297 12.10 11.94 1.35 rnd-1_family-1#LINE/L2 2 68 (59) L2d2_3end#LINE/L2 435 508 (47) m_b1s601i0 rnd-1_family- 2 TAGATTGTAAGCTCTTTG-GGGCAGGGACCGTCTTTTGTTCTGTGTTTGT 50 i - i v i i v - v L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACT-TCTTTGT 483 rnd-1_family- 51 -------ACAGCGCCTAGCACAATG 68 ------- i L2d2_3end#LIN 484 ATCCCCCACAGCGCCTAGCACAGTG 508 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 13.35 CpG sites = 5, Kimura (unadjusted) = 13.35 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (3 / 66), avg. gap size = 3.00 (9 / 3) 229 20.65 9.78 5.21 rnd-1_family-1#LINE/L2 2 93 (34) L2b_3end#LINE/L2 345 440 (26) m_b1s601i1 rnd-1_family- 2 TAGATTGTAAGCTCTTTG-GGGCAGGGACCG--TCT--TTTGTTCTGTGT 46 i i iv - -- --i vvi i L2b_3end#LINE 345 TAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGC 394 rnd-1_family- 47 TTGTA----CAGCGCCTAGCACAATGGGGTCCTGGTCCATGACTGGGGCT 92 - ---- i? ---- iv iiiiv v L2b_3end#LINE 395 T-GTATCCCCAGCGCCTAGCACAGNG----CCTGGCACACAGTAGGCGCT 439 rnd-1_family- 93 C 93 L2b_3end#LINE 440 C 440 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.09 CpG sites = 12, Kimura (unadjusted) = 25.21 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.10 (9 / 91), avg. gap size = 1.56 (14 / 9) 4364 5.61 2.35 0.18 rnd-1_family-10#LINE/CR1 3 556 (0) CR1-L3A_Croc#LINE/CR1 3716 4281 (7) m_b1s551i0 rnd-1_family- 3 TTACCTCTGTATTTGGCACTGGTGCGACCGCTGCTGGAATACTGTGTCCA 52 i CR1-L3A_Croc# 3716 TTACCTCTGTATTTGGCACTGGTGCGACCGCTACTGGAATACTGTGTCCA 3765 rnd-1_family- 53 GTTCTGGTGTCCACAATTCAAGAAGGATGTTGATAAATTGGAGAGGGTTC 102 ? ? CR1-L3A_Croc# 3766 GTTCTGGTGTCCACANTTCAAGAAGGATGTTGANAAATTGGAGAGGGTTC 3815 rnd-1_family- 103 AGAGAAGAGCCACGAGAATGATTAAAGGATTAGAAAACATGCCTTATAGT 152 i i CR1-L3A_Croc# 3816 AGAGAAGAGCCACGAGAATGATTAAAGGACTGGAAAACATGCCTTATAGT 3865 rnd-1_family- 153 GATAGACTCAAGGAGCTCAATCTATTTAGCTTAACAAAGAGAAGGTTAAG 202 v v CR1-L3A_Croc# 3866 GAGAGACTCAAGGAGCTCAATCTATTTAGCTTATCAAAGAGAAGGTTAAG 3915 rnd-1_family- 203 GGGTGACTTGATTACAGTCTATAAGTACCTACATGGGGAACAAATATTTA 252 ii i i v i CR1-L3A_Croc# 3916 GGGTGACTTGATCGCAGTCTATAAGTACCTACACGGGGAACAGAAATTTG 3965 rnd-1_family- 253 ATAAT---GGGCTCTTCAGTCTAGCAGAGAAAGGTATAACACGATCCAAT 299 --- v v CR1-L3A_Croc# 3966 ATAATAGAGGGCTCTTCAGTCTAGCAGACAAAGGTATAACAAGATCCAAT 4015 rnd-1_family- 300 GGCTGGAAGTTGAAGCTAGACAAATTCAGACTGGAAATAAGGCGTACATT 349 i ? i v? CR1-L3A_Croc# 4016 GGCTGGAAGTTGAAGCTAGACAAATTCAGACTAGAAATAAGGNGCAANTT 4065 rnd-1_family- 350 TTTAACAGTGAGAGTAATTAACCATTGGAACAATTTACCAAGGGTCGTGG 399 i i i ?i CR1-L3A_Croc# 4066 TTTAACAGTGAGGGTAATTAACCACTGGAACAACTTACCAAGGGNTGTGG 4115 rnd-1_family- 400 TGGATTCTCCATCACTGGCAATTTTTAAATCAAGATTGGATGTTTTTCTA 449 v CR1-L3A_Croc# 4116 TGGATTCTCCATCACTGGAAATTTTTAAATCAAGATTGGATGTTTTTCTA 4165 rnd-1_family- 450 AAAGATCTGCTCT---------AGGAATTATTTTGGGGAAGTTCTATGGC 490 v --------- v i i CR1-L3A_Croc# 4166 AAAGATATGCTCTAGTTCAAACAGGAATTAATTCGGGGAAGTCCTATGGC 4215 rnd-1_family- 491 CTGTGTTATACAGGAGGTCAGACTAGATGATC-ACAATGGTCCCTTCTGG 539 i -i i - i? i CR1-L3A_Croc# 4216 CTGCGTTA-GCAGGAGGTCGGACTAGATGATCTACAGNGGTCCCTTCCGG 4264 rnd-1_family- 540 CCTTGGAATCTATGAAT 556 i? CR1-L3A_Croc# 4265 CCTTANAATCTATGAAT 4281 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.84 CpG sites = 22, Kimura (unadjusted) = 5.94 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.01 (4 / 553), avg. gap size = 3.50 (14 / 4) 676 2.50 0.00 2.50 rnd-1_family-103#LINE/L2 2 83 (35) L2-1_AMi#LINE/L2 1156 1235 (0) m_b1s551i1 rnd-1_family- 2 AAACTCTCCTTTGCCGTGATGCCTACAAAAAACTTGACAACGGTTAGGCT 51 --i L2-1_AMi#LINE 1156 AAACTCTCCTTTGCCGTGATGCCTACAAAAA--CTGACAACGGTTAGGCT 1203 rnd-1_family- 52 GCTGGTGTGCTGAGACCACTGCCTATCATGCT 83 i? L2-1_AMi#LINE 1204 GCTGGTGTGCTGAGACCACTGCCTATTNTGCT 1235 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.60 CpG sites = 2, Kimura (unadjusted) = 2.60 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 309 22.73 0.00 0.00 rnd-1_family-11#LINE/CR1 11 76 (116) tRNA-Thr-ACA#tRNA 7 72 (3) m_b1s502i0 rnd-1_family- 11 ATAGCTCAGTGGTTTGAGCATTGGCCTGCTAAACCCAGGGTTGTGAGTTC 60 v v i i vv vi i i tRNA-Thr-ACA# 7 ATAGCTCAGGGGTTAGAGCACTGGTCTTGTAAACCAGGGGTCGCGAGTTC 56 rnd-1_family- 61 AATCCTTGAGGGGGCC 76 vi i vv tRNA-Thr-ACA# 57 AAATCTCGCTGGGGCC 72 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.43 CpG sites = 7, Kimura (unadjusted) = 27.21 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 403 11.68 0.00 3.33 rnd-1_family-11#LINE/CR1 110 171 (21) Plat_L3#LINE/CR1 3499 3558 (15) m_b1s551i2 rnd-1_family- 110 CCTGCTAGTGAAGGCAGGGGGCTGGACTCGATGACCTTTCAAGGTCCCTT 159 i-- i iv i i Plat_L3#LINE/ 3499 CCTGCC--TGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTT 3546 rnd-1_family- 160 CCAGTTCTAGGA 171 i ? Plat_L3#LINE/ 3547 CCAGCTCTANGA 3558 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.39 CpG sites = 6, Kimura (unadjusted) = 13.31 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 17 30.34 2.22 3.37 rnd-1_family-110#DNA/hAT-Charlie 139 228 (0) (CCCCCG)n#Simple_repeat 1 89 (0) m_b1s252i12 rnd-1_family- 139 CCCCTGGCTCTGCCACAGGCCCCGCCCCCACTCCACCCCTTCCCGCCCCC 188 i v i i v v v i - - v -i (CCCCCG)n#Sim 1 CCCCCGCCCCCGCCCCCGCCCCCGCCCCCGC-CC-CCGC-CCCCGCCCCC 47 rnd-1_family- 189 TCCCCTGAGCCTG-CCGTGCCCTCG-CTCCTCCCCCTCCCCC 228 v i vv i - vi i - i v v (CCCCCG)n#Sim 48 GCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCC 89 Matrix = Unknown Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.00 (5 / 5) 17 23.14 3.12 3.12 rnd-1_family-110#DNA/hAT-Charlie 164 227 (1) (CCCCT)n#Simple_repeat 1 64 (0) m_b1s252i13 rnd-1_family- 164 CCCCACTCCACCCCTTCCCGCCCCCTCCCCTGAGCCTGCCGTGCCCT-CG 212 v i v - vi -vv v v v - v (CCCCT)n#Simp 1 CCCCTCCCCTCCCC-TCCCCTCCCCTCCCCT-CCCCTCCCCTCCCCTCCC 48 rnd-1_family- 213 CTCCTC-CCCCTCCCC 227 i - (CCCCT)n#Simp 49 CTCCCCTCCCCTCCCC 64 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.00 (4 / 4) 15 19.85 0.00 0.00 rnd-1_family-118#Unknown 1 29 (299) (G)n#Simple_repeat 1 29 (0) m_b1s252i10 rnd-1_family- 1 GGGGGGGGGAGGGGGAGGGAGCGGGCGGG 29 i i i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 25.74 0.00 2.08 rnd-1_family-118#Unknown 1 49 (279) (GGGAGG)n#Simple_repeat 1 48 (0) m_b1s252i9 rnd-1_family- 1 GGGGGGGGGAGGGGGAGGGAGCGGGCGGGAGAGAGAGAGAAGGGGGCGG 49 i i v v i i i - i i v (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAG-GGGGAGGGGGAGG 48 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 12 17.65 5.00 2.44 rnd-1_family-118#Unknown 68 107 (221) (CGC)n#Simple_repeat 1 41 (0) m_b1s252i11 rnd-1_family- 68 CGCTGCC-ACGCGGCCCCTCCCGCCG-CGCCGCCGCCTGCCG 107 i -v v v iv - - (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC-GCCG 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 338 15.71 1.41 1.41 rnd-1_family-119#DNA/hAT-Blackjack 107 177 (570) BLACKJACK#DNA/hAT-Blackjack 1 71 (2898) m_b1s502i1 rnd-1_family- 107 TAGGGTGACCAGACGTCCCGATTTTATCGGGACNGTCCCGATATTTNCTT 156 v i vvi ? i v vi? i BLACKJACK#DNA 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCCGGTTTACGCCT 50 rnd-1_family- 157 GTTTGTCCC-GCGTCCCGACCG 177 - - v BLACKJACK#DNA 51 G-TTGTCCCGGCGTCCCGTCCG 71 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.57 CpG sites = 5, Kimura (unadjusted) = 18.27 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 17 22.55 0.00 0.00 rnd-1_family-119#DNA/hAT-Blackjack 244 279 (468) (C)n#Simple_repeat 1 36 (0) m_b1s252i8 rnd-1_family- 244 CCCCCCCCCGCCCCGACTCCGCCCCCTCCTCCCCCC 279 v vv i v i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 36 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 487 8.83 0.00 1.47 rnd-1_family-123#LINE/CR1 18 86 (0) Plat_L3#LINE/CR1 3499 3566 (7) m_b1s551i3 rnd-1_family- 18 CCTGCCATGAGTGCAGGGGACTGGACTAGATGACCTCTCGAGGTCCCTTC 67 vv - i i Plat_L3#LINE/ 3499 CCTGCCTGGAG-GCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTTC 3547 rnd-1_family- 68 CAGTCCTATGATTCTATGA 86 ii ? Plat_L3#LINE/ 3548 CAGCTCTANGATTCTATGA 3566 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.62 CpG sites = 4, Kimura (unadjusted) = 9.62 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 325 10.20 2.04 0.00 rnd-1_family-126#DNA/PIF-Harbinger 2 50 (4) C Chompy-6_Croc#DNA/PIF-Harbinger (815) 165 116 m_b1s502i2 rnd-1_family- 2 GGTCTCCCACATCCCAGGTGAGTGCCCTAACCACTGGGCTA-AAAGTTAT 50 ? v v i - i i C Chompy-6_Croc 165 GGNCTCCCCCCTCCCAGGTGAGTGCCCTAACCACTAGGCTACAGAGTCAT 116 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.29 CpG sites = 3, Kimura (unadjusted) = 11.29 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 16 28.25 1.47 2.99 rnd-1_family-16#Unknown 279 346 (73) (CCCCCT)n#Simple_repeat 1 67 (0) m_b1s252i7 rnd-1_family- 279 CCCCCTCCCGC-GCCCCAACCCCACCCCCTGCCCCAGCCCTGATCCCCCT 327 v -v vv v - vv -vv (CCCCCT)n#Sim 1 CCCCCTCCCCCTCCCCCTCCCCCTCCCCCT-CCCCCTCCC-CCTCCCCCT 48 rnd-1_family- 328 CCCGCCCTCCGAACCCCTC 346 v i i vvv (CCCCCT)n#Sim 49 CCCCCTCCCCCTCCCCCTC 67 Matrix = Unknown Transitions / transversions = 0.15 (2/13) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 11 17.73 5.00 2.44 rnd-1_family-17#PLE/Naiad 419 458 (729) (CACCAA)n#Simple_repeat 1 41 (0) m_b1s252i6 rnd-1_family- 419 CACCAGCAACTACACACCACACC-ACAGAAACACCAAC-CCA 458 i v v - v - vv - (CACCAA)n#Sim 1 CACCAACACCAACAC-CAACACCAACACCAACACCAACACCA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 2859 20.47 0.18 1.08 rnd-1_family-19#LINE/CR1 10 572 (0) Plat_L3#LINE/CR1 3007 3564 (9) m_b1s551i4 rnd-1_family- 10 GCAAGACACGAGAAGTAATTCTTCCGCTCTACTCCGCGCTGATNAGGCCT 59 vv i i v i i i ? i i Plat_L3#LINE/ 3007 GCAAGAGTCGGGAAGTAATCCTTCCGCTATACTCTGCACTGGTCAGACCC 3056 rnd-1_family- 60 CAGCTGGAGTACTGTGTCCAGTTCTGGGCGCCACATTTCAGGAAAGATGT 109 ivii i i v i i i i ii i Plat_L3#LINE/ 3057 TTATTAGAGTACTGTGTCCAGTTTTGGTCACCGCACTTTAAAAAGGATGT 3106 rnd-1_family- 110 GGACAAATTGGAGAAAGTCCAGAGAAGAGCAACAAAAATGATTAA-GGTC 158 v i ii i - vv Plat_L3#LINE/ 3107 GGAGAAACTGGAGAGGGTCCAGAGAAGAGCGACAAAAATGATTAAAGGGA 3156 rnd-1_family- 159 TAGAAAACATGACCTATGAGGGAAGATTGAAAAAACTGGGTTTGTTTAGT 208 i i v v i i i ii i v i Plat_L3#LINE/ 3157 TGGAAAATAGGTCCTATGAGGAAAGGTTAAAGGAATTGGGGTTGTTTAGC 3206 rnd-1_family- 209 CTGGAGAAGAGAAGACTGAGGGGGGACATGATAACAGTTTTCAAGTACGT 258 i i v v i v i ii Plat_L3#LINE/ 3207 CTGGAGAAGAGAAGGCTAAGGGGTGACTTAATAACTGTCTTCAAGTATAT 3256 rnd-1_family- 259 AAAAGGTTGTTACAAGGAGGAGGGAGAAAAATTGTTCTCCTTAACCTCTG 308 i i v iii v vv vv i v iv v ? Plat_L3#LINE/ 3257 GAAGGGTTTTTATGGGGAGGACGCTGACCAGTTGTTCTCCATGTCCACNG 3306 rnd-1_family- 309 AGGATAGGACAAGAAGCAATGGGCTTAAATTGCAGCAAGGGAGGTTTAGG 358 iv i i v iv i i i v Plat_L3#LINE/ 3307 AGGACCGAACAAGAGGAAATGGGCTTAAATTAAAGCAGGAGAGATTTCGG 3356 rnd-1_family- 359 TTGGACATTAGGAAAAACTTCCTAACTGTCAGGGTGGTTAAGCACTGGAA 408 v i i i i v i Plat_L3#LINE/ 3357 TTGGACATAAGGAAGAACTTCTTGACTGTCAGGGTGATAAAACACTGGAA 3406 rnd-1_family- 409 TAAATTGCCTAGGGAGGTTGTGGAATCTCCATCATTGGAGATTTTTAAGA 458 iiiii i v i vi i Plat_L3#LINE/ 3407 CGGGCTACCGAGGGAGGTTGTGGAGTCTCCATCCCTGGAGATCTTTAAGA 3456 rnd-1_family- 459 GCAGGTTAGACAAACACCTGTCAGGGATGGTCTAGATAATACTTAGTCCT 508 iv iv ?v i vv i - v -- i -- Plat_L3#LINE/ 3457 AAAGAATAGACANCCATCTGTCCTGGATGGTTTAG-TCAT--TCA--CCT 3501 rnd-1_family- 509 GCCATGAGTGCAGGGGACTGGACTAGATGACCTCTCGAGGTCCCTTCCAG 558 vv - i i Plat_L3#LINE/ 3502 GCCTGGAG-GCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTTCCAG 3550 rnd-1_family- 559 TCCTACGATTCTAT 572 ii ? Plat_L3#LINE/ 3551 CTCTANGATTCTAT 3564 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.95 CpG sites = 75, Kimura (unadjusted) = 24.71 Transitions / transversions = 1.92 (75/39) Gap_init rate = 0.01 (7 / 562), avg. gap size = 1.00 (7 / 7) 675 26.70 0.56 0.56 rnd-1_family-2#LINE/CR1 136 312 (3799) CR1-L3A_Croc#LINE/CR1 235 411 (3877) m_b1s551i5 rnd-1_family- 136 GATCAGCTGTTGTAACCTGCACAGGTTGTGCCATGTTTGTCTTTCTT-CC 184 ? iv i vv v i i - i - CR1-L3A_Croc# 235 GANCAGTGGTTGTGACCTGCAACGGATGCGCCACGTTT-TCTTTCCTGCC 283 rnd-1_family- 185 ACAGGACAGAAGCGACTTTGTCTGTACAAAGTGCAAGCTGGTCTCCATAT 234 vv i v v iv v ii i vv ii ii CR1-L3A_Croc# 284 TGAAGCCAGAAGGGACTTCCTGTGTATGAAGTGCAAGTTGGTGGCTGTGC 333 rnd-1_family- 235 TGGAAGAGAAGGTTCGAGGNCTGGAGAAACGAGTATCGACTCTGCGTTGC 284 i i v ?i iii i ii v vv CR1-L3A_Croc# 334 TGGAAGAAAAGATTCGTGGTTTGGAAGGACAAGTACTGACGCTGCGGAGC 383 rnd-1_family- 285 ATAAGGGAAAATGAAGATTTCCTGGACA 312 v i iiv i v i CR1-L3A_Croc# 384 ATCAGAGAGGCTGAGGAGTTCTTGGACA 411 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 28, Kimura (unadjusted) = 34.36 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.01 (2 / 176), avg. gap size = 1.00 (2 / 2) 1690 25.90 0.84 0.84 rnd-1_family-2#LINE/CR1 695 1169 (2942) Plat_L3#LINE/CR1 138 612 (2961) m_b1s551i6 rnd-1_family- 695 CCGAGAGGTCTGCTGCTTGCCAGGAGCTAGGATACACGATGTGACGGAGA 744 i v ? i ? ii i vi i viiv ?i iv i ? Plat_L3#LINE/ 138 CCGGGAGGTGTGNTGCCTGNCGAGAACTCAGGTCTGAGNCGCCACGAAGN 187 rnd-1_family- 745 GACTGCCGAGACTCATCAAGCCCTCGGATCGCTACCCCTTCCTGCTTCTC 794 i vvvi ?i vvv ii? i v v v v Plat_L3#LINE/ 188 GATTGGACGGACTCATCNGGCCCGACGACTNCTGCCCCGTGCTTCTTATC 237 rnd-1_family- 795 CACGTGGGCACCAATGATACTGCCAAGAATGACCTTGAGCGGATCACTGC 844 i v v vi vv v iv ?v -- v Plat_L3#LINE/ 238 CATGTGGGAACGAATGATACTGCCCGGTCTCACCCGGAGCNTATCA--GG 285 rnd-1_family- 845 AG--ACTACGTGGCTCTGGGAAGAAGGATAAAGGAGTTTGAGGCGCAAGT 892 -- i iv ivi i i viv i v i Plat_L3#LINE/ 286 AGTGACTGCAGGGCTCTGGGAGCGAGGGTGAAGGAGGCGGGGGCTCAGGT 335 rnd-1_family- 893 GGTGTTCTCGTCCATCCTCCCTGTGCAAGGAAAAGGCCCGGGTAGAGACC 942 v v vv i i i vv i i v Plat_L3#LINE/ 336 GGTGTTCTCGTCGATCCTCCCAGTCGAGGGGAAAGGCTCCCGCAGGGACA 385 rnd-1_family- 943 GTCGAATCGTGGAAGTCAACGAATGGCTACGCAGGTGGTGTCGGAGAGAA 992 v v v ii v vv i iiv i Plat_L3#LINE/ 386 GACGCATCCTGGAGATGAACGCCTGGCTGCGCGACTGGTGTCGAAGAGAA 435 rnd-1_family- 993 GGCTTTGGATTCTTCGACCATGGGATGGTGTTCCAAGAAGGAGGAGTGCT 1042 v i i v i vi i v vii ii vv v Plat_L3#LINE/ 436 TGCTTCGGATTCCTCGACAACGGTGTGATCTTCAGGGAAGAGGGCCTCCT 485 rnd-1_family- 1043 AGGCAGAGACGGGCTCCACCTAACGAAGAGAGGGAAGAGCATCTTCGCAA 1092 ii v i v i vi i i vi Plat_L3#LINE/ 486 GAGCCGGGACGGGATCCATCTCGCGAAGAAAGGGAAGAGTATCTTCGGGA 535 rnd-1_family- 1093 GCAGGCTGGCTAACCTAGTGAGGAGGGCTTTAAACTAGGTTCACCGGGGG 1142 i i iiv - Plat_L3#LINE/ 536 GCAGACCGGCTAACCTAGTGAGGAGGGCTTTAAACTAGGTTTGGC-GGGG 584 rnd-1_family- 1143 AAGGA--GACCAAAGCCCTGAGGTAAGTG 1169 v --? i- vi Plat_L3#LINE/ 585 ATGGATCNACT-AAGCCCAAAGGTAAGTG 612 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 64, Kimura (unadjusted) = 32.90 Transitions / transversions = 1.10 (64/58) Gap_init rate = 0.01 (6 / 474), avg. gap size = 1.33 (8 / 6) 8818 28.05 1.71 1.57 rnd-1_family-2#LINE/CR1 1246 4110 (1) Plat_L3#LINE/CR1 705 3573 (0) m_b1s551i7 rnd-1_family- 1246 GGGACGATCGGCGAGTTATCTTAAGTGCCTATACACAAATGCAAGAAGCC 1295 i i vii - i ii v i ii i i i v Plat_L3#LINE/ 705 GGGACAACCCATG-GCTACTTGAAATGTTTGTACGCAAATGCAAGGAGCA 753 rnd-1_family- 1296 TGGGAAACAAGCAGGGAGAACTGGAAGTCCTGGCACAGTCAGGG----AA 1341 i i ii i i i ---- i---- i Plat_L3#LINE/ 754 TGGGAAATAAACAGGAGGAACTGGAGGTCTTAGC----TCAGGACCACAG 799 rnd-1_family- 1342 CTATGATGTGATTGGAATAACAGAGACTTGGTGGGATAACTCACATGACT 1391 i i i v v i i v v Plat_L3#LINE/ 800 TTATGATGTAACTGGAATAACTGAGACGTGGTGGGACAGCACTCATGACT 849 rnd-1_family- 1392 GGAGTACTGTCATGGATGGATATAAACTGTTCAGGAAGGACAGGCAGGGC 1441 i vvv i v i viii i i v Plat_L3#LINE/ 850 GGAGTGCTGGACTAGAAGGGTATCGGTTGTTCAGGAAAGATAGGCAGGGA 899 rnd-1_family- 1442 AGAAAAGGTGGGGGAGTTGCGTTGTATGTAAGAGAGGAGTATGACTGCTC 1491 i i v v v v ii v ii vi?v iivv Plat_L3#LINE/ 900 AAAAAGGGAGGTGGTGTTGCCTTGTACATCAAGGATANCTACACATGCTC 949 rnd-1_family- 1492 AGAGCTCCGGTATGAAACTGCAGAAA---AAC---CTGAGAGTCTCTGGA 1535 vi i --- v v i i--- ---iv v i Plat_L3#LINE/ 950 AGAGGCCCAG---GAAACAGAAGGAGGCCAACAGGTAGAGAGTGTCTGGG 996 rnd-1_family- 1536 TNAAGTTGAGAAGTGTGAGCAACAAGGGTGATGTCGTGGTNGGAGTCTGC 1585 ? ivi i i vi iv i i i i ? ii Plat_L3#LINE/ 997 TTAAAGCGAAAGGTGAAAAGAATAAGGGCGACGTCATGGTAGGAGTCTAT 1046 rnd-1_family- 1586 TATAGACCACCAGACCAGGGGGATGAGGTGGACGAGGCTTTCTTCCGGCA 1635 v i ii vi i i iv v Plat_L3#LINE/ 1047 TATAGACCTCCAAACCAGGAAGAGAAGGTGGATGAGGCCTTCTTTGGTCA 1096 rnd-1_family- 1636 ACTAGCAGAAGTTGCTAGATCG---CAGGCCCTGGTTCTCATGGGAGACT 1682 vi vi iv --- --- vi vv v Plat_L3#LINE/ 1097 ACTCACCAAAGCGGCT---TCGGGTCAGGATCTGGTGGTGATGGGAGACT 1143 rnd-1_family- 1683 TTAATCACCCTGATATCTGCTGGGAGAGCAATACAGCGGTGCACAGACAA 1732 ii v i i v vv ivi Plat_L3#LINE/ 1144 TTAACTACCCAGATATCTGCTGGAAAAGCAATTCAGCGGGCCACAGATCG 1193 rnd-1_family- 1733 TCCAGGAAGTTTTTGGAAAGTGTAGGGGACAATTTCCTGGTGCAAGTGCT 1782 v iv i vv ii v i iiviv Plat_L3#LINE/ 1194 TCAAACAGGTTTTTGGATTGCATTGGGGACAATTTCCTAGTGCAGAAAGT 1243 rnd-1_family- 1783 GGAGGAACCAACTAGGGGCAGA-GCTCTTCTTGACCTGCTGCTCACAAAC 1831 i i - - i ii v v i v Plat_L3#LINE/ 1244 AGAGGAATCAACTAGGG-CAGATGCCCTTCTTGATTTGATTCTTACTAAC 1292 rnd-1_family- 1832 AGGGAAGAATTAGTAGGGGAAGCAAAAGTGGATGGGAACCTGGGAGGCAG 1881 i v i vvi i i v v v Plat_L3#LINE/ 1293 GGGGAAGAATTAGTCGAGGATCTAAAGGTGGATGGAAACCTTGGTGGAAG 1342 rnd-1_family- 1882 TGACCATGAGATGGTCGAGTTCAGGATCCTGACACAAGGAAGAAAGGAGA 1931 i i ii i vi i i ----i ii Plat_L3#LINE/ 1343 CGATCACAAGATGATCGTATTCAAGATCCTAA----GGGAAGGGAGGAGA 1388 rnd-1_family- 1932 G----CAGCAGAATACGGACCCTGGACTTCAGAAAAGCAGACTTTGACTC 1977 ---- ii vi vvv i i i i i i vv Plat_L3#LINE/ 1389 GAAGTCAGCAAGATAAAGAAAATGAACTTTAGGAAAGCAAATTTTAACAG 1438 rnd-1_family- 1978 CCTCAGGGAACNGATGGGCAGGATCCCCTGGGAGAATAACATGAGGGGNA 2027 v i v ?ii i v i vv i i v i v i i ? Plat_L3#LINE/ 1439 GCTTAGGGCACTAGTAGGAAGGACCCGATGGAAGGAAAGCCTAAGAGGCA 1488 rnd-1_family- 2028 AAGGGGTCCAGGAGAGCTGGCTGTATTTTAAAGAATCCTTATTG-AGGTT 2076 i i i vi i i iv vv vi - i Plat_L3#LINE/ 1489 AAGGAGTCCAAGAAAGCTGGCTGTTCTTCAAAAAGACAGTTCTGCAGGCT 1538 rnd-1_family- 2077 GCAGGAACAAACCATCCCGATGTGTAGAAAGAATAGTAAATATGGCAGGC 2126 - i v ii ii? i i i iv ivi ii i v Plat_L3#LINE/ 1539 -CAGGAACAAACTATACCAGTGCANAGGAAGGACAAGAAGGGTAACAAGA 1587 rnd-1_family- 2127 GACCAGCTTGGCTTAACAGTGAAATCCTTGCTGATCTTAAACGCAAAAAA 2176 vi iv v vvv v i?iivv i v iv vii Plat_L3#LINE/ 1588 TGCCAAGTTGGCTAAACCCAGAACTCTNCAGAGACCTGAAGGGCAAATGG 1637 rnd-1_family- 2177 GAAGCTTACAAGAAGTGGAAGATTGGACAAATGACCAGGGAGGAGTATAA 2226 ivi i iv v v i v i ii i Plat_L3#LINE/ 1638 GAAAGCTACAAAAAGTGGAAATTAGGCCAGATCACTAAAGAAGAGTATAA 1687 rnd-1_family- 2227 AAATATTGCTCAGGCATGCAGGAGTGAAATCAGGAAGGCCAAATC---AC 2273 i v v v iivii i iiii i i i i ? v --- v Plat_L3#LINE/ 1688 AGAAATAGCACGATTGTGTAGGGACAAGATTAGAAAAGCNAAAGCCGGAA 1737 rnd-1_family- 2274 ACTTGGAGTTGCAGCTAGCAAGAGATGTTAAGAGTAACAAGAAGGGTTTC 2323 --- v i v ii v ii i iivv Plat_L3#LINE/ 1738 A---GGAGATGCAACTAGCACGAGACATAAAAGGTAACAAAAAAACATTC 1784 rnd-1_family- 2324 TTCAGGTATGTTAG-CAACAAGAAGAAAGTCAAGGAAAGTGTGGGCCCCT 2372 iv i - - i iiii i i v vi i Plat_L3#LINE/ 1785 TTCAATTATATTAGGCAA-AAGAGGAGGACCAGGGAAAATGTCGCTCCCC 1833 rnd-1_family- 2373 TACTGAATGAGGGAGGCAACCTAGTGACAGAGGA-TGTGGAAAAAGCTAA 2421 iiv ii iii iii v v ii i v - - i vi Plat_L3#LINE/ 1834 CGGTAGACAGGAAGGGAAAGCTGATAACAGATGACTGTG-AAAAGGCGGA 1882 rnd-1_family- 2422 TGTACTCAATGCTTTTTTTGCCTCTGTCTTCACGAACAAGGTCAGCTCCC 2471 v ivi i ?vvi ii i i v i iv viv Plat_L3#LINE/ 1883 GGCTTTTANATTTTTTTTCACTTCTGTCTTTACGAAAAAGATCAAATGTG 1932 rnd-1_family- 2472 AGACTGCTGCACTGGGCAG--CACAGTATGGGGAGGAGG--TGACCAGCC 2517 - v vv v i-- v v - ? iv i -- ivv Plat_L3#LINE/ 1933 A-ACAGCTGACCAGGGCAAGTCCCACT-TGNGATGGAAGGTTGGAAAGCC 1980 rnd-1_family- 2518 ---CTCTG-TGGAGAAAGAAGTGGTTCGGGACTATTTAGAAAAGCTGGAC 2563 --- vvi- i i iii vii v i ?i i i i Plat_L3#LINE/ 1981 AAACTAGAATAGGGAAAGAAACAGTTAAAGAGTATCTNAAAAAACCGGAT 2030 rnd-1_family- 2564 GNGCACAAGTCCATGGGGCCGGATGCGCTGCATCCGAGGGTGCTAAAGGA 2613 ?iivi i viii v vvv v i v Plat_L3#LINE/ 2031 GTATTTAAATCAGCAGGGCCTGATGACATGCATCCTAGGGTACTTAAGGA 2080 rnd-1_family- 2614 GTTGGCGGATGTGATTGCAGAGCCATTGGCCATTATCTTTGAAAACTCAT 2663 i v i i i i i ii Plat_L3#LINE/ 2081 ATTGGCGGATGTTATTGCAGAGCCACTAGCTATTATTTTTGAGAACTCGC 2130 rnd-1_family- 2664 GGCGATCGGGGGAGGTCCCGGATGACTGGAAAAAGGCTAATGTAGTGCCC 2713 v iv i i v v i i v i v Plat_L3#LINE/ 2131 GGAGGACGGGAGAAGTCCCTGAGGATTGGAAAAGGGCAAACGTTGTGCCC 2180 rnd-1_family- 2714 ATCTTTAAAAAAGGGAAGAAGGAGGATCCGGGGAACTACAGGCCAGTCAG 2763 i v i v v i i i Plat_L3#LINE/ 2181 ATCTTTAAAAAAGGGAAAAAGGACGACCCTGGTAATTACAGACCGGTCAG 2230 rnd-1_family- 2764 CCTCACCTCAGTCCCTGGAAAAATCATGGAGCAGGTCCTCAAGGAATCAA 2813 i v v ii v i i vv i i ii v iv Plat_L3#LINE/ 2231 CTTAACATCGATACCTGGGAAGATACTAGAACAAATCATCAAACAATCAA 2280 rnd-1_family- 2814 TTNTGAAGCACTTAGAGGAGAGGAAAGTGATCAGGAA-CAGTCAGCATGG 2862 ?vv v i i viv ii - ii - ii i i Plat_L3#LINE/ 2281 TTTGCAACCACCTAGAAGAGCATAAGAT-ACTAGGAAGCAACCAACGTGG 2329 rnd-1_family- 2863 ATTCACCAAGGGCAAGTCGTGCCTGACTAACCTAATTGCCTTCTATGATG 2912 v iiiv i i v ? ii v i Plat_L3#LINE/ 2330 CTTTGTGAAGAGCAAATCGTGCCAGACNAATTTAATTTCCTTCTATGATA 2379 rnd-1_family- 2913 AGATAACTGGCTCTGTGGATGAGGGGAAAGCAGTGGACGTGTTATTCCTT 2962 iii i v ivi i ii i i i i iv v vi v Plat_L3#LINE/ 2380 GAGTGACAGGCCACGTAGACAAGGGGGAAGCAATAGATGTAATCTATCTA 2429 rnd-1_family- 2963 GACTTTAGCAAAGCTTTTGATACGGTCTCCCACAGTATTCTTGCCGGCAA 3012 i i i v v i v iiii i iii i Plat_L3#LINE/ 2430 GACTTCAGTAAGGCTTTTGATTCCGTCCCACATGACATCCTCATCGACAA 2479 rnd-1_family- 3013 GTTAAAGAAGTATGGGCTGGATGAATGGACTATAAGGTGGATAGAAAGCT 3062 i iiii v v iv vvvv ii v i iv v Plat_L3#LINE/ 2480 GCTGGGAAAGTATGGTCTTGACCATACTACCGTTAGGTGGGTGCACAGCT 2529 rnd-1_family- 3063 GGCTAGATCGTCGGGCTCAACGGGTAGTGATCAATGGCTCCATGTCTAGT 3112 v vv vi i v v vi v vi Plat_L3#LINE/ 2530 GGCTCGAGGGTCGCACCCAAAGGGTAGTCATCAATGGCTCGGTGTCAACC 2579 rnd-1_family- 3113 TGGCAGCCGGTNTCAAGCGGAGTGCCCCAAGGGTCGGTCCTGGGGCCGGT 3162 vi vv?i ? i i v v v i i i Plat_L3#LINE/ 2580 TGGAGGGANATATCGAGTGGTGTCCCACAGGGATCGGTCCTGGGACCGGT 2629 rnd-1_family- 3163 TTTGTTCAATATCTTCATTAATGATCTGGAGGATGGCGTGGACTGCACTC 3212 i i i ii i v v vi v vv iv Plat_L3#LINE/ 2630 TCTATTCAATATCTTTATCGATGACCTGGACGAAGGAATCGAGAGCATGC 2679 rnd-1_family- 3213 TCAGCAAGTTTGCAGATGACACTAAACTGGGAGGAGTGGTAGATACGCTG 3262 v i i i v i v ivi i vi Plat_L3#LINE/ 2680 TCATCAAATTTGCAGATGATACTAAATTGGGCGGGGTTGCTAACACTTTG 2729 rnd-1_family- 3263 GAGGGTAGGGATAGGATACAGAGGGACCTAGACAAATTAGAGGATTGGGC 3312 i ii i ii v i v ? i ii v v Plat_L3#LINE/ 2730 GAAGACAGGAATAAAATTCAAAGTGACCTNGACAAATTGGAAAAATGGTC 2779 rnd-1_family- 3313 CAAAAGAAACCTGATGAGGTTCAACAAGGACAAGTGCAGAGTCCTGCACT 3362 v?v i vv ii i i ii vv Plat_L3#LINE/ 2780 CTNCAAAAACAGGATGAAATTCAATAGGGACAAGTGCAAGGTAGTGCACT 2829 rnd-1_family- 3363 TA-GGACGGAAG--AATCCCATGCACTGCTACAGACTAGGGACCGAATGG 3409 - i i-- v --- viv iv i vv v Plat_L3#LINE/ 2830 TAGGGACGAAAAACAAACC---GCACAAATACAGGATGGGGAAAGACTGG 2876 rnd-1_family- 3410 CTAGGCAGCAGTTCTGCAGAAAAGGACCTAGGGGTTACAGTGGACGAGAA 3459 vv v v i i i i v v ? Plat_L3#LINE/ 2877 CTAGGCACAAGTACAGCAGAAAAAGACCTGGGGGTCATAGTCGACCANAA 2926 rnd-1_family- 3460 GCTGGATATGAGTCAACAGT---GTGCCCTTGTTGCCAAGAAGGCTAACG 3506 i i i --- v i --- i i i Plat_L3#LINE/ 2927 GCTGAATATGAGTCAGCAATGTAGTGCCGTTATT---AAAAAAGCCAACG 2973 rnd-1_family- 3507 GCATTTTGGGCTGTATAAGTAGGGGCAT----TGCCAGCAGATCGAGGGA 3552 vvi vi v v ii i i ---- v - - -- Plat_L3#LINE/ 2974 TGGTACTGGGATGTATTAACAGGAGTATGACATGCAAG-AG-TC--GGGA 3019 rnd-1_family- 3553 CGTGATCGTTCCCCTCTATTCGACATTGGTGAGG-CCTCATCTGGAGTAC 3601 v i v v v i vi i v i- i - i Plat_L3#LINE/ 3020 AGTAATCCTTCCGCTATACTCTGCACTGGTCAGACCCTTAT-TAGAGTAC 3068 rnd-1_family- 3602 TGTGTCCAGTTTTGGGCCCCACACTACAAGAAGGATGTGGAAAAATTGGA 3651 v v i vi i i i Plat_L3#LINE/ 3069 TGTGTCCAGTTTTGGTCACCGCACTTTAAAAAGGATGTGGAGAAACTGGA 3118 rnd-1_family- 3652 AAGAGTCCAGCGGAGGGCAACAAAAATGATTAGGGGGCTGGAGCACATGA 3701 i i v i i i ii v iv i v v Plat_L3#LINE/ 3119 GAGGGTCCAGAGAAGAGCGACAAAAATGATTAAAGGGATGGAAAATAGGT 3168 rnd-1_family- 3702 CTTATGAGGAGAGGCTGAGGGAACTGGGATTGTTTAGTCTGCAGAAGAGA 3751 i i i i i i i i v Plat_L3#LINE/ 3169 CCTATGAGGAAAGGTTAAAGGAATTGGGGTTGTTTAGCCTGGAGAAGAGA 3218 rnd-1_family- 3752 AGAATGAGGGGGGATTTGATAGCNGCCTTCAACTACCTGAAGGGGGGTTC 3801 iv i v i i i ? i v iv vvv v Plat_L3#LINE/ 3219 AGGCTAAGGGGTGACTTAATAACTGTCTTCAAGTATATGAAGGGTTTTTA 3268 rnd-1_family- 3802 CAAAGAGGATG--GAGCTAGGCTGTTCTCAGTGGTGGCAGATGACAGAAC 3849 iiii i -- - i - i vi vivi ? v v Plat_L3#LINE/ 3269 TGGGGAGGACGCTGA-CCA-GTTGTTCTCCATGTCCACNGAGGACCGAAC 3316 rnd-1_family- 3850 AAGGAGCAATGGTCTCAAGTTGCAGTGGGGGAGGTCTAGGTTGGATATTA 3899 ii v v i i iv ii i i i v i v Plat_L3#LINE/ 3317 AAGAGGAAATGGGCTTAAATTAAAGCAGGAGAGATTTCGGTTGGACATAA 3366 rnd-1_family- 3900 GGAAAAACTATTTCACTAGGAGGGTGGTGAAGCACTGGAATGGGTTACCT 3949 i vi v ivv i i i i i v Plat_L3#LINE/ 3367 GGAAGAACTTCTTGACTGTCAGGGTGATAAAACACTGGAACGGGCTACCG 3416 rnd-1_family- 3950 AGGGAGGTGGTGGAATCTCCTTCCTTGGAGGTTTTTAAGGCCCGGCTTGA 3999 v i v i i i ivvv iv v Plat_L3#LINE/ 3417 AGGGAGGTTGTGGAGTCTCCATCCCTGGAGATCTTTAAGAAAAGAATAGA 3466 rnd-1_family- 4000 CAAAGCC--CTGGCTGGGATGATTTAGTTGGGAATTGGTCCTGCTTTGA- 4046 -- ? -- v iv i i---- vi- i v - Plat_L3#LINE/ 3467 C--ANCCATCTGTCCTGGATGGTTTAGTC----ATTCA-CCTGCCTGGAG 3509 rnd-1_family- 4047 GCAGGGGGTTGGACTAGATGACCTCCTGAGGTCCCTTCCAACCCTGATAT 4096 i i ii i i i?v Plat_L3#LINE/ 3510 GCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANGAT 3559 rnd-1_family- 4097 TCTATGATTCTATG 4110 i Plat_L3#LINE/ 3560 TCTATGATTCTACG 3573 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 489, Kimura (unadjusted) = 36.67 Transitions / transversions = 1.62 (489/302) Gap_init rate = 0.02 (68 / 2864), avg. gap size = 1.38 (94 / 68) 264 18.18 0.00 0.00 rnd-1_family-22#DNA/hAT-Blackjack 1 44 (79) MER94#DNA/hAT-Blackjack 1 44 (90) m_b1s502i3 rnd-1_family- 1 TAGGGTGACCAGATGTCCCGATTTTATAGGGACAGTCCCGATTT 44 v i i vviv i MER94#DNA/hAT 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCCGGTTT 44 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.20 CpG sites = 4, Kimura (unadjusted) = 20.94 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 16 28.51 0.00 4.55 rnd-1_family-25#LTR/DIRS 1365 1433 (4818) (CCGGCA)n#Simple_repeat 1 66 (0) m_b1s252i5 rnd-1_family- 1365 CCGGCTCCCGGCACCGACGAGGTCATCGGCACCGATCGCGGTCCCGGCAC 1414 -v i ivv v i iivv iv (CCGGCA)n#Sim 1 CCGGC-ACCGGCACCGGCACCGGCACCGGCACCGGCACCGGCACCGGCAC 49 rnd-1_family- 1415 CGNTCGCCGGCACCGCGCA 1433 -v i - (CCGGCA)n#Sim 50 CG-GCACCGGCACCG-GCA 66 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 5937 4.49 0.56 0.00 rnd-1_family-26#LINE/CR1 1 713 (0) CR1-L3A_Croc#LINE/CR1 3340 4056 (232) m_b1s551i8 rnd-1_family- 1 TGACCTGGAAGAAAACATAAAATCATCACTGATAAAGTTTGCAGATGACA 50 i CR1-L3A_Croc# 3340 TGACCTGGAAGAAAACATAAAATCATTACTGATAAAGTTTGCAGATGACA 3389 rnd-1_family- 51 CAAAAATTGGGG-AGTGGTAAATAATGAAGAGGACAGGTCACTGATACAG 99 i - CR1-L3A_Croc# 3390 CAAAGATTGGGGGAGTGGTAAATAATGAAGAGGACAGGTCACTGATACAG 3439 rnd-1_family- 100 AGCGATCTGGATCGCTTGGTAAACTGGGCGCAAGCAAACAATATGCGTTT 149 i CR1-L3A_Croc# 3440 AGCGATCTGGATCGCTTGGTAAGCTGGGCGCAAGCAAACAATATGCGTTT 3489 rnd-1_family- 150 TAATACGGCTAAATGTAAATGTATACATCTAGGAACAAAGAATGTAGGCC 199 i i vvi i CR1-L3A_Croc# 3490 CAATACGGCCAAATGTAAAGTCATACATCTAGGAACAAAGAATGCAGGCC 3539 rnd-1_family- 200 ATACTTACAGGATGGGGGACTCTATCCTGGGAAGCAGTGACTCTGAAAAA 249 i i CR1-L3A_Croc# 3540 ATACTTACAGGATGGGGGACTCTATCCTGGGAAGCAGCGACTCTGAAAAG 3589 rnd-1_family- 250 GATTTGGGGGTCGTGGTGGATAATCAGCTGAACATGAGCTCCCAGTGCGA 299 i ii CR1-L3A_Croc# 3590 GACTTGGGGGTCACGGTGGATAATCAGCTGAACATGAGCTCCCAGTGCGA 3639 rnd-1_family- 300 CGCTGTGGCCAAAAGGGCTAATGCGATCCTNGGATGCATAAACAGGGGAA 349 ? i CR1-L3A_Croc# 3640 CGCTGTGGCCAAAAGGGCTAATGCGATCCTTGGATGTATAAACAGGGGAA 3689 rnd-1_family- 350 TCTCGAGTAGGAGTAGAGAGGTTATTTTACCTCTGTATTTGGCACTGGTG 399 ? i v CR1-L3A_Croc# 3690 TNTCGAGTAGGAGTAGGGAGGTTATATTACCTCTGTATTTGGCACTGGTG 3739 rnd-1_family- 400 CGACCGCTGCTGGAATACTGTGTCCAGTTCTGGTGCCCACAATTCAAGAA 449 i i ? CR1-L3A_Croc# 3740 CGACCGCTACTGGAATACTGTGTCCAGTTCTGGTGTCCACANTTCAAGAA 3789 rnd-1_family- 450 GGATGTTGATAAATTGGAGAGGGTTCAGAGAAGAGCCACGAGAATGATTA 499 ? CR1-L3A_Croc# 3790 GGATGTTGANAAATTGGAGAGGGTTCAGAGAAGAGCCACGAGAATGATTA 3839 rnd-1_family- 500 AAGGATTAGAAAACATGCCTTATAGTGATAGACTCAAGGAGCTCAATCTA 549 i i v CR1-L3A_Croc# 3840 AAGGACTGGAAAACATGCCTTATAGTGAGAGACTCAAGGAGCTCAATCTA 3889 rnd-1_family- 550 TTTAGCTTAACAAAGAGAAGGTTAAGGGGTGACTTGATTACAGTCTATAA 599 v ii CR1-L3A_Croc# 3890 TTTAGCTTATCAAAGAGAAGGTTAAGGGGTGACTTGATCGCAGTCTATAA 3939 rnd-1_family- 600 GTACCTACATGGGGAACAAATATTTAATAAT---GGGCTCTTCAGTCTAG 646 i i v i --- CR1-L3A_Croc# 3940 GTACCTACACGGGGAACAGAAATTTGATAATAGAGGGCTCTTCAGTCTAG 3989 rnd-1_family- 647 CAGAGAAAGGTATAACACGATCCAATGGCTGGAAGTTGAAGCTAGACAAA 696 v v CR1-L3A_Croc# 3990 CAGACAAAGGTATAACAAGATCCAATGGCTGGAAGTTGAAGCTAGACAAA 4039 rnd-1_family- 697 TTCAGACTGGAAATAAG 713 i CR1-L3A_Croc# 4040 TTCAGACTAGAAATAAG 4056 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.12 CpG sites = 24, Kimura (unadjusted) = 4.68 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.00 (2 / 712), avg. gap size = 2.00 (4 / 2) 211 19.15 2.08 2.08 rnd-1_family-28#Unknown 15 62 (2) L2c_3end#LINE/L2 357 404 (74) m_b1s601i2 rnd-1_family- 15 TGTCTGTCTTGTCTATTTAGATTGTAAGCTCTTCG-GGGCAGGGACTGT 62 iv i i - i i i i - i L2c_3end#LINE 357 TGTCTGTCTCCTCCACT-AGACTGTGAGCTCCTTGAGGGCAGGGACCGT 404 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.62 CpG sites = 8, Kimura (unadjusted) = 23.53 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 759 1.00 0.00 0.00 rnd-1_family-3#SINE/MIR 1 100 (42) MIR1_Amn#SINE/MIR 71 170 (60) m_b1s601i3 rnd-1_family- 1 CTCTGCCACTGGCCTGCTGGGTGACCTTGGGCAAGTCACTTCACCTCTCT 50 ? ? ? ? MIR1_Amn#SINE 71 CTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCT 120 rnd-1_family- 51 GTGCCTCAGTTTCCCCATCTGTAAAATGGGGATAATGATACTGACCTCCT 100 ? i MIR1_Amn#SINE 121 GNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTGACCTCCT 170 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 1.06 CpG sites = 1, Kimura (unadjusted) = 1.06 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 261 4.99 9.52 4.55 rnd-1_family-3#SINE/MIR 101 142 (0) AmnSINE1#SINE/5S-Deu-L2 510 553 (22) m_b1s502i4 rnd-1_family- 101 TTGTAAAGCGCTTTGAGATCTACT----GATGAAAAGCGCTATATA 142 i -- ---- i AmnSINE1#SINE 510 TTGTAAAGCGCTTTGGGATC--CTTCGGGATGAAAGGCGCTATATA 553 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.27 CpG sites = 2, Kimura (unadjusted) = 5.27 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (3 / 41), avg. gap size = 2.00 (6 / 3) 264 18.37 0.00 0.00 rnd-1_family-30#DNA/TcMar-Tigger 10 58 (136) X10b_DNA#DNA/TcMar-Tigger 8 56 (123) m_b1s502i5 rnd-1_family- 10 ACCCCGATATAACGCGACCCGATATAACACGAATTCGGATATAACGCGG 58 v i i i iv v i v X10b_DNA#DNA/ 8 ACCCCGTTATAACACGGCTCATTATTACACGGATTCGGATATACCGCGG 56 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.28 CpG sites = 5, Kimura (unadjusted) = 21.28 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 303 22.73 0.00 0.00 rnd-1_family-30#DNA/TcMar-Tigger 117 182 (12) UCON55#DNA/TcMar-Tigger 117 182 (10) m_b1s502i6 rnd-1_family- 117 TATAACGCGGTTTCACCTATAACGCGGTAAGATTTTTTGGCTCCCGAGGA 166 v i v vvv ivviv vi UCON55#DNA/Tc 117 TATAAGGCGGTCTCACCTATAAGGCGGTCCCACGGCATGGACCCCGAGGA 166 rnd-1_family- 167 CAGCGTTATATCGGGG 182 v i UCON55#DNA/Tc 167 CAGCGTTATAGCGAGG 182 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.16 CpG sites = 5, Kimura (unadjusted) = 27.08 Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 374 25.55 0.00 1.11 rnd-1_family-32#DNA 1 91 (83) Eulor9A#DNA 32 121 (180) m_b1s502i7 rnd-1_family- 1 ATGTTAAGGTTGCAAAGTCAAGCACTCAAAAGTTAGGAAATGCCAGAATT 50 i v i vi v i i i v i -i i i Eulor9A#DNA 32 ACGTTATGGCTGAGAATTTAAACGCACAAAAGTCAGGAAAT-TCAAAGTT 80 rnd-1_family- 51 AAGGTTGCCCGTGCAACCTTAATTCGGCCCCCTTGTGCGTA 91 v v vvv v i i i Eulor9A#DNA 81 ACGGTTCCCACAGCAACCGTAACTCGGCCCCCTTGCGCATA 121 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.06 CpG sites = 13, Kimura (unadjusted) = 31.82 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 663 6.17 0.00 0.00 rnd-1_family-33#DNA/hAT-Charlie 238 318 (7) UCON81#DNA/hAT-Charlie 4 84 (0) m_b1s502i8 rnd-1_family- 238 TATTACTGGCACGCGAAACCTTAAATTAGAGTGAATAAATGAAGACTCGG 287 ?i i UCON81#DNA/hA 4 TATTACTGGCACGNAAAACCTTAAATTAGAGTGAATAAATGAAGACTTGG 53 rnd-1_family- 288 CACACCACTTCTGAAAGGTTGCCGACCCCTG 318 ii i UCON81#DNA/hA 54 CATGCCACTTCTGAAAGGTTGCCAACCCCTG 84 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.68 CpG sites = 5, Kimura (unadjusted) = 6.68 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 1181 2.84 1.42 0.00 rnd-1_family-38#LINE/CR1 1 141 (0) CR1-L3B_Croc#LINE/CR1 3127 3269 (8) m_b1s551i9 rnd-1_family- 1 TGCCTTTCTGGAAGATATGCTTTAGTCAAACA--AGTTATTGGGCTCGAT 48 -- i CR1-L3B_Croc# 3127 TGCCTTTCTGGAAGATATGCTTTAGTCAAACACAAGTTATTGGGCTCAAT 3176 rnd-1_family- 49 GCAGGGGTAACTGGGTGAAATTCTATGGCCTGTGTTATACAGGAGGTCAG 98 i iv ? CR1-L3B_Croc# 3177 ACAGGGGTAACTGGGTGAAATTTAATGGCCTGTGNTATACAGGAGGTCAG 3226 rnd-1_family- 99 ACTAGATGATCTAATGGTCCCTTCTGGCCTTAAAATCTATGAA 141 ? CR1-L3B_Croc# 3227 ACTAGATGATCTAATGGTCCCTTCTGGCCTTAAANTCTATGAA 3269 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.95 CpG sites = 3, Kimura (unadjusted) = 2.95 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.01 (1 / 140), avg. gap size = 2.00 (2 / 1) 358 16.92 0.00 0.00 rnd-1_family-4#SINE/MIR 11 75 (39) C Chompy-6_Croc#DNA/PIF-Harbinger (432) 548 484 m_b1s502i9 rnd-1_family- 11 ATGGTCCAGTGGTTAGGGCGCTAGCCTGGGACTTGGGAGACCTGGGTTCA 60 i i i i i v ii ?v i C Chompy-6_Croc 548 ATAGCCTAGTGGTTAGAGCACTCGCCCAGGANGTGGGAGACCCGGGTTCA 499 rnd-1_family- 61 ATTCCCTGCTCTGCC 75 v ? C Chompy-6_Croc 498 ATTCCCTCCTCNGCC 484 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.44 CpG sites = 8, Kimura (unadjusted) = 20.45 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 221 8.57 0.00 0.00 rnd-1_family-4#SINE/MIR 80 114 (0) MIR3#SINE/MIR 77 111 (97) m_b1s601i4 rnd-1_family- 80 ACTTCCTGTGTGACCTTGGGCAAGTCACTTAGCCT 114 ?v vi MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCT 111 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 9.39 CpG sites = 1, Kimura (unadjusted) = 9.39 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 232 3.33 0.00 0.00 rnd-1_family-4#SINE/MIR 85 114 (0) MIRc#SINE/MIR 85 114 (154) m_b1s601i5 rnd-1_family- 85 CTGTGTGACCTTGGGCAAGTCACTTAGCCT 114 i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCT 114 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 3.45 CpG sites = 1, Kimura (unadjusted) = 3.45 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 317 14.81 1.85 0.00 rnd-1_family-40#DNA/hAT 1 54 (54) UCON69#DNA/hAT 107 161 (325) m_b1s502i10 rnd-1_family- 1 AAGTTTCTAGCCCTCGTGGTTGCGGAGAAAG-CTTGAAAACGTGACCCGA 49 ii i i- v i v UCON69#DNA/hA 107 AAGTTTCTAGCCCTTATGGTTGCGAAGAAAACCTTCAAAATGTGAACCGA 156 rnd-1_family- 50 GTGCA 54 i UCON69#DNA/hA 157 GTGTA 161 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.93 CpG sites = 6, Kimura (unadjusted) = 16.93 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 6262 1.98 0.14 0.28 rnd-1_family-41#LINE/CR1 1 709 (0) CR1-L3A_Croc#LINE/CR1 2733 3440 (848) m_b1s551i10 rnd-1_family- 1 CAGCAGGTCCGGATAACTTGCATCCAAGAGTTTTAAAAGAGCTGGCTGAG 50 i CR1-L3A_Croc# 2733 CAGCAGGTCCGGATAACTTGCATCCAAGAGTTTTAAAAGAGCTGGCCGAG 2782 rnd-1_family- 51 GAGCTCGCTGGACCGTTAATGTTGATTTTCAATAAGTCTTGGAACACTGG 100 v CR1-L3A_Croc# 2783 GAGCTCTCTGGACCGTTAATGTTGATTTTCAATAAGTCTTGGAACACTGG 2832 rnd-1_family- 101 GGAAGTTCCAGAAGACTGGAAGAAAGCTAATGTTGTGCCAATATTTAAAA 150 i CR1-L3A_Croc# 2833 GGAAGTTCCAGAGGACTGGAAGAAAGCTAATGTTGTGCCAATATTTAAAA 2882 rnd-1_family- 151 AGGGTAAACGGGATGACCCGGGTAATTATAGGCCTGTCAGCCTGACATCG 200 CR1-L3A_Croc# 2883 AGGGTAAACGGGATGACCCGGGTAATTATAGGCCTGTCAGCCTGACATCG 2932 rnd-1_family- 201 ATCCCGGGCAAGATAATGGAGCGGCTGATACGGGACTCGATTAATAAAGA 250 i i CR1-L3A_Croc# 2933 ATCCCGGGCAAAATAATGGAACGGCTGATACGGGACTCGATTAATAAAGA 2982 rnd-1_family- 251 ATTAAAGGAGGGTAATATAATTAATGCCAATCAACATGGGTTTATGGAAA 300 CR1-L3A_Croc# 2983 ATTAAAGGAGGGTAATATAATTAATGCCAATCAACATGGGTTTATGGAAA 3032 rnd-1_family- 301 ATAGATCCTGTCAAACTAACTTGATATCTTTTTTGATGAGATTACAAGTT 350 i -- CR1-L3A_Croc# 3033 ATAGATCTTGTCAAACTAACTTGATATC--TTTTGATGAGATTACAAGTT 3080 rnd-1_family- 351 TGGTTGATAAAGGTAATAGTGTTGATGTAATATACTTAGACTTCTGTAAG 400 i CR1-L3A_Croc# 3081 TGGTTGATAAAGGTAATAGCGTTGATGTAATATACTTAGACTTCTGTAAG 3130 rnd-1_family- 401 GCGTTTGACTTGGTACCGCACGACATTTTGATTAAAAAACTAGAACGATA 450 i i CR1-L3A_Croc# 3131 GCATTTGACTTGGTACCGCACGACATTTTGATTAAGAAACTAGAACGATA 3180 rnd-1_family- 451 TAAAATTAACATGGCACACATTAAATGGATTAAAAACTGGCTAACTGATA 500 i i CR1-L3A_Croc# 3181 CAAAATCAACATGGCACACATTAAATGGATTAAAAACTGGCTAACTGATA 3230 rnd-1_family- 501 GGTCTCAAAATGTAATTGTAAACGGGGAATCATCATCGAGCGGGTGTGTT 550 i i CR1-L3A_Croc# 3231 GGTCTCAAAATGTAATTGTAAATGGGGAATCATCATCGAGCGGGCGTGTT 3280 rnd-1_family- 551 TCTAGTGGGGTCCCGCAGGGATCGGTTCTTGGCCCTACGCTATTTAACAT 600 CR1-L3A_Croc# 3281 TCTAGTGGGGTCCCGCAGGGATCGGTTCTTGGCCCTACGCTATTTAACAT 3330 rnd-1_family- 601 TTTTATCAATGACCTGGAAGAAAACATAAAATCATCACTGATAAAGTTTG 650 i CR1-L3A_Croc# 3331 TTTTATCAATGACCTGGAAGAAAACATAAAATCATTACTGATAAAGTTTG 3380 rnd-1_family- 651 CAGATGACACAAA-ATTGGGGGAGTGGTAAATAATGAAGAGGACAGGTCA 699 - CR1-L3A_Croc# 3381 CAGATGACACAAAGATTGGGGGAGTGGTAAATAATGAAGAGGACAGGTCA 3430 rnd-1_family- 700 CTGATACAGA 709 CR1-L3A_Croc# 3431 CTGATACAGA 3440 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 1.62 CpG sites = 13, Kimura (unadjusted) = 2.02 Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.00 (3 / 708), avg. gap size = 1.00 (3 / 3) 755 28.96 4.67 4.03 rnd-1_family-44#LINE/CR1 71 563 (3337) CR1-L3A_Croc#LINE/CR1 817 1312 (2976) m_b1s551i11 rnd-1_family- 71 TTGGGGACTCCTTACTGAGGAGATTGGACAGGCC--TGTGACCAGGG-CG 117 i i iv i i v v iv -- v - v - i CR1-L3A_Croc# 817 TCGGGGATTCTATACTAAGAAGAATGGAAAGAACGTTCTG-CAAGGGACA 865 rnd-1_family- 118 GACCCGGAGAACAGAAGGGTGTGCTGTCTGCCGGGCGCNAAGATACGGGA 167 i -- v i v v v v ? i i CR1-L3A_Croc# 866 GGC--GGACAACAGGACGGTGTGCTGTCTTCCCGGAGCCAAGACACGAGA 913 rnd-1_family- 168 TGTGGACCTGCGGCTGAAAAGGATCCTAANAGGAGCGGGNAAGAACCCCT 217 i ivi iv i i v v i i ?ivvi ? i i vi CR1-L3A_Croc# 914 TGCGACTCTAAGACTGGATAGGCTTCTGAAGTCGGCGGGCAAGGATCCAC 963 rnd-1_family- 218 TGATNATCCTTCATGTGGGAACGAATGACACGGCTAGGTTCTCGTTGGAG 267 i ? vv v i v v v v ------ i-- ? CR1-L3A_Croc# 964 TGGTGATGGTGCATATCGGCACTAATGACACTGCT------TCGC--GNG 1005 rnd-1_family- 268 AGAA-TCAAGGGAGATTATG-------CCAGG---CTGGGGAAGACGCTC 306 v v- v--- i-------i --- v i i ii v CR1-L3A_Croc# 1006 ATACCTCAC---AGATTATAGACGACTTCAGGGAACTCGGAAGGGTGCTG 1052 rnd-1_family- 307 AAGGAGATAGAGGCTCAGGTNATCTTCAGTGGGATTCTGCCTGTTCCN-- 354 vii v ii i ? vvv i i v i ?-- CR1-L3A_Croc# 1053 AAGGAGAAGAATGTCCAAGTGATCTTCTCGGAGATCCTTCCTGTCCCACG 1102 rnd-1_family- 355 AGGGAAGGGCAGCAAAGGGCTGACAGGATTGTGACGATNAATAGNTGGCT 404 v ivii i i -- v i v ivii ? iv ? CR1-L3A_Croc# 1103 AGCGAAGGAAGACAGAAGGC--AGAAGATTCTGGAAGTGAACCGCTGGCT 1150 rnd-1_family- 405 AAGGGAGTGGTGCTATAAGG---AGGGCTTTGGGATGTATGGC-CACTGG 450 i vi --- --- i v- v i v- CR1-L3A_Croc# 1151 AGGTAAGTGGTG---TAAGGTAGAGGGTTTTGGT-TTTGTGGAACACTGG 1196 rnd-1_family- 451 GAGGCNTTC---GNGGACAGACGACTGTTCTCGCGGGATGGGCTTCACCT 497 vvvi ? --- ? v iiv i v vvviv v i i CR1-L3A_Croc# 1197 TCCACCTTCTATGGGGAGAAGGGGCTGTACAGTTTGGATGGCCTCCATCT 1246 rnd-1_family- 498 GAGTAGGGAGGGAAATAGACTTCTGGGANGGAGGCTGGCNCANCTNATCA 547 v iii vi v i i?iv ?vi? ?i CR1-L3A_Croc# 1247 CAGTAGAAGGGGAACCAGTCTTCTAGGGGACAGGCTGGCTAGACTAGTCA 1296 rnd-1_family- 548 AAAGAGCTTTAAACTA 563 ii i v CR1-L3A_Croc# 1297 GGAGGGCGTTAAACTA 1312 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.48 CpG sites = 74, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.17 (74/63) Gap_init rate = 0.06 (29 / 492), avg. gap size = 1.48 (43 / 29) 384 32.41 3.08 2.68 rnd-1_family-44#LINE/CR1 704 963 (2937) CR1-3_Croc#LINE/CR1 185 445 (3160) m_b1s551i12 rnd-1_family- 704 AGGCCCGCAACATATAGTGCTACTAATGGGAGAC----AGGCCAAACGGC 749 v i --- --i i vi ii ---- i vv CR1-3_Croc#LI 185 AGGACTGCAACA---AGTG--GCCAAAAGGAAGCGAGTAGGTCAAAATGC 229 rnd-1_family- 750 A---TACATTAGGATGTTTGTACACCAATGCGAGGAGCCTAGGTAACAAA 796 --- i iv - iv i v i iv i v i CR1-3_Croc#LI 230 AAAATACGTCCG-ATGCATGTATACAAATGCGAGAAGTATGGGGAATAAA 278 rnd-1_family- 797 ATGGAGGAACTGGA-GCTNCTGGTCCAGGAAGTGAAACCGGATATCGTAG 845 vvi v i - ? -i i iiv iv vivv v vi v CR1-3_Croc#LI 279 CAAGATGAGCTGGAAGCTGC-AGCCTGTGAAAAGAACTATGATCTGATTG 327 rnd-1_family- 846 GGATAACAGAAACGTGGTGGAATGGCAGTCACGACTGGAGCACAGGTATN 895 v v i v i ii vv i i iiiiviii ? CR1-3_Croc#LI 328 GCATCACAGAGACCTGGTGGGACAGCTCTTATGACTGGAATGTCAACATC 377 rnd-1_family- 896 GAAGGGTATGCGCTGTTTAGGAAAGACCGGAATAAAGGTAAAGGTGGGGG 945 i v ii v v i v iv iiii v v CR1-3_Croc#LI 378 GAGGGTTACACTCTGTTTCGGAAGGACAGGGTTGGGAGAAAAGGTGGTGG 427 rnd-1_family- 946 GGTGGCATTGTATGTCAA 963 v v v CR1-3_Croc#LI 428 TGTTGCCTTGTATGTCAA 445 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 46, Kimura (unadjusted) = 44.12 Transitions / transversions = 1.28 (46/36) Gap_init rate = 0.04 (10 / 259), avg. gap size = 1.50 (15 / 10) 561 27.82 1.73 3.52 rnd-1_family-44#LINE/CR1 733 963 (2937) Plat_L3#LINE/CR1 705 931 (2642) m_b1s551i13 rnd-1_family- 733 GAGACAGGCCAAACGGCATACATTAGGATGTTTGTACACCAATGCGAGGA 782 i iv --i - - iii i v i Plat_L3#LINE/ 705 GGGACAACCCA--TGGC-TAC-TTGAAATGTTTGTACGCAAATGCAAGGA 750 rnd-1_family- 783 GCCTAGGTAACAAAATGGAGGAACTGGAGCTNCTGGTCCAGGA----AGT 828 v i v i vv v ?i i ii ---- Plat_L3#LINE/ 751 GCATGGGAAATAAACAGGAGGAACTGGAGGTCTTAGCTCAGGACCACAGT 800 rnd-1_family- 829 GAAACCGGATATCGTAGGGATAACAGAAACGTGGTGGAATGGCAGTCACG 878 v ----v i viiv i v i i ii v i Plat_L3#LINE/ 801 TA----TGATGTAACTGGAATAACTGAGACGTGGTGGGACAGCACTCATG 846 rnd-1_family- 879 ACTGGAGCACAGGTATNGAAGGGTATGCGCTGTTTAGGAAAGACCGGAAT 928 ii v vv ? vv i i iv v v Plat_L3#LINE/ 847 ACTGGAGTGCTGGACTAGAAGGGTATCGGTTGTTCAGGAAAGATAGGCAG 896 rnd-1_family- 929 AAAGGTAAAGGTGGGGGGGTGGCATTGTATGTCAA 963 ii iiv i v v v v v ii Plat_L3#LINE/ 897 GGAAAAAAGGGAGGTGGTGTTGCCTTGTACATCAA 931 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 35, Kimura (unadjusted) = 35.90 Transitions / transversions = 1.30 (35/27) Gap_init rate = 0.04 (9 / 230), avg. gap size = 1.33 (12 / 9) 226 32.56 4.40 6.90 rnd-1_family-44#LINE/CR1 1161 1546 (2354) Plat_L3#LINE/CR1 1121 1497 (2076) m_b1s551i14 rnd-1_family- 1161 GGAACTGTGTGATTATGGGAGACTTTAACTTCCCGGATATAGATTGGGGG 1210 v - i v v i ---i vv Plat_L3#LINE/ 1121 GGATCTG-GTGGTGATGGGAGACTTTAACTACCCAGATAT---CTGCTGG 1166 rnd-1_family- 1211 ACAAGCGCTAGTAATAATAATAGGGCTCAGATN----------TTCCTGG 1250 v ------ v-i iii v v ?---------- ii Plat_L3#LINE/ 1167 AAAAGC------AATT-CAGCGGGCCACAGATCGTCAAACAGGTTTTTGG 1209 rnd-1_family- 1251 ATGTG-ATAGCTGATCGATTCCTTCAC-CAAGTAGTNGCTGAACCGACGA 1298 - - v vv - i i i vii- iiv ? vv i i v Plat_L3#LINE/ 1210 AT-TGCATTGGGGA-CAATTTCCTAGTGCAGAAAGTAGAGGAATCAACTA 1257 rnd-1_family- 1299 GGGGGGATGCCATTTTAGATTTGGTTTTGGTGAGTAGTGAGGACCTCGTN 1348 vi v i v i i viiv iii v i vi v ? Plat_L3#LINE/ 1258 GGGCAGATGCCCTTCTTGATTTGATTCTTACTAACGGGGAAGAATTAGTC 1307 rnd-1_family- 1349 GAGGAAGTGGTTGTAGGGGACAACCTTGGCTCGAGTGATCATGAGCTAAT 1398 vv iivv i iv iv ivvi i ii v i Plat_L3#LINE/ 1308 GAGGATCTAAAGGTGGATGGAAACCTTGGTGGAAGCGATCACAAGATGAT 1357 rnd-1_family- 1399 TCGGTTTAAA---CTAAATGGAAGGANTAACAGAANTAAGTCNGNGACTA 1445 ivvi i i--- i- i?vi v ? v iv? ?--- Plat_L3#LINE/ 1358 CGTATTCAAGATCCTAAG-GGAAGGGAGGAGAGAAGTCAGCAAGA---TA 1403 rnd-1_family- 1446 GGGTTTNTG-ATTTCAAAAGGGCCAACTTTAANAAATTAAGGGGACTGGT 1494 ii vvv? - i i ii ii v i ? iii v v i Plat_L3#LINE/ 1404 AAGAAAATGAACTTTAGGAAAGCAAATTTTAACAGGCTTAGGGCACTAGT 1453 rnd-1_family- 1495 NAGGGAAGTGGATTGGACTGAAGAACTNANGGATCTAA-AGGCGGAGGAG 1543 ?-- -- iiv iv i --- ? --i - ii Plat_L3#LINE/ 1454 A--GGAA--GGACCCGATGGAAGGA---AAG--CCTAAGAGGCAAAGGAG 1494 rnd-1_family- 1544 GCC 1546 v Plat_L3#LINE/ 1495 TCC 1497 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 68, Kimura (unadjusted) = 46.00 Transitions / transversions = 1.39 (68/49) Gap_init rate = 0.08 (32 / 385), avg. gap size = 1.34 (43 / 32) 319 32.18 1.72 0.00 rnd-1_family-44#LINE/CR1 1791 1964 (1936) CR1_Mam#LINE/CR1 593 769 (1435) m_b1s551i15 rnd-1_family- 1791 ACCTTGCGAGGGGAATTAAAACCAATAGTAAGAGGTTCTATAGCCATATA 1840 i ivvii i i i v ivi i v CR1_Mam#LINE/ 593 ACCTTGCAAGGGACTCCAAAGCCAATAATAAAAGGTTCTTTAAATACATC 642 rnd-1_family- 1841 AATAGGAAGAAAACAAAGAAAGAAGAAGTGGGACCG-CTGAAGACTGTGG 1889 vi ? i iv ivv i vv i-i v iiii CR1_Mam#LINE/ 643 AAAGGNAGGAAGCCAGCTAGAGAATCAGTGGGACCATTTGATGATCACGG 692 rnd-1_family- 1890 -NCGGAGTGGAGATTAAAGATAATCTAGG-CATGGCCCAATATCTAAACG 1937 -? ii iv vi? i v i vvv -v i vv iviv ? i CR1_Mam#LINE/ 693 TGCAAAAGGTGNACTCAAGATGAAAAAGGAGATAGCAGAGAGACTNAATG 742 rnd-1_family- 1938 AATACTTTGCNTCGGTNTTTAATGAGG 1964 v ? ? v CR1_Mam#LINE/ 743 AATTCTTTGCTTCGGTCTTTACTGAGG 769 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.21 CpG sites = 31, Kimura (unadjusted) = 45.31 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.02 (3 / 173), avg. gap size = 1.00 (3 / 3) 585 28.22 0.84 2.12 rnd-1_family-44#LINE/CR1 2074 2312 (1588) CR1-12_AMi#LINE/CR1 378 613 (1) m_b1s551i16 rnd-1_family- 2074 AAATCGGGGGGACCGGACGATCTTCATCCGAGAATATTAAAGGAACTGGC 2123 i v v i iv v v ii ii i i i i CR1-12_AMi#LI 378 AAATCAGCGGGTCCGGATGACATGCATCCCAGGGTGCTGAGGGAATTAGC 427 rnd-1_family- 2124 GCGNGAAATTGCAAGCCCATTAGCGANAATTTTTAATGAATC-TGTA-AA 2171 vvi? -i i ?iiv i i i ?v i vi i - v - CR1-12_AMi#LI 428 TAATGAA-CTACNGAACCACTGGCAATTATTTTTGAAAAGTCATGGAGAA 476 rnd-1_family- 2172 CTCGGGGGTNGTACCGTNTGACTGGAGAATNGCTAACGTGGTTCCTATTT 2221 -- v? - iv?v v? v i i v ? i CR1-12_AMi#LI 477 CT--GGGGAGGT-CCAGAGGACTGGAGAAAAGCAAATGTAGTACCNATCT 523 rnd-1_family- 2222 TCAAGAAAGGGAAAAAAAGTGATCCGGGTAACTACAGGCCTGTTAGTTTG 2271 i i i ? ? i i - v i i ? CR1-12_AMi#LI 524 TCAAAAAAGGGAAGAAGAGNGATCCNGGCAATTACA-GCCAGTCAGTCTN 572 rnd-1_family- 2272 ACATCTGTAGTATGCAAGGTCTTGGAAAAAATTTTGAAGGA 2312 v vi vvivv ? ii vv v v i CR1-12_AMi#LI 573 ACCTCAATCCCTGGNAAAATAATGGAACAAATATTAAAGGA 613 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.63 CpG sites = 38, Kimura (unadjusted) = 38.63 Transitions / transversions = 1.36 (38/28) Gap_init rate = 0.03 (7 / 238), avg. gap size = 1.00 (7 / 7) 7354 16.78 0.21 3.11 rnd-1_family-44#LINE/CR1 2101 3521 (379) CR1-11_Crp#LINE/CR1 1 1381 (80) m_b1s551i17 rnd-1_family- 2101 CCGAGAATATTAAAGGAACTGGCGCGNGAAATTGCAAGCCCATTAGCGAN 2150 v vi i i i i? i i i iv i ? CR1-11_Crp#LI 1 CCCAGAATTCTGAAAGAACTGGCACATGAAATCGCAGGTCCGGTAGCAAG 50 rnd-1_family- 2151 AATTTTTAATGAATCTGTAAACTC-GGGGGTNGTACCGTNTGACTGGAGA 2199 i i i v v - i ? i ? CR1-11_Crp#LI 51 GATTTTTAATAAATCTATCAAGTCAGAGGGTGGTACCATATGACTGGAGA 100 rnd-1_family- 2200 ATNGCTAACGTGGTTCCTATTTTCAAGAAAGGGAAAAAAAGTGATCCGGG 2249 -? v v i ----- ---------- v i CR1-11_Crp#LI 101 A-AGCAAACTTAG-----AT----------GTGGAAAAAAGTGATCCGGG 134 rnd-1_family- 2250 TAACTACAGGCCTGTTAGTTTGACATCTGTAGTATGCAAGGTCTTGGAAA 2299 i i i v vi ii i v CR1-11_Crp#LI 135 CAACTACAGGCCCGTTAGTCTGACCTCAATAGTATGCAAGGCTTTAGAAC 184 rnd-1_family- 2300 AAATTTTGAAGGAGAAAGTAGTTAAGGACNTTGAGGTCAATGGCAATTGG 2349 i i i i i ? v v v v CR1-11_Crp#LI 185 AAATTTTGAAGGAAAGAATAATTAAAGACATGGAGGTAAATGGAAAATGG 234 rnd-1_family- 2350 GATAAANTACAACATGGTTTTACGAAAGGTAGATCGTGCCAAACCAACCT 2399 ? i v v i i CR1-11_Crp#LI 235 GATAAAATGCAACATGGGTTTACCAAAGGTAGATCGTGCCAGACTAACCT 284 rnd-1_family- 2400 GATCTCCTTCTTTGAGAAGGTAACGGATTTTTTAGACAAGG--GAAATGC 2447 v- i v i v i i -- CR1-11_Crp#LI 285 GATA-CTTTCTTTGATAAGATAACTGATTTTCTAGACAAAGNAGAAATGC 333 rnd-1_family- 2448 GGTGGATCTAATNTACCTGGATTTCAGTAAGGCGTTTGATACGGTNCCAC 2497 i ? ? i i i i ? CR1-11_Crp#LI 334 GGTAGATCTNATCTATCTGGACTTCAGTAAAGCATTTGATACGGTGCCAC 383 rnd-1_family- 2498 ATGGGGAATTATTGGTTAAATTGGAAAAGATGGGGATCGATATGAAAATC 2547 i - i ii i iii ii i i CR1-11_Crp#LI 384 ATGGGAAA-TATTAGTTAAGCTGGAGAAGATGGGGATTAGTACAAGAATT 432 rnd-1_family- 2548 GAGAGGTGGATAAGGAACTGGTTAAAGGGGAGACTGCAGCGGGTCGTACT 2597 vi - i ------ i ivi i ? i CR1-11_Crp#LI 433 GTAAGGTGG-TAAGGAGCT------AAGGGAGATGACAACGGGTNGTGCT 475 rnd-1_family- 2598 GAAAGGTGAACTGTCAGGCTGGAGGGAGGTTACTAGTGGAGTTCCTCAGG 2647 - ? i - - - i CR1-11_Crp#LI 476 GAAAGG-GAANTATC-GGCTGGA-GGAGGTTACTAGTGGAGTT-CTCAAG 521 rnd-1_family- 2648 GNTCGGTTTTGGGACCAATCTTATTTAATCTNTTTATTACTGACCTCGGN 2697 ? i i v ? i v i ? CR1-11_Crp#LI 522 GATCGGTCTTGGGACCGATCTTATTTAATATTTTCATTAATGACCTTGGC 571 rnd-1_family- 2698 ACCGAANGCGGGAGTGGGCTGATAAAGTTTGCGGATGACACGAAGNTGGG 2747 - i ? ii v i i i v i ? CR1-11_Crp#LI 572 A-CAAAAGTAGGAGTGTGCTAATGAAATTTGCTGATGACACAAAGTTGGG 620 rnd-1_family- 2748 AGGCGTTGCCAATNCGGAGGAGGACCGGGATATCCTGCAGGGAGACCTGG 2797 i i i ? i i v i i v CR1-11_Crp#LI 621 AGGCATCGTCAATACAGAGGAGGATCGGGATATCATACAGGAAGAACTGG 670 rnd-1_family- 2798 ATGACCTTGTGAACTGGAGTANCAGAAATAGGATGAAATTTAATAGTGAA 2847 v - ?i i i iv CR1-11_Crp#LI 671 ATGACCTTGAG-ACTGGAGTAATAGAAATGGGATGAAATTCAATAGTACA 719 rnd-1_family- 2848 AAGTGCAAGGTNATGCATTTAGGGACGAATAACAAGAATTTTNGTTACAA 2897 ? i --- i i? i i CR1-11_Crp#LI 720 AAGTGCAAGGTCATGCACTTAGGGAC---TAATAAGAATTTCTGCTATAA 766 rnd-1_family- 2898 GCTGGGGACGCATCGGTTGGAAGTAACGGAGGAGGAGAAGGACCTNGGGG 2947 ii v i iii? ------ i ? v CR1-11_Crp#LI 767 GCTGGGAGCTCATCAGTTGGAAACGNC------GGAGAAAGACCTGGGTG 810 rnd-1_family- 2948 TNCTNGTNGACCGCAGGATGACTATGAGCCGNCAATGTGACGTGGCNGTG 2997 ? ? ? i i i? i i ? CR1-11_Crp#LI 811 TACTAGTCGATCACAGGATGACTATGAGCCACCAATGTGATGCGGCCGTG 860 rnd-1_family- 2998 AAAAAAGCCAATGCGGTCTTGGGATGCATTAGGCGAGGTATNTCCAGTAG 3047 i v i i i ? --i ? CR1-11_Crp#LI 861 AAAAAGGCAAATGCGATCCTAGGATGCATNAG--AAGGTATTTCCAGTAG 908 rnd-1_family- 3048 GGATAAGGAGGTGCTGCTNCCGTTGTACAAGGCGCTGGTGAGACCTCATT 3097 i i i ii iv ? i -i i CR1-11_Crp#LI 909 AGATAGGGAAGTATTAATGCCATTGTACAAGG-ACTGGTGAGACCTCATC 957 rnd-1_family- 3098 TGGAGTACTGTGTGCAGTTCTGGTCTCCCATGTTTAAAAAAGATGAACTC 3147 i i v i i i CR1-11_Crp#LI 958 TGGAATACTGTGTACAGTTCTGGTCACCCATGTTCAAGAAAGATGAATTC 1007 rnd-1_family- 3148 AAACTGGAACGGGTGCAGAGAAGGGCCACTAGGATGATCAGAGGAATGGA 3197 i i i CR1-11_Crp#LI 1008 AAACTGGAACAGGTGCAGAGAAGGGCTACTAGGATGATCAGGGGAATGGA 1057 rnd-1_family- 3198 AAACCTGTCGTATGAAAGGAGACTAGAGGAGCTTGGGTTGTTTAGTCTGA 3247 i i i v i i i i v i ii CR1-11_Crp#LI 1058 GAGCCTATCTTACGAGAGGAGACTAAAAGAGCTTGGCTTGTTTAGCCTAG 1107 rnd-1_family- 3248 CAAAGCGAAGGCTGAGGGGGGATATGATTGCTNTCTTTAAATATATCAGA 3297 i i v i i CR1-11_Crp#LI 1108 CAAAACGAAGGCTGAGAGGGGATATGATTGCTNTCTATAAATACATCAGG 1157 rnd-1_family- 3298 GGGATNAATACAAGGGAGGGAGAGGAATTATTCCAGCTTAGTACTAATGT 3347 i ? i v i ii iv v ivivi CR1-11_Crp#LI 1158 GGGGTAAACACCAGGGAGGGAGAAGAGCTATTTAAGCTAAAGGACAATGT 1207 rnd-1_family- 3348 GGACACGAGAACGAATGGATATAAACTGGCCGTGGGGAAGTTTAGGCTTG 3397 v i i i i i iiv i v CR1-11_Crp#LI 1208 TGGCACAAGAACAAATGGGTATAAACTGGCCATGAATAAATTTAGGCTGG 1257 rnd-1_family- 3398 AAATTAGACGAAGGTTTCTGACCGTCAGAGGGGTGAAATATTGGAACGGC 3447 v i i vi ii vi i CR1-11_Crp#LI 1258 AAATTAGAAGAAGGTTTCTAACCATCAGAGCAGTGAGGTTCTGGAACAGC 1307 rnd-1_family- 3448 CTTCCGAGGGAAACGGTGGGGGCGACGGACCTGTCTGGTTTTAAGATTAA 3497 i vi i iii i vii iv i vi CR1-11_Crp#LI 1308 CTTCCAATAGGAGTAGTGGGGGCAAAAAACCTAACTAGTTTTAAGATGGA 1357 rnd-1_family- 3498 GTTNGATAAGTTTATGGAGGGAAT 3521 i ? v i i i CR1-11_Crp#LI 1358 GCTTGATCAGTTTATGAAAGGGAT 1381 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.41 CpG sites = 177, Kimura (unadjusted) = 20.18 Transitions / transversions = 3.28 (177/54) Gap_init rate = 0.03 (45 / 1420), avg. gap size = 1.02 (46 / 45) 580 23.19 0.65 1.97 rnd-1_family-44#LINE/CR1 3598 3751 (149) CR1-3_Croc#LINE/CR1 3213 3364 (241) m_b1s551i18 rnd-1_family- 3598 GGCTGGAGACTCTTGCCTACATGCTCGGGGTCTTACTGATCGCCATATTT 3647 i iv ivivi i vv i CR1-3_Croc#LI 3213 GGCTAGAGGGTCTTGCCCCTCCGCTCAGGGTCAGACCGATCGCCATATTT 3262 rnd-1_family- 3648 GGGGTCGGGAAGGAATTTTCCTCCA-GGGCAGATTGGCTGAGCCTCTGGA 3696 i v i - v ivvi v v i CR1-3_Croc#LI 3263 GGGGTCAGGAAGGAATTTTACCCCATGGTCAGATTGGTACGGACTGTGGG 3312 rnd-1_family- 3697 GGTTTTTCGCCTTCCTCCGCAGCATGGGGCAGGGATCACTAGCAGGAGGG 3746 - i i iv iv vi v v v -- i CR1-3_Croc#LI 3313 GGTTTTT-GCCTTCCTCTGTAGCGGGGGGCGTGGCCCTCTACCCG--GGA 3359 rnd-1_family- 3747 TCTCT 3751 CR1-3_Croc#LI 3360 TCTCT 3364 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.60 CpG sites = 18, Kimura (unadjusted) = 27.99 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.03 (4 / 153), avg. gap size = 1.00 (4 / 4) 237 26.32 2.20 8.14 rnd-1_family-44#LINE/CR1 3810 3900 (0) CR1-3_Croc#LINE/CR1 3519 3604 (1) m_b1s551i19 rnd-1_family- 3810 GGGTAGGGACGGTTTTGTGGCCTGCAGCATGCAGGGGGTCAGACCAGATG 3859 i i i ------- vv v ii i CR1-3_Croc#LI 3519 GGATAGGGATGAT-------CCTGCCTCAGGCAGGGGGTTGGACTAGATG 3561 rnd-1_family- 3860 ATC-ATAATGGTCCCTTCTGACCTTAA-AGTCTATGAGTCTAT 3900 i -v iiv iii i v-vv v CR1-3_Croc#LI 3562 ACCTCTGGAGGTCCCTTCCAGCCCTACTTCTCTATGATTCTAT 3604 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 13, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.10 (9 / 90), avg. gap size = 1.00 (9 / 9) 501 12.82 0.00 1.28 rnd-1_family-44#LINE/CR1 3822 3900 (0) CR1-L3B_Croc#LINE/CR1 3197 3274 (3) m_b1s551i20 rnd-1_family- 3822 TTTTGTGGCCTGCAGCATGCAGGGGGTCAGACCAGATGATCATAATGGTC 3871 vi ii?i i i i - CR1-L3B_Croc# 3197 TTTAATGGCCTGTGNTATACAGGAGGTCAGACTAGATGATC-TAATGGTC 3245 rnd-1_family- 3872 CCTTCTGACCTTAAAGTCTATGAGTCTAT 3900 i ? i CR1-L3B_Croc# 3246 CCTTCTGGCCTTAAANTCTATGAATCTAT 3274 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.05 CpG sites = 9, Kimura (unadjusted) = 15.05 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 464 7.14 0.00 0.00 rnd-1_family-45#SINE/MIR 1 70 (0) MIR1_Amn#SINE/MIR 14 83 (147) m_b1s601i6 rnd-1_family- 1 TGGTCTTGTGGNTAAGGCACTGGACTGGGACTCAGGAGACCTGGGTTCTA 50 v ? ii i ? MIR1_Amn#SINE 14 TGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNA 63 rnd-1_family- 51 TTCCCGGCTCTGCCACTGAC 70 ? ?i MIR1_Amn#SINE 64 NTCCCGGCTCTGCCACTNGC 83 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 6.54 CpG sites = 4, Kimura (unadjusted) = 8.10 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 344 19.05 0.00 0.00 rnd-1_family-50#DNA/hAT-Charlie 8 70 (355) Charlie2a#DNA/hAT-Charlie 1 63 (2798) m_b1s502i11 rnd-1_family- 8 CAGTGGTTCTCAACCAGGGGTACGCGTACCCCTGGGGGTACGCAGAGGTC 57 ii v v i i ii iii Charlie2a#DNA 1 CAGTGGTCTTCAAACTGGGGTATGCATACCCCTGGGGGTACGCGAAGACT 50 rnd-1_family- 58 TTCCAGGGGGTAC 70 i Charlie2a#DNA 51 TTCCAAGGGGTAC 63 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 10, Kimura (unadjusted) = 23.12 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 245 26.43 2.25 2.25 rnd-1_family-54#DNA 19 107 (98) MER131#DNA 49 137 (78) m_b1s601i7 rnd-1_family- 19 TTCCCATTATAAGACCCTGTTTTCAGTTGCTTATAACTTTGCC--AAACT 66 i iv i vv i iv -- vv MER131#DNA 49 TTTCCATTATAAACCCCTATTTTCAGGGGTTTATAACTCGGCCGTAAAAA 98 rnd-1_family- 67 TTAACCGTTTGGGCTGAAATTTTCCATGCCGGGTGTCTGCC 107 vi -- ii i vv i vi v v MER131#DNA 99 TTCGC--TCCGGGCTGAAACTTGGCATACAAGGTCTCAGCC 137 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.00 CpG sites = 11, Kimura (unadjusted) = 32.85 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.33 (4 / 3) 342 18.39 3.33 3.33 rnd-1_family-54#DNA 115 204 (1) C UCON60#Unknown (14) 286 197 m_b1s502i12 rnd-1_family- 115 GAATTTTTTTGGAAAGTTTCAGCCAAAACGGTTCAGCCGTTTCCGAG--A 162 i v v ? v ii -- C UCON60#Unknow 286 GAATTTCTTTTGAAAGTTTGAGCNAAATCGGTTCAGCCGTTTTTGAGTTA 237 rnd-1_family- 163 -ACGAGGCTAGGGAAAAATACGTTGTTTTGCCATGTTAAAAAA 204 -i v - i i ii-- v v? vi C UCON60#Unknow 236 TGCGAGGATA-GAAGAAATACAC--TTTTCCANTTCTAAAAAA 197 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.91 CpG sites = 9, Kimura (unadjusted) = 21.91 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.20 (6 / 5) 264 18.18 0.00 0.00 rnd-1_family-60#DNA/hAT-Blackjack 164 207 (327) MER94#DNA/hAT-Blackjack 1 44 (90) m_b1s502i13 rnd-1_family- 164 TAGGGTGACCAGATGTCCCGATTTTATAGGGACAGTCCCGATTT 207 v i i vviv i MER94#DNA/hAT 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCCGGTTT 44 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.20 CpG sites = 4, Kimura (unadjusted) = 20.94 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 492 28.88 2.93 2.93 rnd-1_family-63#LINE/CR1 1036 1274 (1966) CR1-L3B_Croc#LINE/CR1 368 606 (2671) m_b1s551i21 rnd-1_family- 1036 GGCAGACAAC-TAAANAGTGACAAGTTTTTAAAGTGCTTGTATACAAATG 1084 i v i- i ? -i v ?i v v i v CR1-L3B_Croc# 368 GGCAAAGAATGTGAAGAG-AAGANATTTTTCAATTGCTTATATACCAATG 416 rnd-1_family- 1085 CTAGAAGTCTAAATAATAAGATGGGTGAACTAGAGTGCCTCGTATTAAAT 1134 i iii i vvi iv i ivvi -- i - CR1-L3B_Croc# 417 CTAGGAGTCTGGGTAACAAGCAAGAGGAACTGGAAATTCTC--ATTGA-T 463 rnd-1_family- 1135 GAGGATA---TTGATATAATAGGCATCACAGAAACTTGGTGGAATGA--- 1178 i v --- v i v i i --- CR1-L3B_Croc# 464 GAGAAGAAATTTGATATAATTGGCATTACTGAAACCTGGTGGGATGATTC 513 rnd-1_family- 1179 GGATAATCAATGGGACACGGTAATACCAGGGTACAAAATATATCGGAAGG 1228 v i i--- i iiiviv v? v v i vv i v v CR1-L3B_Croc# 514 GCATGAC---TGGAATGTTAAAATCNCTGGTTATAACCTGTTTAGGAAGG 560 rnd-1_family- 1229 ACAGAACAGGTCGTGCTGGTGGGGGAGTGGCACTATATGTGAAAGA 1274 i i vivivv i i v ii v CR1-L3B_Croc# 561 ACAGAGCGGGTAAAAGAGGCGGGGGAGTGGCGCTCTACATTAAAGA 606 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 38, Kimura (unadjusted) = 37.97 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.04 (10 / 238), avg. gap size = 1.40 (14 / 10) 5540 25.45 1.16 3.02 rnd-1_family-63#LINE/CR1 1516 3233 (7) CR1_Mam#LINE/CR1 21 1707 (497) m_b1s551i22 rnd-1_family- 1516 TCAGGACGGGATGCAGAGATAAAATTTCTNGACACCTTAAATGACTGCTT 1565 i ii ii iivi ?ii i ? i vvvi ? i CR1_Mam#LINE/ 21 TCGGGACGAAATATAGAAGAGANGCTTTTCGATAAGACAAATNACCGCTT 70 rnd-1_family- 1566 CTTGGAGCAGCTAGTCCTGGAACCCACAAGGGGAGAGGCAATT--CTTGA 1613 i i ii v ii i -- i v v-- v CR1_Mam#LINE/ 71 CCTAGAATAGGTAGTTTTAGAACCCACAAGG--AAAGGAAATANACTGGA 118 rnd-1_family- 1614 TTTAGTCCTAAGTGGAGCACAGGATCTGGTCCAAGAGGTGAATATAGCTG 1663 i i i i ?i v v v iv i i ivv i i v CR1_Mam#LINE/ 119 CTTGGTTCTGAGNAGTGAACAGGAACTGGCGCAGGAAGTATCTGTGGGTG 168 rnd-1_family- 1664 GACCGCTCGGTAATAGTGACCATAATA-TAATTAAATTTAACATCCCTGT 1712 i i ----- - -- -ii i i --- CR1_Mam#LINE/ 169 AACCACT-----AT-GTGACCA--ATAACGATTAAATTCAACATTC---T 207 rnd-1_family- 1713 GGCGGGAA--GAACACCACAGCAG-CCCAACACNGTAGCATTTAATTTCA 1759 -- v v iv i-i v ?- ivi i i i CR1_Mam#LINE/ 208 GGCGGGAAAGGAAAACCAAAAAAAATCCATCACA-TGTTACTCAATTTTA 256 rnd-1_family- 1760 GAAAGGGGAACTACGCAAAAATGAGGAGGTTAGTTAAACGGAAATTAAAA 1809 i i vv v ivi i-- i v i CR1_Mam#LINE/ 257 GAAAAGGGAACTATGACAAAATGTGGGCATTAGTTAG--GAAAAATGAAA 304 rnd-1_family- 1810 GGTACAGTGACAAAAGTGAAATCCCTGCAAGCTGCATGGAAACTTTTTAA 1859 i ? ? vvv i vvv ii i vv v i v ? CR1_Mam#LINE/ 305 AGNANAGTTTAAAAAGTAAATAACCCACAGGAAGCCTGGAGACTATTTNA 354 rnd-1_family- 1860 AGACACCATAATAGAGGCTCAANTTAAATGTATACCCCAAATTAAAAAAC 1909 i v v i i i i?vv i i v?ii i ?v CR1_Mam#LINE/ 355 AAACACCTTATTGGAAGCCCAGGAAAAATGTGTGCCANGGATCAAAAANA 404 rnd-1_family- 1910 ACAG----TAAGAGAACCAAAAAAGNGCCACCGTGGCTAAACAACAAAGT 1955 v ---- vi i --- v?v ?v i viii CR1_Mam#LINE/ 405 CCAGGCGCTTGGAAAA---AAAAATACCCNGCATGGCTAACTGGCAAAGT 451 rnd-1_family- 1956 AAAAGAAGCAGTNAGAGGCAAAAAGGCATCCTTTAAAAAGTGGAA-GTCA 2004 v i vi ?iv vi i i i - v? CR1_Mam#LINE/ 452 CAAAGAGGCTATTGTAGGGGAAAAGGCATCTTTCAAAAAATGGAAAGANA 501 rnd-1_family- 2005 AATCCTANTGAGGAAAATAGAAAGGAGCATAAACTCTGGCAAGTNAAGTG 2054 ? v ? i i ii i vv ii v v i ? i i CR1_Mam#LINE/ 502 ANTCCAAGTGAGGAGAACAGGGAAGCCCGCAAAGTATGGCAGGTCAGGTA 551 rnd-1_family- 2055 TAAAAATATAATTAGGAAGGCCAAAAAAGAATTTGAAGAACAGCTAGCCA 2104 i vvviv vi i i v v v CR1_Mam#LINE/ 552 CAAACTAGAAATTAGGCGGGCCAAAAAAGAATTTGAGGAGCACCTTGCAA 601 rnd-1_family- 2105 AAGACTCAAAAAGTAATAGCAAAATNTTTTTTAAGTACATCAGAAGCAGG 2154 ii v ivi ii v? i i i i ? CR1_Mam#LINE/ 602 GGGACTCCAAAGCCAATAATAAAAGGTTCTTTAAATACATCAAAGGNAGG 651 rnd-1_family- 2155 AAGCCTGCTAAACAACCAGTGGGGCCACTGGACGATCGAGATGCTAAAGG 2204 v i v i i i v i iv i v CR1_Mam#LINE/ 652 AAGCCAGCTAGAGAATCAGTGGGACCATTTGATGATCACGGTGCAAAAGG 701 rnd-1_family- 2205 AGCACTCAAGGACGATAAGGCCATTGCGGAGAAACTAAATGAATTCTTTG 2254 v ? ivvi v vv v i i ? CR1_Mam#LINE/ 702 TGNACTCAAGATGAAAAAGGAGATAGCAGAGAGACTNAATGAATTCTTTG 751 rnd-1_family- 2255 CNTCGGTCTTCACGGCTGAGGATGTGAGGGAGATTCCCAAACCTGAGCCA 2304 ? i v vv i i v vv ii iiii CR1_Mam#LINE/ 752 CTTCGGTCTTTACTGAGGAAGACGTTAGGGAGATTCCCACTCCCAAATTG 801 rnd-1_family- 2305 TTCTTTTTAGGT-GACAAATCTGAGGAACTGTCCCAGATTGAGGTGTCAN 2353 - v i i- ii v v ivvi i v v ivvv? CR1_Mam#LINE/ 802 T-CTTTTGAAGCAGACAGGTCAGAGGTACTAGATCAAATAGTGGTAAACG 850 rnd-1_family- 2354 TAGAGGAGGTTTTGGAACAAATTGATAAACTNAACAGTA-ATAAGTCACC 2402 i v v i i v v i ?i i- - i CR1_Mam#LINE/ 851 CACAGGATGTTCTAGACCTAATTGACAAACTAGAT-GTAGATAAATCACC 899 rnd-1_family- 2403 GGGACCAGATGGTATTCACCCAAGAGTTCTGAAGGAACTCAAATGTGAAA 2452 - i i i iv CR1_Mam#LINE/ 900 GG-ACCAGATGGCATCCACCCAAGAGTTTTGAAGGAACTCAAGGGTGAAA 948 rnd-1_family- 2453 TTGCGGAACTACTAACTGTGGTNTGTAACCTGTCNTTTAAATCAGCTTCT 2502 i iv ---- v v ----- v? vi - i iv CR1_Mam#LINE/ 949 CTGTTGA----CAAAATGTG-----TAACCTGTATTACAAA-CGGCCACT 988 rnd-1_family- 2503 GTACC-AGATGACTGGAGGATAGCTAATGTGACGCCGATTTTTAAAAAGG 2551 i - -- ?-- vi ivii - i v - iiv i CR1_Mam#LINE/ 989 GTGCCNAGA--ACN--AGTGTGTTCAATG-GGCTCC-ATCCATAAGAAGG 1032 rnd-1_family- 2552 GCTCCAGAGGTGATCCCGGCAATTACAGGCCGGTAAGCCTAACTTCAGTA 2601 iv --- - i - i i i i v vi CR1_Mam#LINE/ 1033 GCTCCAGAGGCCAT---GG-AACTA-AAGCCAGTGAGTCTCACTTCCATA 1077 rnd-1_family- 2602 CCGGGCAAATTGGTCGAAACTATA-GTAAAGAACAGAATTGTCAGACACA 2650 ? ii v ? -- - i ii ? i ?---i? i i CR1_Mam#LINE/ 1078 CCNGGCAAGCTGGTGGNA--TATAAGCAAAGAGTAGNACTN---ANCGCG 1122 rnd-1_family- 2651 TAGATGAACATAANNTGTTGGGGAAGAGTCAACATGGTTTTTGTAAAGGG 2700 i ??ii ?? ii i ii i v i i CR1_Mam#LINE/ 1123 CANNCAAACATAACCTACTAGGAGAAAGGCAACATGGTTTCTGTAAGGGG 1172 rnd-1_family- 2701 AAATCATGCCTCACCAATCTATTAGAATTCTTTGAGGGGGTCAACAAGCA 2750 v i i v i - CR1_Mam#LINE/ 1173 AAATCATGCCTGACTAATCTATTAGAGTTCTTTGAGGGGGTAAATAA-CA 1221 rnd-1_family- 2751 TGTGGACAAGGGNGATCCAGTGGATATAGTGTACTTAGATTTTCAGAAAG 2800 i?i v i v i i i CR1_Mam#LINE/ 1222 TGTGGACAAGGAGAAACCAGTGGATATAATTTATTTAGACTTTCAAAAAG 1271 rnd-1_family- 2801 CCTTTGACAAGGTCCCTCACCAAAG----GCTCTTAAGCAAAGTAAGCNG 2846 i v i----ii i -- v i i?i CR1_Mam#LINE/ 1272 CCTTTGACAAGGTTCCACACCAAAACTTTATTTTTAA--AAATTGAGTCA 1319 rnd-1_family- 2847 TCATGGGATAAGAGGGAAGGTCCTCTCATGGATCGGTAACTGGTTAAAAG 2896 i v? i v ii v v v i v i CR1_Mam#LINE/ 1320 CCATGGGATTNGGGGGAATGTTTTGTCATGGATAGGGAACTGGCTTAGAG 1369 rnd-1_family- 2897 ACAGGAAACAAAGGGTAG-GAATAAATGGTCAGTTTTCAGAATGGAGAGA 2945 i - i v v i v i ii CR1_Mam#LINE/ 1370 ACAGGAAACAAAAGGTAGAGAATAAACGGGCACTTCTCTGGATGGAGAAG 1419 rnd-1_family- 2946 GGTAAATAGCGGTGTCCCCCAGGGGTCTGTACTGGGACCAGTNCTGTTCA 2995 v i i v i v i i ?i i i CR1_Mam#LINE/ 1420 TGTAAACAGTGGGGTCCCCCAGGGATCAGTGCTGGGACTAGTCTTATTTA 1469 rnd-1_family- 2996 ACATATTCATAAATGATCTGGAAAAAGGGGTAAACAGTGAGGTGGCAAAA 3045 v i i i i iv ii vv v i CR1_Mam#LINE/ 1470 ACATTTTTATAAATGATCTGGAAGAGGGAGTGCACAGTGAAATCTCCAAG 1519 rnd-1_family- 3046 TTTGCAGATGATACAAAACTACTCAAGATAGTTAAGTCCAAAGCAGACTG 3095 i v i vi vi i v i v v v iv CR1_Mam#LINE/ 1520 TTTGCAGATGACACTAAGCTCTTCCGGGTAGTGAAATGCCAAGCCGATGG 1569 rnd-1_family- 3096 CGAAGAGCTACAAAGGGATCTCACAAAACTGGGTGACTGGGCAACAAAAT 3145 v vi i i iiii i ii v v iv i CR1_Mam#LINE/ 1570 GGATAAACTGCAGGAAGATCTCACGAGGCTGTGTGAGTGGGCAGAAAAGT 1619 rnd-1_family- 3146 GGCAGATGAAATTCAATGTTGATAAATGCAAAGTAATGCACATTGGAAAA 3195 iv i v ii i i i iv v i CR1_Mam#LINE/ 1620 GGCAGATGAGCTTCAGTGTGGGCAAGTGTAAGGTAATGCATTTAGGGAAA 1669 rnd-1_family- 3196 NATAACCCCAACTATACATACAATATGATGGGGNCTAA 3233 ? i v v i v v? i CR1_Mam#LINE/ 1670 AATAATCCAAACTATACTTATAAGATGATGGGCTCTGA 1707 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 264, Kimura (unadjusted) = 33.01 Transitions / transversions = 1.65 (264/160) Gap_init rate = 0.04 (63 / 1717), avg. gap size = 1.13 (71 / 63) 16 5.61 7.32 4.76 rnd-1_family-64#Unknown 117 157 (133) (GCGCGCT)n#Simple_repeat 1 42 (0) m_b1s252i4 rnd-1_family- 117 GCGC-CTGCAGCGCTGCGCGCT-CGCTC-GCAGCGCTGCGAGCT 157 - - - v - - v (GCGCGCT)n#Si 1 GCGCGCTGC-GCGCTGCGCGCTGCGCGCTGC-GCGCTGCGCGCT 42 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.12 (5 / 40), avg. gap size = 1.00 (5 / 5) 240 16.92 0.00 0.00 rnd-1_family-73#DNA/hAT-Charlie 3 67 (267) Charlie1b#DNA/hAT-Charlie 1 65 (458) m_b1s502i14 rnd-1_family- 3 CAGCGGTTCTCAACCAGGGGTCCGGGGCCCCCTGGGGGGCCGCGAGCAGG 52 vvv v v v v vvvv Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 rnd-1_family- 53 TTTCAGGGGGTCCGC 67 Charlie1b#DNA 51 TTTCAGGGGGTCCGC 65 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.60 CpG sites = 0, Kimura (unadjusted) = 19.60 Transitions / transversions = 0.00 (0/11) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 15 4.77 0.00 0.00 rnd-1_family-76#DNA/PIF-Harbinger 979 1000 (4573) (CCTC)n#Simple_repeat 1 22 (0) m_b1s252i0 rnd-1_family- 979 CCCCCCTCCCTCCCTCCCTCCC 1000 i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 28 0.00 0.00 0.00 rnd-1_family-76#DNA/PIF-Harbinger 1916 1942 (3657) (CCCT)n#Simple_repeat 1 27 (0) c_b1s251i0 rnd-1_family- 1916 CCCTCCCTCCCTCCCTCCCTCCCTCCC 1942 (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 8.18 3.85 0.00 rnd-1_family-76#DNA/PIF-Harbinger 3398 3423 (2176) (CCACC)n#Simple_repeat 1 27 (0) m_b1s252i1 rnd-1_family- 3398 CCACCCCACCCCA-CCCTCCCCTCCCC 3423 - v v (CCACC)n#Simp 1 CCACCCCACCCCACCCCACCCCACCCC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 12 25.32 2.38 0.00 rnd-1_family-76#DNA/PIF-Harbinger 4332 4373 (1226) (CACACA)n#Simple_repeat 1 43 (0) m_b1s252i2 rnd-1_family- 4332 CACAAACACAAGTAAAC-CACCCCCCCCCACACACACACACAC 4373 v vii v - v v v v (CACACA)n#Sim 1 CACACACACACACACACACACACACACACACACACACACACAC 43 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 12 25.32 2.38 0.00 rnd-1_family-76#DNA/PIF-Harbinger 4332 4373 (1226) (CACA)n#Simple_repeat 1 43 (0) m_b1s252i3 rnd-1_family- 4332 CACAAACACAAGTAAAC-CACCCCCCCCCACACACACACACAC 4373 v vii v - v v v v (CACA)n#Simpl 1 CACACACACACACACACACACACACACACACACACACACACAC 43 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 503 16.34 1.90 0.94 rnd-1_family-8#SINE/MIR 1 105 (38) MIR#SINE/MIR 110 215 (47) m_b1s601i8 rnd-1_family- 1 TCTCTGTGCCTCAGTTCCC-CATCTGTAAAATGGGGATAATAGCACTTCC 49 i - ii -v v MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA-GTAC 158 rnd-1_family- 50 CTACCTCACAGGGGTGTTGTGAGGA-TAAATACATTAAAGATTGTGAGGC 98 i v - ivi vivv i i MIR#SINE/MIR 159 CTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGC 208 rnd-1_family- 99 GCTCAGA 105 i MIR#SINE/MIR 209 GCTTAGA 215 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.64 CpG sites = 10, Kimura (unadjusted) = 18.64 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.00 (3 / 3) 187 16.63 8.93 3.39 rnd-1_family-83#Unknown 206 261 (1) MIR3#SINE/MIR 12 70 (138) m_b1s601i9 rnd-1_family- 206 GCTGACAGCAGAG---GAATGG--TGAGACTCAGGAATCCTGGGTTCCAT 250 -- --- v i -- i v iv i v MIR3#SINE/MIR 12 GCTGA--GCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAG 59 rnd-1_family- 251 TCCAGGCTCTG 261 v MIR3#SINE/MIR 60 TCCCGGCTCTG 70 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.74 CpG sites = 4, Kimura (unadjusted) = 18.89 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.75 (7 / 4) 221 14.89 4.26 0.00 rnd-1_family-83#Unknown 215 261 (1) MIR1_Amn#SINE/MIR 27 75 (155) m_b1s601i10 rnd-1_family- 215 AGAGGAATGG--TGAGACTCAGGAATCCTGGGTTCCATTCCAGGCTCTG 261 v v -- i i iv ? ? v MIR1_Amn#SINE 27 AGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTG 75 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.95 CpG sites = 3, Kimura (unadjusted) = 17.46 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1) 1576 5.59 0.51 0.51 rnd-1_family-84#LINE/CR1 1 198 (0) CR1-L3A_Croc#LINE/CR1 4078 4275 (13) m_b1s551i23 rnd-1_family- 1 GGTAATTAACCATTGGAACAACTTACCAAGGGATGTGGTGGATTCTCCAT 50 i ? CR1-L3A_Croc# 4078 GGTAATTAACCACTGGAACAACTTACCAAGGGNTGTGGTGGATTCTCCAT 4127 rnd-1_family- 51 CACTTGNAGTCTTTAAATCAAGACTGGATGTTTTTCTAAAAGATATGCTC 100 v ? i i i CR1-L3A_Croc# 4128 CACTGGAAATTTTTAAATCAAGATTGGATGTTTTTCTAAAAGATATGCTC 4177 rnd-1_family- 101 TAGTTCAAACAGGAATTAATTCAGGGAAGTTCTATGGCCTGTGTTATGCA 150 i i i - CR1-L3A_Croc# 4178 TAGTTCAAACAGGAATTAATTCGGGGAAGTCCTATGGCCTGCGTTA-GCA 4226 rnd-1_family- 151 GGAGGTCAGACTAGATGATC-ACAATGGTCCCTTCTGGCCTTAAAATCT 198 i - i? i ? CR1-L3A_Croc# 4227 GGAGGTCGGACTAGATGATCTACAGNGGTCCCTTCCGGCCTTANAATCT 4275 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.97 CpG sites = 10, Kimura (unadjusted) = 6.02 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.01 (2 / 197), avg. gap size = 1.00 (2 / 2) 620 5.00 0.00 1.25 rnd-1_family-94#LINE/CR1 1 81 (0) CR1-L3B_Croc#LINE/CR1 3194 3273 (4) m_b1s551i24 rnd-1_family- 1 AAATTCTGTGGCCTGTGTTATGCAGGAGGTCAGACTAGATGATCATAATG 50 ivi ? i - CR1-L3B_Croc# 3194 AAATTTAATGGCCTGTGNTATACAGGAGGTCAGACTAGATGATC-TAATG 3242 rnd-1_family- 51 GTCCCTTCTGGCCTTAAAATCTATGAATCTA 81 ? CR1-L3B_Croc# 3243 GTCCCTTCTGGCCTTAAANTCTATGAATCTA 3273 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.35 CpG sites = 3, Kimura (unadjusted) = 5.35 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 275 6.98 0.00 0.00 rnd-1_family-98#DNA/hAT-Charlie 8 50 (205) MER58A#DNA/hAT-Charlie 1 43 (181) m_b1s502i15 rnd-1_family- 8 CAGAGGTGGGCAAACTACGGCCCGCGGGCCACATCCGGCCCGC 50 i v v MER58A#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGC 43 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.32 CpG sites = 1, Kimura (unadjusted) = 7.32 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 265 15.94 1.43 1.43 rnd-1_family-98#DNA/hAT-Charlie 8 77 (178) MER58C#DNA/hAT-Charlie 1 70 (145) m_b1s502i16 rnd-1_family- 8 CAGAGGTGGGCAAACTACGGCCCGCGGGCCACATCCGGCCCGCGGGACCG 57 i v v - v i MER58C#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGC-GGCCTG 49 rnd-1_family- 58 -TCCTGCCCGGCCCCTGAGCT 77 - ii iv vi MER58C#DNA/hA 50 TTTTTGTACGGCCCGCGAGCT 70 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.36 CpG sites = 6, Kimura (unadjusted) = 18.06 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 888 1.67 0.00 0.00 rnd-1_family-0#SINE/MIR 1 120 (0) MIR1_Amn#SINE/MIR 34 153 (77) m_b2s601i0 rnd-1_family- 1 TGGACTGGGACTCAGGAGACCTGGGTTCTATTCCCGGCTCTGCCACTGGC 50 i ? ? ? MIR1_Amn#SINE 34 TGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGC 83 rnd-1_family- 51 CTGCTGGGTGACCTTGGGCAAGTCACTTCACCTCTCTGTGCCTCAGTTTC 100 ? ? ? ? MIR1_Amn#SINE 84 CNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTC 133 rnd-1_family- 101 CCCATCTGTAAAATGGGGAT 120 i MIR1_Amn#SINE 134 CTCATCTGTAAAATGGGGAT 153 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 0.98 CpG sites = 2, Kimura (unadjusted) = 1.80 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0) 16 27.97 1.35 4.17 rnd-1_family-113#Unknown 5 78 (256) (CCGCT)n#Simple_repeat 1 72 (0) m_b2s252i8 rnd-1_family- 5 CCGCCCCAGCTCACCTCCGCTCCGCCTCCTCCCCTGAGCGCGCCGCGCCC 54 i - vv - v i vvvv v -i (CCGCT)n#Simp 1 CCGCTCC-GCTCCGCTCCGCTCCG-CTCCGCTCCGCTCCGCTCCGC-TCC 47 rnd-1_family- 55 GCTCCGCTTCTC-CCCCCCCCCTCC 78 i v - v i v (CCGCT)n#Simp 48 GCTCCGCTCCGCTCCGCTCCGCTCC 72 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 2895 25.09 1.36 1.49 rnd-1_family-12#LINE/CR1 1 809 (853) C CR1-1_Amn#LINE/CR1 (5) 808 1 m_b2s551i0 rnd-1_family- 1 ATAAGAACATAAGAACGGCCATACTGGGTCAGACCAAAGGTCCATCTAGC 50 v ? C CR1-1_Amn#LIN 808 ATAAGAACATAAGAACTGCCATACTGGGTCAGACCAANGGTCCATCTAGC 759 rnd-1_family- 51 CCAGTATCCTGTCTTCCGACAGTGGCCAATGCCAGGTGCCCCAGAGGGAA 100 ? i i i ii i C CR1-1_Amn#LIN 758 CCAGTATCCTGTCTNCCGACAGTGGCCAGTACCAGATGCTTCAGAGGGAG 709 rnd-1_family- 101 TGAACAGAACAGGTAATCATCAAGTGATCCATCCCCTGTCGCCCATTCCC 150 vv v i? i i ii ? ii C CR1-1_Amn#LIN 708 TGAACCTAACAGGTAATGATCAAGTGATCTNTCTCCTGCCATCCNTCTCC 659 rnd-1_family- 151 AGCTTCTGGCAAACAGAGGCTAGGGACACCA-TCCCTGCCCATCCTGGCT 199 v i i i ? ? - i i? i i vi C CR1-1_Amn#LIN 658 ACCCTCCGACAANCAGAGGCTAGGGACANCATTCCTTANCCGTTCTGTTT 609 rnd-1_family- 200 AATAGCCATTGATGGACCTATCCTCCATGAACTTATCTAGTTCTTTTTTG 249 i i i i i ii C CR1-1_Amn#LIN 608 AATAGCCACTAATGGACCTATCCTCCATGAATTTATCCAGTCCCCTTTTG 559 rnd-1_family- 250 AACCCTGTTATAGTCTTGGCCTTCACAACATCCTCTGGCAANGAGTTCCA 299 v ? ?i ? i i ? v ? C CR1-1_Amn#LIN 558 AACCCGGTTATANTNCTNGCCTCCACGACNTCCTGTGGCAATGAGTTCCA 509 rnd-1_family- 300 CAGGTTGACTGTGCGTTGTGTGAAGAAATACTTCCT---TTTGTTT-GTT 345 i vi i i ? vi i i v iv --- iv - v C CR1-1_Amn#LIN 508 TATATTAACTATNCTCTGCGTAAAGAAATTCCGCCTAAATTCCTTTAGTG 459 rnd-1_family- 346 TTAAACCTGCTGCCTATTAATTTCATTTGGTGACCCCTAGTTCTTGTGTT 395 iivii -- v -- ii ? v v v v i C CR1-1_Amn#LIN 458 CCCGGCC--CTTCC--TTAGCTTNAGTTCGTGCCCCCTTGTTCTTGTATT 413 rnd-1_family- 396 ATGAGAA-GGAGTAAATAACACTTCCTTATTTACTTTCTCCACACCAGTC 444 - v v-i vvi i vi vivvi i iii i iv vv C CR1-1_Amn#LIN 412 -TGACACTAGCTCAAATAGCCTTGTAGCATCTATCCTCTCTATTCCCTTC 364 rnd-1_family- 445 ATGATTTTATAGACCTCTATCATATCCCCCCTTAGTCGTCTCTTTTCCAA 494 vi ? i v vi v vi i i vi C CR1-1_Amn#LIN 363 AGAATTNTGTATACCTCAGTGAGGTCCCCTCTTAATCTCCTCTTTTCCAA 314 rnd-1_family- 495 GCTGA--AAAGTCCCAGTCTTATTAATCTCTCCTCATACGGAAG--CCGT 540 i-- -- v v i i ivi i i ivv vvv -- -- C CR1-1_Amn#LIN 313 A--GAATACAGACCTAGTTTCTCTAACCTTTCTGAATAACTAAGATCC-- 268 rnd-1_family- 541 TCCATACCCCTA-ATCATTTTTGTTGCCCTTTTCTGAACCTTTTCCAATT 589 - ivii i- i v iiv v i v C CR1-1_Amn#LIN 267 -CCGAGTCCCTGTATCATTCTGGTTGCCCTCCGCTGTACCTTCTCCATTT 219 rnd-1_family- 590 CCAATATATCTTTTTTGAGATGGGGCGACCACATCTGCACGCAGTATTCA 639 i vv i ivi ii i v v i i v C CR1-1_Amn#LIN 218 CTATAATATCCTTTTTATAATAAGGTGACCAGAACTGCGCACAGTATTCC 169 rnd-1_family- 640 AGATGTGGGCGTACCATGGATTTATATAGAGGCAATATGATATTTTCTGT 689 i v vi i vvvvi i v vi iv i v ii i v C CR1-1_Amn#LIN 168 AAATGTGGCCTCACTAGTCCCTTATACAGTGCTAGAATAATTTCCTCCGA 119 rnd-1_family- 690 CTTATTATCTATCCCTTTCTTAATGATTCCCAACATTCTGTTCGCTTTTT 739 vv v v i v v vv i? i i C CR1-1_Amn#LIN 118 CTTATATTCGATACCTCTATTTATGCATCCCAGNATTTTGTTTGCTTTTT 69 rnd-1_family- 740 TGACTGCCGCTGCACATTGAGTGGATGTTTTCAGAGAACTATCCACAATG 789 ? i i ivi i v iv v v i vvi v i? C CR1-1_Amn#LIN 68 TNACTGCTGTTAAGCACTGTGCCGAAGGTTTTAGAGTTTTATCCACCACN 19 rnd-1_family- 790 ACTCCAAGATCTCTTTCTTG 809 i - - i C CR1-1_Amn#LIN 18 ACCCCAAG-TC-CTTTCTCG 1 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.02 CpG sites = 117, Kimura (unadjusted) = 32.11 Transitions / transversions = 1.41 (117/83) Gap_init rate = 0.02 (19 / 808), avg. gap size = 1.21 (23 / 19) 2299 32.71 1.63 1.71 rnd-1_family-12#LINE/CR1 220 1510 (152) C X2_LINE#LINE/CR1 (118) 1290 1 m_b2s551i1 rnd-1_family- 220 TCCTCCATGAACTTATCTAGTTCTTTTTTGAACCCTGTTATAGTCTTGGC 269 i vi vv v v i i i vv v v C X2_LINE#LINE/ 1290 TTCTCCAGAAACAAATCTAGGTGTCTCTTGAACTCATTTATACTCTTTGC 1241 rnd-1_family- 270 CTTCACAACATCCTCTGGCAANGAGTTCCACAGGTTGACTGTGCGTTGTG 319 i iv ivi v i i i i ?vvi i v v i iiv v i C X2_LINE#LINE/ 1240 TTCAATCGCCTTCCCCGGTAACTTATTCCATATGTTTATTACCCTTTGCG 1191 rnd-1_family- 320 TGAAGAAATACTTCCTT--TTGTTTGTTTTAAACCT-GCTGCCTATTAAT 366 iv i v v v-- vii i - vv - i v v -- C X2_LINE#LINE/ 1190 TGAAATAGTTCTGCCTGAGTTCCCTATTT-ACTCCTAGTTTCCTAAT--T 1144 rnd-1_family- 367 TTCATTTGGTGACCCCTAGTTCTTGTGTTATGAGAAGGAGTAAATAACAC 416 i vv v v i ii viiivivv ?vi v i ? iivi C X2_LINE#LINE/ 1143 TTTAGATCGTGTCCCCTGGTTTCTGAACCCCTCGNCAGTGTGAANAGTTT 1094 rnd-1_family- 417 TTCCTTATTTACTTTCTCCACACCAGTCATGATTTTATAGACCTCTATCA 466 v ii?? iv v v iv vv iii iv i i v i C X2_LINE#LINE/ 1093 ATCTCNNTCAACTTTATCAATCCCTTTCGCAATTTTGAAAACTTCAATTA 1044 rnd-1_family- 467 TATCCCCCCTTAGTCGTCTCTTTTCCAAGCTGAAAAGTCCCAGTCTTATT 516 vi v i vv v ivvv v iv i iv C X2_LINE#LINE/ 1043 GGTCACCTCGAAGTCTTCTCTTTTCCAGTGAGAATAAGCCCAGTTTCCTT 994 rnd-1_family- 517 AATCTCTCCTCATACGGAAGCCGTTCCATACCCCTAATCATTTTTGTTGC 566 i i vv?v vivi iv v vv? i i C X2_LINE#LINE/ 993 AACCTTTCCTCATAACNTAGATTCTTGAGACCCGGNATCATCTTTGCTGC 944 rnd-1_family- 567 CCTTTTCTGAACCTTTTCCAATTCCAATA-TATCTTTTTTGAGATGGGGC 615 v v v i i vv - i - i ii v i??v i C X2_LINE#LINE/ 943 CCTATGCTGCACCCTCTCCAAGGC-AGTAATATCCTTCCTGTGGNNCGGT 895 rnd-1_family- 616 GACCACATCTGCACGCAGTATTCAAGATGTGGGCGTA-CCATGGATTTAT 664 vvv i? vi - iv - ? vv vi C X2_LINE#LINE/ 894 GACCAGTACTGCACANAGTATTCCGGATG-GGGTCTAGCNAGTGCCTTAT 846 rnd-1_family- 665 ATAGAGGCAATATGATATTTTCTGTCTTATTATCTATCCCTTTCTTAATG 714 i vii i viiv i ii ?i i vv ? i vi i C X2_LINE#LINE/ 845 ACAGTAACAGTATCGCCTCTTTCGNTTTGTATTCTNTCCCTCTGCTAATA 796 rnd-1_family- 715 ATTCCCAACATTCTGTTCGCTTTTTTGACTGCCGCTGCACATTGAGTGGA 764 vvv ii i i i v v ii i i iv C X2_LINE#LINE/ 795 CAACCCAGTATCCTGTTTGCCTTTTTTACTGCAGCTGTGCACTGGGCTGA 746 rnd-1_family- 765 TGTTTTCAGAGAACTATCCACAATGACTCCAAGATCTCTTTCTTGAGTGG 814 v iv vi v i i v i i i vii C X2_LINE#LINE/ 745 TGGTTTCAATGATTTTTCCACAATAACCCCCAAATCCCTTTCCTGATCAG 696 rnd-1_family- 815 TAACAGCTAATTTAGACCCCATCATTTTATATGTAT-----AGTTGGGAT 859 iv-- iiv -- ivivi vii i ----- ? v v C X2_LINE#LINE/ 695 TGT--GCTGGAT--GACTGTTCCATTTAGCACGTATTCCCTAGNTTGGTT 650 rnd-1_family- 860 TATGTTTTCCAATGTGCATTACTTTGCATTTATCAACATTGAATTTCATC 909 iv vvi i ivv i- i i i v i v i C X2_LINE#LINE/ 649 CCTTGCTCCCAGACTA-ATTATTTTACATTTGTCTACATTGAACTGCATT 601 rnd-1_family- 910 TGCCATTTTGTTGCCCAGTCACCCA---GTTTTGTGAGATCCCTTTGTAG 956 i vv v i --- v ii--- i i v v C X2_LINE#LINE/ 600 TGCCATCTGCTGGCCCAGTCACCTAAACGATCC---AAATCCTTTTGAAT 554 rnd-1_family- 957 CTCTTCGCAGTCTGCTTTGG-ACTTAA-CTATCTTGAGTAGTTTTGTATC 1004 vv i v v v i i v- i iv- ii iv i -- v C X2_LINE#LINE/ 553 CTGGTTGCATTGTTCCTCGTTATTTGCTCTGCCTCCAAT--TTTAGTATC 506 rnd-1_family- 1005 ATCTGCAAATTTTGCCACCTCACTGTTTACCCCTTTTTCCAGATCATTTA 1054 i ? v? i ii v iv iv i iv i C X2_LINE#LINE/ 505 ATCTGCAAACTTNGANATCTTGCTTTCAATACCCTCGTCCAAATCATTTA 456 rnd-1_family- 1055 TGAATATGTTGAACAGNACTGGTCCCAGTACAGACCCCTGGGGGACACCA 1104 i? ? ?i?v ii? v i v v C X2_LINE#LINE/ 455 TANATATNTTGAACAGCGNAGGTCCCGANACTGATCCCTGGGGTACCCCA 406 rnd-1_family- 1105 CTATTTACCTCTCTCCATTCTGAAAACTGACCATTTATTCCTACCCTTTG 1154 vv v i i vii ? vv i ivv ? i C X2_LINE#LINE/ 405 CTTGTAACCCCTTTCCAGCTTGAAAANTTTCCATCTACGGCTNCTCTTTG 356 rnd-1_family- 1155 TTTCCTATCTTTTAACCAGTTACCGATCCATGAGAGGACCTTCCCTCTTA 1204 i iiii ? i ? vi v vv vvvv ?i v i ? C X2_LINE#LINE/ 355 TCTCCTGCTCTTNAGCCANTTTTCTATCCAGCACTCTANTTTACCTCCTN 306 rnd-1_family- 1205 TCCCATGACAGCTTACTTT-GC--TTAAGAGCCTTTGGTGAGGGACCTTG 1251 i i vvi i - -- ---i ii i v i C X2_LINE#LINE/ 305 TTCCGTGACTCTTTACCTTAGCCATTAA---TCTCCGATGTGGAACCTTG 259 rnd-1_family- 1252 TCAAAGGCTTTCTGAAAGTCCAAGTACACTATATCCACTGGATCNCCCTT 1301 v i i i ? i ii i? C X2_LINE#LINE/ 258 TCAAATGCTTTTTGAAAATCTAAGTANACTACATCCACTGAGTTTCCCTT 209 rnd-1_family- 1302 GTCCA-CATGCTTGTTGACCCCCTCAAAGAATTCTAGTAGATTGGTGAGG 1350 i i?- viv -i ivi i i i i i i v i C X2_LINE#LINE/ 208 ATCTNTCATGGCAGT-AATATCTTCAAAGAACTCCAGCAGGTTAGTTAAG 160 rnd-1_family- 1351 CATGATTTCCCTTTACAAAAACCGTGTTGACTCTTCCCCAACAAATTATG 1400 ii ? vv vi v i i i ? i iiv v i C X2_LINE#LINE/ 159 CATGACCTCCCNTGCCTGAATCCATGCTGGCTNTCCTTAATCAAACTATG 110 rnd-1_family- 1401 TTCATCTATGTGTCTGACAATTCTGTTCTTTACTATAGTTTCAACCAA-- 1448 i iv i v iivv v iiv?i i i vv ? -- -- C X2_LINE#LINE/ 109 CTTTTCCAGGTGTTCTCCCACCGNATCCCTTAAGATNGTTTC--CCAANA 62 rnd-1_family- 1449 TTTGCCCGGTACTGAAGTCAGGCTTACCGGCCTGTAATTGCCGGGATCGC 1498 v vii?vi v i i ? i v iv vii i C X2_LINE#LINE/ 61 TTTTCCCCACNGCGATGTTAAGCTNACTGGCCTGTAATTTCTTGGTCTGT 12 rnd-1_family- 1499 CTCTGGAGCCCT 1510 v - C X2_LINE#LINE/ 11 CTCTTGA-CCCT 1 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.41 CpG sites = 230, Kimura (unadjusted) = 45.94 Transitions / transversions = 1.24 (230/185) Gap_init rate = 0.03 (34 / 1290), avg. gap size = 1.26 (43 / 34) 4714 24.57 0.70 4.11 rnd-1_family-12#LINE/CR1 380 1661 (1) C CR1_Mam#LINE/CR1 (70) 2134 895 m_b2s551i2 rnd-1_family- 380 CCCTAGTTCTTGTGTTATGAGAAGGAGTAAATAACACTTCCTTATTTACT 429 v i v i vvvi i i v--- v i i i C CR1_Mam#LINE/ 2134 CCCTAGTTCTAGTATTCTGGGATTTGGTGAACAAG---TCCGTGTTCACC 2088 rnd-1_family- 430 TTCTCCACACCAGTCATGATTTTATAGACCTCTATCATATCCCCCCTTAG 479 v i vv i iv i i C CR1_Mam#LINE/ 2087 TTATCCATACCCTTCATGATTTTATAGACTTTGATCATATCCCCTCTCAG 2038 rnd-1_family- 480 TCGTCTCTTTTCCAAGCTGAAAAGTCCCAGTCTTATTAATCTCTCCTCAT 529 i v vii ii -- iii iv vv ?i iiiivv v C CR1_Mam#LINE/ 2037 CCTTCGTCTTTCCAGACT--AAAGTTTTAAACAAANCAGCTCAGCCTCTT 1990 rnd-1_family- 530 ACGGAAGCCGTTCCATACCCCTAATCATTTTTGTTGCCCTTTTCTGAACC 579 i?i - v i i vi i i ------ C CR1_Mam#LINE/ 1989 ATNAAAGCC-TTCCATCCCCTTGATCATTTTAATTACCCTTCTC------ 1947 rnd-1_family- 580 TTTTCCAATTCCAATATATCTTTTTTGAG--ATGGGGCGACCACATCTGC 627 ------ ii iiv i i -- v v v C CR1_Mam#LINE/ 1946 ------AGCTCTGTTATGTCTTTCTTGAGGGATGCGGCGACCAGAACTGC 1903 rnd-1_family- 628 ACGCAGTATTCAAGATGTGGGCGTACCATGGATTTATATAGAGGCAATAT 677 i v i i iiii v i i i i iv C CR1_Mam#LINE/ 1902 ACACAGTATTCCAGGTGCGGATACACCATGGTTTTGTACAAAGGTAGGAT 1853 rnd-1_family- 678 GATATTTTCTGTCTTATTATCTATCCCTTTCTTAATGATTCCCAACATTC 727 i i i i vi v v i i i v i i C CR1_Mam#LINE/ 1852 AATGTTTTCTGTTTTGTTTCCAATACCCTTCCTGATGATGCCCAGCATTT 1803 rnd-1_family- 728 TGTTCGCTTTTTTGACTGCCGCTGCACATTGAGTGGATGTTTTCAGAGAA 777 v i i i v --- i iv i i C CR1_Mam#LINE/ 1802 TGTTGGCCTTTTTGGCTACAGC---ACATTGGGCTGATGTCTTCAGGGAA 1756 rnd-1_family- 778 CTATCCACAATGACTCCAAGATCTCTTTCTTGAGTGGTAACAGCTAATTT 827 vi i v i i i v v v ii i C CR1_Mam#LINE/ 1755 CAGTCTACAATGACTCCTAGATCCCTTTCCTGGGTCGTAACTGATAGCTC 1706 rnd-1_family- 828 AGACCCCATCATTTTATATGTATAGTTGGGATTATGTTTTCCAATGTGCA 877 v i v v v i v vi C CR1_Mam#LINE/ 1705 AGAGCCCATCATCTTATAAGTATAGTTTGGATTATTTTTCCCTAAATGCA 1656 rnd-1_family- 878 TTACTTTGCATTTATCAACATTGAATTTCATCTGCCATTTTGTTGCCCAG 927 i i i ii v i vi i vi v C CR1_Mam#LINE/ 1655 TTACCTTACACTTGCCCACACTGAAGCTCATCTGCCACTTTTCTGCCCAC 1606 rnd-1_family- 928 TCACCCAGTTTTGTGAGATCCCTTTGTAGCTCTTCGCAGTCTGCTTTGGA 977 v ii i iiii i i iv v vi v v v C CR1_Mam#LINE/ 1605 TCACACAGCCTCGTGAGATCTTCCTGCAGTTTATCCCCATCGGCTTGGCA 1556 rnd-1_family- 978 CTTAACTATCTTGAGTAGTTTTGTATCATCTGCAAATTTTGCCACCTCAC 1027 i v i iv iv i v i i v vv ii C CR1_Mam#LINE/ 1555 TTTCACTACCCGGAAGAGCTTAGTGTCATCTGCAAACTTGGAGATTTCAC 1506 rnd-1_family- 1028 TGTTTACCCCTTTTTCCAGATCATTTATGAATATGTTGAACAGNACTGGT 1077 vi i i i i v i i i? i C CR1_Mam#LINE/ 1505 TGTGCACTCCCTCTTCCAGATCATTTATAAAAATGTTAAATAAGACTAGT 1456 rnd-1_family- 1078 CCCAGTACAGACCCCTGGGGGACACCACTATTTACCTCTCTCCATTCTGA 1127 i v i v i vii i v C CR1_Mam#LINE/ 1455 CCCAGCACTGATCCCTGGGGGACCCCACTGTTTACACTTCTCCATCCAGA 1406 rnd-1_family- 1128 AAACTGACCATTTATTC-CTACCCTTTGTTTCCTATCTTTTAACCAGTTA 1176 i v v i - i i i v i v C CR1_Mam#LINE/ 1405 GAAGTGCCCGTTTATTCTCTACCTTTTGTTTCCTGTCTCTAAGCCAGTTC 1356 rnd-1_family- 1177 CCGATCCATGAGAGGACCTTCCCTCTTATCCCATGACAGCTTACTTTGCT 1226 v v ii v i ?v iiii i v -- C CR1_Mam#LINE/ 1355 CCTATCCATGACAAAACATTCCCCCNAATCCCATGGTGACTCAATTT--T 1308 rnd-1_family- 1227 TAAGAGC----CTTTGGTGAGGGACCTTGTCAAAGGCTTTCTGAAAGTCC 1272 i ii----i v i i i C CR1_Mam#LINE/ 1307 TAAAAATAAAGTTTTGGTGTGGAACCTTGTCAAAGGCTTTTTGAAAGTCT 1258 rnd-1_family- 1273 AAGTACACTATATCCACTGGATCNCCCTTGTCCACATGCTTGTTGACCCC 1322 i v i v i?i - i v C CR1_Mam#LINE/ 1257 AAATAAATTATATCCACTGGTTTCTCCTTGTCCACATG-TTATTTACCCC 1209 rnd-1_family- 1323 CTCAAAGAATTCTAGTAGATTGGTGAGGCATGATTTCCCTTTACAAAAAC 1372 i i i v i i C CR1_Mam#LINE/ 1208 CTCAAAGAACTCTAATAGATTAGTCAGGCATGATTTCCCCTTACAGAAAC 1159 rnd-1_family- 1373 CGTGTTGACTCTTCCCCAACAAATTATGTTCATCTATGTGTCTGACAATT 1422 i v i ii i ii ii ii?? ii i ?i---? i ? C CR1_Mam#LINE/ 1158 CATGTTGCCTTTCTCCTAGTAGGTTATGTTTGNNTGCGCGNT---NAGTN 1112 rnd-1_family- 1423 CTGTTCTTTAC-TATAGTTTCAACCAATTTGCCCGGTACTGAAGTCAGGC 1471 ii i - -- ? v ii ? iv v i C CR1_Mam#LINE/ 1111 CTACTCTTTGCTTATA--TNCCACCAGCTTGCCNGGTATGGAAGTGAGAC 1064 rnd-1_family- 1472 TTACCGGCCTGTAATTGCCGGGATCGCCTCTGGAGCCCTTTTTAAAAATT 1521 i i i - i - --- v i vii - C CR1_Mam#LINE/ 1063 TCACTGGCTT-TAGTT-CC---ATGGCCTCTGGAGCCCTTCTTATGGA-T 1020 rnd-1_family- 1522 GGCGTCACATTAGCTATCCTCCAGTCATCT-GGTACAGAAGCTGATTTAA 1570 v i - iivi iv --? -- - i vi i v vv C CR1_Mam#LINE/ 1019 GGAGCC-CATTGAACACACT--NGT--TCTNGGCACAGTGGCCGTTTGTA 975 rnd-1_family- 1571 ATGATAGGTTACANACCACAGTTAGTAGTTCTGCAATTTCATATTTGAGT 1620 - i ----- v v ---- vi i ivi C CR1_Mam#LINE/ 974 AT-ACAGGTTA-----CACATTTTG----TCAACAGTTTCACCCTTGAGT 935 rnd-1_family- 1621 TCCTTCAGAACTCTTGGGTGAATACCATCTGGTCCTGGTGA 1661 i i i - C CR1_Mam#LINE/ 934 TCCTTCAAAACTCTTGGGTGGATGCCATCTGGTCC-GGTGA 895 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.29 CpG sites = 201, Kimura (unadjusted) = 31.17 Transitions / transversions = 1.99 (201/101) Gap_init rate = 0.04 (56 / 1281), avg. gap size = 1.07 (60 / 56) 281 12.50 12.50 0.00 rnd-1_family-120#LINE/L2 1 64 (5) L2d_3end#LINE/L2 396 467 (49) m_b2s601i1 rnd-1_family- 1 ATTGTAAGCTCTTTG-GGGCAGGGAC--TGTCTCTTACTNTGTGTTTGT- 46 i - -- iv v v? i - L2d_3end#LINE 396 ATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTT 445 rnd-1_family- 47 ----ACAGCACCTAGCACAATG 64 ---- i i L2d_3end#LINE 446 CCCCACAGCGCCTAGCACAGTG 467 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 10.77 CpG sites = 5, Kimura (unadjusted) = 14.31 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (4 / 63), avg. gap size = 2.00 (8 / 4) 2086 2.69 1.15 0.00 rnd-1_family-127#LINE/CR1 1 260 (0) CR1-L3A_Croc#LINE/CR1 2356 2618 (1670) m_b2s551i3 rnd-1_family- 1 ATGGAAGAAAGGGGAAGTTGATAGTAATGAATATAAATCAGAAGTTAGGA 50 i i i i CR1-L3A_Croc# 2356 ATGGAAAAAAGGGGAAGTTGATAGCAATGAATATAAATTAGAAGCTAGGA 2405 rnd-1_family- 51 ANTGTAGAAAATTGATAAGGGAAGCAAAGGGACACAAGGAGAAATCTATG 100 ? i CR1-L3A_Croc# 2406 ATTGTAGAAAATTGATAAGGGAAGCAAAAGGACACAAGGAGAAATCTATG 2455 rnd-1_family- 101 GCCAGCAGAGTTAAGGACAATAAG---GAGTTTTTNAAATATATTAGGAA 147 --- i CR1-L3A_Croc# 2456 GCCAGCAGAGTTAAGGACAATAAGAAGGAGTTTTTNAAGTATATTAGGAA 2505 rnd-1_family- 148 CAAAAGGAATCCTAACAATGGTATTGGTCCATTACTAGATGGAAATGGTA 197 CR1-L3A_Croc# 2506 CAAAAGGAATCCTAACAATGGTATTGGTCCATTACTAGATGGAAATGGTA 2555 rnd-1_family- 198 GAATTATCAATAATAATGCAGAAAAGGCAGAAGTGTTCAATAAATATTTC 247 i CR1-L3A_Croc# 2556 GAATTGTCAATAATAATGCAGAAAAGGCAGAAGTGTTCAATAAATATTTC 2605 rnd-1_family- 248 TGTTCTGTATTTG 260 CR1-L3A_Croc# 2606 TGTTCTGTATTTG 2618 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.79 CpG sites = 7, Kimura (unadjusted) = 2.79 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (1 / 259), avg. gap size = 3.00 (3 / 1) 321 12.50 3.57 0.00 rnd-1_family-128#SINE/MIR 2 57 (0) AmnSINE1#SINE/5S-Deu-L2 510 567 (8) m_b2s502i0 rnd-1_family- 2 TTGTAAAGCGCTTTGAGATC--TACNGATGAAAAGCGCTATATAAGAGCT 49 i -- vv? i iv v AmnSINE1#SINE 510 TTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATGCA 559 rnd-1_family- 50 AGGTATTA 57 AmnSINE1#SINE 560 AGGTATTA 567 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.96 CpG sites = 3, Kimura (unadjusted) = 13.96 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 55), avg. gap size = 2.00 (2 / 1) 2406 25.32 1.13 3.63 rnd-1_family-13#LINE/CR1 1 705 (0) CR1-1_Amn#LINE/CR1 116 803 (10) m_b2s551i4 rnd-1_family- 1 AAGACAGAAAATATCATAATGCCACTATATAAATCCATGGTACGCCCACA 50 v i ii v i vv iv i ivvvv i iv v CR1-1_Amn#LIN 116 AAGTCGGAGGAAATTATTCTAGCACTGTATAAGGGACTAGTGAGGCCACA 165 rnd-1_family- 51 CCTTGAATACTGCGTGCAGTTCTGGTCGCCCCATCTCAAAAAAGATATAT 100 ii v i i i ii ivi i vv CR1-1_Amn#LIN 166 TTTGGAATACTGTGCGCAGTTCTGGTCACCTTATTATAAAAAGGATATTA 215 rnd-1_family- 101 TAGAATTGGAAAAGGTACAGAGAAGGGCAACAAAAATGAT-TAGGGGTAT 149 v i v i v i -i iivi CR1-1_Amn#LIN 216 TAGAAATGGAGAAGGTACAGCGGAGGGCAACCAGAATGATACAGGGACTC 265 rnd-1_family- 150 GGAACAGCTTCCATACGAGGAGAGATTAAAAAGACTGGGACTGT--TCAG 197 ii- v vvv ivvi i i i i i i v -- -- CR1-1_Amn#LIN 266 GGGG-ATCTTAGTTATTCAGAAAGGTTAGAGAAACTAGGTCTGTATTC-- 312 rnd-1_family- 198 CTTGGAAAAGAGACGACTAAGGGGGGATATGATAGAGGTCTATAAAATCA 247 i iv i i iv v iv v i ? iv CR1-1_Amn#LIN 313 TTTGGAAAAGAGGAGATTAAGAGGGGACCTCACTGAGGTATACANAATTC 362 rnd-1_family- 248 TGAATGGTGTGGAGAAAGTGAATAGGGAAGTGTTATTT-ACCCCTTCACA 296 v vi i iii ii ivviv iv i - v ivv vv CR1-1_Amn#LIN 363 TGAAGGGAATAGAGAGGATAGATGCTACAAGGCTATTTGAGCTAGTGTCA 412 rnd-1_family- 297 TAACACAAGAACCAGGGGTCACCCAATGAAATTAATAGGCAGCAGGTTTA 346 - i v v vv v ? ii -- v -- iivi CR1-1_Amn#LIN 413 -AATACAAGAACAAGGGGGCACGAACTNAAGCTAA--GGAAG--GGCCGG 457 rnd-1_family- 347 AAAC-AAACAAA---AGGAAGTACTTCTTCACACAACGCACAGTCAACCT 392 iv - vi --- vi v i i i iv ? i i iv CR1-1_Amn#LIN 458 GCACTAAAGGAATTTAGGCGGAATTTCTTTACGCAGAGNATAGTTAATAT 507 rnd-1_family- 393 GTGGAACTCGTTGCCAGGGGATGTTGTGAAGGCCAAAAGTATAACTGGGT 442 i i vi ? i i ? i? ? i CR1-1_Amn#LIN 508 ATGGAACTCATTGCCACAGGANGTCGTGGAGGCNAGNANTATAACCGGGT 557 rnd-1_family- 443 TCAAAAAAGAATTAGATAAGTTCATGGAGGATAGGTCCATCAATGGCTAT 492 ii i i i i i i CR1-1_Amn#LIN 558 TCAAAAGGGGACTGGATAAATTCATGGAGGATAGGTCCATTAGTGGCTAT 607 rnd-1_family- 493 TAGCCAAGATGGTCAGGGATGCAACCCCATGCTCTGGGTGTCCCTAAACC 542 iv ii i ?i i --------- ? ------ i- CR1-1_Amn#LIN 608 TAAACAGAACGGNTAAGGA---------ATGNT------GTCCCTAG-CC 641 rnd-1_family- 543 TCTGACTGCCAGAAGCTGGGACTGGACGACAGGGGATGGATCACTCGATA 592 ?i i i i v iiv? i i i ?i i v CR1-1_Amn#LIN 642 TCTGNTTGTCGGAGGGTGGAGANGGATGGCAGGAGANAGATCACTTGATC 691 rnd-1_family- 593 ATTGCCCTGTTCTGTTCATTCCCTCTGAAGCATCTGGCACTGGCCACTGT 642 i - vv i i CR1-1_Amn#LIN 692 ATTACC-TGTTAGGTTCACTCCCTCTGAAGCATCTGGTACTGGCCACTGT 740 rnd-1_family- 643 CGGAAGACAGGATACTGGGCTAGATGGACCATTGGTCTGACCCAGTATGG 692 ? ? CR1-1_Amn#LIN 741 CGGNAGACAGGATACTGGGCTAGATGGACCNTTGGTCTGACCCAGTATGG 790 rnd-1_family- 693 CCGTTCTTATGTT 705 v CR1-1_Amn#LIN 791 CAGTTCTTATGTT 803 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.33 CpG sites = 108, Kimura (unadjusted) = 32.61 Transitions / transversions = 1.69 (108/64) Gap_init rate = 0.04 (30 / 704), avg. gap size = 1.10 (33 / 30) 19 19.89 0.00 2.13 rnd-1_family-130#DNA/hAT-Charlie 1 48 (82) (CCCCAC)n#Simple_repeat 1 47 (0) m_b2s252i7 rnd-1_family- 1 CCGCACCCCCAGCCGGAGCCCTCACCCCCTCCCGCACCCCAACCCCCA 48 v v vv - i v v v (CCCCAC)n#Sim 1 CCCCACCCCCACCCCCA-CCCCCACCCCCACCCCCACCCCCACCCCCA 47 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 2036 4.55 0.00 0.00 rnd-1_family-136#LINE/CR1 1 242 (0) CR1-L3A_Croc#LINE/CR1 2655 2896 (1392) m_b2s551i5 rnd-1_family- 1 ATGATAACACTCTTTCCATTCCACTAGTATCTCAGGAGGATGTTAAACAG 50 i v iv vi v v CR1-L3A_Croc# 2655 ATGATGAAATACTTTCCATTCCAACAGTAACTAAGGAGGATGTTAAACAG 2704 rnd-1_family- 51 CAGCTACTAAAGTTAGACATTTTTAAATCAGCAGGTCCGGATAACTTGCA 100 CR1-L3A_Croc# 2705 CAGCTACTAAAGTTAGACATTTTTAAATCAGCAGGTCCGGATAACTTGCA 2754 rnd-1_family- 101 TCCAAGAGTTTTAAAAGAGCTGGCTGAGGAGCTCGCTGGACCGTTAATGT 150 i v CR1-L3A_Croc# 2755 TCCAAGAGTTTTAAAAGAGCTGGCCGAGGAGCTCTCTGGACCGTTAATGT 2804 rnd-1_family- 151 TGATTTTCAATAAGTCTTGGAACACTGGGGAAGTTCCAGAAGACTGGAAG 200 i CR1-L3A_Croc# 2805 TGATTTTCAATAAGTCTTGGAACACTGGGGAAGTTCCAGAGGACTGGAAG 2854 rnd-1_family- 201 AAAGCTAATGTTGTGCCAATATTTAAAAAGGGTAAACGGGAT 242 CR1-L3A_Croc# 2855 AAAGCTAATGTTGTGCCAATATTTAAAAAGGGTAAACGGGAT 2896 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.29 CpG sites = 5, Kimura (unadjusted) = 4.69 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 241), avg. gap size = 0.0 (0 / 0) 3237 22.46 1.62 1.62 rnd-1_family-24#LINE/CR1 1 801 (2007) C CR1-1_Amn#LINE/CR1 (11) 802 2 m_b2s551i6 rnd-1_family- 1 ACATAAGAACGGCCGTACTGGGTCAGACCAAAGGTCCATCTAGCCCAGTA 50 v i ? C CR1-1_Amn#LIN 802 ACATAAGAACTGCCATACTGGGTCAGACCAANGGTCCATCTAGCCCAGTA 753 rnd-1_family- 51 TCCTGTCTACCGACAGTGGCCAATGCCAGGTGCCCCAGAGGGAGTGAACC 100 ? i i i ii C CR1-1_Amn#LIN 752 TCCTGTCTNCCGACAGTGGCCAGTACCAGATGCTTCAGAGGGAGTGAACC 703 rnd-1_family- 101 TAACAGGCAATGATCAAGTGATCTCTCTCCTGCCATCCATCTCCACCCTC 150 i ? ? C CR1-1_Amn#LIN 702 TAACAGGTAATGATCAAGTGATCTNTCTCCTGCCATCCNTCTCCACCCTC 653 rnd-1_family- 151 TGACAAACAGAGGCTAGGGACACCATTCCTTACCCATCCTGGCTAATAGC 200 i ? ? ? i i vi C CR1-1_Amn#LIN 652 CGACAANCAGAGGCTAGGGACANCATTCCTTANCCGTTCTGTTTAATAGC 603 rnd-1_family- 201 CATTAATGGACTTAACCTCCATGAATTTATCCAGTTCTCTTTTAAACCCT 250 i i v i i i v C CR1-1_Amn#LIN 602 CACTAATGGACCTATCCTCCATGAATTTATCCAGTCCCCTTTTGAACCCG 553 rnd-1_family- 251 GTTATAGTCCTAGCCTTCACAACCTCCTCAGGCAAGGAGTTCCACAGGTT 300 ? ? ? i i ? vv v i vi C CR1-1_Amn#LIN 552 GTTATANTNCTNGCCTCCACGACNTCCTGTGGCAATGAGTTCCATATATT 503 rnd-1_family- 301 GACTGTGCGCTGCGTGAAGAAGAACTTCCTTTTATTTGTTTTAA-ACCTG 349 i i ? v i -- i i vii v v vi i-i i C CR1-1_Amn#LIN 502 AACTATNCTCTGCGTAAAGAA--ATTCCGCCTAAATTCCTTTAGTGCCCG 455 rnd-1_family- 350 ---CTGCCTATTAATTTCATTTGGTGGCCCCTAGTTCTTGTATTATGGGA 396 --- v -- ii ? v v v v - iv C CR1-1_Amn#LIN 454 GCCCTTCCT--TAGCTTNAGTTCGTGCCCCCTTGTTCTTGTATT-TGACA 408 rnd-1_family- 397 ACAAGT-AAATAACTTTTCCTTATCCACTTTCTCCACACCACTCATGATT 445 vi iv - i i vivvi i iii i iv vi vi C CR1-1_Amn#LIN 407 CTAGCTCAAATAGCCTTGTAGCATCTATCCTCTCTATTCCCTTCAGAATT 358 rnd-1_family- 446 TTATATACCTCTATCATATCCCCCCTTAGTCTCCTCTTTTCCAAGCTGAA 495 ? i vi v vi i i i-- C CR1-1_Amn#LIN 357 NTGTATACCTCAGTGAGGTCCCCTCTTAATCTCCTCTTTTCCAAA--GAA 310 rnd-1_family- 496 --AAGTCCTAGCCTCTTTAATCTCTCCTCATA--TGGGACCCGTTCCAAA 541 --v v ii i i i ivv -- ii i --- i i C CR1-1_Amn#LIN 309 TACAGACCTAGTTTCTCTAACCTTTCTGAATAACTAAGATCC---CCGAG 263 rnd-1_family- 542 CCCCTA-ATCATTTTAGTTGCCCTTCTCTGAACCTTTTCTAATGCCAGTA 590 i i- i i i v v i i v v i vv C CR1-1_Amn#LIN 262 TCCCTGTATCATTCTGGTTGCCCTCCGCTGTACCTTCTCCATTTCTATAA 213 rnd-1_family- 591 TATCTTTTTTGAGATGAGGAGACCACATCTGTACGCAGTATTCAAGATGT 640 i ivi i v v v ii i v i C CR1-1_Amn#LIN 212 TATCCTTTTTATAATAAGGTGACCAGAACTGCGCACAGTATTCCAAATGT 163 rnd-1_family- 641 GGGCGTACCATGGATTTATATAAGGGC---AATAAGATATTCTCCGTCTT 687 v vi i vvvvi i - v --- -- v i v C CR1-1_Amn#LIN 162 GGCCTCACTAGTCCCTTATACA-GTGCTAGAATAA--TTTCCTCCGACTT 116 rnd-1_family- 688 ATTCTCTATCCCCTTTTTAATGATTCCTAACATCCTGTTTGCTTTTTTGA 737 vi v v ii v v vv i i? ii ? C CR1-1_Amn#LIN 115 ATATTCGATACCTCTATTTATGCATCCCAGNATTTTGTTTGCTTTTTTNA 66 rnd-1_family- 738 CCGCCGCTGCACACTGCGTGGACGTCTTCAGAGAACTATCCACGATGACT 787 i i i ivi i iv v vi i vvi v i? i C CR1-1_Amn#LIN 65 CTGCTGTTAAGCACTGTGCCGAAGGTTTTAGAGTTTTATCCACCACNACC 16 rnd-1_family- 788 CCAAGATCTCTTTC 801 vi i i C CR1-1_Amn#LIN 15 CCAAGTCCTTTCTC 2 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.89 CpG sites = 108, Kimura (unadjusted) = 28.00 Transitions / transversions = 1.57 (108/69) Gap_init rate = 0.03 (20 / 800), avg. gap size = 1.30 (26 / 20) 6593 26.34 1.04 3.57 rnd-1_family-24#LINE/CR1 326 2538 (270) C CR1_Mam#LINE/CR1 (25) 2179 21 m_b2s551i7 rnd-1_family- 326 TTCCTTTTATTTGTTT-TAAACCTGCTGCCTATTAATTTCATTTGGTGGC 374 i ii- vi v vi - -- ii vvv ? -- C CR1_Mam#LINE/ 2179 TTTCTTTTATTTGTCCCTAAAATTTCTTTC-A--AGCTTCAAAGGNTG-- 2135 rnd-1_family- 375 CCCTAGTTCTTGTATTATGGGAACAAGTAAATAACTTTTCCTTATCCACT 424 v v vivi i i v --- v i i i C CR1_Mam#LINE/ 2134 CCCTAGTTCTAGTATTCTGGGATTTGGTGAACAAGT---CCGTGTTCACC 2088 rnd-1_family- 425 TTCTCCACACCACTCATGATTTTATATACCTCTATCATATCCCCCCTTAG 474 v i vi v i iv i i C CR1_Mam#LINE/ 2087 TTATCCATACCCTTCATGATTTTATAGACTTTGATCATATCCCCTCTCAG 2038 rnd-1_family- 475 TCTCCTCTTTTCCAAGCTGAAAAGTCCTAGCCTCTTTAATCTCTCCTCAT 524 i i vii ii -- ii iv vvv?i iiiivv v C CR1_Mam#LINE/ 2037 CCTTCGTCTTTCCAGACT--AAAGTTTTAAACAAANCAGCTCAGCCTCTT 1990 rnd-1_family- 525 ATGGGACCCGTTCCAAACCCCTAATCATTTTAGTTGCCCTTCTCTGAACC 574 ?ii v - vv i i i i -- i i C CR1_Mam#LINE/ 1989 ATNAAAGCC-TTCCATCCCCTTGATCATTTTAATTACCCTTCTC--AGCT 1943 rnd-1_family- 575 TTTTCTAATGCCAGTATATCTTTTTTGAG--ATGAGGAGACCACATCTGT 622 i v ---------- i i -- v v v v i C CR1_Mam#LINE/ 1942 CTGT----------TATGTCTTTCTTGAGGGATGCGGCGACCAGAACTGC 1903 rnd-1_family- 623 ACGCAGTATTCAAGATGTGGGCGTACCATGGATTTATATAAGGGCAATAA 672 i v i i iiii v i i i i iv v C CR1_Mam#LINE/ 1902 ACACAGTATTCCAGGTGCGGATACACCATGGTTTTGTACAAAGGTAGGAT 1853 rnd-1_family- 673 GATATTCTCCGTCTTATTCTCTATCCCCTTTTTAATGATTCCTAACATCC 722 i i i i i i ii v v ii i v i i ii C CR1_Mam#LINE/ 1852 AATGTTTTCTGTTTTGTTTCCAATACCCTTCCTGATGATGCCCAGCATTT 1803 rnd-1_family- 723 TGTTTGCTTTTTTGACCGCCGCTGCACACTGCGTGGACGTCTTCAGAGAA 772 v i --- ii v i v iv i i C CR1_Mam#LINE/ 1802 TGTTGGCCTTTTTG---GCTACAGCACATTGGGCTGATGTCTTCAGGGAA 1756 rnd-1_family- 773 CTATCCACGATGACTCCAAGATCTCTTTCCTGANTNGTTGTAGCTAAATT 822 vi i i v i i? ? viiv v iv i C CR1_Mam#LINE/ 1755 CAGTCTACAATGACTCCTAGATCCCTTTCCTGGGTCGTAACTGATAGCTC 1706 rnd-1_family- 823 AGCCCCCATCATATTGTATGTATAGTTGGGGTTATTTTTTCCAATGTGCA 872 vv v i v v i i v vi C CR1_Mam#LINE/ 1705 AGAGCCCATCATCTTATAAGTATAGTTTGGATTATTTTTCCCTAAATGCA 1656 rnd-1_family- 873 TTACTTTACATTTATCCACATTAAATTTCATTTGCCATTTTGTTGCCCAA 922 i i ii i i vi i i vi v C CR1_Mam#LINE/ 1655 TTACCTTACACTTGCCCACACTGAAGCTCATCTGCCACTTTTCTGCCCAC 1606 rnd-1_family- 923 TCACTTAGTTTTGTGAGATCTTTTTGAAGTTCTTCACAGTCTGCTTTGGT 972 vi ii i ii v iv v vi v v vv C CR1_Mam#LINE/ 1605 TCACACAGCCTCGTGAGATCTTCCTGCAGTTTATCCCCATCGGCTTGGCA 1556 rnd-1_family- 973 CTTAACTATCTTGAGCAGTTTAGTATCATCTGCAAACTTTGCCACCTCAC 1022 i v i iv iv i i v vv ii C CR1_Mam#LINE/ 1555 TTTCACTACCCGGAAGAGCTTAGTGTCATCTGCAAACTTGGAGATTTCAC 1506 rnd-1_family- 1023 TGTTTACCCCTTTCTCCAGATCATTTATGAATAAGTTGAATAGGATTGGT 1072 vi i i ii i v v i i i i C CR1_Mam#LINE/ 1505 TGTGCACTCCCTCTTCCAGATCATTTATAAAAATGTTAAATAAGACTAGT 1456 rnd-1_family- 1073 CCCAGGACTGACCCTTGGGGAACACCACTAGTTACCCCTCTCCATTCTGA 1122 v i i i v iv v i i v C CR1_Mam#LINE/ 1455 CCCAGCACTGATCCCTGGGGGACCCCACTGTTTACACTTCTCCATCCAGA 1406 rnd-1_family- 1123 AAATTTACCATTTATTC-CTACCCTTTGTTCCCTGTCTTTTAACCAGTTC 1171 i v vv i - i i i v i C CR1_Mam#LINE/ 1405 GAAGTGCCCGTTTATTCTCTACCTTTTGTTTCCTGTCTCTAAGCCAGTTC 1356 rnd-1_family- 1172 TCAATCCATGAAAGGACCTTCCCTCTTATCCCATGACAGCTTAATTT--- 1218 i v v ii v i ?v iiii i --- C CR1_Mam#LINE/ 1355 CCTATCCATGACAAAACATTCCCCCNAATCCCATGGTGACTCAATTTTTA 1306 rnd-1_family- 1219 -ACNTAAGAGCCTTTGGTGAGGGACCTTGTCAAAGGCTTTCTGGAAATCT 1267 - v? - -i v i i i i C CR1_Mam#LINE/ 1305 AAAATAA-AG-TTTTGGTGTGGAACCTTGTCAAAGGCTTTTTGAAAGTCT 1258 rnd-1_family- 1268 AAGTACACTATGTCCACTGGATCCCCCTTGTCCACATGTTTGTTGACCCC 1317 i v i i v i i - i v C CR1_Mam#LINE/ 1257 AAATAAATTATATCCACTGGTTTCTCCTTGTCCACATG-TTATTTACCCC 1209 rnd-1_family- 1318 TTCAAAGAACTCTAATAGATTAGTAAGACACGATTTCCCTTTACAGAAAC 1367 i v i i i C CR1_Mam#LINE/ 1208 CTCAAAGAACTCTAATAGATTAGTCAGGCATGATTTCCCCTTACAGAAAC 1159 rnd-1_family- 1368 CATGTTGACTCTTGCCCAACAANTTATGTTCNTCTATGTGTCTGACAATT 1417 v i iv i ii i? i??? ii i ?i---? i ? C CR1_Mam#LINE/ 1158 CATGTTGCCTTTCTCCTAGTAGGTTATGTTTGNNTGCGCGNT---NAGTN 1112 rnd-1_family- 1418 TTATTCTTTAC-TATNGTTTCAACCAATTTGCCCGGTACTGACGTTAGAC 1466 i i i - ?-- ? v ii ? iv v v C CR1_Mam#LINE/ 1111 CTACTCTTTGCTTATA--TNCCACCAGCTTGCCNGGTATGGAAGTGAGAC 1064 rnd-1_family- 1467 TTACCGGCCTGTAATTGCCGGGATCACCTCTGGAGCCCTTTTTAAANATT 1516 i i i - i - --- vi i vi? - C CR1_Mam#LINE/ 1063 TCACTGGCTT-TAGTT-CC---ATGGCCTCTGGAGCCCTTCTTATGGA-T 1020 rnd-1_family- 1517 GGCGTTACATTAGCTATCCTCCAGTCATTNGGTACAGAAGCCGATTTAAA 1566 v ii- iivi iv --? i-i i vi - iv C CR1_Mam#LINE/ 1019 GGAGCC-CATTGAACACACT--NGTT-CTNGGCACAGTGGCCG-TTTGTA 975 rnd-1_family- 1567 NGACAGGTTACAAACCACAGTTAGTAGTTCCGCAATTTCACATTTGAGTT 1616 ?v ----- v v ---- vi i vi C CR1_Mam#LINE/ 974 ATACAGGTTA-----CACATTTTG----TCAACAGTTTCACCCTTGAGTT 934 rnd-1_family- 1617 CCTTCAGAACTCTTGGGTGAATGCCATCTGGTCCCGGTGACTTGT-TACT 1665 i i - i i - - C CR1_Mam#LINE/ 933 CCTTCAAAACTCTTGGGTGGATGCCATCTGGT-CCGGTGATTTATCTAC- 886 rnd-1_family- 1666 GTTNAGTTTATCAATTNGTTCCAAAACCTCCTCTA-GTGACACCTCAATC 1714 i i? i ? v i i v v i- v-i v v i C CR1_Mam#LINE/ 885 ATCTAGTTTGTCAATTAGGTCTAGAACATCCTGTGCGTT-TACCACTATT 837 rnd-1_family- 1715 TGNGACAGTTCCTCAGATTTGTCACCTANAAAGGACGGCTCAGGTTTGGG 1764 ?vvi v v ii vv v? i iii ii vv C CR1_Mam#LINE/ 836 TGATCTAGTACCTCTGACCTGTCTGCTTCAAAAGACAATTTGGGAGTGGG 787 rnd-1_family- 1765 AATCTCCCTNACATCCTCAGCCGTGAAGACCGANGCAAAGAATTCATTTA 1814 ? i i vv v i ? ? C CR1_Mam#LINE/ 786 AATCTCCCTAACGTCTTCCTCAGTAAAGACCGAAGCAAAGAATTCATTNA 737 rnd-1_family- 1815 GTTTCTCCGCAATGGCCTTATCGTCCTTGAGCGCTCCTTTNGCATCTCGA 1864 i i v vv v ivvi i? v ? i vi C CR1_Mam#LINE/ 736 GTCTCTCTGCTATCTCCTTTTTCATCTTGAGTNCACCTTTTGCACCGTGA 687 rnd-1_family- 1865 TCGTCCAGNGGCCCCACTGGTTGTTTAGCAGGCTTCCTGCTTCTGATGTA 1914 i v i? i i v i v ? i i C CR1_Mam#LINE/ 686 TCATCAAATGGTCCCACTGATTCTCTAGCTGGCTTCCTNCCTTTGATGTA 637 rnd-1_family- 1915 CTTAAAAAACATTTTGCTATTACCTTTTGAGTCTTTGGCTAGCTGTTCTT 1964 i i v ii iv v ii v v v i i C CR1_Mam#LINE/ 636 TTTAAAGAACCTTTTATTATTGGCTTTGGAGTCCCTTGCAAGGTGCTCCT 587 rnd-1_family- 1965 CAAACTCCTTTTTGGCCTTCCTNATTACATTTTTACACTTNATTTGCCAG 2014 i i iv ? v vvv ii i ? ii v C CR1_Mam#LINE/ 586 CAAATTCTTTTTTGGCCCGCCTAATTTCTAGTTTGTACCTGACCTGCCAT 537 rnd-1_family- 2015 NGTTTATGCTCCTTTCTATTTTCCTCACTAGGATTTGAC-TTCCACTTTT 2063 ?v ii vv i ii i i v ? ?v - i C CR1_Mam#LINE/ 536 ACTTTGCGGGCTTCCCTGTTCTCCTCACTTGGANTTNTCTTTCCATTTTT 487 rnd-1_family- 2064 TAAAGGATGCCTTTTTGTCTCTCACTGCTTCTTTTACTTNGTTGTTNAGC 2113 i i ivi viv iv i v ? iiiv ? C CR1_Mam#LINE/ 486 TGAAAGATGCCTTTTCCCCTACAATAGCCTCTTTGACTTTGCCAGTTAGC 437 rnd-1_family- 2114 CACGGTGGCTCTTTTTTGGTTCTCTTA----CTGTGTTTTTTAATTTGGG 2159 i v? v v --- i iv ---- vv? i ii?v C CR1_Mam#LINE/ 436 CATGCNGGGTATTTTT---TTTTCCAAGCGCCTGGTNTTTTTGATCCNTG 390 rnd-1_family- 2160 GTATACATTTAAGTTGGGCCTCTATTATGGTGTCTTTAAAAAGTTTCCAT 2209 i i vvvi i i v v i ? v i v C CR1_Mam#LINE/ 389 GCACACATTTTTCCTGGGCTTCCAATAAGGTGTTTTNAAATAGTCTCCAG 340 rnd-1_family- 2210 GCAGCTTGCAGGGATTTCACTTTNGTCACTGTACCTTTTAATTTCTGTTT 2259 vv i ii vvv i ?vvv ? -? v i -ii C CR1_Mam#LINE/ 339 GCTTCCTGTGGGTTATTTACTTTTTAAACTNT-NCTTTTCATTTTT-CCT 292 rnd-1_family- 2260 AACTAACCTCCTCATTTTTGCGTAGTTCCCCTTTCTGAAATTAAATGCTA 2309 ivi v vv i i i i i i-- C CR1_Mam#LINE/ 291 AACTAATGCCCACATTTTGTCATAGTTCCCTTTTCTAAAATTGAGTA--A 244 rnd-1_family- 2310 CA-GTGTTGGG-CTGCTGNGGTGTTC--TTCCCACCACAGGGATGTTAAA 2355 - v i-i vi v? v -- i --- i i C CR1_Mam#LINE/ 243 CATGTGATGGATTTTTTTTGGTTTTCCTTTCCCGCCA---GAATGTTGAA 197 rnd-1_family- 2356 TGTTATTA-TATTATGGTCACTATTNCCAAGCGGTCCNGCTATATTCACC 2404 v v ii- -- - ----- i i ?v i i vvi i C CR1_Mam#LINE/ 196 TTTAATCGTTAT--TGGTCAC-AT-----AGTGGTTCACCCACAGATACT 155 rnd-1_family- 2405 TCTTGGACCAGATCCTGCGCTCCACTCAGGACTAAATCGAG--AATTGCC 2452 i vi v iv v i? i i i v --v v C CR1_Mam#LINE/ 154 TCCTGCGCCAGTTCCTGTTCACTNCTCAGAACCAAGTCCAGTNTATTTCC 105 rnd-1_family- 2453 TCTCCCCTTGTGGGTTCCNGNACCAGCTGCTCCAAGAAGCAGTCATTTAA 2502 i -- i?i? i v ii i i i ? iv C CR1_Mam#LINE/ 104 TTT--CCTTGTGGGTTCTAAAACTACCTATTCTAGGAAGCGGTNATTTGT 57 rnd-1_family- 2503 GGTGTCGAGAAATTTTATCTCTGCATCCCGTCCTGA 2538 vv i i ii? ivii ii ii i C CR1_Mam#LINE/ 56 CTTATCGAAAAGCNTCTCTTCTATATTTCGTCCCGA 21 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 348, Kimura (unadjusted) = 34.46 Transitions / transversions = 1.63 (348/214) Gap_init rate = 0.04 (92 / 2212), avg. gap size = 1.09 (100 / 92) 254 35.97 0.71 0.71 rnd-1_family-24#LINE/CR1 2551 2690 (118) C L3#LINE/CR1 (2394) 1705 1566 m_b2s601i2 rnd-1_family- 2551 CCAGTCAATATGGGGATAGTTGAAATCCCCCACTATTATTGAGTTCTTTA 2600 ivi i vv i ii i i ?i ii viv C L3#LINE/CR1 1705 CCAGCAGATGTCCGGATAGTTGAAGTCCCCCATCACTACTGNATCTTGCC 1656 rnd-1_family- 2601 TTT-TGATAGCCTCTCTAATCTCCCTGAGCATTTCATCGTCACTATCACC 2649 i - vi -i i v viv v v vvv i vv ? vi C L3#LINE/CR1 1655 TCTGTGCCAG-TTTTGTAATCTGTATCAGGAAAGCATCATCCATNTCCTC 1607 rnd-1_family- 2650 GTCCTGGTCAGGTGGTCGGTAATANATCCCTACTGCTATAT 2690 vvi i i i v i ? ii i vi v C L3#LINE/CR1 1606 CATCTGGCCGGGCGGTCTGTAGTATACTCCCACAACGATAT 1566 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.37 CpG sites = 28, Kimura (unadjusted) = 52.38 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.01 (2 / 139), avg. gap size = 1.00 (2 / 2) 4988 10.47 0.00 1.70 rnd-1_family-27#LINE/CR1 1 719 (430) CR1-11_Crp#LINE/CR1 702 1408 (53) m_b2s551i8 rnd-1_family- 1 ATGAAATTTAATAGTGCAAAGTGCAAGGTCATGCATTTAGGGACTAACAA 50 i i i i CR1-11_Crp#LI 702 ATGAAATTCAATAGTACAAAGTGCAAGGTCATGCACTTAGGGACTAATAA 751 rnd-1_family- 51 CAAGAATTTTTGCTATAAGCTGGGGACNTATCAGTTGGAAGTGACAGAGG 100 --- i ii ?i ii ? ----- CR1-11_Crp#LI 752 ---GAATTTCTGCTATAAGCTGGGAGCTCATCAGTTGGAAACGNC----- 793 rnd-1_family- 101 AGGAGAAAGACCTGGGTGTATTGGTTGATCACAGGATGACTATGAGCCGC 150 - i i i i CR1-11_Crp#LI 794 -GGAGAAAGACCTGGGTGTACTAGTCGATCACAGGATGACTATGAGCCAC 842 rnd-1_family- 151 CAATGTGATGCGGCCGTGAAAAAGGCTAATGCGGTCCTAGGATGCATCAG 200 v i ? CR1-11_Crp#LI 843 CAATGTGATGCGGCCGTGAAAAAGGCAAATGCGATCCTAGGATGCATNAG 892 rnd-1_family- 201 GCGAGGTATTTCCAGTAGAGATAGGGAAGTGTTAGTACCGTTATACAAGG 250 i-- i i i i i CR1-11_Crp#LI 893 A--AGGTATTTCCAGTAGAGATAGGGAAGTATTAATGCCATTGTACAAGG 940 rnd-1_family- 251 CACTGGTGAGACCTCATCTGGAATACTGTGTGCAGTTCTGGTCTCCCATG 300 - i v CR1-11_Crp#LI 941 -ACTGGTGAGACCTCATCTGGAATACTGTGTACAGTTCTGGTCACCCATG 989 rnd-1_family- 301 TTTAAGAAAGATGAATTCAAACTGGAACAGGTGCAGAGAAGGGCTACTAG 350 i CR1-11_Crp#LI 990 TTCAAGAAAGATGAATTCAAACTGGAACAGGTGCAGAGAAGGGCTACTAG 1039 rnd-1_family- 351 GATGATCNGAGGAATGGAAAACCTACCTTATGAGAGGAGACTCAAAGAGC 400 ? i i i i i v CR1-11_Crp#LI 1040 GATGATCAGGGGAATGGAGAGCCTATCTTACGAGAGGAGACTAAAAGAGC 1089 rnd-1_family- 401 TTGGCTTGTTTAGCCTAACCAAAAGAAGGCTGAGGGGAGATATGATTGCT 450 i v v i i CR1-11_Crp#LI 1090 TTGGCTTGTTTAGCCTAGCAAAACGAAGGCTGAGAGGGGATATGATTGCT 1139 rnd-1_family- 451 CTCTATAAATACATCAGAGGGATAAATACCAGGGAGGGAGAGGAGTTATT 500 ? i i i i i CR1-11_Crp#LI 1140 NTCTATAAATACATCAGGGGGGTAAACACCAGGGAGGGAGAAGAGCTATT 1189 rnd-1_family- 501 TAAGTTAAGCGCCAATGTGGACACAAGAACAAATGGATATAAACTGGCCA 550 i iv v v i i CR1-11_Crp#LI 1190 TAAGCTAAAGGACAATGTTGGCACAAGAACAAATGGGTATAAACTGGCCA 1239 rnd-1_family- 551 TCAACAAGTTTAGGCTTGAAATTAGACGAAGGTTTCTAACCATCAGAGGA 600 v i i v v v CR1-11_Crp#LI 1240 TGAATAAATTTAGGCTGGAAATTAGAAGAAGGTTTCTAACCATCAGAGCA 1289 rnd-1_family- 601 GTGAAGTTCTGGAACAGCCTTCCAAGGGGAGCAGTGGGGGCAAAAAACCT 650 i vi i CR1-11_Crp#LI 1290 GTGAGGTTCTGGAACAGCCTTCCAATAGGAGTAGTGGGGGCAAAAAACCT 1339 rnd-1_family- 651 ANCTGGCTTCAAGACTGAGCTTGATAAGTTTATGGAGGGGATGGTATGAT 700 ? i i i iv v i i vi i CR1-11_Crp#LI 1340 AACTAGTTTTAAGATGGAGCTTGATCAGTTTATGAAAGGGATTATATGAC 1389 rnd-1_family- 701 GGGATTGCCTACAATGGCA 719 v i i i i CR1-11_Crp#LI 1390 GTGGTTGCCTGCGATAGCA 1408 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.80 CpG sites = 57, Kimura (unadjusted) = 11.59 Transitions / transversions = 3.35 (57/17) Gap_init rate = 0.02 (12 / 718), avg. gap size = 1.00 (12 / 12) 730 16.55 0.71 0.71 rnd-1_family-27#LINE/CR1 820 959 (190) CR1-3_Croc#LINE/CR1 3206 3345 (260) m_b2s551i9 rnd-1_family- 820 GGTGTCTGGCTGGTGGGTCTTGCCCACATGCTCAGGGTCTAACTGATCGC 869 vi i v vivi vi i CR1-3_Croc#LI 3206 GGTTCCTGGCTAGAGGGTCTTGCCCCTCCGCTCAGGGTCAGACCGATCGC 3255 rnd-1_family- 870 CATATTTGGGGTCGGGAAGGAATTTTCCCCCG-GGTCAGATTGGCAGAGA 918 i v i- i vi CR1-3_Croc#LI 3256 CATATTTGGGGTCAGGAAGGAATTTTACCCCATGGTCAGATTGGTACGGA 3305 rnd-1_family- 919 CCCTGGGGGTTTTTCGCCTTCCTCTGCAGCGTGGGGCACGG 959 iv - i v ii CR1-3_Croc#LI 3306 CTGTGGGGGTTTTT-GCCTTCCTCTGTAGCGGGGGGCGTGG 3345 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.53 CpG sites = 14, Kimura (unadjusted) = 18.94 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (2 / 139), avg. gap size = 1.00 (2 / 2) 664 21.66 7.18 0.52 rnd-1_family-27#LINE/CR1 969 1149 (0) CR1-L3B_Croc#LINE/CR1 3084 3276 (1) m_b2s551i10 rnd-1_family- 969 TGGAGGATTCTCTGTAACTTGAAGTCTTTAAACCATGATTTGAGGACTTC 1018 v ii vv v i i v i v v v i CR1-L3B_Croc# 3084 TGGTGGATTCTCCATCTCTTGATGTCTTCAAATCAAGACTGGATGCCTTT 3133 rnd-1_family- 1019 -----AG-TA------ACTCAGCCAGAGGTTAG-GGGTCTATTACAGGAG 1055 ----- - ------ v iv v i v- iii v i CR1-L3B_Croc# 3134 CTGGAAGATATGCTTTAGTCAAACACAAGTTATTGGGCTCAATACAGGGG 3183 rnd-1_family- 1056 TGGGTGGGTGAGGTTCTGTGGCCTGCGNTGTGCAGGAGGTCAGACTAGAT 1105 iiv ii ivi i i i CR1-L3B_Croc# 3184 TAACTGGGTGAAATTTAATGGCCTGTGNTATACAGGAGGTCAGACTAGAT 3233 rnd-1_family- 1106 GATCATGATGGTCCCTTCTGACCTTAAAGTCTATGAGTCTATGA 1149 - i i ? i CR1-L3B_Croc# 3234 GATC-TAATGGTCCCTTCTGGCCTTAAANTCTATGAATCTATGA 3276 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.46 CpG sites = 24, Kimura (unadjusted) = 26.46 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.03 (5 / 180), avg. gap size = 2.80 (14 / 5) 258 13.51 0.00 0.00 rnd-1_family-39#DNA/PIF-Harbinger 27 63 (23) MER133B#DNA/PIF-Harbinger 42 78 (37) m_b2s502i1 rnd-1_family- 27 GCGCCTAACTCCCATTGAAATCAATGGGAGTTAGGCG 63 vi i iv MER133B#DNA/P 42 GCGCGCAACTCCCATTGAAGTCAATGGGAGTTGTGCG 78 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.04 CpG sites = 3, Kimura (unadjusted) = 15.04 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 2033 10.96 1.93 4.24 rnd-1_family-47#LINE/CR1 714 1075 (89) CR1-13_AMi#LINE/CR1 371 724 (0) m_b2s551i11 rnd-1_family- 714 TCACACAGCGCNCAATTAGCCTGTGGAACTCACTGCCACANGATATCANT 763 i ii ?i i ? ? CR1-13_AMi#LI 371 TTACACAATGCATAATTAACCTGTGGAACTCACTGCCACAAGATATCACT 420 rnd-1_family- 764 GAGGCCAAGAGCTTAGCAGGATTCAAAGAGGGACTGGACGTTTATATGGA 813 - i i i i CR1-13_AMi#LI 421 GAGGCCAAGAGCTTAGCAGGATTCAAA-AAGGATTAGACATTTATATGGA 469 rnd-1_family- 814 TAACGAGAATATC--CAGTTAAACAAGTGANGATTTTTAAAAAGAGTTTT 861 i -- v iv vv ? ---- i----- CR1-13_AMi#LI 470 TAACGAGAACATCCGCAGTTACATTAGATAGGA----TAAAAAA-----T 510 rnd-1_family- 862 GGAAGGGATATAAACCCTCATGCTTCAGGGCATAAGCCAACT-CTAACTA 910 iv - ? i- i CR1-13_AMi#LI 511 ATAAGGGATAT-AANCCTCATGCTTCAGGGCATAAGCCAACCACTAACTG 559 rnd-1_family- 911 NTGGGGTTAGGAGGAAACTTTCCCTGGGGGCAGGTTATCCCATAACTGCC 960 ?i i i iv i i CR1-13_AMi#LI 560 ACGGGGTTAGGAAGAAACTTCCCCTATGGGCAGGTTATTCCATAATTGCC 609 rnd-1_family- 961 TACTGCAGGGTTTCTTGCACCTTCCTCTGAAGCATCTGGTACTGGCCACT 1010 - i iii ? - CR1-13_AMi#LI 610 -ATTATGGGGNTT-TTGCACCTTCCTCTGAAGCATCTGGTACTGGCCACT 657 rnd-1_family- 1011 GTCAGA---AGGATACTGGACTAGATGGACCACTGGTCTGATCCAGTCTG 1057 --- -iv v v ? CR1-13_AMi#LI 658 GTCAGAGACAGGATACTGGACTAGATGGACCACTGGTC-ATTCCACTATN 706 rnd-1_family- 1058 GC-AATTCCTATGTTCCTA 1075 - vv - i CR1-13_AMi#LI 707 GCGAATTAAT-TGTTCTTA 724 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.99 CpG sites = 27, Kimura (unadjusted) = 12.32 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.05 (19 / 361), avg. gap size = 1.16 (22 / 19) 343 25.50 1.97 1.97 rnd-1_family-49#LTR/Gypsy 3729 3880 (1109) MamGyp-int#LTR/Gypsy 2459 2610 (2492) m_b2s551i12 rnd-1_family- 3729 TAGATCTTAGCAAAGGGTACTGGCAGATCCCCCT---CGAGGAGACCTCA 3775 i i v v iv i iv v iv ---i ? iv --- MamGyp-int#LT 2459 TGGATTTGAGGAGTGGGTATTATCAGATACCTATGGCTGANGAGGAC--- 2505 rnd-1_family- 3776 AAGGAGAAGACCGCNTTCGCCACNCCANCGGGNCTNTNCCAATTCACACG 3825 i i v ? ii vv? ??i ?i ? ?i iiv v MamGyp-int#LT 2506 AAAGAAAAGACAGCCTTCATCTGTCCNGTGGGGTTCTATCAATTTGAAAG 2555 rnd-1_family- 3826 GATGCCNTTCGGNCTCCATGGGGCCCCAGCCACCTTCCAGCGCCTGATGG 3875 ?ivv ?v iv? v v MamGyp-int#LT 2556 GATGCCTCAGGGTATCTCNGGGGCCCCTGCCACCTTCCAGCGGCTGATGG 2605 rnd-1_family- 3876 ACNAG 3880 v? MamGyp-int#LT 2606 AAAAG 2610 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 19, Kimura (unadjusted) = 35.02 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.03 (4 / 151), avg. gap size = 1.50 (6 / 4) 262 29.70 0.00 3.30 rnd-1_family-5#LINE/CR1 741 834 (3442) L3#LINE/CR1 568 658 (3441) m_b2s601i3 rnd-1_family- 741 CTGCTGCCACCACTGCGAATAGGAAACGTAGGGTAGTGGTGGTCGGAGAC 790 i i ii? v iiv iv i i i--- v i v L3#LINE/CR1 568 CTGTTACTGNCCCCAGGAGGAAGAGACGC---GTCGTGGTGGTTGGTGAC 614 rnd-1_family- 791 TCTCTGCTGAGGGGGACGGAGGCGCCCATCTGTCGCCCTGACAT 834 i i iv v i v iv v i L3#LINE/CR1 615 TCCCCGCTGAGGGATACGGAGGCGGCCGTATGCAGACCTGACGT 658 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 17, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.00 (3 / 3) 12179 27.81 0.93 0.81 rnd-1_family-5#LINE/CR1 839 4272 (4) Plat_L3#LINE/CR1 136 3573 (0) m_b2s551i13 rnd-1_family- 839 TCTCGGGAGGTATGCTGCCTGCCGGGGGCCCGTATCCGAGACGTTACGGA 888 i i ? ? i ii i ivi i ? ii i Plat_L3#LINE/ 136 TCCCGGGAGGTGTGNTGCCTGNCGAGAACTCAGGTCTGAGNCGCCACGAA 185 rnd-1_family- 889 GGCATTGTCGA-GGATT-ATCCGGCCCTCTGACTACTACCCCATGCTACT 936 ?v -- - i - ? vvi ? i i v Plat_L3#LINE/ 186 GNGATTG--GACGGACTCATCNGGCCCGACGACTNCTGCCCCGTGCTTCT 233 rnd-1_family- 937 CATCCATGTGGGCACAAATGATACTGCGCGGTGTGACACTGAGCGGATCA 986 i v i v v v v v ?v Plat_L3#LINE/ 234 TATCCATGTGGGAACGAATGATACTGCCCGGTCTCACCCGGAGCNTATCA 283 rnd-1_family- 987 AGAGTGACTACAGGGCTCTGGGAGTACGGGTGAAGGAGTTTGGAGCGCAG 1036 i i iiv viv i v Plat_L3#LINE/ 284 GGAGTGACTGCAGGGCTCTGGGAGCGAGGGTGAAGGAGGCGGGGGCTCAG 333 rnd-1_family- 1037 GTGGTATTCTCTTCGATTCTTCCTGTCAAAGGTAGGGGCCCGGGCAGAGA 1086 i v i i v i i v ii i vv i Plat_L3#LINE/ 334 GTGGTGTTCTCGTCGATCCTCCCAGTCGAGGGGAAAGGCTCCCGCAGGGA 383 rnd-1_family- 1087 CAGATGCATCATGGAGGTGAATGCCTGGCTGCGAAGATGGTGTCGCCAGG 1136 i v i i viiv vvii Plat_L3#LINE/ 384 CAGACGCATCCTGGAGATGAACGCCTGGCTGCGCGACTGGTGTCGAAGAG 433 rnd-1_family- 1137 AGGGCTTTGGCTTCCTAGACCACGGGATGCTATTCGAGGAAG---GACTG 1183 iv i v v v vi v v ii --- v v Plat_L3#LINE/ 434 AATGCTTCGGATTCCTCGACAACGGTGTGATCTTCAGGGAAGAGGGCCTC 483 rnd-1_family- 1184 CTAGGCAGAGATGGCGTTCACCTTTCGAGGAGAGGGAAGACCCTATTCGG 1233 ii v i i vi i i iv i i viv v Plat_L3#LINE/ 484 CTGAGCCGGGACGGGATCCATCTCGCGAAGAAAGGGAAGAGTATCTTCGG 533 rnd-1_family- 1234 ACACAGACTGGCTAACCTAGTGAGGAGGGCTTTAAACTAGGTTCGACGGG 1283 ivi i i i Plat_L3#LINE/ 534 GAGCAGACCGGCTAACCTAGTGAGGAGGGCTTTAAACTAGGTTTGGCGGG 583 rnd-1_family- 1284 GACAGGTGAGCAAAGCCCACAGGTAAGTGGGGAA----CATGGAGACCGG 1329 ii i v?i v v i-- ---- v v- i Plat_L3#LINE/ 584 GATGGATCNACTAAGCCCAAAGGTAAGTGA--AATTTNCATTGAT-CTGG 630 rnd-1_family- 1330 GGAGATGGGTCGGAAA-CGAGAGGGAGCGTGGGCTATATTGGCA-GAGAG 1377 i -- i v v- v iviii v vv vi i i- i v Plat_L3#LINE/ 631 GGGGA--GGCCTGAACTCTAGAATAGACTTGGGAAATTCTAGCGTGGGTG 678 rnd-1_family- 1378 AAAGGAGAGTCAGGACAAAACTGGGAGGAAAGATCAAACCA--G-TATCT 1424 v i iv iiv vi vii i i ---- v -- - ii Plat_L3#LINE/ 679 ACAAGGTAACAAGGAGGAAAACAGAAGGGA----CAACCCATGGCTACTT 724 rnd-1_family- 1425 TAGATGCCTATATACAAATGCGAGAAGTATGGGGAATAAGCAGGAAGAAC 1474 v i ii i ii i i i i i i Plat_L3#LINE/ 725 GAAATGTTTGTACGCAAATGCAAGGAGCATGGGAAATAAACAGGAGGAAC 774 rnd-1_family- 1475 TGGAAGTGCTAATAAATAAATACAACTATGACATTGTTGGCATCACTGAA 1524 i vi iivv vi vi ii ii vii v v i Plat_L3#LINE/ 775 TGGAGGTCTTAGCTCAGGACCACAGTTATGATGTAACTGGAATAACTGAG 824 rnd-1_family- 1525 ACTTGGTGGGATAATACACATGATTGGAATGTTGGTGTGGATGGGTACAG 1574 v i ii v i i i vv i v iv Plat_L3#LINE/ 825 ACGTGGTGGGACAGCACTCATGACTGGAGTGCTGGACTAGAAGGGTATCG 874 rnd-1_family- 1575 CTTGCTCAGGAAGGATAGACAGGGGAAAAAGGGAGGAGGTGTTGCCTTAT 1624 v i i i i v i Plat_L3#LINE/ 875 GTTGTTCAGGAAAGATAGGCAGGGAAAAAAGGGAGGTGGTGTTGCCTTGT 924 rnd-1_family- 1625 ATATTAAAAATGTACACACTTGGACTGAGGT---AGAGATGGACATAGGA 1671 i i ii i?vi v vv v i---i i ii --- Plat_L3#LINE/ 925 ACATCAAGGATANCTACACATGCTCAGAGGCCCAGGAAACAGA---AGGA 971 rnd-1_family- 1672 GACGGAAGTGTTGAGAGTCTCTGGGTTAGGCTNAAAGGGGCAAAAAACAA 1721 i vi viv v v iivi? v v i i Plat_L3#LINE/ 972 GGCCAACAGGTAGAGAGTGTCTGGGTTAAAGCGAAAGGTGAAAAGAATAA 1021 rnd-1_family- 1722 GGGAGATGTCATGCTAGGAGTCTACTACAGGCCACCTAACCAGGTGGAAG 1771 v i v i i i v v vi ii Plat_L3#LINE/ 1022 GGGCGACGTCATGGTAGGAGTCTATTATAGACCTCCAAACCAGGAAGAGA 1071 rnd-1_family- 1772 AGGTGGATGAGGCTTTTTTCAAGCAACTAACAAAATCATCCAAAGCCCAA 1821 i i iiiv v v v iv ivvi vi i Plat_L3#LINE/ 1072 AGGTGGATGAGGCCTTCTTTGGTCAACTCACCAAAGCGGCTTCGGGTCAG 1121 rnd-1_family- 1822 GATTTGGTGGTGATGGGGGACTTCAACTATCCGGATATATGTTGGGAAAA 1871 i i i i i v i i i Plat_L3#LINE/ 1122 GATCTGGTGGTGATGGGAGACTTTAACTACCCAGATATCTGCTGGAAAAG 1171 rnd-1_family- 1872 TAACACAGCGGGGCACAGACTATCCAACAAATTCTTGGACTGCATTGGAG 1921 i iv v iii v ii i i i Plat_L3#LINE/ 1172 CAATTCAGCGGGCCACAGATCGTCAAACAGGTTTTTGGATTGCATTGGGG 1221 rnd-1_family- 1922 ACAACTTTTTATTTCAGAAGGTTGAAAAAGCTACTAGGGGGGAAGCTGTT 1971 i ii v v i v ii v v vi v iv Plat_L3#LINE/ 1222 ACAATTTCCTAGTGCAGAAAGTAGAGGAATCAACTAGGGCAGATGCCCTT 1271 rnd-1_family- 1972 CTAGACTTGATTTTAACAAATAGGGAGGAACTCGTTGAGAATTTGAAAGT 2021 v i i v v ii i i v i i i i i Plat_L3#LINE/ 1272 CTTGATTTGATTCTTACTAACGGGGAAGAATTAGTCGAGGATCTAAAGGT 1321 rnd-1_family- 2022 AGAAGGCAGCCTGGGTGAAAGTGATCATGAAATCATAGAGTTCGCGATTC 2071 i v v i v i i ii i v v vi iv i Plat_L3#LINE/ 1322 GGATGGAAACCTTGGTGGAAGCGATCACAAGATGATCGTATTCAAGATCC 1371 rnd-1_family- 2072 TAAGGAAGGGTAGAAGGGAGAACAGCAAAATAGAGACAATGGATTTCAGG 2121 i i v i i iiv i i v i i i Plat_L3#LINE/ 1372 TAAGGGAAGGGAGGAGAGAAGTCAGCAAGATAAAGAAAATGAACTTTAGG 1421 rnd-1_family- 2122 AAGGCAGATTTTGGNAAGCTCAGAGAGCTGATAGGTAAGGTCCCATGGGA 2171 i i ii? i i i vi ii v i ii v i Plat_L3#LINE/ 1422 AAAGCAAATTTTAACAGGCTTAGGGCACTAGTAGGAAGGACCCGATGGAA 1471 rnd-1_family- 2172 ATCAAGACTGAGGGGAAAAACAACTGAGGAGAGTTGGCAGTTTTTCAAAG 2221 ivv v i i v iv iiiv i i i v i i Plat_L3#LINE/ 1472 GGAAAGCCTAAGAGGCAAAGGAGTCCAAGAAAGCTGGCTGTTCTTCAAAA 1521 rnd-1_family- 2222 GGACACTATTAAGGGCCCAAAAGCAAGCTATTCCGCTGGTTAGGAAAGAT 2271 i v vi ivi i ii i i v iv vv? i i Plat_L3#LINE/ 1522 AGACAGTTCTGCAGGCTCAGGAACAAACTATACCAGTGCANAGGAAGGAC 1571 rnd-1_family- 2272 AGAAAATGTGGCAAAAGACCACCTTGGCTTAACCACGAGATCTTGCACGA 2321 ii iv ii i vi vv v vv iv ?vviv Plat_L3#LINE/ 1572 AAGAAGGGTAACAAGATGCCAAGTTGGCTAAACCCAGAACTCTNCAGAGA 1621 rnd-1_family- 2322 TCTAAAAAATAAAAAGGAGTCATATAAAAAATGGAAACTAGGACAGATTA 2371 i i iiii vi ivvv i i i v i Plat_L3#LINE/ 1622 CCTGAAGGGCAAATGGGAAAGCTACAAAAAGTGGAAATTAGGCCAGATCA 1671 rnd-1_family- 2372 CAAAGGATGAATATAGGCAAACAACACAGGAATGCAGGGGCAAGATTAGA 2421 v i v i iiv i i iivvi i i Plat_L3#LINE/ 1672 CTAAAGAAGAGTATAAAGAAATAGCACGATTGTGTAGGGACAAGATTAGA 1721 rnd-1_family- 2422 AAGGCAAAGGCACAAAATGAGCTCAAACTAGCTACGGGA-ATAAAGGGAA 2470 i ? i vvi v v vv - i - i v Plat_L3#LINE/ 1722 AAAGCNAAAGCCGGAAAGGAGATGCAACTAGC-ACGAGACATAAAAGGTA 1770 rnd-1_family- 2471 ACAAGAAGACTTTTTATCAAT-ACATTAGAAGCAAGAGGAAGACCAAAGA 2519 i i v i - - i iviv i ii Plat_L3#LINE/ 1771 ACAAAAAAACATTCT-TCAATTATATTAGGCAAAAGAGGAGGACCAGGGA 1819 rnd-1_family- 2520 CAGGGTAGGCCCACTGCTCAGTGAAGAGGGAGAAACAG-TAACAGGAAAC 2568 v iv v vi v i v - vv i i ii i v - ivi Plat_L3#LINE/ 1820 AAATGTCGCTCCCCCGGT-AGACAGGAAGGGAAAGCTGATAACAGATGAC 1868 rnd-1_family- 2569 TTGGAAATGGCAGAGATGCTTAATGACTTCTTTGTTTCGGTCTTCACCGA 2618 vv v i iivi ?vvvi i iii v i vi Plat_L3#LINE/ 1869 TGTGAAAAGGCGGAGGCTTTTANATTTTTTTTCACTTCTGTCTTTACGAA 1918 rnd-1_family- 2619 GAAG-TCTGAAG-GAATGCCTAAC-ATAGTGAATGCTAATGGGAAGGGGG 2665 i - vi v - iiv i - vi ii i v i v v ?i v i- Plat_L3#LINE/ 1919 AAAGATCAAATGTGAACAGCTGACCAGGGCAAGTCCCACTTGNGATGGA- 1967 rnd-1_family- 2666 TAGGTTT---AGCGGA--TAAAATAAAAAAAGAACAAGTTAAAAATCACT 2710 - v--- vi -- i iii vv i vi ii Plat_L3#LINE/ 1968 -AGGTTGGAAAGCCAAACTAGAATAGGGAAAGAAACAGTTAAAGAGTATC 2016 rnd-1_family- 2711 TAGAAAAGTTAGATGCCTGCAAGTCACCAGGGCCTGATGAAATGCATCCT 2760 ?i iiii iv vi i v v Plat_L3#LINE/ 2017 TNAAAAAACCGGATGTATTTAAATCAGCAGGGCCTGATGACATGCATCCT 2066 rnd-1_family- 2761 AGAATACTCAAGGAGCTAATAGAGGA-GGTAT--CTGAGCCTCTAGCTAT 2807 ii i --- v i v - v -- v v Plat_L3#LINE/ 2067 AGGGTACTTAAGGA---ATTGGCGGATGTTATTGCAGAGCCACTAGCTAT 2113 rnd-1_family- 2808 TATCTTTGGAAAGTCATGGGAGACGGGAGAGATTCCAGAAGACTGGAAAA 2857 i ii v ii ii ii i v i i Plat_L3#LINE/ 2114 TATTTTTGAGAACTCGCGGAGGACGGGAGAAGTCCCTGAGGATTGGAAAA 2163 rnd-1_family- 2858 GGGCAAATATAGTGCCCATCTATAAAAAGGGAAATAAAAACAACCCAGGN 2907 ii v v i i v ii i v ? Plat_L3#LINE/ 2164 GGGCAAACGTTGTGCCCATCTTTAAAAAAGGGAAAAAGGACGACCCTGGT 2213 rnd-1_family- 2908 AACTACAGACCAGTTAGTTTAACTTCTGTGCCAGGGAAGATAATGGAGCA 2957 i i i i v vi i v v i i Plat_L3#LINE/ 2214 AATTACAGACCGGTCAGCTTAACATCGATACCTGGGAAGATACTAGAACA 2263 rnd-1_family- 2958 AGTAATTAAGGAAATCATCTGCAAACACTTGGAAGGTGGTAAGGTGATAG 3007 i v i iv viv i v i i ivvi i iv Plat_L3#LINE/ 2264 AATCATCAAACAATCAATTTGCAACCACCTAGAAGAGCATAAGATACTAG 2313 rnd-1_family- 3008 GGAACAGCCAGCATGGATTTGTGAAGAACAAATCATGTCAAACCAATCTG 3057 i i i i i v i i i i ? i i Plat_L3#LINE/ 2314 GAAGCAACCAACGTGGCTTTGTGAAGAGCAAATCGTGCCAGACNAATTTA 2363 rnd-1_family- 3058 ATAGCTTTCTTTGATAGGATAACGAGCCTTGTGGATAAGGGTGAAGCGGT 3107 vv i v ii i ii vi i i v ii Plat_L3#LINE/ 2364 ATTTCCTTCTATGATAGAGTGACAGGCCACGTAGACAAGGGGGAAGCAAT 2413 rnd-1_family- 3108 GGATGTGGTATACCTAGACTTTAGTAAGGCATTTGATACGGTCTCGCATG 3157 i ii v i i v v v i i Plat_L3#LINE/ 2414 AGATGTAATCTATCTAGACTTCAGTAAGGCTTTTGATTCCGTCCCACATG 2463 rnd-1_family- 3158 ATATTCTTATCGATAAACTAGGCAAATACAANTTAGATGGGGCTACTATA 3207 i i i i i i v i iii?i v ivivi ii v Plat_L3#LINE/ 2464 ACATCCTCATCGACAAGCTGGGAAAGTATGGTCTTGACCATACTACCGTT 2513 rnd-1_family- 3208 AGGTGGGTGCATAACTGGCTGGATAACCGTACTCAGAGAGTTGTTATTAA 3257 i i v viii i i i i v i i Plat_L3#LINE/ 2514 AGGTGGGTGCACAGCTGGCTCGAGGGTCGCACCCAAAGGGTAGTCATCAA 2563 rnd-1_family- 3258 TGGTTCCCAATCCTGCTGGAAAGGCGTAACGAGTGGGGTNCCGCAGGGGT 3307 i vvvi vvv ii i?i v v ? i i Plat_L3#LINE/ 2564 TGGCTCGGTGTCAACCTGGAGGGANATATCGAGTGGTGTCCCACAGGGAT 2613 rnd-1_family- 3308 CTGTTTTGGGACCGGCTCTGTTCAATATCTTCATCAACGACTTAGATATT 3357 v ii i i i i i i i iivv Plat_L3#LINE/ 2614 CGGTCCTGGGACCGGTTCTATTCAATATCTTTATCGATGACCTGGACGAA 2663 rnd-1_family- 3358 GGCATAGAAAGTACGCTTATTAAGTTTGCGGATGATACCAAACTGGGAGG 3407 v v i i i i i i i i i v Plat_L3#LINE/ 2664 GGAATCGAGAGCATGCTCATCAAATTTGCAGATGATACTAAATTGGGCGG 2713 rnd-1_family- 3408 GATTGCAACTGCTTTGGAGGACAGGGTCATAATTCAAAATGATCTGGACA 3457 i v vii i ivi v i i ? Plat_L3#LINE/ 2714 GGTTGCTAACACTTTGGAAGACAGGAATAAAATTCAAAGTGACCTNGACA 2763 rnd-1_family- 3458 AATTGGAGAAATGGTCTGAGGTAAACAGGATGAAGTTTAACAAAGACAAA 3507 i iv?viv i i i ii i Plat_L3#LINE/ 2764 AATTGGAAAAATGGTCCTNCAAAAACAGGATGAAATTCAATAGGGACAAG 2813 rnd-1_family- 3508 TGCAAAGTGCTCCACTTAGGAAGGAAAAATCAGTTTCACACATACAGAAT 3557 i iv v i v iv iiiv v i Plat_L3#LINE/ 2814 TGCAAGGTAGTGCACTTAGGGACGAAAAACAAACCGCACAAATACAGGAT 2863 rnd-1_family- 3558 GGGAAAAGACTGTCTAGGAAGGAGTACGGCAGAAAGGGATCTAGGGGTTA 3607 i v v vi i ii i i i Plat_L3#LINE/ 2864 GGGGAAAGACTGGCTAGGCACAAGTACAGCAGAAAAAGACCTGGGGGTCA 2913 rnd-1_family- 3608 TAGTGGACCACAAGCTAAATATGAGTCAACAGTGTGATGCTGTTGCAAAA 3657 v ? i i i ii i iiv Plat_L3#LINE/ 2914 TAGTCGACCANAAGCTGAATATGAGTCAGCAATGTAGTGCCGTTATTAAA 2963 rnd-1_family- 3658 AAAGCAAACATGATTCTGGGATGCATTAACAGGTGTGTTGTGAGCAAGAC 3707 v i i v i v i viiiv v Plat_L3#LINE/ 2964 AAAGCCAACGTGGTACTGGGATGTATTAACAGGAGTATGACATGCAAGAG 3013 rnd-1_family- 3708 ACGAGAAGTCATTCTTCCGCTCTACTCTGCTCTGGTTAGGCCTCAGCTGG 3757 v i v i v v i i iivii i Plat_L3#LINE/ 3014 TCGGGAAGTAATCCTTCCGCTATACTCTGCACTGGTCAGACCCTTATTAG 3063 rnd-1_family- 3758 AGTATTGTGTCCAGTTCTGGGCGCCGCATTTCAAAAAAGATGTGGAGAAA 3807 i i v i i i i Plat_L3#LINE/ 3064 AGTACTGTGTCCAGTTTTGGTCACCGCACTTTAAAAAGGATGTGGAGAAA 3113 rnd-1_family- 3808 TTGGAAAGGGTCCAGAGAAGAGCAACAAGAATGATTAAAGGTCTTGAGAA 3857 i i i i vv v i Plat_L3#LINE/ 3114 CTGGAGAGGGTCCAGAGAAGAGCGACAAAAATGATTAAAGGGATGGAAAA 3163 rnd-1_family- 3858 CATGACCTATGAAGGAAGGCTGAAAGAATTGGGTTTGTTTAGTTTGGAAA 3907 i v v i i i i i v ii i Plat_L3#LINE/ 3164 TAGGTCCTATGAGGAAAGGTTAAAGGAATTGGGGTTGTTTAGCCTGGAGA 3213 rnd-1_family- 3908 AGAGAAGACTGAGAGGGGACATGATAGCAGTTTTCAGGTATNTAAAAGGG 3957 i i i v v i i v i i ? i i v Plat_L3#LINE/ 3214 AGAGAAGGCTAAGGGGTGACTTAATAACTGTCTTCAAGTATATGAAGGGT 3263 rnd-1_family- 3958 TGTCATAAGGAGGAGGGAGAGAACTTGTTCACCTTAGCCTCTAAGGATAG 4007 v i ii v vv vv v v v iv v ?i iv Plat_L3#LINE/ 3264 TTTTATGGGGAGGACGCTGACCAGTTGTTCTCCATGTCCACNGAGGACCG 3313 rnd-1_family- 4008 AACNAGAAGCAATGGGTTTAAACTGCAGCAAGGGAGGTCTAGGTTGGACA 4057 ? i v i i iv i i i i v Plat_L3#LINE/ 3314 AACAAGAGGAAATGGGCTTAAATTAAAGCAGGAGAGATTTCGGTTGGACA 3363 rnd-1_family- 4058 TTAGGAAAAAGTTCCTAACTGTCAGGGTGGTTAAACACTGGAACAAATTG 4107 v i v i i i v iiii i Plat_L3#LINE/ 3364 TAAGGAAGAACTTCTTGACTGTCAGGGTGATAAAACACTGGAACGGGCTA 3413 rnd-1_family- 4108 CCTAGGGAGGTTGTGGAATCTCCGTCTCTGGAGATATTTAAGAGTAGGTT 4157 v i i i v iv iv Plat_L3#LINE/ 3414 CCGAGGGAGGTTGTGGAGTCTCCATCCCTGGAGATCTTTAAGAAAAGAAT 3463 rnd-1_family- 4158 AGATAAATGTCTATCAGGGATGGTCTAGACAGTATTTGGTCCTGCCATGC 4207 i ?vii i vv i v --- ii-- - v Plat_L3#LINE/ 3464 AGACANCCATCTGTCCTGGATGGTTTAGTC---ATTCA--CCTGCC-TGG 3507 rnd-1_family- 4208 GGGCAGGGGACTGGACTCGATGACCTCTCGAGGTCCCTTCCAGTCCTAGA 4257 i i iv ii ?i Plat_L3#LINE/ 3508 AGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANG 3557 rnd-1_family- 4258 A-TCTATGAATCTATG 4272 - v i Plat_L3#LINE/ 3558 ATTCTATGATTCTACG 3573 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.30 CpG sites = 608, Kimura (unadjusted) = 36.47 Transitions / transversions = 1.79 (608/339) Gap_init rate = 0.01 (48 / 3433), avg. gap size = 1.25 (60 / 48) 386 16.67 0.00 0.00 rnd-1_family-51#DNA/PIF-Harbinger 1 66 (8) Chompy-6_Croc#DNA/PIF-Harbinger 489 554 (426) m_b2s502i2 rnd-1_family- 1 AGAAGGGATTTGAACAGGGGTCTCCCACCTCTCAGGTGAGTGCCCTAACC 50 i v vv ? iii i i Chompy-6_Croc 489 AGGAGGGAATTGAACCCGGGTCTCCCACNTCCTGGGCGAGTGCTCTAACC 538 rnd-1_family- 51 ACTGGGCTATGGGATA 66 i v ? Chompy-6_Croc 539 ACTAGGCTATTGNATA 554 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.93 CpG sites = 7, Kimura (unadjusted) = 19.85 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 20 23.55 1.47 2.99 rnd-1_family-59#Unknown 10 77 (120) (CCGCT)n#Simple_repeat 1 67 (0) m_b2s252i5 rnd-1_family- 10 CCGCCCCAGCTCACCTCCGCTCCGCCTCCTCCCCTGAGCGCGCCGCCCCG 59 i - vv - v i vvvv v i (CCGCT)n#Simp 1 CCGCTCC-GCTCCGCTCCGCTCCG-CTCCGCTCCGCTCCGCTCCGCTCCG 48 rnd-1_family- 60 CTCCGCTTCTCTCC-CTCC 77 i v - (CCGCT)n#Simp 49 CTCCGCTCCGCTCCGCTCC 67 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 12 19.18 5.88 3.85 rnd-1_family-59#Unknown 138 188 (9) (GCG)n#Simple_repeat 1 52 (0) m_b2s252i6 rnd-1_family- 138 GCGGCGGCGGC-GCGCTCGG-GGAGGAGGCGG-AGCGGAGGTGAGCTGGG 184 - -v - v v -i v i - v v (GCG)n#Simple 1 GCGGCGGCGGCGGCG-GCGGCGGCGGCGGCGGCGGCGGCGGCG-GCGGCG 48 rnd-1_family- 185 GCGG 188 (GCG)n#Simple 49 GCGG 52 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 362 19.74 0.00 1.32 rnd-1_family-7#SINE/MIR 953 1029 (1087) CR1-3_Croc#LINE/CR1 3528 3603 (2) m_b2s551i14 rnd-1_family- 953 TGGTCCTGCCTCAGCGTAGGGGGCTGGACTTGATGATTTCTCGAGGAGCC 1002 i - i i v ii v vv CR1-3_Croc#LI 3528 TGATCCTGCCTCAG-GCAGGGGGTTGGACTAGATGACCTCTGGAGGTCCC 3576 rnd-1_family- 1003 GTCCAGCCCCACAGTTCTGTGATTCTA 1029 v i vvi i CR1-3_Croc#LI 3577 TTCCAGCCCTACTTCTCTATGATTCTA 3603 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.11 CpG sites = 8, Kimura (unadjusted) = 23.11 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 912 10.30 3.03 0.00 rnd-1_family-7#SINE/MIR 1257 1421 (695) MIR1_Amn#SINE/MIR 6 175 (55) m_b2s601i4 rnd-1_family- 1257 AGGCAGTGTGGTCTAGTGGNTAGAGCACGGGACTGGNANTCAGGAAACA- 1305 ? v ? ? i i v- MIR1_Amn#SINE 6 AGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCT 55 rnd-1_family- 1306 GTGTTCTNNTCCTGGCTCTGCCACTGACTCGCTGNGTGACCTTGGGCAAG 1355 v ?? i ?i i? MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAG 105 rnd-1_family- 1356 TCACGTCCCCGCCCCGTGCCTCAGTTTCCCCATCTGTAAAATAGGG---A 1402 v ?v v i i ? i i --- MIR1_Amn#SINE 106 TCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 155 rnd-1_family- 1403 TGATACTGACC-CTTCTGTA 1421 - i i MIR1_Amn#SINE 156 TGATACTGACCTCCTTTGTA 175 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 10.65 CpG sites = 11, Kimura (unadjusted) = 12.06 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (3 / 164), avg. gap size = 1.67 (5 / 3) 816 17.55 4.35 0.93 rnd-1_family-7#SINE/MIR 1257 1463 (653) MIRc#SINE/MIR 3 216 (52) m_b2s601i5 rnd-1_family- 1257 AGGCAGTGTGGTCTAGTGGNTAGAGCACGGGACTGGNANTCAGGAAA--C 1304 vi ?v v v ? ? i-- MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 rnd-1_family- 1305 AGTGTTCTNNTCCTGGCTCTGCCACTGACTCGCTGNGTGACCTTGGGCAA 1354 v v v?? i v v ? MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 rnd-1_family- 1355 GTCACGTCCCCGCCCCGTGCCTCAGTTTCCCCATCTGTAAAATAGGGATG 1404 v vv v i i v i i i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 rnd-1_family- 1405 ATA----CTGACCCTTCTGTACCTCCCAGGGATG--AGGAAGGTT-ACTT 1447 ---- - v i- v v --iv i i i- v v MIRc#SINE/MIR 153 ATAATACCTG-CCCTGCC-TACCTCACAGGGTTGTTGTGAGGATCAAATG 200 rnd-1_family- 1448 AGTTAATGTTTGTAAA 1463 v v i MIRc#SINE/MIR 201 AGATAATGTATGTGAA 216 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.11 CpG sites = 14, Kimura (unadjusted) = 20.71 Transitions / transversions = 0.64 (14/22) Gap_init rate = 0.03 (6 / 206), avg. gap size = 1.83 (11 / 6) 12 19.61 0.00 0.00 rnd-1_family-72#Unknown 86 114 (0) (CCCCT)n#Simple_repeat 1 29 (0) m_b2s252i4 rnd-1_family- 86 CCCATCCCCTCAGCTCCCCTCCTCCCCCC 114 v vv i i (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCCCTCCCC 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 3.70 rnd-1_family-77#DNA/PIF-Harbinger 284 311 (4218) (CCTC)n#Simple_repeat 1 27 (0) m_b2s252i0 rnd-1_family- 284 CCTCACCTCCCTCCCTCCCTCCCTCCCT 311 - (CCTC)n#Simpl 1 CCTC-CCTCCCTCCCTCCCTCCCTCCCT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 16 10.08 2.94 2.94 rnd-1_family-77#DNA/PIF-Harbinger 493 526 (4003) (GGC)n#Simple_repeat 1 34 (0) m_b2s252i1 rnd-1_family- 493 GGAGGCGGCGGCGGCGGCAGC-GCGGCGACGAGCG 526 v i - i - (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG-GCG 34 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 17 18.53 0.00 0.00 rnd-1_family-77#DNA/PIF-Harbinger 2945 2975 (1554) (C)n#Simple_repeat 1 31 (0) m_b2s252i2 rnd-1_family- 2945 CCCCCCCCGCCGCCGACCCCCCCCCCCCGCC 2975 v v vv v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 20 3.81 0.00 0.00 rnd-1_family-77#DNA/PIF-Harbinger 3731 3757 (772) (CTC)n#Simple_repeat 1 27 (0) m_b2s252i3 rnd-1_family- 3731 CTCATCCTCCTCCTCCTCCTCCTCCTC 3757 v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 413 17.33 1.33 0.00 rnd-1_family-93#DNA/PIF-Harbinger 1 75 (0) Chompy-6_Croc#DNA/PIF-Harbinger 378 453 (527) m_b2s502i3 rnd-1_family- 1 AGCTTCAACAGGAGAGACTGAGGGAGCCCC-ACATCAGAATATCCCATAG 49 i iiv i v - vi v i Chompy-6_Croc 378 AGCTTCAACAGGAGGGGTGGAGAGTGCCCCCACCCCAGAATAGCCTATAG 427 rnd-1_family- 50 CCCAGTGGTTAGGGCACTCNCCTGAG 75 ii ? i Chompy-6_Croc 428 CCTGGTGGTTAGGGCACTCTCCTGGG 453 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.50 CpG sites = 9, Kimura (unadjusted) = 20.50 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 967 7.35 0.74 0.00 rnd-1_family-97#DNA/PIF-Harbinger 1 136 (0) Chompy-6_Croc#DNA/PIF-Harbinger 751 887 (93) m_b2s502i4 rnd-1_family- 1 CACACCCCTCTCCTCGGCATCTCCCATTGGCTAGCTTAGGCGGCTCCCCG 50 v i i i i Chompy-6_Croc 751 CACACCCCTGTCCTCAGCGTTTCCTATTGGCTAGCTTAGGCGGCTCCCCG 800 rnd-1_family- 51 CCTAGCGTGCTGGCTTTTGTGGATCCCATTCTNAGGCGCCTATCTCTCCC 100 ii ? ? v Chompy-6_Croc 801 CTCAGCGTGCTGGCTNTTGTGGATCCCATTCTGAGGCGCCTAACTCTCCC 850 rnd-1_family- 101 CATNCATTGTATA-GGAGCCTGGGCGCCTAACTCAGG 136 ? i - i Chompy-6_Croc 851 CATGCACTGTATAGGGAGCCTAGGCGCCTAACTCAGG 887 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.26 CpG sites = 8, Kimura (unadjusted) = 8.03 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.01 (1 / 135), avg. gap size = 1.00 (1 / 1) 14 12.68 0.00 0.00 rnd-1_family-141#Unknown 141 166 (130) (TGCT)n#Simple_repeat 1 26 (0) m_b3s252i14 rnd-1_family- 141 TGCTTGATTGCTTGCTTGTTTGTTTG 166 v i i (TGCT)n#Simpl 1 TGCTTGCTTGCTTGCTTGCTTGCTTG 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 14 15.91 0.00 0.00 rnd-1_family-151#DNA/PIF-Harbinger 1337 1364 (769) (CTC)n#Simple_repeat 1 28 (0) m_b3s252i13 rnd-1_family- 1337 CTCGTCCTCCTCCTCCTCTTCCCCGTCC 1364 v i i v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCC 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 230 23.45 0.00 1.56 rnd-1_family-154#DNA/hAT-Charlie 6 70 (73) MER112#DNA/hAT-Charlie 1 64 (197) m_b3s502i0 rnd-1_family- 6 CAGCGGTTCTCAAACTGTGGGTCGGGACCCCAAAGTGGGTCGCGACCCCG 55 i v i i v vvv i vvi i MER112#DNA/hA 1 CAGTGTTTTTCAAACTGCGGGTCGCGACCCATTAGTGGGTCGTGAAATCA 50 rnd-1_family- 56 TTTTAATGGGGTCGC 70 v i - MER112#DNA/hA 51 ATTTAGT-GGGTCGC 64 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 7, Kimura (unadjusted) = 28.25 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 12 20.33 0.00 7.14 rnd-1_family-154#DNA/hAT-Charlie 96 140 (3) (GCCCGA)n#Simple_repeat 1 42 (0) m_b3s252i12 rnd-1_family- 96 GCCCGGGGCCGAAGCCGAAGCCCGAGCCCCACCGCCCGGGGCCGA 140 i v - vi v -- i v (GCCCGA)n#Sim 1 GCCCGAGCCCG-AGCCCGAGCCCGAGCCCGA--GCCCGAGCCCGA 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 26 27.21 3.96 1.94 rnd-1_family-159#Unknown 11 111 (1345) (CT)n#Simple_repeat 1 103 (0) m_b3s252i10 rnd-1_family- 11 CTTTCTTTTTCTCTCTC-CTCCATCTCTTTTTCTTTCAGCTCCATCTCTC 59 i i i - iv i i i -v iv (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTC 49 rnd-1_family- 60 TCT-TGTGGGCCTC-CTCTTTGGCTTTCTCT-TCTCTTTCTCTCTGCTCT 106 - v vvvi - i vv i - i - (CT)n#Simple_ 50 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 98 rnd-1_family- 107 GTCTC 111 v (CT)n#Simple_ 99 CTCTC 103 Matrix = Unknown Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.06 (6 / 100), avg. gap size = 1.00 (6 / 6) 12 20.84 0.00 2.94 rnd-1_family-159#Unknown 1237 1271 (185) (AACA)n#Simple_repeat 1 34 (0) m_b3s252i11 rnd-1_family- 1237 AACGAACACACTCCCAAACAAAGAACACAAACAAA 1271 i v vvv v - (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAA-ACAAACAAA 34 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 350 15.71 0.00 0.00 rnd-1_family-161#DNA/hAT-Charlie 1 70 (74) MER58D#DNA/hAT-Charlie 1 70 (316) m_b3s502i1 rnd-1_family- 1 CAGGGGTGGGCAAACTACGGCCCGCGGGCCGCATCCGGCCCNCCAGACGT 50 v iv ? ivvi MER58D#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCCGCCTGT 50 rnd-1_family- 51 TTTAATCCGGCCCTCGAGCT 70 vi v v MER58D#DNA/hA 51 TTTTGTACGGCCCGCGAGCT 70 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.29 CpG sites = 4, Kimura (unadjusted) = 17.93 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 12 19.52 6.06 6.06 rnd-1_family-161#DNA/hAT-Charlie 75 140 (4) (CCGGGGT)n#Simple_repeat 1 66 (0) m_b3s252i9 rnd-1_family- 75 CCGGGGAGCGGGGTCCGGGGCTTGCCCCGCTCCGGCGCTCC--AG-CCGG 121 vv -- - vv v - v --i - (CCGGGGT)n#Si 1 CCGGGGTCCGGGGTCCGGGG--T-CCGGGGTCCGG-GGTCCGGGGTCCGG 46 rnd-1_family- 122 GGAGCGGGGT-CGGGGGCCG 140 vv - v (CCGGGGT)n#Si 47 GGTCCGGGGTCCGGGGTCCG 66 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.11 (7 / 65), avg. gap size = 1.14 (8 / 7) 256 19.26 9.52 1.10 rnd-1_family-164#DNA/PIF-Harbinger 16 99 (0) Chompy-6_Croc#DNA/PIF-Harbinger 890 980 (0) m_b3s502i2 rnd-1_family- 16 TGTGAATCCCAGT---GGGGCCTGAN-TCTGGGATTTAGGCGCC-TAAAG 60 ? i i v --- v i?-i iii v i-i v Chompy-6_Croc 890 TNTGGATTCCACTCCGGGGGCCAGGCGCCTAAAAGTTAGGCGCTGCAACG 939 rnd-1_family- 61 T--GGCAGTTA-GGCGCCTAAGTCCCTTTGTGGATCTAGCCC 99 i--i - i- Chompy-6_Croc 940 CTCAGC-GTTGCGGCGCCTAAGTCCCTTTGTGGATCTAGCCC 980 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 12, Kimura (unadjusted) = 23.81 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.50 (9 / 6) 14 20.24 2.04 4.17 rnd-1_family-173#rRNA 1554 1602 (5579) (GCCCCGT)n#Simple_repeat 1 48 (0) m_b3s252i8 rnd-1_family- 1554 GCCCCGTCGCCCCATCCACTCTCCCGTTGTGCCCC-TGCCCCGTGCCCCG 1602 - i v v iv v -ii - (GCCCCGT)n#Si 1 GCCCCGT-GCCCCGTGCCCCGTGCC-CCGTGCCCCGTGCCCCGTGCCCCG 48 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 3918 4.32 0.96 2.14 rnd-1_family-173#rRNA 2200 2719 (4462) LSU-rRNA_Hsa#rRNA 2 515 (4520) m_b3s551i0 rnd-1_family- 2200 GCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA 2249 LSU-rRNA_Hsa# 2 GCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA 51 rnd-1_family- 2250 GCGGAGGAAAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACA 2299 LSU-rRNA_Hsa# 52 GCGGAGGAAAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACA 101 rnd-1_family- 2300 GGGAAGAGCCCAGCGCCGAATCCCCGTCCCGCGGTGGGGCGCGGGAAATG 2349 i --- LSU-rRNA_Hsa# 102 GGGAAGAGCCCAGCGCCGAATCCCCGCCCCGCGG---GGCGCGGGAAATG 148 rnd-1_family- 2350 TGGCGTACAGAAGACCCACTCCCCGGTGCCGCTC-TCGGGGGCCCAAGTC 2398 i i - v LSU-rRNA_Hsa# 149 TGGCGTACGGAAGACCCACTCCCCGGCGCCGCTCGTGGGGGGCCCAAGTC 198 rnd-1_family- 2399 CTTCTGATCGAGGCACAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCCCC 2448 v -- LSU-rRNA_Hsa# 199 CTTCTGATCGAGGCCCAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCC-- 246 rnd-1_family- 2449 CGGCGCGCCGGGACCGGGTCTTCTTGGAGTCGGGTTGCTTGGGAATGCAG 2498 - i --- v ii LSU-rRNA_Hsa# 247 -GGCGCAC---GCCCGGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAG 292 rnd-1_family- 2499 CCCAAAGCTGGTGGTAAACTCCATCTAAGGCTAAATACCGGCACGAGACC 2548 v LSU-rRNA_Hsa# 293 CCCAAAGCGGGTGGTAAACTCCATCTAAGGCTAAATACCGGCACGAGACC 342 rnd-1_family- 2549 GATAGTCAACAAGTACCGTAAGGGAAAGTTGAAAAGAACTTTGAAGAGAG 2598 i LSU-rRNA_Hsa# 343 GATAGTCAACAAGTACCATAAGGGAAAGTTGAAAAGAACTTTGAAGAGAG 392 rnd-1_family- 2599 AGTTCAAGAGGGCGTGAAACCGTTAAGAGGTAAACGGGTGGGGTCCGCGC 2648 ? LSU-rRNA_Hsa# 393 AGTTCAAGAGGGCGTGAAACCGTTAAGANGTAAACGGGTGGGGTCCGCGC 442 rnd-1_family- 2649 AGTCTGCCCGGAGGATTCAACC---CGGCGGGTTCGGTCG-GCCGGCCCG 2694 i --- ii i - ? -- LSU-rRNA_Hsa# 443 AGTCCGCCCGGAGGATTCAACCNGGCGGCGGGTCTGGCCGTGNCGG--CG 490 rnd-1_family- 2695 GGACGACGGATCCCCCTCGCCCCCC 2719 vv i iii i LSU-rRNA_Hsa# 491 GTCCGGCGGATCTTTCCCGCCCCCC 515 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.73 CpG sites = 16, Kimura (unadjusted) = 4.49 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.03 (14 / 519), avg. gap size = 1.14 (16 / 14) 273 22.76 1.63 0.00 rnd-1_family-173#rRNA 2724 2846 (4335) LSU-rRNA_Hsa#rRNA 623 747 (4288) m_b3s551i1 rnd-1_family- 2724 GGGGGTGTCGGGAGGGGACCGCCGCCCGGACGGCC-CCGGCCCCCGTCGG 2772 v vvvi ? i i vi i v- i v i i LSU-rRNA_Hsa# 623 GGGGGAGTCCTTGGGGNACTGTCCTCCAGACGGCGACTGGCCACCGCCAG 672 rnd-1_family- 2773 GCGCATTTCCACCGAGGCGGTGCGCCGCGACCGGCTCTGGGTCGGCTGGG 2822 ii i v i v i i v i LSU-rRNA_Hsa# 673 ATGCATTTCCACTGTGGTGCTGCGCCGTGACTGGCTCTGGGACGGCTGGA 722 rnd-1_family- 2823 AAGGCCTGGT-GGGCAGGTGGCTCG 2846 i i- v LSU-rRNA_Hsa# 723 AAGGCCCGGCAGGGAAGGTGGCTCG 747 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.83 CpG sites = 17, Kimura (unadjusted) = 27.98 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.02 (2 / 122), avg. gap size = 1.00 (2 / 2) 5335 11.01 5.13 1.26 rnd-1_family-173#rRNA 2917 3910 (3271) LSU-rRNA_Hsa#rRNA 1080 2111 (2924) m_b3s551i2 rnd-1_family- 2917 GACCGCCGCCGCACCTTCCCCCGTGGCCCCCTGCCCCCTCCCTTCCG--- 2963 ivi v iii i ----- vi v ivv --- LSU-rRNA_Hsa# 1080 GACCGCTCTCCCACCCCTCCTC-----CCCGCGCCCCCGCCCCGGCGACG 1124 rnd-1_family- 2964 -GGGGGGTGCGGTACGGGGGCCGTGGCGGGGGACGG---GTCCCCC-TGC 3008 - v ii v i v v v i --- v- LSU-rRNA_Hsa# 1125 GGGGGGGTGCCGCGCGCGGGTCGGGGGGCGGGGCGGACCGTCCCCAGTGC 1174 rnd-1_family- 3009 -TCCCGG------CGCGACTGTCAA--CCGGGGCGGACTGTCCTCAGTGC 3049 -i ------ - i ii-- vi ii v - i - - LSU-rRNA_Hsa# 1175 GCCCCGGGCGGGTCGCG-CCGTCGGGCCCGGGGGAGGTTCTC-TCGG-G- 1220 rnd-1_family- 3050 GCCCCGACCGCGTCGCGCCGCCGGGCGGGGAGGGCCACGCCAGGGTGCCC 3099 v vv v - vv i - v viv -- i i v LSU-rRNA_Hsa# 1221 GCCACGCGCGCGTCCC-CCGAAGAG-GGGGACGGCGGAGC--GAGCGCAC 1266 rnd-1_family- 3100 GGGGTCTGCGGCGATGTCGGCAACCCACCCGACCCGTCTTGAAACACGGA 3149 v i v i i LSU-rRNA_Hsa# 1267 GGGGTCGGCGGCGACGTCGGCTACCCACCCGACCCGTCTTGGAACACGGG 1316 rnd-1_family- 3150 CCAAGGAGTCTAACACGTGCGCGAGTCACAGGCTCGAACGAAAGCC---C 3196 ? ? ??? ? ?vi vvi v ? ---? LSU-rRNA_Hsa# 1317 CCAAGGAGNCTNACNNNTNCGNCGGTCCGGGGCTCGCACGAAAGNCGNCN 1366 rnd-1_family- 3197 ATGGCGCAATGAAGGTGAGGGCCG-GCGCGCGCCGGCTGAGGTGGGATCC 3245 ?? ? ? i ? ? - ???v ? i? v? i? LSU-rRNA_Hsa# 1367 NNGNCGCANTGAGGNTGAGGNCCGCGNNNCCGCCNGCCNAGGGNGGGNCC 1416 rnd-1_family- 3246 CGAGG---CCACTGATTCGCGGAGGGCGCACCACCGGCCCGTCTCGCCCG 3292 ? --- v i ? i?? v i ?? ? ?? ?? LSU-rRNA_Hsa# 1417 CNAGGGCCCCCCCGNTCNNCCGGGGGNNCNCCACCGGCCNNTCTCGCCNN 1466 rnd-1_family- 3293 CCCCGTCGGGGAGGTGGAGCATGAGCGTACGTGCTAGGACCCGAAAGATG 3342 ?v ii i i i i ? i ? LSU-rRNA_Hsa# 1467 CNGCGCTGGGAAGGTGGGGCACGAGCGCANGTGTTAGGACCCGAAAGNTG 1516 rnd-1_family- 3343 GTGAACTATGCCTGGGCAGGGCGAAGCCAGAGGAAACTCTGGTGGAGGTC 3392 ? i i ? LSU-rRNA_Hsa# 1517 GTGAACTNTGCCTGGGCGGGGCGAAGCCGGAGGAAACTCNGGTGGAGGTC 1566 rnd-1_family- 3393 CGTAGCGGTCCTGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCG 3442 i i ? LSU-rRNA_Hsa# 1567 CGTAGCGGTCCTGATGTGCAAATCGGTCGTCCAACCTGGGTNTAGGGGCG 1616 rnd-1_family- 3443 AAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCA 3492 i i i LSU-rRNA_Hsa# 1617 AAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCAAGGTTTCCCTCG 1666 rnd-1_family- 3493 GGATAGCTGGCACTC------------GT----CCGTCTCCGCAGTTTTA 3526 i ------------ i---- i iv i ? LSU-rRNA_Hsa# 1667 GGATAGCTGGCGCTCTCNCGAACCGACGCACCCCCGCCCACGCGGTTTTN 1716 rnd-1_family- 3527 TCTGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAACCT 3576 i LSU-rRNA_Hsa# 1717 TCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAACCT 1766 rnd-1_family- 3577 ATTCTCAAACTTTAAATGGGTAAGAAGCCCGGCTCGCTGGCGTGGAGCCG 3626 ? iv i LSU-rRNA_Hsa# 1767 ATTCTNAAACTTTAAATGGGTAAGAAGCCCGGCCGGCTGGCATGGAGCCG 1816 rnd-1_family- 3627 GGCGTGGAATGCGAGTGCCTAGTGGGCCACTTTTGGTAAGCAGAACTGGC 3676 ? LSU-rRNA_Hsa# 1817 GGCGTGGAATGCGAGTGCCTAGTGGGCNACTTTTGGTAAGCAGAACTGGC 1866 rnd-1_family- 3677 GCTGCGGGATGAACCGAACGCCGGGTTAAGGCGCCCGATGCCGACGCTCA 3726 i ? i ?? ?i LSU-rRNA_Hsa# 1867 GCTGCGGGATGAACCAAANGCCGGGTTAGGNNGCCCGATGCNAACGCTCA 1916 rnd-1_family- 3727 TCAGACCCCAGAAAAGGTGTTGGTTGATATAGACAGCAGGACGGTGGCCA 3776 i i i LSU-rRNA_Hsa# 1917 TCGGACCCCGGAAAGGGTGTTGGTTGATATAGACAGCAGGACGGTGGCCA 1966 rnd-1_family- 3777 TGGAAGTTGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCA 3826 i LSU-rRNA_Hsa# 1967 TGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCA 2016 rnd-1_family- 3827 ACTAGCCCTGAAAATGGATGGCGCTGGAGCGTCGGGCCCATACCCGGCCG 3876 ?? ? LSU-rRNA_Hsa# 2017 ACTAGCCCTGAAAATGGATGGCGCTGGAGCGTCGGGCCNNTACCNGGCCG 2066 rnd-1_family- 3877 TCGCCGGC-----------AATGAGAGCCGCGGGGGCTACGCCGC 3910 i -----------i i i v vi?? LSU-rRNA_Hsa# 2067 TTGCCGGCGGTCGAGAGNGGACGGGAGCGGCGGGGGCGGNNCCGC 2111 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.17 CpG sites = 69, Kimura (unadjusted) = 12.75 Transitions / transversions = 1.77 (69/39) Gap_init rate = 0.03 (26 / 993), avg. gap size = 2.46 (64 / 26) 4681 9.30 0.36 2.20 rnd-1_family-173#rRNA 3862 4696 (2485) LSU-rRNA_Hsa#rRNA 2213 3032 (2003) m_b3s551i3 rnd-1_family- 3862 GCCCATACCCGGCCGTC-GCCGGCAATGAGAGCCGCGGG-GGCTACGCCG 3909 ii v vi - vv i-- ?v v - ? ? ? LSU-rRNA_Hsa# 2213 GCCCACGCCCCGCCCCCCGCCCCCG--GAGNCCCCCGGGAGNCTANGCNG 2260 rnd-1_family- 3910 CGACGAGTAGGAGGGCCGCTGCGGTGCGCCTTGAAGCCTAGGGCGCGGGC 3959 v ?v i ?i ? v ?i i LSU-rRNA_Hsa# 2261 GGNGGGGNGGGAGGGCCGCTGCGNTGAGCCTTGAAGCCNGGGGCGTGGGC 2310 rnd-1_family- 3960 CCGGGTGGAGCCGCCGCAGGTGCAGATCTTGGTGGTAGTAGCAAATATTC 4009 LSU-rRNA_Hsa# 2311 CCGGGTGGAGCCGCCGCAGGTGCAGATCTTGGTGGTAGTAGCAAATATTC 2360 rnd-1_family- 4010 AAACGAGAACTTTGAAGGCCGAAGTGGAGAAGGGTTCCATGTGAACAGCA 4059 ? LSU-rRNA_Hsa# 2361 AAACGAGANCTTTGAAGGCCGAAGTGGAGAAGGGTTCCATGTGAACAGCA 2410 rnd-1_family- 4060 GTTGAACATGGGTCAGTCGGTCCTAAGAGATAGGCGAGTGCCGTTCCGAA 4109 ii ?i i LSU-rRNA_Hsa# 2411 GTTGAACATGGGTCAGTCGGTCCCGAGAGANGGGCGAGCGCCGTTCCGAA 2460 rnd-1_family- 4110 GGGACGGGCGATGGCCTCCGTTGCCCTCAGCCGATCGAAAGGGAGTCGGG 4159 ? ?? i iv LSU-rRNA_Hsa# 2461 GGGACGGGCGATGNCCTCNNTTGCCCTCGGCCGACGGAAAGGGAGTCGGG 2510 rnd-1_family- 4160 TTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCGTCCA 4209 i ? ??? i ?i i LSU-rRNA_Hsa# 2511 TTCGGATCCCCGAATCCGGAGTGGCGGAGATGGGCNCNNNGGGGCNCCCG 2560 rnd-1_family- 4210 GTGCGGTAACGCAACCGATCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGA 4259 ? i ? i LSU-rRNA_Hsa# 2561 GNGCGGTAACGCGACNGACCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGA 2610 rnd-1_family- 4260 GTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCG 4309 i LSU-rRNA_Hsa# 2611 GTTCTCTTTTCTTTGCGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCG 2660 rnd-1_family- 4310 AGAGAGGGGCCCGAGCCTTGGAAAGCGTCGCGGTTCCGGCGGCGTCCGGT 4359 v ? ? LSU-rRNA_Hsa# 2661 AGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCNGGCGGCNTCCGGT 2710 rnd-1_family- 4360 GAGCTCTCGCTGGCCCTTGAAAATCCGGGGGAGATGGTGTAAATCTCGCG 4409 iv v ? v ? v LSU-rRNA_Hsa# 2711 GAGCTCCGGCGGGCCCTTGAAANTCCGGGGGAGAGGGTGTAANTCTCCCG 2760 rnd-1_family- 4410 CCGGGCCGTACCCATATCCGCAGCAGGTCTCCAAGGTGAACAGCCTCTGG 4459 v ? ? ? i i ?i ?? ? i v LSU-rRNA_Hsa# 2761 CGGGGCCNTACCCNTNTCCGCGGCGGNCCTCCAAGNNGANCGGCCTCGGG 2810 rnd-1_family- 4460 CATGTTAGAACAATGTAGGTAAGGGAAGTCGGCAAGCCGGATCCGTAACT 4509 ?? i v i?i v? i ?i v? LSU-rRNA_Hsa# 2811 NNTGTTGGAACAAGGTAGGTAAGGGAGNCCGCNAGGCCGGNCCGNTAACT 2860 rnd-1_family- 4510 TCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGGGCGCGA 4559 i ? i ? ?i ?i - LSU-rRNA_Hsa# 2861 CCGGGNTAAGAATNGGCTCTAAGGGCTGGNCCGNCCGGGCT-GGGCGCGA 2909 rnd-1_family- 4560 AGCGGGGCTGGGCGCGAGCCGCGGCTGGACGAGGCGCCGCCCTCTCCCGG 4609 ???? ? ?? ?i i i ?? ??? i i -? LSU-rRNA_Hsa# 2910 AGCGGGGCTGGGCNNNNGNCGNNGNCGGGCGGGGNNCCNNNCCCCCCC-N 2958 rnd-1_family- 4610 GGGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCTGTGGATCGCCC 4659 v ?v - ?i? i i--- v ----?? ? i ------i ?? LSU-rRNA_Hsa# 2959 CGNCCGG-GGNANCCCC---CTCG----NNGNCCTCCC------CCNNCC 2994 rnd-1_family- 4660 CAGCTGCGGCGGGCG-TCGCTCGCCTCTCCCCCTCCGC 4696 v i ?v???? ?- i v i i ? i LSU-rRNA_Hsa# 2995 CACCCGCNCNNNNCNCTCGCCCCCCCCCCNCCCCCCGC 3032 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.74 CpG sites = 50, Kimura (unadjusted) = 11.04 Transitions / transversions = 1.92 (50/26) Gap_init rate = 0.03 (21 / 834), avg. gap size = 1.00 (21 / 21) 3410 5.55 3.40 0.41 rnd-1_family-173#rRNA 4659 5128 (2053) LSU-rRNA_Hsa#rRNA 3484 3967 (1068) m_b3s551i4 rnd-1_family- 4659 CCAGCTGCGGCGGGCGTCGCTCGCCTCTCCCCCTCCGCGGGG-------A 4701 i v v - i vv vv - v -------v LSU-rRNA_Hsa# 3484 CCGGCGGCGGAGGG-GCCGCGGGCCGGTCCCCC-CCGCCGGGTCCGCCCC 3531 rnd-1_family- 4702 TGGGG--GGGG-----CCGGCGTTCCGCCTCGGCCGGCGCCT-AGCAGCT 4743 i -- v ----- ??? iii ? ? ? ?? -i i i LSU-rRNA_Hsa# 3532 CGGGGCCGCGGTTCCNCNNNCGCCTCGNCTCGGNCNGCNNCTTGGCGGCC 3581 rnd-1_family- 4744 GACTTAGAACTGGTGCGGACCAGGGGAATCCGACTGTTTAATTAAAACAA 4793 ? ? ?? i i ? ? LSU-rRNA_Hsa# 3582 GNCTNAGAACTGNNGCGAACCGGGGGAATCCGACTNTTTAATNAAAACAA 3631 rnd-1_family- 4794 AGCATCGCGAAGGCCCGCGGTGGGTGTTGACGCGATGTGATTTCTGCCCA 4843 i LSU-rRNA_Hsa# 3632 AGCATCGCGAAGGCCCGCGGCGGGTGTTGACGCGATGTGATTTCTGCCCA 3681 rnd-1_family- 4844 GTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAAACGGC 4893 LSU-rRNA_Hsa# 3682 GTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAAACGGC 3731 rnd-1_family- 4894 GGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATT 4943 LSU-rRNA_Hsa# 3732 GGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATT 3781 rnd-1_family- 4944 AGTGACGCGCATGAATGGATGAACGAGATTCCCACTGTCCCTACCTACTA 4993 LSU-rRNA_Hsa# 3782 AGTGACGCGCATGAATGGATGAACGAGATTCCCACTGTCCCTACCTACTA 3831 rnd-1_family- 4994 TCTAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAA 5043 i i LSU-rRNA_Hsa# 3832 TCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAA 3881 rnd-1_family- 5044 AGAAGACCCTGTTGAGCTTGACTCTAGTCTGGCACTGTGAAGAGACATGA 5093 v LSU-rRNA_Hsa# 3882 AGAAGACCCTGTTGAGCTTGACTCTAGTCTGGCACGGTGAAGAGACATGA 3931 rnd-1_family- 5094 GAGGTGTAGAATAAGTGGGAGGCCTCCGG-GCCGCC 5128 i - v LSU-rRNA_Hsa# 3932 GAGGTGTAGAATAAGTGGGAGGCCCCCGGCGCCCCC 3967 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.47 CpG sites = 15, Kimura (unadjusted) = 5.97 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.01 (7 / 469), avg. gap size = 2.57 (18 / 7) 6086 4.03 0.13 0.54 rnd-1_family-173#rRNA 5114 5861 (1320) LSU-rRNA_Hsa#rRNA 4004 4748 (287) m_b3s551i5 rnd-1_family- 5114 GGCCTC-CGGGCCGCCGGTGAAATACCACTACTCTTATCGTTTTTTCACT 5162 i- ? v LSU-rRNA_Hsa# 4004 GGCCTTGCGGGCCGCCGGTGAAATNCCACTACTCTGATCGTTTTTTCACT 4053 rnd-1_family- 5163 TACCCGGTGAGGCGGGGGGGCGAGCCCCGAGGGGCTCTCGCTTCTGGCTC 5212 v - v LSU-rRNA_Hsa# 4054 GACCCGGTGAGGCGGGGGGGCGAGCCC-GAGGGGCTCTCGCTTCTGGCGC 4102 rnd-1_family- 5213 CAAGCGCCCGGCGCGTGCCGGGTGCGACCCGCTCCGGGGACAGTGTCAGG 5262 v - - i i i i LSU-rRNA_Hsa# 4103 CAAGCGCCCGCC-CG-GCCGGGCGCGACCCGTTCCGGGGACGGTGCCAGG 4150 rnd-1_family- 5263 TGGGGAGTTTGACTGGGGCGGTACACCTGTCAAACCGTAACGCAGGTGTC 5312 v i LSU-rRNA_Hsa# 4151 TGGGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAATGCAGGTGTC 4200 rnd-1_family- 5313 CTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAA 5362 LSU-rRNA_Hsa# 4201 CTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAA 4250 rnd-1_family- 5363 AAGCTCGCTTGATCTTGATTTTCAGTATGAATACAGACCGTGAAAGCGGG 5412 i LSU-rRNA_Hsa# 4251 AAGCTCGCTTGATCTTGATTTTCAGTACGAATACAGACCGTGAAAGCGGG 4300 rnd-1_family- 5413 GCCTCACGATCCTTCTGACTTTTTGGGTTTTAAGCAGGAGGTGTCAGAAA 5462 i i LSU-rRNA_Hsa# 4301 GCCTCACGATCCTTCTGACCTTTTGGGTTTTAAGCAGGAGGTGTCGGAAA 4350 rnd-1_family- 5463 AGTTACCACAGGGATAACTGGCTTGTGGCGGCCAAGCGTTCATAGCGACG 5512 LSU-rRNA_Hsa# 4351 AGTTACCACAGGGATAACTGGCTTGTGGCGGCCAAGCGTTCATAGCGACG 4400 rnd-1_family- 5513 TCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAA 5562 ? ? ? i i i ? LSU-rRNA_Hsa# 4401 TCGCTTTTTGATCCTTNGNTGTNGGTTCTTCCTATCATTGTGAGGCGGAN 4450 rnd-1_family- 5563 TTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGT 5612 ? ?ii ?? ? LSU-rRNA_Hsa# 4451 TTCACCAAGCGTNGGATTGTTCACCCACTANCGGGGAANNTGAGCTGGNT 4500 rnd-1_family- 5613 TTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGATGTGTTGTT 5662 ??i ? ? LSU-rRNA_Hsa# 4501 TTAGACCNNTGTGAGACAGGTTAGTTTTACCCTNCTGNTGATGTGTTGTT 4550 rnd-1_family- 5663 GCAATAGTAATCCTGCTCAGTACGAGAGGAACCGCAGGTTCAGACATTTG 5712 v i LSU-rRNA_Hsa# 4551 GCCATGGTAATCCTGCTCAGTACGAGAGGAACCGCAGGTTCAGACATTTG 4600 rnd-1_family- 5713 GTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGGG 5762 LSU-rRNA_Hsa# 4601 GTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGGG 4650 rnd-1_family- 5763 ATTATGACTGAACGCCTCTAAGTCAGAATCCCCCCTAAACGTAACGATAC 5812 v i ii - LSU-rRNA_Hsa# 4651 ATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCG-AACGATAC 4699 rnd-1_family- 5813 GGCAGCGCCGTGGAGCCTCGGTTGGCCCCGGATAGCCGGCCCCCCCCCT 5861 i i i v LSU-rRNA_Hsa# 4700 GGCAGCGCCGCGGAGCCTCGGTTGGCCTCGGATAGCCGGTCCCCCGCCT 4748 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.31 CpG sites = 22, Kimura (unadjusted) = 4.25 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.01 (5 / 747), avg. gap size = 1.00 (5 / 5) 1258 17.36 2.89 0.00 rnd-1_family-173#rRNA 5837 6078 (1103) LSU-rRNA_Hsa#rRNA 4787 5035 (0) m_b3s551i6 rnd-1_family- 5837 GCCCCGGATAGCCG---GCCCCCCCCCTC-CGGGGGGTAGGGCTCGGTGA 5882 v i?i v --- v v v - v ivii ii v LSU-rRNA_Hsa# 4787 GCCGCGGGNGGGCGCNTGCCCCGCCGCGCGCCGGGACCGGGGTCCGGTGC 4836 rnd-1_family- 5883 GGAGAGCCATTCGTGTCGGGAC-CGGAGTGCGGACAGAAGGG-AGCCGCC 5930 vi vii v- i v i i -i LSU-rRNA_Hsa# 4837 GGAGAGCCCCTCGTCCTGGGAAACGGGGTGCGGCCGGAAAGGCGGCCGCC 4886 rnd-1_family- 5931 TC-TCACCCGTTGCGCACCGCATGTTCGTGGGGAACCTGGTGCTAAATCA 5979 i - i ii v i i i LSU-rRNA_Hsa# 4887 CCCTCGCCCGTCACGCAACGCACGTTCGTGGGGAACCTGGCGCTAAACCA 4936 rnd-1_family- 5980 TTCGTAGACGACCTGATTCTGGGTCAGGGTTTCGTGCGTAGCAGAGCAGC 6029 v i i LSU-rRNA_Hsa# 4937 TTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGC 4986 rnd-1_family- 6030 TACCTCGCTGCGATCTATTGAAAGTCAGCCTTTGACACAAGACTTTGTC 6078 v i i iv LSU-rRNA_Hsa# 4987 TCCCTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTC 5035 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.09 CpG sites = 26, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.02 (5 / 241), avg. gap size = 1.40 (7 / 5) 636 20.67 7.39 1.07 rnd-1_family-174#LINE/CR1 54 229 (0) CR1-L3B_Croc#LINE/CR1 3081 3267 (10) m_b3s551i7 rnd-1_family- 54 AAATGGTGGATTCTCTGTAACTTGAAGTCTTTAAATCATGATTTGAGGAC 103 i ii vv v i v i v v v CR1-L3B_Croc# 3081 AAGTGGTGGATTCTCCATCTCTTGATGTCTTCAAATCAAGACTGGATGCC 3130 rnd-1_family- 104 TTC-----AG-TA------ACTCAGCCAGAGGTTAG-GGGTCTATTACAG 140 i----- - ------ v iv v i v- iii v CR1-L3B_Croc# 3131 TTTCTGGAAGATATGCTTTAGTCAAACACAAGTTATTGGGCTCAATACAG 3180 rnd-1_family- 141 GAGTGGGTGGGGTGAGGTTCTGTGGCCTGCGATGTGCAGGAGGTCAGACT 190 i iiv - ii ivi i ? i i CR1-L3B_Croc# 3181 GGGTAACTGGG-TGAAATTTAATGGCCTGTGNTATACAGGAGGTCAGACT 3229 rnd-1_family- 191 AGATGATCATGATGGTCCCTTCTGGCCTTAAAGTCTATG 229 - i ? CR1-L3B_Croc# 3230 AGATGATC-TAATGGTCCCTTCTGGCCTTAAANTCTATG 3267 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.01 CpG sites = 22, Kimura (unadjusted) = 25.01 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.03 (6 / 175), avg. gap size = 2.50 (15 / 6) 20 0.00 0.00 0.00 rnd-1_family-182#Unknown 1 22 (138) (G)n#Simple_repeat 1 22 (0) m_b3s252i7 rnd-1_family- 1 GGGGGGGGGGGGGGGGGGGGGG 22 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGG 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 259 25.00 0.00 0.00 rnd-1_family-188#DNA/TcMar-Tigger 1 60 (313) MER6B#DNA/TcMar-Tigger 65 124 (86) m_b3s502i3 rnd-1_family- 1 TACAGTAACTCCTCACTTAAAGTCGTCCCGGTTAACGTTGTTTCGTTGTT 50 i iv ivv v ii v i i i v MER6B#DNA/TcM 65 TACAGCAGGTCCTCGAATAACGTCGTTTCGTTCAACGTCGTTTCGTTATA 114 rnd-1_family- 51 ACGTTGCTGA 60 v MER6B#DNA/TcM 115 ACGTTGATGA 124 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.17 CpG sites = 8, Kimura (unadjusted) = 30.81 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 12 18.17 0.00 7.50 rnd-1_family-188#DNA/TcMar-Tigger 283 325 (48) (CTGCCCT)n#Simple_repeat 1 40 (0) m_b3s252i6 rnd-1_family- 283 CTGTCCCTCCCCCCACTGCCATGTGCTGCTCCTGCCCTCTGCC 325 - iv v v v -v - (CTGCCCT)n#Si 1 CTG-CCCTCTGCCCTCTGCCCTCTGC-CCT-CTGCCCTCTGCC 40 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 6779 11.53 0.00 2.52 rnd-1_family-190#LINE/CR1 1 1059 (445) CR1-11_Crp#LINE/CR1 358 1390 (71) m_b3s551i8 rnd-1_family- 1 CAGTAAGGCATTTGATACGGTTCCACATGGGAAATTATTAGTTAAATTGG 50 i v - ii CR1-11_Crp#LI 358 CAGTAAAGCATTTGATACGGTGCCACATGGGAAAT-ATTAGTTAAGCTGG 406 rnd-1_family- 51 AGAAGATGGGGATTAATATGAGAATCGAAAGGTGGATAAGGAACTGGTTA 100 i ii i v - i ----- CR1-11_Crp#LI 407 AGAAGATGGGGATTAGTACAAGAATTGTAAGGTGG-TAAGGAGCT----- 450 rnd-1_family- 101 AAGGGGAGACTACAACGGGTCGTACTGAAAGGTGAACTGTCAGGCTGGAG 150 - i iv ? i - ? i - CR1-11_Crp#LI 451 -AAGGGAGATGACAACGGGTNGTGCTGAAAGG-GAANTATC-GGCTGGAG 497 rnd-1_family- 151 GGAGGTTACTAGTGGAGTTCCTCAGGGATCGGTCTTGGGACCAATCTTAT 200 - - i i CR1-11_Crp#LI 498 G-AGGTTACTAGTGGAGTTC-TCAAGGATCGGTCTTGGGACCGATCTTAT 545 rnd-1_family- 201 TTAACATTTTTATTACTGACCTTGGCACAAAAAGTGGGAGTGTGCTAATA 250 i i v - i i CR1-11_Crp#LI 546 TTAATATTTTCATTAATGACCTTGGCACAAAA-GTAGGAGTGTGCTAATG 594 rnd-1_family- 251 AAATTTGCGGATGACACAAAGTTGGGAGGTATTGCCAATACGGAGGAGGA 300 v i i i i CR1-11_Crp#LI 595 AAATTTGCTGATGACACAAAGTTGGGAGGCATCGTCAATACAGAGGAGGA 644 rnd-1_family- 301 CCGGAATATCATACAGGAAGATCTGGATGACCTTGTAAACTGGAGTAATA 350 i i v - i CR1-11_Crp#LI 645 TCGGGATATCATACAGGAAGAACTGGATGACCTTG-AGACTGGAGTAATA 693 rnd-1_family- 351 GAAATGGGATGAAATTTAATAGTGNAAAGTGCAAGGTCATGCATTTAGGG 400 i i? i CR1-11_Crp#LI 694 GAAATGGGATGAAATTCAATAGTACAAAGTGCAAGGTCATGCACTTAGGG 743 rnd-1_family- 401 ACTAATAACAAGAATTTTTGCTATAAGCTGGGGACGCATCAGTTGGAAGT 450 --- i ii v ii CR1-11_Crp#LI 744 ACTAATAA---GAATTTCTGCTATAAGCTGGGAGCTCATCAGTTGGAAAC 790 rnd-1_family- 451 GACAGAGGAGGAGAAAGACCTCGGNGTATTGGTTGATCACAGGATGACTA 500 ? ------ v ? i i i CR1-11_Crp#LI 791 GNC------GGAGAAAGACCTGGGTGTACTAGTCGATCACAGGATGACTA 834 rnd-1_family- 501 TGAGCCGCCAATGTGATGCGGCCGTGAAAAAGGCTAATGCGGTCTTGGGA 550 i v i i i CR1-11_Crp#LI 835 TGAGCCACCAATGTGATGCGGCCGTGAAAAAGGCAAATGCGATCCTAGGA 884 rnd-1_family- 551 TGCATCAGGCGAGGTATTTCCAGTAGAGATAGGGAGGTGTTAGTACCGTT 600 ? i-- i i i i i CR1-11_Crp#LI 885 TGCATNAGA--AGGTATTTCCAGTAGAGATAGGGAAGTATTAATGCCATT 932 rnd-1_family- 601 ATACAAGGCACTGGTGAGACCTCATCTGGAATACTGTGTGCAGTTCTGGT 650 i - i CR1-11_Crp#LI 933 GTACAAGG-ACTGGTGAGACCTCATCTGGAATACTGTGTACAGTTCTGGT 981 rnd-1_family- 651 CTCCCACGTTTAAGAAGGATGAATTCAAACTGGAACAGGTGCAGAGAAGG 700 v i i i CR1-11_Crp#LI 982 CACCCATGTTCAAGAAAGATGAATTCAAACTGGAACAGGTGCAGAGAAGG 1031 rnd-1_family- 701 GCTACTAGGATGATCNGAGGAATGGAAAACCTGCCTTATGAGAGGAGACT 750 ? i i i ii i CR1-11_Crp#LI 1032 GCTACTAGGATGATCAGGGGAATGGAGAGCCTATCTTACGAGAGGAGACT 1081 rnd-1_family- 751 CGAGGAGCTTGGCTTGTTTAGCCTAACCAAAAGAAGGCTGAGGGGGGATA 800 vi i i v v i CR1-11_Crp#LI 1082 AAAAGAGCTTGGCTTGTTTAGCCTAGCAAAACGAAGGCTGAGAGGGGATA 1131 rnd-1_family- 801 TGATTGCTCTCTATAAATATATCAGAGGGATAAATACCAGGGAGGGAGAG 850 ? i i i i i CR1-11_Crp#LI 1132 TGATTGCTNTCTATAAATACATCAGGGGGGTAAACACCAGGGAGGGAGAA 1181 rnd-1_family- 851 GAGTTATTTAAGCTCAGTACCAATGTGGACACGAGAACGAATGGATATAA 900 i v iviv v i i i i CR1-11_Crp#LI 1182 GAGCTATTTAAGCTAAAGGACAATGTTGGCACAAGAACAAATGGGTATAA 1231 rnd-1_family- 901 ACTGGCCGTCGGGAAGTTTAGGCTTGAAATTAGACGAAGGTTTCTAACCA 950 i viiv i v v CR1-11_Crp#LI 1232 ACTGGCCATGAATAAATTTAGGCTGGAAATTAGAAGAAGGTTTCTAACCA 1281 rnd-1_family- 951 TCAGAGGGGTGAAGTTCTGGAACAGCCTTCCGAGGGGAGCAGTGGGGGCG 1000 vi i i vi i i CR1-11_Crp#LI 1282 TCAGAGCAGTGAGGTTCTGGAACAGCCTTCCAATAGGAGTAGTGGGGGCA 1331 rnd-1_family- 1001 AAAGACCTATCTGGCTTTAAGACTAAGCTTGATAAGTTTATGGAGGGGAT 1050 i v i i ivi v i i CR1-11_Crp#LI 1332 AAAAACCTAACTAGTTTTAAGATGGAGCTTGATCAGTTTATGAAAGGGAT 1381 rnd-1_family- 1051 GGTNTGATG 1059 vi ? i CR1-11_Crp#LI 1382 TATATGACG 1390 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.23 CpG sites = 92, Kimura (unadjusted) = 12.89 Transitions / transversions = 3.41 (92/27) Gap_init rate = 0.02 (26 / 1058), avg. gap size = 1.00 (26 / 26) 601 21.83 2.10 0.69 rnd-1_family-190#LINE/CR1 1176 1318 (186) CR1-3_Croc#LINE/CR1 3201 3345 (260) m_b3s551i9 rnd-1_family- 1176 CCGAGGGT--CTGGCTGGAGAGTCTTGCCCGCATGCTCGGGGTTCAGCTG 1223 ii -- i i vivi i ivii i CR1-3_Croc#LI 3201 CCGGAGGTTCCTGGCTAGAGGGTCTTGCCCCTCCGCTCAGGGTCAGACCG 3250 rnd-1_family- 1224 ATCGCCATATTTGGGGTCGGGAAGGAATTTTCCTCCA-GGGCAGATTGGC 1272 i v i - v i CR1-3_Croc#LI 3251 ATCGCCATATTTGGGGTCAGGAAGGAATTTTACCCCATGGTCAGATTGGT 3300 rnd-1_family- 1273 AGAGGCCCTGGAGGTTTTTCGCCTTCCTCCGCAGCATGGGGCAGGG 1318 vi i iv i - i i iv iv CR1-3_Croc#LI 3301 ACGGACTGTGGGGGTTTTT-GCCTTCCTCTGTAGCGGGGGGCGTGG 3345 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.93 CpG sites = 22, Kimura (unadjusted) = 26.75 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.02 (3 / 142), avg. gap size = 1.33 (4 / 3) 590 22.15 9.60 0.52 rnd-1_family-190#LINE/CR1 1328 1504 (0) CR1-L3B_Croc#LINE/CR1 3084 3276 (1) m_b3s551i10 rnd-1_family- 1328 TGGAGGATTCTCTGCGACTTGAAGTCTTTAAATCACGATTTGGGGACTTC 1377 v iiivv v i v i v iv v i CR1-L3B_Croc# 3084 TGGTGGATTCTCCATCTCTTGATGTCTTCAAATCAAGACTGGATGCCTTT 3133 rnd-1_family- 1378 ----AACA---GCTG-AGTCAAGGGAGAGTTATTN---------CAGGAG 1410 ---- v --- v- ivivi ?--------- i CR1-L3B_Croc# 3134 CTGGAAGATATGCTTTAGTCAAACACAAGTTATTGGGCTCAATACAGGGG 3183 rnd-1_family- 1411 TGGGTGGGTCAGCTTTTGTGGCCTGCATCGTGCGGGAGGTCAGACTAGAT 1460 iiv v iv vi ii?ii i i CR1-L3B_Croc# 3184 TAACTGGGTGAAATTTAATGGCCTGTGNTATACAGGAGGTCAGACTAGAT 3233 rnd-1_family- 1461 GATCATAATGGTCCCTTCTGACCTTAAAGTCTATGAGTCTATGA 1504 - i ? i CR1-L3B_Croc# 3234 GATC-TAATGGTCCCTTCTGGCCTTAAANTCTATGAATCTATGA 3276 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.30 CpG sites = 23, Kimura (unadjusted) = 27.30 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.03 (5 / 176), avg. gap size = 3.60 (18 / 5) 14 15.49 0.00 0.00 rnd-1_family-191#DNA/PIF-Harbinger 282 310 (4555) (TCCC)n#Simple_repeat 1 29 (0) m_b3s252i5 rnd-1_family- 282 TCCGTCCATCACTCCCGCCCTCCCTCCCT 310 v v v v (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 697 14.03 0.87 0.87 rnd-1_family-192#LINE/CR1 1 115 (0) CR1-L3B_Croc#LINE/CR1 3119 3233 (44) m_b3s551i11 rnd-1_family- 1 AGACTGGATGTCTTTCTAAAAGATACGCTCTAGCTCAACCAGAAGTTAT- 49 i ii i i - v v - CR1-L3B_Croc# 3119 AGACTGGATGCCTTTCTGGAAGATATGCTTTAG-TCAAACACAAGTTATT 3167 rnd-1_family- 50 GGGCTTGATGCAGGAATCACTGGGTGAAATTCTNTGGCCTGTGTTATGCA 99 ii i ii v iv? ? i CR1-L3B_Croc# 3168 GGGCTCAATACAGGGGTAACTGGGTGAAATTTAATGGCCTGTGNTATACA 3217 rnd-1_family- 100 GGAGGTCAGACTAGAT 115 CR1-L3B_Croc# 3218 GGAGGTCAGACTAGAT 3233 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.24 CpG sites = 12, Kimura (unadjusted) = 16.24 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.00 (2 / 2) 17 26.95 1.92 1.92 rnd-1_family-193#LTR/Gypsy 1 52 (5217) (AG)n#Simple_repeat 1 52 (0) m_b3s252i3 rnd-1_family- 1 AGAGAGAGATGGAGCTGAAAGAAAAAGAGATGGAG-GAGAGAGAAAAAGA 49 vi -v i i i vi - i i (AG)n#Simple_ 1 AGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 rnd-1_family- 50 AAG 52 i (AG)n#Simple_ 50 GAG 52 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 17 27.52 1.59 1.59 rnd-1_family-193#LTR/Gypsy 1383 1445 (3824) (CCAGAA)n#Simple_repeat 1 63 (0) m_b3s252i4 rnd-1_family- 1383 CCAGAGACC-CAGCCAAAGCCAGTCCCAGAACCGGAACTGGCAACGCAAC 1431 - -v i i i vv i ii v v iv (CCAGAA)n#Sim 1 CCAGA-ACCAGAACCAGAACCAGAACCAGAACCAGAACCAGAACCAGAAC 49 rnd-1_family- 1432 CAGCACCAGAACCA 1445 v (CCAGAA)n#Sim 50 CAGAACCAGAACCA 63 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 1934 14.38 0.33 0.00 rnd-1_family-203#LINE/CR1 1 306 (0) CR1-1_Amn#LINE/CR1 497 803 (10) m_b3s551i12 rnd-1_family- 1 ACAGTCAACCTGTGGAACTCTTTGCCAGGGGATGTTGTGAAGGCCAAGAC 50 i i iv i v vi ? i i ? i? ? CR1-1_Amn#LIN 497 ATAGTTAATATATGGAACTCATTGCCACAGGANGTCGTGGAGGCNAGNAN 546 rnd-1_family- 51 TATAACAGGGTTCAAAAAAGAACTAGATAAGTTCATGGAGGATAGGTCCA 100 v ii i i i CR1-1_Amn#LIN 547 TATAACCGGGTTCAAAAGGGGACTGGATAAATTCATGGAGGATAGGTCCA 596 rnd-1_family- 101 TCAATGGCTATTAGCCAGGATGGGCAGGGA-TGGTGTCCCTAGCCTCTGT 149 i i iv i i ?i i - ? ? CR1-1_Amn#LIN 597 TTAGTGGCTATTAAACAGAACGGNTAAGGAATGNTGTCCCTAGCCTCTGN 646 rnd-1_family- 150 TTGCCAGAAGCTGGGAATGGGCGACAGGGGATGGATCACTTGATGATTAC 199 i i i v ii ? ii i i ?i v CR1-1_Amn#LIN 647 TTGTCGGAGGGTGGAGANGGATGGCAGGAGANAGATCACTTGATCATTAC 696 rnd-1_family- 200 CTGTTCTGTTCATTCCCTCTGAAGCACCTGGCATTGGCCACTGTCGGAAG 249 vv i i i i ? CR1-1_Amn#LIN 697 CTGTTAGGTTCACTCCCTCTGAAGCATCTGGTACTGGCCACTGTCGGNAG 746 rnd-1_family- 250 ACAGGATACTGGGCTAGATGGACCTTTGGTCTGACCCAGTATGGCCGTTC 299 ? v CR1-1_Amn#LIN 747 ACAGGATACTGGGCTAGATGGACCNTTGGTCTGACCCAGTATGGCAGTTC 796 rnd-1_family- 300 TTATGTT 306 CR1-1_Amn#LIN 797 TTATGTT 803 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.88 CpG sites = 34, Kimura (unadjusted) = 17.11 Transitions / transversions = 3.40 (34/10) Gap_init rate = 0.00 (1 / 305), avg. gap size = 1.00 (1 / 1) 920 6.61 0.82 0.82 rnd-1_family-204#LINE/CR1 1 122 (0) CR1-13_AMi#LINE/CR1 326 447 (277) m_b3s551i13 rnd-1_family- 1 AATTGAAAGGCAGCAAATTTAAAACTGATAAAAGGAAATAC-TTTTTCAC 49 i - - i CR1-13_AMi#LI 326 AATTGAAAGGCAAC-AATTTAAAACTGATAAAAGGAAATACTTTTTTTAC 374 rnd-1_family- 50 ACAACGCATAATTAGCCTGTGGAACTCATTGCCACAGGATATCGTTGAGG 99 i i i i ii CR1-13_AMi#LI 375 ACAATGCATAATTAACCTGTGGAACTCACTGCCACAAGATATCACTGAGG 424 rnd-1_family- 100 CCAAGAGCTTAGCAGGATTCAAA 122 CR1-13_AMi#LI 425 CCAAGAGCTTAGCAGGATTCAAA 447 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.09 CpG sites = 8, Kimura (unadjusted) = 7.09 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 235 24.30 1.39 2.82 rnd-1_family-206#DNA/hAT-Tip100 1 72 (230) MamTip2b#DNA/hAT-Tip100 1 71 (378) m_b3s601i0 rnd-1_family- 1 CAGGGCCGGTGCTACCATTTAGGCAAACTAGGCGGTTGCCTAGGGCGCCA 50 iv -iiv i v ii v -i vii MamTip2b#DNA/ 1 CAGGGCCGGCCCTAC-GCGTAGGCAGAGTAGGCGGCCGCCTACG-TGGTG 48 rnd-1_family- 51 AGATTTG-GGGGCGCCAAAAAGC 72 v - i i MamTip2b#DNA/ 49 TGATTTGAGGGGCGCCGAAAGGC 71 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.33 CpG sites = 11, Kimura (unadjusted) = 30.24 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 215 12.20 0.00 0.00 rnd-1_family-216#SINE/MIR 69 109 (59) MIR3#SINE/MIR 30 70 (138) m_b3s601i1 rnd-1_family- 69 GGGCTGGGAGTCAGGACTCCTGGGTTCTATCCCCGGCTCTG 109 i vv vi MIR3#SINE/MIR 30 GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTG 70 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 13.32 CpG sites = 2, Kimura (unadjusted) = 13.32 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 22 10.01 0.00 0.00 rnd-1_family-217#Unknown 701 732 (118) (GT)n#Simple_repeat 1 32 (0) m_b3s252i2 rnd-1_family- 701 GTGTGTGTGTGTGTGTGTGTGAGTGTAAGTGT 732 v iv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 20.93 2.50 0.00 rnd-1_family-227#DNA/TcMar-Tigger 405 444 (151) (TATATG)n#Simple_repeat 1 41 (0) m_b3s252i1 rnd-1_family- 405 TATACGTGTGTGTGTGTGTATATGTATAT-TATATAAATAT 444 i i i i i - iv (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATGTATATGTATAT 41 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 558 20.51 1.68 1.68 rnd-1_family-227#DNA/TcMar-Tigger 475 593 (2) MER6A#DNA/TcMar-Tigger 487 605 (0) m_b3s502i4 rnd-1_family- 475 GGAACCTAACCCCCCCATTTACATTAATT--CTTATGGGGAAATTGGATT 522 i i ii--i i i -- i vi v MER6A#DNA/TcM 487 GGAACTTAACTCTT--GTTTATATCAATTAGCCTATGGTAAAATTGGTTT 534 rnd-1_family- 523 CGCTTAACATCGTTTCGCTTAAAGTCGCATTTTTCAGGAACATAACTACA 572 i vv i v i i v v v i MER6A#DNA/TcM 535 CGTTATACGTCGTTTCGCTTAAAGTCGCAGTTTCCAAGAACCTATCGACG 584 rnd-1_family- 573 ACGTTAAGCGAGGAGTTACTG 593 i v MER6A#DNA/TcM 585 ACGTTAAGTGAGGACTTACTG 605 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.19 CpG sites = 15, Kimura (unadjusted) = 24.45 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.33 (4 / 3) 473 14.86 0.00 0.00 rnd-1_family-228#LINE/CR1 2 75 (0) CR1-3_Croc#LINE/CR1 3528 3601 (4) m_b3s551i14 rnd-1_family- 2 TGGTCCTGCTTCGAGCAGGGGGCTGGACTAGATGACCTCCCGAGGTCCCT 51 i i ii i iv CR1-3_Croc#LI 3528 TGATCCTGCCTCAGGCAGGGGGTTGGACTAGATGACCTCTGGAGGTCCCT 3577 rnd-1_family- 52 TCCAGCCCTGATATTCTATGATTC 75 iv vi CR1-3_Croc#LI 3578 TCCAGCCCTACTTCTCTATGATTC 3601 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.95 CpG sites = 8, Kimura (unadjusted) = 16.95 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 18 21.68 1.56 4.84 rnd-1_family-229#Simple_repeat 4 67 (3) (GGCCGGC)n#Simple_repeat 1 62 (0) m_b3s252i0 rnd-1_family- 4 GGCCGGCAGCGGGCTGAGCGG-GGCCGGCGGCCGGGACCCCGGCTGGCAA 52 i v - iv - - vvv - vi (GGCCGGC)n#Si 1 GGCCGGCGGCCGGC-GGCCGGCGGCCGGCGGCC-GGCGGCCGGC-GGCCG 47 rnd-1_family- 53 GGGGCCGGCAGCCGG 67 v i (GGCCGGC)n#Si 48 GCGGCCGGCGGCCGG 62 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.00 (4 / 4) 449 1.61 0.00 0.00 rnd-1_family-236#SINE/MIR 1 62 (1) MIR1_Amn#SINE/MIR 6 67 (163) m_b4s601i0 rnd-1_family- 1 AGGCAGTGTGGTCTAGTGGNTAGAGCACTGGACTGGGANTCAGGAGACCT 50 ? ? i MIR1_Amn#SINE 6 AGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCT 55 rnd-1_family- 51 GGNTTCTATTCC 62 ? ? ? MIR1_Amn#SINE 56 GGGTTCNANTCC 67 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 0.18 CpG sites = 1, Kimura (unadjusted) = 1.79 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 346 27.52 0.00 0.00 rnd-1_family-237#SINE/MIR 25 133 (0) MIR1_Amn#SINE/MIR 5 113 (117) m_b4s601i1 rnd-1_family- 25 GAGAAAGGATGGTCTCGTGGTTAAGGCAGTTGAATGCTGCCCTGGAGAAC 74 iv vi v v ii v v v vvi i v v MIR1_Amn#SINE 5 GAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACC 54 rnd-1_family- 75 TGGATTCTATCCCTGCCTCTGCCACAGAGTTCCTATGTGATGCTGGGCAA 124 i ? ?i i v v?ivi?v i? ivi MIR1_Amn#SINE 55 TGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAA 104 rnd-1_family- 125 GTCACTTAA 133 ? MIR1_Amn#SINE 105 GTCACTTNA 113 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 14, Kimura (unadjusted) = 37.16 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0) 1262 3.36 0.00 0.00 rnd-1_family-238#LINE/CR1 1 149 (0) CR1-L3A_Croc#LINE/CR1 2109 2257 (2031) m_b4s551i0 rnd-1_family- 1 ACACTTGGTGCTTTAAAAGGGCCAATTTCACAAAGCTGAAAACAATTATG 50 i i CR1-L3A_Croc# 2109 ATACTTGGTGCTTTAAAAGGGCCAGTTTCACAAAGCTGAAAACAATTATG 2158 rnd-1_family- 51 AGCCAAATCAGCTGGGAGGAAGAATTTAANCAGAAAAATGTGAATGATAA 100 i ? CR1-L3A_Croc# 2159 AGCCAAATCAGCTGGGAGAAAGAATTTAAACAGAAAAATGTGAATGATAA 2208 rnd-1_family- 101 TTGGGAATTGTTTAAGAACACTTTACTAGATGCCCAAAAAGCCACAATC 149 i i CR1-L3A_Croc# 2209 TTGGGAACTGTTTAAGAACATTTTACTAGATGCCCAAAAAGCCACAATC 2257 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.50 CpG sites = 5, Kimura (unadjusted) = 3.50 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0) 19 4.35 0.00 0.00 rnd-1_family-239#Unknown 53 76 (599) (GA)n#Simple_repeat 1 24 (0) m_b4s252i9 rnd-1_family- 53 GAGAGAGAGAGAGGGAGAGAGAGA 76 i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 706 21.53 1.83 3.73 rnd-1_family-242#LINE/CR1 4 167 (0) Plat_L3#LINE/CR1 3403 3563 (10) m_b4s551i1 rnd-1_family- 4 GGAACAGACTGCCTAGGGAGGTCGTGGAAGCTCCTTCACTGGAGGTTTTC 53 i i i v i iv v v i i i Plat_L3#LINE/ 3403 GGAACGGGCTACCGAGGGAGGTTGTGGAGTCTCCATCCCTGGAGATCTTT 3452 rnd-1_family- 54 AAAAGGAGGCTGGATAGCCATCTGTCTTGGATGGTTTAGACA--CAACAA 101 i ii iv i i ? i v -- ---- Plat_L3#LINE/ 3453 AAGAAAAGAATAGACANCCATCTGTCCTGGATGGTTTAGTCATTCA---- 3498 rnd-1_family- 102 ATCCTGCATCTTGGCAGGGGGTTAGACTAGATGACC-CTTGCGGTCCCTT 150 -- v vvv i i i - i v Plat_L3#LINE/ 3499 --CCTGCCTGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTT 3546 rnd-1_family- 151 CTAACCCTATGGTTCTA 167 i i i ? i Plat_L3#LINE/ 3547 CCAGCTCTANGATTCTA 3563 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.75 CpG sites = 23, Kimura (unadjusted) = 26.54 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.05 (8 / 163), avg. gap size = 1.12 (9 / 8) 513 9.23 0.00 0.00 rnd-1_family-244#DNA/PIF-Harbinger 5 69 (0) Chompy-6_Croc#DNA/PIF-Harbinger 910 974 (6) m_b4s502i0 rnd-1_family- 5 CTAGGCGCCTAAAAGTTAGGCGTTGCGACGCTCAGCGTCGCAACGCCTAA 54 i i i i ii Chompy-6_Croc 910 CCAGGCGCCTAAAAGTTAGGCGCTGCAACGCTCAGCGTTGCGGCGCCTAA 959 rnd-1_family- 55 GTCCCTTTGTGGATC 69 Chompy-6_Croc 960 GTCCCTTTGTGGATC 974 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.53 CpG sites = 6, Kimura (unadjusted) = 10.20 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 287 30.53 0.76 0.76 rnd-1_family-247#LINE/L2 7 138 (1) UCON86#LINE/L2 102 233 (449) m_b4s502i1 rnd-1_family- 7 GTACAGAACGCTGCAGCNCGTCTCCTCAGCA-ACACAGGCTACCGCGAGC 55 i i v ? i i - -i iivv vi v UCON86#LINE/L 102 GTGCAGAATGCTGCTGCCCGCCTTCTCA-CACGCACAAAGAAGTGCGACC 150 rnd-1_family- 56 ACATCANACCTGTNCTCCGCTCTCTACACTGGCTTCCCATAGAATACCGA 105 ?v ii ? vivivv v i vv v v v i UCON86#LINE/L 151 ACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAGG 200 rnd-1_family- 106 ATCAAGTTCAAGGTCTCGGTCCTTATCTTCAAA 138 v ii iv vv i i i UCON86#LINE/L 201 ATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAA 233 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.69 CpG sites = 20, Kimura (unadjusted) = 40.99 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.02 (2 / 131), avg. gap size = 1.00 (2 / 2) 286 22.43 0.00 5.26 rnd-1_family-248#DNA 1 80 (13) Eulor9A#DNA 14 89 (212) m_b4s502i2 rnd-1_family- 1 AAAAACTACGTTAAAAGAACGTTATTAAGGTTGCAAAGTCAAGCACTCAA 50 viv --- i vi v i i i v Eulor9A#DNA 14 AAAAACTACGTTAATGCAACGTTAT---GGCTGAGAATTTAAACGCACAA 60 rnd-1_family- 51 AAGTTAGGAAATGCCAGAATTAAGGTTGCC 80 i -i i i v v Eulor9A#DNA 61 AAGTCAGGAAAT-TCAAAGTTACGGTTCCC 89 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.23 CpG sites = 10, Kimura (unadjusted) = 27.04 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 228 8.11 0.00 2.70 rnd-1_family-249#DNA/hAT-Charlie 300 337 (5) Charlie32a#DNA/hAT-Charlie 300 336 (0) m_b4s502i3 rnd-1_family- 300 AAGTGGTCCGCGGAAAAAAAAAAGTTTGAGAACCACTG 337 vvi ?- Charlie32a#DN 300 AAGTGGTCCGCGGACCGAAAAN-GTTTGAGAACCACTG 336 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.10 CpG sites = 1, Kimura (unadjusted) = 8.83 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 466 4.13 2.56 6.67 rnd-1_family-254#LINE/L2 1 78 (0) L2-1_AMi#LINE/L2 1034 1108 (127) m_b4s551i2 rnd-1_family- 1 CATCGCCCACTTGTTAAATTTTCAAACAAGCACCTTCGTGCTTTCTCCCA 50 - - --- i i L2-1_AMi#LINE 1034 CATCGCCCACTTGTTAAATTTTCAAAC-AGCA-CTTC---CTTTTTCCTA 1078 rnd-1_family- 51 TGCTG--CCCCTCACGCTTGGGAGGAGCTC 78 -- i L2-1_AMi#LINE 1079 TGCTGCTCCCCTCATGCTTGGGAGGAGCTC 1108 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.29 CpG sites = 3, Kimura (unadjusted) = 4.29 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.17 (7 / 6) 16 14.48 5.26 0.00 rnd-1_family-258#LTR/DIRS 1475 1512 (976) (CCTC)n#Simple_repeat 1 40 (0) m_b4s252i8 rnd-1_family- 1475 CCTCGCCCCCTCCCTCCCACCC-CCCTTCC-CCGTCCCTC 1512 v i v - i - v (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 501 30.65 2.99 5.50 rnd-1_family-266#DNA/hAT-Tip100 196 530 (1257) Zaphod2#DNA/hAT-Tip100 2059 2385 (1207) m_b4s502i4 rnd-1_family- 196 TGAGAGGTCAGGGCTACGATAATGGTGCCAACATGAGAGGAAAGAACAGA 245 i v i vii v i viv iv i iv Zaphod2#DNA/h 2059 TGAGAGGCCAGGGATACGACAATGCCACAAATATGCATGGAAAACATAAC 2108 rnd-1_family- 246 GGAGTGCAGACACG-GATCCGAGAGTTAAACCCTCGAGCTTTTTTTGTCC 294 v - vi- vv ivv v ii v i v i v i i Zaphod2#DNA/h 2109 GGATTGCA-ACAGAAGATCCTCGAAAAATATTCTAGGGCATTCTATATTC 2157 rnd-1_family- 295 CATGCAGTTCT---CATTCATTGAACTTGGTGGTCAGTGATGCAGCATCA 341 v --- --- v i i v ii vv Zaphod2#DNA/h 2158 CTTG---TTCTGCGCATTCTTTAAACTTGGTAGTGAACGATGCAGCAAAA 2204 rnd-1_family- 342 GCTTCTAGTGAGGCTGCTGAATTTTTTTAATGTAATTCAAAGCATCTATG 391 iii vv vi ii - i ? i i-- v i Zaphod2#DNA/h 2205 ATCTCTTTTGACACCACTGAATTTTTTTA-TATNATCCAAG--AACTATA 2251 rnd-1_family- 392 TATTT--TTCTCTGCATCAACTCATCGATGGCAAATTTTGAAGCAACATC 439 i vi -- i v v vv v v vivi v ivv i Zaphod2#DNA/h 2252 CAACTACTTTTCAGCTTCAACGAAACGTTGGAGTGTATTGAAAACACATT 2301 rnd-1_family- 440 TGG-GAACATCCTCTCTGACACTGAAACCACTG---AGTGCCACACGATG 485 iv-i -------i vvi i --- i --- i Zaphod2#DNA/h 2302 TACCAAACAT-------AAATTTGAAACCATTGTCGAAT---ACGCGATG 2341 rnd-1_family- 486 GGAAAGTCGAGTGGAGGCGATAAAGCCTATCAAACACCAAATTGG 530 v v v v v - ii v iv i Zaphod2#DNA/h 2342 GGAAAGTCGAGTTGATGCCATCATGCC-ACTAAAAACTCAATTAG 2385 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.00 CpG sites = 49, Kimura (unadjusted) = 40.05 Transitions / transversions = 1.02 (49/48) Gap_init rate = 0.07 (23 / 334), avg. gap size = 1.22 (28 / 23) 552 28.79 1.00 1.00 rnd-1_family-266#DNA/hAT-Tip100 1229 1428 (359) Zaphod2#DNA/hAT-Tip100 3079 3278 (314) m_b4s502i5 rnd-1_family- 1229 TGGAATATATGTGCACAAATAAGATGACCACCCTC-TTTCCAAATGCTTT 1277 v v vv v- v ivv v - i i Zaphod2#DNA/h 3079 TGCAATATATTTGCAGCAATAAT-TTACCGGACACATTTCCGAATACTTT 3127 rnd-1_family- 1278 TGTTGCTCTGCGCATACTTCTAACACTTCCTGTAACAGTTGCCAGTGGAG 1327 v vv v iv i vi v vi v i i Zaphod2#DNA/h 3128 TGTAGCTCTCAGGATATATTTAACTTTGCCAATATCGGTCGCCAGTGGAG 3177 rnd-1_family- 1328 AACGCAGCTTCTCCAAGCTGAAG-TTAATAAAAACACATCTACGCTCCAC 1376 i v ii i i- v -i ii v v i Zaphod2#DNA/h 3178 AACGTAGCTTCTCAAAATTAAAATTTATTAAAAAC-TACTTAAGGTCTAC 3226 rnd-1_family- 1377 AATGACACAGGAGAGGCTGGTCGGCCTTGCAACCATCTCAATAGAGCATG 1426 v i i i viviii v i i v iv i Zaphod2#DNA/h 3227 AATGTCACAAGAAAGACTGTCAAATCTAGCGACCATTTCTATAGAAAACG 3276 rnd-1_family- 1427 AG 1428 Zaphod2#DNA/h 3277 AG 3278 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.20 CpG sites = 29, Kimura (unadjusted) = 36.80 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.02 (4 / 199), avg. gap size = 1.00 (4 / 4) 514 4.29 0.00 4.29 rnd-1_family-268#LINE/CR1 2 74 (743) CR1-L3B_Croc#LINE/CR1 3203 3272 (5) m_b4s551i3 rnd-1_family- 2 GGCCTGCGNTATGCAGGGGGTCAGACTAGATGATCATAATGGTCCCTTCT 51 i i i - CR1-L3B_Croc# 3203 GGCCTGTGNTATACAGGAGGTCAGACTAGATGATC-TAATGGTCCCTTCT 3251 rnd-1_family- 52 GGCCTTAAAGTCTATGATAATCT 74 ? -- CR1-L3B_Croc# 3252 GGCCTTAAANTCTATG--AATCT 3272 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.62 CpG sites = 3, Kimura (unadjusted) = 4.62 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.00 (3 / 3) 16 24.51 3.49 4.71 rnd-1_family-268#LINE/CR1 695 780 (37) (TTTCTCC)n#Simple_repeat 1 85 (0) m_b4s252i7 rnd-1_family- 695 TTTGTCCTTT-TTGTTTTACCTTT-TCCTCCATCCCTCCCTCCTTTCT-C 741 v - iv iv - iiv - ii - (TTTCTCC)n#Si 1 TTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCT-CCTTTCTCCTTTCTCC 49 rnd-1_family- 742 TTCNTCTCTTGCTTCTTTTGTCCTTTCCCCTGTTCCCCT 780 i? - v - i v i - i (TTTCTCC)n#Si 50 TTTCTC-CTTTC-TCCTTTCTCCTTTCTCCT-TTCTCCT 85 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 592 1.54 0.00 0.00 rnd-1_family-269#LINE/CR1 1 65 (0) CR1-13_AMi#LINE/CR1 622 686 (38) m_b4s551i4 rnd-1_family- 1 TTGCACCTTCCTCTGAAGCATCTGGTACTGGCCACTGTCGGAGACAGGAT 50 i CR1-13_AMi#LI 622 TTGCACCTTCCTCTGAAGCATCTGGTACTGGCCACTGTCAGAGACAGGAT 671 rnd-1_family- 51 ACTGGACTAGATGGA 65 CR1-13_AMi#LI 672 ACTGGACTAGATGGA 686 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 1.56 CpG sites = 1, Kimura (unadjusted) = 1.56 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 17 19.53 2.04 2.04 rnd-1_family-275#Unknown 192 240 (122) (TAGGGGG)n#Simple_repeat 1 49 (0) m_b4s252i6 rnd-1_family- 192 TAGGGGGTAGGTGGGAGGGGGCAGTGGGGT-GAGAAGAGGGGGTGGGGGG 240 v v i - - i iiv i (TAGGGGG)n#Si 1 TAGGGGGTAGGGGGTAGGGGGTAG-GGGGTAGGGGGTAGGGGGTAGGGGG 49 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 13 37.12 0.00 1.37 rnd-1_family-287#Unknown 57 130 (79) (CCCGCTC)n#Simple_repeat 1 73 (0) m_b4s252i5 rnd-1_family- 57 CCCCCCCCCCGCTCCCCGTCTCTTGACTGCCCCCCCCCCGAACCTCCCTG 106 v i - iivi v v i vv i v v (CCCGCTC)n#Si 1 CCCGCTCCCCGCTCCCCG-CTCCCCGCTCCCCGCTCCCCGCTCCCCGCTC 49 rnd-1_family- 107 CCCCTTCTCCGACCCCCGGCCCCC 130 vi i vi vi (CCCGCTC)n#Si 50 CCCGCTCCCCGCTCCCCGCTCCCC 73 Matrix = Unknown Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 1590 5.08 0.00 0.00 rnd-1_family-289#LINE/CR1 1 197 (0) CR1-L3A_Croc#LINE/CR1 1911 2107 (2181) m_b4s551i5 rnd-1_family- 1 TAAATATTATAGATGACAATTTCCTAACTCAAAAAGTGTTGCANCCAACA 50 v ? CR1-L3A_Croc# 1911 TAAAAATTATAGATGACAATTTCCTAACTCAAAAAGTGTTGCATCCAACA 1960 rnd-1_family- 51 CGGGGGAATTCTATATTAGACCTCGTCTTGACAGATAAAGAGGAACTGAT 100 i i CR1-L3A_Croc# 1961 CGGGGGAATTCTATATTAGACCTCATCTTGACAGATAAAGAGGAATTGAT 2010 rnd-1_family- 101 CACAGAACTAAAAATTAATGGTAGCTTAGGTACAAGTGATCATGACTTGA 150 i v i CR1-L3A_Croc# 2011 CACAGAACTAAAAATTAGTGGTTGCTTAGGTGCAAGTGATCATGACTTGA 2060 rnd-1_family- 151 TCACATTTATAATGTGCAAACAGAATAAAGTCCAGACCAGTAATATA 197 i i v i CR1-L3A_Croc# 2061 TTACATTTGTTATGTGCAAACAGAATAAAGTCCAAACCAGTAATATA 2107 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.31 CpG sites = 7, Kimura (unadjusted) = 5.31 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 196), avg. gap size = 0.0 (0 / 0) 1331 1.31 0.00 0.00 rnd-1_family-293#LINE/CR1 1 153 (0) CR1-L3A_Croc#LINE/CR1 2497 2649 (1639) m_b4s551i6 rnd-1_family- 1 TATTAGGAACAAAAGGAATCCTAACAATGGTATTGGTCCATTACTAGATG 50 CR1-L3A_Croc# 2497 TATTAGGAACAAAAGGAATCCTAACAATGGTATTGGTCCATTACTAGATG 2546 rnd-1_family- 51 GAAATGGTAGAATTGTCAATAATAATGCAGAAAAGGCAGAAGTGTTCAAT 100 CR1-L3A_Croc# 2547 GAAATGGTAGAATTGTCAATAATAATGCAGAAAAGGCAGAAGTGTTCAAT 2596 rnd-1_family- 101 AAATATTTCTGTTCTGTATTTGGAAAAAAGCCAGATGATGTANTCGTATC 150 i CR1-L3A_Croc# 2597 AAATATTTCTGTTCTGTATTTGGGAAAAAGCCAGATGATGTANTCGTATC 2646 rnd-1_family- 151 ATA 153 i CR1-L3A_Croc# 2647 ACA 2649 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 1.33 CpG sites = 2, Kimura (unadjusted) = 1.33 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 152), avg. gap size = 0.0 (0 / 0) 571 2.99 0.00 0.00 rnd-1_family-297#LINE/CR1 1 67 (0) CR1-L3B_Croc#LINE/CR1 3202 3268 (9) m_b4s551i7 rnd-1_family- 1 TGGCCTGTGATATACAGGAGGTCAGACTAGATGATCTGGTGGTCCCTTCT 50 ? ii CR1-L3B_Croc# 3202 TGGCCTGTGNTATACAGGAGGTCAGACTAGATGATCTAATGGTCCCTTCT 3251 rnd-1_family- 51 GGCCTTAAACTCTATGA 67 ? CR1-L3B_Croc# 3252 GGCCTTAAANTCTATGA 3268 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.18 CpG sites = 2, Kimura (unadjusted) = 3.18 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 16 5.27 0.00 0.00 rnd-1_family-307#Unknown 308 327 (237) (G)n#Simple_repeat 1 20 (0) m_b4s252i4 rnd-1_family- 308 GGAGGGGGGGGGGGGGGGGG 327 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 235 16.67 0.00 1.85 rnd-1_family-308#DNA/hAT-Charlie 1 55 (47) MER102c#DNA/hAT-Charlie 1 54 (277) m_b4s502i6 rnd-1_family- 1 CAGGGGTAGTCAATAGGCGGACCGCGGGCCAAATCCGGACCGCCAGACGC 50 i v iv iv v v - ?? MER102c#DNA/h 1 CAGAGGTTGCAAACTGGCGGCCCGCGGGCCAAATCCGGCCCG-CAGACNN 49 rnd-1_family- 51 TTTTG 55 v MER102c#DNA/h 50 GTTTG 54 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.68 CpG sites = 3, Kimura (unadjusted) = 19.68 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 231 18.46 2.99 2.99 rnd-1_family-308#DNA/hAT-Charlie 1 67 (35) MER58D#DNA/hAT-Charlie 1 67 (319) m_b4s502i7 rnd-1_family- 1 CAGGGGTAGTCAA--TAGGCGGACCGCGGGCCAAATCCGGACCGCCAGAC 48 v v -- -- v v ivvi MER58D#DNA/hA 1 CAGGGGTCGGCAAACTA--CGGCCCGCGGGCCAAATCCGGCCCGCCGCCT 48 rnd-1_family- 49 GCTTTTGAACGGACCCCGA 67 i v v v MER58D#DNA/hA 49 GTTTTTGTACGGCCCGCGA 67 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.46 CpG sites = 3, Kimura (unadjusted) = 21.22 Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.33 (4 / 3) 12 12.08 0.00 6.90 rnd-1_family-308#DNA/hAT-Charlie 72 102 (0) (TTA)n#Simple_repeat 1 29 (0) m_b4s252i3 rnd-1_family- 72 TTTTTATTTACTTATTATCATTATTGTTATT 102 v - - i i (TTA)n#Simple 1 TTATTA-TTA-TTATTATTATTATTATTATT 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 15 14.49 8.77 3.33 rnd-1_family-310#Unknown 370 426 (6) (GCGGC)n#Simple_repeat 1 60 (0) m_b4s252i2 rnd-1_family- 370 GCGG-GCTGGGCGGCGCGGCCGCAGC-CTGCTCCGGCG-GGC-CGG-GCC 414 - v v - i - v -v - - - v (GCGGC)n#Simp 1 GCGGCGCGGCGCGGCGCGG-CGCGGCGCGGC-GCGGCGCGGCGCGGCGCG 48 rnd-1_family- 415 GGGCGGCGCGGC 426 v (GCGGC)n#Simp 49 GCGCGGCGCGGC 60 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.12 (7 / 56), avg. gap size = 1.00 (7 / 7) 17 30.80 0.00 0.00 rnd-1_family-318#Unknown 82 127 (7) (GG)n#Simple_repeat 1 46 (0) m_b4s252i1 rnd-1_family- 82 GGGGGGAGGGGGGGGAGGGAGCGGGGGGAGAGAGAGAAGGGGGCGG 127 i i i v i i i i ii v (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 46 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 795 3.09 0.00 0.00 rnd-1_family-320#LINE/L2 1 97 (0) L2-1_AMi#LINE/L2 655 751 (484) m_b4s551i8 rnd-1_family- 1 CTATGTCTAAATCTTGCCGATTCTTTCTGCATAACATCTCTAAGATACGG 50 v L2-1_AMi#LINE 655 CTATGTCTAAATCTTGCAGATTCTTTCTGCATAACATCTCTAAGATACGG 704 rnd-1_family- 51 CCTTTCCTATCCATCCACACAGCTAAAACTCTCGTCCAGGCTCTCAT 97 v v L2-1_AMi#LINE 705 CCTTTCCTATCCATCCACACAGCTAAAACTCTCGTCCAGTCTCACAT 751 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.17 CpG sites = 0, Kimura (unadjusted) = 3.17 Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0) 5383 9.77 5.65 4.29 rnd-1_family-325#DNA/hAT-Tag1 3 922 (0) hAT-5_Mam#DNA/hAT-Tag1 50 981 (2559) m_b4s502i8 rnd-1_family- 3 TTTTTTATTTAAATCGGATTTTTT---------TGATAAAATGCTTTTTG 43 v v ? ---------? v i i ? v hAT-5_Mam#DNA 50 TTTTTTAATTTAATCGGATTTTNTANTTTTTNTNGTTAAGATGTTTTNTT 99 rnd-1_family- 44 AGGAAAAA---ACCTATCTAAAGATAGTTTTAATT-AAGATACATTATAG 89 i --- v - ii v hAT-5_Mam#DNA 100 AAGAAAAAGAAACCTATATAAAGATAGTTTTAATTTAAGATATGTTAAAG 149 rnd-1_family- 90 CTCAAAGATATCTCATCATGGAATAGGGATTATAAATTCTAATTCTATAG 139 -- v v ? hAT-5_Mam#DNA 150 CTCAAAGATATC--ATCATGGAATAGGGATTATAACTTCTAATTATATAN 197 rnd-1_family- 140 TA--TGAGACAATATATTCATGTAA-TGTTTAAGAAAAGTTTTGTAAATG 186 -- -iv v i i hAT-5_Mam#DNA 198 TATTTGAGACAATATATTCATGTAACCTTTTTAGAAAAGTTTTATAAATA 247 rnd-1_family- 187 AGTTCCAATAGTTCATGG-----ATTAGGGACCCAATCTTATGGGGTT-C 230 i iv i vi i ----- i - hAT-5_Mam#DNA 248 GGTCACAACAGGCCACGGACTATATTAGGGGCCCAATCTTATGGGGTTCC 297 rnd-1_family- 231 CAGGGGCTTCTGTATAGATTATTTAGGTTAATCTT--------TCTATCT 272 i i v ? ? i-- vv --------i vv hAT-5_Mam#DNA 298 CAGAGGCTCCTCTATAGATTANTNAGA--AAGATTAAAGAAAACCACTCT 345 rnd-1_family- 273 ACCCAATGGGACTCAGTGCTCAG----TCTAGAAGATACCATCA------ 312 ---- v i ------ hAT-5_Mam#DNA 346 ACCCAATGGGACTCAGTGCTCAGTCGATCTAGAAGATCCCATTAAGCATC 395 rnd-1_family- 313 ---GAGATGCTTAGTTTTGCAGTTCTCAAACTGTGGATTTGTGTCTCCAG 359 --- v -- hAT-5_Mam#DNA 396 TCTGTGATGCTTAGTTT--CAGTTCTCAAACTGTGGATTTGTGTCTCCAG 443 rnd-1_family- 360 AGATAACATGCTTGTTAACAGCAAAAATGTTTTTAAATAAATAAATAAAT 409 v ---------------------------- hAT-5_Mam#DNA 444 AGATAACATCCTTGTTAACAGC---------------------------- 465 rnd-1_family- 410 AATATATAGAGGTGAGAAATAACAGACC---TCAACCCTATTGTCCCTCT 456 i i i i --- i i hAT-5_Mam#DNA 466 AGTATATGGAGATGAGAGATAACAGACCTGATCAGCCCTATTGTCTCTCT 515 rnd-1_family- 457 GCAAATTTGTGTACACAGAGTCAATCCCTTACCTCTCTCTAAAAGTGCAA 506 i v hAT-5_Mam#DNA 516 GCAAGTTTGTGTACACAGAGTCAAGCCCTTACCTCTCTCTAAAAGTGCAA 565 rnd-1_family- 507 AGTTTCAAAAAGTTCAATGAATAGAAGATTGTTGGGGGCGGAATAGATCT 556 i v i i i hAT-5_Mam#DNA 566 AGTTTCAAGAAGTTAAATGAATAGAGGATTGTTGGGGGTGGAGTAGATCT 615 rnd-1_family- 557 GGACAAGGAGAAGAAGTCTGGAGATAAATGTGAGAAGGGAGGGACAGGCA 606 i i i ii i ---- hAT-5_Mam#DNA 616 GGGCAAGGAGGAGGAGTCTGGAGATAAATGCAAGGAGGGAGG----GGCA 661 rnd-1_family- 607 GTAGAAACAAAAGTGAAAC-TGTTTGAGCAGCATATTCCAGAAGTCTTGA 655 v - v i v hAT-5_Mam#DNA 662 GTAGAAACAAAAGAGAAACATTTTCGAGCAGAATATTCCAGAAGTCTTGA 711 rnd-1_family- 656 GGT----CTTTCTGAGTGTAGCCTTCATTGATTTGAGATCTA-CCATACC 700 v----v i i i -iv vivv hAT-5_Mam#DNA 712 GGGATAAGTTTCTGAGTATAGCTTCCATTGATTTGAGATCTAGTGAGGGA 761 rnd-1_family- 701 ATTCTCTCACTAGAAGGGAAAACCTATAATGGCAGCAGGCCGTAAAAGAG 750 vv v -iv v hAT-5_Mam#DNA 762 ATGGTAT-GGTAGAAGGGAAAACCTATCATGGCAGCAGGCCGTAAAAGAG 810 rnd-1_family- 751 ACCCAGTTTGGGAATATTTTAATGAAGTTCCTCTACCTGTGGGTAAGACA 800 - ? i hAT-5_Mam#DNA 811 ACCC-GTTTGGGAATATTTTAATGAAGTTCCTCTNCCTGTGGGTAAGATA 859 rnd-1_family- 801 GGCACGCGTGCAAAATGCAAACAGTGCAACAAAGAAATGCAAGGCCTGGT 850 i hAT-5_Mam#DNA 860 GGCATGCGTGCAAAATGCAAACAGTGCAACAAAGAAATGCAAGGCCTGGT 909 rnd-1_family- 851 TGCCCGAATGAAACAACATCATGAGAAGTGTTCCTTCTCAGGAGGAAGCT 900 i i i hAT-5_Mam#DNA 910 TGCCCGAATGAAACAGCATCGTGAGAAGTGCTCCTTCTCAGGAGGAAGCT 959 rnd-1_family- 901 GCGTTGAAGATGATGAAAGGAA 922 v v hAT-5_Mam#DNA 960 GCTTTGAAGATGATGAATGGAA 981 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.24 CpG sites = 48, Kimura (unadjusted) = 10.61 Transitions / transversions = 1.26 (48/38) Gap_init rate = 0.06 (55 / 919), avg. gap size = 1.67 (92 / 55) 264 15.38 3.85 0.00 rnd-1_family-329#SINE/MIR 1 52 (0) AmnSINE1#SINE/5S-Deu-L2 521 574 (1) m_b4s502i9 rnd-1_family- 1 TTTGAGATCTATTG--ATGAAAAGCGCTATATAAGAGCTAGGTATTATTA 48 i iv i -- i iv v AmnSINE1#SINE 521 TTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATGCAAGGTATTATTA 570 rnd-1_family- 49 TTAT 52 AmnSINE1#SINE 571 TTAT 574 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.19 CpG sites = 5, Kimura (unadjusted) = 17.45 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1) 6342 9.74 1.68 5.21 rnd-1_family-341#DNA/hAT-Tag1 1 1073 (2) hAT-5_Mam#DNA/hAT-Tag1 2465 3501 (39) m_b4s502i10 rnd-1_family- 1 AATGGGACAAGCACTATCTCCAGCTCATTTTCTTGCAAATATTCTCAATA 50 i iv i ? v hAT-5_Mam#DNA 2465 AACGGATCAAGCGCTATNTCCAGCTCATTTTCTTGCCAATATTCTCAATA 2514 rnd-1_family- 51 CTCGGTACCAGGGTCAAACCTTAACTGCTGAAGAAGAGGAGTTGGCTATG 100 v i --- hAT-5_Mam#DNA 2515 CTCGGTACCAGGGTCAATCCTTAACCGCTGAAGAAGAG---TTGGCTATG 2561 rnd-1_family- 101 ACATGGACATCCAGCAATCATCCCTCCATAATGCCAACTATAATAAACTT 150 i i i hAT-5_Mam#DNA 2562 ACATGGGCATCCAGCAATCATCCCTCCATAATACCAACTATAATAAATTT 2611 rnd-1_family- 151 CAGAGCTAAGGGTGAACCATTCAAGAAATATATGTTTGCTGNCGATGTTT 200 i i ?i v i hAT-5_Mam#DNA 2612 CAGGGCTAAGGGCGAACCATTCAAGAAATATATGTTTGCTGATGAGGCTT 2661 rnd-1_family- 201 TAAAGAAAGTCANACCAGTGAACTGGTGGAAGTCACTTAAGCACTTGGAN 250 ?i ? i ? hAT-5_Mam#DNA 2662 TAAAGAAAGTCACGCNAGTGAACTGGTGGAAGTCACTTAAGCACCTGGAT 2711 rnd-1_family- 251 ---TCAGAGACTGTTGAAGTGNTAANCTCACTTTTGACAGCAGTAGCTTC 297 --- ? ii ? ? ivi i hAT-5_Mam#DNA 2712 CCATCANAGACTACTGAAGTGATAATCCAGCTTTTAACAGCAGTAGCTTC 2761 rnd-1_family- 298 TTCTGCNGGTGTAGAAAGAATATTTTCTTCCTTTGGACTAATTCATTCCA 347 ? i i hAT-5_Mam#DNA 2762 TTCTGCAGGCGTAGAAAGAATATTTTCTTCCTTTGGACTAATTCATTCTA 2811 rnd-1_family- 348 AATTGAGAAATCGTTTGGGACCTGAAAAAGCAGGAAAGCTTGTTTTTCTT 397 i v i hAT-5_Mam#DNA 2812 AATTGAGAAATCGCTTGGGAACTGAAAAAGCAGGAAAGCTTGTCTTTCTT 2861 rnd-1_family- 398 TTCCAGNCTATGAACAAACAGGAAAATGAAGGTGAAGACGACTGAGTTAG 447 ? i i v --- i ? hAT-5_Mam#DNA 2862 TTCCAGTCTATGAATAAACAGGAAGAGGAAGGTGAA---GACTGAATTNG 2908 rnd-1_family- 448 CTGCAGAAGCCAATATTTTAAGTTTCTCATGTTGACCTGGCTGACATAGT 497 iv v i ? v i hAT-5_Mam#DNA 2909 CTGCGTAACCCAGTATTTTAAGTTTCTCATGTTGACNTGGCTGAAATAAT 2958 rnd-1_family- 498 CGATTTAATTTTTGTTTTTTAAATATTTCATTTAACTATTTTAGTTAAAA 547 v --- ?v ? -iv vi vv v i? - hAT-5_Mam#DNA 2959 CTATTTAATTTTTG---TNAAAANA-CACATTTCGCGTTTATAANT-AAA 3003 rnd-1_family- 548 ACAATTTTAACAAAAACAAACCTGATTTTAAAAA---ACTTGAATGTTTA 594 i?i ----- ---------- i --- v vv v hAT-5_Mam#DNA 3004 ATNGTT-----AAAAA----------TTCAAAAATACACGTGCTTGTTTT 3038 rnd-1_family- 595 ACTAAATTCAAAAATTCATATGCTTGTTTTGTTAAAATATTATATGTTTG 644 ii ---- v - ii v v v i -------------- hAT-5_Mam#DNA 3039 GTTAA----AATAATT-ATACACGTTTGTTGTTGAA-------------- 3069 rnd-1_family- 645 CTGTTGAAGAAAAAAATCCAGAATACATAACGTTGTTGTTTTAGTTAAAT 694 -------- v i vv hAT-5_Mam#DNA 3070 --------GAAAAATATCCAAAATACATAAGCTTGTTGTTTTAGTTAAAT 3111 rnd-1_family- 695 AAAACAATTTAAATGTCTG-----TCTGGTGA----TGTTCTCCTCCTAA 735 i ----- i ---- v ? hAT-5_Mam#DNA 3112 AAAATAATTTAAATGTCTGTTGCCTTTGGTGACGGTTGTTGTCCTCCNAA 3161 rnd-1_family- 736 TACAGCATGGCAAGAAAATCCTCCAAATATTAATGATTAACCTGTTGAAT 785 ? i v i iv i ?i? hAT-5_Mam#DNA 3162 TACAGNATGGCAAAAATATCCCCCAAATATCCATGATTAATCNANTGAAT 3211 rnd-1_family- 786 TGGAGATAGTTCACCTCCCAATGACTTCATAAATATCTGCTTCAATTACC 835 i i v hAT-5_Mam#DNA 3212 TGGAGATAGTTCACCTCCCAATGACTTCACAAGTATCTGCTTCAATTAGC 3261 rnd-1_family- 836 TTTGGTAAATGAAATAACCAAACAATCATTCA-TTTTCTGATATAGCTGT 884 i iv v - i i hAT-5_Mam#DNA 3262 TTTGGTAAATAAAATAACCAAATCATAATTCAGTTTTCTGATGTAGCTGC 3311 rnd-1_family- 885 AAAACTAATCTGAAAAGTTTTCAAAATAAATCACT--TTAAAAATGTATA 932 i iv v -- v hAT-5_Mam#DNA 3312 AAAATTAATCTGAAAAAATATCAAAATAAATCACTGCTTTAAAATGTATA 3361 rnd-1_family- 933 GTGTGTACCTTCTAAAAATGAAACCTACATCTATCTCTGAGTTGTGAAGA 982 v hAT-5_Mam#DNA 3362 GTGTGTACCTTCTAAAAATGAAACCTACATCTATCTCTGAGTTGTGAATA 3411 rnd-1_family- 983 ATATGTATTAAGGTTATAACAACCAACAAGAATGCACTTTTATGTAGAAA 1032 v v - hAT-5_Mam#DNA 3412 ATATGTATTAAGGTTATATCAAACAACAAGAATGCACTTTT-TGTAGAAA 3460 rnd-1_family- 1033 TCCATGATTAAATCGAGTCTTCCTGACTAGTGATTTAAATC 1073 v v v i hAT-5_Mam#DNA 3461 ACAATGATTAAATCGAGGCTTCCTGACCAGTGATTTAAATC 3501 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.83 CpG sites = 56, Kimura (unadjusted) = 10.68 Transitions / transversions = 1.30 (56/43) Gap_init rate = 0.06 (60 / 1072), avg. gap size = 1.20 (72 / 60) 11 14.08 0.00 8.82 rnd-1_family-347#Unknown 362 398 (341) (AAAAGG)n#Simple_repeat 1 34 (0) m_b4s252i0 rnd-1_family- 362 AAAAGAATAAGGAAAAATGGGAAAGGTTAAAGGAAAA 398 i v - - i -v (AAAAGG)n#Sim 1 AAAAGGAAAAGG-AAAA-GGAAAAGG-AAAAGGAAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 654 26.50 0.83 2.54 rnd-1_family-348#LINE/CR1 132 371 (379) CR1-12_AMi#LINE/CR1 378 613 (1) m_b4s551i9 rnd-1_family- 132 AAATCGGGGGGNCCGGATAATCTCCATCCAAGAATATTAAAGGAACTGGC 181 i v ? i iv v v ii ii i i i i CR1-12_AMi#LI 378 AAATCAGCGGGTCCGGATGACATGCATCCCAGGGTGCTGAGGGAATTAGC 427 rnd-1_family- 182 ACATGAAATTGCAAGCCCAATAGCAAGGATTTTTAATGAATC-TGTA-AA 229 vv -i i ?iiv v i vv i vi i - v - CR1-12_AMi#LI 428 TAATGAA-CTACNGAACCACTGGCAATTATTTTTGAAAAGTCATGGAGAA 476 rnd-1_family- 230 CTCAGGGGTCGTACCCTGTGACTGGAGAATTGCTAATATAGTACCTATAT 279 -- vv - vviv vv v i ? v CR1-12_AMi#LI 477 CT--GGGGAGGT-CCAGAGGACTGGAGAAAAGCAAATGTAGTACCNATCT 523 rnd-1_family- 280 TTAAGAAAGGGGGGGAAAAGTGATCCGGGNAACTACAGGCCCGTTAGTTT 329 i - i ii i ? ? ? i - v i i CR1-12_AMi#LI 524 TCAA-AAAAGGGAAGAAGAGNGATCCNGGCAATTACA-GCCAGTCAGTCT 571 rnd-1_family- 330 GACCTCAATNGTATGCAAGGTCTTGGAACAAATTTTGAAAGA 371 ? ?vivv ? ii vv v i i CR1-12_AMi#LI 572 NACCTCAATCCCTGGNAAAATAATGGAACAAATATTAAAGGA 613 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 34, Kimura (unadjusted) = 34.97 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.03 (8 / 239), avg. gap size = 1.00 (8 / 8) 3456 11.42 0.51 5.31 rnd-1_family-348#LINE/CR1 159 750 (0) CR1-11_Crp#LINE/CR1 1 565 (896) m_b4s551i10 rnd-1_family- 159 CCAAGAATATTAAAGGAACTGGCACATGAAATTGCAAGCCCAATAGCAAG 208 v vi i i i i i ii CR1-11_Crp#LI 1 CCCAGAATTCTGAAAGAACTGGCACATGAAATCGCAGGTCCGGTAGCAAG 50 rnd-1_family- 209 GATTTTTAATGAATCTGTAAACTCAG-GGGTCGTACCCTGTGACTGGAGA 257 i i v v - v v i CR1-11_Crp#LI 51 GATTTTTAATAAATCTATCAAGTCAGAGGGTGGTACCATATGACTGGAGA 100 rnd-1_family- 258 ATTGCTAATATAGTACCTATATTTAAGAAAGGGGGGGAAAAGTGATCCGG 307 v- v iv ----- i ----------- ii CR1-11_Crp#LI 101 AA-GCAAACTTAG-----ATGT-----------GGAAAAAAGTGATCCGG 133 rnd-1_family- 308 GNAACTACAGGCCCGTTAGTTTGACCTCAATNGTATGCAAGGTCTTGGAA 357 ? i ? ii i CR1-11_Crp#LI 134 GCAACTACAGGCCCGTTAGTCTGACCTCAATAGTATGCAAGGCTTTAGAA 183 rnd-1_family- 358 CAAATTTTGAAAGAGAAAGTAGTTAAGGACATAGAGGTAAACGGTAATTG 407 i i i i i i i i v v CR1-11_Crp#LI 184 CAAATTTTGAAGGAAAGAATAATTAAAGACATGGAGGTAAATGGAAAATG 233 rnd-1_family- 408 GGATAAAATACAACATGGTTTTACAAAAGGTAGATCATGCCAGACCAACC 457 i v v i i CR1-11_Crp#LI 234 GGATAAAATGCAACATGGGTTTACCAAAGGTAGATCGTGCCAGACTAACC 283 rnd-1_family- 458 TGATCTCCTTCTTTGAGAAGATAACTGATTTTTTAGACAAAG--GAAATG 505 v- i v i -- CR1-11_Crp#LI 284 TGATA-CTTTCTTTGATAAGATAACTGATTTTCTAGACAAAGNAGAAATG 332 rnd-1_family- 506 CAGTAGATCTAATCTACCTGGATTTCAGTAAGGCATTTGATACGGTTCCA 555 i ? i i i v CR1-11_Crp#LI 333 CGGTAGATCTNATCTATCTGGACTTCAGTAAAGCATTTGATACGGTGCCA 382 rnd-1_family- 556 CATGGGAAATTATTAGTTAAATTGGAGAAGATGGGGATTAATACGAGAAT 605 - ii i i CR1-11_Crp#LI 383 CATGGGAAA-TATTAGTTAAGCTGGAGAAGATGGGGATTAGTACAAGAAT 431 rnd-1_family- 606 TGAAAGGTGGATAAGGAACTGGTTAAAGGGGAGACTACAACGGGTCGTGC 655 v - i ------ i iv ? CR1-11_Crp#LI 432 TGTAAGGTGG-TAAGGAGCT------AAGGGAGATGACAACGGGTNGTGC 474 rnd-1_family- 656 TGAAAGGTGAACTGTCGGGCTGGAGGGAGGTTACTAGTGGAGTTCCTCAG 705 - ? i - - - i CR1-11_Crp#LI 475 TGAAAGG-GAANTATC-GGCTGGA-GGAGGTTACTAGTGGAGTT-CTCAA 520 rnd-1_family- 706 GGATCGGTCTTGGGACCAATCTTATTTAATATTTTCATTAATGAC 750 i CR1-11_Crp#LI 521 GGATCGGTCTTGGGACCGATCTTATTTAATATTTTCATTAATGAC 565 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.67 CpG sites = 46, Kimura (unadjusted) = 12.67 Transitions / transversions = 2.56 (46/18) Gap_init rate = 0.05 (32 / 591), avg. gap size = 1.03 (33 / 32) 1838 21.14 1.81 1.58 rnd-1_family-344#LINE/CR1 6 447 (3) Plat_L3#LINE/CR1 1857 2299 (1274) m_b5s551i0 rnd-1_family- 6 ATAACNGANAAC-GTGGAAATGGCNGAGG-TGCTNAATGCCTTTTTGCTT 53 ? ?i - i - ? - vi ?? vii ii Plat_L3#LINE/ 1857 ATAACAGATGACTGTGAAAA-GGCGGAGGCTTTTANATTTTTTTTCACTT 1905 rnd-1_family- 54 CAGTTTTCACCAAAAAGGTTAGTGGCGACCGGACGTCTAAC-ACAGTNAA 102 v i i v i i ivv i v i ---- i - vi i? i Plat_L3#LINE/ 1906 CTGTCTTTACGAAAAAGATCAAATGTGAACAG----CTGACCAGGGCAAG 1951 rnd-1_family- 103 TATCA---GCGA--AAANGGGGNAGGANCAGAGGCTAAAATAGGGAAAGA 147 vi --- ? --i ? vv ? iii? i -- i Plat_L3#LINE/ 1952 TCCCACTTGNGATGGAAGGTTGGAAAGCCAAA--CTAGAATAGGGAAAGA 1999 rnd-1_family- 148 ACAAGTTAAAGAATACTTAGACAAGTTAGATGTNTTCAAGTCGGCAGGGC 197 vv i ii ?i v iiii ? i i i Plat_L3#LINE/ 2000 AACAGTTAAAGAGTATCTNAAAAAACCGGATGTATTTAAATCAGCAGGGC 2049 rnd-1_family- 198 CTGATGAAATNCATCCTAGGGTACTTAAGGAACTAGCTGAAGNGATCTCN 247 v ? i i v v ?v iv ? Plat_L3#LINE/ 2050 CTGATGACATGCATCCTAGGGTACTTAAGGAATTGGCGGATGTTATTGCA 2099 rnd-1_family- 248 GAACCATTAGCGATTATCTTCGAGAACTCATGGAGGACGGGNGAGGTCCC 297 i i v i i ii ? i Plat_L3#LINE/ 2100 GAGCCACTAGCTATTATTTTTGAGAACTCGCGGAGGACGGGAGAAGTCCC 2149 rnd-1_family- 298 AGAGGACTGGAAAAGGGCAAATATAGTGCCTATCTTTAAAAAGGGGAACA 347 v i ii v i i v Plat_L3#LINE/ 2150 TGAGGATTGGAAAAGGGCAAACGTTGTGCCCATCTTTAAAAAAGGGAAAA 2199 rnd-1_family- 348 AGGAGGACCCGGGGAATTATAGACCAGTCAGCCTAACTTCGGTACCCGGA 397 v v v i i i v i i i Plat_L3#LINE/ 2200 AGGACGACCCTGGTAATTACAGACCGGTCAGCTTAACATCGATACCTGGG 2249 rnd-1_family- 398 AAGATAATGGAGCAAATAATTAAGCAATCAATTTGTAAGCACCTAGAAGA 447 v i i v i i i v Plat_L3#LINE/ 2250 AAGATACTAGAACAAATCATCAAACAATCAATTTGCAACCACCTAGAAGA 2299 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.03 CpG sites = 62, Kimura (unadjusted) = 26.77 Transitions / transversions = 2.07 (62/30) Gap_init rate = 0.03 (12 / 441), avg. gap size = 1.25 (15 / 12) 262 21.54 0.00 0.00 rnd-1_family-356#DNA/hAT-Charlie 7 71 (2) MER58C#DNA/hAT-Charlie 1 65 (150) m_b5s502i0 rnd-1_family- 7 CAGGGGTCGGCAACCTACGGCACGCGTGCCAAACACGGCACGCGAGCCGA 56 v v v iv v iv i v MER58C#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCGGCCTGT 50 rnd-1_family- 57 TTTTGAGTGGCACGC 71 vii v MER58C#DNA/hA 51 TTTTGTACGGCCCGC 65 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.47 CpG sites = 5, Kimura (unadjusted) = 25.39 Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 295 15.25 0.00 18.03 rnd-1_family-360#DNA/TcMar-Tigger 12 83 (79) MamRep137#DNA/TcMar-Tigger 69 129 (381) m_b5s502i1 rnd-1_family- 12 AAAAAGAGAAAAATAACAATTTNAATACTGTACCTGTAGTGCGGGCGATT 61 i i i i i v ? ----------- MamRep137#DNA 69 AGAGAGAAAGAGAGAACAATTTAAATA-----------GTGCGGGCGATT 107 rnd-1_family- 62 CCGCCCGCCATTGAACTCAATG 83 i vv MamRep137#DNA 108 CTGCCCGCCATTCCACTCAATG 129 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.02 CpG sites = 6, Kimura (unadjusted) = 17.02 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.15 (11 / 71), avg. gap size = 1.00 (11 / 11) 498 11.27 0.00 0.00 rnd-1_family-360#DNA/TcMar-Tigger 83 153 (9) MamRep137#DNA/TcMar-Tigger 433 503 (7) m_b5s502i2 rnd-1_family- 83 GTAATTTTGACTATACGCGGTTTTCGCTTTACGCGCTGACCGCGGAACGT 132 i i ivii v MamRep137#DNA 433 GTAATTTTGACTATACGCGATTTTCGCCTTACGCGCTGACTTTAGAACCT 482 rnd-1_family- 133 AACCCCNGCGTAAGATGAGAC 153 ? v MamRep137#DNA 483 AACCCCCGCGTAAGATGCGAC 503 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.51 CpG sites = 5, Kimura (unadjusted) = 12.51 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 274 14.84 0.00 3.70 rnd-1_family-363#DNA/hAT 362 417 (1385) UCON69#DNA/hAT 70 123 (363) m_b5s502i3 rnd-1_family- 362 TTGTTCTGCAGCATCTAAGCTTTCATTTAGAAACAATGTAAGTCTCTAGC 411 v v v i v --? i UCON69#DNA/hA 70 TTGTGCTCCAGAATCTAAGCTTTCATTTAAAAAAA--NTAAGTTTCTAGC 117 rnd-1_family- 412 TGTTAT 417 iv UCON69#DNA/hA 118 CCTTAT 123 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.86 CpG sites = 3, Kimura (unadjusted) = 16.86 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 337 12.99 2.04 13.64 rnd-1_family-370#DNA/hAT-Blackjack 1 98 (74) BLACKJACK#DNA/hAT-Blackjack 1 88 (2881) m_b5s502i4 rnd-1_family- 1 TAGGGTGACCATACGTCCCGTTTTGGCCGGGACAGTCCCTTTTTTAAGCC 50 v v -vv v BLACKJACK#DNA 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCC-GGTTTACGCC 49 rnd-1_family- 51 --CTGTCCCGGCCGTCCCGACTTTTTTGGCAAAAGTGGGCATTTGTCCCG 98 --i - v ivv ----------i BLACKJACK#DNA 50 TGTTGTCCCGG-CGTCCCGTCCGGTTT----------AGCATTTGTCCCG 88 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.80 CpG sites = 3, Kimura (unadjusted) = 14.03 Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.13 (13 / 97), avg. gap size = 1.08 (14 / 13) 718 16.55 2.68 2.68 rnd-1_family-375#LINE/CR1 107 255 (876) CR1-L3B_Croc#LINE/CR1 3123 3271 (6) m_b5s551i1 rnd-1_family- 107 TGGATGTCGTTCCAAAAGACGTGCTCTGGCTCAGTCCCATGCTATGGTTG 156 i v iii ii i i - iv v v i v -- CR1-L3B_Croc# 3123 TGGATGCCTTTCTGGAAGATATGCTTTAG-TCAAACACAAGTTATTG--G 3169 rnd-1_family- 157 GCTGAA----GGAACCACTTGGTGAAATTCTATGGCCTGCGTTATACAGG 202 v ---- iiiv v iv i ? CR1-L3B_Croc# 3170 GCTCAATACAGGGGTAACTGGGTGAAATTTAATGGCCTGTGNTATACAGG 3219 rnd-1_family- 203 AGGTCAGACTAGATGATCATAATGGTCCCTTCTGGCCTTAANNTCTATGA 252 - ? CR1-L3B_Croc# 3220 AGGTCAGACTAGATGATC-TAATGGTCCCTTCTGGCCTTAAANTCTATGA 3268 rnd-1_family- 253 ATC 255 CR1-L3B_Croc# 3269 ATC 3271 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.44 CpG sites = 15, Kimura (unadjusted) = 19.44 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (5 / 148), avg. gap size = 1.60 (8 / 5) 217 22.73 1.49 1.49 rnd-1_family-375#LINE/CR1 821 887 (244) C MIR3#SINE/MIR (66) 142 76 m_b5s601i0 rnd-1_family- 821 ATTTGATAGTGGAGAAGACTGATGCCGTAAGGGG-GAAGTGAGTTACCCC 869 v i vv i i v vvi i - v i - C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCC- 94 rnd-1_family- 870 AAGGTCACCCAGTGAGTT 887 v i? C MIR3#SINE/MIR 93 AAGGTCACACAGCNAGTT 76 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.72 CpG sites = 7, Kimura (unadjusted) = 27.72 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 878 15.44 0.00 15.66 rnd-1_family-377#DNA/hAT-Tag1 3 194 (13) hAT-5_Mam#DNA/hAT-Tag1 2714 2879 (661) m_b5s502i5 rnd-1_family- 3 ACCAGAGTTTGTTGAAGTGCTAAACCAGCTTTTGACAGCAGTAGCCTCTT 52 i ? vi ii v v i i hAT-5_Mam#DNA 2714 ATCANAGACTACTGAAGTGATAATCCAGCTTTTAACAGCAGTAGCTTCTT 2763 rnd-1_family- 53 CTGCAGGTGCAGAGAGAATATTTTCTTCATTTCAGTTTATTCAACTAGTT 102 i i i v ------------------ hAT-5_Mam#DNA 2764 CTGCAGGCGTAGAAAGAATATTTTCTTCCTTT------------------ 2795 rnd-1_family- 103 CAGTTCAATGACTAGTTCATTCAAAGTTAAGAAACCGATTGGGAGTTGAA 152 -- ------ i v i i i v ii hAT-5_Mam#DNA 2796 --G------GACTAATTCATTCTAAATTGAGAAATCGCTTGGGAACTGAA 2837 rnd-1_family- 153 AAAGCAGGAAAGCTTGTTTTCCTCTTCCAATCTATGAATAAA 194 i i i i hAT-5_Mam#DNA 2838 AAAGCAGGAAAGCTTGTCTTTCTTTTCCAGTCTATGAATAAA 2879 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.66 CpG sites = 19, Kimura (unadjusted) = 17.40 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.14 (26 / 191), avg. gap size = 1.00 (26 / 26) 14 18.80 4.55 2.22 rnd-1_family-378#DNA/hAT-Charlie 454 497 (182) (ATA)n#Simple_repeat 1 45 (0) m_b5s252i8 rnd-1_family- 454 ATAAT-GTAATAAAAATACT-GTAATGATAAATAATAATTAAAATA 497 -i v v -i i - v v (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAAT-AATAATAATAATAATA 45 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 286 24.02 0.00 2.67 rnd-1_family-378#DNA/hAT-Charlie 597 673 (6) Charlie21a#DNA/hAT-Charlie 1139 1213 (0) m_b5s502i6 rnd-1_family- 597 ATTTTTAGGAGGGGGTTCGCGAGACTTGACATTTTAGTGAAAGGGGTTCA 646 ii -- i vv i viv i Charlie21a#DN 1139 ATTCCTA--AGGGGGTTCGCGAGATTATATATTACTGTGAAAGGGGTTCG 1186 rnd-1_family- 647 CGGGTTGTTAAAGTTTGGGAACCACTG 673 i iivv v v i Charlie21a#DN 1187 CGAGTCAAAAAAGGTTGGGAAACGCTG 1213 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 10, Kimura (unadjusted) = 29.37 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 494 26.43 4.38 7.74 rnd-1_family-380#LTR/ERV1 1846 2325 (1579) ERV24_Prim#LTR/ERV1 2760 3224 (4351) m_b5s701i0 rnd-1_family- 1846 CACTGATGTTGGCCTGCTCCTTTCGGCAGAGCCAGTAAGGATTCAAGTGA 1895 i vvviv iv i ? vv ?i v ii i ii ERV24_Prim#LT 2760 CACTGATATTGGGAAAATTATCTCGGCNGCCCCNATTAAAATTCAAATAG 2809 rnd-1_family- 1896 AGCCCTCCTTAACCCCCCCGTCAGTCCCT---CAATACCCCCTGTCGCTG 1942 v v ?v- i i? -- ?iv i --- i ivvi ii ERV24_Prim#LT 2810 ATCCATCNA-AACCTCTNC--CNAACCTTAANCAATACCCTCTAAGACCA 2856 rnd-1_family- 1943 GAAGCCCGGGAGGGCATCCGCCCCATTATCGAGGGATTCATTGCACAAAA 1992 i iv i v ?v v i v iv? ----- ii i ERV24_Prim#LT 2857 GAGGCCTCGGAAGGGATNAGACCTATAATTTNGG-----ATTATATAAAA 2901 rnd-1_family- 1993 ----GCT-AGTCCGCCCTCAGCGCACT---CCCTGTAACACCCCTATACT 2034 ---- -?i ivvi i--- ?--- ? i v v ERV24_Prim#LT 2902 AGAGGCTTNATTATTCCTT---GCACNAGCCCNTGTAACACTCCAATCCT 2948 rnd-1_family- 2035 GCCTGTCAAAAAGCCTCCTAAAAAGGACGGAGACCCTATTCGTTGGCGCT 2084 ? ? ? i i ----- v ?? ii ---------- v v ERV24_Prim#LT 2949 NCCNGTNAGAAAACC-----AAATGGNNGAGGA----------TGGAGAT 2983 rnd-1_family- 2085 TTGTACAGGATCTACGGGTTGTTAATCAGTATGTGGTCCCTCTTCATGCA 2134 ? ?v i i?i v ?vv? ?i ? vv ? v ? ERV24_Prim#LT 2984 TTGTNCAGGATCTNAGAGCNATTAATAANATNGTNATNCCTCGACNTCCN 3033 rnd-1_family- 2135 GTAGTTCCTGATCCAGCTAC--TATCATCAGCCAAATCCC--CTGGGATG 2180 v vi i ??v -- i iiv v -- -- -- v ERV24_Prim#LT 3034 GTAGTACCAAACCCNNATACNTTGTTGACTGCCA--TCCCAACTG--AAG 3079 rnd-1_family- 2181 CTGAGTGGTTCACTGTTATTGACTTAAAATCAGCCTTTTTCAGCATTCCT 2230 v vv v v i ?viv?vv ? i i ERV24_Prim#LT 3080 GTGAGTTCTTCACTGTAATAGACCTNTGCNGTGCNTTCTTTAGCATTCCT 3129 rnd-1_family- 2231 GTGCACCCAGACTCTCAGTATCTCTTTGGTTTCACCTGGGAGG---GACA 2277 ?v ivv ?vv i ? ? vi i i --- ERV24_Prim#LT 3130 GTNGATAAAGANAGTCAATNTCTNTTTGCCTTCACTTGGGAAGACAGACA 3179 rnd-1_family- 2278 AAGTTATGTCTGG-CAACGACTTCCTCAAGG--CTACAGAGACAGCCCCA 2324 --- iii - ?ii? - v i --? v -- ? ERV24_Prim#LT 3180 A---TACACCTGGACNGTNA-TGCCTCAGGGGTNTACTGAG--AGCCCNA 3223 rnd-1_family- 2325 C 2325 ERV24_Prim#LT 3224 C 3224 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.75 CpG sites = 60, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.05 (60/57) Gap_init rate = 0.09 (45 / 479), avg. gap size = 1.27 (57 / 45) 598 23.09 2.89 8.11 rnd-1_family-380#LTR/ERV1 2015 2325 (1579) ERV24B_Prim#LTR/ERV1 2940 3235 (4378) m_b5s701i1 rnd-1_family- 2015 CCCTGTAACACCCCTATACTGCCTGTCAAAAAGCCTCCTAAAAAGGACGG 2064 i i i ? v ? ? v i ?----- v ?? i ERV24B_Prim#L 2940 CCTTGTAATACTCCNATCCTNCCNGTAAAAAAACCN-----AATGGNNGA 2984 rnd-1_family- 2065 AGACCCTATTCGTTGGCGCTTTGTACAGGATCTACGGGTTGTTAATCAGT 2114 i ---------- v v ? i i v i iii - i? ERV24B_Prim#L 2985 GGA----------TGGAGATTTGTNCAAGACCTAAGAGCCATTAA-CAAN 3023 rnd-1_family- 2115 AT-GTGGTCCCTCTTCATGCAGTAGTTCCTGATCCAGCTAC--TATCATC 2161 - ?i i v? v ? ? vi i ?vv -- ? ii? ERV24B_Prim#L 3024 ATNGTNATTCCTCGNCATCCNGTAGTNCCAAACCCNCATACNTTNTTGNC 3073 rnd-1_family- 2162 AGCCAAATCCCCTGGGATGCTGAGTGGTTCACTGTTATTGACTTAA--AA 2209 v? -- ??vv v vi ? vv ? ? ii v-- i ERV24B_Prim#L 3074 TNCCA--TCCCNNCTGAAGGCGANTTCTTCACTGTNATNGATCTATGTAG 3121 rnd-1_family- 2210 TCAGCCTTTTTCAGCATTCCTGTGCACCCAGACTCTCAGTATCTCTTTGG 2259 -- ? i i ?v i?v vv i ? v ERV24B_Prim#L 3122 T--GCNTTCTTTAGCATTCCTGTNGATNAAGACAGTCAATATCTNTTTGC 3169 rnd-1_family- 2260 TTTCACCTGGGAGG---GACAAAGTTATGTCTGG-CAACGACTTCCTCAA 2305 i i i --- --- iii - iiv - v i ERV24B_Prim#L 3170 CTTCACTTGGGAAGACCGACAA---TACACCTGGACAGTCA-TGCCTCAG 3215 rnd-1_family- 2306 GGCTACAGAGACAGCCCCAC 2325 ? i vv v ?? ERV24B_Prim#L 3216 GGNTATACTGAAAGCCCNNC 3235 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.11 CpG sites = 37, Kimura (unadjusted) = 31.69 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.09 (29 / 310), avg. gap size = 1.14 (33 / 29) 497 30.39 3.79 4.09 rnd-1_family-380#LTR/ERV1 2081 2423 (1481) MER34-int#LTR/ERV1 3403 3744 (4463) m_b5s701i2 rnd-1_family- 2081 CGCTTTGTACAGGATCTACGGGTTGTTAATCAGTATGTGGTCCCTCTTCA 2130 v i v i ii v i vv - ii i vi MER34-int#LTR 3403 CGATTTGTACAAGATCTAAGAGCCGTAAACCCTT-TGTAATTCCTCGCCA 3451 rnd-1_family- 2131 TGCAGTAGTTCCTGATCCAGCTACTATCATCAGCCAAATCCCCTGGGATG 2180 iv v i i iv i v iv i ivvv MER34-int#LTR 3452 CCCCGTAGTCCCTAATCCAGCTACTATTCTTACCTCAATTCCTGCTGATG 3501 rnd-1_family- 2181 CTGAGTGGTTCACTGTTATTGACTTAAAATCAGCCT--TTTTCAGCATTC 2228 v vv i v v i vviv i -- i-- MER34-int#LTR 3502 CAGCCTGGTTTACAGTAATTGACCTCTGCTCAGCTTTCTTTTCG--ATTC 3549 rnd-1_family- 2229 CTGTGCACCCAGACTCTCAGTATCTCTTTGGTTTCAC-CTGGGAGGGACA 2277 vv v v? i v vv i -i vi v MER34-int#LTR 3550 CGTTGCACCCTGACTCGNAATTTCTCTTTGCATTTACATTTAGAGGGAGA 3599 rnd-1_family- 2278 AAGTTATGTCTGGCAACGACTTCCTCAAGGCTAC--AGAGACAGCCCCAC 2325 v i -iiv vvv vv v ? i v i--v v vv i v MER34-int#LTR 3600 CAATTA-ACATGGACTCGCATACNTCAGGGATATTGTGAGTCCCCCTCAA 3648 rnd-1_family- 2326 GATTTTCAGCCAATGCCTC--CGCCACGACTTGGA------AGGCTTCAC 2367 v -- vv i--v -- i ------ v i MER34-int#LTR 3649 TATTTTC--CCAAGTCCTTAAAGC--CGACTTAGACTCTGTAGCCTTTAC 3694 rnd-1_family- 2368 CAGTCCGCAGGGATCCACGTTAGTCCTATACGTAGATGACATCCTATTAG 2417 ------ i v vi v i v i v v ii i vv MER34-int#LTR 3695 C------CAAGGCTCCACTCTTGTTCAATATGTTGATGACCTTTTACTTT 3738 rnd-1_family- 2418 GTAACC 2423 MER34-int#LTR 3739 GTAACC 3744 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 42, Kimura (unadjusted) = 39.43 Transitions / transversions = 0.72 (42/58) Gap_init rate = 0.06 (19 / 342), avg. gap size = 1.42 (27 / 19) 306 28.39 5.08 5.08 rnd-1_family-380#LTR/ERV1 3282 3537 (367) MER52-int#LTR/ERV1 4845 5100 (1991) m_b5s701i3 rnd-1_family- 3282 TGGACAACCCTGATTGCATCCTCTTCTCGGACGGAAGCTCCTTCTATGTT 3331 i v v i v i iv i i --- v MER52-int#LTR 4845 TAGAGAACCCAGACTGGATTCTCTTTACGGACGGAAGTTCTTT---TGTA 4891 rnd-1_family- 3332 GATGGCAAGCGTTTCA-----CCGGTTATGCA---GTCACCTCTGAATGG 3373 --i v v i ----- v v --- i - - MER52-int#LTR 4892 GA--ACAAGGGATCCATAAAGCAGGGTATGCAATAGTTACC-CTGAATG- 4937 rnd-1_family- 3374 GACATT--CAAGAGGCCGCCTCACTGC-CAGGCAACTGGGGAGCCCAAGC 3420 - --ii vv v v - i - --ii v i vi MER52-int#LTR 4938 -ACATTGTTGAGAGCGCGCCTCTCTCCTCGGGCA-C--AAGTGCTCAACT 4983 rnd-1_family- 3421 CGCCGAACTCTATGCCCTGGCCCGAGCTTGCCAGTTGGCCGCTGGTAAGA 3470 v i vvv vi vv i viv v i iiv ivv v ii MER52-int#LTR 4984 AGCCGAGCTAATTGCCCTCACGAGGGCGCTCGAATTAAGCAAAGGGAAAG 5033 rnd-1_family- 3471 CCGTTACCATTTTTACTGATAGCAAGTATGCTTTTGGAGTTGTGCATTGT 3520 v v v vvi ivv iv v - i MER52-int#LTR 5034 CAGTTAACATTTATACTGATTCTAAGTATGCTTTCCTAGTCCTCCA-TGC 5082 rnd-1_family- 3521 CACAT-CCACC-TCTGGAA 3537 - - i- MER52-int#LTR 5083 C-CATGCCACTATCTGGAA 5100 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 31, Kimura (unadjusted) = 35.89 Transitions / transversions = 0.82 (31/38) Gap_init rate = 0.07 (19 / 255), avg. gap size = 1.37 (26 / 19) 358 28.02 3.68 3.68 rnd-1_family-380#LTR/ERV1 3412 3574 (330) MER34-int#LTR/ERV1 4743 4905 (3302) m_b5s701i4 rnd-1_family- 3412 AGCCCAAGCCGCCGAACTCTAT-GCCCTGGCCCGAGCTTGCCAGTTGGCC 3460 i i - - i vi iv vvi v MER34-int#LTR 4743 AGCCCAAGCTGCTGAACTC-ATAGCTCTTACTAGAGCTTGCACATTGGCA 4791 rnd-1_family- 3461 GCTGGTAAGACCGTTACCATTTTTACTGATAGCAAGTATGCTTTTGGAGT 3510 ivv v i i ii i vi ivv ii MER34-int#LTR 4792 AAAGGAAAAACTGCCACTATTTACACTGACTCCAGATATGCTTTTGGAGT 4841 rnd-1_family- 3511 -TG---TGC-ATTGTCACATCCACCTCTGGAAGTTTCGAGGTTTCCAGAC 3555 - --- -i v -----v i ii v v ivi MER34-int#LTR 4842 CTGTCATGCTGTTGGCACA-----ATCTGGAAATCCCGCGGATTCTTAAC 4886 rnd-1_family- 3556 AGCTGCCGGTAAACCCATT 3574 vv i vv i MER34-int#LTR 4887 CTCTGCTGGTACTCCTATT 4905 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 24, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.06 (10 / 162), avg. gap size = 1.20 (12 / 10) 385 28.30 0.00 0.00 rnd-1_family-380#LTR/ERV1 3412 3517 (387) PRIMA4-int#LTR/ERV1 4774 4879 (3391) m_b5s701i5 rnd-1_family- 3412 AGCCCAAGCCGCCGAACTCTATGCCCTGGCCCGAGCTTGCCAGTTGGCCG 3461 i iv i vvv i i i vi PRIMA4-int#LT 4774 AGCTCAAGTGGCCGAATTGATTGCCCTGACCCGAGCTTGTCAATTGGCAA 4823 rnd-1_family- 3462 CTGGTAAGACCGTTACCATTTTTACTGATAGCAAGTATGCTTTTGGAGTT 3511 vv ii i i iv v vi i viv ? i PRIMA4-int#LT 4824 AAGACAAGGCTGCGAACATTTACACTGACAGCCGCTATGCNTTTGGGGTT 4873 rnd-1_family- 3512 GTGCAT 3517 iv PRIMA4-int#LT 4874 GCTCAT 4879 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 17, Kimura (unadjusted) = 36.79 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0) 227 33.54 1.83 1.83 rnd-1_family-390#DNA/hAT-Tip100 357 520 (871) Zaphod2#DNA/hAT-Tip100 1194 1357 (2235) m_b5s502i7 rnd-1_family- 357 CCACAGCAAGTGAAAAACTTCATGTTCCCCAAAGACAATGAAAATAG-AA 405 vv i i i i vv i v i iv ii - Zaphod2#DNA/h 1194 CCACCTCAAGTAAGAAATTTTAACTTTCCAAAAGACAGTACAGGTAGGAA 1243 rnd-1_family- 406 GTTTCCATCCAACACATTACTGGCGTGAAATC--CCCAATGGTGACAAAG 453 i ivv- vi ?--i ii v -- v v i Zaphod2#DNA/h 1244 GTTTTCGGA-AACTTATTAN--ACACGAATTCTTCCAAATGGTGAAAAAA 1290 rnd-1_family- 454 TGGAGAGGCCATGGCTTATGTACTCAAAAACCCAGAATGCTGCATACTGT 503 vivv ii v i vv v i v vvv vv i v i vi Zaphod2#DNA/h 1291 TCACTAGATCCTGGTTACTTTATTCTACCTCAAAGGATTCTGTATTTTGT 1340 rnd-1_family- 504 TTTTGTTGCAAACTCTT 520 i v i Zaphod2#DNA/h 1341 CTATATTGCAAACTCTT 1357 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.23 CpG sites = 26, Kimura (unadjusted) = 45.43 Transitions / transversions = 0.93 (26/28) Gap_init rate = 0.03 (5 / 163), avg. gap size = 1.20 (6 / 5) 227 30.99 4.24 5.36 rnd-1_family-390#DNA/hAT-Tip100 815 1097 (294) Zaphod#DNA/hAT-Tip100 2050 2329 (1750) m_b5s502i8 rnd-1_family- 815 AAACAATGGAAACTTCCTTAAAATT--GTGGAGCTGATGGCTGAGTTTGA 862 v i -- ii -- i iv vv vi i Zaphod#DNA/hA 2050 AAACAATGGAAAATTTCT--AGGTTTAGTAGAAATGATTTCGAAATTTGA 2097 rnd-1_family- 863 TGCTGTACT--CCAGGAGCATCTAAGAAGAGTCACCACCCAAGA-AATGT 909 iv v -- -- i v v ii v ------ i - v Zaphod#DNA/hA 2098 TGCTAGAATGGCC--GAACATGTAAGACGGATAA------AAAATAATGA 2139 rnd-1_family- 910 A-CACAC-ACCACTACCTTGGAAAAACAATTCAAAATGAGATCATACAGT 957 - v i- i i v vii v i vv v Zaphod#DNA/hA 2140 AACAAATGATCACTATCTAGGATGGAGAATTCAAAATGAGATTATTAATT 2189 rnd-1_family- 958 TACTGGCAACAAAAGTCAAACAGAAGATTGTGGCAGATCTGAAGTCAGCA 1007 v vv vv v i v ii i ii --- v vv? v i iv Zaphod#DNA/hA 2190 TAATGGGTAATAAAGTGAGAGAAGAAATCAT---ACATAANAATTTAAAA 2236 rnd-1_family- 1008 AG---ATATTACTCTGTTATTCTGGACTGCACACCTGACATCAGCCATAC 1054 --- v vvv i i i ?vvvv vv i iii Zaphod#DNA/hA 2237 AGTAAATATTACTCAGTTCAACTAGATTGTANCAGGGACAAAAGTCACGT 2286 rnd-1_family- 1055 GGAACAAATGACTTTAATGGTGCGTTTTGT--AACAACAACAGAA 1097 v v i v v vi i v -- v -- Zaphod#DNA/hA 2287 TGAACAACTAACATTTATTATACGTATTGTTGAACTAC--CAGAA 2329 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.88 CpG sites = 36, Kimura (unadjusted) = 40.55 Transitions / transversions = 0.77 (36/47) Gap_init rate = 0.08 (22 / 282), avg. gap size = 1.23 (27 / 22) 307 29.50 2.80 2.80 rnd-1_family-390#DNA/hAT-Tip100 1237 1379 (12) Zaphod2#DNA/hAT-Tip100 2059 2201 (1391) m_b5s502i9 rnd-1_family- 1237 TGAGAGGTCAGGGCTACGATAATGGTGCCAACATGAGAGGAAAGAACAGA 1286 i v i vii v i viv iv i iv Zaphod2#DNA/h 2059 TGAGAGGCCAGGGATACGACAATGCCACAAATATGCATGGAAAACATAAC 2108 rnd-1_family- 1287 GGAGTGCAGACACG-GATCCGAGAGTTAAACCCTCGAGCTTTTTTTGTCC 1335 v - vi- vv ivv v ii v i v i v i i Zaphod2#DNA/h 2109 GGATTGCA-ACAGAAGATCCTCGAAAAATATTCTAGGGCATTCTATATTC 2157 rnd-1_family- 1336 CATGCAGTTCT---CATTCATTGAACTTGGTGGTCAGTGATGCAGCA 1379 v --- --- v i i v ii Zaphod2#DNA/h 2158 CTTG---TTCTGCGCATTCTTTAAACTTGGTAGTGAACGATGCAGCA 2201 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 21, Kimura (unadjusted) = 38.02 Transitions / transversions = 1.05 (21/20) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.33 (8 / 6) 19 22.28 2.20 8.14 rnd-1_family-391#Unknown 92 182 (318) (TGTT)n#Simple_repeat 1 86 (0) m_b5s252i7 rnd-1_family- 92 TGTCTGTAGTGTGTGTTTGTTTG--TGTTTGAGGGTTACTTGCTGTGTGC 139 i -v v -- vvv vv -- v - (TGTT)n#Simpl 1 TGTTTGT-TTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTT--TGTTTG- 46 rnd-1_family- 140 TGAGCTTGTGTTTGTCAGTCTGTTTGTTTGTTTTGGTTGTTTG 182 vv - - iv i - v (TGTT)n#Simpl 47 TTTG-TT-TGTTTGTTTGTTTGTTTGTTTG-TTTGTTTGTTTG 86 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.09 (8 / 90), avg. gap size = 1.12 (9 / 8) 1469 20.22 0.36 0.00 rnd-1_family-393#LINE/CR1 1 277 (2) Plat_L3#LINE/CR1 2196 2473 (1100) m_b5s551i2 rnd-1_family- 1 AACAAAGAAGACCCGGGGAATTATAGACCAGTCAGCCTAACTTCGATACC 50 v i v v v i i i v Plat_L3#LINE/ 2196 AAAAAGGACGACCCTGGTAATTACAGACCGGTCAGCTTAACATCGATACC 2245 rnd-1_family- 51 TGGAAAGATACTGGAACAAATTATTAAACAATCAGTTTGTAAGCACCTAG 100 i i i i i i v Plat_L3#LINE/ 2246 TGGGAAGATACTAGAACAAATCATCAAACAATCAATTTGCAACCACCTAG 2295 rnd-1_family- 101 AGGACAATAGGGTNATAAGNAATAGCCAGCATGGATTTGTCAAGAACAAA 150 i vv i i ?v i ? ii i i i v v i Plat_L3#LINE/ 2296 AAGAGCATAAGATACTAGGAAGCAACCAACGTGGCTTTGTGAAGAGCAAA 2345 rnd-1_family- 151 TCATGCCAAACCAACCTAATTTCCTTCTTTGACAGGGTTACTGGCCTAGT 200 i i ? ii v i i v v vv Plat_L3#LINE/ 2346 TCGTGCCAGACNAATTTAATTTCCTTCTATGATAGAGTGACAGGCCACGT 2395 rnd-1_family- 201 GGAT-GGGGGGAAGCAGTAGACGTGATATATCTTGATTTTAGTAAGGCTT 249 i i-i i i i v v i i Plat_L3#LINE/ 2396 AGACAAGGGGGAAGCAATAGATGTAATCTATCTAGACTTCAGTAAGGCTT 2445 rnd-1_family- 250 TTGACACAGTCCCACATGACATTCTCAT 277 iv v i Plat_L3#LINE/ 2446 TTGATTCCGTCCCACATGACATCCTCAT 2473 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.94 CpG sites = 36, Kimura (unadjusted) = 24.40 Transitions / transversions = 1.80 (36/20) Gap_init rate = 0.00 (1 / 276), avg. gap size = 1.00 (1 / 1) 293 34.85 3.87 4.66 rnd-1_family-398#LINE/RTE-BovB 33 962 (277) MamRTE2#LINE/RTE-BovB 359 1281 (271) m_b5s551i3 rnd-1_family- 33 GGCGTCAAGCAAGGGTGTGTTCTAGCNCC--CACTCTGTTCAGCATGATA 80 v i v i iv v ? -- vi iii vviv MamRTE2#LINE/ 359 GGAGTTAAGCAAGGCTGCGTCATCGCTCCAACACTCTTCTCGATATTTCT 408 rnd-1_family- 81 TTCT---CTGCCAC-TCTGACTGATGCCTTTCAACACTGCACTGAAGGAG 126 ---i i - ii--- vv v v i- iv-- MamRTE2#LINE/ 409 TTCTACGTTGCTACATCTGACCA---CCGATAAACTCC-CACCC--GGAG 452 rnd-1_family- 127 TAGGCATGAAGTATAGAACTGACGGGAAACTNTTCAATCTGAGGCGACTG 176 ivv i v iv v i i v ? v v i v MamRTE2#LINE/ 453 TAGAATTAAATTACCGAACGGATGGAAATCTGTTCAATCTCAGCCGGCTT 502 rnd-1_family- 177 CGTGCCANCACCAAGGTG----AAGG---AA--ACTGTACTTCGAGACTT 217 v i ?v i i iiv----v v--- -- i v i v -- MamRTE2#LINE/ 503 CGAGCTAAAACTAGGACCTCCTCAGTCTCAATCATTGAACTTCAATAC-- 550 rnd-1_family- 218 TCTCTTTGCCGATGATTGTGCCCTGAATGCTAGTACAGAGCCAGANATGC 267 ------- i vvi ivv vi viiv iv ?v v MamRTE2#LINE/ 551 -------GCTGATGATGCCGTAGTGTGTGCTCACTCAGAAGCAGATCTCC 593 rnd-1_family- 268 AAGCCANTATGGACAAGTTTTCAANTGCATGCAACAACTTCGG--TCTCA 315 v ?iiiv ivv v vi?v iii v vv v -- v i MamRTE2#LINE/ 594 AAGCAATCGCTGACGTCTTTACCGAGGCATATGAAAAAATGGGATTGTCG 643 rnd-1_family- 316 CCATCAGCATCGAGAAGACTGAGGTNNTGCACCAGCCAGCTCCCCACAAG 365 -- i i v i i ?? v i ivv iv ii MamRTE2#LINE/ 644 C--TTAACATCCAAAAGACTAAGGTACTTCATCAAAAAGCTCCTAATGAG 691 rnd-1_family- 366 CTCCGTACTCAGAACCGTCCATCACTGTAAAT----GGACAGAGACTTCA 411 ---i v- -- iv v vi i ---- vv vi vv MamRTE2#LINE/ 692 C---ATACTCC-AACC--CCGGCAATTCAGATTCATGGTGAGACGCTGGA 735 rnd-1_family- 412 GACAGTGGACCACTTTACNTACCTNGGCAGCACCCTCTCCCGAGCAG-TG 460 vv vi i iv ? ? v vvi v iiiv - MamRTE2#LINE/ 736 GAACGTGGAATATTTCCCGTACCTAGGAAGCCATCTCTCACAGAAAGCTG 785 rnd-1_family- 461 TCAATCGACGATGAAGT-CANNACCGCAGAATTGCTAAA----GCCAGCT 505 v - i i v i - ?? i ------- v ---- v v MamRTE2#LINE/ 786 ACA-TTGATGAAGAAATTCAACATCGC-------CTCAAATGTGCAAGCG 827 rnd-1_family- 506 CTGCATTTGGCCGACTGC-GCNNCGCAACGTTTGGGAACGTCGNGGGATC 554 v v i v v v- v?? -iii i i i --i ? iv i MamRTE2#LINE/ 828 CAGCCTTCGGACGCCTGAAGAAACG-GGTGTTCGAGGAC--TGCGACATT 874 rnd-1_family- 555 AG-CCTACCAACGAAGCTNAAGGTCTACAGAGCAGTNGTGCTCCCAACTC 603 -i iv- v i ? v i vii i? v v ii MamRTE2#LINE/ 875 AGATCTGA-AACCAAACTTATGGTTTACCAGGCAGCTGTGATCCCCACCT 923 rnd-1_family- 604 TNCTGTACGGCTGCGAGACNTGGACNGCCTATCGGCGTCACGCGAGAAGG 653 ? vvvi ? ?i v iv iv v iviv iiiv MamRTE2#LINE/ 924 TGCTGTACGGAGCTGAGACGTGGACAACATACAGAAGACATCTTAAGGTG 973 rnd-1_family- 654 CTCGANCGCTTCCACATNCGCTGTCTGCGAAAG--CTTCTGAAGATCAGA 701 v ?viv v ivv? i i -- i i --i i MamRTE2#LINE/ 974 CTGGAAAAATACCATCAACGCTGCCTGCGGAAGATCCTCCGA--GTCAAA 1021 rnd-1_family- 702 TGGCAGGACAAAGTGC-CCAATACCGANGTCCTCGCTAGAGCCAGTCTAG 750 v i -i - i iivii?i v vvii v i--- MamRTE2#LINE/ 1022 TGGGAGGACAGA-CGCACTAATGTGAGCATCCTCTCGCAGGCGAGC---G 1067 rnd-1_family- 751 CCGTCAGT-TC-ANGCATTGCTGATGAGAGCCCAGCTCNGNTGGGCCGGA 798 iiiv - - ? v v vi v i vv i? ? i i MamRTE2#LINE/ 1068 CTACAAGTATCGAGGCAATGATTGTCAAACACCAGCTTCGCTGGACTGGA 1117 rnd-1_family- 799 CATGTCGTGNGGATGCCAGA--CGAACGCATCCCCAAACAGCTCTTCTAC 846 i vi v? i i v -- v i- - v i iv vi v MamRTE2#LINE/ 1118 CACGTGATCAGAATGTCTGATTCCAG-GC-TCCCAAAGCAAGTGCTGTAC 1165 rnd-1_family- 847 GGAGAACTCACTCAGGGAAAGCGCTCCCATGGAGGNCAAAAGAAGCGNTT 896 vvvv i v vi i i ii iivviv ? i ii i ? MamRTE2#LINE/ 1166 TCCCAATTAAGCCAAGGGAGACGCCTAAGAGGAGGGCAGAGAAAACGTTT 1215 rnd-1_family- 897 CAAGGACACGCTGAAGACCTCTTTGAAGTCCTTCGAGATCAACACCGCCA 946 i i iiiv v v ivv v? ivvv v i i v i v vv MamRTE2#LINE/ 1216 TAAAGATGTCCTCAAGTCTAATTTTNAAAAATGCAAAATAAATACAGCAT 1265 rnd-1_family- 947 CATGGGAAACCTTCGC 962 v i v MamRTE2#LINE/ 1266 CTTGGGAGACCTTGGC 1281 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 46.77 CpG sites = 155, Kimura (unadjusted) = 50.11 Transitions / transversions = 1.01 (155/154) Gap_init rate = 0.07 (61 / 929), avg. gap size = 1.30 (79 / 61) 908 29.18 0.00 1.60 rnd-1_family-400#LINE/RTE-BovB 3 319 (1318) MamRTE1#LINE/RTE-BovB 1011 1322 (2490) m_b5s601i1 rnd-1_family- 3 GGCGATTTTAACGCAAGAGTTGGNCGAGATGCCGCAGCCTGGGAAGGAGT 52 v i v v i ?v v v i v ii ii MamRTE1#LINE/ 1011 GGAGATTTCAACGCACGTGTCGGCAGCGATGCCGAAACGTGGAGAAAAGT 1060 rnd-1_family- 53 CATCGGGAAAAATGGAGTGGGAAAGTGTAACAGCAATGGCCTNCTACTGC 102 ivv?v i ii v iv? i ? v MamRTE1#LINE/ 1061 CATCGGACCNCACGGGATTGGAAAGCTNAACAGCAATGGTCTACTCCTGC 1110 rnd-1_family- 103 TGAAAACTTGTGCAGAACATGACCTTCTGATCAGCAATACGGTCTTCCGC 152 v ivivv vi i v v iv i v i vi MamRTE1#LINE/ 1111 TCAGCGAATGTGCCAAGCATCAGCTCGTAATCACCAACACCATCTTCCGC 1160 rnd-1_family- 153 CTTCCTACACGTAACAAATCAGGACTTCGTGGATGCATCCCCGNTCCAAG 202 v v ---i v i -- i v i i vv ? i MamRTE1#LINE/ 1161 CTACCGA---ATAAGAGA--AAGACATCATGGATGCACCCAAGGTCTAAG 1205 rnd-1_family- 203 CACTGGCATCTGATCGATTATGTCATCGTCAGGAGACGGGACAGACGAGA 252 v v i i iv ivii vvivii MamRTE1#LINE/ 1206 CAGTGGCATCTCATTGATTATATCATCGTTCGACAGCGGGACCTGAAGGA 1255 rnd-1_family- 253 CGTCAGGGTTACAAAAGCTATGCGTGGCGCTGACTGTTGGACGGATCATA 302 i ivi i viv i v i v i v MamRTE1#LINE/ 1256 TGTTTAGATTACTGCAGCTATGCGTGGCGCCGAGTGCTGGACCGACCATC 1305 rnd-1_family- 303 GGCTCATAGTATCCAAA 319 v v vvv MamRTE1#LINE/ 1306 GCCTGATACGCTCCAAA 1322 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 44, Kimura (unadjusted) = 38.11 Transitions / transversions = 0.94 (44/47) Gap_init rate = 0.02 (5 / 316), avg. gap size = 1.00 (5 / 5) 310 34.41 3.79 4.58 rnd-1_family-400#LINE/RTE-BovB 551 946 (691) MamRTE1#LINE/RTE-BovB 1563 1955 (1857) m_b5s601i2 rnd-1_family- 551 CAAGACTGGTTTGACGAAAATGACGCNGAAATCCAGGCCTTACTTGCTGA 600 ii i i v ? i iv ivvi v v MamRTE1#LINE/ 1563 CAGAACTGGTTTGATGAGAATGACTCAGAGATTAAGAAGCTACTTGCAGC 1612 rnd-1_family- 601 GAAGCACCGCCTGCATCGTGCATATCAAAACGATCCA--TCCTCA-GCGN 647 i vv?vv ? ------ i v vv v -- - vv? MamRTE1#LINE/ 1613 AAAGCAAGNAATGCNT------TGTCAACACCTTGCAGCTCCTCATGATC 1656 rnd-1_family- 648 CAAAGAAGACCGNC-TTTATCAACGCTCG---CAGAACAGTACAGAACCG 693 i vi i vv ? -i ivi v ii --- ivi - i v vi MamRTE1#LINE/ 1657 CAGACGAAAGAGACGCTTACAGAAGCCTGTATCGTGACA-TGCAGATCAA 1705 rnd-1_family- 694 ACTGCGCNAGATGCGG--GACTTGTGGCTGAGCGCCAAAGCAGATGAAAT 741 ii iv -- i i ?-- iv iv iii i v v i MamRTE1#LINE/ 1706 GTTAAG--AAACGCGNATGACCAGTGGTGGGATGCCAAGGCTGAAGAGAT 1753 rnd-1_family- 742 ACAGGCATATGCGGACAGGAACGACTATAAGCAGTTTTATGANGCCCTCA 791 v vv i v ?v v vvvi v v i v?? v MamRTE1#LINE/ 1754 CCAGGACTATGCAGACCGNCACCAAACCAAGGACTTCTATGCGNCCCTAA 1803 rnd-1_family- 792 ANACACTCTATGGTCCACTA---GTCTTC-TGGGAGCTTTCCCCTCCTGA 837 ? iii v ? vi --- i v -i v ----- v vvv MamRTE1#LINE/ 1804 AGATGTTATATGGNCCAACACACGCCATCACGGCA-----CCGCTGAGGA 1848 rnd-1_family- 838 ACTCTGATGGTACTGTGCTCCTTACAGANAAGACGACGGCATTCTCCAGA 887 iiv?v iv i iv v i ?ii v -- v i v i MamRTE1#LINE/ 1849 GTGNAGATGGCTCCGCCCTCATCACAGACGGGAAG--GGAATCCTACGGA 1896 rnd-1_family- 888 GATGG--GCTGAACACTTTGAAGCAATTCTCAATNGCCCCTCAGTCGTCA 935 -- -- ii v vvv ? i?vv i vii i i MamRTE1#LINE/ 1897 GATGGCAGC--AACACTTCAACGATCTTCTNAACACGCCTTCTACCATCG 1944 rnd-1_family- 936 ATGACGAGGCC 946 v i i i MamRTE1#LINE/ 1945 AGGATGAAGTC 1955 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.44 CpG sites = 64, Kimura (unadjusted) = 49.52 Transitions / transversions = 0.97 (64/66) Gap_init rate = 0.07 (26 / 395), avg. gap size = 1.27 (33 / 26) 398 24.79 3.75 4.18 rnd-1_family-400#LINE/RTE-BovB 1009 1248 (389) MamRTE1#LINE/RTE-BovB 2013 2251 (1561) m_b5s601i3 rnd-1_family- 1009 GACGAAGTGAAGAAAGCTATCAANCAGCTGTCAAG--TGGCAAAGCNCCA 1056 v v ?v vv i i-- ii v -- i ? iv MamRTE1#LINE/ 2013 GAAGAAGTCANCACCGCTGTCAG--AGCCATGAAGAATGGTAAAGCTCTC 2060 rnd-1_family- 1057 GGNCCAGATGGCATNCCAGCAGAGGTGTACAAAGTCGGTGGAACCCGTGA 1106 ? v ? v v i v v ---- vv vvv v MamRTE1#LINE/ 2061 GGACCTGATGGCATACCTGCTGAGATTTTCAA----GCAGGAAGGGGAGA 2106 rnd-1_family- 1107 C-CTGCTACGGAAGCTCAC-TGAGCTGCTTCGTC--CTTCTGGA--AGCA 1150 - -ii v iiii - ii -i v -- v v -- v i MamRTE1#LINE/ 2107 CGCTGCT-TAGACGTCTGCATAGGCT-TTTCTTCAGCATATGGAGTACCG 2154 rnd-1_family- 1151 GGGAACCATNCCACAAGAANTNAGAGACGCCNNCATCGTCACC-TCTATA 1199 i -- ? i i v? ? i i ??i i - vi MamRTE1#LINE/ 2155 AGGAA--ATGCCGCAGGATTTCAAAGATGCCACTATCATCACCATCTTCA 2202 rnd-1_family- 1200 AGAGNAAGGGCGANAGNNNGGNNTGCGACAACTACCGTGGNATCTCCCT 1248 i? i ? i???v ?? i i i ? ? MamRTE1#LINE/ 2203 AGAAGAAAGGCGAGAAAGCTGACTGCGGCAACTATCGCGGCATCTCNCT 2251 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 31, Kimura (unadjusted) = 33.85 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.07 (16 / 239), avg. gap size = 1.19 (19 / 16) 883 25.35 0.98 2.31 rnd-1_family-400#LINE/RTE-BovB 1250 1556 (81) MamRTE2#LINE/RTE-BovB 2 304 (1248) m_b5s551i4 rnd-1_family- 1250 CTNTCCGTNGCGGGGAAAGTTCTTGCNCGGGTCCTNTTGAACCGACTGAT 1299 ? ii? v i ii iv ?v ii ?i --i MamRTE2#LINE/ 2 CTTTCCACCGCCGGAAAGATCATTGCAAGAATCCTCCTGAACCGACT--C 49 rnd-1_family- 1300 CNCTCACCTGGAGAAGGGCTTATCTGCCNGAGTCACAGTGTGGCTTCCGN 1349 ? i i vv i v -- ? i v i v iv ? MamRTE2#LINE/ 50 CTCCCACTTGCTGAAGAGCTTCTC--CCGGAATCTCAGCGTGGGTTTAGA 97 rnd-1_family- 1350 CCGGGNCGTGGNACTATCGACATGATCTTCGCNGCGCGNCAGNTACAGGA 1399 v ivv v v ?i v ii i i i i ? v ? ? ? MamRTE2#LINE/ 98 GCATCNAGAGGCGCAACTGATACGGTCTTCACTGCTCGCCAGCTNCAGGA 147 rnd-1_family- 1400 GAAATGTCGNGAGCAGAACCGNGAAC---TGTACACGGCCTTTATCGACC 1446 i i i? i i--- i?i --- v i i iv ? MamRTE2#LINE/ 148 AAAATGCCAAGAACAA---CATAAACCTCTTTATATGGCCTTCCTCGACN 194 rnd-1_family- 1447 TNACNAAAGCCTTTGACTCNGTCAATCGCGANGCCCTNTGGANGATCCTG 1496 ? v? i ? i i ? vi ? ? i v MamRTE2#LINE/ 195 TCAGGAAGGCCTTTGACTCTGTCAGTCGTGAAGCATTGTGGAGGATTCTT 244 rnd-1_family- 1497 TCNAAGTTTGGCTGTCCAGACAAATTTATNNNNATCGTACGNCTATTCCA 1546 ii? v v i vvv ii ???? iv v ? ii i MamRTE2#LINE/ 245 CTGAAGTATGGATGCCCACCAAAATTCGTCACCATTCTCCGCCTGCTCTA 294 rnd-1_family- 1547 TGACGGNATG 1556 ? MamRTE2#LINE/ 295 TGACGGTATG 304 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.92 CpG sites = 48, Kimura (unadjusted) = 36.37 Transitions / transversions = 1.71 (48/28) Gap_init rate = 0.03 (8 / 306), avg. gap size = 1.25 (10 / 8) 185 27.96 0.00 2.94 rnd-1_family-400#LINE/RTE-BovB 1563 1632 (5) MamRTE1#LINE/RTE-BovB 2565 2632 (1180) m_b5s601i4 rnd-1_family- 1563 CGCGTNCTGGATGACGGTGAGTCACATCTGAGCCCTTCCCAGTCACCAAC 1612 ?vvi v i -- vii i v v vi i MamRTE1#LINE/ 2565 CGCGTCAGAGTTGACGGCG--TCCTGTCCGACCCATTCCCCATCACCAAT 2612 rnd-1_family- 1613 GGCGTCAAGCAAGGNTGTGT 1632 v v i i? i MamRTE1#LINE/ 2613 GGAGTGAAGCAGGATTGCGT 2632 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.09 CpG sites = 10, Kimura (unadjusted) = 36.90 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 12 15.30 3.45 0.00 rnd-1_family-403#LTR/ERV1 351 379 (454) (GGGAA)n#Simple_repeat 1 30 (0) m_b5s252i6 rnd-1_family- 351 GGGAAGGGAGGGGTAGGGGA-GGAACGGAA 379 i v i - v (GGGAA)n#Simp 1 GGGAAGGGAAGGGAAGGGAAGGGAAGGGAA 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 233 23.03 9.09 5.26 rnd-1_family-403#LTR/ERV1 444 553 (280) LTR26B#LTR/ERV1 405 518 (13) m_b5s502i10 rnd-1_family- 444 GATTTGAGACATGC--CGGTCTCCTAGCGCCNNTTCAG-AGCTCT-CGAA 489 iiv v -- v ------?? i -i i - v LTR26B#LTR/ER 405 GATTTGAGGTTTCCTCCCGTCTCCT------CGTTCGGCGGCCCTACGAT 448 rnd-1_family- 490 TAAACTTGGTTTGCTTCTCCACCCCGGTGTGTC----TATTGG--TGCGA 533 i vv iv v v v v ---- i-- vi LTR26B#LTR/ER 449 TAAACCTCTTTCTCTGCTGCAACCCGGTGTCTCGGCGTATTGACTTGCCG 498 rnd-1_family- 534 CGCACACCGGGCAACGAACC 553 i i i LTR26B#LTR/ER 499 CGCGCATCGGGCAACGGACC 518 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.30 CpG sites = 12, Kimura (unadjusted) = 28.47 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.10 (11 / 109), avg. gap size = 1.45 (16 / 11) 354 19.48 0.00 4.17 rnd-1_family-411#DNA/TcMar-Tigger 10 84 (3) MamRep137#DNA/TcMar-Tigger 8 79 (431) m_b5s502i11 rnd-1_family- 10 GTCGCATCTTACGCGCATTTAACATGCGCGATTTCAGCTTTACGCGGTCG 59 v v i v i v v MamRep137#DNA 8 GTCGCATCATACGCGCATTTAACTTACGCGAATTCAACTATACGCGCTCG 57 rnd-1_family- 60 GCAAAAACAAAAAAAAAGAGAAAAA 84 --- i v i i i i i MamRep137#DNA 58 G---AGAGAGAGAGAGAGAGAAAGA 79 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.79 CpG sites = 8, Kimura (unadjusted) = 22.79 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.00 (3 / 3) 310 33.52 4.21 4.21 rnd-1_family-422#LTR/ERV1 28 407 (1860) C HERV3#LTR/ERV1 (2863) 5563 5184 m_b5s701i6 rnd-1_family- 28 CGGAGTAANACAAGGGGCAAAGCATCAGGCCACCTAAGAGAGGCCTCCTG 77 v i? v v ii v v vv i v vii ii C HERV3#LTR/ERV 5563 CGGAGGAGGACCATGGGCAAGACCTGATCCCATCTCAGATGAGTTTCCTG 5514 rnd-1_family- 78 ACAGACCTTTGAGAGGTGTCGCTTGAGTGTCTGATTTGTGCGTTCCACTA 127 i ivvi ivvv vv ii i i ii i v C HERV3#LTR/ERV 5513 GCAATATTTCTTCAGTAGCTGCTTGAGTGTCCGGTTCATGCGCTCCACTT 5464 rnd-1_family- 128 CTCCACTG-GCT-TGCGGTCGCCATGGTGTGTGGAGCTTCCAGGGGATTT 175 i -- - - i vi v v v i vvvv C HERV3#LTR/ERV 5463 TTC--CTGAGCTCTGCGGCCGGTAGGCTGTGTGTAACTTCCATTTTATTT 5416 rnd-1_family- 176 GCAG-GGCACTCGATATCTTTTGAACAACTTGAGATGTGAAGTG-TGTTC 223 vi i-i - vi v v? ii v i v v ii- i -i v C HERV3#LTR/ERV 5415 TTAACAGC-CGTGTTAGNTCCTGAACTATTTCAGCTAC-AAATGCCGGTC 5368 rnd-1_family- 224 CGTTATCAGATTCCATCCACT--GGGGGAGTCCGAAGCGAGGAATGATCT 271 i i v ii i --v v -- i v i v vi i i v C HERV3#LTR/ERV 5367 CATTGTCTGACCCTA--GAGTTAGAGGCAGTCCAAATCTGGGGATAATGT 5320 rnd-1_family- 272 C-CTTGACAA-ACTTAAGAGCCAC----CGT--TTTGGCAGTGTTGTTAC 313 - i i- --v i ---- -- vv v vi v i- C HERV3#LTR/ERV 5319 CTCTTAACAGTACTT--TAGTCACTTCTCGTGCTTTCTCTGTCCTGGTG- 5273 rnd-1_family- 314 GACATGGGAAGGCTTCGGGCCATCCGCTGAATCGAT-CCACCAAG-ACGA 361 ----- i i iv -- vv i - v v i - v C HERV3#LTR/ERV 5272 -----GGGAAAGCCTCGACCCATC--CTGAAAAGGTGCAAACGAGCACCA 5230 rnd-1_family- 362 GGAGGTACCTGTACCCTTGGGTCCGGGGAAACTCAGTAAAGTCTAT 407 v v vi v iiv? ii v ii i i i C HERV3#LTR/ERV 5229 GCATGTACCGATAGCCCCCNGCTCGGGGCAGTTCGGTGAAGTCCAT 5184 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.88 CpG sites = 64, Kimura (unadjusted) = 45.90 Transitions / transversions = 1.10 (64/58) Gap_init rate = 0.07 (27 / 379), avg. gap size = 1.19 (32 / 27) 477 28.01 2.11 1.04 rnd-1_family-422#LTR/ERV1 129 413 (1854) C PABL_B-int#LTR/ERV1 (2131) 4991 4704 m_b5s701i7 rnd-1_family- 129 TCCACTGGCTTGCGGTCGCCATGGTGTGTGGAGCTTCCAGGGGATTTGCA 178 v?i v ? v ? ? v v i vvvv iv? C PABL_B-int#LT 4991 TCCAGNAGATTGNGGTCTCCANGNTGAGTGTAGTTTCCATTTTATTCCNA 4942 rnd-1_family- 179 GGGCACTCGAT-ATCTTTTGAACAACTTGAGATGTGAAGTGTGTTCCGTT 227 ? -i v - ii ?i ?ii? vi ?i ?viv v? i C PABL_B-int#LT 4941 GNGC-TTCGCTTACTTNCTGNGTNACTTCGGANATGAANGAAGGNCCATT 4893 rnd-1_family- 228 ATCAGATTCCATCCACTGGGGGAGTCCGAAGCGAGGAATGATCTCCTTGA 277 i vv v? ivvv vi i v i v C PABL_B-int#LT 4892 GTCACTTTGNATTGCGTCAGGGAGCCCGAACCGAGGAATGATTTCCTTTA 4843 rnd-1_family- 278 -CAAA-CTTAAGAGCCACCGTTTTGGCAGTGTTGTTACGACATGGGAAGG 325 - - --v i ivi?v ? vv?v i v ?i i v ? C PABL_B-int#LT 4842 GCAAAGCTT--TAGCTACTTCNGTNGCTCNTTCGGTNTGGCATGGGTANG 4795 rnd-1_family- 326 CTTCGGGCCATCCGCTGAATCGATCCACCAAGACGAGGAGGTACCTGTAC 375 i ?iv ?vv vvvi i ? i? v ii i? ? C PABL_B-int#LT 4794 CCTCNACCCATCCNGAGAAGGTGTCTACNAGNACCAGGAGGTATTTANAN 4745 rnd-1_family- 376 CCTT--GGGTCCGGGGAAA-CTCAGTAAAGTCTATTTGCCA 413 i i-- ?v ?? iv - ?vi i ? C PABL_B-int#LT 4744 CTTCCAGGNGCCGNNGGCATCNGGGTGAAGTCNATTTGCCA 4704 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.46 CpG sites = 37, Kimura (unadjusted) = 40.76 Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.03 (8 / 284), avg. gap size = 1.12 (9 / 8) 2046 30.21 2.59 2.88 rnd-1_family-422#LTR/ERV1 808 2235 (32) C PRIMA41-int#LTR/ERV1 (2752) 5004 3581 m_b5s701i8 rnd-1_family- 808 GCAGCGCGCTTGGCTTCCCTGTCTGCTCTGGCATTGCCCTTGGTTACATC 857 v vv i v i?i ?vv vi v i ? ?- C PRIMA41-int#L 5004 GCTGCGGCCTTAGCTGCTNCGTCTGCNAGGGAGTTTCCCTTAGTNACAN- 4956 rnd-1_family- 858 TTGA-TCTTCCTTTTGATGGGCTCTGCAATGCACCACCGCTACTGCTGAG 906 v - ii i vv v i? ? v ivv C PRIMA41-int#L 4955 TGGAGTCCCCTTTTTGATGTCCTCTGCAATGAATNACNGCTACTTCCTTG 4906 rnd-1_family- 907 GGGAGTTGTACCGCTTCTAAAAGCCGGAGAATTTGAGACCCATGCTTAAC 956 v i?iv v v ? vivv vv viv i v i C PRIMA41-int#L 4905 GGCAGCNAAACAGCATCTAANAGATTCAGAATTTCTGAGTGATGTTTTAT 4856 rnd-1_family- 957 CGGGGAGCCTTGGGCTGTTAGCATCCCTCTTTGCTTCCACAGACCAGCGT 1006 v ? i vi ? ? vi i ? v ? viv ? i C PRIMA41-int#L 4855 GGGGGANCCCTTAGCNGTTAGNAGTCCCCNTTCCTTCCANATGGCNGCAT 4806 rnd-1_family- 1007 GAGCATGCAATACCCCAAAAGCATACTTTGAGTCAGTAAAGATATTAACC 1056 v ii vv ?? v i i? ? i i i C PRIMA41-int#L 4805 GAGCATGGAGCACCAGAAANNCATACTTGGAATCAGTGNANATGTTGACT 4756 rnd-1_family- 1057 CGTTTGTCTTTTGCCAGCTCGAGTGCACGAGTCAGGGCCACTAGTTCGGC 1106 v vv i v ii v? v v v i ? i ? i i v C PRIMA41-int#L 4755 CTTAAGTCCTTTCCCAATTGNAGGGCCCTAATNAGAGCNATTAATTCCGC 4706 rnd-1_family- 1107 NAGCTGGGCAGATGTCCCAGCAGGTAAACTCTCAGCTTCCACGGTATCGT 1156 ?vvi i v v ?vv v ivi ?? i v i?iiv ? C PRIMA41-int#L 4705 CTTTTGAGCTGAGGTNGAAGCCGGTAAGGCCTNNGCCTCGATNACCTCNT 4656 rnd-1_family- 1157 GAAGAGTCACAATAGCATAACCCGCCCTCCT-TTGCCC--ATCCACAACG 1203 vv iv v ? i v ? i i - v --i v v C PRIMA41-int#L 4655 GTTGGCTAACNACAGCATACCCNGCCTTTCTGTTTCCCTNGTGCACAAAG 4606 rnd-1_family- 1204 GCACTACTGCCATCGGTATACCATTCCAAGTCAGCATTTGGGAGTGGTTG 1253 --- v v v i vv i v vvvv v i v C PRIMA41-int#L 4605 ---CTACTTCCATCTGTAAACCATTCTACCTCGGGATTATCTAGGGGCTC 4559 rnd-1_family- 1254 ATCTTTTAAATCTGGGCGGCTGGAGTA---TTGGGCATCTATGATTTCCA 1300 i i i v ? --- -- - i i i vi C PRIMA41-int#L 4558 ATCCTTTAAGTCCGGCCNGCTGGAGTAAATTT--GC-TCCATAACTTGTA 4512 rnd-1_family- 1301 GACAGTCATGTTCCTGCTTTTCTGT---CTCCGGTAGCAGGGTAGCTGGA 1347 v ivv v iv vv vi ---i ? i iv?i i C PRIMA41-int#L 4511 TACAAGAATGATCTAGGGTGCCTGTGGGTTCNGGCAAANAGGTAGCTGGG 4462 rnd-1_family- 1348 TTAAGGGAGGGACAGGTCTGCAGGGTAACTTCAGGGTTCTCTAACAGTTT 1397 v ii vvv i viii vv i v v i - v i i?vv C PRIMA41-int#L 4461 TTCAAAGTTTGGCATACTTTAAGAGTTACATCGGGG-TGTCTAGCAANAA 4413 rnd-1_family- 1398 TGCCTGGTA-CCGAGCAACCCGAGCCTGTGTGAGCCAGAGACCACCCTTA 1446 v i -ii? i -?i vv iv v ? vv iivv i ? C PRIMA41-int#L 4412 AGCCTGATATTTNAGTAA-NTGTCCCCCTGTCANCCACTGGTGTCCTTTN 4364 rnd-1_family- 1447 GTGTCCAGCAGGGCTTGGACCATATGGGGAATATACACTTGCACAGTTCC 1496 iv i v vvv i v ivvi ? ii vv v i vi v?vv iv C PRIMA41-int#L 4363 GCTTCTAGGACCCCCTGTACTTGGTGNGGGGTCAAAACCTCTAGNTGTTG 4314 rnd-1_family- 1497 TCCCAGTGTCAGTTTTTCAGCTTCCCCAAGCACTAGGGCAGTGGCTGCGA 1546 i? ? viii ?i v v v? i i ? ? ? C PRIMA41-int#L 4313 TCCCAANGTNAGTTTACTGGCTTCNTCTACCAANAGAGCGGTNGCNGCNA 4264 rnd-1_family- 1547 CCGCCCNCAAGCATGCTGGCCACCCCTTTGCAACTTGATCCAGTTGTTTA 1596 ? ?? i v ? vv? v i i i i i C PRIMA41-int#L 4263 CNGCCCTNAGGCATCCNGGCCACCCCGANGCCACCTGGTCTAGCTGCTTA 4214 rnd-1_family- 1597 GAGAAATATGCCAC------GGGACGTTTCCAGGCGCCTAATAACTGAGT 1640 i ? ------ ii vi-- -----i i i C PRIMA41-int#L 4213 GAAAAATANGCCACTGGTCGGGGATATTTCCCA--GCCT-----TTGGGC 4171 rnd-1_family- 1641 AAGCACTCCCAGGGCTACCCCTTTCCTTTCATGCACATACAGTTGGAACG 1690 ? v v -ii vii vv v -- i ? C PRIMA41-int#L 4170 NAGGACACCCAGGGC-GTCCCTTGTTTTTCAGCCACATAAAG--GAAANG 4124 rnd-1_family- 1691 GCTTAGAAAGATCCGGCAGACCCAGGGCTGGGGCTTCCATCAGCTTTCTT 1740 ?vv? i? iv v ?v i ? i v?ivi i iii C PRIMA41-int#L 4123 GCTTNTCNAANTTGGGGANTCCCAAGGCNGGAGCTGNTCCCAGTTTCTCT 4074 rnd-1_family- 1741 TTCAAGATTTTAAA----TGCCCTGTCCGCTTCTGGGGACCAGTGAAAGG 1786 ? i i v ---- iii - v i ? --ivv v v? C PRIMA41-int#L 4073 TTNAGGGTATTAAAAGTNTGTTTTG-CAGTTNCT--ATCCCATTCNAAGG 4027 rnd-1_family- 1787 GGTCATGATCCGCTCCCTTAACACATTCATACAGNGGTTTAGCCCACAGT 1836 ? i - i v v vvi i i? i ? ivvv? i C PRIMA41-int#L 4026 GNTCACG-TCCGCTCCTTTTAGAGCCTCATATAAAGGCTTNGCTATANGC 3978 rnd-1_family- 1837 CCATACTCTGGGATCCATATTCTGCAAAAGCCTGCCATGCCCAGAAATGC 1886 v ii v ? i ?vv?v i v ? v i v C PRIMA41-int#L 3977 CCAAATCCGGGNACCCATNAANAGCAGAATCCNGCCATTCCCAAAAAAGC 3928 rnd-1_family- 1887 CCTGAGCCGTTTA-CGGTTGCTTGGGAT-AGGAACTTGGCAGATAGCCTC 1934 ?v i v-i -- v ? -v i ???vvv i C PRIMA41-int#L 3927 CCNCAGCTGTTTCTTGGT--CTGGGGNTCCGGGANNNCCAAGATGGCCTC 3880 rnd-1_family- 1935 CTTCCTTTCGTTTGAGAGCTGCCTCTC----TCCCTGCCTTATGTGAA-- 1978 i i ? --- ?i i i?iv i ----? vv vv --- ? -- C PRIMA41-int#L 3879 TTTTCNTTC---TNGGGGCTANTGCCCGGGTNCCAGGGGTTA---GNACG 3836 rnd-1_family- 1979 -ATCCCAGATACTGTA--CTTCTGAGAGNGCAATTTGAGCCTTGCTCCGA 2025 - i i - -- i -v v i i iv v ? C PRIMA41-int#L 3835 TATCCCAAATATT-TAACCTTTTGAG-TNGAAATCTGGGCCTTGTGCGGN 3788 rnd-1_family- 2026 GCTACCCGGTATCCTCGGAGTCCAACAAAGTTCAGGAGGCTCACAGTGGC 2075 v? vi i viviiv v vi i i ? ivi v ii -ii C PRIMA41-int#L 3787 GANACCCTATACCCGTTAGTTCCCAGGAAATTTAGNAACTTAATGGT-AT 3739 rnd-1_family- 2076 TTTGAGACAAG---GGATTAGACCCACAGC-AGCAATTAGCAAGTCATCT 2121 v vv i ---vvv ---i?vi - ? ? i i C PRIMA41-int#L 3738 TTTTATCCGAGTCTTCTTTAG---TNGGGCTAGNAATNAACAAGTCATCC 3692 rnd-1_family- 2122 ACATATTGCAGGAGGAGGACTCTGTCCGAATTGTCCCACTCCTCCAAGTC 2171 v vi vii? v i i i - i --vi i iii v C PRIMA41-int#L 3691 ACATATTGAATAATAGNGCCCCTATTC-AACTGT--AGCTTCCTTAATTC 3645 rnd-1_family- 2172 TCTGGCCAGAGCCTGGCCGAACAGAGTGGGGGA-ATTTTTAAATCCCTGG 2220 i ? i? v vv i ? - v-i iii ? C PRIMA41-int#L 3644 TTTNGCCAANGCATTTCCAAANAGA-TGGGGGCTGTCCCTAAANCCCTGG 3596 rnd-1_family- 2221 GCCAATACTGTCCAG 2235 vv iv C PRIMA41-int#L 3595 GGAAGGACTGTCCAG 3581 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 207, Kimura (unadjusted) = 42.99 Transitions / transversions = 0.98 (207/212) Gap_init rate = 0.04 (58 / 1427), avg. gap size = 1.34 (78 / 58) 14 12.19 5.26 2.56 rnd-1_family-423#Unknown 105 142 (3) (CCGGGCC)n#Simple_repeat 1 39 (0) m_b5s252i5 rnd-1_family- 105 CCGGGCCCCGGGCCCC--CTTCCGGACCGCCGGGCCCCGG 142 --vii i - (CCGGGCC)n#Si 1 CCGGGCCCCGGGCCCCGGGCCCCGGGCC-CCGGGCCCCGG 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.50 (3 / 2) 352 30.78 2.22 6.15 rnd-1_family-424#LTR/ERV1 112 381 (93) MER110-int#LTR/ERV1 2594 2853 (1794) m_b5s701i9 rnd-1_family- 112 CAAGCAACTATGAGATCTGCAAAACACTGCCAGGCATTAATGAAATGTGT 161 ivi ------ v i v v i v v iiii MER110-int#LT 2594 CAAGCAGACATG------GCCAAATACTGCAAGGGACTCATGCAATACAC 2637 rnd-1_family- 162 TAGGTTTCTTTTC-TCA-CAGGTAAAAGAAGTGCTACCCAAAGACCCT-- 207 ivi -- v - - vi v ivi v iv v i -- MER110-int#LT 2638 CCAGT--CTTATCATCAACAGGTACGAGCAGCCTTTCCTCAACATCCTCC 2685 rnd-1_family- 208 --AGCAGCCCTGCCATTCATTGAAACCAGGAGACTGGGTCTACGTAAAGT 255 -- i i vv vvvi i v i?vvv --- - MER110-int#LT 2686 TAAACAACCCTTGCATGACCTAAAACCTGGAGATNTTCTCTA---AAAG- 2731 rnd-1_family- 256 CCATCAACGAAAGACTGCCTTGGCTCCACGCTGGAAAGGCCCTTTCCAAG 305 v i iv i v vv v v v vi i MER110-int#LT 2732 ACACCAGAGAAAGACTGCCCTTGAACCCCGATGGAAAGGACCTTATCAGG 2781 rnd-1_family- 306 TCCTGTTAACCACCAACACCGCTGTGAAGTGCCAAGGACTGCCTGCCTGG 355 v --- i v v i iiv ?v vvv v i MER110-int#LT 2782 TACTGTTA---ACTAACACAGCAGTAAAACTCCAAGGNGTTGATCCTTGG 2828 rnd-1_family- 356 ACCCATGCTTCTCACTGCAAAAAGAC 381 -i iiv ? ivv MER110-int#LT 2829 A-TCATATGTCTCNCTAGCAAAAGAC 2853 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 34, Kimura (unadjusted) = 40.34 Transitions / transversions = 0.77 (34/44) Gap_init rate = 0.07 (20 / 269), avg. gap size = 1.10 (22 / 20) 966 29.90 0.66 0.66 rnd-1_family-426#LINE/CR1 1 303 (45) CR1-3_Croc#LINE/CR1 1156 1458 (2147) m_b5s551i5 rnd-1_family- 1 ACAAAAAGTGGAAACATGGACAAATTGCTAAGGANGAGTACAAAAGAATA 50 iiv i iv i ii ii i ? v v iii CR1-3_Croc#LI 1156 ACAGGCAATGGAAGAATGGGCAGGTCACCAAGGAAGCGTACCAGGAAATA 1205 rnd-1_family- 51 GCACAAGCATGTAGGGACAAAATCAGAAAGGCTAAGGCACAAAATGAGTT 100 vi i v i i v ii v i i i CR1-3_Croc#LI 1206 GCAAGAACCTGCAGGGACAAAATCAGGAAGGCAAAGATAAAGAACGAGCT 1255 rnd-1_family- 101 ACACCTAGCAAGGGACATAAAAGGCAATAAGAAGAGGTTCTNTAAATACA 150 i i i i vi v i i i ? i ii CR1-3_Croc#LI 1256 GCACCTGGCGAAGGAGGTTAAGGACAACAAGAAGAGGTTCTATAAGTATG 1305 rnd-1_family- 151 TTAGGAGCAAGAGAAAGACGAAGGAAAGTGTAGGTCCTCTACTTAGCGGG 200 i vviv i i v iv i ? i- i ii CR1-3_Croc#LI 1306 TTGGCCAGAAAAGAAGGACCAAGGAAGCTGTGGGTCCNCTG-TTAACAAG 1354 rnd-1_family- 201 -GAAGGAGAGCTAATAACTGACGACATCAAGAAGGCTGAGGTGTTTAATG 249 -v i i i vv ? v iiiv v v ii i ii CR1-3_Croc#LI 1355 CCAGGGGGAACTCCTAACNGAAGATGCAAAGAAGGCGGAGCTACTCAACA 1404 rnd-1_family- 250 CCTATTTTGCTTCAGTCTTCACTAAAAAGGTTAA-TGGTGACCAGATACT 298 v i i - ii -iv iii i i CR1-3_Croc#LI 1405 GCTACTTTGCCTCAGTCTTCAC-AAAAAAATTAAGCTGCAGCCAGACACC 1453 rnd-1_family- 299 CAACA 303 i i CR1-3_Croc#LI 1454 TAATA 1458 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 66, Kimura (unadjusted) = 41.66 Transitions / transversions = 2.75 (66/24) Gap_init rate = 0.01 (4 / 302), avg. gap size = 1.00 (4 / 4) 19 15.75 1.82 5.66 rnd-1_family-428#Unknown 37 91 (132) (ATAACT)n#Simple_repeat 1 53 (0) m_b5s252i4 rnd-1_family- 37 ATAACTATATACATGAAATTACAACCTATAACTTTTACTATAAC-ATTAC 85 - - iv i i - v v - v (ATAACT)n#Sim 1 ATAACTATA-AC-TATAACTATAA-CTATAACTATAACTATAACTATAAC 47 rnd-1_family- 86 TATAAC 91 (ATAACT)n#Sim 48 TATAAC 53 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 996 18.72 0.53 0.00 rnd-1_family-437#LINE/CR1 3 189 (1) Plat_L3#LINE/CR1 2631 2818 (755) m_b5s551i6 rnd-1_family- 3 CTATTCAATATTTTCATTAATGACTTGGATAATGGAGTGGA-AGTATGCT 51 i i ii i ii v i v - i Plat_L3#LINE/ 2631 CTATTCAATATCTTTATCGATGACCTGGACGAAGGAATCGAGAGCATGCT 2680 rnd-1_family- 52 NATAAAATTTGCGGATGACACCAAGCTGGGAGGGGTTGCAAGCACTTTGG 101 ? v i i i ii v v i Plat_L3#LINE/ 2681 CATCAAATTTGCAGATGATACTAAATTGGGCGGGGTTGCTAACACTTTGG 2730 rnd-1_family- 102 AGGACAGGATTAGAATTCAAAATGACCTTGACAAATTGGAGAATTGGTCT 151 i v i i ? i v i Plat_L3#LINE/ 2731 AAGACAGGAATAAAATTCAAAGTGACCTNGACAAATTGGAAAAATGGTCC 2780 rnd-1_family- 152 GAAATCAACAAGATGAAATTCAATAAAGACAAGCGCAA 189 v?v vv i ii i Plat_L3#LINE/ 2781 TNCAAAAACAGGATGAAATTCAATAGGGACAAGTGCAA 2818 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.94 CpG sites = 24, Kimura (unadjusted) = 22.51 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.01 (1 / 186), avg. gap size = 1.00 (1 / 1) 1311 14.10 1.47 11.69 rnd-1_family-439#DNA/hAT-Tag1 1 273 (0) hAT-5_Mam#DNA/hAT-Tag1 2632 2879 (661) m_b5s502i12 rnd-1_family- 1 TCAAGCAGTACATGTTTGCTGCCGAG-TTTTAAAGAAAGTCAAACCACTG 49 v i i vi -i vi ? v hAT-5_Mam#DNA 2632 TCAAGAAATATATGTTTGCTGATGAGGCTTTAAAGAAAGTCACGCNAGTG 2681 rnd-1_family- 50 AACTGGTGGAAGTCACTGGCTAAGCACCTGGA---ACCAGAGTTTGTTGA 96 --- --- i ? vi ii hAT-5_Mam#DNA 2682 AACTGGTGGAAGTCACT---TAAGCACCTGGATCCATCANAGACTACTGA 2728 rnd-1_family- 97 AGTGCTAAACCAGCTTTTGACAGCAGTAGCCTCTTCTGCAGGTGCAGAGA 146 v v i i i i i hAT-5_Mam#DNA 2729 AGTGATAATCCAGCTTTTAACAGCAGTAGCTTCTTCTGCAGGCGTAGAAA 2778 rnd-1_family- 147 GAATATTTTCTTCATTTCAGTTTATTCAACTAGTTCAGTTCAATGACTAG 196 v -- ------------------------ i hAT-5_Mam#DNA 2779 GAATATTTTCTTCCTTT--G------------------------GACTAA 2802 rnd-1_family- 197 TTCATTCAAAGTTGAGAAACCAATTGGGAGTTGAAAAAGCAGGAAAGCTT 246 v i i iv ii hAT-5_Mam#DNA 2803 TTCATTCTAAATTGAGAAATCGCTTGGGAACTGAAAAAGCAGGAAAGCTT 2852 rnd-1_family- 247 GTTTTCCTCTTCCAATCTATGAATAAA 273 i i i i hAT-5_Mam#DNA 2853 GTCTTTCTTTTCCAGTCTATGAATAAA 2879 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.41 CpG sites = 24, Kimura (unadjusted) = 15.86 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.11 (31 / 272), avg. gap size = 1.06 (33 / 31) 15 20.03 0.00 0.00 rnd-1_family-440#Unknown 308 336 (200) (A)n#Simple_repeat 1 29 (0) m_b5s252i2 rnd-1_family- 308 AAACAAATAAACAAACAAACAAAAAAAAA 336 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 17 7.81 0.00 0.00 rnd-1_family-440#Unknown 308 334 (202) (AAAC)n#Simple_repeat 1 27 (0) m_b5s252i3 rnd-1_family- 308 AAACAAATAAACAAACAAACAAAAAAA 334 i v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 20 11.06 2.56 0.00 rnd-1_family-442#Unknown 711 749 (169) (TCTGTGT)n#Simple_repeat 1 40 (0) m_b5s252i1 rnd-1_family- 711 TCTGTGTTCAGTGTTCTGTGTTGCATGTTCTGTG-TCTGT 749 v vii - (TCTGTGT)n#Si 1 TCTGTGTTCTGTGTTCTGTGTTCTGTGTTCTGTGTTCTGT 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 185 24.28 1.41 1.41 rnd-1_family-443#DNA/hAT-Tip100 103 173 (0) C MamTip2b#DNA/hAT-Tip100 (378) 71 1 m_b5s601i5 rnd-1_family- 103 GCTTTTTGGCGCCCC-CAAATCTTGGCGCCCTAGGCGGCCGCCTAGTTCG 151 i i - viiv i v- v ii C MamTip2b#DNA/ 71 GCCTTTCGGCGCCCCTCAAATCACACCACG-TAGGCGGCCGCCTACTCTG 23 rnd-1_family- 152 CCTAGTGGTTGCACCGGCCCTG 173 vvv v vi C MamTip2b#DNA/ 22 CCTACGCGTAGGGCCGGCCCTG 1 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.56 CpG sites = 8, Kimura (unadjusted) = 29.52 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 565 19.66 1.68 1.68 rnd-1_family-447#DNA/TcMar-Tigger 42 160 (2) MER6A#DNA/TcMar-Tigger 487 605 (0) m_b5s502i13 rnd-1_family- 42 GGAACCTAACCCCCCCATTTACATTAANT--CTTATGGGGAAATTGGATT 89 i i ii--i i i ? -- i vi v MER6A#DNA/TcM 487 GGAACTTAACTCTT--GTTTATATCAATTAGCCTATGGTAAAATTGGTTT 534 rnd-1_family- 90 CGCTTAACATCGTTTCGCTTAAAGTCGCATTTTTCAGGAACATAACTACA 139 i vv i v i i v v v i MER6A#DNA/TcM 535 CGTTATACGTCGTTTCGCTTAAAGTCGCAGTTTCCAAGAACCTATCGACG 584 rnd-1_family- 140 ACGTTAAGTGAGGAGTTACTG 160 v MER6A#DNA/TcM 585 ACGTTAAGTGAGGACTTACTG 605 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.19 CpG sites = 14, Kimura (unadjusted) = 23.42 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.33 (4 / 3) 971 24.88 0.00 0.00 rnd-1_family-452#LINE/CR1 1 201 (0) Plat_L3#LINE/CR1 2402 2602 (971) m_b5s551i7 rnd-1_family- 1 GGAGGGAGCAGTAGACGTGATATATCTTGATTTTAGTAAGGCTTTTGACA 50 i i i i i v v i i iv Plat_L3#LINE/ 2402 GGGGGAAGCAATAGATGTAATCTATCTAGACTTCAGTAAGGCTTTTGATT 2451 rnd-1_family- 51 CAGTCCCACATGACATTCTCATAAGCAAACTAGGGAAATGTGGTCTAGAT 100 v i vii i i i i i v i Plat_L3#LINE/ 2452 CCGTCCCACATGACATCCTCATCGACAAGCTGGGAAAGTATGGTCTTGAC 2501 rnd-1_family- 101 GAAATTACTATAAGGTGGGTGCACAACTGGTTGAAAGACCGTACTCAAAG 150 v v i ii v i i vi i ii i i Plat_L3#LINE/ 2502 CATACTACCGTTAGGTGGGTGCACAGCTGGCTCGAGGGTCGCACCCAAAG 2551 rnd-1_family- 151 AGTAGTTATCAATGGTTCGCTGTCGAACTGGGAGGGCGTATCTAGTGGGG 200 i i i v i v ii i?i v v Plat_L3#LINE/ 2552 GGTAGTCATCAATGGCTCGGTGTCAACCTGGAGGGANATATCGAGTGGTG 2601 rnd-1_family- 201 T 201 Plat_L3#LINE/ 2602 T 2602 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.48 CpG sites = 36, Kimura (unadjusted) = 31.88 Transitions / transversions = 2.57 (36/14) Gap_init rate = 0.00 (0 / 200), avg. gap size = 0.0 (0 / 0) 14 23.60 0.00 2.44 rnd-1_family-458#Unknown 1 42 (251) (TCA)n#Simple_repeat 1 41 (0) m_b5s252i0 rnd-1_family- 1 TCATCACCATCACCTTCCTCATCATCACCAGTGGCCATCATC 42 i i v v i - vii (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCA-TCATCATCATC 41 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 966 28.28 2.79 2.79 rnd-1_family-464#LTR/ERVK 346 847 (3123) HERVK14C#LTR/ERVK 2906 3407 (4027) m_b5s701i10 rnd-1_family- 346 AGCCCGTATGGGTTGCGCAGTGGCCGCTTCCTTTAGAAAAGCTGGAGGCC 395 ? ? v ? v? ?? ivi i i HERVK14C#LTR/ 2906 ANCCNGTTTGGGTNGANCAGTGGCCGCTNNCTCAGGAAAAACTGGGGGCC 2955 rnd-1_family- 396 CTCCAGCACTTGGTTAATGACCAGCTGAAGGCAGGACGTTTGGAGGAGTC 445 i v v v i i v v ii ii ?iv iiv ---? i HERVK14C#LTR/ 2956 TTACAGGAATTAGTCAAAGAACAATTAGANAAAGGACACAT---NGAGCC 3002 rnd-1_family- 446 CAC--TAGCCCCTT-TAATACCCCCGTGTTTGTGATTAAAAAGAAATCTG 492 -- vv i ? -v v ? v i ? i i i HERVK14C#LTR/ 3003 CACATTTTCTCCNTGGAATTCNCCAGTGTTTGTAATNAAGAAAAAATCCG 3052 rnd-1_family- 493 GCAAGTGGCGCCTCCTGCAGGACCTTCGCGCCATTAACAAAATTATACAG 542 ii ?v v ivvv i v v i i iiv i i ? i HERVK14C#LTR/ 3053 GCAGATGGCGNATGCTAACCGACTTACGAGCCGTCAATGCAGTCATNCAA 3102 rnd-1_family- 543 CCTATGGGTCCCCTGCAGT--GTGGTACCCCTAATCCCAACCTTATTCCC 590 ? vv ? i-- v v i ?ii--i iv v v i HERVK14C#LTR/ 3103 CCNATGGGGGCNCTGCAGCCAGGGCTGCCNTC--CCCCGCCATGATTCCT 3150 rnd-1_family- 591 TGTGATTACCGGTTATTTGTAATAGATTTAAAGGATTGTTTTTTTACCA- 639 v v i iv v? v v v i i i i i - HERVK14C#LTR/ 3151 AGAGACTGGCCNTTAATAGTTATAGATTTGAAGGACTGCTTCTTTACTAT 3200 rnd-1_family- 640 TCCCCTTGCACCCTGAGGACCGGGT-----GCACTTTGCCTTCACTGTTC 684 i v ---- -- ? i -----iv v i i i HERVK14C#LTR/ 3201 TCCTCTAGCA----GAG--CCNGATTTTGAAAAATTTGCTTTTACTATTC 3244 rnd-1_family- 685 CGGTTTTGAATCACTCCCAGCCCAC-TCCACGCTATCAGTGGAATGTGCT 733 v i v iv vvvv i ?i -v - ? v v ?i HERVK14C#LTR/ 3245 CTGCTATGAACAACAAGGAACCNGCAGCCA-GNTATCATTGGAAAGTNTT 3293 rnd-1_family- 734 CCCTCAAGGCATGTTGAATAGCCCCACCTTGTGTCAGCATTTTGTTGCGC 783 v v i i ? ?v v ivv ? v v ? HERVK14C#LTR/ 3294 GCCGCAGGGCATGTTGAATAGTCCNACNATTTGTCAAACTTNTGTGGGGN 3343 rnd-1_family- 784 AGGCCCTACGGCCCTTCCGCG--CAGCACACCCAGATGCCTTAATTTACC 831 iv v ii iv ?v v -- --ivi v ? vv ivvi HERVK14C#LTR/ 3344 AGGCTATTCAACCTGTNAGAGATCAG--TTTCCAGATTCNTATATCATTC 3391 rnd-1_family- 832 ACTACATGGATGACAT 847 i i HERVK14C#LTR/ 3392 ATTATATGGATGACAT 3407 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.64 CpG sites = 69, Kimura (unadjusted) = 38.70 Transitions / transversions = 1.00 (69/69) Gap_init rate = 0.04 (21 / 501), avg. gap size = 1.33 (28 / 21) 717 25.51 4.94 4.01 rnd-1_family-464#LTR/ERVK 2127 2571 (1399) HERVK14C#LTR/ERVK 4657 5105 (2329) m_b5s701i11 rnd-1_family- 2127 CAGGCGCAGGCCATTGTTCGCCAGTGTGACCTTTGCGCTTCTCTCTCCAA 2176 ?v ? ? iv v i-- ?? i ivvviv v HERVK14C#LTR/ 4657 CAGGCNAAGGNCATTGTNCAACATTGC--CCTNNGTGCCAGGTGCTACAA 4704 rnd-1_family- 2177 TAGCC-CG--GAGGTA--GGGGTTAACCCTCGTGGAACCTCGGCC---AA 2218 iv - i--i v -- ? ? v --- i ?--- HERVK14C#LTR/ 4705 CTGCCACATCAAGGGACTGGNGTTAACCCNCGAGGA---TTGGCNCCTAA 4751 rnd-1_family- 2219 CCAGCTCTGGCAAATGGATGTTACACATTTCCCTCCCTTTG-----CCCC 2263 i?v ? i ? v v v ? v ----- i?i HERVK14C#LTR/ 4752 TNCGCTNTGGCAAATGGACGTNACCCATGTACCTNCATTTGGGAAACTNT 4801 rnd-1_family- 2264 CTGGCAGTATCTTCACGTGTGTGTAGATACCTTTTCCCATTATGTGTGGG 2313 ?----- iv i i ?vv i v ? HERVK14C#LTR/ 4802 CN-----TACGTCCATGTNACTGTAGATACCTTTTCTCATTTTGTNTGGG 4846 rnd-1_family- 2314 TCACCCCCCAGAAGGGTGAGGCCTCTCGTCATGTTATTAATCACATGATT 2363 i? iiv i vi ? ?v vv i vv iv iv v HERVK14C#LTR/ 4847 CNACTTGCCAAACAGGNGAGGCNGCTGCTCGTGTTAAAAGACATTTGCTT 4896 rnd-1_family- 2364 CGCGCTATGGCAATCATGGGTCACCCATCCCATCTTAAGACCGACAACGG 2413 iv vv v v ?i ivvi ivvv ?v i ? i HERVK14C#LTR/ 4897 TCCTGTTTCGCNGTCATGGGCATTCCACAAAANATTAAAACNGACAATGG 4946 rnd-1_family- 2414 CCCCGCCTACTGTAGCTCGGCCTTT----GC-CTCCTTCTGTACCACGTG 2458 v v ?? - vii? ---- -i --- v -i HERVK14C#LTR/ 4947 CCCAGGCTACNNTAG-TAAANCTTTANANGCGTTCCTTC---AACA-ATG 4991 rnd-1_family- 2459 GGACATTGTCCACACGTTTGGTATCCCGTATAACCCCACAGGCCAGGCCA 2508 ? ivv ?vvi ? v ii ivv ? i HERVK14C#LTR/ 4992 GNACATTAAACACANTACTGGNATCCCCTATAATTCTCAAGGNCAAGCCA 5041 rnd-1_family- 2509 TTGTGGAACGAGCCAATCGTGCGCTCAAACAAGCCCTGGTCC----GCCA 2554 v i vi - i -- ? i viv v ----i v HERVK14C#LTR/ 5042 TTGTTGAACGAGCTAATCGAAC-CTTAA--AANCTCAATTACAAAAACAA 5088 rnd-1_family- 2555 AAAACAGAAAGGGGGGA 2571 i i i HERVK14C#LTR/ 5089 AAGACAGAAGGGGGGAA 5105 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.31 CpG sites = 51, Kimura (unadjusted) = 34.43 Transitions / transversions = 0.88 (51/58) Gap_init rate = 0.06 (26 / 444), avg. gap size = 1.54 (40 / 26) 5168 13.49 3.22 3.95 rnd-1_family-465#DNA/hAT-Tag1 1 995 (1) hAT-5_Mam#DNA/hAT-Tag1 971 1958 (1582) m_b5s502i14 rnd-1_family- 1 GATGAAAGGAACATGTCTGAACATGCAGGATCTTCAGGTTGGTAAACTTT 50 v i ? ? ii i hAT-5_Mam#DNA 971 GATGAATGGAACATGTCTGAACATGCGGNATNTCTAGGTTAGTAAACTTT 1020 rnd-1_family- 51 TTTATTTCATACTTCTTTCTTAAGGACTGCCTGTCTTC-----------C 89 i ? v i v i ? ----------- hAT-5_Mam#DNA 1021 CTTATTNCATTCTTTTTACTCAAGGACTGCCTGNCTTCTCTGTTGACATC 1070 rnd-1_family- 90 TTCTGGAC----TATT------CTTGAATTCTCAT------GTTTGAGCA 123 i ---- ?i ------ ------ ? hAT-5_Mam#DNA 1071 TTTTGGACGGANTNCTAGATTACTTGAATTCTCATAAAAATGTTTGAGNA 1120 rnd-1_family- 124 AAAAATATAGTTGTTACTCTATGGTACTATCAT--TTTAGATGCAGTTGT 171 i-i ?? i i v v? -- i??i i?i ? hAT-5_Mam#DNA 1121 AAAG-CATANNTGTTATTTTAAGGANCTATCATATTCNNAATGTNATNGT 1169 rnd-1_family- 172 GATAAAAATAAATAGCTGAAATAGGCAGATCTTCCTTTTACAATTTCACC 221 ??vi v?i ii i i i i i hAT-5_Mam#DNA 1170 GANNTGAAANGATGACTGAAATAAGCAGACCTTCCTTTTGCAGTTTCACT 1219 rnd-1_family- 222 TTTAAAGTAGTACTGAGTGTCAGTGAATGCAATGAGTAATACTAAATGAG 271 i? ? --- ? ?------- ? i? ?? ?? hAT-5_Mam#DNA 1220 TCNAAAGTAGTNCTG---GNCN-------CNATGAGCNANNCTAAATGNN 1259 rnd-1_family- 272 CAGTATGGTAATAATAATTAAATAACTGCATTGACTTATTTTGTTTAGGA 321 ???? iii ----------- ? i ?v i hAT-5_Mam#DNA 1260 CAGTNNNNTAGCGA-----------CTNCATTAACTNCTTTTGTTCAGGA 1298 rnd-1_family- 322 GAATCCATCCTCAACATACAGGATTCTGAAGACTATCCACCTTCAAGATC 371 i ? ? v --- i i i i--- hAT-5_Mam#DNA 1299 GGATCNANCCTGAACATACAGGATTCTGA---CTGTTCATCTTCAG---C 1342 rnd-1_family- 372 ACCATCATTTTCTATAGTTTCAGAGTTATCTGCCAATGATA---GTGTTT 418 ii i v i i ? ii ?? i i --- i hAT-5_Mam#DNA 1343 ATTATCACTGTCCACAGTNTCGAANNTATCTGCTAACGATACNAGTGTTC 1392 rnd-1_family- 419 CAGTCACATCATGTATGTCACATAGCCACAGTATATCACCTGTAGCAAAA 468 v i ?v --- i vi i v------ i ? vi ???i? hAT-5_Mam#DNA 1393 GAATCNAAT---GCAAATCGCATAT------TATACCNCCTGGGGNNNGN 1433 rnd-1_family- 469 AGAAAAAAAAAAATCTCCATCATCCAGAAACAACCATAGATAAGTTTGTG 518 v ii vvi -- i i v ii hAT-5_Mam#DNA 1434 TGGGATTGAAA--TCTCCGTTATCCAGAAACTACCATAGATAAGTTTGCA 1481 rnd-1_family- 519 ATAAGAACCAGCAGATTACAAAAAGAGGTAATTGATGAAAAAATTGCCCG 568 i ? ivi ? i hAT-5_Mam#DNA 1482 ATAAGAGCCAGCAGATTNCAGCGAGNGGTAATTGATGAAAAAATTGCTCG 1531 rnd-1_family- 569 GTTTGTTTATGCAACAAACTCTCCTTTCCGTATGATTGAGAACCCACACT 618 i v i hAT-5_Mam#DNA 1532 GTTTGTTTATGCAACAAACTCTCCTTTCCGTATGGTTGAGAACACACGCT 1581 rnd-1_family- 619 TCATTAACATGGTTCAGTCATTAAGACCAGGATACAGTCCACCCAACAGA 668 i i i iv i i hAT-5_Mam#DNA 1582 TCACTGACGTGGTTCAGTCATTGCGATCAGGATACAGTCCACCCGACAGA 1631 rnd-1_family- 669 GCAGACGTCGCAGGCAAATTGCTGGATAAAGTGTATGAAAGAGAAATTGA 718 ii v ? v i?i ? hAT-5_Mam#DNA 1632 GCAGATATAGCAGGCAAATTGCTGGANAAAGTGTAAGAGNAAGAAATTNA 1681 rnd-1_family- 719 GCAGTGTGCAAAAGGTCTAGAGGGTAAAATTGTTAACCTGAGTCTTGATG 768 i i v ? ? ? i v v v ?? i hAT-5_Mam#DNA 1682 ACGGGGTNCANAANGCCTAGAGGGAAAAATTGTGAACCTGAGGCNNGATA 1731 rnd-1_family- 769 GGTGGAGCAATGTCCACAATGATCCTGTTGTATGTGCTTGTGTGACAACA 818 ? i i i vi vi ? hAT-5_Mam#DNA 1732 GGTGGAGCAATGNCCGCAGTGGTCCAATAATATGNGCTTGTGTGACAACA 1781 rnd-1_family- 819 GAAGAAGGGAATGTCTTCCTTACAGAAACAATTGATACATCAGGAAATGC 868 ? ?v ? ? ? i hAT-5_Mam#DNA 1782 GAANAAGGGNCTNTCTNCCTTNCAGAAACAATCGATACATCAGGAAATGC 1831 rnd-1_family- 869 ACACACAGCAGAATACTTACAAGAAGTAGCAGTAAAAGCTATAACAAACT 918 i ? i ? i i hAT-5_Mam#DNA 1832 ACGCANAGCAGAATATTTNCAAGAAATAGCAGTAAAAGCTGTAACAAACT 1881 rnd-1_family- 919 GTGAAAAAAAATTCAAATGTCTAGTACGCAGCTTGGTCACAGACAATGCT 968 i i ? v i hAT-5_Mam#DNA 1882 GCGAAAAAAAATTCAGATGTCTANTACGCAGCTTCGTCACAGACAACGCT 1931 rnd-1_family- 969 GCAAATGTATCCAAGATGAGAAGAAAT 995 v i ? hAT-5_Mam#DNA 1932 GCAAATGTATCAAAGGTNAGAAGAAAT 1958 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.20 CpG sites = 96, Kimura (unadjusted) = 16.46 Transitions / transversions = 2.91 (96/33) Gap_init rate = 0.05 (45 / 994), avg. gap size = 1.58 (71 / 45) 326 15.87 0.00 1.59 rnd-1_family-466#DNA/hAT-Charlie 6 69 (0) MER112#DNA/hAT-Charlie 1 63 (198) m_b5s502i15 rnd-1_family- 6 CAGTGGTTTTCAAACTGCGGGTCGCGACCCAGTACTGGGTCGCGGAATGT 55 v v v i i -i MER112#DNA/hA 1 CAGTGTTTTTCAAACTGCGGGTCGCGACCCATTAGTGGGTCGTGAAAT-C 49 rnd-1_family- 56 AAGGCACTGGGTCG 69 vvi v MER112#DNA/hA 50 AATTTAGTGGGTCG 63 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.85 CpG sites = 4, Kimura (unadjusted) = 17.85 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 357 8.33 0.00 0.00 rnd-1_family-456#SINE/MIR 1 60 (0) MIR1_Amn#SINE/MIR 15 74 (156) m_b6s601i0 rnd-1_family- 1 GGTCCAGTGGNTAGGGCACTGGGCTGGGAGTCAGGAGACCTGGGTTCTAG 50 i ? i i v i ? ? MIR1_Amn#SINE 15 GGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNAN 64 rnd-1_family- 51 TCCCGGCTCT 60 MIR1_Amn#SINE 65 TCCCGGCTCT 74 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 7.64 CpG sites = 4, Kimura (unadjusted) = 9.49 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 1408 2.47 0.00 1.23 rnd-1_family-468#LINE/CR1 1 164 (0) CR1-L3A_Croc#LINE/CR1 1625 1786 (2502) m_b6s551i0 rnd-1_family- 1 CTCTATGTCAAAAATGGCGCATTACCTGTTTCCGAGTCACTGATAACTCG 50 -- i CR1-L3A_Croc# 1625 CTCTATGTCAAAAATGGC--ATTACCTGTTTCCGAGTCACTGACAACTCG 1672 rnd-1_family- 51 GAAGAAAATGATCTTGAATGCTTATGGATCAATGTCCTAACAGATAAAGC 100 v i CR1-L3A_Croc# 1673 GAAGCAAATGATCTTGAATGCTTATGGATCAATGTTCTAACAGATAAAGC 1722 rnd-1_family- 101 ACAAGATGGGGTACTAGTTGGTGTCTGCTACAGACCACCAAATCACACTA 150 CR1-L3A_Croc# 1723 ACAAGATGGGGTACTAGTTGGTGTCTGCTACAGACCACCAAATCACACTA 1772 rnd-1_family- 151 GGGAACAGGATGAC 164 i CR1-L3A_Croc# 1773 GAGAACAGGATGAC 1786 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.52 CpG sites = 3, Kimura (unadjusted) = 2.52 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.01 (2 / 163), avg. gap size = 1.00 (2 / 2) 1414 3.11 0.00 0.00 rnd-1_family-471#LINE/CR1 1 161 (0) CR1-L3A_Croc#LINE/CR1 1658 1818 (2470) m_b6s551i1 rnd-1_family- 1 GTCACTGATAACTCGGAAGAAAATGATCTTGAATGCTTATGGATCAATGT 50 i v CR1-L3A_Croc# 1658 GTCACTGACAACTCGGAAGCAAATGATCTTGAATGCTTATGGATCAATGT 1707 rnd-1_family- 51 CCTAACAGATAAAGCACAAGATGGGGTATTAGTTGGTGTCTGCTACAGAC 100 i i CR1-L3A_Croc# 1708 TCTAACAGATAAAGCACAAGATGGGGTACTAGTTGGTGTCTGCTACAGAC 1757 rnd-1_family- 101 CACCAAATCACACTAGGGAACAGGATGACCGGCTCCTTANGCACCTATCT 150 i ? CR1-L3A_Croc# 1758 CACCAAATCACACTAGAGAACAGGATGACCGGCTCCTTAAGCACCTATCT 1807 rnd-1_family- 151 ATAATGTGTAG 161 CR1-L3A_Croc# 1808 ATAATGTGTAG 1818 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.21 CpG sites = 4, Kimura (unadjusted) = 3.21 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 160), avg. gap size = 0.0 (0 / 0) 830 24.26 0.00 0.00 rnd-1_family-472#LINE/CR1 2 170 (10) CR1-3_Croc#LINE/CR1 2841 3009 (596) m_b6s551i2 rnd-1_family- 2 TTCAAACTACAGCANAGCAGATTTAGATTAAATCTCAGGAAAAACTTCCT 51 v ii i ? i i ii v v i CR1-3_Croc#LI 2841 TTGAAGTTGCAGCAAAGTAGGTTTAGATTGGATATCCGGAAAAACTTCTT 2890 rnd-1_family- 52 AACTGTAAGAACAGTAGGACGATGGAACAGGCTGCCTAGGGAGGTCGTGG 101 v v ii i ii i i i i CR1-3_Croc#LI 2891 CACTGTTAGAACAGTGAGGCAGTGGAATAGACTGCCTAGGGAAGTTGTGG 2940 rnd-1_family- 102 AAGCTCCTTCACTGGAGGTTTTCAAAAGGAGGCTGGATAGCCATCTGTCT 151 vv v v i i i i iiv v CR1-3_Croc#LI 2941 ACTCTCCATCACTGGAGGTGTTCAAGAAGAGGTTGGACAGCCACTGGTCG 2990 rnd-1_family- 152 TGGATGGTTTAGACACAAC 170 v i i i ii i CR1-3_Croc#LI 2991 GGGATGATCTAGGCGTAGC 3009 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.89 CpG sites = 29, Kimura (unadjusted) = 30.80 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.00 (0 / 168), avg. gap size = 0.0 (0 / 0) 613 0.00 1.45 0.00 rnd-1_family-473#LINE/L2 1 69 (0) L2-1_AMi#LINE/L2 447 516 (719) m_b6s551i3 rnd-1_family- 1 TGTCTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTCAAGCTCAA 50 L2-1_AMi#LINE 447 TGTCTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTCAAGCTCAA 496 rnd-1_family- 51 CATGG-CTAAAACAGAGCTC 69 - L2-1_AMi#LINE 497 CATGGCCTAAAACAGAGCTC 516 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.00 CpG sites = 0, Kimura (unadjusted) = 0.00 Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 255 24.24 0.00 0.00 rnd-1_family-476#LINE/CR1 95 160 (1110) CR1-L3A_Croc#LINE/CR1 293 358 (3930) m_b6s551i4 rnd-1_family- 95 AAAGAGCTTCGTNTGTATGAAGTGCCGCCTGATAGAGCTGATGGAAGAAA 144 i ii v ? vivi i i vvv v CR1-L3A_Croc# 293 AAGGGACTTCCTGTGTATGAAGTGCAAGTTGGTGGCTGTGCTGGAAGAAA 342 rnd-1_family- 145 AGATCCGAGGNTTGGA 160 i v ? CR1-L3A_Croc# 343 AGATTCGTGGTTTGGA 358 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 8, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 797 30.52 4.26 3.63 rnd-1_family-476#LINE/CR1 654 1146 (124) CR1-L3A_Croc#LINE/CR1 817 1312 (2976) m_b6s551i5 rnd-1_family- 654 TTGGGGACTCCTTACTGAGAAGAACGGACAGGCC-TGTNACCAGAG-CTG 701 i i iv i i v iv - vi?i v i - v CR1-L3A_Croc# 817 TCGGGGATTCTATACTAAGAAGAATGGAAAGAACGTTCTGCAAGGGACAG 866 rnd-1_family- 702 ATCCGGAGAACAGAAGGGTGTGCTGTCTGCCGGGNGCTAAGATACGGGAT 751 i-- v i v v v ? i i i CR1-L3A_Croc# 867 G--CGGACAACAGGACGGTGTGCTGTCTTCCCGGAGCCAAGACACGAGAT 914 rnd-1_family- 752 GTGGACCTGAGGCTGAAGAGGATCCTAACGGGAGCGGGAAAGAATCCACT 801 i ivi i i i v v i i v vvi v i CR1-L3A_Croc# 915 GCGACTCTAAGACTGGATAGGCTTCTGAAGTCGGCGGGCAAGGATCCACT 964 rnd-1_family- 802 GATTGTCCTTCATGTGGGAACGAATGATACGGCTAGATTCTCGCTGGA-- 849 i vi vv v i v v v i v ------ v? -- CR1-L3A_Croc# 965 GGTGATGGTGCATATCGGCACTAATGACACTGCT------TCGCGNGATA 1008 rnd-1_family- 850 ----ACGNATCAAGGGAGACTATGCCAGG---CTGGGGAAGACGCTTAAG 892 ---- i? i vi iv ---i --- v i i ii v CR1-L3A_Croc# 1009 CCTCACAGATTATAGACGACT---TCAGGGAACTCGGAAGGGTGCTGAAG 1055 rnd-1_family- 893 GAAATGGAGGCTCAGGTGATCTTCAGTGGGATTCTGCCTGTTC--CTAGA 940 i v i v ii i vvv i i v i -- v v CR1-L3A_Croc# 1056 GAGAAGAATGTCCAAGTGATCTTCTCGGAGATCCTTCCTGTCCCACGAGC 1105 rnd-1_family- 941 GAAGGGCAGCA-AAGGCGTGACAAGATTATGACGATCAACAGATGGCTCA 989 ivii - --- v v ivii v v v vi CR1-L3A_Croc# 1106 GAAGGAAGACAGAAGGC---AGAAGATTCTGGAAGTGAACCGCTGGCTAG 1152 rnd-1_family- 990 GGCAGTGGTGCTATAAG---GAGGGCTTTGGGATGTATGG-CCACTGGGA 1035 vv --- --- i v- v i -v vv CR1-L3A_Croc# 1153 GTAAGTGGTG---TAAGGTAGAGGGTTTTGGT-TTTGTGGAACACTGGTC 1198 rnd-1_family- 1036 GGCATTC---GTGGACAGAGGACTGTTCTCNCGGGATGGACTTCACCTGA 1082 vi v --- v v ii i v vv?iv v i i v CR1-L3A_Croc# 1199 CACCTTCTATGGGGAGAAGGGGCTGTACAGTTTGGATGGCCTCCATCTCA 1248 rnd-1_family- 1083 GTAGGGAGGGAAATAGACTTCTGGGATGGAGGCTGGCACAACTGATTAAA 1132 iii vi v i iviv vvi ii i ii CR1-L3A_Croc# 1249 GTAGAAGGGGAACCAGTCTTCTAGGGGACAGGCTGGCTAGACTAGTCAGG 1298 rnd-1_family- 1133 AGAGCTTTAAACTA 1146 i v CR1-L3A_Croc# 1299 AGGGCGTTAAACTA 1312 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 75, Kimura (unadjusted) = 40.40 Transitions / transversions = 1.07 (75/70) Gap_init rate = 0.06 (28 / 492), avg. gap size = 1.39 (39 / 28) 18 16.33 2.27 2.27 rnd-1_family-478#DNA/PIF-Harbinger 278 321 (84) (GGA)n#Simple_repeat 1 44 (0) m_b6s252i16 rnd-1_family- 278 GGGGGGGAAGGAGGAGGAGGAGGAGGAGGA-AAGCGGGAGCGAGG 321 i i i -i vi - (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGG 44 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 888 30.18 0.00 0.00 rnd-1_family-480#LINE/CR1 2 276 (0) Plat_L3#LINE/CR1 1857 2131 (1442) m_b6s551i6 rnd-1_family- 2 ATAACTGATGACATCAAGAAGGCTGAGGTGTTTAATGCCTATTTTGCTTC 51 v vvii i v iv ?vvii v ii Plat_L3#LINE/ 1857 ATAACAGATGACTGTGAAAAGGCGGAGGCTTTTANATTTTTTTTCACTTC 1906 rnd-1_family- 52 AGTCTTCACTAAAAAGGTTAATGGTGACCAGATACTCAACACAATTAATA 101 v i v i i vv v v ivi ivi v vvi Plat_L3#LINE/ 1907 TGTCTTTACGAAAAAGATCAAATGTGAACAGCTGACCAGGGCAAGTCCCA 1956 rnd-1_family- 102 TTAACAACAAGGGGGAAGGAACGCAAGCCAAAATAGGGAAAGAACAGGTT 151 i vi?i iiiii vvi i vv i i i vvi Plat_L3#LINE/ 1957 CTTGNGATGGAAGGTTGGAAAGCCAAACTAGAATAGGGAAAGAAACAGTT 2006 rnd-1_family- 152 AAAGAATATTTAGATAAGTTAGATGTATTCAAGTCAGCAGGGCCTGATGA 201 i i ?i v iiii i i Plat_L3#LINE/ 2007 AAAGAGTATCTNAAAAAACCGGATGTATTTAAATCAGCAGGGCCTGATGA 2056 rnd-1_family- 202 AATTCATCCTAGGGTACTTAAGGAACTAGCTGAAGCAATCTCGGAACCGT 251 v v i i v v iv iv i i ii Plat_L3#LINE/ 2057 CATGCATCCTAGGGTACTTAAGGAATTGGCGGATGTTATTGCAGAGCCAC 2106 rnd-1_family- 252 TAGCAATTATCTTTGAGAACTCNTG 276 v i ?i Plat_L3#LINE/ 2107 TAGCTATTATTTTTGAGAACTCGCG 2131 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 49, Kimura (unadjusted) = 40.61 Transitions / transversions = 1.44 (49/34) Gap_init rate = 0.00 (0 / 274), avg. gap size = 0.0 (0 / 0) 17 8.91 0.00 0.00 rnd-1_family-481#Unknown 476 499 (69) (G)n#Simple_repeat 1 24 (0) m_b6s252i15 rnd-1_family- 476 GGCGGGGGGGGGTGGGGGGGGGGG 499 v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 18.80 8.82 1.37 rnd-1_family-482#LTR/ERVL 1327 1394 (241) (TTATTG)n#Simple_repeat 1 73 (0) m_b6s252i14 rnd-1_family- 1327 TTATTGCTA-TGGGAATGTTATTG--CTTG-TATTGTTATTAGTTA-GCT 1371 i - vv v --v - - -vv (TTATTG)n#Sim 1 TTATTGTTATTGTTATTGTTATTGTTATTGTTATTGTTATT-GTTATTGT 49 rnd-1_family- 1372 TAGGATTA-TGTTATTGTTGTTGT 1394 vvi - i (TTATTG)n#Sim 50 TATTGTTATTGTTATTGTTATTGT 73 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.09 (6 / 67), avg. gap size = 1.17 (7 / 6) 388 29.07 3.65 6.93 rnd-1_family-502#LINE/RTE-BovB 1 521 (4) MamRTE2#LINE/RTE-BovB 1035 1539 (13) m_b6s551i7 rnd-1_family- 1 GCACTAACGTCAGTGTCCTCGCAGAGGCCAACATCATCAGCGTCGAGGCN 50 i v ii v iv v i iii iv ii ? MamRTE2#LINE/ 1035 GCACTAATGTGAGCATCCTCTCGCAGGCGAGCGCTACAAGTATCGAGGCA 1084 rnd-1_family- 51 CTGATCATCCAGCACCAGCTGAGGCTGAGC-GGGCACTGTG-TGCGNATG 98 v ii v i v-v ii - i - - vv ? MamRTE2#LINE/ 1085 ATGATTGTCAAACACCAGCTT-CGCTGGACTGGACAC-GTGATCAGAATG 1132 rnd-1_family- 99 CCTGACGCNCGCCTCCCAAAACAAGTNCTGTNCTCTCAGCTCACCGAAGG 148 i iv ?v v i ? ? i ii v v v MamRTE2#LINE/ 1133 TCTGATTCCAGGCTCCCAAAGCAAGTGCTGTACTCCCAATTAAGCCAAGG 1182 rnd-1_family- 149 AGAAAGGAC-NCGCGGAGGNCAGAAGAAACGCTNCAAAGACACNCTGAAG 197 - i v v -?v v ? ii i ?i iii? v MamRTE2#LINE/ 1183 -GAGACGCCTAAGAGGAGGGCAGAGAAAACGTTTTAAAGATGTCCTCAAG 1231 rnd-1_family- 198 GTAAACNTCAAGAGATGTGGCATCGACACCACACACTGGGAGACAGCAGC 247 viv i? i? i i iiiv vi i vi ivi vvii MamRTE2#LINE/ 1232 TCTAATTTTNAAAAATGCAAAATAAATACAGCATCTTGGGAGACCTTGGC 1281 rnd-1_family- 248 CCAGGACAGGNNNAAATGG-GCAGGAAGACTTGTCAGNGAGGGANCGCCC 296 v iviv??? vi - v v ? ---- v v?v i ?i- v MamRTE2#LINE/ 1282 CAAGGATCACTCCACGTGGAGGAGTAANA----TAACACAAGGAGT-CCA 1326 rnd-1_family- 297 GCATTTTGAGGAAAATCGCCTCGCCACNGGTCGANAGAAAAACGNCAGAG 346 ? i------- i- i ?- - ? ii i ?----? MamRTE2#LINE/ 1327 GCNTTTTGAA-------GCCTCA-CGCT-GTC-AGAGGGAGACGG----N 1362 rnd-1_family- 347 GAGGAAGGAAAGGCAAACTGTCNCNCAGC-AATCGCG-GCCCAACCCCTG 394 ii ii v ii ------v? - i v -i i v -i MamRTE2#LINE/ 1363 GAAAAGAGAACGGCGGA------AGCAGCGAATTGAGAACCCGAACCC-A 1405 rnd-1_family- 395 TCTTCCGACACCACCT-GCAACGTCTGC--------CAATGAGCC-TGTG 434 i ----? ? v - v i -------- iii i - iv MamRTE2#LINE/ 1406 CCTTCC----NCNCGTGGAAATGTCTGCCCAAGTTGCAGCAAACCTTGCC 1451 rnd-1_family- 435 GNTCAAGGATCGGACTCCTCAGTCACCTAAGGACCCATAAAAATAAAACC 484 ? vv v iv i ? i? i ? -- ivv v MamRTE2#LINE/ 1452 GGTCTCGGATCGGCCTTATTAGTCACNTGNGAACNCAT--AAATAGCCCA 1499 rnd-1_family- 485 CGT-GAAAG--AGATCATCCTCGACNTCGAGGGATCGCCG 521 i - -- i i v ?v i i i MamRTE2#LINE/ 1500 CATGGAAAGAAAAATCATTCTCGTCCGCGAGAGATTGCTG 1539 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 85, Kimura (unadjusted) = 41.27 Transitions / transversions = 1.52 (85/56) Gap_init rate = 0.09 (46 / 520), avg. gap size = 1.17 (54 / 46) 227 33.54 1.83 1.83 rnd-1_family-506#DNA/hAT-Tip100 856 1019 (73) Zaphod2#DNA/hAT-Tip100 1194 1357 (2235) m_b6s502i0 rnd-1_family- 856 CCACAGCAAGTGAAAAACTTCATGTTCCCCAAAGACAATGAAAATAG-AA 904 vv i i i i vv i v i iv ii - Zaphod2#DNA/h 1194 CCACCTCAAGTAAGAAATTTTAACTTTCCAAAAGACAGTACAGGTAGGAA 1243 rnd-1_family- 905 GTTTCCATCCAACACATTACTGGCGTGAAATC--CCCAATGGTGACAAAG 952 i ivv- vi ?--i ii v -- v v i Zaphod2#DNA/h 1244 GTTTTCGGA-AACTTATTAN--ACACGAATTCTTCCAAATGGTGAAAAAA 1290 rnd-1_family- 953 TGGAGAGGCCATGGCTTATGTACTCAAAAACCCAGAATGCTGCATACTGT 1002 vivv ii v i vv v i v vvv vv i v i vi Zaphod2#DNA/h 1291 TCACTAGATCCTGGTTACTTTATTCTACCTCAAAGGATTCTGTATTTTGT 1340 rnd-1_family- 1003 TTTTGTTGCAAACTCTT 1019 i v i Zaphod2#DNA/h 1341 CTATATTGCAAACTCTT 1357 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.23 CpG sites = 26, Kimura (unadjusted) = 45.43 Transitions / transversions = 0.93 (26/28) Gap_init rate = 0.03 (5 / 163), avg. gap size = 1.20 (6 / 5) 3766 8.94 0.00 0.00 rnd-1_family-512#DNA/hAT-Tag1 1 492 (0) hAT-5_Mam#DNA/hAT-Tag1 1971 2462 (1078) m_b6s502i1 rnd-1_family- 1 GAAGAGAGTCCCAAGCTAATAACATACGGTTGCAGTGCTCATTTGATGCA 50 i i i i i hAT-5_Mam#DNA 1971 GAAGAAAGCCCCAAGCTAATAACATATGGCTGCAGCGCTCATTTGATGCA 2020 rnd-1_family- 51 CCTCCTAGCCAAAGACTTCAGTGTTCCAGAAATAAAGGCTAATGTTGTTG 100 i i i i? hAT-5_Mam#DNA 2021 CCTCTTAGCCAAAGACTTCGGTGCTCCAGAAATAAAGGCTAATGTTGCNG 2070 rnd-1_family- 101 AAATTGCAAAATACTTCCGTAACAACCACTTTGCAGCAGCTGCTCTGAAA 150 i ? i i hAT-5_Mam#DNA 2071 AAATTGCAAAATACTTCCATAACAACCANTTTGCAGCAGCTGCTCCGAAG 2120 rnd-1_family- 151 AAAGCGGGAGGAACCAAGCTAACTCTCCCACAAGACGTGCGATGGAACTC 200 i i hAT-5_Mam#DNA 2121 AAAGCAGGAGGAACCAAACTAACTCTCCCACAAGACGTGCGATGGAACTC 2170 rnd-1_family- 201 AGTAGTGGACTGTTTTGAGCACTATATCAAGAACTGGCCTAATCTGATGA 250 i i ? iiv ii i hAT-5_Mam#DNA 2171 AGTAGCGGATTGTTTTGNGTGATATATTGAGAACTGGCCTAATCTGACGA 2220 rnd-1_family- 251 CAGTTTGTGAACAAAATCGTGAAAAAATAGATGGCACTGTCACAGCCAAA 300 i v v hAT-5_Mam#DNA 2221 CAATTTGTGAACAAAATCGTGACAAAATAGATGGAACTGTCACAGCCAAA 2270 rnd-1_family- 301 GTTCTCAACATTGGGCTTAAGAGAAATGTTGAACACATGCTGAGTACCCT 350 i? ? v v iii v i i hAT-5_Mam#DNA 2271 GTTTNCAANATTGGGCTAAAGAGAAATGTAGAACGTGTGCTGACTATCCC 2320 rnd-1_family- 351 GAAGCCTATTTCCGTAGCCTTGAACAAAATGCAGGGAAATAGCTGTTTTA 400 i v i hAT-5_Mam#DNA 2321 GAAGCCTATTTCCGTAGCCTTGAACAAAGTGCAGGGAAATCGCCGTTTTA 2370 rnd-1_family- 401 TTGCTGACGCTGTTGAAATTTGGAAGGAACTGAGTGAGATCTTAAAAAGA 450 i ? i i hAT-5_Mam#DNA 2371 TTGCTGATGCTGTTGAAATTTGGAAGGNACTGAGTGAGACCTTGAAAAGA 2420 rnd-1_family- 451 GAAATATGCAACGACAGAGTTAAATTACAAGCATTAAAAAAA 492 i ? i ? ii hAT-5_Mam#DNA 2421 GAAATGTNCAATGACAGAGTNAAATTACGGGCATTAAAAAAA 2462 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.92 CpG sites = 37, Kimura (unadjusted) = 9.89 Transitions / transversions = 5.29 (37/7) Gap_init rate = 0.00 (0 / 491), avg. gap size = 0.0 (0 / 0) 607 24.62 0.00 0.00 rnd-1_family-513#LINE/CR1 2 131 (0) Plat_L3#LINE/CR1 3243 3372 (201) m_b6s551i8 rnd-1_family- 2 GTCTTCAAATACGTTAAGGGCTGTTATAAAGAGGACGGTGATCAATTGTT 51 i ii v i v iii v i i Plat_L3#LINE/ 3243 GTCTTCAAGTATATGAAGGGTTTTTATGGGGAGGACGCTGACCAGTTGTT 3292 rnd-1_family- 52 CTCCATGTCCACTGAAGGTAGGACAAGAAGTAATGGGCTTAATCTGCAGC 101 ? i iiv i i v vi iv Plat_L3#LINE/ 3293 CTCCATGTCCACNGAGGACCGAACAAGAGGAAATGGGCTTAAATTAAAGC 3342 rnd-1_family- 102 GAGGGAGATTTAGGTTAGATGTTAGGAAAA 131 ii i v i ii v i Plat_L3#LINE/ 3343 AGGAGAGATTTCGGTTGGACATAAGGAAGA 3372 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.54 CpG sites = 23, Kimura (unadjusted) = 31.54 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.00 (0 / 129), avg. gap size = 0.0 (0 / 0) 592 29.79 4.42 3.56 rnd-1_family-519#LINE/CR1 3 364 (726) CR1-L3A_Croc#LINE/CR1 948 1312 (2976) m_b6s551i9 rnd-1_family- 3 GCGGGAAAGAATCCACTGATTGTCCTTCATGTGGGAACAAATGATACNGC 52 v i i vi vv v i v v v i ? CR1-L3A_Croc# 948 GCGGGCAAGGATCCACTGGTGATGGTGCATATCGGCACTAATGACACTGC 997 rnd-1_family- 53 TAGATTCTCGCTGGAACGCATCAAGGG----AGACTATGCCAGG---CTG 95 ------ - ?i ii v vi i---- v ivi --- v CR1-L3A_Croc# 998 T------TCGC-GNGATACCTCACAGATTATAGACGACTTCAGGGAACTC 1040 rnd-1_family- 96 GGGAAGACGCTTAAGGAAATGGAGGCTCAGGTGATCTTCAGTGGGATTCT 145 i i ii v i v i v ii i vvv i i CR1-L3A_Croc# 1041 GGAAGGGTGCTGAAGGAGAAGAATGTCCAAGTGATCTTCTCGGAGATCCT 1090 rnd-1_family- 146 GCCTGTCCC--TAGAGANGAGCGAC-GAAGGCGAGACAAGATTATGATGA 192 v --v v ? iiv - - -- v ivii CR1-L3A_Croc# 1091 TCCTGTCCCACGAGCGAAGGAAGACAGAAGGC-AGA--AGATTCTGGAAG 1137 rnd-1_family- 193 TCAACAGATGGCTCAGGCAGTGGTGCTATAAGG---AGGGCTTTGGGATG 239 v v v vi vv --- --- i vv v CR1-L3A_Croc# 1138 TGAACCGCTGGCTAGGTAAGTGGTG---TAAGGTAGAGGGTTTTGGTTTT 1184 rnd-1_family- 240 TTTGACCACTGGGAGGCATTC-ATGGACAGA--GGACTGTTCTCATGGGA 286 v v v vvvi v - iv -- i v vvv v CR1-L3A_Croc# 1185 GTGGAACACTGGTCCACCTTCTATGGGGAGAAGGGGCTGTACAGTTTGGA 1234 rnd-1_family- 287 TGGACTCCACCTGAGTAGGGAGGGAAATAGACTTCTGGGATGGAGGCTGG 336 v i v iii vi v i iviv CR1-L3A_Croc# 1235 TGGCCTCCATCTCAGTAGAAGGGGAACCAGTCTTCTAGGGGACAGGCTGG 1284 rnd-1_family- 337 CACAACTGATTAAAAGAGCTTTAAACTA 364 vvi ii i ii i v CR1-L3A_Croc# 1285 CTAGACTAGTCAGGAGGGCGTTAAACTA 1312 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.71 CpG sites = 48, Kimura (unadjusted) = 38.71 Transitions / transversions = 0.86 (48/56) Gap_init rate = 0.06 (20 / 361), avg. gap size = 1.45 (29 / 20) 601 28.85 3.80 6.18 rnd-1_family-519#LINE/CR1 587 1033 (57) Plat_L3#LINE/CR1 723 1159 (2414) m_b6s551i10 rnd-1_family- 587 TTAAGATGCTTGTACACCAATGCNAGGAGCCTGGGTAACAAAATGGAGGA 636 i i i i v ? v v i vv Plat_L3#LINE/ 723 TTGAAATGTTTGTACGCAAATGCAAGGAGCATGGGAAATAAACAGGAGGA 772 rnd-1_family- 637 ACTAGAGTTACTGGTGCAGGA----AGTGAAACCAGATATNATAGGNATA 682 i v vi i iv ---- v v---- i ? iv ? Plat_L3#LINE/ 773 ACTGGAGGTCTTAGCTCAGGACCACAGTTAT----GATGTAACTGGAATA 818 rnd-1_family- 683 ACAGAAACATGGTGGAATAGTAGTCATGACTGGAGTACAGGTATTGAAGG 732 v i i i i i v i v vv v Plat_L3#LINE/ 819 ACTGAGACGTGGTGGGACAGCACTCATGACTGGAGTGCTGGACTAGAAGG 868 rnd-1_family- 733 GTACGTGCTGTTTAGGAAGGA----CAGAGAATAAAGGTAAAGGTGGTGG 778 ivv i i i ---- i v --i -- Plat_L3#LINE/ 869 GTATCGGTTGTTCAGGAAAGATAGGCAGGGAAAAAAGG--GAGGTGGT-- 914 rnd-1_family- 779 AGTGGCACTGTATATCAAAGANAAGGTAGAC-TGTAAAGAAG--TAAGAA 825 - v vi i i ?- ?v v - ivv i --i i Plat_L3#LINE/ 915 -GTTGCCTTGTACATCAAGGAT-ANCTACACATGCTCAGAGGCCCAGGAA 962 rnd-1_family- 826 GT-GATGGAATGGATA--AGACAGAGTCTGTCTGGGTAAAAATCNCATTG 872 ii- v -- vi -- ii vv v iiv?v -- Plat_L3#LINE/ 963 ACAGAAGGA--GGCCAACAGGTAGAGAGTGTCTGGGTTAAAGCGAAA--G 1008 rnd-1_family- 873 GGGAAGAAAGCTACNAGAGGCTCCCCTGGGATAGTGCTTGGGGTGTGCTA 922 v i i --- i? - ------ ivi vi v v i v ii Plat_L3#LINE/ 1009 GTGAAAAGA---ATAAG-GGC------GACGTCATGGTAGGAGTCTATTA 1048 rnd-1_family- 923 CAGACCNCCGGGATCC--GATTTGGATATGGATAGAGACC-TCTTTAATG 969 i ? --i v -- vvv i vi - i - ii v Plat_L3#LINE/ 1049 TAGACCTCC--AAACCAGGAAGAGAAGGTGGAT-GAGGCCTTCTTTGGTC 1095 rnd-1_family- 970 TTTTTAATGAAGTAAANACTANTGGGAATTGTGTGATCATGGGAGACTTT 1019 vvi i vii iiiv?v vi? vi i ivv i v Plat_L3#LINE/ 1096 AACTCACCAAAGCGGCTTCGGGTCAGGATCTGGTGGTGATGGGAGACTTT 1145 rnd-1_family- 1020 AACTTCCCAGATAT 1033 v Plat_L3#LINE/ 1146 AACTACCCAGATAT 1159 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 65, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.16 (65/56) Gap_init rate = 0.08 (35 / 446), avg. gap size = 1.26 (44 / 35) 19 0.00 0.00 0.00 rnd-1_family-521#Unknown 1 21 (240) (AC)n#Simple_repeat 1 21 (0) m_b6s252i13 rnd-1_family- 1 ACACACACACACACACACACA 21 (AC)n#Simple_ 1 ACACACACACACACACACACA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 461 16.66 6.02 0.71 rnd-1_family-529#SINE/MIR 4 136 (6) MIR1_Amn#SINE/MIR 28 167 (63) m_b6s601i1 rnd-1_family- 4 GGGCACTGGCCTGNGACTCGGGAGATCTGGGTTCGATTCCCNNCNC-GCC 52 i v ? i ? ? ?? ? - MIR1_Amn#SINE 28 GAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCC 77 rnd-1_family- 53 ATCT------CGTGTGACCNTGGGCAAGCCATTGGCTGTCTCTGCGCCTC 96 ii?------i ? ? i i v?viv ? MIR1_Amn#SINE 78 ACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTC 127 rnd-1_family- 97 AG-TCCCCCATCTGCACAGGTGGGGATAATAGCCCTGCCCT 136 - i i i - ii iiiv v MIR1_Amn#SINE 128 AGTTTCCTCATCTGTA-AAATGGGGATAATGATACTGACCT 167 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.46 CpG sites = 16, Kimura (unadjusted) = 21.46 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.03 (4 / 132), avg. gap size = 2.25 (9 / 4) 249 16.33 0.00 2.04 rnd-1_family-550#DNA/hAT-Blackjack 1 50 (139) MER94#DNA/hAT-Blackjack 1 49 (85) m_b6s502i2 rnd-1_family- 1 TAGGGTGACCAGACGTCCCGTTTTTAAAGGGACAGTCCCGTATTTAAGCC 50 v v vvvv -i v MER94#DNA/hAT 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCCG-GTTTACGCC 49 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.56 CpG sites = 1, Kimura (unadjusted) = 18.56 Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 247 21.22 1.49 1.49 rnd-1_family-550#DNA/hAT-Blackjack 1 67 (122) BLACKJACK#DNA/hAT-Blackjack 1 67 (2902) m_b6s502i3 rnd-1_family- 1 TAGGGTGACCAGACGTCCCGTTTTTAAAGGGACAGTCCCGTATTTAAGCC 50 v v vvvv -i v BLACKJACK#DNA 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCCG-GTTTACGCC 49 rnd-1_family- 51 C-TCCTGCAGGTGTCCCG 67 i- iv v v i BLACKJACK#DNA 50 TGTTGTCCCGGCGTCCCG 67 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.11 CpG sites = 4, Kimura (unadjusted) = 24.95 Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 324 16.44 0.00 0.00 rnd-1_family-558#LINE/CR1 2 74 (655) C CR1-L3A_Croc#LINE/CR1 (1869) 2419 2347 m_b6s551i11 rnd-1_family- 2 CAATTTTCTACAATTCTGACCTTCTAACTTATATTCTTTACTATTGACTT 51 iv v i v i ii C CR1-L3A_Croc# 2419 CAATTTTCTACAATTCCTAGCTTCTAATTTATATTCATTGCTATCAACTT 2370 rnd-1_family- 52 CCCCTTTCTTCCATATATTTTAT 74 i v i v C CR1-L3A_Croc# 2369 CCCCTTTTTTCCATTTGTTATAT 2347 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.76 CpG sites = 7, Kimura (unadjusted) = 18.76 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 543 4.55 0.00 0.00 rnd-1_family-564#DNA/hAT-Charlie 4 69 (4) Charlie7a#DNA/hAT-Charlie 207 272 (0) m_b6s502i4 rnd-1_family- 4 GGGGGTGCGTGCTCAAAANTTTTTTACTGATAGGGGTGCGCGATCAAAAA 53 i ? ii Charlie7a#DNA 207 GGGGGTGCATGCTCAAAAATTTTTTACTGATAGGGGTGCATGATCAAAAA 256 rnd-1_family- 54 AGTTTGGAGACCACTG 69 Charlie7a#DNA 257 AGTTTGGAGACCACTG 272 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.84 CpG sites = 3, Kimura (unadjusted) = 4.84 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 283 20.90 1.49 0.00 rnd-1_family-567#DNA/hAT-Charlie 1 67 (267) Charlie1a#DNA/hAT-Charlie 1 68 (1387) m_b6s502i5 rnd-1_family- 1 CAGTGGTTCCCAAACTGGGGTTCGTGAACCCCTGGGGGTTCGCG-GAACG 49 i i v v i i i i v - v v Charlie1a#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGCGGACCCCTGGGGGTCCCCGAGACCC 50 rnd-1_family- 50 TTACAGGGGGTTCNCGGG 67 v i ? i Charlie1a#DNA 51 TTTCAGGGGGTCCGCGAG 68 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.36 CpG sites = 8, Kimura (unadjusted) = 25.29 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 291 16.95 1.69 0.00 rnd-1_family-567#DNA/hAT-Charlie 7 65 (269) Charlie21a#DNA/hAT-Charlie 7 66 (1147) m_b6s502i6 rnd-1_family- 7 TTCCCAAACTGGGGTTCGTGAACCCCTGGGGGTTCGCGGA-ACGTTACAG 55 v v v i ii i -ii v Charlie21a#DN 7 TTCCCAACCGGTGGTTTGTGAACCCCCAGGGGTTCGCGAAGGTGTTCCAG 56 rnd-1_family- 56 GGGGTTCNCG 65 ? Charlie21a#DN 57 GGGGTTCACG 66 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.85 CpG sites = 6, Kimura (unadjusted) = 19.85 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 12 18.29 0.00 3.12 rnd-1_family-570#LINE/RTE-BovB 382 414 (36) (ATCAAA)n#Simple_repeat 1 32 (0) m_b6s252i12 rnd-1_family- 382 ATCAAAATACAACACCAAAACCAAACTCAAGAT 414 - v i i v i (ATCAAA)n#Sim 1 ATCAAAAT-CAAAATCAAAATCAAAATCAAAAT 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 12 19.14 4.35 4.35 rnd-1_family-573#LTR/ERV1 259 304 (206) (GAGAG)n#Simple_repeat 1 46 (0) m_b6s252i10 rnd-1_family- 259 GAGAGGGGAGGGGGAGTAGAGGGGGGGAGTGGTAGA-GAGGGGA-AGG 304 i - i v i i v - - i - (GAGAG)n#Simp 1 GAGAGGAGA-GGAGAGGAGAGGAGAGGAGAGG-AGAGGAGAGGAGAGG 46 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 15 34.95 0.00 0.00 rnd-1_family-573#LTR/ERV1 263 311 (199) (GG)n#Simple_repeat 1 49 (0) m_b6s252i11 rnd-1_family- 263 GGGGAGGGGGAGTAGAGGGGGGGAGTGGTAGAGAGGGGAAGGGGGGGGG 311 i i vi i i v vi i i ii (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 49 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 20 13.69 0.00 0.00 rnd-1_family-575#Unknown 112 143 (282) (GT)n#Simple_repeat 1 32 (0) m_b6s252i9 rnd-1_family- 112 GTGTGTTTGTGTGTGTGTGTGAGTGTAAGTGT 143 v v iv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 14 20.96 3.77 3.77 rnd-1_family-576#LINE/L1-Tx1 508 560 (1255) (GCC)n#Simple_repeat 1 53 (0) m_b6s252i8 rnd-1_family- 508 GCGGCGGCC-CCCCCGCCTGCCGCC-ACGTCGTCTCCCCCGTCCGCCGCC 555 v v - v - -v i i v v - (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCC-GCCGCCGCCGCCGCCGCCGCCG-CCGCCGCC 48 rnd-1_family- 556 TCCGC 560 v (GCC)n#Simple 49 GCCGC 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 206 20.32 2.74 5.63 rnd-1_family-583#LINE/I-Jockey 20 92 (3) AmnL2-1#LINE/L2 1521 1591 (1022) m_b6s601i2 rnd-1_family- 20 CTCCACCACCAGANCCCTCACCTGTGGAGTCCCACAAGGATCAATTCTC- 68 v i -- ? vi i v i - AmnL2-1#LINE/ 1521 CTGCGCCA--AGACCCCTCCTCTATGGAGTCCCACAAGGTTCAGTTCTCG 1568 rnd-1_family- 69 -TCTCCNGTCCTATTCAACATCTAC 92 -i ii ? ii v --i AmnL2-1#LINE/ 1569 GCCCTCTGCTCTTTTC--TATCTAC 1591 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.30 CpG sites = 10, Kimura (unadjusted) = 25.35 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.00 (6 / 6) 3021 8.84 2.78 0.63 rnd-1_family-586#DNA/hAT-Tag1 1 467 (13) hAT-5_Mam#DNA/hAT-Tag1 3025 3501 (39) m_b6s502i7 rnd-1_family- 1 CATATGCTTGTTTTTTTTAAAAATA-TTATAT--GTTTGCTGTTGAAGAA 47 ii v -- - i-- i hAT-5_Mam#DNA 3025 CACGTGCTTGTTTTGTT--AAAATAATTATACACGTTTGTTGTTGAAGAA 3072 rnd-1_family- 48 AAAAATCCAGAATACTTAACGTTGTTGTTTTAGTTAAATAAAACAATTTA 97 v i v vv i hAT-5_Mam#DNA 3073 AAATATCCAAAATACATAAGCTTGTTGTTTTAGTTAAATAAAATAATTTA 3122 rnd-1_family- 98 AATGTCTGTC-----TGGTGA----TGTTCTCCTCCTAATACAGCATGGC 138 i----- ---- v ? ? hAT-5_Mam#DNA 3123 AATGTCTGTTGCCTTTGGTGACGGTTGTTGTCCTCCNAATACAGNATGGC 3172 rnd-1_family- 139 AAGAAAATCCTCCAAATATTAATGATTAACCTGTTGAATTGGAGATAGTT 188 i v i iv i ?i? hAT-5_Mam#DNA 3173 AAAAATATCCCCCAAATATCCATGATTAATCNANTGAATTGGAGATAGTT 3222 rnd-1_family- 189 CACCTCCCAATGACTTCATAAATATCTGCTTCAATTACCTTTGGTAAATG 238 i i v i hAT-5_Mam#DNA 3223 CACCTCCCAATGACTTCACAAGTATCTGCTTCAATTAGCTTTGGTAAATA 3272 rnd-1_family- 239 AAATAACCAAACAATCATTCA-TTTTCTGATATAGCTGTAAAACTAATCT 287 iv v - i i i hAT-5_Mam#DNA 3273 AAATAACCAAATCATAATTCAGTTTTCTGATGTAGCTGCAAAATTAATCT 3322 rnd-1_family- 288 GAAAAGTTTTCAAAATAAATCACTGTTTAAAAATGTATAGTGTGTACCTT 337 iv v i v hAT-5_Mam#DNA 3323 GAAAAAATATCAAAATAAATCACTGCTTTAAAATGTATAGTGTGTACCTT 3372 rnd-1_family- 338 CTAAAAATGAAACCTACATCTATCTCTGAGTTGTGAAGAATATGTATTAA 387 v hAT-5_Mam#DNA 3373 CTAAAAATGAAACCTACATCTATCTCTGAGTTGTGAATAATATGTATTAA 3422 rnd-1_family- 388 GGTTATAACAACCAACAAGAATGCACTTTTATGTAGAAANCCATGATTAA 437 v v - ? v hAT-5_Mam#DNA 3423 GGTTATATCAAACAACAAGAATGCACTTTT-TGTAGAAAACAATGATTAA 3471 rnd-1_family- 438 ATCGAGTCTTCCTGACTAGTGATTTAAATC 467 v i hAT-5_Mam#DNA 3472 ATCGAGGCTTCCTGACCAGTGATTTAAATC 3501 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.29 CpG sites = 22, Kimura (unadjusted) = 9.54 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.02 (8 / 466), avg. gap size = 2.00 (16 / 8) 1252 30.60 0.20 2.61 rnd-1_family-589#LTR/Gypsy 5 514 (1738) MamGyp-int#LTR/Gypsy 3232 3729 (1373) m_b6s551i12 rnd-1_family- 5 AAACCTGTAGCCTTTGCCAGCCGAGGACTGTCTGATAGTGAAACTCGCTA 54 i ?i i i ?? i v i v MamGyp-int#LT 3232 AAGCCNATAGCTTTCGCCAGCNNAAGTCTGTCTGATAGTGAGACTCGATA 3281 rnd-1_family- 55 TCCCACCCACAAGCTGGAGTTCTTGGCCTTGAAATGGGCCATCACTGAGA 104 i i ii ii i i ?i i ? v v MamGyp-int#LT 3282 CCCTATTCACAAATTAGAGTTCCTGGCNCTAAAATGGGCNATCACGGACA 3331 rnd-1_family- 105 AATTTCGAGACTACTTGTATGGTGCTCAGTTCCAGGTGTGGACAGACAAC 154 i ?ii v iv i v iv vv i i v MamGyp-int#LT 3332 AGTTTNAGGAGTATGTATATGGAGTGCCTTTTCAAGTGTGGACTGACAAC 3381 rnd-1_family- 155 AACCCACTGACCTATGCGTTAACAAGTGCTAAGCTGGATGCTACAGGGCA 204 i ? v ? i i i v v i i i MamGyp-int#LT 3382 AATCCNCTCACNTACGTGCTCACCAGTGCCAAACTGGATGCTACGGGGCA 3431 rnd-1_family- 205 AAGATGGGTGGCCGCCTTGGCTAGCTATGACTTCAGCATTCAATACCGAT 254 iv i vi i ii i i i v v MamGyp-int#LT 3432 GCGGTGGGTGGCCGCACTAGCTGACTATAATTTCAGCGTTCATTACAGAT 3481 rnd-1_family- 255 CAGGGAGAAGCAATGTAGATGCAGATGCATTGTCCAGGCGTCCACAGGCA 304 ?vvv iivi i vi v i v v v v vv ? MamGyp-int#LT 3482 CAGGNCTCAGCAACAAGGATGCGGATGCTCTTTTCCGCCGGCCCCATCCN 3531 rnd-1_family- 305 CCAGGAGTTGCTGTGATACCCACGGATGGAGTGAGGGCTATTTGCAGTGT 354 vi ?vii vviiv v vv v v i i ---- v MamGyp-int#LT 3532 CAGGNCACTGAAACTATCCCCAGCGAGGGAGTCAGGGCCATCTG----GG 3577 rnd-1_family- 355 GAGTCGCCGGGAGCCAGA-GTCCCATGAGAGTCTTCATGGATGTGCTGCA 403 ? v v?vi iii? i- ?i -------- ?v v v iiv ? MamGyp-int#LT 3578 NACTCCNAAGGGATNAGGCGTNTC--------CTNAAGGGAGGTATGGCN 3619 rnd-1_family- 404 GAAGCTTTGGGCCTGCCCCCTGAATGCGTGCCTTCTGCTTCAGTGAACTA 453 ivi v ? i - ivvi viv ivv v v i MamGyp-int#LT 3620 GAAAGCTTGGGGCTNCCTCC-GAGACTGTGCCTATGGTAGCCGTCAATTA 3668 rnd-1_family- 454 TATTGCGTTGGACCAATCTCCTTTGCCCATGCTCAATGCGGCTGACTGGC 503 i v vii i v vi vi vv iviiv i vv v MamGyp-int#LT 3669 TGTGGCCCCGGGCAAATCGTCACTGCCCCAGCCGGGAGTGGAGGACTGGA 3718 rnd-1_family- 504 AGGAAGCCCAG 514 i i v MamGyp-int#LT 3719 GGAAAGCGCAG 3729 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 81, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.14 (81/71) Gap_init rate = 0.03 (14 / 509), avg. gap size = 1.00 (14 / 14) 3827 27.54 1.04 1.04 rnd-1_family-589#LTR/Gypsy 615 1770 (482) MamGyp-int#LTR/Gypsy 3830 4985 (117) m_b6s551i13 rnd-1_family- 615 GAGAATGGACCAAACTAAAACTGATTCAGGGAGTGCTACATCGAGTGACC 664 ? vvv i ?? v v i ii ii iiii ?- i MamGyp-int#LT 3830 GAGANTGGCAGAAATTANNACTGATTAATGGGGTATTGTACTAGGTN-CT 3878 rnd-1_family- 665 ACAG-ACCCTTTACAAAAGCAACGAGCACAGCTGGTGCTGCCAAAAGAGT 713 ? -i iv v vii vii iiv i ?i vv i i MamGyp-int#LT 3879 NCAGTGCCCCGTAAATGGGCTGTGGAAACAACTGGTNTTGCCCCAGGAAT 3928 rnd-1_family- 714 ACAGAGCCCTGGCCATGAGGGCCCTGCACGATGACTTTGGACATTTAGGG 763 v vv ?i i?v i vii i v i i MamGyp-int#LT 3929 ACCGCCCCNCGGTNCTGAGAGCATCGCATGATGACTTTGGCCATCTGGGG 3978 rnd-1_family- 764 ATGGAGAGGACCCTGGAACTTATTCGTAGTAGATTCTATTGGCCCCGGAT 813 v i ? i v v viv?v i vi vi MamGyp-int#LT 3979 AGGGAAAGGACNCTAGAACTAATTAGGGCNCGGTTCTTCTGGCCCAAGAT 4028 rnd-1_family- 814 GGCTGAAGATGTTCGCAGG---AAATGTGAGACCTGCGCTCGATGTGTTC 860 v i i --- i --- i i i v ii MamGyp-int#LT 4029 GGCAGAGGACGT---CAAGTCCAAATGTGAGACTTGTGCCCGCTGCATTC 4075 rnd-1_family- 861 AAAGGAAAACTCTGCCCACGAGGGCTGCATATCTCGAGAACATCACCAGC 910 iv ii ? iv v v v i vi ivvv MamGyp-int#LT 4076 AGCGGAAAACCTTGCCNACACGGGCAGCTTATCTGGAAACTATTCAGAGC 4125 rnd-1_family- 911 ANCAAACCTCTGGAACTGGTATGCATCGATTTCTTGTCTTTAGAAGTAGA 960 ? i? i i ii i ii ? i i i vii MamGyp-int#LT 4126 AGCAAGNCCCTAGAGTTAGCGTGCATNGACTTCTTGTCCTTGGAACCGGA 4175 rnd-1_family- 961 CAAGAGGAATATTGGGAACATTCTAGTAGTGACTGACCATTNTACGCGAT 1010 ivv iv ? v v ii ? i i ?i v vi MamGyp-int#LT 4176 CAGCCGGAACCTNGGGAACATACTTGCGGTGACNGATCACTTCACCCGCC 4225 rnd-1_family- 1011 ATGCGCAGGCATATCCCACGCGTGATCAGAGGGCCACCACTGTTGCTCGA 1060 i ? ? vv v i ii vv v ? i MamGyp-int#LT 4226 GTGCNCAGGCNTATCCCACCAGGGACCAGAAAGCATCCACAGTTGCNCGG 4275 rnd-1_family- 1061 GTACTGTGGGAGAAATATTTCTCAGTTTATGGATTTCCGGCCCGGATACA 1110 ii i ?i ? i v i? i v MamGyp-int#LT 4276 GTGTTATGGGAGAAATNCTTCTCAGTNTATGGGTTTCCTGCTNGAATTCA 4325 rnd-1_family- 1111 CTCGGATCAGGGGCGGGACTTTGAGAGTCATCTTCTGAAGGAGGTGCTGA 1160 i i v i i i?i v vi i i vv MamGyp-int#LT 4326 CTCAGATCAAGGGAGAGATTTTGAGAGTCGNTTACTGCGGGAAGTACTTC 4375 rnd-1_family- 1161 GGATAGCGGGAATTAAGAAGTCTAGGACAACGCCTTATCACCCGCAAGGT 1210 i?v v i vv i i v v i i v v MamGyp-int#LT 4376 ANTTAGCTGGGATACAGAAATCCAGGACTACTCCCTATCATCCCCAAGGG 4425 rnd-1_family- 1211 GATCCTCAGCCAGAGAGGTTCAACCGAACCCTATTAGATATGTTGGGGAC 1260 i ? i ? i i v ii i i i MamGyp-int#LT 4426 GACCCNCAACCNGAGAGATTTAACAGAACTTTATTAAACATGCTGGGGAC 4475 rnd-1_family- 1261 TTTGCGGCCAGAGCAGAAAG--CAACCTGGAGCCAACATGTCGCATATCT 1308 vi ? v v i -- i-- i i v vi MamGyp-int#LT 4476 GCTNCGCCCTGAGCAGAAGGGGCAG--TGGAGCCAGCACGTGGCATTCCT 4523 rnd-1_family- 1309 GGTGCACGCCTACAATGCCACAAAGAATGATGCTACAGGAGTCACCCCAT 1358 ? i v i i i v vv i i vi MamGyp-int#LT 4524 GGTNCATGCCTACAATGCCACCAGGAACGATGCCACTGGCTTTACCTCTC 4573 rnd-1_family- 1359 ATCTCTTAATGTTTGGGCGAGAACCAAGATTACCCATAGACCTGTGCTTT 1408 i i i i vv ii i v i v MamGyp-int#LT 4574 ATTTCTTGATGTTTGGGCGGGAGCCTCGGCTGCCCATTGATCTCTGCTTT 4623 rnd-1_family- 1409 GGTGTATCAGAGGATGGAGAT-AGCTAT---GAAA-CTCATCAGCAGTAT 1453 v ---i iv ? i - v?? --- - ii-- MamGyp-int#LT 4624 GGGGT---GGGCGANGGAGGTGAGANNTCGGGAAACCTCACT--CAGTAT 4668 rnd-1_family- 1454 GTATCCCGACTAAGAGAAAAGCTGCGGGATGCTTATCACTTAGCTACATC 1503 i v ivi? ? i v i ? i v? i iv i vv MamGyp-int#LT 4669 GCAGCTAANCTNAGGGACAAACTNCAGGAANCTTACCGGTTAGCCACCGC 4718 rnd-1_family- 1504 TGCGGCTCGGAAGAACGCAGACCGCAACAAACATCGATATGATGCTAGGG 1553 i ?viv i ?i v i i iiii i MamGyp-int#LT 4719 TGCAGCTCGNCGCAACACAGANTGGAATAAGCACTAGTATGATGCCAGGG 4768 rnd-1_family- 1554 TACGTCTGCAAGAACTCCAGCCGGGGGACAGAGTCCTGCTGCGAAATTTG 1603 viv? i i v vvi v ? i i MamGyp-int#LT 4769 TACGGTGNCAGGAGCTGCAGGAAGGGGACCGAGTNCTGCTGTGGAATTTG 4818 rnd-1_family- 1604 GGTATTG-CTGGCAAACACAAGATAGCTGACAGATGGAAGGCAATACCTT 1652 -ii - i i i i i v v ? i? ? MamGyp-int#LT 4819 GG-GCTGCCCGGTAAGCACAAAATAGCCGACCGCTGGAAGGCNACNCCNT 4867 rnd-1_family- 1653 ACTTGGTGATGGAAAAGCTAGGAGACCTGCCGGTCTACAAGATCAAACCT 1702 ii i i i i ii v iiv? ? v ii vv iv v MamGyp-int#LT 4868 ATCTAGTGGTAGAGAGACTTGGGACNCTGCCNGTGTACAAAGTGCAGGCA 4917 rnd-1_family- 1703 GAAGAGGGTCCAGGGCAGACAAAGACGGTGCATAGAAACCTTTTGCTCCC 1752 ii v v? iiiv ii i v iv ivvi ? iv MamGyp-int#LT 4918 GAGAATGGGNCAGGGCAAGTCAAGGTGATCCACCGAAATAACTTNCCGCC 4967 rnd-1_family- 1753 TGTGGGGGAATTGGTAGG 1770 ?i i i i MamGyp-int#LT 4968 NATAGGGGAACTGGTGGG 4985 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.94 CpG sites = 198, Kimura (unadjusted) = 37.57 Transitions / transversions = 1.69 (198/117) Gap_init rate = 0.02 (19 / 1155), avg. gap size = 1.26 (24 / 19) 18 0.00 0.00 0.00 rnd-1_family-592#Unknown 94 113 (0) (AC)n#Simple_repeat 1 20 (0) m_b6s252i7 rnd-1_family- 94 ACACACACACACACACACAC 113 (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 21 20.58 3.17 1.56 rnd-2_family-128#Unknown 37 99 (183) (CCCCG)n#Simple_repeat 1 64 (0) m_b6s252i4 rnd-2_family- 37 CCTCGCCCCGCCCCTTCCC-CGAGGCCCCGCCCCTGCCCCGCCCCTTCCC 85 i vi - vvv - vi (CCCCG)n#Simp 1 CCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCC-GCCCCGCCCCGCCCC 49 rnd-2_family- 86 -CGAGGCCCCGCCCC 99 - vvv (CCCCG)n#Simp 50 GCCCCGCCCCGCCCC 64 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 13 29.67 1.56 1.56 rnd-2_family-128#Unknown 92 155 (127) (CCCT)n#Simple_repeat 1 64 (0) m_b6s252i5 rnd-2_family- 92 CCCGCCCCCCGCTCACTACATTCC-CCCTCCCTCTGTNGCTCGCTCTCCC 140 v i - v v v i - iv ?v v i i (CCCT)n#Simpl 1 CCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 49 rnd-2_family- 141 CCACCCTCACTCACT 155 v v v (CCCT)n#Simpl 50 CCTCCCTCCCTCCCT 64 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 23 20.11 5.66 3.70 rnd-2_family-128#Unknown 161 266 (16) (CGGGGTG)n#Simple_repeat 1 108 (0) m_b6s252i6 rnd-2_family- 161 CGGGCTG-GGGCAG-GGGGT-TGGGGTGC-GGGAG-GGGGTGAGGGCTCC 205 v - vv - -i - v - v v v (CGGGGTG)n#Si 1 CGGGGTGCGGGGTGCGGGGTGCGGGGTGCGGGGTGCGGGGTGCGGGGTGC 50 rnd-2_family- 206 GGGCGGGGGNNTGCGGGGGCTCTGGGGGGACGGGG-CCGGGAATGAGGGG 254 vv v ?? - - vi v - -v -i v (CGGGGTG)n#Si 51 GGGGTGCGGGGTGC-GGGG-TGCGGGGTG-CGGGGTGCGGG-GTGCGGGG 96 rnd-2_family- 255 TGCGGGGTGCGG 266 (CGGGGTG)n#Si 97 TGCGGGGTGCGG 108 Matrix = Unknown Transitions / transversions = 0.21 (3/14) Gap_init rate = 0.10 (10 / 105), avg. gap size = 1.00 (10 / 10) 16 14.45 2.50 2.50 rnd-2_family-665#Unknown 40 79 (175) (GCCCC)n#Simple_repeat 1 40 (0) m_b6s252i0 rnd-2_family- 40 GCCCCGCCCCTGCCCCGCCCCTTCCC-CGAGGCCCCGCCCC 79 - vi - vvv (GCCCC)n#Simp 1 GCCCCGCCCC-GCCCCGCCCCGCCCCGCCCCGCCCCGCCCC 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 18 25.25 1.19 6.25 rnd-2_family-665#Unknown 41 124 (130) (CCCCGC)n#Simple_repeat 1 80 (0) m_b6s252i1 rnd-2_family- 41 CCCCGCCCCTG-CCCCGCCCCTTCCCCGAGGCCCCGCCCCCGCTCACTCC 89 i - iv -v v i v v (CCCCGC)n#Sim 1 CCCCGCCCCCGCCCCCGCCCCCGCCCC-CGCCCCCGCCCCCGCCCCCGCC 49 rnd-2_family- 90 ATCCCCCTCCCTCCGTCGCTCGCTCTCCCCCACCC 124 -- v i v vi - - i v i (CCCCGC)n#Sim 50 --CCCGCCCCCGCCCCCGC-C-CCCGCCCCCGCCC 80 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.00 (6 / 6) 19 24.66 3.23 0.00 rnd-2_family-665#Unknown 72 133 (121) (CCCT)n#Simple_repeat 1 64 (0) m_b6s252i2 rnd-2_family- 72 CCCGCCCCCGCTCACTCCAT-CC-CCCTCCCTCCGTCGCTCGCTCTCCCC 119 v i v v v - - v v v i i (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 50 rnd-2_family- 120 CACCCTCACTCACT 133 v v v (CCCT)n#Simpl 51 CTCCCTCCCTCCCT 64 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 22 24.52 0.00 4.29 rnd-2_family-665#Unknown 141 213 (41) (GGGCTG)n#Simple_repeat 1 70 (0) m_b6s252i3 rnd-2_family- 141 GGGCTGGGGCAGGGGGTTGGGGTGCGGGAGGGGGCGAGGGCTCTGGCTGG 190 v v v v - vv vi vv (GGGCTG)n#Sim 1 GGGCTGGGGCTGGGGCTGGGGCTG-GGGCTGGGGCTGGGGCTGGGGCTGG 49 rnd-2_family- 191 GGGTGCGGGCTCCGGGGTAGGGC 213 v - -v v i (GGGCTG)n#Sim 50 GGCTG-GGGCT-GGGGCTGGGGC 70 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.00 (3 / 3) 2723 5.58 1.22 3.50 rnd-2_family-68#LINE/L2 2 410 (4) L2-1_AMi#LINE/L2 744 1143 (92) m_b6s551i14 rnd-2_family- 2 TCTCGCGTCTCGATTACTGCAGCATCCTTCTCTCCGGCCTTGACAAATGC 51 i i i i i L2-1_AMi#LINE 744 TCTCACATCTCGATTACTGCAACATCCTTTTCTCTGGCCTTGACAAATGC 793 rnd-2_family- 52 AGTCTTGCCCTGCTCATATCCATTCAGAATGCTGCTGCAAAGATCATTTT 101 i i L2-1_AMi#LINE 794 AATCTTGCCCCGCTCATATCCATTCAGAATGCTGCTGCAAAGATCATTTT 843 rnd-2_family- 102 CCTAGCCCGTCGCTTTGACCACGTCACCCCTCTCTTTGNATCCCTCCACT 151 ? -- L2-1_AMi#LINE 844 CCTAGCCCGTCGCTTTGACCACGTCACCCCTCTCTTTGCATCCCT--ACT 891 rnd-2_family- 152 GGCTCCCCCTTCTCCATCGCATCAAACNTAAGCTNCTTGTCTTCACTTTC 201 i - ? ? L2-1_AMi#LINE 892 GGCTCCCCCTTCTCTATCG-ATCAAACATAAGCTACTTGTCTTCACTTTC 940 rnd-2_family- 202 AAGGCCCTTCACGGCCTATCCCCACCCTACCTATCATCTCTCATTCACTA 251 i--v ii L2-1_AMi#LINE 941 AAGGCCCTTCACGGCCTATCCT--ACCTGTCTATCATCTCTCATTCACTA 988 rnd-2_family- 252 TCGAGTGTCGACT---GCTTCCGCTCGGCCCATGATGCCAGCCTCCATCG 298 v i --- i v L2-1_AMi#LINE 989 TCGAGAGTTGACTCCCGCCTCCGATCGGCCCATGATGCCAGCCTCCATCG 1038 rnd-2_family- 299 CCCACTTGTTAAATTTTCAAACAAGCACCTTCGTGCTTTCTCCCATGCTG 348 - - --- i i L2-1_AMi#LINE 1039 CCCACTTGTTAAATTTTCAAAC-AGCA-CTTC---CTTTTTCCTATGCTG 1083 rnd-2_family- 349 --CCCCTCACGCTTGGGAGGAGCTCCCCGTAAACATCCGCAAAGCTACCT 396 -- i ---- i v L2-1_AMi#LINE 1084 CTCCCCTCATGCTTGGGAGGAGCTCCCCGTAAACATCCGCAA----ATCA 1129 rnd-2_family- 397 CATTATCCTCCTTC 410 i L2-1_AMi#LINE 1130 CATTATTCTCCTTC 1143 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.64 CpG sites = 18, Kimura (unadjusted) = 5.90 Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.04 (16 / 408), avg. gap size = 1.19 (19 / 16) 305 27.14 14.90 2.58 rnd-2_family-76#LINE/CR1 3 210 (5) CR1-L3A_Croc#LINE/CR1 4037 4269 (19) m_b6s551i15 rnd-2_family- 3 AAATTTAGGCN-GATATCAGGAA-AAATTCCTGACAGTGAGATCTATTAG 50 i i ?- v v ?i- ? ii i iviv i CR1-L3A_Croc# 4037 AAATTCAGACTAGAAATAAGGNGCAANTTTTTAACAGTGAGGGTAATTAA 4086 rnd-2_family- 51 ACTGTGGAATAGTCTCCCAAGGGAAGTGGTGGAAGCCCCATCGCTTGAGN 100 v vv i iii v ?v vv i i v i? CR1-L3A_Croc# 4087 CCACTGGAACAACTTACCAAGGGNTGTGGTGGATTCTCCATCACTGGAAA 4136 rnd-2_family- 101 CATTTAAAACTAGACTGGA--------CAAA------GCACTGG------ 130 iv v v i --------i ------ v i ------ CR1-L3A_Croc# 4137 TTTTTAAATCAAGATTGGATGTTTTTCTAAAAGATATGCTCTAGTTCAAA 4186 rnd-2_family- 131 --AGAATATACTGTAGGGAA---CAAT--CCTGCATTGGCAGGTGGGAAG 173 --i - v vii --- v -- i i ----- CR1-L3A_Croc# 4187 CAGGAAT-TAATTCGGGGAAGTCCTATGGCCTGCGTTAGCAGG-----AG 4230 rnd-2_family- 174 GATGAACTAGATGACCT--AACAGTCTTTTCCGTCTCTA 210 vi i i -- i?i ii v ii CR1-L3A_Croc# 4231 GTCGGACTAGATGATCTACAGNGGTCCCTTCCGGCCTTA 4269 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.74 CpG sites = 34, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.07 (15 / 207), avg. gap size = 2.47 (37 / 15) 381 25.86 0.85 0.85 rnd-2_family-76#LINE/CR1 14 130 (85) CR1-3_Croc#LINE/CR1 2871 2987 (618) m_b6s551i16 rnd-2_family- 14 GATATCAGGAAAAA-TTCCTGACAGTGAGATCTATTAGACTGTGGAATAG 62 v - i v v v v vi v i v CR1-3_Croc#LI 2871 GATATCCGGAAAAACTTCTTCACTGTTAGAACAGTGAGGCAGTGGAATAG 2920 rnd-2_family- 63 TCTCCCAAGGGAAGTGGTGGAAGCCCCATCGCTTGAGNCATTTAAAACTA 112 v v v v vv i i v ?ii i i vv CR1-3_Croc#LI 2921 ACTGCCTAGGGAAGTTGTGGACTCTCCATCACTGGAGGTGTTCAAGAAGA 2970 rnd-2_family- 113 GACTGGACAAAGCACTGG 130 ii - iv CR1-3_Croc#LI 2971 GGTTGGAC-AGCCACTGG 2987 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.11 CpG sites = 12, Kimura (unadjusted) = 32.11 Transitions / transversions = 0.67 (12/18) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 349 30.00 0.00 0.00 rnd-2_family-76#LINE/CR1 25 144 (71) CR1-L3B_Croc#LINE/CR1 3032 3151 (126) m_b6s551i17 rnd-2_family- 25 AAATTCCTGACAGTGAGATCTATTAGACTGTGGAATAGTCTCCCAAGGGA 74 ? ii i iviv iv vv i iv v CR1-L3B_Croc# 3032 ANATTTTTAACAGTGAGGGTGATTAACCACTGGAACAAACTACCAAGGGA 3081 rnd-2_family- 75 AGTGGTGGAAGCCCCATCGCTTGAGNCATTTAAAACTAGACTGGACAAAG 124 vv i v v?iv i v v iivvv CR1-L3B_Croc# 3082 AGTGGTGGATTCTCCATCTCTTGATGTCTTCAAATCAAGACTGGATGCCT 3131 rnd-2_family- 125 CACTGGAGAATATACTGTAG 144 iv ii i v CR1-L3B_Croc# 3132 TTCTGGAAGATATGCTTTAG 3151 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 17, Kimura (unadjusted) = 39.53 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0) 62 24.61 3.39 3.74 rnd-2_family-173#DNA/hAT-Charlie 124 418 (72) (CCCGGC)n#Simple_repeat 1 294 (0) m_b7s252i24 rnd-2_family- 124 CCCAGCCCC-GCTCTGCCCCCAGCTCNCGCTCCGGCCCCCAGCCGCGGCC 172 i - i i v i i ?v i - i v (CCCGGC)n#Sim 1 CCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG-CCCCGGCCCCGGCC 49 rnd-2_family- 173 CCAGCCCCGGGCCCTGACTCCCAG-CCCGGCCGCGGCTCCACNCCTGGCC 221 i - i i - i - v i iv? i (CCCGGC)n#Sim 50 CCGGCCCC-GGCCCCGGC-CCCGGCCCCGGCCCCGGCCCCGGCCCCGGCC 97 rnd-2_family- 222 NCGNGCCCACGCCGCTCCTGCCCCGNCCCCAGCCCTGNCCCCGGCCCC-G 270 ? - - -- i v ? i i ? - (CCCGGC)n#Sim 98 CCG-GCCC-CG--GCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG 143 rnd-2_family- 271 ACGCAGCTCCGCTCCCGGCAGCCCCGCTCCTGGCCCCAGCCCCGCTCCCG 320 v v i i vi -- v - i i vi (CCCGGC)n#Sim 144 CCCCGGCCCCGGCCCCGGC--CCCGGC-CCCGGCCCCGGCCCCGGCCCCG 190 rnd-2_family- 321 GCTGCNGCCCCAGCCTCNGCCCC-NCCTCCGCCCC-G-CCTTACCCCTG- 366 iv ? i i ? -? i v - - ivi v - (CCCGGC)n#Sim 191 GCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGC 240 rnd-2_family- 367 TCCGNTCCC-TCCCC-CCCCCGAGCCGTGG-CCCAGCCCAGTTCCGGGCC 413 i ?i -v -v - vi - i v vi v (CCCGGC)n#Sim 241 CCCGGCCCCGGCCCCGGCCCCG-GCCCCGGCCCCGGCCCCGGCCCCGGCC 289 rnd-2_family- 414 CCGGC 418 (CCCGGC)n#Sim 290 CCGGC 294 Matrix = Unknown Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.07 (21 / 294), avg. gap size = 1.00 (21 / 21) 13 15.44 6.67 2.13 rnd-2_family-173#DNA/hAT-Charlie 279 323 (167) (CCGCTCC)n#Simple_repeat 1 47 (0) m_b7s252i25 rnd-2_family- 279 CCGCTCCCGGCAGCCCCGCTCCTGGC-CCCAG--CCCCGCTCCCGGCT 323 v -v iv - v -- v (CCGCTCC)n#Si 1 CCGCTCCCCGC-TCCCCGCTCCCCGCTCCCCGCTCCCCGCTCCCCGCT 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.33 (4 / 3) 1679 13.31 13.80 0.50 rnd-2_family-195#SINE/tRNA 87 441 (19) LFSINE_Vert#SINE/tRNA 46 447 (12) m_b7s601i0 rnd-2_family- 87 CCTTTNATTTCTAGGTCACCGGTTNAAATCCGGCCCGGGCTAGTAATGAC 136 ? ii i ?i i i ii i LFSINE_Vert#S 46 CCTTTCACCTCTAGGTCACTGGTTCGAATCCAGCCCAGGTCAGTAGTGAC 95 rnd-2_family- 137 TGAAAGTTGTTACTATCTG-----------GTGGCTTGTGTGAAATGGAG 175 i ii i ----------- i i - LFSINE_Vert#S 96 CGAAAGTCATTACCATCTGACGGCTGTTCGGTGGCCTATGTGAAATG-AG 144 rnd-2_family- 176 TTGGTGGTCTCGGTCCAGTTCCTAGGGCAGAGGTCGTCTTCACCA-AAAA 224 i v v v - iv i - LFSINE_Vert#S 145 TTGGTGGTCTCAGTCCAGTTCCTAGTGGACAGGT-GTCCACATCACAAAA 193 rnd-2_family- 225 CGCCCAT----------AC-AATTGGCACCCTTGTTGGCAGTCTCAGCAG 263 vv ---------- - LFSINE_Vert#S 194 CCACCATCACAATTGGCACTAATTGGCACCCTTGTTGGCAGTCTCAGCAG 243 rnd-2_family- 264 AGAGGCCAAGGACTGAATGGGCATGGAGACTGAACCNCCCTCTCACCCTT 313 i? ii LFSINE_Vert#S 244 AGAGGCCAAGGACTGAATGGGCATGGAGACTGAACTACCCTCTCACCTCT 293 rnd-2_family- 314 AGAAGCAGT-----------GGGGTTGAGGCACACT-------------- 338 i ii -----------i i -------------- LFSINE_Vert#S 294 AGAGGTGGTCCCTCCAGGTCAGGGTTGAGGCACATTGGCGGGGCAGTGTG 343 rnd-2_family- 339 GGGAAGCTTTCANNGCTGCTGCNCGTGCTATNCCTGTTCTGTGGGTAGA- 387 v ?? i ? i ? i i - LFSINE_Vert#S 344 GGGAAGCTTGCACTGCCGCTGCCCGTGCTGTACCTGTTCTGTGGATAAAC 393 rnd-2_family- 388 GGAAGNGTTCGGTNTCCAGGGCTGCCAATCTGGCACCNTTAAGAAACNCT 437 i i ?v i ? i i ? v vi i ? LFSINE_Vert#S 394 AGAGGACTTCAGTCTCCAGGGCTGTCAATCCGGCACCTTTCACGAGCACT 443 rnd-2_family- 438 AAAT 441 LFSINE_Vert#S 444 AAAT 447 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 13.88 CpG sites = 37, Kimura (unadjusted) = 15.60 Transitions / transversions = 3.70 (37/10) Gap_init rate = 0.03 (9 / 354), avg. gap size = 5.67 (51 / 9) 2341 12.69 2.05 1.27 rnd-2_family-202#SINE/5S-Deu-L2 1 391 (112) AmnSINE1#SINE/5S-Deu-L2 107 500 (75) m_b7s502i0 rnd-2_family- 1 GCTGCAGGAAGTAGCGCTGATGATTCAGNAGGTGGCANTCTTCCCTCCGA 50 i i i ? ? i AmnSINE1#SINE 107 GCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCTGA 156 rnd-2_family- 51 GTCAGTANTGAATCANTACCNCTGCACGGTGTTGGGGGACAC-NCACTGC 99 ? i ? i ? v ii i i -?ii AmnSINE1#SINE 157 GTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGCTGC 206 rnd-2_family- 100 TGGANGGGCCGNCTTTCGGAGAGAGNTGTAAAANCAGAGNNCCTGACCAC 149 ? v ? v- ?i ? - ?? AmnSINE1#SINE 207 TGGAGGTGCCGTCTTTCGGAT-GAGACGTAAAACC-GAGGTCCTGACCAC 254 rnd-2_family- 150 TTCAAGCTATCNA-------ATGGCNCTCTTCGCAAGAGCANGGACGNTA 192 vvi ii i? ------- ? i i ? ii ? AmnSINE1#SINE 255 TTGTGGTCATTAAAGATCCCATGGCACTTTTCGCAAGAGTAGGGGTGTTA 304 rnd-2_family- 193 ATCCCAGTGTCCTGGNCAAATTCTAACTTGGGNNATTACACTCTGTTACA 242 i i ? i i ?? i ii-i AmnSINE1#SINE 305 ACCCCGGTGTCCTGGCCAAATTCCAATTTGGGTAATTACATTCTGCC-TA 353 rnd-2_family- 243 CCTAAATTCCCCCTGCAGTTTCAGTTGAGTACAGCGTTCTTCACTTCCTG 292 i ii i ii AmnSINE1#SINE 354 CCTAAATTCCCCCTGCAGTTTCAATTGGATACGGTATTCTTCACTTCCTG 403 rnd-2_family- 293 CCCTAAANTGTTGTGTAGTGNTGGTTGTGCACTGTTANATAGCCGCTGTG 342 i ? ? - i i ? i i i i AmnSINE1#SINE 404 TCCTAAACTGTTGTGTAGTGTT-GCTGTGCGCTGTTAAACAGCTGCCGCG 452 rnd-2_family- 343 TTCCACTTCCAGAGGCGGCTGCATTTCAGTGGTGGGTGAAGTGATCCCT 391 -i i AmnSINE1#SINE 453 TTCCAC-CCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTGATCCCT 500 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.18 CpG sites = 44, Kimura (unadjusted) = 15.45 Transitions / transversions = 8.80 (44/5) Gap_init rate = 0.02 (7 / 390), avg. gap size = 1.86 (13 / 7) 368 12.50 3.12 0.00 rnd-2_family-202#SINE/5S-Deu-L2 440 503 (0) AmnSINE1#SINE/5S-Deu-L2 506 571 (4) m_b7s502i1 rnd-2_family- 440 TAGTTTTNAAAGTGCTTTGAGATCCTC--GGATGAAATGCGCTAGAGAAA 487 i v? i i i-- v v v AmnSINE1#SINE 506 TAGCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAA 555 rnd-2_family- 488 TGCAANGTATTATTAT 503 ? AmnSINE1#SINE 556 TGCAAGGTATTATTAT 571 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.44 CpG sites = 4, Kimura (unadjusted) = 14.21 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 63), avg. gap size = 2.00 (2 / 1) 1246 13.38 1.34 3.18 rnd-2_family-268#DNA/Kolobok 1 224 (342) UCON29#DNA/Kolobok 1 220 (219) m_b7s502i2 rnd-2_family- 1 TTGAAGTGCAGTTCCGCTCTGAAAAGTGACTATGTAAAAACGGCACCTTC 50 i i vi v v i i UCON29#DNA/Ko 1 TTAAAGTGCGGTTATGGTCAGAAAAGTGACTGTGTAAAAATGGCACCTTC 50 rnd-2_family- 51 TTACTCAACAGATCTGCTCCCTGTGCTGTATTCAGAGTCATANCTGCATA 100 i ? - ? v ? v UCON29#DNA/Ko 51 TTACTCAGCANATCTGCTCCCTGTG-TGTNTTCTGAGTCATATCTGCTTA 99 rnd-2_family- 101 A--CAGNAACNAAANTAAGTTTGCTTTTACTCCCGTTAGCCCTGCAGAGC 148 v--i v?i ? ?i ---- ? i v UCON29#DNA/Ko 100 CTTTACTGACAAAAACAAGT----TTTTACTNCTGTTAGCACTGCAGAGC 145 rnd-2_family- 149 CAACACAGCTACGGGAGAGTGAAAGCTGGATTCTATTCC-TCTCGCGCAT 197 i i i -- i-i ii UCON29#DNA/Ko 146 CAATACAGCTACGGAAGAGCG--AGCTGGATTCTATTCTGCCTCATGCAT 193 rnd-2_family- 198 CATCAACAGAATTGTTTACTAAGTTCC 224 i ivi UCON29#DNA/Ko 194 CATCAACAAAATTGTCAGCTAAGTTCC 220 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.42 CpG sites = 20, Kimura (unadjusted) = 15.53 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (9 / 223), avg. gap size = 1.11 (10 / 9) 697 13.97 5.41 3.31 rnd-2_family-268#DNA/Kolobok 340 487 (79) UCON29#DNA/Kolobok 223 373 (66) m_b7s502i3 rnd-2_family- 340 TTGNAGAAT----ATTCCCGGTGATGATGCACGAGAAAGAAAGAACTCAG 385 ? ---- v i i ? iv v UCON29#DNA/Ko 223 TTGCAGAATCTTTATTACTGGTGATGATGTANGAGGCAGAAAGAACACAG 272 rnd-2_family- 386 CTTGACTCTCAGATCCAAGGTTGAGTTTGCAGGGCTGGTAGTTAGAAGAA 435 i i v ? i --- UCON29#DNA/Ko 273 CTTGATTTTCAGATCCCAGGTTGAGTTTGCAGNGCTGGCAGTTAGAA--- 319 rnd-2_family- 436 CAAAACATTTTTACGAAT----AACTGATCACATTTGATNCGGAGGTANC 481 - v i -i v ---- v v i i v?i UCON29#DNA/Ko 320 -AAATCATCTTT-TGACTTGTAAACTGAGCAAATTTGATNTGGAAGTCAT 367 rnd-2_family- 482 TGAGAG 487 UCON29#DNA/Ko 368 TGAGAG 373 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.22 CpG sites = 11, Kimura (unadjusted) = 16.22 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (7 / 147), avg. gap size = 1.86 (13 / 7) 1674 13.97 16.97 0.66 rnd-2_family-289#SINE/tRNA 154 542 (9) LFSINE_Vert#SINE/tRNA 5 456 (3) m_b7s601i1 rnd-2_family- 154 GGGAACTGGATGGCTCAGGGGATTG-TAA-GGGATGCGGAATCTTTTACT 201 i - - i ii i i LFSINE_Vert#S 5 GGGGACTGGATGGCTCAGGGGATTGGTAATGGGATACGGAGCCTTTCACC 54 rnd-2_family- 202 TCTAGGTCGCCGGTTCAAATCCAGCCCAGGTCGGTAGTGACCGAAAGTTT 251 i i i i i- LFSINE_Vert#S 55 TCTAGGTCACTGGTTCGAATCCAGCCCAGGTCAGTAGTGACCGAAAGTC- 103 rnd-2_family- 252 GCTGCCATCTG---------TAATGGTC-----------AGTTGGTGGTC 281 ii i ---------iii i ----------- LFSINE_Vert#S 104 ATTACCATCTGACGGCTGTTCGGTGGCCTATGTGAAATGAGTTGGTGGTC 153 rnd-2_family- 282 TCAGTCCATTTCCGAG-GGGCAGGAGTCCACATCACAAAGCCACCACNAC 330 v v - i v i i? LFSINE_Vert#S 154 TCAGTCCAGTTCCTAGTGGACAGGTGTCCACATCACAAAACCACCATCAC 203 rnd-2_family- 331 GTTTGGCACCAATTGGCGATCTT------AGTC------GAGAGGCCATA 368 iv i ivi ------ ------ vi LFSINE_Vert#S 204 AATTGGCACTAATTGGCACCCTTGTTGGCAGTCTCAGCAGAGAGGCCAAG 253 rnd-2_family- 369 AACTGAATNAGCATAGGG------CAAATCTGT-ATC-CTAGAGGTGGTC 410 i ?i i i ------ v vi v - i - LFSINE_Vert#S 254 GACTGAATGGGCATGGAGACTGAACTACCCTCTCACCTCTAGAGGTGGTC 303 rnd-2_family- 411 TCTTCAGGTCAGGGTTNAGACACAGTGGCAGG-TAGTATCAGAGGNA--- 456 i i ? i v i -i i -- i ? --- LFSINE_Vert#S 304 CCTCCAGGTCAGGGTTGAGGCACATTGGCGGGGCAGTGT--GGGGAAGCT 351 rnd-2_family- 457 --TACTA----TGCCCGTG-----------CTGTGGATAAACAGAGGACT 489 --i i---- ----------- LFSINE_Vert#S 352 TGCACTGCCGCTGCCCGTGCTGTACCTGTTCTGTGGATAAACAGAGGACT 401 rnd-2_family- 490 TCAGTCTCCAGAGCTGTCAATCCGGCACCTTTCACNAGCACTAAG--CAC 537 i ? i-- LFSINE_Vert#S 402 TCAGTCTCCAGGGCTGTCAATCCGGCACCTTTCACGAGCACTAAATTCAC 451 rnd-2_family- 538 ATAAA 542 v LFSINE_Vert#S 452 TTAAA 456 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.20 CpG sites = 43, Kimura (unadjusted) = 16.18 Transitions / transversions = 3.91 (43/11) Gap_init rate = 0.05 (19 / 388), avg. gap size = 3.63 (69 / 19) 232 11.43 0.00 0.00 rnd-2_family-98#Unknown 48 82 (41) C MER133B#DNA/PIF-Harbinger (41) 74 40 m_b7s502i4 rnd-2_family- 48 CAGCTCCCATTGACTTCAGTGGGAGTTGAGGGCGC 82 i i v v C MER133B#DNA/P 74 CAACTCCCATTGACTTCAATGGGAGTTGCGCGCGC 40 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.44 CpG sites = 2, Kimura (unadjusted) = 12.44 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 40.43 0.00 0.00 rnd-3_family-1110#Unknown 50 126 (235) (CCC)n#Simple_repeat 1 77 (0) m_b7s252i23 rnd-3_family- 50 CCCCCCCTTGGCTCCTCCTCCGGCCGCCCACGCCCCCCCCCTTGGCTCCT 99 iivv i i i vv v v v iivv i i (CCC)n#Simple 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 rnd-3_family- 100 CCTCCGGCCGCGCCGCCCCCCCCCCCC 126 i vv v v v (CCC)n#Simple 51 CCCCCCCCCCCCCCCCCCCCCCCCCCC 77 Matrix = Unknown Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 244 22.41 0.00 0.00 rnd-3_family-1181#Simple_repeat 4 61 (428) HSAT5v1#Satellite 5222 5279 (619) m_b7s502i5 rnd-3_family- 4 TGTGCGTGTGTGTGCGCGTGCATATGTGTGTGCGTGTGTATGCACGTGTG 53 i iii iiii i ? i ii HSAT5v1#Satel 5222 TGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTGNACGCGTGTGTG 5271 rnd-3_family- 54 TGCGTNTG 61 i ? HSAT5v1#Satel 5272 CGCGTGTG 5279 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.44 CpG sites = 13, Kimura (unadjusted) = 31.21 Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 258 21.74 4.35 0.00 rnd-3_family-1181#Simple_repeat 14 82 (407) HSAT5v1#Satellite 5209 5280 (618) m_b7s502i6 rnd-3_family- 14 TGTGCGCGTGCA-TATGTGTGTGC--GTGTGTATGCACGTGTGTGCGTNT 60 i i i - i -- i i ii i i ? HSAT5v1#Satel 5209 TGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGT 5258 rnd-3_family- 61 GCGCGTGTATGTGTGCATGTGT 82 ?i i i i i HSAT5v1#Satel 5259 GNACGCGTGTGTGCGCGTGTGT 5280 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.25 CpG sites = 15, Kimura (unadjusted) = 29.69 Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2) 293 19.71 4.11 2.70 rnd-3_family-1181#Simple_repeat 24 96 (393) HSAT5v1#Satellite 5207 5280 (618) m_b7s502i7 rnd-3_family- 24 CATATGTGTGTGC---GTGTGTATGCACGTGTGTGCGTNTGCGCGTGTAT 70 ii ii --- i i i i-- i i HSAT5v1#Satel 5207 CATGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGC--GCGTGTGTGT 5254 rnd-3_family- 71 GTGTGCATGTGTGTGTGCATGTGTGT 96 ? i i ii HSAT5v1#Satel 5255 GTGTGNACGCGTGTGTGCGCGTGTGT 5280 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.80 CpG sites = 14, Kimura (unadjusted) = 25.54 Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.67 (5 / 3) 270 26.39 1.39 0.00 rnd-3_family-1181#Simple_repeat 37 108 (381) HSAT5v1#Satellite 5210 5282 (616) m_b7s502i8 rnd-3_family- 37 GTGTGTATGCA-CGTGTGTGCGTNTGCGCGTGTATGTGTGCATGTGTGTG 85 i i -i i i?i iii i ii HSAT5v1#Satel 5210 GCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTG 5259 rnd-3_family- 86 TGCATGTGTGTATGCGTGCATCT 108 ?i ii ii ii HSAT5v1#Satel 5260 NACGCGTGTGTGCGCGTGTGTCT 5282 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.34 CpG sites = 19, Kimura (unadjusted) = 39.14 Transitions / transversions = 1.00 (19/0) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 229 15.94 4.35 0.00 rnd-3_family-1181#Simple_repeat 118 186 (303) HSAT5v1#Satellite 5209 5280 (618) m_b7s502i9 rnd-3_family- 118 TGTGTGCGTGCG-TGTGTGTGTGCATGCGTGTGCGCGTGTGCGTGTGCGT 166 i i i- i i i i i HSAT5v1#Satel 5209 TGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGT 5258 rnd-3_family- 167 G--CGTGTGTGTGCGTGTGCGT 186 -- i i i HSAT5v1#Satel 5259 GNACGCGTGTGTGCGCGTGTGT 5280 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.86 CpG sites = 11, Kimura (unadjusted) = 19.20 Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2) 37 23.24 0.00 1.16 rnd-3_family-1181#Simple_repeat 220 306 (183) (GT)n#Simple_repeat 1 86 (0) m_b7s252i20 rnd-3_family- 220 GTGTGTGTGTGTGCATGTGTGTGTGTGTGCGCGCGCGCGTACTGTGTGTC 269 ii i i i i i -v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-GTGTGTGTG 49 rnd-3_family- 270 TGTGTACGTGTGCGTGTGTGTATNTGCGCGCGTGTGT 306 ii i i ? i i i (GT)n#Simple_ 50 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 86 Matrix = Unknown Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 304 21.13 1.41 0.00 rnd-3_family-1181#Simple_repeat 312 382 (107) HSAT5v1#Satellite 5209 5280 (618) m_b7s502i10 rnd-3_family- 312 TGCGTGTGTGCA-TGTGTGTGTGTATGTATGTGTGCATGTNTGTGTGTGT 360 ii - i i iii i ii ? HSAT5v1#Satel 5209 TGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGT 5258 rnd-3_family- 361 GCATACGTGTGTGTGCATGCGT 382 ? ii i i i HSAT5v1#Satel 5259 GNACGCGTGTGTGCGCGTGTGT 5280 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.80 CpG sites = 15, Kimura (unadjusted) = 28.53 Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 237 24.68 1.32 4.05 rnd-3_family-1181#Simple_repeat 322 397 (92) HSAT5v1#Satellite 5207 5280 (618) m_b7s502i11 rnd-3_family- 322 CATGTGTGTGTGTA-TGTATGTGTGCATGTNTGTGTGTGTGCATACGTGT 370 i ii i - i i --i i i i i ii HSAT5v1#Satel 5207 CATGCGTGCATGCAATGTGTGTGTGCACG--CGCGTGCGCGCGTGTGTGT 5254 rnd-3_family- 371 GTGTGCATGCGTGCGCGTACGGTGTGT 397 ? i i i ii - HSAT5v1#Satel 5255 GTGTGNACGCGTGTGTGCGC-GTGTGT 5280 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.89 CpG sites = 18, Kimura (unadjusted) = 34.66 Transitions / transversions = 1.00 (18/0) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 20 23.06 3.03 0.00 rnd-3_family-1181#Simple_repeat 420 485 (4) (TGTGCG)n#Simple_repeat 1 68 (0) m_b7s252i21 rnd-3_family- 420 TGTGCGCGTNTGCGCACGCGTGCGTGTGC--GTACGTGTGCGTGTNCGTA 467 i ?i i ii i -- i ? i (TGTGCG)n#Sim 1 TGTGCGTGTGCGTGTGCGTGTGCGTGTGCGTGTGCGTGTGCGTGTGCGTG 50 rnd-3_family- 468 CGTGTGTTCGTGTGTGTG 485 i i v i (TGTGCG)n#Sim 51 TGCGTGTGCGTGTGCGTG 68 Matrix = Unknown Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.02 (1 / 65), avg. gap size = 2.00 (2 / 1) 15 20.84 4.26 0.00 rnd-3_family-1181#Simple_repeat 437 483 (6) (GCGT)n#Simple_repeat 1 49 (0) m_b7s252i22 rnd-3_family- 437 GCGTGCGT--GTGCGTACGTGTGCGTGTNCGTACGTGTGTTCGTGTGTG 483 -- i i i i ? i i v i (GCGT)n#Simpl 1 GCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTG 49 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1) 1646 13.83 17.56 1.83 rnd-3_family-1244#DNA/PIF-Harbinger 18 444 (0) Chompy-6_Croc#DNA/PIF-Harbinger 481 973 (7) m_b7s502i12 rnd-3_family- 18 TCCGGCAGAGCGGGGACTTGAGCCCGGGT----------------GAGTG 51 v ? vi v i ---------------- Chompy-6_Croc 481 TCAGGCNGAGGAGGGAATTGAACCCGGGTCTCCCACNTCCTGGGCGAGTG 530 rnd-3_family- 52 CTCTAACCACCGGGCTGTTGGGCGTAATAGG---GCGGT-----C-TCTC 92 ii i ?i-- v --- i----- -i Chompy-6_Croc 531 CTCTAACCACTAGGCTATTGNA--TAAAAGGGGGGCGGCACCACCACCTC 578 rnd-3_family- 93 CTTT-------TTTTGA--GAAAGGGCTGACCT----------------- 116 ii------- i -- i iv ? i----------------- Chompy-6_Croc 579 CTCCGGCCGCGTTTTAAAAGAAAAGAGTGANCCCTGCTCCGTTTTTGAAA 628 rnd-3_family- 117 -----GGCTTAGGCGCCTAACTCCAGGAGAGGGTTCACGGCTGTGAATCC 161 ----- ? vv Chompy-6_Croc 629 GAAAGGGCTTAGGCGCCTANCTCCAGGAGAGGGTTCCGGGCTGTGAATCC 678 rnd-3_family- 162 CGAGCAGAGGNAGGCGCCTCCCNCTGGCCCAGAGTTAGGCGCCTAACTCC 211 ii v ? ?vii v ? vi Chompy-6_Croc 679 CGAGTGGACGGAGGCGCCTCCCTGCAGCCCTGAGTNAGGCGCCTAAGCCC 728 rnd-3_family- 212 CTTTGAGGGGCAGGGAGGGGCTTAAGCCACGTCC-TCTTCTCGGCATTTC 260 vvv ----- ii v ii - v i i i Chompy-6_Croc 729 CGGAGAGGGGC-----GGGATTTAAGACACACCCCTGTCCTCAGCGTTTC 773 rnd-3_family- 261 CTACTG-CTAGCT---ACAG-TCCCCGCTCAGCNTGCTGGCTCCTGTGAA 305 i - ---i i - ? ?i i Chompy-6_Croc 774 CTATTGGCTAGCTTAGGCGGCTCCCCGCTCAGCGTGCTGGCTNTTGTGGA 823 rnd-3_family- 306 TCCCNTTCTTAGNNGCCTAACTCTCCCCATGCATTGTATCGGGAGCCTGG 355 ? v ?? i v i Chompy-6_Croc 824 TCCCATTCTGAGGCGCCTAACTCTCCCCATGCACTGTATAGGGAGCCTAG 873 rnd-3_family- 356 GCGCCTAACTCGGGGCTGTGGATTCCACT--GGGTGGCAGGGCGCCTAAA 403 i ? -- - vi Chompy-6_Croc 874 GCGCCTAACTCAGGGCTNTGGATTCCACTCCGGG-GGCCAGGCGCCTAAA 922 rnd-3_family- 404 ACTTAGGCNTTGCAATGCT-----------AGCCTAAGTCCCCTTTGTGG 442 v ?i i -----------v - Chompy-6_Croc 923 AGTTAGGCGCTGCAACGCTCAGCGTTGCGGCGCCTAAGT-CCCTTTGTGG 971 rnd-3_family- 443 AT 444 Chompy-6_Croc 972 AT 973 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.00 CpG sites = 37, Kimura (unadjusted) = 16.15 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.05 (23 / 426), avg. gap size = 3.65 (84 / 23) 358 32.97 0.63 5.28 rnd-3_family-132#LINE/L2 273 589 (124) X24_LINE#LINE/L2 12 314 (0) m_b7s601i2 rnd-3_family- 273 GGGGCTGCCGTTGNAAGCAACNCNNAGGCNGCAGNTTGCGACTATTAGAG 322 v ? ii v ? ?? i ?v ? v i -----i - X24_LINE#LINE 12 GGGGCTGCCCTTGAAGACCACCCGGAAGCTTCAGCTGGTG-----CAGA- 55 rnd-3_family- 323 ATGCAGCAGCCCCTGAACCCATCTCCACAGCGGGACGTGTCTCCGGGAGC 372 i i --------i v vv i? vii?v i v v? X24_LINE#LINE 56 ATGCAGCGGCTC--------GTCTGCTGAANGGTGTNAGCCACANGGAGC 97 rnd-3_family- 373 ACATCACTCCTNTGCTTCACACCCTCCACTGGCTCCCAGTTCTCCCCC-A 421 i v ? i i vi v v ?i iv ii - X24_LINE#LINE 98 ACATTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCTTCCGA 147 rnd-3_family- 422 TTGCCAGTTCAAGGCCTTGGTCCTGATCTTCGAAGCCATCAGTGGGTCAG 471 v - i iv iiii i vii v vvi v ii X24_LINE#LINE 148 GTG-CAATTCAAGGTGTTGACTTTAATCTATAAAGCCCTATATGGTTTGG 196 rnd-3_family- 472 GACCCAGCTACATNAGCGACCGCATCTCCATCTACGACCCGCCAAGACAG 521 v ii i v ? v i v ivi ?i vv i v i i X24_LINE#LINE 197 GCCCTGGTTACCTTAGAGATCGCCTCTCTCCCTNTGCACCGTCACGGCAA 246 rnd-3_family- 522 CTGCGCTCCTCTGGGACAATGCAGNTNACAAAGCCCAGG-GCGAAGCGCG 570 i v v vv i iiv v v ? ? iivv i-vi ?iv X24_LINE#LINE 247 TTGAGATCAGCTAGGATGCTCCTGCTAACGGTTCCCAGATTTGAANTTCG 296 rnd-3_family- 571 TGAGAGACGGAGGTAAAAT 589 - i ?v ii ii X24_LINE#LINE 297 -GGGANCCGGAGGCGAGGT 314 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.03 CpG sites = 56, Kimura (unadjusted) = 48.48 Transitions / transversions = 1.30 (56/43) Gap_init rate = 0.06 (18 / 316), avg. gap size = 1.00 (18 / 18) 37 0.00 0.00 0.00 rnd-3_family-136#DNA/CMC-EnSpm 114 149 (557) (TG)n#Simple_repeat 1 36 (0) c_b7s251i0 rnd-3_family- 114 TGTGTGTGNGTGTGTGTGTGTGTGTGTGTGTGTGTG 149 ? (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 32 3.23 0.00 0.00 rnd-3_family-136#DNA/CMC-EnSpm 445 476 (230) (TG)n#Simple_repeat 1 32 (0) c_b7s251i1 rnd-3_family- 445 TGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTG 476 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 5.00 0.00 0.00 rnd-3_family-136#DNA/CMC-EnSpm 520 540 (166) (GA)n#Simple_repeat 1 21 (0) m_b7s252i17 rnd-3_family- 520 GAGAGAGAGAGAGGGAGAGAG 540 i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAG 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 19 22.78 0.00 1.85 rnd-3_family-136#DNA/CMC-EnSpm 622 676 (30) (TG)n#Simple_repeat 1 54 (0) m_b7s252i18 rnd-3_family- 622 TGCGTGTGTGTGNCACTCTGTGTGTGTGTGACACCNGTGCGTGTGTGTGT 671 i ?vvv v -iiiv? i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGT 49 rnd-3_family- 672 GTGTG 676 (TG)n#Simple_ 50 GTGTG 54 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 15 5.48 0.00 0.00 rnd-3_family-136#DNA/CMC-EnSpm 676 694 (12) (GA)n#Simple_repeat 1 19 (0) m_b7s252i19 rnd-3_family- 676 GAGAGAGAGAGAGAGACAG 694 v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAG 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 916 20.16 3.37 3.37 rnd-3_family-1500#DNA/PIF-Harbinger 1 267 (0) Chompy-6_Croc#DNA/PIF-Harbinger 481 747 (233) m_b7s502i13 rnd-3_family- 1 TCAGGCACTAGGGGGAAACTGAACCAGGGTCTCCCANAT-------GAGN 43 ?v- i i i v ?? ------- ? Chompy-6_Croc 481 TCAGGCNG-AGGAGGGAATTGAACCCGGGTCTCCCACNTCCTGGGCGAGT 529 rnd-3_family- 44 NCCCTAACCACTGGGCTAAAGGTTATAAGGGAGGCTGTGCCACCACCCTC 93 ? i i vv ?v v i v ii --- Chompy-6_Croc 530 GCTCTAACCACTAGGCTATTGNATAAAAGGGGGGCGGCACCACCACC--- 576 rnd-3_family- 94 CTCCTCCCCGGCCGTTTTGTGTGGAGTTAGGCACGTGCCTAACTC-ATTC 142 - -- iv v i-ii vv i vii v? ivi -i i Chompy-6_Croc 577 -TCCTCC--GGCCGCGTTTTA-AAAGAAAAGAGTGANCCCTGCTCCGTTT 622 rnd-3_family- 143 TCGCAAGAAACGGCTTAGGCGCCTGACTCCAGGAGAGGGTTCCCGGCTGT 192 i v v i? v Chompy-6_Croc 623 TTGAAAGAAAGGGCTTAGGCGCCTANCTCCAGGAGAGGGTTCCGGGCTGT 672 rnd-3_family- 193 GGATCGCAAGCAGAGATAGGCGCCTCCCTGCAGCCCGGACTTAGGCGCCT 242 i v i ii viv v v ? Chompy-6_Croc 673 GAATCCCGAGTGGACGGAGGCGCCTCCCTGCAGCCCTGAGTNAGGCGCCT 722 rnd-3_family- 243 -ANCTCCGTGAGAGGGGCAGGGCTTA 267 - ? i - i ii Chompy-6_Croc 723 AAGCCCCG-GAGAGGGGCGGGATTTA 747 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.31 CpG sites = 30, Kimura (unadjusted) = 24.95 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.05 (12 / 266), avg. gap size = 1.50 (18 / 12) 1065 19.38 12.73 3.05 rnd-3_family-1516#DNA/PIF-Harbinger 4 333 (5) Chompy-6_Croc#DNA/PIF-Harbinger 376 736 (244) m_b7s502i14 rnd-3_family- 4 ACAGCTTCAGCAGGAGAGACTGAGGGAGCCCC-ACCCATCAGAATATCCC 52 i i iiv i v - -- v i Chompy-6_Croc 376 ACAGCTTCAACAGGAGGGGTGGAGAGTGCCCCCACCC--CAGAATAGCCT 423 rnd-3_family- 53 ACAGTCCAGCGGTTAGGGCACTCGCCTGAGAGGTGGGA-ACCT--GTTCA 99 i i ii i v i - iv -- ii Chompy-6_Croc 424 ATAGCCTGGTGGTTAGGGCACTCTCCTGGGAGGTGGGAGATGTGGGTTTG 473 rnd-3_family- 100 AATCCCTTCTCCCCATCAGGCGGAGGGGGGACTTGAACTGGGGGTCTCCC 149 i-------- ? i v i-v Chompy-6_Croc 474 AATCCCC--------TCAGGCNGAGGAGGGAATTGAACC-CGGGTCTCCC 514 rnd-3_family- 150 GCGTCCCAGGTGAGTGCCCTAACCACTGGGCTAAAAGTTATGAGGGAGNT 199 i ? ii i i i vvi?v vi i ?i Chompy-6_Croc 515 ACNTCCTGGGCGAGTGCTCTAACCACTAGGCTATTGNATAAAAGGGGGGC 564 rnd-3_family- 200 G----CTCCTCCTCCTC----------------------AGCGGTTCTTG 223 ---- v v ---------------------- i i?i i Chompy-6_Croc 565 GGCACCACCACCTCCTCCGGCCGCGTTTTAAAAGAAAAGAGTGANCCCTG 614 rnd-3_family- 224 C------------NAAAACGNCNTAGGCGCCTAACTCCAGGAGAGGGTTC 261 ------------?i v ? ? ? Chompy-6_Croc 615 CTCCGTTTTTGAAAGAAAGGGCTTAGGCGCCTANCTCCAGGAGAGGGTTC 664 rnd-3_family- 262 GCAGCTGAGAATCCCAAGCAGAGANAGGCGCCTCCCTGCAGCCCGGACTT 311 vvi v i ii vi? v v ? Chompy-6_Croc 665 CGGGCTGTGAATCCCGAGTGGACGGAGGCGCCTCCCTGCAGCCCTGAGTN 714 rnd-3_family- 312 AGGTGCCTANCTCCGNGAGAGG 333 i ?vi v? Chompy-6_Croc 715 AGGCGCCTAAGCCCCGGAGAGG 736 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.00 CpG sites = 40, Kimura (unadjusted) = 24.15 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.05 (17 / 329), avg. gap size = 3.12 (53 / 17) 23 21.00 0.00 2.00 rnd-3_family-1772#Unknown 87 137 (574) (TC)n#Simple_repeat 1 50 (0) m_b7s252i16 rnd-3_family- 87 TCACTCCGTCTCTCTCTCTGTCTCTCTCTCTCTGCAGCCCCTCTCTCGCT 136 v iv v - vvi i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCT 49 rnd-3_family- 137 C 137 (TC)n#Simple_ 50 C 50 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 750 10.27 8.78 1.26 rnd-3_family-187#DNA/PIF-Harbinger 1 148 (377) Chompy-6_Croc#DNA/PIF-Harbinger 53 211 (769) m_b7s502i15 rnd-3_family- 1 TGTTCCACTTTGTATAAA-TAATTAAATATTCATTGGGCC-GAGAGA--- 45 ? ? i ? -v ? v - --- Chompy-6_Croc 53 TGTNCCACTNTGCANAAAAGAATTNAAGATTCATTGGGCCAGAGAGAGGG 102 rnd-3_family- 46 ---AAGNGAG----TGACTCTGTAGCCCGGTGGTTAGGGCACTCACCTGG 88 --- ? ? ---- ii Chompy-6_Croc 103 AGCAAGAGNGAGCATGACTCTGTAGCCTAGTGGTTAGGGCACTCACCTGG 152 rnd-3_family- 89 GANGTGGGAGACCCAGGNTCCAGTCTCCCTGCTCCAATGAATATTTAATT 138 ? v ? ii ? i -- v v i vv Chompy-6_Croc 153 GAGGGGGGAGNCCTGGGTTCCGG--TCCCTGCTCCAAGGACTGTTTATGT 200 rnd-3_family- 139 A-TTTATACAA 148 - v Chompy-6_Croc 201 ATTTTATCCAA 211 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.08 CpG sites = 7, Kimura (unadjusted) = 11.86 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.05 (8 / 147), avg. gap size = 1.88 (15 / 8) 974 19.38 8.57 3.10 rnd-3_family-187#DNA/PIF-Harbinger 112 356 (169) Chompy-6_Croc#DNA/PIF-Harbinger 332 589 (391) m_b7s502i16 rnd-3_family- 112 TCTCCCTGCTCCAATGAATATTTAATTATTT-ATACAAAGTGGAACAGCT 160 i vi v v v -v i ? ? Chompy-6_Croc 332 TCTCTCTGGCCCAATGAATCTTGAATTCTTTTCTGCANAGTGGNACAGCT 381 rnd-3_family- 161 TCAACAGGAGAGACTGAGAGAGACCC-ACCCCAGAATACCCCGTAGCCCG 209 i iiv v v - v ii i Chompy-6_Croc 382 TCAACAGGAGGGGTGGAGAGTGCCCCCACCCCAGAATAGCCTATAGCCTG 431 rnd-3_family- 210 GTGG-----------------GAGGTGGGAGACCCGGGTTCAAATCCCTG 242 ----------------- ivi ii i- Chompy-6_Croc 432 GTGGTTAGGGCACTCTCCTGGGAGGTGGGAGATGTGGGTTTGAATCCCC- 480 rnd-3_family- 243 CTCCGAATCAGGCAGAGCGGGGATTTGAACCTGGGTCTCCCACATCCCAG 292 ------- ? vi v i ? ii Chompy-6_Croc 481 -------TCAGGCNGAGGAGGGAATTGAACCCGGGTCTCCCACNTCCTGG 523 rnd-3_family- 293 GTGAGTGCCCTAACCACTGGGCTATAAGANCGTATAGGGGT--CATCACC 340 i i i vi? ?viv vi i-- i Chompy-6_Croc 524 GCGAGTGCTCTAACCACTAGGCTATTGNATAAAAGGGGGGCGGCACCACC 573 rnd-3_family- 341 TCCTCCTCNTGCTGTG 356 v ?v i i Chompy-6_Croc 574 ACCTCCTCCGGCCGCG 589 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.86 CpG sites = 28, Kimura (unadjusted) = 23.67 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.05 (12 / 244), avg. gap size = 2.42 (29 / 12) 12 17.04 2.22 6.98 rnd-3_family-190#Unknown 104 148 (252) (CCGC)n#Simple_repeat 1 43 (0) m_b7s252i14 rnd-3_family- 104 CCTCCC-CCAGCCAGCCCTTCCGCGCTGCCCGGCCCGCGCCGCCCG 148 v - v v vi - i - - (CCGC)n#Simpl 1 CCGCCCGCCCGCCCGCCCGCCCGC-CCGCCC-GCCCGC-CCGCCCG 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 13 22.31 5.66 0.00 rnd-3_family-190#Unknown 174 226 (174) (CCGCGG)n#Simple_repeat 1 56 (0) m_b7s252i15 rnd-3_family- 174 CCGGGGCTCCGGCCGCTGCCACGGCAGC-G--GCGGCCGNGGCGGGGGCC 220 v iv v i v - -- ? v v (CCGCGG)n#Sim 1 CCGCGGCCGCGGCCGCGGCCGCGGCCGCGGCCGCGGCCGCGGCCGCGGCC 50 rnd-3_family- 221 CGGGCC 226 vv (CCGCGG)n#Sim 51 GCGGCC 56 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.50 (3 / 2) 22 0.00 0.00 0.00 rnd-3_family-288#Unknown 2 25 (346) (T)n#Simple_repeat 1 24 (0) m_b7s252i13 rnd-3_family- 2 TTTTTTTTTTTTTTTTTTTTTTTT 25 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 208 5.12 7.50 2.38 rnd-3_family-368#Unknown 20 59 (1268) C L2c_3end#LINE/L2 (69) 409 368 m_b7s601i3 rnd-3_family- 20 AAGACA--GTCCCTGCCC-CAAAGAGCTCACAGTCTAAGTGAA 59 -- - i - i C L2c_3end#LINE 409 AAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT-AGTGGA 368 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 5.41 CpG sites = 2, Kimura (unadjusted) = 5.41 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.33 (4 / 3) 185 25.86 3.45 0.00 rnd-3_family-368#Unknown 1270 1327 (0) C MER131#DNA (154) 61 2 m_b7s601i4 rnd-3_family- 1270 TTTA-AACAGAAGTCGTGATGCAACCTTAACTATAGTGGCGC-NGCCGTN 1317 - ii iivv iiv ? i -?i v i? C MER131#DNA 61 TTTATAATGGAAACGCTGACAGANCCTTAACTATAGCGGCGCGAACGGCG 12 rnd-3_family- 1318 CCACTGTAAT 1327 i i C MER131#DNA 11 CCGCTATAAT 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 11, Kimura (unadjusted) = 35.93 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 2913 9.65 1.88 11.41 rnd-3_family-404#LINE/L2 3 692 (111) L2-1_Crp#LINE/L2 610 1240 (1) m_b7s551i0 rnd-3_family- 3 CTCCCATCTTAAAAAAACCCACCTTTGACCCCACTTGCCTCTCCAACTAC 52 --- i ---- L2-1_Crp#LINE 610 CTCCCATCTTAAAAAAA---ACCCTTGACCCCACTTGCCTCTCCA----C 652 rnd-3_family- 53 CGCCCCA-CTCCCTTCTCCCTTTCATCTCTAAGCTCATTGAACGCGCTGT 101 i - ?i L2-1_Crp#LINE 653 CACCCCATCTCCNCTCTCCCTTTCATCTCTAAGCTCATTGAACGCGCTGT 702 rnd-3_family- 102 CTACAATCGCTGTCTGGAGTTCCTCTCCTCCAGTTCCATCCTAGACCCTC 151 i -- ---- - L2-1_Crp#LINE 703 TTACAATCGCTGTCTGGAGTTCCTCTCCTCCAGTTCC--C----ACCCT- 745 rnd-3_family- 152 TCCAATCCGGCTTCCGCCCCTTGCACTCCACTGAAAC----TGCTCTCAC 197 -- v i i - -i i---- - ii L2-1_Crp#LINE 746 --CACTCCAGCTTCTGCCCCTT-C-TTCCACTGAAATCTAATG-TCTTGC 790 rnd-3_family- 198 CAAAGTCTCTAATGACCTCTTCCTGGCCAAAGCTCAGAGCCAGTACTCCA 247 - i i ? i L2-1_Crp#LINE 791 CAAAGTCTCTAATGA-CTCTTTCTAGCCAAANCTCAGAACCAGTACTCCA 839 rnd-3_family- 248 TCCTCATCCTCCTTGACCTGTCAGCTGCCTTTGACACNGTCGACCA-TGC 296 --- i ? - L2-1_Crp#LINE 840 TCCTCATCCTCCTTGACCTGTCA---GCCTTCGACACAGTCGACCACTGC 886 rnd-3_family- 297 TCTTCTTGAAATCTTGTCCTCCCTTGGCTTCTCGTGACTTCTGTCCTCTC 346 - --- L2-1_Crp#LINE 887 TCTTCTTGAAATCTTGTCCTCCCTTGGCTTC-CGTGA---CTGTCCTCTC 932 rnd-3_family- 347 CTGGTTCTCCTNCCTCTCTAATCGCTCCTTCAGCATGTCCTTCGGAGGAT 396 ? i ii -v i - i ------- L2-1_Crp#LINE 933 CTGGTTCTCCTTCTTTCCT-CTTGC-CTTT-------TCCTTCGGAGGAT 973 rnd-3_family- 397 CCTCCTCATCCNCCCTCCAGCTTTCTGTGGGGGTTCCACAGGGCTCTGTC 446 - - i i - i? iiiii i---- ii-- L2-1_Crp#LINE 974 -CTCCTCATCC-CCTTCCAACTTTC-GCNGAAACCCT----GGCTCCA-- 1014 rnd-3_family- 447 CTGGNTCCCTTCTCTTCTCCCTCTACACCT-TATCTCTGGGTAATCTCAT 495 v ? ii iii i? vi?-i L2-1_Crp#LINE 1015 CTTGCTCCCTTTCCTTTCTCCTCCNCAGTNACATCTCTGGGTAATCTCAT 1064 rnd-3_family- 496 CCGCAAACACGAATTCAACTACC----ATCTCTATGCTGACGACTCACAG 541 i ------- -- ---- ii ----- i L2-1_Crp#LINE 1065 CTGCAAAC-------CAA--ACCGTATATCTTCATG-----GACTCGCAG 1100 rnd-3_family- 542 ATCTAC-CTCTCTACTCCAGACCTGTCTCCTTCTGTCCAAACTAAAATCT 590 - - L2-1_Crp#LINE 1101 ATCTACACTCTCTACTCCAGACCTGTCTCCTTCTGTCCAAA-TAAAATCT 1149 rnd-3_family- 591 CGGCCTGTCCTTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTCA 640 -- i i - i ivv --------- L2-1_Crp#LINE 1150 CGGCCTGTC--TCTCCGACGTCTCCTCGTGG-TATTGTGCC--------- 1187 rnd-3_family- 641 AGCTCAACATGGCTAAAAC-AGAGCTCTTAATCTTCCCCCCCAAGCCCTC 689 -i v ? v i? vv v L2-1_Crp#LINE 1188 AGCTCAACATGGCTAAAACGGGATCTNTTAATCTACCTNCCCATCCCCAC 1237 rnd-3_family- 690 CCC 692 L2-1_Crp#LINE 1238 CCC 1240 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.89 CpG sites = 48, Kimura (unadjusted) = 10.60 Transitions / transversions = 4.36 (48/11) Gap_init rate = 0.11 (79 / 689), avg. gap size = 1.08 (85 / 79) 4049 3.29 0.96 7.48 rnd-3_family-404#LINE/L2 178 803 (0) L2-1_AMi#LINE/L2 65 652 (583) m_b7s551i1 rnd-3_family- 178 TCCACTGAAACTGCTCTCACCAAAGTCTCTAATGACCTCTTCCTGGCCAA 227 - v---- iv i L2-1_AMi#LINE 65 TCCACTGAA-CTGCTG----CAGCGTCTCTAATGACCTCTTCCTAGCCAA 109 rnd-3_family- 228 AGCTCAGAGCCAGTACTCCATCCTCATCCTCCTTGACCTGTCAGCTGCCT 277 v i i L2-1_AMi#LINE 110 ATCTCAGAACCAGTACTCCATCCTCATCCTCCTTGACCTGTCAGCCGCCT 159 rnd-3_family- 278 TTGACACNGTCGACCATGCTCTTCTTGAAATCTTGTCCTCCCTTGGCTTC 327 ? L2-1_AMi#LINE 160 TTGACACAGTCGACCATGCTCTTCTTGAAATCTTGTCCTCCCTTGGCTTC 209 rnd-3_family- 328 TCGTGACTTCTGTCCTC--TCCTGGTTCTCCTNCCTCTCTAATCGCTCCT 375 - - -- ---- i ? L2-1_AMi#LINE 210 -CGTGACT-CTGTCCTCCGTC----TCCTCCTACCTCTCTAATCGCTCCT 253 rnd-3_family- 376 TCAGCATGTCCTTCGGAGGATCCTCCTCATCCNCCCTCCAGCTTTCTGTG 425 -i ------------- i ----- ?i vi L2-1_AMi#LINE 254 T-GGCA-------------ATTCT-----TCCTTCCTCCCACTTTCTGTG 284 rnd-3_family- 426 GGGGTTCCACAGGGCTCTGTCCT-GGNTCCCTTCTCTTCTCCCTCTACAC 474 - ?i -- L2-1_AMi#LINE 285 GGGGTTCCACAGGGCTCTGTCCTTGGTCCCCTTCTCTTCTC--TCTACAC 332 rnd-3_family- 475 CTTATCTCTGGGTAATCTCATCCGCAAACACGAATTCAACTACCATCTCT 524 i -- L2-1_AMi#LINE 333 CTTATCTCTGGGTAATCTCATCCGCAAACACAAATTCAACTACCATCT-- 380 rnd-3_family- 525 ATGCTGACGACTCACAGATCTACCTCTCTACTCCAGACCTGTCTCCTTCT 574 -- i --- L2-1_AMi#LINE 381 --GTTGAC---TCACAGATCTACCTCTCTACTCCAGACCTGTCTCCTTCT 425 rnd-3_family- 575 GTCCAAACTAAAATCTCGGCCTGTCCTTCTCTGACATCTCCTCGTGGATG 624 -- L2-1_AMi#LINE 426 GTCCAAACTAAAATCTCGGCCTGTC--TCTCTGACATCTCCTCGTGGATG 473 rnd-3_family- 625 TCTAGCCGTCAGCTCAAGCTCAACATGG-CTAAAACAGAGCTCTTAATCT 673 - L2-1_AMi#LINE 474 TCTAGCCGTCAGCTCAAGCTCAACATGGCCTAAAACAGAGCTCTTAATCT 523 rnd-3_family- 674 TCCCCCCCAAGCC--CTCCCCGCTACCTCCTTTCTCGATCACTGTGGACA 721 - -- ii v -- L2-1_AMi#LINE 524 T-CCCCCCAAGCCTNCTCCCCATTCCCT--TTTCTCGATCACTGTGGACA 570 rnd-3_family- 722 ACACCACCATCCTGCCTGTCACTCAGGCCCGTAACCTGGGCGTCATCTTC 771 L2-1_AMi#LINE 571 ACACCACCATCCTGCCTGTCACTCAGGCCCGTAACCTGGGCGTCATCTTC 620 rnd-3_family- 772 GACTCGGACCTCTCTCTAGGTCCTCACATCCA 803 L2-1_AMi#LINE 621 GACTCGGACCTCTCTCTAGGTCCTCACATCCA 652 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.21 CpG sites = 14, Kimura (unadjusted) = 3.38 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.08 (48 / 625), avg. gap size = 1.04 (50 / 48) 32 13.22 3.12 7.61 rnd-3_family-442#Unknown 1 96 (372) (GCAGGGG)n#Simple_repeat 1 92 (0) m_b7s252i9 rnd-3_family- 1 GCAGGGGGTCGGGGTGCAGGGTGCGGCAGGGGGCTCAGGGCAGGGGGTTG 50 - i v - - - vvi iv (GCAGGGG)n#Si 1 GCAGGGGG-CAGGGGGCA-GG-G-GGCAGGGGGCAGGGGGCAGGGGGCAG 46 rnd-3_family- 51 GGGTGCA-GGAG--GGGTGCGGGGGGCAGGGGGCTCAGGGGGCAGGGGG 96 - - i -- v i -- (GCAGGGG)n#Si 47 GGG-GCAGGGGGCAGGGGGCAGGGGGCAGGGGG--CAGGGGGCAGGGGG 92 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.09 (9 / 95), avg. gap size = 1.11 (10 / 9) 19 3.67 0.00 3.45 rnd-3_family-442#Unknown 114 143 (325) (CTGC)n#Simple_repeat 1 29 (0) m_b7s252i10 rnd-3_family- 114 CTCCCTGCCTGCCTGCCTGCCTGCCCTGCC 143 v - (CTGC)n#Simpl 1 CTGCCTGCCTGCCTGCCTGCCTG-CCTGCC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 12 4.69 0.00 8.33 rnd-3_family-442#Unknown 312 337 (131) (GCAG)n#Simple_repeat 1 24 (0) m_b7s252i11 rnd-3_family- 312 GCAGGGCAGGGCAGGCAGGCAGGGAG 337 - - v (GCAG)n#Simpl 1 GCA-GGCA-GGCAGGCAGGCAGGCAG 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 14 0.00 8.33 0.00 rnd-3_family-442#Unknown 312 335 (133) (GCAGG)n#Simple_repeat 1 26 (0) m_b7s252i12 rnd-3_family- 312 GCAGGGCAGGGCA-GGCA-GGCAGGG 335 - - (GCAGG)n#Simp 1 GCAGGGCAGGGCAGGGCAGGGCAGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 34 18.27 1.16 3.57 rnd-3_family-447#Unknown 46 131 (189) (CCCCGC)n#Simple_repeat 1 84 (0) m_b7s252i7 rnd-3_family- 46 CCCCGGCCCCGCCCCCAGCCCCGCCCACGCCCCCG-CCCCAACCCCGCCC 94 v iv v - iv (CCCCGC)n#Sim 1 CCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCC 50 rnd-3_family- 95 CCTCCCCAAAGTCTCCGCCCCCTCCCCTGCTTCCCGC 131 v --v i i v i -i (CCCCGC)n#Sim 51 CCGCCCC--CGCCCCCGCCCCCGCCCCCGC-CCCCGC 84 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 21 24.64 6.96 2.50 rnd-3_family-447#Unknown 202 316 (4) (GGCGCCCC)n#Simple_repeat 1 120 (0) m_b7s252i8 rnd-3_family- 202 GGCCCCCCGGCGGCTCCAGC-CTGGGTCGGCTCGG-GCCCTGGGGTGCC- 248 v - i i - ivv v v i - i v iv - (GGCGCCCC)n#S 1 GGCGCCCCGGC-GCCCCGGCGCCCCGGCGCCCCGGCGCCCCGGCGCCCCG 49 rnd-3_family- 249 G-GCCCCGGC-CCCCGGC-CGACCAC-CCCCGGCCCGCCCAGCACTGCCG 294 - - - vv vi - v - i i -v (GGCGCCCC)n#S 50 GCGCCCCGGCGCCCCGGCGCCCCGGCGCCCCGGCGC-CCCGGCGC-CCCG 97 rnd-3_family- 295 GC-CCCCGGCGGCCCGGCGCACC 316 - v v (GGCGCCCC)n#S 98 GCGCCCCGGCGCCCCGGCGCCCC 120 Matrix = Unknown Transitions / transversions = 0.64 (9/14) Gap_init rate = 0.10 (11 / 114), avg. gap size = 1.00 (11 / 11) 244 18.42 0.00 0.00 rnd-3_family-4534#Unknown 77 114 (0) MER1B#DNA/hAT-Charlie 302 339 (0) m_b7s502i17 rnd-3_family- 77 AAGCCGGTCCCTGGTATCAAAAAGGTTGAGAAACACTG 114 i ii i i v i MER1B#DNA/hAT 302 AAACCGGTCCCTGGTGCCAAAAAGGTTGGGGACCGCTG 339 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.81 CpG sites = 6, Kimura (unadjusted) = 22.29 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 21 26.06 1.56 0.00 rnd-3_family-454#DNA/hAT-Tip100 80 143 (400) (GCCCCG)n#Simple_repeat 1 65 (0) m_b7s252i3 rnd-3_family- 80 GCTCCAGCCCCTGCTCCGGCTCTTCCCCAGGCCCCCGCCCCTGCTCC-GC 128 i i v i i ivv v v v i - (GCCCCG)n#Sim 1 GCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGC 50 rnd-3_family- 129 CCCAGCCCCGCCCCC 143 i v (GCCCCG)n#Sim 51 CCCGGCCCCGGCCCC 65 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 16 3.83 0.00 6.90 rnd-3_family-454#DNA/hAT-Tip100 112 142 (401) (CCCCG)n#Simple_repeat 1 29 (0) m_b7s252i4 rnd-3_family- 112 CCCCGCCCCTGCTCCGCCCCAGCCCCGCCCC 142 - i - (CCCCG)n#Simp 1 CCCCGCCCC-GCCCCGCCCC-GCCCCGCCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 15 13.53 0.00 8.89 rnd-3_family-454#DNA/hAT-Tip100 207 255 (288) (CCCCG)n#Simple_repeat 1 45 (0) m_b7s252i5 rnd-3_family- 207 CCCGGCCCCAGCCCGCGCTCCGCTCCGNCCGGCCCCAGCCGCGCCGCCG 255 v - - i i ? v - v - (CCCCG)n#Simp 1 CCCCGCCCC-GCCC-CGCCCCGCCCCGCCCCGCCCC-GCCCCGCC-CCG 45 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 12 21.12 6.00 0.00 rnd-3_family-454#DNA/hAT-Tip100 207 256 (287) (CCCGGC)n#Simple_repeat 1 53 (0) m_b7s252i6 rnd-3_family- 207 CCCGGCCCCAGCCCGCGCTCC-GCTCC-G-NCCGGCCCCAGCCGCGCCGC 253 i vv i - i - -? i v v v (CCCGGC)n#Sim 1 CCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCC 50 rnd-3_family- 254 CGG 256 (CCCGGC)n#Sim 51 CGG 53 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 240 23.67 3.09 4.17 rnd-3_family-496#LINE/L2 534 630 (342) X24_LINE#LINE/L2 146 241 (73) m_b7s601i5 rnd-3_family- 534 GAGTNCAGTTCAAGTCTCTGTCCT-GATATTCAAAGCCCTCCATACGTGG 582 ? i vivi v i -i v vi -- -- X24_LINE#LINE 146 GAGTGCAATTCAAGGTGTTGACTTTAATCTATAAAGCCCT--ATA--TGG 191 rnd-3_family- 583 ACTGG-CCCTAACTACCTGAGAGATCGCCTCTCCCTCCGTG-ACCATGAC 630 vi - iii v i i i? - i v X24_LINE#LINE 192 TTTGGGCCCTGGTTACCTTAGAGATCGCCTCTCTCCCTNTGCACCGTCAC 241 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 14, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.07 (7 / 96), avg. gap size = 1.00 (7 / 7) 444 16.44 0.00 0.00 rnd-3_family-53#LINE/CR1 1 73 (2) CR1-L3A_Croc#LINE/CR1 2260 2332 (1956) m_b7s551i2 rnd-3_family- 1 ACAACTGAGGAAGAAGGCCGTACTGGTTAAAAAAACGACCTGGTTTAGAG 50 ii i iiii v ii i CR1-L3A_Croc# 2260 ACAATCGAGAAAGAAGGCTACGCTGGTTAAAAAACCAGCCTGGCTTAGAG 2309 rnd-3_family- 51 GGGAAGTGAAGGCAGCTATAAAA 73 i CR1-L3A_Croc# 2310 GGGAAGTGAAAGCAGCTATAAAA 2332 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.95 CpG sites = 11, Kimura (unadjusted) = 19.62 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 271 17.91 0.00 0.00 rnd-3_family-555#DNA/Merlin 1 67 (202) C MER136#DNA/Merlin (3) 315 249 m_b7s502i18 rnd-3_family- 1 GTCACGCTTTATATTAAGGTTCCATTTATAAATAGTTTATAAAGGGTTAA 50 v i v v iv v? viv v C MER136#DNA/Me 315 GTAACACTTTAAATTAAGGTGCCATTTATAAATGCTTTATTNATATTTAT 266 rnd-3_family- 51 TAAATGATTAATAGATG 67 ? v C MER136#DNA/Me 265 NAAATGATTACTAGATG 249 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.22 CpG sites = 3, Kimura (unadjusted) = 21.22 Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 1455 16.54 8.33 2.72 rnd-3_family-583#DNA/PIF-Harbinger 291 638 (327) C Chompy-6_Croc#DNA/PIF-Harbinger (387) 593 227 m_b7s502i19 rnd-3_family- 291 AAAACGCAG----AGGAGGTGGTGGTGCGCGTTCCCCTTCCACCCAGTAA 336 i ---- - ii ii i? i i C Chompy-6_Croc 593 AAAACGCGGCCGGAGGAGGTGGTGGTGC-CGCCCCCCTTTTATNCAATAG 545 rnd-3_family- 337 C---------AGAGCACTCACCCGCNATGNGGGAGACCCGGGTTCAAATC 377 --------- i iv? ? ? v C Chompy-6_Croc 544 CCTAGTGGTTAGAGCACTCGCCCAGGANGTGGGAGACCCGGGTTCAATTC 495 rnd-3_family- 378 CCCACTCTGCCTGATNTGGAGCAGGGATTTGAACCCAGGTCTCTCTAATC 427 iv ? --------i ii vi i vvv C Chompy-6_Croc 494 CCTCCTCNGCCTGA--------GGGGATTCAAACCCACATCTCCCACCTC 453 rnd-3_family- 428 TCACG-GAGTGCCCTAACCACCGGGCTATAGGGTATTCCGGGGTGGGTGT 476 i v - i v i v i C Chompy-6_Croc 452 CCAGGAGAGTGCCCTAACCACCAGGCTATAGGCTATTCTGGGGTGGGGGC 403 rnd-3_family- 477 -CTCTCAGTCTCTCCTGTTGAAGCTGTTCCACTTTGTATGAAATACTTAA 525 - vii i ? ? i vi v v v C Chompy-6_Croc 402 ACTCTCCACCCCTCCTGTTGAAGCTGTNCCACTNTGCAGAAAAGAATTCA 353 rnd-3_family- 526 ATATTCANTGGGCCAGAGAG--AGAGCGAGAGAGAAAGTCATTNT-TA-C 571 v ? -- i ? ivi v i ? - - C Chompy-6_Croc 352 AGATTCATTGGGCCAGAGAGAGAGAGCAAGAGNGAGCATGACTCTGTAGC 303 rnd-3_family- 572 TCAGTGGCTAGGGCAC---CCT-------GGGAGACCCAGGNTCCAGTCC 611 ii i --- ------- ? ii ? i - C Chompy-6_Croc 302 CTAGTGGTTAGGGCACTCACCTGGGAGGGGGGAGNCCTGGGTTCCGGT-C 254 rnd-3_family- 612 CCTGCTCCAATGGCTTTTTANNTATTT 638 v i v ?? C Chompy-6_Croc 253 CCTGCTCCAAGGACTGTTTATGTATTT 227 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.84 CpG sites = 36, Kimura (unadjusted) = 19.99 Transitions / transversions = 1.80 (36/20) Gap_init rate = 0.05 (19 / 347), avg. gap size = 2.05 (39 / 19) 1113 18.22 12.39 4.18 rnd-3_family-583#DNA/PIF-Harbinger 611 965 (0) Chompy-6_Croc#DNA/PIF-Harbinger 335 717 (263) m_b7s502i20 rnd-3_family- 611 CCCTGCTCCAATGGCTTTTTANNTATTT-ATNCAAAGTGGAACAGCTTCA 659 i vi iv i v ?? v -v ? ? ? Chompy-6_Croc 335 CTCTGGCCCAATGAATCTTGAATTCTTTTCTGCANAGTGGNACAGCTTCA 384 rnd-3_family- 660 ACAGGTGAGATTGAGAG------CAGCCNATCACAGNATATANCTCAGTG 703 v i i v ------ v ? vv i ?v ? iii Chompy-6_Croc 385 ACAGGAGGGGTGGAGAGTGCCCCCACCCCAGAATAGCCTATAGCCTGGTG 434 rnd-3_family- 704 GTCGNGGCACTCACGTGGGACGNGGGAGANCTNCGTTCAAGTCCCTGCTC 753 ii? v v v ? ?v ?v ii i ----- Chompy-6_Croc 435 GTTAGGGCACTCTCCTGGGAGGTGGGAGATGTGGGTTTGAATCCC----- 479 rnd-3_family- 754 CAGCTCACGCAGNGAGANNGAGAACTGGACC-AGGTCTCCCACGTCNCGG 802 --- v ? ? ---?? i i i -i ? ?i Chompy-6_Croc 480 ---CTCAGGCNGAG---GAGGGAATTGAACCCGGGTCTCCCACNTCCTGG 523 rnd-3_family- 803 GCGAGTGCTCTAACTACCGGGCC------TAAA-----GGTGGCACCACC 841 i ii i------ ----- i Chompy-6_Croc 524 GCGAGTGCTCTAACCACTAGGCTATTGNATAAAAGGGGGGCGGCACCACC 573 rnd-3_family- 842 ACCAATTTTTCTCCATTT---TTTTATGAGAAAGGGCTGACCT------- 881 ----- i ivii--- vi i iv ? i------- Chompy-6_Croc 574 ACC-----TCCTCCGGCCGCGTTTTAAAAGAAAAGAGTGANCCCTGCTCC 618 rnd-3_family- 882 ---------------GGCTTAGGCGCCTAACTCCAGGAGAGGGTTCACGG 916 --------------- ? vv Chompy-6_Croc 619 GTTTTTGAAAGAAAGGGCTTAGGCGCCTANCTCCAGGAGAGGGTTCCGGG 668 rnd-3_family- 917 CTGTGAATCNCAAGCGGAGANAGGCGCCTCCCTGCGGCCCGGACTTAGG 965 ? i i vi? i v v ? Chompy-6_Croc 669 CTGTGAATCCCGAGTGGACGGAGGCGCCTCCCTGCAGCCCTGAGTNAGG 717 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.67 CpG sites = 37, Kimura (unadjusted) = 23.10 Transitions / transversions = 1.48 (37/25) Gap_init rate = 0.07 (24 / 354), avg. gap size = 2.50 (60 / 24) 16 5.20 0.00 0.00 rnd-3_family-623#Unknown 256 275 (322) (GA)n#Simple_repeat 1 20 (0) m_b7s252i2 rnd-3_family- 256 GAGAGAGAGAGAGACAGAGA 275 v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 2068 8.14 1.95 7.65 rnd-3_family-624#DNA 1 359 (10) MER126#DNA 26 365 (84) m_b7s502i21 rnd-3_family- 1 AGAACTTCGAAAAACGTTCTATGTAAAGCGAATCGGAACTCTGTTTAT-- 48 i i i v ---- v -- i i -- MER126#DNA 26 AAAACTTTGAAAAACATTCTATTTA----GAAAC--AATTCTGCTTATAT 69 rnd-3_family- 49 --CTTATATTTTCTGTATTTCTCTTCGTATGCTTTTTNTTCTTGTTTTT- 95 -- v -------------i i - MER126#DNA 70 ATCGTATATTTTCTGTATTTCTCTTC-------------CCTCGTTTTTT 106 rnd-3_family- 96 ATTACTACGGAAGGCTATTTGCATNAAAACAGGATCTTTGTTTCTTAAGA 145 v ----i ? MER126#DNA 107 ATTACTAGGGA----CATTTGCATGAAAACAGGATCTTTGTTTCTTAAGA 152 rnd-3_family- 146 GTTCATCTGCTCCTGCTGCTTATTCCCCANCGGAAGTCATAATNNTCTGT 195 ? v ?? MER126#DNA 153 GTTCATCTGCTCCTGCTGCTTATTCCCCACCTGAAGTCATAATCCTCTGT 202 rnd-3_family- 196 CTGTGACATCACAATTGGCTGCTGTGGAAATGTTCGATGGTGTCACAAAG 245 i i v i- i v MER126#DNA 203 TTGTGACATCACAATTGGTTGCTGTGGAAATGATT-ATGATGTCACAAAC 251 rnd-3_family- 246 AGAGGATTATGACTTCAGGTGGGGAATAAGCAGCAGGAGCAGATGAACTC 295 MER126#DNA 252 AGAGGATTATGACTTCAGGTGGGGAATAAGCAGCAGGAGCAGATGAACTC 301 rnd-3_family- 296 TTNAGAAATCAAAGACTCATTTTTCATACAAA--TCNCTAGTNATAAAGA 343 ? - ii vv i -- ?i ? i MER126#DNA 302 TTAAGAAA-CAAAGATCCTGTTTTCATGCAAATGTCCTTAGTAATAAAAA 350 rnd-3_family- 344 ACGAGGGGAAGAAAAA 359 - i MER126#DNA 351 ACGA-GGGAAGAGAAA 365 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.53 CpG sites = 18, Kimura (unadjusted) = 8.85 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (29 / 358), avg. gap size = 1.14 (33 / 29) 14 21.51 3.39 5.17 rnd-3_family-666#Unknown 292 350 (167) (CGCC)n#Simple_repeat 1 58 (0) m_b7s252i1 rnd-3_family- 292 CGCGCCGCCCGCCCGCCCACCCG-GCGCTCG-GGGCTGGGGCCGCGCCGC 339 - i -v i -vv -vv v - (CGCC)n#Simpl 1 CGC-CCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGC-CCGCCCGC-CCGC 47 rnd-3_family- 340 CCACGCGCCCG 350 i v (CGCC)n#Simpl 48 CCGCCCGCCCG 58 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 243 13.66 0.00 8.47 rnd-3_family-746#Unknown 57 120 (139) UCON80_AMi#Unknown 1 59 (163) m_b7s601i6 rnd-3_family- 57 ATGAGGGACACAAAANAATTATTCATGCAGGAAACTTAAAATGCTGTGGG 106 -- i ? v v- v i i v UCON80_AMi#Un 1 ATGAGG--CACAAGAAAAATAG-CAGGCAGGAAGCTTGAAATGATGTGGG 47 rnd-3_family- 107 ATTCGTTCCTTTAG 120 i -- UCON80_AMi#Un 48 ATTCATT--TTTAG 59 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.30 CpG sites = 4, Kimura (unadjusted) = 15.30 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 781 15.79 0.00 0.00 rnd-3_family-746#Unknown 123 255 (4) UCON80#DNA/hAT-Blackjack 2 134 (8) m_b7s502i22 rnd-3_family- 123 TAAATAACTCTTTCTATAACCTCAGTTTCATGATTCTTTATTTCTGATGT 172 vvi vvi UCON80#DNA/hA 2 TAAATAAAATTTTCTATAACCTCAGTTTCATGATTCAGCATTTCTGATGT 51 rnd-3_family- 173 AAATAATTTTCAACAATAAAAGTGAGGGGACACCAAATTTGTGTGGAACG 222 v i ivi ii i i UCON80#DNA/hA 52 AAATAATTTACAATAATAAAAGTGAGATAACACCAGGTTTGTGTGGGATG 101 rnd-3_family- 223 TAGGTAACTTTGGGACTAAAATGAGNGACATTT 255 v v v ? ii i UCON80#DNA/hA 102 GAGGTAAATTTGGGTCTAAAATGAGGGATGTCT 134 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.05 CpG sites = 12, Kimura (unadjusted) = 18.05 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0) 2080 5.34 1.04 2.82 rnd-3_family-784#DNA/hAT 13 301 (353) UCON69#DNA/hAT 68 351 (135) m_b7s502i23 rnd-3_family- 13 AACTGTGCTCCAGAATCTANNCTTTCGTTTAAAANAGAAATTAAGTTTCT 62 i ?? i --- ? UCON69#DNA/hA 68 AATTGTGCTCCAGAATCTAAGCTTTCATTTAAAA---AAANTAAGTTTCT 114 rnd-3_family- 63 AGCCCTTATGGTTGCGNAGAAAACCTTNAAAATATGAGCTGAATGTAAAC 112 ? ? i i i i UCON69#DNA/hA 115 AGCCCTTATGGTTGCGAAGAAAACCTTCAAAATGTGAACCGAGTGTAAAC 164 rnd-3_family- 113 CGATGCAGTGTTGTCTTCCTGAGTCTGCAGGCAGCCTGAAACAATAGCTC 162 ? v i UCON69#DNA/hA 165 CGATGCAGTGNTGTCTGCCTGAGTCTGCAGACAGCCTGAAACAATAGCTC 214 rnd-3_family- 163 TGAGAGGTGTGAACTGCCCCCATTCATCTCAGTGTGGNNTATTTAACTCT 212 - i v ??--- UCON69#DNA/hA 215 TGAGAGGTGTGAACTG-CCCCATTCATCTCAATGGGGTG---TTAACTCT 260 rnd-3_family- 213 GAAACCTAANGATGGCAATTTAAATGTCAACA---TTAACTATTTCACTG 259 i ? i --- UCON69#DNA/hA 261 GAAGCCTAATGATGACAATTTAAATGTCAACATTGTTAACTATTTCACTG 310 rnd-3_family- 260 CTGATCATTTTAGCAGAAAAACCTTAGCTANTGTGCTTATCC 301 v i -i ? UCON69#DNA/hA 311 CTGATCATTTTAGCAGAAACATC-CAGCTAATGTGCTTATCC 351 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.44 CpG sites = 12, Kimura (unadjusted) = 5.81 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.03 (9 / 288), avg. gap size = 1.22 (11 / 9) 250 5.41 0.00 2.70 rnd-3_family-79#DNA/PIF-Harbinger 30 67 (30) MER133B#DNA/PIF-Harbinger 42 78 (37) m_b7s502i24 rnd-3_family- 30 GCGCCCAACTCCCATTGAAANTCAATGGGAGTTGGGCG 67 v - ? v MER133B#DNA/P 42 GCGCGCAACTCCCATTG-AAGTCAATGGGAGTTGTGCG 78 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.80 CpG sites = 0, Kimura (unadjusted) = 5.80 Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 983 14.19 0.65 0.00 rnd-3_family-804#Unknown 667 821 (7) UCON64#Unknown 219 374 (18) m_b7s502i25 rnd-3_family- 667 ATGTGGTACATACAGAATACACGATGACGTGGTGTGA-ATAAAGGTTTTA 715 ? i i v i ii i v v- ? UCON64#Unknow 219 ANGTGGCATAAACAAAATACGTGATGGCGTGGGGTGCTATAAAGNTTTTA 268 rnd-3_family- 716 TCGGCACTCGTTTGGGATGACCTGCATAACTCACTCGTGGCTTTGCCACT 765 i v i i ? ii UCON64#Unknow 269 TTGCCACTTGTTTGAGANGACCTGCATAACTCACTCGTGGCTCCGCCACT 318 rnd-3_family- 766 CGTGAGTAATGCGGCCATCCCAAACTCATGCTGATAAAACCTTTATACCA 815 i i vii ? v UCON64#Unknow 319 CGTGAGTAATGCGGTCATCCCAAACTCGTGGCAATAAAANCTTTATAGCA 368 rnd-3_family- 816 CACCAC 821 v UCON64#Unknow 369 CCCCAC 374 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.17 CpG sites = 15, Kimura (unadjusted) = 16.49 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.01 (1 / 154), avg. gap size = 1.00 (1 / 1) 231 28.40 0.00 2.70 rnd-3_family-885#Unknown 5 80 (46) C DNM1r#Unknown (2111) 2551 2478 m_b7s502i26 rnd-3_family- 5 TGTTCATTTACATTAGTGTGTGTGTGTGTGTGTATACACACACACACACA 54 - v ? vv i i i iiiii i i i i i C DNM1r#Unknown 2551 TGTTC-TATANATACGTATATATACACATATATACACACATACACACATA 2503 rnd-3_family- 55 CACACACATCNTATATATATGTACAC 80 i -? i i ii C DNM1r#Unknown 2502 TACACACAT-ATATACACACATACAC 2478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 18, Kimura (unadjusted) = 41.18 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 253 23.34 0.00 1.67 rnd-3_family-885#Unknown 30 90 (36) C DNM1r#Unknown (2125) 2537 2478 m_b7s502i27 rnd-3_family- 30 GTGTGTGTATACACACACACACACACACACACATCNTATATATATGTACA 79 i i i i i i i i -? i i i i i C DNM1r#Unknown 2537 GTATATATACACATATATACACACATACACACAT-ATACACACATATATA 2489 rnd-3_family- 80 CACACATATAC 90 i C DNM1r#Unknown 2488 CACACATACAC 2478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 14, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 13 16.86 3.85 5.88 rnd-3_family-942#Unknown 354 405 (245) (CTCCCCT)n#Simple_repeat 1 51 (0) m_b7s252i0 rnd-3_family- 354 CTCACCCTCTGCCCCATATCCCCTCTCCCC-C-CAATTCTCCCCCCCCCC 401 - - - v - - vvi i i (CTCCCCT)n#Si 1 CTC-CCCTCT-CCCC-TCTCCCCTCTCCCCTCTCCCCTCTCCCCTCTCCC 47 rnd-3_family- 402 CACT 405 v (CTCCCCT)n#Si 48 CTCT 51 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.10 (5 / 51), avg. gap size = 1.00 (5 / 5) 731 13.81 11.04 2.26 rnd-3_family-947#Unknown 624 786 (0) UCON64#Unknown 212 388 (4) m_b7s502i28 rnd-3_family- 624 GTAAAATATGTGGCATATNCAGAATACATGATGGTGTGGTGTGGTGATAA 673 ?? ? v? i i i v v - UCON64#Unknow 212 GNNAAATANGTGGCATAAACAAAATACGTGATGGCGTGGGGTGCT-ATAA 260 rnd-3_family- 674 NNGTTTTATTGGCACTTGTTTGGGGTGATCTGCATAACTCACTTGTGAAG 723 ??? v i i? i i --- UCON64#Unknow 261 AGNTTTTATTGCCACTTGTTTGAGANGACCTGCATAACTCACTCGTG--- 307 rnd-3_family- 724 GTTCN-------------AATGCAGCCACCCCANACTCAAGCCAATAAAA 760 i ?------------- i i i ? iv v UCON64#Unknow 308 GCTCCGCCACTCGTGAGTAATGCGGTCATCCCAAACTCGTGGCAATAAAA 357 rnd-3_family- 761 CCTTT-----ACGCCACAGCATCANGTATTC 786 ? ----- v v i ?i UCON64#Unknow 358 NCTTTATAGCACCCCACACCGTCACATATTC 388 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.28 CpG sites = 14, Kimura (unadjusted) = 16.93 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.04 (6 / 162), avg. gap size = 3.67 (22 / 6) 320 16.09 0.00 3.57 rnd-3_family-99#DNA/PIF-Harbinger 11 68 (149) C Chompy-6_Croc#DNA/PIF-Harbinger (13) 967 912 m_b7s502i29 rnd-3_family- 11 AAAGGTATTTAGGCGTTGCTGCGCTCAGCGTTGCAACGCCTAACTGATTT 60 v i ii vi v i -- C Chompy-6_Croc 967 AAAGGGACTTAGGCGCCGCAACGCTGAGCGTTGCAGCGCCTAACT--TTT 920 rnd-3_family- 61 AGGAGCCT 68 v C Chompy-6_Croc 919 AGGCGCCT 912 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.14 CpG sites = 5, Kimura (unadjusted) = 18.24 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 342 25.02 0.00 2.63 rnd-3_family-99#DNA/PIF-Harbinger 138 215 (2) Chompy-6_Croc#DNA/PIF-Harbinger 902 977 (3) m_b7s502i30 rnd-3_family- 138 TNTGGGATTTAGGCTCCTAAATCAGTTAGGCGTTGCAACGCTGAGCGCAG 187 ?i ivii v -- i v iv Chompy-6_Croc 902 TCCGGGGGCCAGGCGCCTAAA--AGTTAGGCGCTGCAACGCTCAGCGTTG 949 rnd-3_family- 188 CAACGCCTAAATACCTTTAAAAATCTGG 215 ii i v ivii i Chompy-6_Croc 950 CGGCGCCTAAGTCCCTTTGTGGATCTAG 977 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.15 CpG sites = 13, Kimura (unadjusted) = 32.17 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 13 21.41 4.65 0.00 rnd-3_family-1060#Unknown 132 174 (1032) (CGGGA)n#Simple_repeat 1 45 (0) m_b8s252i10 rnd-3_family- 132 CGGGA-GGGAAGGGACGGGA-GCTGCGGGAGAGGAGGGGAAGGGA 174 - v - vvi vi v v (CGGGA)n#Simp 1 CGGGACGGGACGGGACGGGACGGGACGGGACGGGACGGGACGGGA 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 233 16.28 2.33 0.00 rnd-3_family-1103#DNA/hAT-Charlie 503 545 (5) Charlie4z#DNA/hAT-Charlie 124 167 (0) m_b8s502i0 rnd-3_family- 503 ATTTACAAATAGGTCC-TGAGCCCGAAAAGGTTGAGAACCACTG 545 iv vi - v i i Charlie4z#DNA 124 ATTCTCAAAGGGGTCCGTGACCCCAAAAAGGTTAAGAACCACTG 167 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.53 CpG sites = 4, Kimura (unadjusted) = 18.53 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 13 17.10 0.00 5.71 rnd-3_family-387#DNA/hAT-Tip100 2227 2263 (0) (AAATT)n#Simple_repeat 1 35 (0) m_b8s252i9 rnd-3_family- 2227 AAATATAAATTAAAAAAAAATATATTTAATTTAAATT 2263 - vv v - v v (AAATT)n#Simp 1 AAAT-TAAATTAAATTAAATTA-AATTAAATTAAATT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 641 7.06 2.33 1.15 rnd-3_family-542#LINE/CR1 5 90 (0) CR1-L3A_Croc#LINE/CR1 1822 1908 (2380) m_b8s551i0 rnd-3_family- 5 AAAAANCTGTGTCGATCATGGGGGACTTCAATTTGAGTGACAT--GCTGG 52 ? i i- i i -- CR1-L3A_Croc# 1822 AAAAAGCTGCGTT-ATCACGGGGGACTTCAATCTGAGTGACATATGCTGG 1870 rnd-3_family- 53 AGGTCTCATGCTGCCAGTACTAAAACATCCTTGGAATT 90 i i CR1-L3A_Croc# 1871 AGGTCTCATGCTGCCAGTACTAAAACGTCCTCGGAATT 1908 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.94 CpG sites = 6, Kimura (unadjusted) = 7.71 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.50 (3 / 2) 12 24.76 2.90 5.97 rnd-3_family-564#Unknown 1 69 (504) (CTGCGCC)n#Simple_repeat 1 67 (0) m_b8s252i8 rnd-3_family- 1 CTGACGCCCAGCACCCTGGGCCCT-CACCCAGCTCTGCCAGTGCCCCTCG 49 - v i v - i v v -- v i iv (CTGCGCC)n#Si 1 CTG-CGCCCTGCGCCCTGCGCCCTGCGCCCTGCGC--CCTGCGCCCTGCG 47 rnd-3_family- 50 CTCCTG-ACCCAGAGCCCTGC 69 - -i v v (CTGCGCC)n#Si 48 C-CCTGCGCCCTGCGCCCTGC 67 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.09 (6 / 68), avg. gap size = 1.00 (6 / 6) 463 12.39 2.75 3.70 rnd-3_family-565#SINE/tRNA 20 128 (144) LFSINE_Vert#SINE/tRNA 133 240 (219) m_b8s601i0 rnd-3_family- 20 ATGCGAAACTGAGTTCGNTGGTCTCAGCCTAGTCCCTTAGTGGACATTTG 69 i - - ? i i i - vv LFSINE_Vert#S 133 ATGTGAAA-TGAGTT-GGTGGTCTCAGTCCAGTTCCT-AGTGGACAGGTG 179 rnd-3_family- 70 TCCACATCACAAAANCACNA-CACAATTTGGCA-TGATTGGCA-TCTGAT 116 ? ? - - - i -i vi LFSINE_Vert#S 180 TCCACATCACAAAACCACCATCACAA-TTGGCACTAATTGGCACCCTTGT 228 rnd-3_family- 117 TGGCAGGCCCGG 128 v i i LFSINE_Vert#S 229 TGGCAGTCTCAG 240 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.19 CpG sites = 9, Kimura (unadjusted) = 14.19 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.00 (7 / 7) 290 23.81 0.00 1.19 rnd-3_family-565#SINE/tRNA 141 225 (47) LFSINE_Vert#SINE/tRNA 296 379 (80) m_b8s601i1 rnd-3_family- 141 AGGTGGGAGTTGCAGGTCAGGATTGAGGTGCATTGGCAGAGCTNATTGNG 190 vvvi v i ii i i -?i vv? LFSINE_Vert#S 296 AGGTGGTCCCTCCAGGTCAGGGTTGAGGCACATTGGCGGGGC-AGTGTGG 344 rnd-3_family- 191 GGAAGCTTGCACAGCACCTGCNCGCGCCATGCCTG 225 v vv ? i ii i LFSINE_Vert#S 345 GGAAGCTTGCACTGCCGCTGCCCGTGCTGTACCTG 379 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.64 CpG sites = 11, Kimura (unadjusted) = 30.40 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 254 18.52 0.00 1.85 rnd-3_family-579#LINE/L2 13 67 (200) L2-1_AMi#LINE/L2 1133 1186 (49) m_b8s551i1 rnd-3_family- 13 TATCCTCCTTCAAATCCCTCCTCAAGACCCACTTCTGCTGCGACGCCTAC 62 i i - i v i i i i i L2-1_AMi#LINE 1133 TATTCTCCTTCAAATCCCTCCTTAA-ACTCTCCTTTGCCGTGATGCCTAC 1181 rnd-3_family- 63 AAGAA 67 i L2-1_AMi#LINE 1182 AAAAA 1186 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.12 CpG sites = 9, Kimura (unadjusted) = 22.63 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 260 11.11 2.22 0.00 rnd-3_family-602#DNA/hAT-Charlie 40 84 (2) Charlie15b#DNA/hAT-Charlie 1 46 (1015) m_b8s502i1 rnd-3_family- 40 CAGTGGTTTTCAACCTGTGGTCCGCGGACCCCTGGGG-TCCGCAGA 84 v v v i - i Charlie15b#DN 1 CAGTGGTTTTCAAACTGTGTTCCGCGGAACCCTAGGGTTCCGCGGA 46 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.72 CpG sites = 2, Kimura (unadjusted) = 12.03 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 241 20.88 5.71 4.23 rnd-3_family-614#DNA/PIF-Harbinger 64 133 (9) MER133B#DNA/PIF-Harbinger 14 84 (31) m_b8s502i2 rnd-3_family- 64 ATGGGCGTGATCCTGCAGTCCT----TACTCAGGCAAAACTCCCACTGAN 109 vvi i --- ---- v iv iv i ? MER133B#DNA/P 14 ATGGGCCAAATTCTGC---CCTCGGATACGCGCGCGCAACTCCCATTGAA 60 rnd-3_family- 110 GTCAATGAGAGTTTTGCCTGAGTA 133 i v v v MER133B#DNA/P 61 GTCAATGGGAGTTGTGCGTGCGTA 84 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.22 CpG sites = 6, Kimura (unadjusted) = 24.99 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.75 (7 / 4) 1123 13.41 2.90 13.60 rnd-3_family-679#DNA/hAT 19 294 (399) UCON69#DNA/hAT 1 250 (236) m_b8s502i3 rnd-3_family- 19 CAGNGTCTCGTGTATTCTATGGTTCCGTAG----GAAATTTGCTGCAGAA 64 ? i i iii i ii ---- i i i UCON69#DNA/hA 1 CAGGGCCCCGTGTATTCCGCGATTCCGCGGCCGCGGAATTTGCCGCGGAA 50 rnd-3_family- 65 TTNACCCCTTGCTGNAGAACTGTGCTCCAGAATCTCAGCTTTCATCATCA 114 i? i ? i v ----- UCON69#DNA/hA 51 TCCACCCCTTGCCGCAGAATTGTGCTCCAGAATCTAAGCTTTCAT----- 95 rnd-3_family- 115 TCGTCATCATAATAATAATAATTAANAATTACAATAAAAATGTTTCTAGC 164 --------------------- ? ---v ? ---- UCON69#DNA/hA 96 ---------------------TTAAAAA---AANTAA----GTTTCTAGC 117 rnd-3_family- 165 CCTTGTGGTTGCAGAGATAACCTTGAAAACGCGAACNGAGCGTAAACCGA 214 i ii v v i i ? i UCON69#DNA/hA 118 CCTTATGGTTGCGAAGAAAACCTTCAAAATGTGAACCGAGTGTAAACCGA 167 rnd-3_family- 215 TGCATGTGGTG-CTG-CTGAGTCTGNAAAGAGCCTGAAACANC-GATNTG 261 - ? - - ? i v ?i- v ? UCON69#DNA/hA 168 TGCA-GTGNTGTCTGCCTGAGTCTGCAGACAGCCTGAAACAATAGCTCTG 216 rnd-3_family- 262 AG-GTTGTGAACTGCCCCAGTCATCTCGNNCGGG 294 - v v i??v UCON69#DNA/hA 217 AGAGGTGTGAACTGCCCCATTCATCTCAATGGGG 250 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.12 CpG sites = 23, Kimura (unadjusted) = 15.70 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.14 (39 / 275), avg. gap size = 1.08 (42 / 39) 272 9.52 0.00 0.00 rnd-3_family-679#DNA/hAT 291 332 (361) UCON69#DNA/hAT 1 42 (444) m_b8s502i4 rnd-3_family- 291 CGGGGCCCCGTGGACTCCGCGATTCCGCGGCCGTGGAATTTG 332 i v i i UCON69#DNA/hA 1 CAGGGCCCCGTGTATTCCGCGATTCCGCGGCCGCGGAATTTG 42 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.83 CpG sites = 3, Kimura (unadjusted) = 10.34 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 312 25.76 11.93 3.83 rnd-3_family-688#LINE/L2 44 261 (389) X24_LINE#LINE/L2 33 267 (47) m_b8s601i2 rnd-3_family- 44 CCAGAAGCTGCAGT--GTTCAGAATCCATTG-CCCACCTGCTAAGCAGCG 90 i v i-- v v vi - i ii i i?i i X24_LINE#LINE 33 CCGGAAGCTTCAGCTGGTGCAGAATGCAGCGGCTCGTCTGCTGAANGGTG 82 rnd-3_family- 91 TC-TCTNTACAGGTGCACATTGNACTAGTTNCTGTGC--CACACCCTGCA 137 ?-v i?i ?- v i? ------ -- i vi X24_LINE#LINE 83 TNAGCCACAN-GGAGCACATTACAC------CTGTGCTCCGCAGTCTGCA 125 rnd-3_family- 138 CTGGCTNCCTGGCTTTCTNCTNGGTGCANTTTAAGGAGATGGTTTTGGTC 187 ? -?ii v ? i?i ? i v v ii ii X24_LINE#LINE 126 CTGGCTACC-NATTTGCTTCCGAGTGCAATTCAAGGTGTTGACTTTAATC 174 rnd-3_family- 188 TANNNTGAACTA-GTGGCCTGGGACCT----------------GCCTCTC 220 ???v vv -i ii v ---------------- X24_LINE#LINE 175 TATAAAGCCCTATATGGTTTGGGCCCTGGTTACCTTAGAGATCGCCTCTC 224 rnd-3_family- 221 CCCATGACATACTGCCACAG---TTGNGGTCAGCGGAGGTGCTC 261 i v -?iii i i i --- ? i vii i X24_LINE#LINE 225 TCCCT-NTGCACCGTCACGGCAATTGAGATCAGCTAGGATGCTC 267 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.83 CpG sites = 38, Kimura (unadjusted) = 36.65 Transitions / transversions = 2.38 (38/16) Gap_init rate = 0.07 (16 / 217), avg. gap size = 2.19 (35 / 16) 522 27.89 2.59 1.54 rnd-3_family-688#LINE/L2 216 408 (242) L2-2_Mam#LINE/L2 19 213 (159) m_b8s601i3 rnd-3_family- 216 CTCTCCCCATGACATACTGCCACAGTTGNGGTCAGCGGAGGTGCTCAAGA 265 i vvvi ii ivi i ? i v i i vv v L2-2_Mam#LINE 19 CTCTCCCTATGCGCCATCGTGGCAATTGAGATCAGCCGGGGCGCTCCTGC 68 rnd-3_family- 266 TGN-AGTCCCTGA--TATATAAG-AGGGGGCGGCTGGTAGGGCGNTCTCC 311 ?-i i ii -- vi vv - i vv iii i ? i L2-2_Mam#LINE 69 TGACGGTTCCCAAATTCCATCCGCAGGGAGCGGAAGACGGGACGTTTTCC 118 rnd-3_family- 312 ATGAGGGGCCCTGGCCNCTT-TGGAATTCACTTCCCCCGTTGGTCCAAAA 360 ii ii --- ?i - v v v vi i iiv L2-2_Mam#LINE 119 GCGGAGGGCCCT---CGTTTGTGGAATTCCCTGCCCGCCCTGGTTCGGCA 165 rnd-3_family- 361 GAGCCCGAGTTTGTTGACCTTCAGGGCACGCTGCAAGGCCCATCTNTT 408 v i v i v ? L2-2_Mam#LINE 166 GAGCCCCAGTTTGCTGACCTTCAGGGCACGGTGCAAGACGCATCTTTT 213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 32, Kimura (unadjusted) = 37.20 Transitions / transversions = 1.52 (32/21) Gap_init rate = 0.04 (7 / 192), avg. gap size = 1.14 (8 / 7) 1028 4.46 6.25 1.80 rnd-3_family-767#LINE/L2 1 160 (108) UCON86#LINE/L2 334 500 (182) m_b8s502i5 rnd-3_family- 1 CTTCACACAA-----CCACTGTTG---CAAGAGCCTTCTCCTCTGCAGCT 42 ----- i --- i UCON86#LINE/L 334 CTTCACACAATCTCGCCGCTGTTGGCGCGAGAGCCTTCTCCTCTGCAGCT 383 rnd-3_family- 43 CCTGCCATCTGGAACAGCCTCCCTGTTCTTTCTCTCTGCCTCATCGACTC 92 i v--- i UCON86#LINE/L 384 CCTGCCATCTGGAACAGCCTTCCTGTA---TCTCTCCGCCTCATCGACTC 430 rnd-3_family- 93 TCCATCTNTTTTCAAATCTCATCTGAAA--ACATATTTTCTCCNTTGCCT 140 ? ? -- v ? UCON86#LINE/L 431 TCCATCTCTTTTCAAATCTCATCTNAAAATACATCTTTTCTCCCTTGCCT 480 rnd-3_family- 141 ATACCTCTTAATTTCTCTCT 160 i UCON86#LINE/L 481 ATGCCTCTTAATTTCTCTCT 500 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.85 CpG sites = 5, Kimura (unadjusted) = 4.71 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.04 (6 / 159), avg. gap size = 2.17 (13 / 6) 568 6.49 1.30 0.00 rnd-3_family-767#LINE/L2 190 266 (2) UCON86#LINE/L2 604 681 (1) m_b8s502i6 rnd-3_family- 190 TGTATTATTTAACTCTGTAAAGCATTT-GGGATACAGTTTGCGTGAAAGA 238 i - ii UCON86#LINE/L 604 TGTATTATTTAACTCTGTAAAGCGTTTTGGGATACAGTTTGTATGAAAGA 653 rnd-3_family- 239 TGCTATGCAAAATAAAGTTGTATTGTAT 266 i i UCON86#LINE/L 654 CGCTATACAAAATAAAGTTGTATTGTAT 681 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.34 CpG sites = 5, Kimura (unadjusted) = 6.96 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 23 26.66 0.90 6.67 rnd-3_family-994#Unknown 46 156 (395) (GCCCC)n#Simple_repeat 1 105 (0) m_b8s252i6 rnd-3_family- 46 GCCCCGGCCCCGCCCCAACTCCGCCCCTTCCCCGGCCCCCCACGCCCCTT 95 - -i i -v v v v vi (GCCCC)n#Simp 1 GCCCC-GCCCCGCCCC-GCCCCGCCCC-GCCCCGCCCCGCCCCGCCCCGC 47 rnd-3_family- 96 CCC-CAAAGTCCCCGCCCCAACTCCGCCCCCTCCCCTGAACGCTCGCCCC 144 - vvv - -i i - v vvvv - v v (GCCCC)n#Simp 48 CCCGCCCCG-CCCCGCCCC-GCCCCG-CCCCGCCCCGCCCCGC-CCCGCC 93 rnd-3_family- 145 CTGCCCCTCCCC 156 i v (GCCCC)n#Simp 94 CCGCCCCGCCCC 105 Matrix = Unknown Transitions / transversions = 0.38 (6/16) Gap_init rate = 0.07 (8 / 110), avg. gap size = 1.00 (8 / 8) 27 25.24 3.97 3.97 rnd-3_family-994#Unknown 47 172 (379) (CCCCGC)n#Simple_repeat 1 126 (0) m_b8s252i7 rnd-3_family- 47 CCCCGGCCCCG-CCCCAACTCCG-CCCCTTCCCCG-GCCC-CCCACGCCC 92 v - iv i - vi -v - v (CCCCGC)n#Sim 1 CCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCC 50 rnd-3_family- 93 CTTCCCCAAAGTCCCCG-CCCCAACTCCGCCCCCTCCCCTGAACGCTCGC 141 iv --v i - iv i v i -- v i (CCCCGC)n#Sim 51 CCGCCCC--CGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCG--CCCCCGC 96 rnd-3_family- 142 CCCCTGCCCCTCCCCCTCCCCTGCTTCCCGC 172 vv v v i -i (CCCCGC)n#Sim 97 CCCCGCCCCCGCCCCCGCCCCCGC-CCCCGC 126 Matrix = Unknown Transitions / transversions = 0.79 (11/14) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 13 26.37 0.00 2.17 rnd-4_family-1218#Unknown 142 188 (2182) (GCCCC)n#Simple_repeat 1 46 (0) m_b8s252i5 rnd-4_family- 142 GCCCCCCCGCGAGCCCTCCCCACCCCACCCCGGCGGCCCCCGCCCCG 188 v v -v v i i v vvv (GCCCC)n#Simp 1 GCCCCGCCCCG-CCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCG 46 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 351 18.33 2.02 6.32 rnd-4_family-1257#LINE/CR1 299 397 (558) CR1-3_Croc#LINE/CR1 3240 3334 (271) m_b8s551i2 rnd-4_family- 299 GGGTCTAGCCGATCGCC-TGTTTAGGGGGTCAGGAAGGAATTTTTTCTCC 347 vii - i -- -- vi CR1-3_Croc#LI 3240 GGGTCAGACCGATCGCCATATTT--GGGGTCAGGAAGGAA--TTTTACCC 3285 rnd-4_family- 348 CATGGGCCAAATTGGCAGAGGACCAGGGAGTTTTTCGCCTTCCTC-GCAG 396 - i i i -v iiv i v i - i CR1-3_Croc#LI 3286 CAT-GGTCAGATTGGTA-CGGACTGTGGGGGTTTTTGCCTTCCTCTGTAG 3333 rnd-4_family- 397 C 397 CR1-3_Croc#LI 3334 C 3334 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.53 CpG sites = 12, Kimura (unadjusted) = 21.53 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.00 (8 / 8) 14 30.30 2.86 1.41 rnd-4_family-14#DNA/hAT 11 80 (613) (CCTC)n#Simple_repeat 1 71 (0) m_b8s252i3 rnd-4_family- 11 CCTGCCACCCCCCCTCTGCGCGTCCCCCCCCCCCGTGGGTCCC-CCCTCC 59 v v i iviv v i i - vvv - (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC-TCCCTCCCTCCCTCC 49 rnd-4_family- 60 CTGCCTGCCTCTC-CCCTGCCT 80 v v i - v (CCTC)n#Simpl 50 CTCCCTCCCTCCCTCCCTCCCT 71 Matrix = Unknown Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 12 18.86 2.63 2.63 rnd-4_family-14#DNA/hAT 55 92 (601) (CCTG)n#Simple_repeat 1 38 (0) m_b8s252i4 rnd-4_family- 55 CCTCCCTGCCTGCCT-CTCCCCTGCCTGCTTGTGCTGCC 92 v - iiv i -v (CCTG)n#Simpl 1 CCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTG-CCTGCC 38 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 356 15.72 4.11 4.11 rnd-4_family-1438#DNA/hAT-Tip100 1 73 (0) MER63D#DNA/hAT-Tip100 4 76 (985) m_b8s502i7 rnd-4_family- 1 TGGTGAGCTGGAGCCGGTTCGCACCGGTTCGCGGGAACCGGTTGTTAAAT 50 v i i i i i i MER63D#DNA/hA 4 TGGTGTGCTGGAGCCGGCTCGTACCGGCTCGCGAGAGCCGATTGTTAAAT 53 rnd-4_family- 51 TT--AGAAGCCGTTTTA-GAACCGGT 73 -- i ---i i- i MER63D#DNA/hA 54 TTTCAGGA---ATTTTGCGAGCCGGT 76 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.56 CpG sites = 10, Kimura (unadjusted) = 18.56 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.07 (5 / 72), avg. gap size = 1.20 (6 / 5) 2203 6.22 10.00 3.49 rnd-4_family-162#DNA/hAT-Ac 3 352 (0) UCON26#DNA/hAT-Ac 12 383 (15) m_b8s502i8 rnd-4_family- 3 GAATCGATTTNAATAAAATAAGA-CCGACCCNAACCTTCGCC------TC 45 i i i?i - i? ------ UCON26#DNA/hA 12 GAACCGGTTCGGATAAAATAAGAACCGACCTGAACCTTCGCCCAAAACTC 61 rnd-4_family- 46 AAACTGAACC-----------TTTTCTGAGGTTCGAAAAN-TTTGGTTAA 83 i i ----------- i ?- i UCON26#DNA/hA 62 GAACCGAACCCGAACCTGAACTTTTTTGAGGTTCGAAAAAGTTCGGTTAA 111 rnd-4_family- 84 CTTTT--------ATTTTTCATTTTCACTGCTTTAGCCTCTGCACT-CCT 124 -------- i - ---- - UCON26#DNA/hA 112 CTTTTTTTNCGTTATTTTTCATTTTCGC-GC----GCCTCTGCACTTCCT 156 rnd-4_family- 125 GGTTTC---TAG--CCGGAAGCGGAAGTGCCAAAATACCGCGAGAAAGGC 169 i ---ii -- i UCON26#DNA/hA 157 GGTTCCGGCCGGGACCGGAAGCGGAAGTGCCGAAATACCGCGAGAAAGGC 206 rnd-4_family- 170 TGTTCTCGCGGTATTTCCGGCCTCGACCGGAAGCAGGGAAGTACCGGAAA 219 - - UCON26#DNA/hA 207 TGTTCTCGCGGTATTTCCGGCC-CGACCGGAAGCAGG-AAGTACCGGAAA 254 rnd-4_family- 220 TCTCGCGAGAGAGCCTGTTCTCGTGAGATTTCCAGCCCAATTTTGCAGA- 268 i i - UCON26#DNA/hA 255 TCTCGCGAGAAAGCCTGTTCTCGCGAGATTTCCAGCCCAATTTTGCAGAC 304 rnd-4_family- 269 CCAGGAGGCTCGGATTTAGATAAGCTTCGGATAAGCATCCGAAC-TTTGG 317 i i ------ - UCON26#DNA/hA 305 CCAAGAGGTTCG------GATAAGCTTCGGATAAGCATCCGAACTTTTGG 348 rnd-4_family- 318 GTGCTTATCTGAACTGAACCTCCGAACTTTTTGAG 352 i i i UCON26#DNA/hA 349 GTGCTTATCCGAACCGAACCTCCGAACCTTTTGAG 383 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.70 CpG sites = 21, Kimura (unadjusted) = 6.72 Transitions / transversions = 1.00 (21/0) Gap_init rate = 0.07 (23 / 349), avg. gap size = 2.09 (48 / 23) 14 18.13 0.00 0.00 rnd-4_family-1914#Unknown 2 33 (115) (ATCCGA)n#Simple_repeat 1 32 (0) m_b8s252i2 rnd-4_family- 2 ATCAGAATCCGAACCCAGATCCGGATCCGAAT 33 v i ii i (ATCCGA)n#Sim 1 ATCCGAATCCGAATCCGAATCCGAATCCGAAT 32 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 668 10.64 19.61 1.67 rnd-4_family-222#DNA/Kolobok 1 153 (2) UCON29#DNA/Kolobok 251 430 (9) m_b8s502i9 rnd-4_family- 1 GTGTGAGCCAGAAAGAACACAGCTCGGCTTTCAGATCCCAGGNTGAG--- 47 i? v i ii ? --- UCON29#DNA/Ko 251 GTANGAGGCAGAAAGAACACAGCTTGATTTTCAGATCCCAGGTTGAGTTT 300 rnd-4_family- 48 GCAGA--TGTAAACTGGAAAAA-----------------AAATGAGC--- 75 ?-- vv ii i ----------------- v --- UCON29#DNA/Ko 301 GCAGNGCTGGCAGTTAGAAAAATCATCTTTTGACTTGTAAACTGAGCAAA 350 rnd-4_family- 76 -----TCTGGAAATCANTGAGAGACAATAAACATGGAAACCCCACGATGC 120 ----- ? i ? v i - i UCON29#DNA/Ko 351 TTTGATNTGGAAGTCATTGAGAGAGAATAAATATGGAA-CCCCACGATGT 399 rnd-4_family- 121 CATTTTTACAGAGTCACTTTTCAGAGTAGAACC 153 -- ? v UCON29#DNA/Ko 400 CATTTTTAC--AGTCACTTTTCNGAGTATAACC 430 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.13 CpG sites = 10, Kimura (unadjusted) = 12.13 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.05 (8 / 152), avg. gap size = 4.12 (33 / 8) 332 26.72 4.27 0.83 rnd-4_family-250#LINE/CR1 1933 2049 (495) X6A_LINE#LINE/CR1 378 498 (580) m_b8s601i4 rnd-4_family- 1933 CTCAGGGAAAAGACCTGGGCGCCATTGATAGCAGCTCAAGAGAAACACCT 1982 i i i i i vvii vii i ii X6A_LINE#LINE 378 CTCAGGAAAAAGATCTAGGCGTCATCGTGGACAGCTCAATGAAGACGTCT 427 rnd-4_family- 1983 GCTC-ATTCGCAGCAGTGGNCAAAA---CAAAAGCAATGTTCAGAT-CNC 2027 - v i ii ? --- i vivi i ?i v -i?i X6A_LINE#LINE 428 GCTCAATGCGCAGCGGCAGTCAAAAAAGCGAATAAGACGTTNGGCTGTAT 477 rnd-4_family- 2028 TAAGATATGGGATGGAGAATAA 2049 - v i X6A_LINE#LINE 478 TAAGA-AGGGAATGGAGAATAA 498 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.21 CpG sites = 23, Kimura (unadjusted) = 36.31 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.50 (6 / 4) 367 25.88 4.86 6.01 rnd-4_family-250#LINE/CR1 2064 2248 (296) CR1-13_AMi#LINE/CR1 78 260 (464) m_b8s551i3 rnd-4_family- 2064 GTGTTCAGTTTTGGTCACCCAGTNTCTATTAAGGATATAGCACATATAAA 2113 i i vi ? v -- iii ? v v - CR1-13_AMi#LI 78 GCGTTCAGTTCTGGTCACCCTATCTCAA--AGAAATANAGCAGAAATAA- 124 rnd-4_family- 2114 AGGGATTTCCAAGACAGGCTCTGAGAATG---------GGGGAGGCTGCC 2154 -- v - i i vvi i ---------i i i v CR1-13_AMi#LI 125 --GGAGTT-CGAGACGGGCGACGAAAATGATTAGAGGCAGAGAGACTTCC 171 rnd-4_family- 2155 ATATGCAAACATATAGAAAAGTCTGGGACTCTTTAGTTTACACAAGAGAC 2204 v i v v ?v i -- - v v v i CR1-13_AMi#LI 172 ATATGAAGAGAGANTGAAGA--CT-GGACTGTTTAGTTTAGAGAGGAGAC 218 rnd-4_family- 2205 AAAGAAGGGAGCATATGATATAGGAGAGGAAAATAAAAAATGAA 2248 i vi i-- i v viviv vi i CR1-13_AMi#LI 219 GAATGAGGGG--ACATGATAGAGGTATACAAAATAATGAATGGA 260 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.65 CpG sites = 24, Kimura (unadjusted) = 32.88 Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.07 (12 / 184), avg. gap size = 1.67 (20 / 12) 1601 13.59 3.07 2.03 rnd-4_family-250#LINE/CR1 2250 2542 (2) CR1-L3B_Croc#LINE/CR1 1025 1320 (1957) m_b8s551i4 rnd-4_family- 2250 CTGATTTACATTCAA-ATGGACAAA-AGAA-ACAGTTCCCAACCGGTACT 2296 - - i - i- - i v CR1-L3B_Croc# 1025 CTGATT-ACATTCAATATGGGCAAACAGAGGACAGT-CCCAACCAGTAAT 1072 rnd-4_family- 2297 ATCTATAGACACTTAGTGCTCCAAGAGGACTAATTCCCCAAAGCTGAGGA 2346 v ---- i i i i i CR1-L3B_Croc# 1073 ATATATA----CTTGGTGCTTCAAAAGGGCTAATTTCCCAAAGCTGAGGA 1118 rnd-4_family- 2347 AAATTGTCAGCAAAACTGACTGGGAGGAAAAANTTNGACAGAAAAATATG 2396 i v i i ? ? i CR1-L3B_Croc# 1119 AAATTATGAGCGAAATTGACTGGGAGGAAAAATTTAGACAGAAAAATGTG 1168 rnd-4_family- 2397 AATGAAAATTGGTAGTTCTTTGATAACAGTTTATTAGATAGCGGAAAANT 2446 v i v v i vi ?i CR1-L3B_Croc# 1169 AATGAAAATTGGGAGTTCTTTAAGAAGAGTTTATTAGATGGCCAAAAAGC 1218 rnd-4_family- 2447 CATGATTCCACAGTCAACAAAGTGAACAACTTTGGGTAAAAACCCA---- 2492 i i v v i v i ---- CR1-L3B_Croc# 1219 CACGATTCCACAATCAAGAAAGAGGACAACTTTGGCTAAAAGCCCATCCT 1268 rnd-4_family- 2493 -GTTCAGTGGCAAAGTGAAGGCAGCAATT-GGGGTGGGGAAGCAATATGT 2540 - i - iii iiii i CR1-L3B_Croc# 1269 GGTTCAGTGGCGAAGTGAAGGCAGCAATTAGAAATAAAAAAGCAATATAT 1318 rnd-4_family- 2541 AA 2542 CR1-L3B_Croc# 1319 AA 1320 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.28 CpG sites = 29, Kimura (unadjusted) = 15.51 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.04 (12 / 292), avg. gap size = 1.25 (15 / 12) 241 20.00 0.00 0.00 rnd-4_family-2774#DNA/PIF-Harbinger 19 63 (19) MER133B#DNA/PIF-Harbinger 37 81 (34) m_b8s502i10 rnd-4_family- 19 TGCGCACCCAAAACTCCCACTGAAGTCAGTGGGAGTTTTGGGTGC 63 i i v iv i i v v MER133B#DNA/P 37 TACGCGCGCGCAACTCCCATTGAAGTCAATGGGAGTTGTGCGTGC 81 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.03 CpG sites = 5, Kimura (unadjusted) = 23.53 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 232 15.68 15.49 1.23 rnd-4_family-297#LINE/L2 141 211 (12) L2c_3end#LINE/L2 371 451 (27) m_b8s601i5 rnd-4_family- 141 ATTAGACTGTAAGCTCTTCG-GGGCAGGGACCGTGTC-TGTTC-----TG 183 i i i i - - i ----- L2c_3end#LINE 371 ACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTG 420 rnd-4_family- 184 TG----AAGCGCCTAGCACACTTTTGGGCGCT 211 i----v i - vv i L2c_3end#LINE 421 TATCCCCAGCGCCTGGCACA-TAGTAGGCGCT 451 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.07 CpG sites = 8, Kimura (unadjusted) = 18.07 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.07 (5 / 70), avg. gap size = 2.40 (12 / 5) 1892 6.12 2.02 0.80 rnd-4_family-298#SINE/tRNA-Deu 1 247 (5) AmnSINE2#SINE/tRNA-Deu 15 264 (94) m_b8s502i11 rnd-4_family- 1 CTTAGTGGTCTAAGCATCAGGTTTGAAATACCTAGACTCCCTGGAACCAC 50 AmnSINE2#SINE 15 CTTAGTGGTCTAAGCATCAGGTTTGAAATACCTAGACTCCCTGGAACCAC 64 rnd-4_family- 51 AGGTTCAAATCCCGGCAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAG 100 i AmnSINE2#SINE 65 AGGTTCAAATCCCAGCAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAG 114 rnd-4_family- 101 ATAAACTGAGTTCCATGCAGTTTACTGGTGNGGGGATCTTTCGGATGAGA 150 i ? i - ? ? i AmnSINE2#SINE 115 ATAAATTGAGTNCCACGCAGTTTACT-GTGTGNGGGTCTTTCGGATGAGA 163 rnd-4_family- 151 CCTTAAAAACCGAGGTCCTGTCTGCTCTGCGTGGACATTAAAGATCCCAT 200 i i i i AmnSINE2#SINE 164 CCTTAAAAACCAAAGCCCTGTCTGCTCTGCGTGGACATTAAAGATCCCGT 213 rnd-4_family- 201 GGCA-TTTCTGACAGAGTAG----TTGCCCCGGTGTCCTTGGCCAAAATT 245 i- ii vv ---- i -i AmnSINE2#SINE 214 GGCGCTTTTCGTAAGAGTAGGGGTTTGCCCCGGTGCCCTTGGCC-GAATT 262 rnd-4_family- 246 TC 247 AmnSINE2#SINE 263 TC 264 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.50 CpG sites = 13, Kimura (unadjusted) = 6.56 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.02 (4 / 246), avg. gap size = 1.75 (7 / 4) 309 25.90 0.00 7.92 rnd-4_family-442#LINE/CR1 7 115 (103) CR1-11_Crp#LINE/CR1 1356 1456 (5) m_b8s551i5 rnd-4_family- 7 GAGCTGGACAAATTTATGAGCGCGATTGTATGACGGGGTTGCTTGTGATG 56 v iv i iv v i v i i i CR1-11_Crp#LI 1356 GAGCTTGATCAGTTTATGAAAGGGATTATATGACGTGGTTGCCTGCGATA 1405 rnd-4_family- 57 GTAGGGGGCAGGGCTCAGCAGCCCTGGGGCTCACTTCCGGTTTATGTCTT 106 i i v i-- ? iiii v i v v i ------ i CR1-11_Crp#LI 1406 GCAGGGGACTGA--TNAATGACCCAGGAGGTCCCTTCCAGT------CCT 1447 rnd-4_family- 107 ATGTTCCTA 115 CR1-11_Crp#LI 1448 ATGTTCCTA 1456 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 17, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.00 (8 / 8) 245 19.04 4.62 3.03 rnd-4_family-442#LINE/CR1 114 178 (40) CR1-13_AMi#LINE/CR1 521 586 (138) m_b8s551i6 rnd-4_family- 114 TAAAGCTCATGCTTCAGGGTTTCAGCCGGCCAC---CTGCAGGGGTCAGG 160 ?v iv v ii --- vv i CR1-13_AMi#LI 521 TAANCCTCATGCTTCAGGGCATAAGCCAACCACTAACTGACGGGGTTAGG 570 rnd-4_family- 161 AAGGGATTCTCCCCCTAT 178 ii -- i CR1-13_AMi#LI 571 AAGAAA--CTTCCCCTAT 586 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.69 CpG sites = 7, Kimura (unadjusted) = 22.69 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.67 (5 / 3) 243 18.75 0.00 0.00 rnd-4_family-466#Unknown 290 337 (548) C DNM1r#Unknown (2126) 2536 2489 m_b8s502i12 rnd-4_family- 290 TATATATATATGTATATATATATATACACACACACACACACATATGTA 337 i ii i i i i i i C DNM1r#Unknown 2536 TATATATACACATATATACACACATACACACATATACACACATATATA 2489 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.50 CpG sites = 9, Kimura (unadjusted) = 23.50 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 976 19.11 0.00 2.25 rnd-4_family-487#DNA/TcMar-Pogo 1 182 (4) MER132#DNA/TcMar-Pogo 1 178 (0) m_b8s502i13 rnd-4_family- 1 CAGTGAAACCTGTACAAGAGACCACCCTTATTAGGCAACCTCCTGTCTTA 50 i v ii iii v i i MER132#DNA/Tc 1 CAGTGAAACCTGCACTAAGGACCACCTCCAATAGGCAGCCCCCTGTCTTA 50 rnd-4_family- 51 AGAGACCGCCCCCCCAAAGTATCCCCAAACGTATTGAGTACAGTTCTGCT 100 --- ?i v iii i- v iv i i i MER132#DNA/Tc 51 AG---CNACCACTTTAAAGTATCCCCAAG-GTTTCCAGTACAATTTTGTT 96 rnd-4_family- 101 CCACCTTTATTAGAAGACCACCTCTGTTAAGCAACCGATTTTTGTTGGTC 150 iv v vi iii i i MER132#DNA/Tc 97 TGACCTTTAGTTAAAGACCACCTCTACCAGGCAACCGATTTTTGCTGGTC 146 rnd-4_family- 151 CCTTGAGTGGTCGCTTAAGACAGGTTTCACTG 182 i i MER132#DNA/Tc 147 CCTTGGGTGGTCGCTTAAGACAGATTTCACTG 178 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.07 CpG sites = 26, Kimura (unadjusted) = 23.07 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.02 (4 / 181), avg. gap size = 1.00 (4 / 4) 17 13.45 4.65 2.27 rnd-4_family-68#Unknown 155 197 (129) (TCAGTT)n#Simple_repeat 1 44 (0) m_b8s252i1 rnd-4_family- 155 TCAGTTTCACTTTCTGTTTCTAG--TCAGTTTCACTTTCTGGTTC 197 v v - -- v v v (TCAGTT)n#Sim 1 TCAGTTTCAGTTTCAGTTTC-AGTTTCAGTTTCAGTTTCAGTTTC 44 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.50 (3 / 2) 12 0.00 0.00 5.26 rnd-4_family-973#Unknown 90 109 (202) (GCA)n#Simple_repeat 1 19 (0) m_b8s252i0 rnd-4_family- 90 GCAGCAAGCAGCAGCAGCAG 109 - (GCA)n#Simple 1 GCAGC-AGCAGCAGCAGCAG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 19), avg. gap size = 1.00 (1 / 1) 372 17.12 22.79 1.21 rnd-4_family-1143#SINE/MIR 17 152 (236) MIR1_Amn#SINE/MIR 3 167 (63) m_b9s601i0 rnd-4_family- 17 GAAAGGCAGTGTG---TAA-GTATGGAAGACTTGGGTCTGCCATATTAGA 62 ii --- i- v i iv -- v vv ivivi MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACT--GGACTGGGACTCGGGA 50 rnd-4_family- 63 GACCTGGGTTCTATTCCCAGCTCTGCCA-------G--AAGTGACCTTGT 103 ? ? i ------- --i? v MIR1_Amn#SINE 51 GACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGG 100 rnd-4_family- 104 GCAA---------CCTCTC--------AGTTACCTTATCTGTAAAATGGG 136 --------- -------- v i MIR1_Amn#SINE 101 GCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 rnd-4_family- 137 GG-AATGATACTTGCCT 152 i- vi MIR1_Amn#SINE 151 GATAATGATACTGACCT 167 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.35 CpG sites = 13, Kimura (unadjusted) = 20.21 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.07 (9 / 135), avg. gap size = 3.67 (33 / 9) 325 10.68 31.07 0.00 rnd-4_family-1143#SINE/MIR 62 164 (224) MIRc#SINE/MIR 48 182 (86) m_b9s601i1 rnd-4_family- 62 AGACCTGGGTTCTATTCCCAGCTCTGCCAG-----AA----GTGACCTTG 102 v v i v----- i---- MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 rnd-4_family- 103 TGCAA---------CCTCTC--------AGTTACCTTATCTGTAAAATGG 135 v --------- -------- v i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 rnd-4_family- 136 GGG-AATGATACTTG-CCTGCCT-CCT---AGGGT 164 i- i i - - --- MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGT 182 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 10.54 CpG sites = 6, Kimura (unadjusted) = 11.57 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.08 (8 / 102), avg. gap size = 4.00 (32 / 8) 269 14.77 1.59 3.23 rnd-4_family-1143#SINE/MIR 219 281 (107) C MIR3#SINE/MIR (123) 85 24 m_b9s601i2 rnd-4_family- 219 ACAGC-AGTCAGTGGAAGAGGTGAGACCNGAACTCATGGTCTCCTGGCTC 267 - i v vi i i? i - i C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA-GGTCTCCTGACTC 37 rnd-4_family- 268 CCAGCCCAGTGCTC 281 i - C MIR3#SINE/MIR 36 CCAGTCC-GTGCTC 24 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.23 CpG sites = 7, Kimura (unadjusted) = 17.23 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 12 12.79 5.56 2.70 rnd-4_family-1213#Unknown 403 438 (204) (GCCCCG)n#Simple_repeat 1 37 (0) m_b9s252i6 rnd-4_family- 403 GCCCCAGCACCCGG-ACCGGCCCC-GCTGCGGCCCCGG 438 i - -v - iv (GCCCCG)n#Sim 1 GCCCCGGC-CCCGGCCCCGGCCCCGGCCCCGGCCCCGG 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 446 19.44 2.73 1.80 rnd-4_family-1258#SINE/MIR 1 110 (46) MIR#SINE/MIR 77 187 (75) m_b9s601i3 rnd-4_family- 1 CTTGCTGCATAACCCTGN-TAAACAACTTTAATCATTCTGTGCCTCAGTT 49 v ii i i ?-i iiv - i vi MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGCAAGTTACTT-AACCTCTCTGTGCCTCAGTT 125 rnd-4_family- 50 TACCCATCTGTAAAATGAATGANAATATT--TACTTACCTCACAGGGGTG 97 v i ii- ? v -- i i v MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGG-GATAATAATAGTACCTACCTCATAGGGTTG 174 rnd-4_family- 98 TTGTGAGGCTTAA 110 v MIR#SINE/MIR 175 TTGTGAGGATTAA 187 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.58 CpG sites = 14, Kimura (unadjusted) = 23.58 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.25 (5 / 4) 276 10.00 5.00 0.00 rnd-4_family-1258#SINE/MIR 116 155 (1) AmnSINE1#SINE/5S-Deu-L2 508 549 (26) m_b9s502i0 rnd-4_family- 116 GTTTGTAAAGCGCTTTGAGATCCTC--GGATGAAAGGTGCTA 155 i i i-- i AmnSINE1#SINE 508 GCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTA 549 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.42 CpG sites = 4, Kimura (unadjusted) = 11.16 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 39), avg. gap size = 2.00 (2 / 1) 301 20.29 1.43 1.43 rnd-4_family-126#DNA 1152 1221 (83) Eulor9B#DNA 165 234 (6) m_b9s502i1 rnd-4_family- 1152 AAGAGGGCAGAGTTAAGGTTGC-ATGGGCAACCTTAACTGTGCATTTCCT 1200 i i v - - v v v Eulor9B#DNA 165 AAGGGGGCGGAGTTACGGTTGCTATGGG-AACCATAACTTTGAATTTCCT 213 rnd-4_family- 1201 GGTTTTCAGAAGTTTGAGTTT 1221 ii iiviv i Eulor9B#DNA 214 GACTTTTGTGCGTTTGAATTT 234 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.10 CpG sites = 8, Kimura (unadjusted) = 23.97 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 282 23.19 2.33 4.76 rnd-4_family-126#DNA 1152 1237 (67) C Eulor9A#DNA (187) 114 31 m_b9s502i2 rnd-4_family- 1152 AAGAGGGCAGAGTTAAGGTTGC-ATGGGCAACCTTAACTGTGCATTTCCT 1200 i v v -i - v v v C Eulor9A#DNA 114 AAGGGGGCCGAGTTACGGTTGCTGTGGG-AACCGTAACTTTGAATTTCCT 66 rnd-4_family- 1201 GGTTTTCAGAAGTTTGAGTTTTGCTCAACT-CAACGTT 1237 ii iiviv i i --- i i-i C Eulor9A#DNA 65 GACTTTTGTGCGTTTAAATT---CTCAGCCATAACGTT 31 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 12, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.00 (6 / 6) 14 20.80 0.00 6.38 rnd-4_family-1326#Unknown 652 701 (1) (GGAGGC)n#Simple_repeat 1 47 (0) m_b9s252i5 rnd-4_family- 652 GGACGCGGCGCGCTGAGGCGCCGGGGGATGGGGGAAGGCGGAGGCGGGGG 701 v v - v vv v - v - i (GGAGGC)n#Sim 1 GGAGGCGGAG-GCGGAGGCGGAGGCGGA-GGCGG-AGGCGGAGGCGGAGG 47 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 1883 4.98 0.81 2.47 rnd-4_family-1338#SINE/5S-Deu-L2 4 250 (15) AmnSINE1#SINE/5S-Deu-L2 9 251 (324) m_b9s502i3 rnd-4_family- 4 CCATACCGCCTTGNGCTGTGATCTCGTCAGATCTCACAAGCTAAGCAGGG 53 i i ? AmnSINE1#SINE 9 CCATACCACCTCGGGCTGTGATCTCGTCAGATCTCACAAGCTAAGCAGGG 58 rnd-4_family- 54 TCGGGCCNGGTCAGTACTTGGATGGGAGACCTCCAAGGAAAACACCAGGT 103 ? - - AmnSINE1#SINE 59 TCGGGCCTGGTCAGTACTTGGATGGGAGACCTCCAAGGAAA-C-CCAGGT 106 rnd-4_family- 104 GCTGCAGCAGGAAG--GTGTTGGTGATTCAGTAGGTGGCACTCTTCCCTC 151 --- -- i AmnSINE1#SINE 107 GCTGCAG---GAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTC 153 rnd-4_family- 152 TGAGTCANTACTGAACCAATGCCCCAGCATGGTGCTAGGGAGCACTGTGC 201 ? i i i i AmnSINE1#SINE 154 TGAGTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGC 203 rnd-4_family- 202 TGCTGGAGGTGCCATCTTTTCAGATGAGATATAAAACCAAGGTCCTGAC 250 i - i ii i AmnSINE1#SINE 204 TGCTGGAGGTGCCGTC-TTTCGGATGAGACGTAAAACCGAGGTCCTGAC 251 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.81 CpG sites = 12, Kimura (unadjusted) = 5.31 Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.03 (7 / 246), avg. gap size = 1.14 (8 / 7) 279 17.23 7.95 1.06 rnd-4_family-1493#LINE/L2 275 362 (14) L2c_3end#LINE/L2 358 451 (27) m_b9s601i4 rnd-4_family- 275 GTCTGTCTG-TCC-TTAGATTGCGAGCTCCTCG-GGGCAGGGACCGTCCC 321 v- -i i i i - vi L2c_3end#LINE 358 GTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTC 407 rnd-4_family- 322 TTCTTGNATGTCTGGA----AAGCGCCTAGCACATCGTGGGCGCT 362 v -? v i v ----v i v i L2c_3end#LINE 408 TTATT-CATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCT 451 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.00 CpG sites = 8, Kimura (unadjusted) = 20.00 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.60 (8 / 5) 242 16.90 6.02 7.32 rnd-4_family-166#DNA/hAT-Tag1 1 166 (819) hAT-5_Mam#DNA/hAT-Tag1 3 166 (3374) m_b9s502i4 rnd-4_family- 1 GGGTGGATAAAAATTCAATNATTTT---AAAAAAAATTAAAATAAATCGG 47 i - ? --- --- hAT-5_Mam#DNA 3 GGGTAGATAAAAAT-CNATNATTTTTNAAAAAAAAATTAAAA---ATCGG 48 rnd-4_family- 48 ATTTTTTAA---AATTTG-TTTTTTATTTAAATTATAATNAGTTTTTCTT 93 --- iv - ? ? --v ? ?i ? ivv v i hAT-5_Mam#DNA 49 ATTTTTTAATTTAATCGGATTTTNTANTT--TTTNTNGTTAAGATGTTTT 96 rnd-4_family- 94 TTT---AAAAATAAACCTGTTTAAAATGAAATCTGAATTTAATACAAAAT 140 ? --- v i v -- ---- iiv vi i hAT-5_Mam#DNA 97 NTTAAGAAAAAGAAACCTATATAAA--GA----TAGTTTTAATTTAAGAT 140 rnd-4_family- 141 ATGTTAAGGCCTAAACTTATTATAAT 166 i ii vv i v hAT-5_Mam#DNA 141 ATGTTAAAGCTCAAAGATATCATCAT 166 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.66 CpG sites = 14, Kimura (unadjusted) = 20.50 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.10 (16 / 165), avg. gap size = 1.38 (22 / 16) 374 26.67 0.00 0.00 rnd-4_family-166#DNA/hAT-Tag1 275 364 (621) hAT-5_Mam#DNA/hAT-Tag1 216 305 (3235) m_b9s502i5 rnd-4_family- 275 CATCTAACTTTTGAGGTCAAGCTTTATAAATATGGCACAATAGGTCATGT 324 v i vvi vv i v v i i i v hAT-5_Mam#DNA 216 CATGTAACCTTTTTAGAAAAGTTTTATAAATAGGTCACAACAGGCCACGG 265 rnd-4_family- 325 ACTGTATTAAGGGCTTGATCCTGTGGGGGACCCAGGGGCT 364 i i iii i i vv i hAT-5_Mam#DNA 266 ACTATATTAGGGGCCCAATCTTATGGGGTTCCCAGAGGCT 305 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.01 CpG sites = 14, Kimura (unadjusted) = 33.71 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 199 20.00 0.00 0.00 rnd-4_family-20#Unknown 47 86 (98) C L2c_3end#LINE/L2 (70) 408 369 m_b9s601i5 rnd-4_family- 47 AAACACAGTCCCTGCCCCAAAAGAGCTTACAGNCTAAGGG 86 i i iv i i ? iv C L2c_3end#LINE 408 AGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.46 CpG sites = 6, Kimura (unadjusted) = 24.94 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 229 22.25 3.16 5.38 rnd-4_family-2797#LTR 55 149 (49) UCON51#LTR 110 202 (48) m_b9s502i6 rnd-4_family- 55 GCCGGGACTAGAACCCTGGTCCTTCAGCTCCAAAAACA-CAGGCCTCTAC 103 i i v vv ?i v? v ?viii - -- UCON51#LTR 110 GCCGAGGCTCGAACCGGGNCCCTTGNGGTCCNCGGGCAGCAG--CTCTAC 157 rnd-4_family- 104 CACTTGAGCTAAAGGAGAGCNCTCCTCAGCTGGCC-AG-CAGTAGTAG 149 vv i i i - i -- - - i v UCON51#LTR 158 CAGGTGAGCCAAAAGGGAGC-CTCCCC--CTGGCCGAGCCGGTAGGAG 202 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 11, Kimura (unadjusted) = 27.82 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.09 (8 / 94), avg. gap size = 1.00 (8 / 8) 15 9.03 2.44 7.69 rnd-4_family-2808#Unknown 167 207 (834) (GCCCCCT)n#Simple_repeat 1 39 (0) m_b9s252i4 rnd-4_family- 167 GCCCCCTGGCCCC-ACCCCCTGCTCCTCTCTGCCCCCTGGCC 207 v -i - - - v (GCCCCCT)n#Si 1 GCCCCCTGCCCCCTGCCCCCTGC-CC-C-CTGCCCCCTGCCC 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 12 13.68 10.00 0.00 rnd-4_family-3530#Unknown 441 480 (624) (AACTTA)n#Simple_repeat 1 44 (0) m_b9s252i3 rnd-4_family- 441 AACTTAGAGTT-TACTT-AAC-T-AACTTAAACTTAAAATCAAA 480 i v -v - - - v i (AACTTA)n#Sim 1 AACTTAAACTTAAACTTAAACTTAAACTTAAACTTAAACTTAAA 44 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 293 28.70 3.70 0.00 rnd-4_family-4049#LINE/CR1 635 742 (3121) C MIR1_Amn#SINE/MIR (74) 156 45 m_b9s601i6 rnd-4_family- 635 ATGATCCCCATTTCAAAGATAGAGAAAGTGAGGCACCAGGTGGGAGAGTG 684 v i v iii v ? vii v v?i C MIR1_Amn#SINE 156 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTG 107 rnd-4_family- 685 ACCTGGCCAGGATCACGTTACCGCTCAGTGGCAGGACTGCAAAC--AACC 732 i v i i ?ivi ? vi? ii i vi ?i-- C MIR1_Amn#SINE 106 ACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACC 57 rnd-4_family- 733 C--GTTCCCTGA 742 -- ii i C MIR1_Amn#SINE 56 CAGGTCTCCCGA 45 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.63 CpG sites = 21, Kimura (unadjusted) = 41.10 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.02 (2 / 107), avg. gap size = 2.00 (4 / 2) 298 22.73 0.00 0.00 rnd-4_family-4049#LINE/CR1 2295 2360 (1503) tRNA-Thr-ACA#tRNA 7 72 (3) m_b9s502i7 rnd-4_family- 2295 ATAGCTCAGTGGTTTGAGCATTGGCCTGCTAAACCCGGGGTTGTGAGCTC 2344 v v i i vv v i i i tRNA-Thr-ACA# 7 ATAGCTCAGGGGTTAGAGCACTGGTCTTGTAAACCAGGGGTCGCGAGTTC 56 rnd-4_family- 2345 AATCCTTGAGGGGGCC 2360 vi i vv tRNA-Thr-ACA# 57 AAATCTCGCTGGGGCC 72 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.43 CpG sites = 7, Kimura (unadjusted) = 27.21 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 502 15.00 0.00 1.25 rnd-4_family-4049#LINE/CR1 2388 2468 (1395) CR1-3_Croc#LINE/CR1 3522 3601 (4) m_b9s551i0 rnd-4_family- 2388 TGGGGATTGGTCCTGCTTTGAGCAGGGGGTTGGACTAGATGACCTCCGGA 2437 i - i i iii i CR1-3_Croc#LI 3522 TAGGGAT-GATCCTGCCTCAGGCAGGGGGTTGGACTAGATGACCTCTGGA 3570 rnd-4_family- 2438 GGTCCCTTCCAACCCTGATATTCTATGATTC 2468 i iv vi CR1-3_Croc#LI 3571 GGTCCCTTCCAGCCCTACTTCTCTATGATTC 3601 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.36 CpG sites = 10, Kimura (unadjusted) = 17.36 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 268 22.39 0.00 0.00 rnd-4_family-4476#DNA/TcMar-Tigger 2 68 (0) Tigger14a#DNA/TcMar-Tigger 256 322 (2) m_b9s502i8 rnd-4_family- 2 TTAACCGGAATTTTTNACTTACCGGCACCCCCCATTCCCCCAACATGCCG 51 i v ? i v i v v i iv v Tigger14a#DNA 256 TTAACCAGAATATTTGATTAACCAGAACACCCCATTTCCTGACCATGCCG 305 rnd-4_family- 52 GATAAAAAAGCTTTTAC 68 v i vv Tigger14a#DNA 306 GATAACAGAGAGTTTAC 322 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.11 CpG sites = 6, Kimura (unadjusted) = 27.11 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 23 25.62 6.86 0.00 rnd-4_family-609#Unknown 216 317 (6) (GGAGCC)n#Simple_repeat 1 109 (0) m_b9s252i2 rnd-4_family- 216 GGAGCTGGAGGCAGAGCAGCAGCAGCAGCC-GTG-CTGAGGCAGAG-TGG 262 i v i v v v v - v - v v i -i (GGAGCC)n#Sim 1 GGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGG 50 rnd-4_family- 263 AGCTGGAGCCGGGGCTGGAG-CAG-TCCGGAGCCGGGGCTGG-GGCAG-T 308 i i i - i -v i i - v i -v (GGAGCC)n#Sim 51 AGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAG 100 rnd-4_family- 309 CCGGAGCCG 317 (GGAGCC)n#Sim 101 CCGGAGCCG 109 Matrix = Unknown Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.07 (7 / 101), avg. gap size = 1.00 (7 / 7) 290 27.46 4.30 2.11 rnd-4_family-762#LINE/L2 7 99 (1220) AmnSINE1#SINE/5S-Deu-L2 149 243 (332) m_b9s601i7 rnd-4_family- 7 CCCTCCAAACCAGTACTAAAACAATGCACCCAATATGAT-TTAGGAAGTA 55 ii ii i v i - iii i - ii i AmnSINE1#SINE 149 CCCTCTGAGTCAGTACTGAACCAGTGC-CCCAGCGTGGTGTTAGGGGGCA 197 rnd-4_family- 56 TTGTGTTGCTGGACCTG--ATC-TTCGGCCTAGATGTCAANATCGGG 99 i i vv --i - viv i - ? i i AmnSINE1#SINE 198 CTGTGCTGCTGGAGGTGCCGTCTTTCGGATGAGACGT-AAAACCGAG 243 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 20, Kimura (unadjusted) = 37.60 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.20 (6 / 5) 278 15.38 0.00 0.00 rnd-4_family-762#LINE/L2 1192 1243 (76) L2-1_AMi#LINE/L2 126 177 (1058) m_b9s551i1 rnd-4_family- 1192 TCCATTCTCATCCTCCTGGACCTCTCTGCAGCATTCGACACTGTCGACCA 1241 i v v v v v i v L2-1_AMi#LINE 126 TCCATCCTCATCCTCCTTGACCTGTCAGCCGCCTTTGACACAGTCGACCA 175 rnd-4_family- 1242 TG 1243 L2-1_AMi#LINE 176 TG 177 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.24 CpG sites = 2, Kimura (unadjusted) = 17.24 Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 17 21.60 1.75 3.57 rnd-4_family-978#Unknown 81 137 (615) (CGCCC)n#Simple_repeat 1 56 (0) m_b9s252i0 rnd-4_family- 81 CGACCCCCCCTGCCCTGCCCCGCGCCCAGCCCGGGGCCGCCGCG-CTCTC 129 v v i i - - v vv v - i v (CGCCC)n#Simp 1 CGCCCCGCCCCGCCCCGCCCCGC-CCC-GCCCCGCCCCGCCCCGCCCCGC 48 rnd-4_family- 130 CCCGCCCC 137 (CGCCC)n#Simp 49 CCCGCCCC 56 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 12 11.65 3.33 3.33 rnd-4_family-978#Unknown 525 554 (198) (CAGCG)n#Simple_repeat 1 30 (0) m_b9s252i1 rnd-4_family- 525 CAG-GCAGCCGCCGCGCTGCGCAGAGCAGCG 554 - - v v v (CAGCG)n#Simp 1 CAGCGCAG-CGCAGCGCAGCGCAGCGCAGCG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 411 26.61 0.00 0.00 rnd-4_family-1089#LTR/ERV1 1328 1436 (740) PRIMA41-int#LTR/ERV1 7173 7281 (475) m_b10s701i0 rnd-4_family- 1328 GATCCGACAGATGGCCCTCCAAAACCGTCAGGCATTGGACATAGTGCTGG 1377 iv i i i v vv v vv ivi? PRIMA41-int#L 7173 GATTAGGCAGGTGGCCTTACAAAACCGTATGGCTTTGGACATTTTAACNG 7222 rnd-4_family- 1378 CGGCCAAAGGAGGGACCTGTGCTCTCATTGGAAAAGAATGTTGTGTGTTT 1427 v i i i i v iii vv v PRIMA41-int#L 7223 CGGCCCAAGGGGGAACTTGTGCTTTGATCAAAACCGAATGTTGTGTGTAT 7272 rnd-4_family- 1428 ATACCTGAC 1436 i v v PRIMA41-int#L 7273 GTTCCAGAC 7281 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.52 CpG sites = 14, Kimura (unadjusted) = 33.52 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0) 383 24.66 5.82 9.89 rnd-4_family-1243#LINE/CR1 25 213 (11) CR1-13_AMi#LINE/CR1 442 623 (101) m_b10s551i0 rnd-4_family- 25 TTTAAAAAGGGCTGGATAATTTTATG---ACCNNTAATA---ACAGTTAT 68 i ii i i v v --- v ??v i ---i i CR1-13_AMi#LI 442 TTCAAAAAGGATTAGACATTTATATGGATAACGAGAACATCCGCAGTTAC 491 rnd-4_family- 69 ACTCGGCAGCAGGCTAAGAAATATTAAGGGTAATCAAATCTCATGCTCCA 118 i v ii --- v i v i i --i ?i i CR1-13_AMi#LI 492 ATTAGATAG---GATAAAAAATATAAGGGATA--TAANCCTCATGCTTCA 536 rnd-4_family- 119 GGGCGTAAGCTGATCGC---CTGCAGGGGTCAGGAAGGAATTTCTCTCCT 165 i ii i i --- vv i i i -- i CR1-13_AMi#LI 537 GGGCATAAGCCAACCACTAACTGACGGGGTTAGGAAGAAACT--TCCCCT 584 rnd-4_family- 166 TCTCATGTACAG--CATTGCACAACTGGCTAGGTGCATTATGGGATTTTT 213 ---- vi --i v i i - ------ i? CR1-13_AMi#LI 585 ----ATGGGCAGGTTATTCCATAATT-GC------CATTATGGGGNTTTT 623 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 31, Kimura (unadjusted) = 32.27 Transitions / transversions = 2.82 (31/11) Gap_init rate = 0.12 (22 / 188), avg. gap size = 1.32 (29 / 22) 227 27.55 2.73 7.62 rnd-4_family-1288#LINE/I 55 164 (1875) L3#LINE/CR1 3122 3226 (873) m_b10s601i0 rnd-4_family- 55 AATGGNACTCCACAGGGGAGTGTTATCAGCCCNACCCTGTTCAACATCAT 104 i ?iiv vvv iv ii ?ii iv L3#LINE/CR1 3122 AGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTT 3171 rnd-4_family- 105 GATNAATGATCTCCCAAGGAGATGAGTGCAGGAATAGGCATCNCNCT--- 151 v ? ii -------i ivi vii - v?i?v --- L3#LINE/CR1 3172 TATCAATGACTT-------GGATGAAGACATAGA-AGGCATGCTTATCAA 3213 rnd-4_family- 152 ATTTGCAGATGAC 164 L3#LINE/CR1 3214 ATTTGCAGATGAC 3226 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 17, Kimura (unadjusted) = 37.60 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (9 / 109), avg. gap size = 1.22 (11 / 9) 255 6.06 0.00 0.00 rnd-4_family-1381#DNA/hAT-Charlie 16 48 (125) Charlie15a#DNA/hAT-Charlie 1 33 (191) m_b10s502i0 rnd-4_family- 16 CAGTGGTTCTCAAACTGTGGTCCGCGGAGCCCT 48 i v Charlie15a#DN 1 CAGTGGTTTTCAAACTGTGTTCCGCGGAGCCCT 33 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.33 CpG sites = 1, Kimura (unadjusted) = 6.33 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 521 16.43 19.89 1.83 rnd-4_family-1815#SINE/MIR 7 192 (0) MIRc#SINE/MIR 25 243 (25) m_b10s601i1 rnd-4_family- 7 GAGCACAGGACTGGGAGCCAGGAACTCCCGAGTTCTAATCCCGGCTCTGA 56 v v i vv i i v i v MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 rnd-4_family- 57 CACGCTGACC-CCTCTGTAGCTTTGGGNAANTCACTTAA----------- 94 -- v i-v v ii i ? ? ----------- MIRc#SINE/MIR 75 CA--CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 rnd-4_family- 95 --CAGTTCCC------ATAAAAC--AGATAAT-ATACCTGCTC------- 126 -- i ------i i--i - i ------- MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTAC 172 rnd-4_family- 127 --CACAGGGGNGTTGTGAGGAT----TGATAATAATGTTTGT-AAAGNNC 169 -- v? ---- -i v - ?? MIRc#SINE/MIR 173 CTCACAGGGTTGTTGTGAGGATCAAATGA-GATAATGTATGTGAAAGCGC 221 rnd-4_family- 170 TTTGAAGGTTGTGAAAGTGCCAT 192 v iii - i MIRc#SINE/MIR 222 TTTGTAAACTGT-AAAGTGCTAT 243 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.46 CpG sites = 18, Kimura (unadjusted) = 19.46 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (13 / 185), avg. gap size = 3.15 (41 / 13) 185 27.44 3.88 0.94 rnd-4_family-1845#LINE/I-Jockey 780 882 (996) L3#LINE/CR1 3122 3227 (872) m_b10s601i2 rnd-4_family- 780 AATGGGNTACCCCAAGGCTCTGTGCTNTCACCAACGCTGTTCAACNTGTA 829 i v? i v i v ?vvv viiv ? v v L3#LINE/CR1 3122 AGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTT 3171 rnd-4_family- 830 CATCAACGACCT-GCCANCNACNNAGTCGCGCAAGTTCATC---TATGCA 875 i i i - vii?v? ?? vv - v i i --- v L3#LINE/CR1 3172 TATCAATGACTTGGATGAAGACATAGAAG-GCATGCTTATCAAATTTGCA 3220 rnd-4_family- 876 GATGACA 882 L3#LINE/CR1 3221 GATGACA 3227 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.60 CpG sites = 12, Kimura (unadjusted) = 37.60 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.67 (5 / 3) 1103 23.47 0.61 0.30 rnd-4_family-1845#LINE/I-Jockey 1543 1871 (7) X12_LINE#LINE/I-Jockey 6 335 (36) m_b10s601i3 rnd-4_family- 1543 TCCGCCACGCCAGGACGTNACGGCGGAANCACTCTGGCGNGAGGAATGGA 1592 ?v ii i ?v v i ? i v ? - X12_LINE#LINE 6 TCNCCCGTGCCAGGACATGCCCGTGGAATCGCGCTGGCGAGAGGAATGG- 54 rnd-4_family- 1593 TATCTGTTA-CAATCNCCAACCAGTCCCTCGTCGCCGACCCGACCATCTG 1641 v iii i - i iv? v v i vi X12_LINE#LINE 55 TCTTCATCAGCGACAACAAACAAGTTCCTCGTCGCCGACCCTGCCATCTG 104 rnd-4_family- 1642 CCCGCCTGGTTTTGACCTGCCACGNCGCCNGTGGTCCCTGCTGAACCGGT 1691 i v iv i ? iv?i v i v X12_LINE#LINE 105 TCCTCCTGGTTTCCACCTACCACGCCGTATATGGGCTCTGCTGAACAGGT 154 rnd-4_family- 1692 TCCGAACNGGGCAGGGTCACTGTGCAGCCAACCTNTACANCTGGGGCCTT 1741 i i ? v i i ? ?v i vv X12_LINE#LINE 155 TTCGGACTGGCCAAGGTCACTGCGCAGCCAACCTTTACAGATGGGGTCAG 204 rnd-4_family- 1742 TGTGACGACCCNNCGTGCGGCTGCGGCC-AACGCAGACGATGTCGCACAT 1790 i i vv i ??vv i i - v i X12_LINE#LINE 205 CGCGAACATCCAAATTGCAGCTGTGGCCAAACGCAGACGATGACGCACAC 254 rnd-4_family- 1791 CGTTGACGANTGCCCGCTGACTAGNTTCGACGGTGGCCTANGGGCTCTGC 1840 i ? vi v i ?i i i ii?v i v v X12_LINE#LINE 255 TGTTGACGAGTGCCCTTTGTCCAGACTTGACGGTGGTCCGATGACACTGA 304 rnd-4_family- 1841 ACCTCGCCGATGANGATGCTATCGCTTGGCT 1871 iv?v vi ? v iii i X12_LINE#LINE 305 ATANAGCAAATGAAGAAGCTGCTGCCTGGCT 335 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 45, Kimura (unadjusted) = 30.66 Transitions / transversions = 1.41 (45/32) Gap_init rate = 0.01 (3 / 328), avg. gap size = 1.00 (3 / 3) 462 26.45 0.00 0.00 rnd-4_family-1916#SINE/MIR 409 529 (505) MIR1_Amn#SINE/MIR 39 159 (71) m_b10s601i4 rnd-4_family- 409 TGAAAATCAGGGCTCTTGGGTCCTATTCCCAACTCTGCCACGGACTGGCT 458 ii v i ivv i i ? ? ii v?i i? MIR1_Amn#SINE 39 TGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCT 88 rnd-4_family- 459 GTGTGACCTAAGACAAGTCAATTCTCCTTTCTCAGCCTTAGCTTCTCCCT 508 ? vi i v ?v i v? i i ii v MIR1_Amn#SINE 89 GNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCAT 138 rnd-4_family- 509 CTTTCAAGTAGGGATAACAAT 529 v v i i ii MIR1_Amn#SINE 139 CTGTAAAATGGGGATAATGAT 159 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 21, Kimura (unadjusted) = 36.63 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 481 24.19 0.81 0.00 rnd-4_family-1916#SINE/MIR 423 546 (488) MIRc#SINE/MIR 51 175 (93) m_b10s601i5 rnd-4_family- 423 CTTGGGTCCTATTCCCAACTCTGCCACGGACTGGCTGTGTGACCTAAGAC 472 i i v v ii vv i vi i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 rnd-4_family- 473 AAGTCAATTCTCCTTTCTCAGCCTTAGCTTCTCCCTCTTTCAAGTAGGGA 522 v vv i v i i ii v v v i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 rnd-4_family- 523 TAACAAT-CCGCCCCTACCTACCTC 546 i - vv i MIRc#SINE/MIR 151 TAATAATACCTGCCCTGCCTACCTC 175 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.44 CpG sites = 16, Kimura (unadjusted) = 29.58 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.01 (1 / 123), avg. gap size = 1.00 (1 / 1) 12 5.48 0.00 0.00 rnd-4_family-2102#Unknown 279 297 (237) (GCT)n#Simple_repeat 1 19 (0) m_b10s252i12 rnd-4_family- 279 GCTGCTGCTGCTGCTTCTG 297 v (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTG 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 1635 10.33 7.81 2.84 rnd-4_family-2208#SINE/5S-Deu-L2 26 294 (0) AmnSINE1#SINE/5S-Deu-L2 7 288 (287) m_b10s502i1 rnd-4_family- 26 AGCCATANCACCTTGGGCTGTGATCTTGTCAGATCTCACAAGCTAAATAA 75 ? i i ii i AmnSINE1#SINE 7 AGCCATACCACCTCGGGCTGTGATCTCGTCAGATCTCACAAGCTAAGCAG 56 rnd-4_family- 76 GGTCAGGCTTGGTCAGTACTTGGATGGGAGACCTCTAAGGAAAACCACGC 125 i i i - --- AmnSINE1#SINE 57 GGTCGGGCCTGGTCAGTACTTGGATGGGAGACCTCCAAGG-AAACC---C 102 rnd-4_family- 126 AGNTACTGCAGGAAGCGGTGNCGGTAANTT-GNAANGGGCGCT-NTCCTT 173 ? i i ?i i ? i- ? i?v i -? i AmnSINE1#SINE 103 AGGTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCT 152 rnd-4_family- 174 -----------CTGAACCAATGCTCCCACAT--------GGNGCACTGTG 204 ----------- i i vi i -------- ? AmnSINE1#SINE 153 CTGAGTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTG 202 rnd-4_family- 205 CTATATGCTGGAGGCGCCATCTTTCGGATGAGATGTAAAACCGAGATCCT 254 ---- i i i i AmnSINE1#SINE 203 C----TGCTGGAGGTGCCGTCTTTCGGATGAGACGTAAAACCGAGGTCCT 248 rnd-4_family- 255 GACCACTTGTGGTCATTAAAGATCCCATGGCACTTTTTGC 294 i AmnSINE1#SINE 249 GACCACTTGTGGTCATTAAAGATCCCATGGCACTTTTCGC 288 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.86 CpG sites = 25, Kimura (unadjusted) = 11.90 Transitions / transversions = 12.50 (25/2) Gap_init rate = 0.04 (12 / 268), avg. gap size = 2.42 (29 / 12) 16 24.62 3.39 1.67 rnd-4_family-228#LINE/L2 17 75 (1510) (TCC)n#Simple_repeat 1 60 (0) m_b10s252i7 rnd-4_family- 17 TCCACCAGCTCTACCTACTCCTCTTCC-CCT-CTCCACCCCGATCTCCTT 64 v vv iv v i - - v i vvi - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-T 49 rnd-4_family- 65 CCTCCTCCTCC 75 (TCC)n#Simple 50 CCTCCTCCTCC 60 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 13 17.47 0.00 3.03 rnd-4_family-228#LINE/L2 147 180 (1405) (CCCT)n#Simple_repeat 1 33 (0) m_b10s252i8 rnd-4_family- 147 CCCTCCCTCCATCCCCACCCTCTCCACCTCCCTC 180 v - v i iv (CCCT)n#Simpl 1 CCCTCCCTCCCT-CCCTCCCTCCCTCCCTCCCTC 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 15 27.60 4.60 2.25 rnd-4_family-228#LINE/L2 155 241 (1344) (CCATCC)n#Simple_repeat 1 89 (0) m_b10s252i9 rnd-4_family- 155 CCATCCCCA-CCCTCTCCACCTCCCTCA-NACCACCTCCA-CCACCTCCG 201 - iv v v - -?v i i - v v - (CCATCC)n#Sim 1 CCATCCCCATCCCCATCCCCATCCC-CATCCCCATCCCCATCCCCATCC- 48 rnd-4_family- 202 CCCTTCTCATTCCCAACCTCATGCCCA-CCTCCTCCCCTTC 241 v i i i v i v - i v v (CCATCC)n#Sim 49 CCATCCCCATCCCCATCCCCATCCCCATCCCCATCCCCATC 89 Matrix = Unknown Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.07 (6 / 86), avg. gap size = 1.00 (6 / 6) 20 14.04 10.91 0.00 rnd-4_family-228#LINE/L2 446 500 (1085) (TC)n#Simple_repeat 1 61 (0) m_b10s252i10 rnd-4_family- 446 TCTCT-TCTCCCGCT-TCTCAC-CCCTCTCT-TCTCTCCCT-TCCCACTC 490 - i v - v - i - i - i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 rnd-4_family- 491 TCTCTCT-TCT 500 - (TC)n#Simple_ 51 TCTCTCTCTCT 61 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.11 (6 / 54), avg. gap size = 1.00 (6 / 6) 15 23.41 4.00 0.00 rnd-4_family-228#LINE/L2 929 978 (607) (TCTCC)n#Simple_repeat 1 52 (0) m_b10s252i11 rnd-4_family- 929 TCTCGTCTGCTCTCAGCCCCTCTCCTC-CCTGCCCTCTCTTC-CCTTTCT 976 v v vv i - vi i - i i (TCTCC)n#Simp 1 TCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC 50 rnd-4_family- 977 TC 978 (TCTCC)n#Simp 51 TC 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 2888 6.32 8.36 5.48 rnd-4_family-228#LINE/L2 999 1584 (1) L2-1_Crp#LINE/L2 6 607 (634) m_b10s551i1 rnd-4_family- 999 CTCTCCATGCTTCACTCTCCTCCACCCTTGACTCTTTTGCCCCTCTCTCC 1048 i ? ii i -- ? L2-1_Crp#LINE 6 CTCTCTATGCTTCNCTCCTCCCCAC--TTNACTCTTTTGCCCCTCTCTCC 53 rnd-4_family- 1049 CATCGCAAGGTCTGC------------CCTGGCTCACCCCCAACATCCGC 1086 i ------------ L2-1_Crp#LINE 54 CATTGCAAGGTCTGCTGCACCTTCAGCCCTGGCTCACCCCCAACATCCGC 103 rnd-4_family- 1087 TTCCTCCGCTCCT---CTCGCGCTGCGGAGCGTCTCTGGNGGAAATCCNA 1133 i --- i i ? ?i L2-1_Crp#LINE 104 TTCCTCTGCTCCTGCTCTCGCGCTGCAGAGCATCTCTGGCGGAAATCCCG 153 rnd-4_family- 1134 TGACCACGCTGACTTCCTCCACTACAAATTCGTTCTCTCCTCCTTCAGTT 1183 v L2-1_Crp#LINE 154 TGACCAGGCTGACTTCCTCCACTACAAATTCGTTCTCTCCTCCTTCAGTT 203 rnd-4_family- 1184 CTGCCATCTTCCTGGCTAAACAACTCTNCTTCTCCAACTTAATTGAATCC 1233 i ? L2-1_Crp#LINE 204 CTGCCATCTTCCTAGCTAAACAACTCTACTTCTCCAACTTAATTGAATCC 253 rnd-4_family- 1234 CACGCCTACAATCCCAGCCGCCTTTTCGCCACCTTTGACTCACTCCTC-- 1281 ii --- -- -- L2-1_Crp#LINE 254 CACGCCCGCAATCCC---CGCCTTTTCGCCAC--TTGACTCACTCCTCAC 298 rnd-4_family- 1282 ----------------CACCTCTCTCTCCGCACAGGATCTTGCTAATTTC 1315 ---------------- i ii ii L2-1_Crp#LINE 299 CACCCTTTCCTGCCTCCACTTCTCTCTCCGCACAGGATCTCACCGATTTC 348 rnd-4_family- 1316 TTCCAAGAGAAAATTGA--------GNCG--ATCTTCAATCCCTCACNTN 1355 i -------- ? -- i i ---i v ? ? L2-1_Crp#LINE 349 TTCCAAGAGAAAACTGACAAAATACGACGTGACCTCC---TCCTCCCCTC 395 rnd-4_family- 1356 ANCTNGCCTTCC--CTTCCC-CTCCTACAACTCTCTCCTCTCTCCCTCCC 1402 i? ? i -- - iii - i - L2-1_Crp#LINE 396 GGCTTGCCTCCCTTCTTCCCTCTCCTACAATCTTCTCCTCT-TCTC-CCC 443 rnd-4_family- 1403 TGTCACAGACGCAGAAGTTTCTCGTCTGNTCTCCTCC-TCTAACCCCTCC 1451 - -- -? i - --- L2-1_Crp#LINE 444 TGTCACAGACGC-GAAGTTTCT--TCT-TTCTCTTCCCTCTAACCCC--- 486 rnd-4_family- 1452 ACTTGCCCCAGTGACCCCATCCCAT-CCATCTCCTGATCTCCCTCGCGCC 1500 ------- ? - - i i i L2-1_Crp#LINE 487 -------CCAGTGACCCCNTCCCATCCCATCTCCTGATC-CCTTCACGTC 528 rnd-4_family- 1501 CACTCTCATCCCCTCCCTTACTCTTCTCCTTAACCTCTCACTCT-CCTCT 1549 --- - L2-1_Crp#LINE 529 CACTCTCATCCCCTCCCTTACTCTTCTCCTTAACCTCT---TCTGCCTCT 575 rnd-4_family- 1550 GGCTCTTTCCCCTCACAATACAAGCATGCTTTAGT 1584 --- i i L2-1_Crp#LINE 576 G---CTTTTCCCTCACAATACAAACATGCTTTAGT 607 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.10 CpG sites = 33, Kimura (unadjusted) = 6.90 Transitions / transversions = 16.50 (33/2) Gap_init rate = 0.08 (44 / 585), avg. gap size = 1.86 (82 / 44) 378 17.90 8.33 1.74 rnd-4_family-2807#LINE/L2 63 170 (10) L2c_3end#LINE/L2 345 459 (19) m_b10s601i6 rnd-4_family- 63 TGTCT-TCTCTGTGTCTGTCTTTTT---TAGACTGTAAGCTCTTCGAGG- 107 - i vi? ii i--- i i i - L2c_3end#LINE 345 TGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGG 394 rnd-4_family- 108 CAGGGACTGTGTTTTTATTTGTGTCTTGTA----CAGCGCCGAGCACATT 153 i i - ii v - ---- vi v L2c_3end#LINE 395 CAGGGACCGTGTCTT-ATTCATCT-TTGTATCCCCAGCGCCTGGCACATA 442 rnd-4_family- 154 GTCGGCGCTNAACAAAT 170 v ? i L2c_3end#LINE 443 GTAGGCGCTCAATAAAT 459 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.36 CpG sites = 14, Kimura (unadjusted) = 21.61 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.06 (6 / 107), avg. gap size = 1.83 (11 / 6) 508 14.59 2.02 3.06 rnd-4_family-281#LINE/CR1 66 164 (42) X6B_LINE#LINE/CR1 974 1071 (1) m_b10s601i7 rnd-4_family- 66 ATAACACTTGCAGCTCTGCA--TTAAGACAATGACTATAATCAAATCTCA 113 i i i v --i i v i--- X6B_LINE#LINE 974 ATAACATTTGTAGTTATGCAAGCTAAGATAAGGG---TAATCAAATCTCA 1020 rnd-4_family- 114 TGCTTCAGGGCTTCAGCCGGTCGCCTGCAGGGGTCAGGAAGGATTTTTTC 163 v v i i v i X6B_LINE#LINE 1021 TGCTTCAGGGCATAAGCTGATCGCCTGCAGGGGTCAGGAAGGAATTTCTC 1070 rnd-4_family- 164 C 164 X6B_LINE#LINE 1071 C 1071 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.44 CpG sites = 9, Kimura (unadjusted) = 16.44 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.25 (5 / 4) 392 14.75 0.00 0.00 rnd-4_family-326#DNA/TcMar-Tigger 1 61 (0) Tigger14a#DNA/TcMar-Tigger 1 61 (263) m_b10s502i2 rnd-4_family- 1 CAGTAAAAGCTGTGTTATCCGGCACTTTACCAACCGGAAAGCTCTATAAA 50 vv i i i v v Tigger14a#DNA 1 CAGTAAAAGCTGGTTTATCCGGCATTCTATCAACCGGAAATCTCTATTAA 50 rnd-4_family- 51 CCGGCATTTCT 61 i i Tigger14a#DNA 51 CTGGCACTTCT 61 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.55 CpG sites = 5, Kimura (unadjusted) = 16.55 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 16 8.72 4.00 0.00 rnd-4_family-3825#Unknown 376 400 (135) (TC)n#Simple_repeat 1 26 (0) m_b10s252i6 rnd-4_family- 376 TCTCTCTCTCTCTC-CCCCCTCTCTC 400 - i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTC 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 15 17.95 5.77 1.85 rnd-4_family-384#Unknown 65 116 (943) (ACCTAAT)n#Simple_repeat 1 54 (0) m_b10s252i5 rnd-4_family- 65 ACC-AATAACTAATATCTTAAT-CCTTATA-CACACACATTATACCTAAT 111 - v - i - v - vv i v v (ACCTAAT)n#Si 1 ACCTAATACCTAATA-CCTAATACCTAATACCTAATACCTAATACCTAAT 49 rnd-4_family- 112 ACCTA 116 (ACCTAAT)n#Si 50 ACCTA 54 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 36 0.00 0.00 0.00 rnd-4_family-384#Unknown 118 152 (941) (AC)n#Simple_repeat 1 35 (0) c_b10s251i1 rnd-4_family- 118 ACACACACACACACACNCACACACACACACACACA 152 ? (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 14 20.12 0.00 0.00 rnd-4_family-3985#Unknown 70 103 (960) (TAAAGA)n#Simple_repeat 1 34 (0) m_b10s252i3 rnd-4_family- 70 TAAATATAATGATAAAGCAAAAGATAAAAGTAAA 103 v v vv ii (TAAAGA)n#Sim 1 TAAAGATAAAGATAAAGATAAAGATAAAGATAAA 34 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 rnd-4_family-3985#Unknown 148 176 (915) (AC)n#Simple_repeat 1 29 (0) c_b10s251i0 rnd-4_family- 148 ACACACACACACACACACACACACACACA 176 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 13.08 0.00 0.00 rnd-4_family-3985#Unknown 194 218 (873) (ATTC)n#Simple_repeat 1 25 (0) m_b10s252i4 rnd-4_family- 194 ATTCATTCACACAATCATTCATTCA 218 iv v (ATTC)n#Simpl 1 ATTCATTCATTCATTCATTCATTCA 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 16 7.83 3.45 3.45 rnd-4_family-4125#DNA/Maverick 1718 1746 (9562) (AG)n#Simple_repeat 1 29 (0) m_b10s252i2 rnd-4_family- 1718 AGACAGAGAGAGA-AGAGAGAGANGAGCGA 1746 v - - v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGA-GAGAGA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 266 12.21 0.00 16.95 rnd-4_family-473#DNA/PIF-Harbinger 43 111 (2) MER133B#DNA/PIF-Harbinger 48 106 (9) m_b10s502i3 rnd-4_family- 43 AACTCCCATTGAAGTCAATGGGAATTTTGNCTGAGTAAAAACTGAGTAAG 92 i v ?v v --- v --- MER133B#DNA/P 48 AACTCCCATTGAAGTCAATGGGAGTTGTGCGTGCGT---ATCTGAG---G 91 rnd-4_family- 93 GACCTCAGGATTTGGCCTT 111 ---- i i MER133B#DNA/P 92 G----CAGAATTTGGCCCT 106 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.17 CpG sites = 3, Kimura (unadjusted) = 13.17 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.15 (10 / 68), avg. gap size = 1.00 (10 / 10) 24 14.43 4.62 3.03 rnd-4_family-9540#Unknown 63 127 (15) (GTTGCTT)n#Simple_repeat 1 66 (0) m_b10s252i1 rnd-4_family- 63 GTTGCTTGTTGGCTAGTT--TT-TGGCTTGTAGCTTGTTGCTTCTTTTTT 109 - v -- - v v -v vi (GTTGCTT)n#Si 1 GTTGCTTGTT-GCTTGTTGCTTGTTGCTTGTTGCTTGTTGCTT-GTTGCT 48 rnd-4_family- 110 TGTAGCTTGTTGCTTCTT 127 v v (GTTGCTT)n#Si 49 TGTTGCTTGTTGCTTGTT 66 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.25 (5 / 4) 16 22.34 4.62 1.49 rnd-4_family-983#Unknown 336 400 (49) (ATTTAA)n#Simple_repeat 1 67 (0) m_b10s252i0 rnd-4_family- 336 ATTTCAAATTTAATTTTAAA--TAGGTTTATTTTTAAAAANAAAAATGTA 383 - v -- ii vv vv? vv iv (ATTTAA)n#Sim 1 ATTT-AAATTTAAATTTAAATTTAAATTTAAATTTAAATTTAAATTTAAA 49 rnd-4_family- 384 TTT-AATTTAAATTAAAA 400 - v (ATTTAA)n#Sim 50 TTTAAATTTAAATTTAAA 67 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.33 (4 / 3) 963 18.41 1.47 1.47 rnd-4_family-110#LINE/L2 2 205 (5) X24_LINE#LINE/L2 88 291 (23) m_b11s601i0 rnd-4_family- 2 CACAGGGAGCACATTACACCTGTGCTCCGTGATCTGCACTGGCTNCCAGT 51 ? iii ? ?i X24_LINE#LINE 88 CACANGGAGCACATTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNAT 137 rnd-4_family- 52 TGGTTTCCAGGTGNAGTTTAAAGTGTTGGTTTTGANCTATAAAGCCCTAA 101 v i ii ? i i i ii i ? v X24_LINE#LINE 138 TTGCTTCCGAGTGCAATTCAAGGTGTTGACTTTAATCTATAAAGCCCTAT 187 rnd-4_family- 102 ATGGNTTGGGNCCTGGCTANCCTGAGAGACCGCCTCTCTCCCCGTGTGAT 151 ? ? i - v i i? iivi X24_LINE#LINE 188 ATGGTTTGGGCCCTGGTTA-CCTTAGAGATCGCCTCTCTCCCTNTGCACC 236 rnd-4_family- 152 ACCGCGGCAGNTGNGATCANCTGAGA---TCCTGAGCTAACAGCCTCTCG 198 ii i i? ? ? ii --- -- i iii iv X24_LINE#LINE 237 GTCACGGCAATTGAGATCAGCTAGGATGCTCCT--GCTAACGGTTCCCAG 284 rnd-4_family- 199 GTTTAAA 205 i i X24_LINE#LINE 285 ATTTGAA 291 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.65 CpG sites = 32, Kimura (unadjusted) = 23.91 Transitions / transversions = 6.40 (32/5) Gap_init rate = 0.02 (4 / 203), avg. gap size = 1.50 (6 / 4) 421 20.58 18.24 2.17 rnd-4_family-1431#SINE/5S-Deu-L2 2705 2863 (753) AmnSINE1#SINE/5S-Deu-L2 26 209 (366) m_b11s502i0 rnd-4_family- 2705 GCGACCATGTCACCTCTCACAAGCTAAGCGGGTTTGGGCCCAGGCAGNGC 2754 i i vi vv i v i ii v ?i AmnSINE1#SINE 26 GTGATCTCGTCAGATCTCACAAGCTAAGCAGGGTCGGGCCTGGTCAGTAC 75 rnd-4_family- 2755 TTGGATGGGAGACCTCCAAGGAAAAGCCAGCGGGTGCTG-GGG----GGC 2799 -- -- i -i ---- i AmnSINE1#SINE 76 TTGGATGGGAGACCTCCAAGGAAA--CC--CAGGTGCTGCAGGAAGTGGT 121 rnd-4_family- 2800 GCTAGTGAGTCAGCAGAGGGTGCTCT------------------------ 2825 i v i iv ii ------------------------ AmnSINE1#SINE 122 GCTGGTGATTCAGTAGGTGGCACTCTTCCCTCTGAGTCAGTACTGAACCA 171 rnd-4_family- 2826 ATTCCCCAGTGCGGCGCTAGGGGGCGCCGTGCTGCGGG 2863 i v i i i i i i v AmnSINE1#SINE 172 GTGCCCCAGCGTGGTGTTAGGGGGCACTGTGCTGCTGG 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.54 CpG sites = 23, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.04 (7 / 158), avg. gap size = 4.71 (33 / 7) 245 20.62 8.25 0.00 rnd-4_family-1431#SINE/5S-Deu-L2 2854 2950 (666) AmnSINE1#SINE/5S-Deu-L2 105 209 (366) m_b11s502i1 rnd-4_family- 2854 GTGCTGCGGGGAGCGG-GCGGGGGGCTCAGCAGGGGGCGCTCTCCCCTNG 2902 i i i - v v ii i v i i ?v AmnSINE1#SINE 105 GTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCT 154 rnd-4_family- 2903 CAGTCAGTGCTGA-------CCCCAGTGCGGCGCTAGGGGGCGCTGTGCT 2945 v i ------- i i i i i AmnSINE1#SINE 155 GAGTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGCT 204 rnd-4_family- 2946 GCAGG 2950 v AmnSINE1#SINE 205 GCTGG 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 14, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (2 / 96), avg. gap size = 4.00 (8 / 2) 257 20.62 8.25 0.00 rnd-4_family-1431#SINE/5S-Deu-L2 2941 3037 (579) AmnSINE1#SINE/5S-Deu-L2 105 209 (366) m_b11s502i2 rnd-4_family- 2941 GTGCTGCAGGGAGCGG-GCGGGGGGCTCAGTAGGGGGCGCTCTCCCCTNG 2989 i i - v v ii v i i ?v AmnSINE1#SINE 105 GTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCT 154 rnd-4_family- 2990 CAGTCAGTGCTG-------GCCCCGGTGCGGCGCTAGGGGGCGCTGTACT 3032 v i ------- i i i i i i i AmnSINE1#SINE 155 GAGTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGCT 204 rnd-4_family- 3033 GCAGG 3037 v AmnSINE1#SINE 205 GCTGG 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 14, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (2 / 96), avg. gap size = 4.00 (8 / 2) 309 20.94 5.66 0.90 rnd-4_family-1431#SINE/5S-Deu-L2 3243 3348 (268) AmnSINE1#SINE/5S-Deu-L2 394 504 (71) m_b11s502i3 rnd-4_family- 3243 TCGCCTCCTGCCCTAGACTCTCGGGCAGTGCTGCTGTGCGGCTGTTAA-C 3291 i i i i v i v i i - - AmnSINE1#SINE 394 TCACTTCCTGTCCTAAACTGTTGTGTAGTGTTGCTGTGCG-CTGTTAAAC 442 rnd-4_family- 3292 AGCTGCC---TGCCGCTCCTCAGGNAGCTGCAATTCAGC-CCCGGTGAGG 3337 --- v i i vv ?i v i-viv i AmnSINE1#SINE 443 AGCTGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAG 492 rnd-4_family- 3338 -GACCCCTGTAT 3348 - i AmnSINE1#SINE 493 TGATCCCTGTAT 504 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.42 CpG sites = 14, Kimura (unadjusted) = 25.42 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.40 (7 / 5) 243 16.36 3.57 1.75 rnd-4_family-1431#SINE/5S-Deu-L2 3343 3398 (218) AmnSINE1#SINE/5S-Deu-L2 434 490 (85) m_b11s502i4 rnd-4_family- 3343 CTGTATAAACCGC--CCGCGCTCCACCCCAGAGGTGGCAGCATCTCAGCA 3390 - v -- i v i ii AmnSINE1#SINE 434 CTGT-TAAACAGCTGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTG 482 rnd-4_family- 3391 CCGGGTAA 3398 vi i AmnSINE1#SINE 483 GTGGGTGA 490 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.81 CpG sites = 6, Kimura (unadjusted) = 18.81 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.50 (3 / 2) 6861 9.70 2.06 0.20 rnd-4_family-1652#LINE/CR1 3 973 (0) CR1-L3A_Croc#LINE/CR1 434 1422 (2866) m_b11s551i0 rnd-4_family- 3 ACTCCAGATTCAAGGAAGAAAGGAGCCGGCCGCCAAGGAGTCAGAGAGAG 52 i i i i i ii i CR1-L3A_Croc# 434 ACCCCAGATTCAAGAAAGAAAGGAACTGGCCACCAAGGAACCAGAAAGAG 483 rnd-4_family- 53 AGGAAGTCAGAGAGGAGGCNTGGCAGTTTGTAACCATCAGAGGNAAGAGG 102 ii ? i i ? CR1-L3A_Croc# 484 AGGAAACCAGAGAGGAGGCTTGGCAGTTCGTAACCACCAGAGGCAAGAGG 533 rnd-4_family- 103 ACGCGGTGGCATTCTACGCGGCTGGAGACAGANGAAGATGGGCAGGCTGT 152 v i i i i CR1-L3A_Croc# 534 ACGAGGCGGCATTCTACACGGCTGGAGGCAGANGAGGATGGGCAGGCTGT 583 rnd-4_family- 153 GGGTACCAGAGAGAAGAGGACCAGGAGGAATTCCACACAGCTAGAAGTTT 202 ivi v CR1-L3A_Croc# 584 GACCACCAGAGAGAAGAGGACCAGGAGGAATTCCACACAGCTAGAAGTAT 633 rnd-4_family- 203 CCAGTCAATACCAGGTCCTCAGCATGGAAACTGTGGAAGATACCTCTCAA 252 i iv i i ii i i v CR1-L3A_Croc# 634 CCAATCGTTACCAGGTTCTCAGCGTGGAAACTGCAGAAAATATCTCTGAA 683 rnd-4_family- 253 GATCCAGCTGGTCNAATGGAACGGAGAGNTGTATGGGACGCGCCTGTGGA 302 ? ? i iii CR1-L3A_Croc# 684 GATCCAGCTGGTCGAATGGAACGGAGAGCTGTACGGGACATACCTGTGGA 733 rnd-4_family- 303 TGGCNGCTCGGCCCAACCCGTAAGAAAATCAAGCGTGCCCACAAAGA--T 350 ? i i vi -- CR1-L3A_Croc# 734 TGGCTGCTCAGCCCAACCCGCAAGACGATCAAGCGTGCCCACAAAGAGAT 783 rnd-4_family- 351 CTNCAACCATCCAAGGAAGACAGACGATCCTTGCCGGGGATTCCGTACTA 400 ? i ii CR1-L3A_Croc# 784 CTCCAACCATCCAAGGAAGACAGACGATCCTTGTCGGGGATTCTATACTA 833 rnd-4_family- 401 AGAAGAATGGAAAGAACATTCTGCAAGGGACAGGCGGACAACAGGACGGT 450 i CR1-L3A_Croc# 834 AGAAGAATGGAAAGAACGTTCTGCAAGGGACAGGCGGACAACAGGACGGT 883 rnd-4_family- 451 GTGCTGCCTTCCCGGAGCCAAGACACGAGACGTCACTCTAAAATTGGACA 500 i i iv i i i CR1-L3A_Croc# 884 GTGCTGTCTTCCCGGAGCCAAGACACGAGATGCGACTCTAAGACTGGATA 933 rnd-4_family- 501 GGCTTCTGAAGTCGATGGGCAAGGATCCACTGGTGATGGTGCATATAGGC 550 ii v CR1-L3A_Croc# 934 GGCTTCTGAAGTCGGCGGGCAAGGATCCACTGGTGATGGTGCATATCGGC 983 rnd-4_family- 551 ACTAATGACACTGC-TCGCAGGATATCTCCNCAGATNGTAGATGACTTCA 599 - i? i - ? ?i i CR1-L3A_Croc# 984 ACTAATGACACTGCTTCGCGNGATACCT-CACAGATTATAGACGACTTCA 1032 rnd-4_family- 600 GGGAACTCGGAAGCGTGCTGAAGAAGAAGAATGTCCAAGCGATCTTCTCG 649 v i i CR1-L3A_Croc# 1033 GGGAACTCGGAAGGGTGCTGAAGGAGAAGAATGTCCAAGTGATCTTCTCG 1082 rnd-4_family- 650 GAGGTCCTTCCTGTCCCGCAAGCGAAGGAAGA-------CAGAAGATTCT 692 i i i ------- CR1-L3A_Croc# 1083 GAGATCCTTCCTGTCCCACGAGCGAAGGAAGACAGAAGGCAGAAGATTCT 1132 rnd-4_family- 693 GGAAGTGAACTGCTGGCTAGGTAAGTGGTGTAGGGT------NTTGGGTT 736 i i ------? v CR1-L3A_Croc# 1133 GGAAGTGAACCGCTGGCTAGGTAAGTGGTGTAAGGTAGAGGGTTTTGGTT 1182 rnd-4_family- 737 TTGTGGAACATTNGTCCACCTTCTATGGGGANAGGGGGCTGTATAGTTTG 786 i ? ? i i CR1-L3A_Croc# 1183 TTGTGGAACACTGGTCCACCTTCTATGGGGAGAAGGGGCTGTACAGTTTG 1232 rnd-4_family- 787 GATGGCCTCCACCCTCAGTAGAAGGGGGACCAATCTTCTCAGGGACAGGC 836 -i i i vi CR1-L3A_Croc# 1233 GATGGCCTCCA-TCTCAGTAGAAGGGGAACCAGTCTTCTAGGGGACAGGC 1281 rnd-4_family- 837 TGGCTAGAGTAGTCAGGAGGGTGTTAAACTAATAACAAAAAGGGAGGGTA 886 v i i i i i i i CR1-L3A_Croc# 1282 TGGCTAGACTAGTCAGGAGGGCGTTAAACTAACAACAAAAGGAGGGAGTG 1331 rnd-4_family- 887 AAAAGAGGGAAGATATGAGCACTC----AGCACAAAATCGAGATGTTGAG 932 iii i v v ---- i i CR1-L3A_Croc# 1332 AAAGAGGGAAACAAATGAGCACTCATTTAGCACAAAATCAAGATGTCGAG 1381 rnd-4_family- 933 AACAAAATTAATCAAGGAACCAAAGGACACGAAGAGAAGAA 973 v i ii CR1-L3A_Croc# 1382 AACAAAATTAATCAAGGCACCAAGGGACGTGAAGAGAAGAA 1422 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.97 CpG sites = 79, Kimura (unadjusted) = 10.78 Transitions / transversions = 5.27 (79/15) Gap_init rate = 0.01 (7 / 970), avg. gap size = 3.14 (22 / 7) 1309 10.17 5.19 2.10 rnd-4_family-1868#DNA 1 231 (25) C Eulor9A#DNA (7) 294 57 m_b11s502i5 rnd-4_family- 1 AAATTAAATGCAAAAANAC-TACGTTAATGCAACGTTATGGTTGAGATTT 49 i v ?? - i C Eulor9A#DNA 294 AAGTAAAATGCAAAAAANCCTACGTTAATGCAACGTTACGGTTGAGATTT 245 rnd-4_family- 50 TAAACGCACAAAAGTCAGGAAATTCAAAGTTATGGTTCCCACAGCAACCG 99 i C Eulor9A#DNA 244 TAAACGCACAAAAGTCAGGAAATTCAAAGTTACGGTTCCCACAGCAACCG 195 rnd-4_family- 100 TAACTCGGCCACATTGCACNTGCATATATATTAAGGCATTAAA--TGACA 147 ? i - i- - -- i C Eulor9A#DNA 194 TAACTCGGCCACATTGCACATAC-TG-ATATTAAGGCA-TAAATTTAACA 148 rnd-4_family- 148 GCATTCACAGTANTACAAAATACTAAATTATGCGCAAGGGGGATGACTT- 196 ? vi ? --?i vi v - C Eulor9A#DNA 147 NCATATACAGTAATACAAAATACT--NCTATGCGCAAGGGGGCCGAGTTA 100 rnd-4_family- 197 ------CTGTGGG-ATTATAATTCTCAA-CTCNTAGCTCTTGT 231 ------ - iii i i v -i ? ii i C Eulor9A#DNA 99 CGGTTGCTGTGGGAACCGTAACTTTGAATTTCCTGACTTTTGT 57 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.50 CpG sites = 18, Kimura (unadjusted) = 11.53 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.05 (11 / 230), avg. gap size = 1.55 (17 / 11) 252 20.00 0.00 0.00 rnd-4_family-1880#LTR/ERV1 2089 2148 (1380) PRIMA41-int#LTR/ERV1 2540 2599 (5157) m_b11s701i0 rnd-4_family- 2089 CCTGGGTCGAAACCAGTGCGCTNTCTGTAGGGAAGAGGGGCACTGGAAGA 2138 i ivv i i ??? i i ?? v PRIMA41-int#L 2540 CTTGGGCATAAATCAGTGTGCNCNCTGTAAGAAAGNNGGCCACTGGAAGA 2589 rnd-4_family- 2139 ATGAATGCCC 2148 iv v PRIMA41-int#L 2590 GGGACTGCCC 2599 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.21 CpG sites = 7, Kimura (unadjusted) = 26.21 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 622 32.66 3.06 2.78 rnd-4_family-1880#LTR/ERV1 2844 3202 (326) HERVIP10F#LTR/ERV1 2739 3098 (4639) m_b11s701i1 rnd-4_family- 2844 AGAATCGGGTTAAAACCTCTGATTCAAAAGTTTCTGCAGTGTGGGTGGCT 2893 i v i v i v iivi v vv ivi ivv HERVIP10F#LTR 2739 AGGATAGGGTTGAAACCTATAATTGAAGGTCTTATTAAAGATGGGCTTCT 2788 rnd-4_family- 2894 CAGGGAAGGCACGTCCCCGTACAATACTCCGATAATGGGGGTGCCTAAGC 2943 ii vvvv i i v i i i i v vvi vvvv ii HERVIP10F#LTR 2789 CGAGCCCTGTATGTCCCCTTATAACACCCCAATACTGCCAGTCAAGAAAT 2838 rnd-4_family- 2944 CTAATGGGCAGTATCGGTTGGTCCAGGACCTGAGACAGATTAACAAGTTA 2993 vi i ivi i i v v vvv i v iv HERVIP10F#LTR 2839 CAGACGGGTCATACCGGCTGGTACAGGACCTTAGAGCTATCAACCAAATA 2888 rnd-4_family- 2994 ATAGAGGCCCCCTATCCAGTCGTCCCGAATCCCCATACTATTCTGGGCCA 3043 i vv i iv i i v i v ii i i vi v HERVIP10F#LTR 2889 GTCCAGACTACCCACCCCGTTGTCCCCAATCCTTACACCATTCTCAGCAA 2938 rnd-4_family- 3044 AGTTCCCAAAAATCACAGTTGGTTCTCTGTCATAGATTTAAAAGATGCCT 3093 ii vv v iviv iv v i i i HERVIP10F#LTR 2939 GATTCCATATAATCATCAATGGTTTACTGTAATAGATTTGAAGGATGCTT 2988 rnd-4_family- 3094 TCTTTTCCATCCCCCTTGATCTGGAG-TCTCAGAGAC-TGTTTGCCTTCG 3141 - vvv vi i i- i - vv v i- i i i HERVIP10F#LTR 2989 T-TTGGGCATGTCCCCTGG-CTGAAGATAGCCGAGATATATTTGCTTTTG 3036 rnd-4_family- 3142 AGTGGGAGGACCCAGATACCCACTACAAGGC-----C--CAATACCTTTG 3184 i ------ - i ----- -- i vv HERVIP10F#LTR 3037 AGTGGGAGGATC------CCCACT-CAGGGCGGAAACAACAATATCGATG 3079 rnd-4_family- 3185 GACCG--TTGTCCCACAGGG 3202 v -- i - HERVIP10F#LTR 3080 GACAGTCTTGCCCCA-AGGG 3098 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.68 CpG sites = 59, Kimura (unadjusted) = 43.69 Transitions / transversions = 1.07 (59/55) Gap_init rate = 0.04 (15 / 358), avg. gap size = 1.40 (21 / 15) 450 32.96 3.68 6.96 rnd-4_family-1880#LTR/ERV1 2909 3397 (131) MER52-int#LTR/ERV1 3586 4059 (3032) m_b11s701i2 rnd-4_family- 2909 CCCGTACAATACTCCGATAATGGGGGTGCCTAAGCCTAATGGGCAGTATC 2958 v ii i v i vv i i i v i ivv MER52-int#LTR 3586 CCCTTGTAATACCCCGATATTGGGGGTACAAAAACCCAACGGGGAATGGA 3635 rnd-4_family- 2959 GGTTGGTCCAGGACCTGAGACAGATTAACAAGTTAATAGAGGCCCC---C 3005 ii vv v vvi ii vivi --- ii ---i MER52-int#LTR 3636 GACTGGTCCAGGACCTCCGCCTCGTTAATGAGGCTGT---GGTTCCAATT 3682 rnd-4_family- 3006 TATCCAGTCGTCCCGAATCCCCATACTATTCTGGGCCAAGTTCCCAA--A 3053 i i i v i v ?i iv v i vi i v ii --i MER52-int#LTR 3683 CACCCGGTGGTTCCCAATCCNTATACCCTGCTAGCTCAAATACCTGAGGG 3732 rnd-4_family- 3054 AATCACAGTTGGTTCTCTGTCATAGATTTAAAAGATGCCTTCTTTTCCAT 3103 ii v -- v v v i ii i i i v MER52-int#LTR 3733 AACTAAA--TGGTTCACAGTCCTGGACCTAAAGGATGCCTTTTTCTGCAT 3780 rnd-4_family- 3104 CCCCCTTGATCTGGAGTCTCAGAGACTGTTTGCCTTCGAGTGGGAGGACC 3153 v vi vv i iv v i vivi v ------ i MER52-int#LTR 3781 ACCGTTACACCCCGACTCCCAGTATTTGTTTGCATTC------GAGGATC 3824 rnd-4_family- 3154 CAGATACCCACTACAAGGCCCAAT--ACCTTTGGACCGTTGTCCCACAGG 3201 ---iv v i v vvi ii-- -- v vv v v MER52-int#LTR 3825 C---CTCCAACCAGACCACCCAGCTAACC--TGGACGGTGTTACCTCAGG 3869 rnd-4_family- 3202 GACTTACCTGTGCA--CCCGAGAT-TTTTGGCAGCCA--GTTAAGAAGGG 3246 i -- vivi -- v vv - v v -- i i --- MER52-int#LTR 3870 GATT--CCGAGACAGCCCCCACCTGTTTGGGCAGGCATTGTCAAAA---G 3914 rnd-4_family- 3247 ACCTCGCCCCATTCCTGGCTAGACACCCCTCATG-TAACATAGTCCAGTA 3295 v ivvi --i -----i v - vi vv v i MER52-int#LTR 3915 ACCTCTCTGAGTTCCT--TTA-----TCCTCAGGTTAAAGTTTTACAATA 3957 rnd-4_family- 3296 TTGCGATGATTTGCTCTTAAGTACTGAAACAGAGGCAGCCTGTAAAGAGC 3345 ivvv iv v i vv i ivv v v ii v v i - MER52-int#LTR 3958 CGTAGATGACATTCTCCTCTGTGCCCCAACTGAGGAAATCTCTCAGGAG- 4006 rnd-4_family- 3346 AAACTGTAGAGCTC--CTTAATTACCTTGGGGC--ACAG-GGGTATAAGG 3390 -ii v ii -- vi --- -- - i MER52-int#LTR 4007 -GGCAGTAAGGCTCTTCTTAATTTTCT---GGCTAACAGAGGATATAAGG 4052 rnd-4_family- 3391 TCTCAAA 3397 MER52-int#LTR 4053 TCTCAAA 4059 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.62 CpG sites = 76, Kimura (unadjusted) = 44.17 Transitions / transversions = 1.03 (76/74) Gap_init rate = 0.09 (43 / 488), avg. gap size = 1.19 (51 / 43) 12 21.20 0.00 5.00 rnd-4_family-2027#SINE/MIR 175 216 (1497) (AGTGGG)n#Simple_repeat 1 40 (0) m_b11s252i6 rnd-4_family- 175 AGTAGGGGCGGGAGTCCCAGCTGGGGGTGGGTAGTGGGAGTG 216 i i i vvv - i - (AGTGGG)n#Sim 1 AGTGGGAGTGGGAGTGGGAG-TGGGAGTGGG-AGTGGGAGTG 40 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 958 7.53 17.20 0.00 rnd-4_family-2027#SINE/MIR 675 860 (853) MIR1_Amn#SINE/MIR 11 228 (2) m_b11s601i1 rnd-4_family- 675 GTGTGGCCTAGTGGAGAGACCGCCGGACTGGGACT--------------- 709 i v v i i --------------- MIR1_Amn#SINE 11 GTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTT 60 rnd-4_family- 710 --ATTCCTGGCTCTGCCACCGGCCTGCTTGGTGNCCT-GGNCAAGTCACT 756 -- ? i i? ? v? ? - ? MIR1_Amn#SINE 61 CNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACT 110 rnd-4_family- 757 TCGCCTCTCTGTGCCTCAGTTTCC-CATNTGTAAAANGGGGATAATGATA 805 ?i ? - ? ? MIR1_Amn#SINE 111 TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 rnd-4_family- 806 -------------TAAAGTNCTTTGAGATCTACTGATGAAAAGTACTATA 842 ------------- ? i i MIR1_Amn#SINE 161 CTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATGAAAAGTGCTACA 210 rnd-4_family- 843 TAAAAGCTAGGTCTTTTT 860 i v v MIR1_Amn#SINE 211 TAAGAGCTAGGTATTATT 228 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 7.93 CpG sites = 9, Kimura (unadjusted) = 8.52 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.03 (5 / 185), avg. gap size = 6.40 (32 / 5) 235 23.59 1.39 5.80 rnd-4_family-2027#SINE/MIR 1110 1181 (532) C Eulor9B#DNA (6) 234 166 m_b11s502i6 rnd-4_family- 1110 AAACTCAAACTTCTGAAAACCAGGAAATACAGAGTTAAGGTAAACGCCCA 1159 i vivii ii v i v ----v C Eulor9B#DNA 234 AAATTCAAACGCACAAAAGTCAGGAAATTCAAAGTTATGGT----TCCCA 189 rnd-4_family- 1160 C-GCAACCTTAACTCTGCCCTCT 1181 i- v i i C Eulor9B#DNA 188 TAGCAACCGTAACTCCGCCCCCT 166 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.85 CpG sites = 10, Kimura (unadjusted) = 28.95 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 21 3.85 0.00 0.00 rnd-4_family-2049#LTR/ERV1 380 407 (3271) (GT)n#Simple_repeat 1 28 (0) m_b11s252i4 rnd-4_family- 380 GTGTGTGTGTGTGTNTGTGTGCGTGTGT 407 ? i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 14 14.94 5.41 0.00 rnd-4_family-2049#LTR/ERV1 3430 3466 (212) (TTGTC)n#Simple_repeat 1 39 (0) m_b11s252i5 rnd-4_family- 3430 TTGTGTTCT-TTGTCCTGTCTTGTGGTGT-TTGTCTTGT 3466 v v - i vv - (TTGTC)n#Simp 1 TTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGT 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 305 20.59 8.08 1.90 rnd-4_family-225#LINE/L2 18 116 (32) L2c_3end#LINE/L2 347 451 (27) m_b11s601i2 rnd-4_family- 18 TCTGCCTCCTTGTCTGTCTGTCTT---TAGATTGTAAGCTCTTCG-GGGC 63 ii v ? -i i--- i i i i - L2c_3end#LINE 347 TCTGTTTACNTGTCTGTCT-CCTCCACTAGACTGTGAGCTCCTTGAGGGC 395 rnd-4_family- 64 AGGGACCGTGCCTTCTTGAATGTTTGCA----AAGCACCTAGCACATTNT 109 i v -v v i ----v i i v? L2c_3end#LINE 396 AGGGACCGTGTCTTATT-CATCTTTGTATCCCCAGCGCCTGGCACATAGT 444 rnd-4_family- 110 GGGTGCT 116 i i L2c_3end#LINE 445 AGGCGCT 451 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.66 CpG sites = 14, Kimura (unadjusted) = 25.53 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.05 (5 / 98), avg. gap size = 2.00 (10 / 5) 242 19.60 3.85 1.89 rnd-4_family-2257#LINE/CR1 6 57 (1) CR1-3_Croc#LINE/CR1 3541 3593 (12) m_b11s551i1 rnd-4_family- 6 GGCAGGGGGATGGACTAGATGA--TCTAATAGGTCTTTTCCATCTCTAAC 53 v -- ii- ii v i vi CR1-3_Croc#LI 3541 GGCAGGGGGTTGGACTAGATGACCTCTGG-AGGTCCCTTCCAGCCCTACT 3589 rnd-4_family- 54 TTTC 57 i CR1-3_Croc#LI 3590 TCTC 3593 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.40 CpG sites = 7, Kimura (unadjusted) = 23.40 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.50 (3 / 2) 15 7.83 0.00 3.45 rnd-4_family-23#Unknown 72 101 (129) (TAT)n#Simple_repeat 1 29 (0) m_b11s252i3 rnd-4_family- 72 TATTATTATTATTATTANTAATTAATANTA 101 - v v ? (TAT)n#Simple 1 TATTATTATTATTATTA-TTATTATTATTA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 14 6.30 8.57 2.70 rnd-4_family-247#Unknown 1526 1560 (1295) (TTGTTT)n#Simple_repeat 1 37 (0) m_b11s252i2 rnd-4_family- 1526 TTG-TTTTCTTTTTGTTTCTTG-TTTTG-TTCTGTTTT 1560 - v - - - i (TTGTTT)n#Sim 1 TTGTTTTTGTTTTTGTTT-TTGTTTTTGTTTTTGTTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 250 27.94 0.00 0.00 rnd-4_family-3413#DNA/TcMar-Tigger 217 284 (153) Tigger13a#DNA/TcMar-Tigger 704 771 (0) m_b11s502i7 rnd-4_family- 217 TTATCCGAATTTTTGATTATCCGATCTGGCCCCGGTCCCAATTAGATCGG 266 v v ? v i i viviv i iivi Tigger13a#DNA 704 TTAACCGACTTTTTNATTAACCAACCAACTACCGGTCCCGATCGCGTCGG 753 rnd-4_family- 267 ATAAACGGGGTTCCACTG 284 iv v i Tigger13a#DNA 754 ATAAGAGGGCTTCTACTG 771 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.30 CpG sites = 10, Kimura (unadjusted) = 36.18 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 271 19.14 17.82 1.71 rnd-4_family-478#DNA/hAT-Ac 171 271 (88) C UCON26#DNA/hAT-Ac (99) 299 183 m_b11s502i8 rnd-4_family- 171 CAAGAT--GGC-GGAAATCTCGCGAGANCAGCTGATCTCGTGAGATTTCC 217 i -- - ? vivv i C UCON26#DNA/hA 299 CAAAATTGGGCTGGAAATCTCGCGAGAACAGGCTTTCTCGCGAGATTTCC 250 rnd-4_family- 218 GCCA--------TTCAGAT-GGGCC-GAAATCTCACGAGAGAACAG---- 253 vi -------- v i - - vi i -- ---- C UCON26#DNA/hA 249 GGTACTTCCTGCTTCCGGTCGGGCCGGAAATACCGC--GAGAACAGCCTT 202 rnd-4_family- 254 -CTCACGAGATTCTGGCGC 271 - i iv ii i C UCON26#DNA/hA 201 TCTCGCGGTATTTCGGCAC 183 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.76 CpG sites = 12, Kimura (unadjusted) = 22.87 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.09 (9 / 100), avg. gap size = 2.22 (20 / 9) 46 27.77 2.97 2.97 rnd-4_family-64#Unknown 267 468 (7) (GGAGGG)n#Simple_repeat 1 202 (0) m_b11s252i1 rnd-4_family- 267 GGTGGGGCTGGGTAAGGGGG-GGGCGGGGGAAATGGGGGGGGGGTGGGGG 315 v vv vi - v i ii v i v (GGAGGG)n#Sim 1 GGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGG 50 rnd-4_family- 316 CGGGGGAAGAGGCAGTGGGGA-AGGAAGGGGGTGGGATA-GGGCA-GGGG 362 v - i v - -i i v iv - v - (GGAGGG)n#Sim 51 AGGGGG-AGGGGGAG-GGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGG 98 rnd-4_family- 363 AGGGGAATGTGG-GAGTGA-GGGGAGGGGGATGGGGATGAGGCAGTGGGG 410 i v v - i v - - -- vi v (GGAGGG)n#Sim 99 AGGGGGAGGGGGAGGGGGAGGGGGAGGGGGA-GGGG--GAGGGGGAGGGG 145 rnd-4_family- 411 GAAGGGGANGATGATGGGGAAGAGAAGGGGATAGGGGAATCGCGGGGGGA 460 i ? iv v i i i -v i vv v i i (GGAGGG)n#Sim 146 GAGGGGGAGGGGGAGGGGGAGGGGGAGGGG-GAGGGGGAGGGGGAGGGGG 194 rnd-4_family- 461 AGCGGGAG 468 v (GGAGGG)n#Sim 195 AGGGGGAG 202 Matrix = Unknown Transitions / transversions = 0.83 (20/24) Gap_init rate = 0.06 (12 / 201), avg. gap size = 1.00 (12 / 12) 181 24.71 5.49 2.13 rnd-4_family-70#SINE/tRNA 2464 2554 (2163) MIR1_Amn#SINE/MIR 41 134 (96) m_b11s601i3 rnd-4_family- 2464 GGGTCCAGGGAAC--AGGCGCTATTCCTG-CCCTGCCACTGTCTGTCTGA 2510 iii i ii --i iv ? ? i - i ?v i?v ? MIR1_Amn#SINE 41 GGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGN 90 rnd-4_family- 2511 GAAACCTTGGCCTTGTCATTC--CCTGGCTCGGTGCCTCAGTTTCC 2554 vi v vv i i-- -- v ? MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCT--CTCTGNGCCTCAGTTTCC 134 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.10 CpG sites = 14, Kimura (unadjusted) = 33.79 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.40 (7 / 5) 185 26.90 13.33 0.85 rnd-4_family-70#SINE/tRNA 4519 4623 (94) LFSINE_Vert#SINE/tRNA 159 276 (183) m_b11s601i4 rnd-4_family- 4519 CCAATTCCTAGTGGTCTGGTGTCTGTGTCACCCGAGCCACCACC-CAG-- 4565 i v v iiii - vi i i - i-- LFSINE_Vert#S 159 CCAGTTCCTAGTGGACAGGTGTCCACATCA-CAAAACCACCATCACAATT 207 rnd-4_family- 4566 ------AGTTGCTCCCGTCACTGGCAGCCT-----GGGAGGCCAAGGACT 4604 ------ i viv v iii i ----- i LFSINE_Vert#S 208 GGCACTAATTGGCACCCTTGTTGGCAGTCTCAGCAGAGAGGCCAAGGACT 257 rnd-4_family- 4605 GACGGGTGATGGCGTCTGA 4623 vv vv v v LFSINE_Vert#S 258 GAATGGGCATGGAGACTGA 276 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.06 CpG sites = 16, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.05 (5 / 104), avg. gap size = 3.00 (15 / 5) 251 21.11 12.22 0.00 rnd-4_family-70#SINE/tRNA 4624 4713 (4) LFSINE_Vert#SINE/tRNA 307 407 (52) m_b11s601i5 rnd-4_family- 4624 CCAGG-CAGGGCTGAGGCACATGGGCGGGG---------GACGCTTGTCC 4663 - i v --------- v iv LFSINE_Vert#S 307 CCAGGTCAGGGTTGAGGCACATTGGCGGGGCAGTGTGGGGAAGCTTGCAC 356 rnd-4_family- 4664 TGCTGCTGGCAAGGCTGGACCCGTTCTGGAGA-GAACAGGAGGATTCAGT 4712 i v viv v i vi -i ii iv LFSINE_Vert#S 357 TGCCGCTGCCCGTGCTGTACCTGTTCTGTGGATAAACAGAGGACTTCAGT 406 rnd-4_family- 4713 C 4713 LFSINE_Vert#S 407 C 407 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.16 CpG sites = 10, Kimura (unadjusted) = 25.03 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.03 (3 / 89), avg. gap size = 3.67 (11 / 3) 12 10.43 3.77 12.24 rnd-4_family-900#LTR/DIRS 63 115 (1172) (TAGT)n#Simple_repeat 1 49 (0) m_b11s252i0 rnd-4_family- 63 TAGTATAGTTAG-TAG-TAGTTTAGTTAGTCTTCGTTAGTNTTAGCTAAT 110 - - - - -- v -- i i (TAGT)n#Simpl 1 TAGT-TAGTTAGTTAGTTAG-TTAGTTAG--TTAGTTAG--TTAGTTAGT 44 rnd-4_family- 111 TAATT 115 i (TAGT)n#Simpl 45 TAGTT 49 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.15 (8 / 52), avg. gap size = 1.00 (8 / 8) 356 12.73 3.64 0.00 rnd-4_family-1042#SINE/5S-Deu-L2 50 104 (0) AmnSINE1#SINE/5S-Deu-L2 508 564 (11) m_b12s502i0 rnd-4_family- 50 GTTTGTAAAGCGCTTTGAGATCCTC--GGATGGAAGGCGCTACAGAAATG 97 i i i-- i i v AmnSINE1#SINE 508 GCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATG 557 rnd-4_family- 98 CAAAGTA 104 i AmnSINE1#SINE 558 CAAGGTA 564 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.41 CpG sites = 6, Kimura (unadjusted) = 14.41 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.02 (1 / 54), avg. gap size = 2.00 (2 / 1) 19 8.35 0.00 0.00 rnd-4_family-1070#Unknown 87 112 (378) (G)n#Simple_repeat 1 26 (0) m_b12s252i13 rnd-4_family- 87 GGGGGGGGGGGGGGGGGGGGAAGGGG 112 ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 62 30.13 6.41 3.20 rnd-4_family-1225#Unknown 30 575 (17) (ATCC)n#Simple_repeat 1 563 (0) m_b12s252i12 rnd-4_family- 30 ATCGATCTATCTGTCC--CCATACA-CC-CCCTTCTATCTATCCATCC-- 73 v i ii -- v - -i v i i -- (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 50 rnd-4_family- 74 CCATACACACCCATCTATCTANTCATCTATCTATCTATCC--CCATACA- 120 - - i i i ?i i i i -- v - (ATCC)n#Simpl 51 CCAT-C-CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 98 rnd-4_family- 121 CC-CCCATCTATCTAATCTATCTATCTCCCCATACNCCCATCTATCTATC 169 -i i -v i i ivi v ?i i i (ATCC)n#Simpl 99 CCATCCATCCATC-CATCCATCCATCCATCCATCCATCCATCCATCCATC 147 rnd-4_family- 170 TNTCTAT-CACCCACACACCCNT-CATCTANCTATCCAGCTA-CCATCCC 216 i? i - i iv i ? - i ? i v i - v (ATCC)n#Simpl 148 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 197 rnd-4_family- 217 CACAACC--CCCTCTATCTATCCCCCCANCCCTACACACCCATCTACCTA 264 iv v -- v i i vi ? v - - i i i i (ATCC)n#Simpl 198 TCCATCCATCCATCCATCCATCCATCCATCCAT-C-CATCCATCCATCCA 245 rnd-4_family- 265 ACTATCTATCTATCTCCCCCATAC-GCCCCCCATTNGTCTATCTATCC-- 311 v i i i - vi v -v vi i?i i i -- (ATCC)n#Simpl 246 TCCATCCATCCATC-CATCCATCCATCCATCCATCCATCCATCCATCCAT 294 rnd-4_family- 312 CCAT-CATCTATCTATCC--CCATACACCCCCGCTATCTATCTATCCATC 358 - i i -- v -i vv i i i (ATCC)n#Simpl 295 CCATCCATCCATCCATCCATCCATCCA-TCCATCCATCCATCCATCCATC 343 rnd-4_family- 359 C--CCGTACACCCCCTNTGGTCTATCTATCTATCTATCC--CCATACACC 404 -- i v -i v -ivi i i i i -- v -i (ATCC)n#Simpl 344 CATCCATCCA-TCCAT-CCATCCATCCATCCATCCATCCATCCATCCA-T 390 rnd-4_family- 405 CCATCTATCTAATCTATCTATCC--CCATACACCCCATCTATCTATCTAT 452 i -v i i -- v -i i i i (ATCC)n#Simpl 391 CCATCCATC-CATCCATCCATCCATCCATCCA-TCCATCCATCCATCCAT 438 rnd-4_family- 453 CC--CCATACACCCCCCCCCGCTATCTATCC--CCATACACCCCATCTAT 498 -- v -i vi vv i i -- v -i i (ATCC)n#Simpl 439 CCATCCATCCA-TCCATCCATCCATCCATCCATCCATCCA-TCCATCCAT 486 rnd-4_family- 499 CCAATCTATCTATCCATCTATCC--CCATACACCCCATCTATCTACTCCC 546 - i i i -- v -i i i - v (ATCC)n#Simpl 487 CC-ATCCATCCATCCATCCATCCATCCATCCA-TCCATCCATCCA-TCCA 533 rnd-4_family- 547 CCCACNCACACCATCTATCCA-CC-TCGATC 575 i i? -v i - - v (ATCC)n#Simpl 534 TCCATCCA-TCCATCCATCCATCCATCCATC 563 Matrix = Unknown Transitions / transversions = 2.21 (84/38) Gap_init rate = 0.08 (41 / 545), avg. gap size = 1.29 (53 / 41) 835 0.00 0.00 0.00 rnd-4_family-1486#LINE/CR1 1 94 (0) CR1-L3B_Croc#LINE/CR1 1228 1321 (1956) m_b12s551i0 rnd-4_family- 1 ACAATCAAGAAAGAGGACAACTTTGGCTAAAAGCCCATCCTGGTTCAGTG 50 CR1-L3B_Croc# 1228 ACAATCAAGAAAGAGGACAACTTTGGCTAAAAGCCCATCCTGGTTCAGTG 1277 rnd-4_family- 51 GCGAAGTGAAGGCAGCAATTAGAAATAAAAAAGCAATATATAAC 94 CR1-L3B_Croc# 1278 GCGAAGTGAAGGCAGCAATTAGAAATAAAAAAGCAATATATAAC 1321 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.00 CpG sites = 0, Kimura (unadjusted) = 0.00 Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0) 1106 8.50 0.58 4.82 rnd-4_family-1532#DNA/hAT 1 173 (43) UCON89#DNA/hAT 11 176 (66) m_b12s502i1 rnd-4_family- 1 TTTATAGGGTGAAGAAGCCAGGGAAATTCCCCCACCCTCTAAACTATCTG 50 i v -- i --- i i UCON89#DNA/hA 11 TTTGTAGGGGG--GAAGCCAAGGAAATTCCCCC---CCCTAAACTATCCG 55 rnd-4_family- 51 TTCCCTGGCTCTAAACGTTCAATAACTTCCCAGCCAGGGAATGCATTTTT 100 i UCON89#DNA/hA 56 TTCCCTGGCTCTAAACGTTCAATAACTTCCCAGCCAGGGAATGTATTTTT 105 rnd-4_family- 101 CCCCTCCCTTTCTCT-CATTTNTCTGTGGTTTGCATTATCATTTGCTAAA 149 --- ? -i ? i UCON89#DNA/hA 106 CCCCTCC---TCTNTATATTTTTCTGTGGTTTGCATTATCGTTTGCTAAA 152 rnd-4_family- 150 TATAGTAAAGCATGCTAATTACCT 173 v vii i v UCON89#DNA/hA 153 TATATTACGACACGCTATTTACCT 176 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.70 CpG sites = 10, Kimura (unadjusted) = 9.22 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.05 (9 / 172), avg. gap size = 1.00 (9 / 9) 34 3.01 0.00 0.00 rnd-4_family-1556#LTR/Gypsy 1293 1326 (1665) (AG)n#Simple_repeat 1 34 (0) c_b12s251i0 rnd-4_family- 1293 AGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGAG 1326 v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 34 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 313 17.71 9.38 0.00 rnd-4_family-1705#SINE/5S-Deu-L2 238 333 (191) AmnSINE1#SINE/5S-Deu-L2 105 209 (366) m_b12s502i2 rnd-4_family- 238 GTGCTGCAGGGAGCGGGGTGGGGG--TCAGTAGGGGGCGCTCTCCCCTGT 285 i i v iv v -- v i i v AmnSINE1#SINE 105 GTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCT 154 rnd-4_family- 286 CAGTCAGTGCTG-------GTCCCAGCGTGGCGCTAGGGGGCGCTGTGCT 328 v i ------- i i i i AmnSINE1#SINE 155 GAGTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGCT 204 rnd-4_family- 329 GCAGG 333 v AmnSINE1#SINE 205 GCTGG 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.45 CpG sites = 10, Kimura (unadjusted) = 20.45 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (2 / 95), avg. gap size = 4.50 (9 / 2) 361 20.18 0.91 0.91 rnd-4_family-1705#SINE/5S-Deu-L2 324 433 (91) AmnSINE1#SINE/5S-Deu-L2 105 214 (361) m_b12s502i3 rnd-4_family- 324 GTGCTGCAGGGAGCGGGG-TGGGGGCTCAGTAGGGGGCGCTCTCCCCTGG 372 i i v - v ii v i i vv AmnSINE1#SINE 105 GTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCT 154 rnd-4_family- 373 CAGTCAGTGCTGGCCCCAGTGCCCCAGCGTGGCACTAGGGGGCGCTGTGC 422 v i iv - iii i AmnSINE1#SINE 155 GAGTCAGTACTGAACC-AGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGC 203 rnd-4_family- 423 TGCAGGNAGCG 433 v ?i i AmnSINE1#SINE 204 TGCTGGAGGTG 214 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.28 CpG sites = 14, Kimura (unadjusted) = 24.28 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2) 190 17.35 11.11 3.90 rnd-4_family-1725#Unknown 296 367 (38) L2d_3end#LINE/L2 360 436 (80) m_b12s601i0 rnd-4_family- 296 TTGTTTCATCCACCTGTTACGTCTTGTCTTT-----TAGACCGCGAGCTC 340 vii-- - ii----- ii ii L2d_3end#LINE 360 TTGTTTCATGTG--TGTTA-GTCTTGTCTCCCCAACTAGATTGTAAGCTC 406 rnd-4_family- 341 TTTG-GGGCAGGGAC--TGTCATTTACTAT 367 i - -- v v ? L2d_3end#LINE 407 CTTGAGGGCAGGGACCATGTCTTATACTNT 436 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.78 CpG sites = 9, Kimura (unadjusted) = 20.78 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.83 (11 / 6) 682 8.43 0.00 2.11 rnd-4_family-1890#LINE/CR1 1 97 (0) CR1-11_Crp#LINE/CR1 1362 1456 (5) m_b12s551i1 rnd-4_family- 1 GATAAATTTACGAATGGGATTATATGACGGGGTTGCCTGCGATAGCAGGG 50 v i i v v CR1-11_Crp#LI 1362 GATCAGTTTATGAAAGGGATTATATGACGTGGTTGCCTGCGATAGCAGGG 1411 rnd-4_family- 51 GACTGGACTCGATGACCCAGGAGGTCCCTTCCAGTCCTATGTCCCTA 97 i-- ?i i CR1-11_Crp#LI 1412 GACTGA--TNAATGACCCAGGAGGTCCCTTCCAGTCCTATGTTCCTA 1456 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.09 CpG sites = 5, Kimura (unadjusted) = 9.09 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2) 636 26.23 10.25 0.00 rnd-4_family-1943#LINE/L2 164 407 (0) X24_LINE#LINE/L2 1 269 (45) m_b12s601i1 rnd-4_family- 164 GCGCTCTACNTGGGGCTACACCTTAAATCCATTCGGAAGCT--------- 204 i ?? ?v i v i v iv ii --------- X24_LINE#LINE 1 GTGCTCNNCTGGGGGCTGCCCTTGAAGACCACCCGGAAGCTTCAGCTGGT 50 rnd-4_family- 205 -------GAAGCCGCTTGT----TAAGCGGTGCATCTCGCTGTGAGCACA 243 ------- v v i ---- i i? i?vvi i v?v X24_LINE#LINE 51 GCAGAATGCAGCGGCTCGTCTGCTGAANGGTGTNAGCCACANGGAGCACA 100 rnd-4_family- 244 TGACACCGGTGCTCCGGGATCTGCACTGGCTGCCTGTTGGTTTCCGGGTG 293 v v vii i ?i v i i X24_LINE#LINE 101 TTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCTTCCGAGTG 150 rnd-4_family- 294 GAGTTTAAGGT-TTGNTNTTGACCTACAAAGCCCTAAATGGCCTGGGCTC 342 v i i - ?i? i i i v ii i X24_LINE#LINE 151 CAATTCAAGGTGTTGACTTTAATCTATAAAGCCCTATATGGTTTGGGCCC 200 rnd-4_family- 343 ---CTACCTGAGAGGCCGCCTCTCCCCCTGTGCA-TACTGCTGCAANCTG 388 ---i v ii i ? -iiiii v ?ivi X24_LINE#LINE 201 TGGTTACCTTAGAGATCGCCTCTCTCCCTNTGCACCGTCACGGCAATTGA 250 rnd-4_family- 389 CATCAGCGGAGGTGTTCTT 407 v vii i i i X24_LINE#LINE 251 GATCAGCTAGGATGCTCCT 269 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.22 CpG sites = 43, Kimura (unadjusted) = 35.71 Transitions / transversions = 2.05 (43/21) Gap_init rate = 0.02 (6 / 243), avg. gap size = 4.17 (25 / 6) 15 26.91 2.04 2.04 rnd-4_family-2053#Unknown 633 730 (367) (CGGGGAC)n#Simple_repeat 1 98 (0) m_b12s252i11 rnd-4_family- 633 CGGNGACCTGGGTCTTCTGACCGGAGACCNGGG-CTGCGGCGCCGGGGTC 681 ? v v ivvv i ? - i - vi v (CGGGGAC)n#Si 1 CGGGGACCGGGGACCGGGGACCGGGGACCGGGGACCG-GGGACCGGGGAC 49 rnd-4_family- 682 CTAGGCCGCGGNGA-CGGGGANCGACGCCTNCGGTCCGGGGACCGGNGAC 730 vi v - ? - ? iv v i?v v ? (CGGGGAC)n#Si 50 CGGGGAC-CGGGGACCGGGGACCGGGGACCGGGGACCGGGGACCGGGGAC 98 Matrix = Unknown Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.00 (4 / 4) 314 29.25 5.39 1.73 rnd-4_family-2231#DNA 15 181 (236) MER131#DNA 30 202 (13) m_b12s601i2 rnd-4_family- 15 AGTTAAGGTTGCAACCAGC--TTCCATTATAAAGCCCTATTTT--AGCCT 60 ? - vii -- v --i vv MER131#DNA 30 AGTTAAGGNT-CTGTCAGCGTTTCCATTATAAACCCCTATTTTCAGGGGT 78 rnd-4_family- 61 TTATGCTTTGGCCCCTANAACTTTGGTTTGGACCTGAAAATTGCCAGATT 110 ivi i - v ? v i v ii i- v v v iv MER131#DNA 79 TTATAACTCGG-CCGTAAAAATTCGCTCCGGG-CTGAAACTTGGCATACA 126 rnd-4_family- 111 A-CTCTGAAGGCAAAGGAGAA-TATTTCTGCAAAGTTTG---AAGAAAAT 155 -v v ivv iiii v - v i i i --- i MER131#DNA 127 AGGTCTCAGCCCGGGAGCGAATTTTTTTTACAAAATTTGAAAAAAAAAAT 176 rnd-4_family- 156 TNATCAAACTGTNTTTCAGTTACGGG 181 i?i ivii i ? v ii MER131#DNA 177 CAGTTCGGCCGTTTTTAAGTTATAGG 202 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 28, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.05 (8 / 166), avg. gap size = 1.50 (12 / 8) 407 19.82 0.00 0.94 rnd-4_family-24#SINE/5S-Deu-L2 106 212 (211) AmnSINE1#SINE/5S-Deu-L2 104 209 (366) m_b12s502i4 rnd-4_family- 106 GGTGCTGCAGGGAGCAGGGTGGGAGGCTCAGCAGGGGGCGCTCTCCCCTC 155 i ii v iv v ii i v i i AmnSINE1#SINE 104 GGTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTC 153 rnd-4_family- 156 GCAGTCAGTGCTGACCCCAGTGCCCCAGCGTGGCGCTAGGGGGCGCTGTG 205 vv i v - i i i AmnSINE1#SINE 154 TGAGTCAGTACTGAACC-AGTGCCCCAGCGTGGTGTTAGGGGGCACTGTG 202 rnd-4_family- 206 CTGCAGG 212 v AmnSINE1#SINE 203 CTGCTGG 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.43 CpG sites = 13, Kimura (unadjusted) = 23.43 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1) 361 20.19 0.95 0.95 rnd-4_family-24#SINE/5S-Deu-L2 203 307 (116) AmnSINE1#SINE/5S-Deu-L2 105 209 (366) m_b12s502i5 rnd-4_family- 203 GTGCTGCAGGGAGCAG-GGTGGGGGCTCAGTAGGGGGCGCTCTCCCCTGG 251 i ii - v v ii v i i vv AmnSINE1#SINE 105 GTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCT 154 rnd-4_family- 252 CAGTCAGTGCTGACCCCAATGCCCCAGGGTGGCGCTAGGGGGCGCTGTGC 301 v i -v i v i i i AmnSINE1#SINE 155 GAGTCAGTACTGA-ACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGC 203 rnd-4_family- 302 TGCAGG 307 v AmnSINE1#SINE 204 TGCTGG 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.84 CpG sites = 12, Kimura (unadjusted) = 23.84 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 248 22.96 0.00 5.93 rnd-4_family-24#SINE/5S-Deu-L2 298 422 (1) AmnSINE1#SINE/5S-Deu-L2 105 222 (353) m_b12s502i6 rnd-4_family- 298 GTGCTGCAGGGAGCGGGGTGGGGGGCTCAGTAGGGGGCGCTCTCCCCTGG 347 i i v iv v ii v i i vv AmnSINE1#SINE 105 GTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCT 154 rnd-4_family- 348 CAGNCGGTGCCTGACCCCAATGACGCAGCCCAGGGTGGCGCTAGGGGGCG 397 v ? i i - v - i --- -- v i i i AmnSINE1#SINE 155 GAGTCAGTAC-TGAACC-AGTG---C--CCCAGCGTGGTGTTAGGGGGCA 197 rnd-4_family- 398 CTGTGCTGCGGGGANTTCCTTCTTT 422 v ii? v v AmnSINE1#SINE 198 CTGTGCTGCTGGAGGTGCCGTCTTT 222 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.27 CpG sites = 15, Kimura (unadjusted) = 28.27 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.00 (7 / 7) 464 11.95 10.00 2.33 rnd-4_family-2407#DNA 25 144 (13) Eulor9A#DNA 167 295 (6) m_b12s502i7 rnd-4_family- 25 TACNAATATGTGCAACGTGGCCGAGTTAATGTTGCTGTAGGAACCTTAAC 74 i? i i vv i v Eulor9A#DNA 167 TATCAGTATGTGCAATGTGGCCGAGTTACGGTTGCTGTGGGAACCGTAAC 216 rnd-4_family- 75 TTTTGCATTTCCTGACTTTT-TAT-TTTAAACTNTGCAACCTTAA---TG 119 - v - ii- v ? - v --- Eulor9A#DNA 217 -TTTGAATTTCCTGACTTTTGTGCGTTTAAAATCT-CAACCGTAACGTTG 264 rnd-4_family- 120 CGATTAAC--AG----CTTTGCA-TTTATTTT 144 - -- ----i - i Eulor9A#DNA 265 C-ATTAACGTAGGNTTTTTTGCATTTTACTTT 295 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.41 CpG sites = 8, Kimura (unadjusted) = 13.37 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.08 (9 / 119), avg. gap size = 1.67 (15 / 9) 17 13.64 8.47 1.59 rnd-4_family-3332#Unknown 13 71 (320) (GTTAACC)n#Simple_repeat 1 63 (0) m_b12s252i10 rnd-4_family- 13 GTTAANCGGTTAACCGGTAAGCATTAGNC-TTACCGGTTAACCG---ACC 58 - v v v i i? - v v --- (GTTAACC)n#Si 1 GTTAA-CCGTTAACCGTTAACCGTTAACCGTTAACCGTTAACCGTTAACC 49 rnd-4_family- 59 -TTAACCGTTAACC 71 - (GTTAACC)n#Si 50 GTTAACCGTTAACC 63 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.50 (6 / 4) 12 7.80 3.23 6.67 rnd-4_family-4842#Unknown 485 515 (27) (TCGGG)n#Simple_repeat 1 30 (0) m_b12s252i9 rnd-4_family- 485 TCGGGTGGCGGT-GGCTCGGGTCCGGGTCGGG 515 v - - v - (TCGGG)n#Simp 1 TCGGGTCG-GGTCGGGTCGGGT-CGGGTCGGG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.10 (3 / 30), avg. gap size = 1.00 (3 / 3) 717 10.17 0.00 1.69 rnd-4_family-604#SINE/5S 21 140 (1497) 5S#rRNA 1 118 (3) c_b12s401i0 rnd-4_family- 21 GCCTACGGCCATACCGGACCCTGAACGCCCCCGATCCCGTCCGATCTCGG 70 i -- v i i 5S#rRNA 1 GTCTACGGCCATACC--ACCCTGAACGCGCCCGATCTCGTCTGATCTCGG 48 rnd-4_family- 71 AAGGTAAGCCGTCCCGGGCCTGGCTAGTACTTGGATGGGNGACCGCCTGG 120 v v vvi i ? 5S#rRNA 49 AAGCTAAGCAGGGTCGGGCCTGGTTAGTACTTGGATGGGAGACCGCCTGG 98 rnd-4_family- 121 GAATCCCGGGTGCCGTAGGC 140 v i 5S#rRNA 99 GAATACCGGGTGCTGTAGGC 118 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 11.06 CpG sites = 6, Kimura (unadjusted) = 11.06 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.00 (2 / 2) 14 7.86 3.70 0.00 rnd-4_family-604#SINE/5S 411 437 (1200) (GGCCA)n#Simple_repeat 1 28 (0) m_b12s252i1 rnd-4_family- 411 GGCCA-CCCAGGCCAGGCCTGGCCAGGC 437 -v v (GGCCA)n#Simp 1 GGCCAGGCCAGGCCAGGCCAGGCCAGGC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 14 7.86 3.70 0.00 rnd-4_family-604#SINE/5S 592 618 (1019) (GGCCA)n#Simple_repeat 1 28 (0) m_b12s252i2 rnd-4_family- 592 GGCCA-CCCAGGCCAGGCCTGGCCAGGC 618 -v v (GGCCA)n#Simp 1 GGCCAGGCCAGGCCAGGCCAGGCCAGGC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 11 15.90 0.00 10.26 rnd-4_family-604#SINE/5S 726 768 (869) (CGCCGGC)n#Simple_repeat 1 39 (0) m_b12s252i3 rnd-4_family- 726 CGCTCGGACCCCCTGCGCCCGGCCGCCGGCTCGCGGGACCGCC 768 - - v v vv - v - (CGCCGGC)n#Si 1 CGC-CGG-CCGCCGGCCGCCGGCCGCCGGC-CGCCGG-CCGCC 39 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 14 7.86 3.70 0.00 rnd-4_family-604#SINE/5S 787 813 (824) (GGCCA)n#Simple_repeat 1 28 (0) m_b12s252i4 rnd-4_family- 787 GGCCA-CCCAGGCCAGGCCTGGCCAGGC 813 -v v (GGCCA)n#Simp 1 GGCCAGGCCAGGCCAGGCCAGGCCAGGC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 17 11.81 5.41 0.00 rnd-4_family-604#SINE/5S 985 1021 (616) (CCTGG)n#Simple_repeat 1 39 (0) m_b12s252i5 rnd-4_family- 985 CCAGGCCAGGCCTGGCCTGGCCTGG-CAGGCC-GGCGTG 1021 v v - v - v (CCTGG)n#Simp 1 CCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTG 39 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 14 18.23 3.64 5.56 rnd-4_family-604#SINE/5S 1081 1135 (502) (CCCGG)n#Simple_repeat 1 54 (0) m_b12s252i6 rnd-4_family- 1081 CCCGGCCCCGGGGCGGACCGGCCCGGGCTCGCTCGAGCCC--CCTGCGCC 1128 - vv v v iv i - -- i - (CCCGG)n#Simp 1 CCCGG-CCCGGCCCGGCCCGGCCCGGCCCGGCCCG-GCCCGGCCCG-GCC 47 rnd-4_family- 1129 CGGCCCG 1135 (CCCGG)n#Simp 48 CGGCCCG 54 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.25 (5 / 4) 15 5.48 0.00 0.00 rnd-4_family-604#SINE/5S 1141 1159 (478) (C)n#Simple_repeat 1 19 (0) m_b12s252i7 rnd-4_family- 1141 CCGCCCCCCCCCCCCCCCC 1159 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 7.56 3.57 0.00 rnd-4_family-604#SINE/5S 1496 1523 (114) (CCCCA)n#Simple_repeat 1 29 (0) m_b12s252i8 rnd-4_family- 1496 CCCCCCCCCACCCCACCCC-CCCCAGCCC 1523 v - v (CCCCA)n#Simp 1 CCCCACCCCACCCCACCCCACCCCACCCC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 274 25.71 2.10 2.10 rnd-4_family-787#LTR/ERV1 1568 1710 (345) PABL_B-int#LTR/ERV1 6542 6684 (438) m_b12s701i0 rnd-4_family- 1568 ATNAGCTCNGAGCTGTACCAGCTCCGGT-TGCTGGCTCTGCAAAACCGCC 1616 ? i v ? iv vv v v-v iv - ?v PABL_B-int#LT 6542 ATGAACGCTGAAATGTACCATATGCGGAAGGCTATCT-TGCAAAACCGNA 6590 rnd-4_family- 1617 AGGCCCTAGATTATGTNTTA--GCCTCNCGGGGCGGGGTGTGTGCCCTTA 1664 v -i -i? ? -- ?v ? i v iiiv i ? ? PABL_B-int#LT 6591 TGGCCCTAGA-CAT-CCTNACTGCNGCCCAGGGGGGAACCTGCGCCNTNA 6638 rnd-4_family- 1665 TTGGAGANGAATGTTGTACTTATGTCCCGGAGNNCTCACAGGACAT 1710 ii iv? iiv i v?? ?viii PABL_B-int#LT 6639 TTAAAACTGAATGTTGTGTGTATATCCCGGATAACTCNGGAAACAT 6684 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.93 CpG sites = 19, Kimura (unadjusted) = 36.17 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.04 (5 / 142), avg. gap size = 1.20 (6 / 5) 18 0.00 3.85 0.00 rnd-4_family-788#DNA/hAT-Tip100 324 349 (1179) (GAAGT)n#Simple_repeat 1 27 (0) m_b12s252i0 rnd-4_family- 324 GAAGTGAAGTGAA-TGAAGTGAAGTGA 349 - (GAAGT)n#Simp 1 GAAGTGAAGTGAAGTGAAGTGAAGTGA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 15 21.84 3.51 3.51 rnd-4_family-1142#Unknown 147 203 (271) (GCCCC)n#Simple_repeat 1 57 (0) m_b13s252i11 rnd-4_family- 147 GCCCCGGGCCG-GCCGCGCCGCGCC-CCCCTCCCCTCCCCGGACCCCAAG 194 vv -v v v - v v - - ivv (GCCCC)n#Simp 1 GCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCC-G-CCCCGCC 48 rnd-4_family- 195 CCGCCCCGC 203 (GCCCC)n#Simp 49 CCGCCCCGC 57 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 187 27.62 2.46 5.04 rnd-4_family-1189#LINE/I-Jockey 994 1115 (1316) L3#LINE/CR1 2592 2710 (1389) m_b13s601i0 rnd-4_family- 994 CCAGAGTTTCTCAAGAATTTGGGGAGACGGGGATG-GGAATGGCTGNCGG 1042 i viivv i v-- i v ivi - iv ? L3#LINE/CR1 2592 CCAGGGTACTGAAAGAACTTGC--AGATGTGATCGCGGAACCGCTGTCGG 2639 rnd-4_family- 1043 CNCTTTTTACTGCCATGCAC--AGAACCGGAGAAGTGCCAGCAAGCTGGC 1090 i?v i iv- vv - -- v i i v ii v L3#LINE/CR1 2640 TAATCTTTGA-GAAAT-CACGGAGAACGGAAGAGGTGCCAGAAGACTGGA 2687 rnd-4_family- 1091 GACAGGCAACAGTGGTNGCCCTACT 1115 i vv ? --? ? L3#LINE/CR1 2688 GACGGGCAAATGTNGT--NCCTANT 2710 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.04 CpG sites = 16, Kimura (unadjusted) = 36.82 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.12 (9 / 8) 15 19.66 0.00 0.00 rnd-4_family-1278#Unknown 215 243 (217) (G)n#Simple_repeat 1 29 (0) m_b13s252i10 rnd-4_family- 215 GGGGGCGCTGGGGGGCGGGGGAGGGGGGG 243 v vv v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 243 23.47 0.00 6.49 rnd-4_family-1516#LINE/L2 3 84 (58) L2d2_3end#LINE/L2 403 479 (76) m_b13s601i1 rnd-4_family- 3 CTTCGCCCATCTNCATGTTCCNTGTTTATCTAATTTAGACTGTAAACTCT 52 iv v i v ?i -- ? i vi i i - i i i L2d2_3end#LIN 403 CTTTTCACGTGTTTATGT--CTTGTCTCCCCAACT-AGATTGTAAGCTCC 449 rnd-4_family- 53 TTGGGGGCAGGGACCGTGNCTTCTTAATTTCT 84 i i ? v -- i L2d2_3end#LIN 450 TTGAGGGCAGGGACCATGTCTTAT--ACTTCT 479 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.72 CpG sites = 13, Kimura (unadjusted) = 30.77 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.00 (5 / 5) 313 22.10 6.78 4.13 rnd-4_family-1516#LINE/L2 20 137 (5) L2c_3end#LINE/L2 352 472 (6) m_b13s601i2 rnd-4_family- 20 TTCCNTGTTTATCTAATT---TAGACTGTAAACTCTTTGGGGGCAGGGAC 66 v i i vv i--- i i i i L2c_3end#LINE 352 TTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGAC 401 rnd-4_family- 67 CGTGNCTTCTTAATTTCTGTA----AAGCACCATGCACAT-CTATGGCAC 111 ? v v i i ----v i vv -v - i L2c_3end#LINE 402 CGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTA-GGCGC 450 rnd-4_family- 112 TATANAAACGACACTTGTTGTAATAA 137 vv ? i ---i - i L2c_3end#LINE 451 TCAATAAATG---TTTGTTG-AATGA 472 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 14, Kimura (unadjusted) = 27.47 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (8 / 117), avg. gap size = 1.62 (13 / 8) 403 18.28 1.53 8.13 rnd-4_family-1531#SINE/tRNA 7 137 (139) LFSINE_Vert#SINE/tRNA 244 366 (93) m_b13s601i3 rnd-4_family- 7 AGAGNCCAAGAACCGCACAGGCCNTGGAGACCGAACTACCTCTGCTANNC 56 ? i i v ii -? i - - v?? LFSINE_Vert#S 244 AGAGGCCAAGGACTGAATGGGC-ATGGAGACTGAACTACC-CT-CTCACC 290 rnd-4_family- 57 TNTGGAGA--ATCCCCATACCCAGATTNGGGTTGAGGCATGCCGGCAGGG 104 ? i i--i i---- i i? iiii i LFSINE_Vert#S 291 TCTAGAGGTGGTCCCT----CCAGGTCAGGGTTGAGGCACATTGGCGGGG 336 rnd-4_family- 105 CAGTGTGTGNGGGAAGCTTGTCCTGCAGCAGCC 137 --- iv v v LFSINE_Vert#S 337 CAGTGTG---GGGAAGCTTGCACTGCCGCTGCC 366 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.81 CpG sites = 17, Kimura (unadjusted) = 22.98 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.09 (12 / 11) 1241 8.87 15.28 0.81 rnd-4_family-1720#SINE/5S-Deu-L2 2 217 (3) AmnSINE1#SINE/5S-Deu-L2 11 257 (318) m_b13s502i0 rnd-4_family- 2 ATACCACCTTGTGCTGTGATCTTGTCAGCTCTCACAAGCTAAGCAGGGTC 51 i v i v AmnSINE1#SINE 11 ATACCACCTCGGGCTGTGATCTCGTCAGATCTCACAAGCTAAGCAGGGTC 60 rnd-4_family- 52 GGGCCTGGTCAGTACTTGGATGGGAGACCTCCAAGGAA---CAGGTACGT 98 --- i - AmnSINE1#SINE 61 GGGCCTGGTCAGTACTTGGATGGGAGACCTCCAAGGAAACCCAGGTGC-T 109 rnd-4_family- 99 GNAGGAAGTGNNATTGGTGGTTCACT--GTGGCATTTT------------ 134 ? ??ii i v -- i i ------------ AmnSINE1#SINE 110 GCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCTGAGTC 159 rnd-4_family- 135 ----------------CCCAGCGTTGGTCCTAGGNGGNACTGNGCTGCTG 168 ---------------- - vi ? ? ? AmnSINE1#SINE 160 AGTACTGAACCAGTGCCCCAGCG-TGGTGTTAGGGGGCACTGTGCTGCTG 208 rnd-4_family- 169 GAGGTGCTGNCTTTNGGATGAGACACAAAACTGAGGTCCTGANTGCTTG 217 i ? ? ii i ?ii AmnSINE1#SINE 209 GAGGTGCCGTCTTTCGGATGAGACGTAAAACCGAGGTCCTGACCACTTG 257 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.50 CpG sites = 15, Kimura (unadjusted) = 10.06 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.03 (6 / 215), avg. gap size = 5.83 (35 / 6) 808 20.71 1.50 1.00 rnd-4_family-183#LINE/L2 30 229 (0) X24_LINE#LINE/L2 13 213 (101) m_b13s601i4 rnd-4_family- 30 GGGCTACACCTTGAA-ACCATTCGGAAACTGAAGCTGGTGCAGAATGCGG 78 i - - ii i vv i X24_LINE#LINE 13 GGGCTGC-CCTTGAAGACCACCCGGAAGCTTCAGCTGGTGCAGAATGCAG 61 rnd-4_family- 79 CNGCCCGCTTGTTAAGCGGAGTTTCACGCCGAGAGCACAT-AT-CCGGTG 126 ? i ii i i i? v ?vvv i v?i - i- v X24_LINE#LINE 62 CGGCTCGTCTGCTGAANGGTGTNAGCCACANGGAGCACATTACACCTGTG 111 rnd-4_family- 127 CTCCGGGATCTGCACTGGCTGCCNGTTGGTTTCCGGGTGGAGTTTAAGGT 176 vii i i v i i v i i X24_LINE#LINE 112 CTCCGCAGTCTGCACTGGCTACCNATTTGCTTCCGAGTGCAATTCAAGGT 161 rnd-4_family- 177 GTTGGTTTTGACCTATAAAGCCCTAAAATGGTTTGGGACCTGGCTACCTG 226 ii i i - v v i v X24_LINE#LINE 162 GTTGACTTTAATCTATAAAGCCCT-ATATGGTTTGGGCCCTGGTTACCTT 210 rnd-4_family- 227 AGA 229 X24_LINE#LINE 211 AGA 213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 27, Kimura (unadjusted) = 25.64 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.03 (5 / 199), avg. gap size = 1.00 (5 / 5) 647 8.33 0.00 0.00 rnd-4_family-1935#Unknown 78 161 (132) C UCON28a#Unknown (702) 93 10 m_b13s502i1 rnd-4_family- 78 GGTTGCAGCATTTTGCGGCATGTGGCATGCCTCTCAGTGAAGCGAAAGGC 127 i i i i i C UCON28a#Unkno 93 GGCTGCAGCATTTCGTGGCATGTGGCACGCCTCTCAGTGAAGTGAAAGGC 44 rnd-4_family- 128 ATGTCACANGCTGGCTTTTCGGCTGTGACATGCC 161 ? i i ? C UCON28a#Unkno 43 ATGTCACAAGCCGGCTTTTCAGCTGTGACANGCC 10 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.54 CpG sites = 7, Kimura (unadjusted) = 9.36 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 747 14.75 2.46 0.00 rnd-4_family-1935#Unknown 172 293 (0) UCON28a#Unknown 14 138 (657) m_b13s502i2 rnd-4_family- 172 TNTCCCAGTCAAAAAANCAGAGTGTGACATGCTTTTCACTTCACTGAGAN 221 ? v iii i? i vv i ? UCON28a#Unkno 14 TGTCACAGCTGAAAAGCCGGCTTGTGACATGCCTTTCACTTCACTGAGAG 63 rnd-4_family- 222 GCATGCCACACGCCACAAAATGCTGCANCCCTCCCTCACATTTTGTATAA 271 i i i ? i v i UCON28a#Unkno 64 GCGTGCCACATGCCACGAAATGCTGCAGCCCCCGCTCACATTTTGCATAA 113 rnd-4_family- 272 GCAATTTTTATTC---TGCGTTCTC 293 ii --- i UCON28a#Unkno 114 GCAATTTCCATTCTGTTGTGTTCTC 138 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.53 CpG sites = 14, Kimura (unadjusted) = 17.57 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.01 (1 / 121), avg. gap size = 3.00 (3 / 1) 14 14.04 10.64 0.00 rnd-4_family-2199#Unknown 131 177 (156) (GGCCTGG)n#Simple_repeat 1 52 (0) m_b13s252i9 rnd-4_family- 131 GGCCGGCGGCCTGGAG-CTGGGGCCT---GCCGGCGGCCAGGGG-CTGGG 175 v v i - --- v v v - (GGCCTGG)n#Si 1 GGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGG 50 rnd-4_family- 176 GC 177 (GGCCTGG)n#Si 51 GC 52 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.67 (5 / 3) 298 25.25 1.98 1.98 rnd-4_family-2426#DNA 14 114 (71) MER131#DNA 48 148 (67) m_b13s601i5 rnd-4_family- 14 GTTTCCATTATAACCTNCTGTTTTCANACGCTCATAACTT-TCCG-AAAC 61 v i? i ?iv i i i-v - v MER131#DNA 48 GTTTCCATTATAAACCCCTATTTTCAGGGGTTTATAACTCGGCCGTAAAA 97 rnd-4_family- 62 ATTCGCNTTTTGGGCTGAAATTTTCCATGCTTGGTCTCTGACCAAAAAAG 111 -- ii i vv i vv v v iii iv MER131#DNA 98 ATTCGC--TCCGGGCTGAAACTTGGCATACAAGGTCTCAGCCCGGGAGCG 145 rnd-4_family- 112 ANT 114 ? MER131#DNA 146 AAT 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.05 CpG sites = 14, Kimura (unadjusted) = 32.57 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.00 (4 / 4) 193 6.67 0.00 0.00 rnd-4_family-243#Unknown 288 317 (815) C AmnSINE1#SINE/5S-Deu-L2 (92) 483 454 m_b13s601i6 rnd-4_family- 288 CCACTGAAATGCAGCCACCTCGGGGCTGGA 317 v v C AmnSINE1#SINE 483 CCACTGAAATGCAGCCACCTCTGGGGTGGA 454 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 7.03 CpG sites = 0, Kimura (unadjusted) = 7.03 Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 220 31.71 1.22 0.00 rnd-4_family-243#Unknown 363 444 (688) C AmnSINE2#SINE/tRNA-Deu (98) 260 178 m_b13s601i7 rnd-4_family- 363 TTTGACCAGTGATNCTNNAGCAAACTCAT-CANCTATGGCAAGGGCCCTG 411 i i iv ii? i??i i v - v?i i iv v vi C AmnSINE2#SINE 260 TTCGGCCAAGGGCACCGGGGCAAACCCCTACTCTTACGAAAAGCGCCACG 211 rnd-4_family- 412 GGATGTTTNATGGCTGTGCAGAGCGGAAAGGAC 444 v ? v iii i v i C AmnSINE2#SINE 210 GGATCTTTAATGTCCACGCAGAGCAGACAGGGC 178 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.79 CpG sites = 17, Kimura (unadjusted) = 47.53 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1) 12 24.23 0.00 5.77 rnd-4_family-2508#Unknown 51 105 (722) (CCCCGAG)n#Simple_repeat 1 52 (0) m_b13s252i8 rnd-4_family- 51 CCCNGAGCCCCGATGCCCCCAGCCGGGAGCGGCGTGGGGCAGAAGCCCTG 100 ? - v vv vv -i vv v - i (CCCCGAG)n#Si 1 CCCCGAGCCCCGA-GCCCCGAGCCCCGAGCCCCG-AGCCCCG-AGCCCCG 47 rnd-4_family- 101 AGCCC 105 (CCCCGAG)n#Si 48 AGCCC 52 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 516 20.00 0.00 0.00 rnd-4_family-288#DNA/hAT 37 141 (2) MER121B#DNA/hAT 303 407 (0) m_b13s502i3 rnd-4_family- 37 CTAAGCGGAACGCGAACCCGANAACGTTCGAGTTCGAGTCGAACTTTCGA 86 i i v v iv ? vv iv v v v MER121B#DNA/h 303 CCAAACGGAACTCGAAGCTCAAAAGTTTCGAGTTCGGTTCTAAATTTAGA 352 rnd-4_family- 87 ACCCACAATGTTTGAGTGGGTTCGAAATTAGGCAAAACGAGTTCACCCAT 136 i i v i v v v MER121B#DNA/h 353 ACCCGCGATTTTCGAGTGGGTTCTAAATTTGGCAAAACGAGTTCTCCCAT 402 rnd-4_family- 137 CCCTA 141 ?i MER121B#DNA/h 403 NTCTA 407 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.28 CpG sites = 8, Kimura (unadjusted) = 23.81 Transitions / transversions = 0.62 (8/13) Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.0 (0 / 0) 1008 13.24 2.64 6.88 rnd-4_family-295#LINE/CR1 193 419 (4) CR1-L3A_Croc#LINE/CR1 1 218 (4070) m_b13s551i0 rnd-4_family- 193 CTCTGACCCTTGGANCTTTGATCAGCCCCGCTGTTTGAAG--TCTGAGTG 240 v i? ? i v -- i CR1-L3A_Croc# 1 CTGTGACCCTTGGGTCTNTGATCAGCCCTGGTGTTTGAAGTCTCTGAGTA 50 rnd-4_family- 241 GTTAATCGCTCCCTGG-TGGCGAGGGGGGAGCTGAGCTAAGCAGGGAGGC 289 v i- i vi--- i v CR1-L3A_Croc# 51 GTTAATCCCTCCCTGATTAGCGAGGGGGTG---GAGCTGAGCAGCGAGGC 97 rnd-4_family- 290 TTGGTA-TAAAANGTCACTTGCCAGGCGAACTCGAGAGCATGAACAGGGG 338 i - -- v ------ ? i v CR1-L3A_Croc# 98 TTAGTAGTAAA--GTCAGTTGCCAGGCGAACT------CNTGAGCAGCGG 139 rnd-4_family- 339 CAGCTAACAGGAGAGTTTCGGAGGGAGTTTAGAGAGGGAGTGTGAG--GC 386 v --- ii v i i - ? -- CR1-L3A_Croc# 140 AA---AACGAGAGCGTTTTGGAGGGAGTTTGGAG-GGGAGTGTGNGAAGC 185 rnd-4_family- 387 TTTCCTTCCAGGTTCAGTTCTACGCGCGATTCC 419 i i v v i v CR1-L3A_Croc# 186 TTTCTTTCTAGGTACAGTTCTACGCTCAATACC 218 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.40 CpG sites = 16, Kimura (unadjusted) = 14.95 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.08 (19 / 226), avg. gap size = 1.11 (21 / 19) 14 23.33 2.22 0.00 rnd-4_family-3323#Unknown 28 72 (261) (TGTAGAA)n#Simple_repeat 1 46 (0) m_b13s252i7 rnd-4_family- 28 TGTATAATTTAGAATGAAGGATAAAGAAT-AATAATGTAGCATGTA 72 v v v i iv -v v v (TGTAGAA)n#Si 1 TGTAGAATGTAGAATGTAGAATGTAGAATGTAGAATGTAGAATGTA 46 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 236 19.05 3.17 0.00 rnd-4_family-3698#DNA/hAT-Tip100 3 65 (121) ORSL#DNA/hAT-Tip100 1 65 (210) m_b13s502i4 rnd-4_family- 3 CAGGGCCGGATTTCCAATTAGGCACAGTAGGCAC-GTGCCTAGGGGCGCC 51 iv vi v - v vv ORSL#DNA/hAT- 1 CAGGGCCGACTTATCCATTAGGCACAGTAGGCACAGTGCCTAGGGCCCAC 50 rnd-4_family- 52 GGCG-TTCTAGGGGC 65 iii- i ORSL#DNA/hAT- 51 GATACTTTTAGGGGC 65 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.11 CpG sites = 6, Kimura (unadjusted) = 22.11 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 18 20.97 1.47 6.15 rnd-4_family-4007#Unknown 226 293 (712) (GCCAGGG)n#Simple_repeat 1 65 (0) m_b13s252i6 rnd-4_family- 226 GCCTGGGGCCAGAACCGAGGGGCCTGGAGCCTGGGAGGCCAGGGG-CAGT 274 v iiv v v i -i - - - (GCCAGGG)n#Si 1 GCCAGGGGCCAGGGGCCAGGGGCCAGGGGCC-AGG-GGCCAGGGGCCAG- 47 rnd-4_family- 275 GAAGCCTGGGGCCAGAGGC 293 -i v i (GCCAGGG)n#Si 48 G-GGCCAGGGGCCAGGGGC 65 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.00 (5 / 5) 13 24.02 5.56 0.00 rnd-4_family-4596#LTR/ERV1 4 57 (2575) (TTGTATG)n#Simple_repeat 1 57 (0) m_b13s252i4 rnd-4_family- 4 TTGTAAGTT-TGTCCTGTATGTCAT-GGGTGT-TGTTTTGTGTTGTATGT 50 v - i vi ii -v v - v i (TTGTATG)n#Si 1 TTGTATGTTGTATGTTGTATGTTGTATGTTGTATGTTGTATGTTGTATGT 50 rnd-4_family- 51 TGTGTGT 57 i (TTGTATG)n#Si 51 TGTATGT 57 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 18 31.27 0.00 6.49 rnd-4_family-4596#LTR/ERV1 2256 2337 (295) (TA)n#Simple_repeat 1 77 (0) m_b13s252i5 rnd-4_family- 2256 TATCATATGTACACATACATACTATACATATATGCCCATACACACTACAA 2305 - i i i i - i iivi i i - i v (TA)n#Simple_ 1 TAT-ATATATATATATATATA-TATATATATATATATATATATA-TATAT 47 rnd-4_family- 2306 ATATATACGCCATATCCATATATCATATATAT 2337 -vvi vi - (TA)n#Simple_ 48 ATATATA-TATATATATATATAT-ATATATAT 77 Matrix = Unknown Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.00 (5 / 5) 13 11.05 0.00 9.38 rnd-4_family-5063#Unknown 916 950 (1038) (TTC)n#Simple_repeat 1 32 (0) m_b13s252i3 rnd-4_family- 916 TTCTTCTTGAGTCTTCTCTCTTTTTCTTCTTTCTT 950 -vv - i - (TTC)n#Simple 1 TTCTTCTT-CTTCTTCT-TCTTCTTCTTC-TTCTT 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 15 14.40 2.38 4.88 rnd-4_family-5663#Unknown 1 42 (293) (GGGAG)n#Simple_repeat 1 41 (0) m_b13s252i2 rnd-4_family- 1 GGGAGGGG-GCGGAGGGGTTTCGAAGGGGGAGGGGAGGGGAGG 42 - v -vvv i - (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGG-AGGGGA-GGGGAGGGGAGGGGAGG 41 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 19 0.00 0.00 0.00 rnd-4_family-602#rRNA 439 459 (3771) (A)n#Simple_repeat 1 21 (0) m_b13s252i1 rnd-4_family- 439 AAAAAAAAAAAAAAAAAAAAA 459 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15392 3.35 2.69 0.00 rnd-4_family-602#rRNA 2122 3941 (289) SSU-rRNA_Hsa#rRNA 1 1869 (0) m_b13s551i1 rnd-4_family- 2122 TACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCA 2171 v SSU-rRNA_Hsa# 1 TACCTGGTTGATCCTGCCAGTACCATATGCTTGTCTCAAAGATTAAGCCA 50 rnd-4_family- 2172 TGCATGTCTAAGTACACACGGCCGGTACAGTGAAACTGCGAATGGCTCAT 2221 i ? SSU-rRNA_Hsa# 51 TGCATGTCTAAGTACGCANGGCCGGTACAGTGAAACTGCGAATGGCTCAT 100 rnd-4_family- 2222 TAAATCAGTTATGGTTCCTTTGGTCGCTC---CAACCCTTACTTGGATAA 2268 --- vv i i ? SSU-rRNA_Hsa# 101 TAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGANAA 150 rnd-4_family- 2269 CTGTGGTAATTCTAGAGCTAATACATGCCGACGAGCGCTGACCTCC---- 2314 i i ---- SSU-rRNA_Hsa# 151 CTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCTTCG 200 rnd-4_family- 2315 ----GGGGATGCGTGCATTTATCAGACCAAAACCAACCCGG---GCTC-- 2355 ---- i --- i -- SSU-rRNA_Hsa# 201 CGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTCAGCCCCT 250 rnd-4_family- 2356 -----GCCC-GGCCG------------------CTTTGGTGACTCTAGAT 2381 ----- - ------------------ SSU-rRNA_Hsa# 251 CTCCGGCCCCGGCCGGGGGGCGGGCGCCGNCGGCTTTGGTGACTCTAGAT 300 rnd-4_family- 2382 AACCTCGGGCCGATCGCACGCCCCC-GTGGCGGCGACGATGCATTCGAAT 2430 - iv i SSU-rRNA_Hsa# 301 AACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAAC 350 rnd-4_family- 2431 GTCTGCCCTATCAACTTTCGATGGTACTTCCTGTGCCTACCATGGTGACC 2480 v iv i SSU-rRNA_Hsa# 351 GTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACC 400 rnd-4_family- 2481 ACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAAC 2530 i SSU-rRNA_Hsa# 401 ACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAAC 450 rnd-4_family- 2531 GGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGA 2580 SSU-rRNA_Hsa# 451 GGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGA 500 rnd-4_family- 2581 CCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCC 2630 SSU-rRNA_Hsa# 501 CCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCC 550 rnd-4_family- 2631 TGTAATTGGAATGAGTACACTTTAAATCCTTTAACGAGGATCCATTGGAG 2680 v SSU-rRNA_Hsa# 551 TGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAG 600 rnd-4_family- 2681 GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATA 2730 SSU-rRNA_Hsa# 601 GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATA 650 rnd-4_family- 2731 TTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGATCGAGCT 2780 v i v SSU-rRNA_Hsa# 651 TTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCG 700 rnd-4_family- 2781 GGCGGTCCGCCGCGAGGCGAGCTACCGCCTGTCCCAGCCCCT-GCCTCTC 2829 i i v - SSU-rRNA_Hsa# 701 GGCGGTCCGCCGCGAGGCGAGCCACCGCCCGTCCCCGCCCCTTGCCTCTC 750 rnd-4_family- 2830 GGCGCTCCCTTGATGCTCTTAACTGAGTGTCCTG-GGGGTCCGAAGCGTT 2878 i i i i - i SSU-rRNA_Hsa# 751 GGCGCCCCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTT 800 rnd-4_family- 2879 TACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCT--GGTCGCCGGAATAC 2926 i--i i v i SSU-rRNA_Hsa# 801 TACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATAC 850 rnd-4_family- 2927 TCCAGCTAGGAATAATGGAATAGGACTCCGGTTCTATTTTGTTGGTTTTC 2976 iv iv SSU-rRNA_Hsa# 851 CGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTC 900 rnd-4_family- 2977 GGAACTGGGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGTGC 3026 i i SSU-rRNA_Hsa# 901 GGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGC 950 rnd-4_family- 3027 CGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAAAGCGAAAGC 3076 i ? i SSU-rRNA_Hsa# 951 CGCTAGAGGTGAAATTCTTGGACCGGCGCAGGNCGGACCAGAGCGAAAGC 1000 rnd-4_family- 3077 ATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAA 3126 SSU-rRNA_Hsa# 1001 ATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAA 1050 rnd-4_family- 3127 GACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTAGCGA 3176 ii SSU-rRNA_Hsa# 1051 GACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACCGGCGA 1100 rnd-4_family- 3177 TCCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTACGGGAAACCAAA 3226 v v SSU-rRNA_Hsa# 1101 TGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAA 1150 rnd-4_family- 3227 GTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAA 3276 SSU-rRNA_Hsa# 1151 GTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAA 1200 rnd-4_family- 3277 TTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCA 3326 SSU-rRNA_Hsa# 1201 TTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCA 1250 rnd-4_family- 3327 ACACGGGAAACCTCACCCGGCCCGGACACGGAAAGGATTGACAGATTGAT 3376 v SSU-rRNA_Hsa# 1251 ACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGAT 1300 rnd-4_family- 3377 AGCTCTTTCTCGATTCTGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGT 3426 i SSU-rRNA_Hsa# 1301 AGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGT 1350 rnd-4_family- 3427 GGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCT 3476 SSU-rRNA_Hsa# 1351 GGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCT 1400 rnd-4_family- 3477 AACTAGTTATGCGACCCCCGAGCGGTCGGCGT---CCAACTTCTTAGAGG 3523 i --- SSU-rRNA_Hsa# 1401 AACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAACTTCTTAGAGG 1450 rnd-4_family- 3524 GACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATG 3573 SSU-rRNA_Hsa# 1451 GACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATG 1500 rnd-4_family- 3574 CCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGACTGGCTCAGCGTG 3623 SSU-rRNA_Hsa# 1501 CCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGACTGGCTCAGCGTG 1550 rnd-4_family- 3624 TGTCTACCCTACGCCGACAGGTGCGGGTAACCCGTTGAACCCCATTCGTG 3673 i i i i SSU-rRNA_Hsa# 1551 TGCCTACCCTACGCCGGCAGGCGCGGGTAACCCGTTGAACCCCATTCGCG 1600 rnd-4_family- 3674 ATGGGGATCGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTA 3723 SSU-rRNA_Hsa# 1601 ATGGGGATCGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTA 1650 rnd-4_family- 3724 AGTGCGGGTCATAAGCTCGCGTTGATTAAGTCCCTGCCCTTTGTACACAC 3773 i SSU-rRNA_Hsa# 1651 AGTGCGGGTCATAAGCTTGCGTTGATTAAGTCCCTGCCCTTTGTACACAC 1700 rnd-4_family- 3774 CGCCCGTCGCTACTACCGATTGGATGGTTTAGTGAGGTCCTCGGATCGGC 3823 i SSU-rRNA_Hsa# 1701 CGCCCGTCGCTACTACCGATTGGATGGTTTAGTGAGGCCCTCGGATCGGC 1750 rnd-4_family- 3824 CCTGCCGGGGTCGG-TCACGGCCCTGGTGGAGCGCCGAGAAGACGGTCGA 3872 i -i i i SSU-rRNA_Hsa# 1751 CCCGCCGGGGTCGGCCCACGGCCCTGGCGGAGCGCTGAGAAGACGGTCGA 1800 rnd-4_family- 3873 ACTTGACTATCTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGA 3922 SSU-rRNA_Hsa# 1801 ACTTGACTATCTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGA 1850 rnd-4_family- 3923 ACCTGCGGAAGGATCATTA 3941 i SSU-rRNA_Hsa# 1851 ACCTGCGGAGGGATCATTA 1869 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.56 CpG sites = 45, Kimura (unadjusted) = 3.45 Transitions / transversions = 2.81 (45/16) Gap_init rate = 0.01 (13 / 1819), avg. gap size = 3.77 (49 / 13) 22 15.19 3.77 1.85 rnd-4_family-6163#Unknown 679 731 (445) (TCTA)n#Simple_repeat 1 54 (0) m_b13s252i0 rnd-4_family- 679 TCTATAGA-CTATCTTTTTATCTATCTATCTATTCTATCT-TCTATCACG 726 vv - v i - - vvv (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTA-TCTATCTATCTATCTAT 49 rnd-4_family- 727 CTATC 731 (TCTA)n#Simpl 50 CTATC 54 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 404 22.12 0.00 2.11 rnd-4_family-793#LINE/CR1 1 97 (47) CR1-11_Crp#LINE/CR1 1097 1191 (270) m_b13s551i2 rnd-4_family- 1 GTATAGCTTGGCCAAACGACGACTGAAGNAATGGATATGATAACNGTCTA 50 v i i v v i --? iv vi ?? CR1-11_Crp#LI 1097 GTTTAGCCTAGCAAAACGAAGGCTGA--GAGGGGATATGATTGCTNTCTA 1144 rnd-4_family- 51 CAAGTATTTGAAGGGTGTAAACACCAAGGAGGGAGAGGAATTATTTA 97 i i iv v i v i i ii CR1-11_Crp#LI 1145 TAAATACATCAGGGGGGTAAACACCAGGGAGGGAGAAGAGCTATTTA 1191 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.84 CpG sites = 13, Kimura (unadjusted) = 27.84 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2) 248 33.58 0.00 1.43 rnd-4_family-793#LINE/CR1 2 143 (1) X21_LINE#LINE/CR1 83 222 (62) m_b13s551i3 rnd-4_family- 2 TATAGCTTGGCCAAACGACGACTGAAGNAATGGATATGATAACNGTCTAC 51 ii i vv iv v i v i ?i-- i v ? i X21_LINE#LINE 83 TATAGTCTAGAAAAGAGAAGGCTCAGGGG--GGACATGATCACGGTCTAT 130 rnd-4_family- 52 AAGTATTTGAAGGGTGTAAACACCAAGGAGGGAGAGGAATTATTTAGNGT 101 i ii vv i ivv i iv v i ii i v? X21_LINE#LINE 131 AAATACCTTCAAGGTAACAATATAAATGAAGGAAGGGAATTATTCACAGT 180 rnd-4_family- 102 GGTACAAGGGGNTATAACTAGGAGTAATGGGATGAAATTAAG 143 vvi v iv ? vi v i vv ii X21_LINE#LINE 181 CTCAGAAGATGGTAGGACAAGGAGCAATGGCCTGAAGCTAAG 222 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.71 CpG sites = 26, Kimura (unadjusted) = 47.71 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.01 (2 / 141), avg. gap size = 1.00 (2 / 2) 794 10.00 0.83 0.83 rnd-4_family-87#DNA 10 130 (121) Eulor9C#DNA 8 128 (142) m_b13s502i5 rnd-4_family- 10 ATTAAATCACAGACAAN-ANATTAAAATAATGTTAAGAGTCTGACTTAAA 58 - i v ?-i?i ? i i Eulor9C#DNA 8 ATTAAAT-ACAAAAAACCGCGTTNAAATAACGTTAAGGGTCTGACTTAAA 56 rnd-4_family- 59 CCCGCAAAAGCAAGGAAATTCAGAGTTAAGGCTGAAACTCTATCCTTAAC 108 i ? v ii Eulor9C#DNA 57 CCCACAAAAGCNAGGAAATTCAGAGTTAAGGCTGACACTCCGTCCTTAAC 106 rnd-4_family- 109 TCACCCCATTGTGCCTGNGTAT 130 i i ? Eulor9C#DNA 107 TCACCCCGTCGTGCCTGGGTAT 128 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.91 CpG sites = 10, Kimura (unadjusted) = 11.50 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.02 (2 / 120), avg. gap size = 1.00 (2 / 2) 496 7.47 0.00 2.99 rnd-4_family-87#DNA 181 249 (2) C Eulor9C#DNA (143) 127 61 m_b13s502i6 rnd-4_family- 181 TACCTAGGCATAACGGGGTGAGTTAAGGACGGAGTTTCAGCCTNAACTCT 230 i ii v ? C Eulor9C#DNA 127 TACCCAGGCACGACGGGGTGAGTTAAGGACGGAGTGTCAGCCTTAACTCT 78 rnd-4_family- 231 GAATTTCCTTACCCTTTTG 249 ?i-- C Eulor9C#DNA 77 GAATTTCCTNG--CTTTTG 61 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.48 CpG sites = 4, Kimura (unadjusted) = 8.23 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 200 33.45 6.33 6.33 rnd-4_family-99#LINE/RTE-BovB 401 700 (176) MamRTE1#LINE/RTE-BovB 3109 3408 (404) m_b13s601i8 rnd-4_family- 401 TGTGGGACTGTCACGTCATNAAGCTTGCTACGGAGCTGTGGATCTACAGA 450 vi iiv ii v ? ivvv vi i ivi i MamRTE1#LINE/ 3109 TGTGGCGCCAACGTGGCATCAAGCTCCAGACCAAACTAAAGGTCTACAGA 3158 rnd-4_family- 451 ACCACGGTTACG-CCAACTCCGTTGTATGGCAGTGAAACATGGGC--GCT 497 i v ii iv?i - - ivi ? i v i v i -- i MamRTE1#LINE/ 3159 GCGATAGCGNTGTCCAAC-CTTCTNTACGGCTGTGAGACCTGGACCTGCC 3207 rnd-4_family- 498 GAGGAAGGCTGAAGAACA-CCGG---ATTGA-CGTTTTCGATTCTCGTTG 542 ivi v v ------ - ---v - iv - ivv ii MamRTE1#LINE/ 3208 ACAGACGTC------ACATCCGGCTTCTTGAGCAGTTTC-ATCAGCGTCA 3250 rnd-4_family- 543 TCTTCGTCAGC--TGCTCCATATCAAGTGGCAGGACAAGATCGGAAATGA 590 i v -- -- i iv i i i i i ivv ii MamRTE1#LINE/ 3251 CCTACG--AGCCATACTTAACATTAAATGGCAAGACAGGATCACCAACAA 3298 rnd-4_family- 591 GGATATTCGAAGCCGAACCCAGCAACCGCCTCCATCAGCACTGGNTCGGT 640 v vi i vi---- v -- v -- i i i?v i MamRTE1#LINE/ 3299 CGAGGTCCTG----GAACGCAGC--CAG--TCTACCAGCACTGAAGCGAT 3340 rnd-4_family- 641 -TTCG-------GCGGCTTTCTTGGTATGGACATATTATTAGAATGGAAG 682 -i ------- i iivi vv i vvvv v MamRTE1#LINE/ 3341 GCTCGCCGCAACGCAGCTCCGCTGGGCTGGACATGTGCGGAGAATGGATG 3390 rnd-4_family- 683 ACCAAC-GAATTCCGAAGC 700 - i - i v v MamRTE1#LINE/ 3391 A-CAGCAGGATACCCAAGC 3408 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.36 CpG sites = 54, Kimura (unadjusted) = 46.73 Transitions / transversions = 1.35 (54/40) Gap_init rate = 0.09 (28 / 299), avg. gap size = 1.36 (38 / 28) 808 25.98 0.37 3.42 rnd-4_family-1008#LINE/L2 4 274 (0) X24_LINE#LINE/L2 1 263 (51) m_b14s601i0 rnd-4_family- 4 GTGCTCTACGTGGGGCTACACCTTGA-GACCATTTGGAAACTGAAGNTAG 52 ?? vv i - - iii i vv ? i X24_LINE#LINE 1 GTGCTCNNCTGGGGGCTGC-CCTTGAAGACCACCCGGAAGCTTCAGCTGG 49 rnd-4_family- 53 TGCAGAATGGCAGCCACCTGCTTATTATAAGTGGAGTTTCGCGCTGGGAG 102 - vi ii ii ii i-- i? v ?vvv i v? X24_LINE#LINE 50 TGCAGAATG-CAGCGGCTCGTCTGCTG--AANGGTGTNAGCCACANGGAG 96 rnd-4_family- 103 CACATTACACCAGTGCCCGGGGATCTGCGCTGGCTGCCAGTAAGTTTCTG 152 v i v vii i i ?i vv i i X24_LINE#LINE 97 CACATTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCTTCCG 146 rnd-4_family- 153 GGTGGAATTCAAGGTGTTGGGTTTGACCTATAAAGTCCCAAGTGGTTCGG 202 i v iv i i i i vi i X24_LINE#LINE 147 AGTGCAATTCAAGGTGTTGACTTTAATCTATAAAGCCCTATATGGTTTGG 196 rnd-4_family- 203 GACCCGGTTACCTGAGAGACAACTGCCTCTCTCCCGTGCCGCCCTACCGC 252 v i v --- ii --v?i v iii i X24_LINE#LINE 197 GCCCTGGTTACCTTAGAG---ATCGCCTCTCTCCC--TNTGCACCGTCAC 241 rnd-4_family- 253 AGGAGNTGAGATCNGCAGAGAT 274 i v i? ? vii X24_LINE#LINE 242 GGCAATTGAGATCAGCTAGGAT 263 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.89 CpG sites = 44, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.83 (44/24) Gap_init rate = 0.04 (10 / 270), avg. gap size = 1.00 (10 / 10) 1083 12.50 7.34 0.53 rnd-4_family-1029#DNA/hAT-Ac 117 293 (70) UCON26#DNA/hAT-Ac 173 361 (37) m_b14s502i0 rnd-4_family- 117 GNAAGTGGGAGTAC-AAAATAGCACAAGAAAGGCTGTTCTCGCGGTATTT 165 ? i i i -i v i i UCON26#DNA/hA 173 GGAAGCGGAAGTGCCGAAATACCGCGAGAAAGGCTGTTCTCGCGGTATTT 222 rnd-4_family- 166 CCGGCCNGGNCCGGAANC-GGAAGTGCTAGAAATCTCACAAGAAAACCTG 214 ?- ? ? - i ii i i i UCON26#DNA/hA 223 CCGGCCC-GACCGGAAGCAGGAAGTACCGGAAATCTCGCGAGAAAGCCTG 271 rnd-4_family- 215 TTCTTGTGAGACTTCCAGCCCAGTTTTGCAGACTCNAGAGG--------- 255 i i i i i ? --------- UCON26#DNA/hA 272 TTCTCGCGAGATTTCCAGCCCAATTTTGCAGACCCAAGAGGTTCGGATAA 321 rnd-4_family- 256 --TTCGGATAAGCATCTGAACTTTGGGATGCTTNTCCAAA 293 -- i v i ? i UCON26#DNA/hA 322 GCTTCGGATAAGCATCCGAACTTTTGGGTGCTTATCCGAA 361 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.52 CpG sites = 20, Kimura (unadjusted) = 14.78 Transitions / transversions = 10.00 (20/2) Gap_init rate = 0.03 (5 / 176), avg. gap size = 2.80 (14 / 5) 272 20.75 0.00 0.00 rnd-4_family-1029#DNA/hAT-Ac 254 306 (57) C UCON26#DNA/hAT-Ac (35) 363 311 m_b14s502i1 rnd-4_family- 254 GGTTCGGATAAGCATCTGAACTTTGGGATGCTTNTCCAAAGCTTTCCAGA 303 i ii vv v ? i vi v C UCON26#DNA/hA 363 GGTTCGGATAAGCACCCAAAAGTTCGGATGCTTATCCGAAGCTTATCCGA 314 rnd-4_family- 304 GCC 306 i C UCON26#DNA/hA 313 ACC 311 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 6, Kimura (unadjusted) = 25.13 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 1145 10.07 0.00 2.37 rnd-4_family-1053#LTR 17 189 (0) UCON51#LTR 74 242 (8) m_b14s502i2 rnd-4_family- 17 TGGATTTGCTGCTTGTGTGCATCCTGCGCATTACCGCAGCTGAGACTCGA 66 i i -- i i i i UCON51#LTR 74 TGGACTCGCTG--TGTGTGCGTCCTGCACATTACCGCAGCCGAGGCTCGA 121 rnd-4_family- 67 ACCGGGACCCTCGTGGNCTGCAGGCAGCAGCTCTACCAGGTGAGCCAAAA 116 ? i ? ? i? i UCON51#LTR 122 ACCGGGNCCCTTGNGGTCCNCGGGCAGCAGCTCTACCAGGTGAGCCAAAA 171 rnd-4_family- 117 GGGAGCCCTCCCCTCGGCTGAGCCAGTAAGAGCTGTGCNNAGCTNTGTCT 166 - ii i i i i ?? ?- UCON51#LTR 172 GGGAG-CCTCCCCCTGGCCGAGCCGGTAGGAGCTGCGCTAAGCTC-GTCT 219 rnd-4_family- 167 CAGCTGGAAGTTGCTCTTTGCAT 189 i i UCON51#LTR 220 CAGCTGGAAGTCGCTCTTCGCAT 242 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.82 CpG sites = 17, Kimura (unadjusted) = 11.78 Transitions / transversions = 1.00 (17/0) Gap_init rate = 0.02 (4 / 172), avg. gap size = 1.00 (4 / 4) 847 28.99 0.32 0.32 rnd-4_family-1385#LTR/Gypsy 279 586 (1678) MamGyp-int#LTR/Gypsy 637 944 (4158) m_b14s551i0 rnd-4_family- 279 GGGGCAGAGGAGTTCGAACCCTGGTTGGAGCATACCACTGAAATGCTGCA 328 v v? i i i ? i i MamGyp-int#LT 637 GGGGAAGAGGCNTTTGAACCCTGGCTGGGGCANACTACTGAGATGCTGCA 686 rnd-4_family- 329 GGAGTGGGCCGTACCTGATGCAGAAAAGCGAAGATGTCTAATAGAGAGCC 378 i vvv v v ? i iv v iv v i i i? MamGyp-int#LT 687 AGAGTGGCAGGTACCAGAGGCNGAGAAAAGACGGAGGCTGATGGAANGCC 736 rnd-4_family- 379 TTAGTGGCCCAGCATTAGATGTGATTCGCACCCTGAAGCTCATTGACCCT 428 ? v v v v v iii v viv vii v MamGyp-int#LT 737 TNAGAGGCCCAGCCTTTGAGGTCATTCGTGTCCTCAAGGCGAACAACGCT 786 rnd-4_family- 429 GGGGTCAGTGTGAAGGACTGCCTGGAGGCCCTCGATCATACCTTTGGGAG 478 vv v v ivv v ii i i ? v vi v ?i MamGyp-int#LT 787 TCGGTGACTGTGGCCGAATGCCTGAGGACTCTNGAGCAGGCGTTTGGGNA 836 rnd-4_family- 479 TGTAGAGGGCCCTGAAGACAGTTACTGT-AAGTTCCTTAATTCCCGACAG 527 i ? i v?- i i v vvvv - ? i v iv iiiv MamGyp-int#LT 837 CGTNGAGAGCCGN-AGGGCTGTGCAGGTCAANTTTCTGAACACTTACCAG 885 rnd-4_family- 528 CAAATTGGCGAGAAGATTTCAGCCTATATACAGAGGCTGGAGAGACTGCT 577 v iii? v i i v v i i ? v vv ? MamGyp-int#LT 886 AAGGCNGGAGAAAAGGTGTCTGCTTATGTNCTGAGGCTGGAGACTCTGNT 935 rnd-4_family- 578 TCAGAGAGC 586 ? i MamGyp-int#LT 936 NCAGAGGGC 944 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.20 CpG sites = 42, Kimura (unadjusted) = 39.30 Transitions / transversions = 0.89 (42/47) Gap_init rate = 0.01 (2 / 307), avg. gap size = 1.00 (2 / 2) 1050 30.44 0.45 0.91 rnd-4_family-1385#LTR/Gypsy 1213 1653 (611) MamGyp-int#LTR/Gypsy 1525 1963 (3139) m_b14s551i1 rnd-4_family- 1213 TCCCCGCAGGACTGATAGGGCCTCGAGCAGAGGTCATGGTGAAGATTGAA 1262 i - i?ii ?? -ii viii i ?v MamGyp-int#LT 1525 TCTCC-CAGGACTANCGGGGCCNNGA-TGGAGGTGGCAGCGAAGANAGAA 1572 rnd-4_family- 1263 GGGGAGGAGTGTAAAGCCGTGCTTGACACTGGATCTCAAGTGACCATTAT 1312 ivvvi ? ivv iv ? v i v i v i vi MamGyp-int#LT 1573 GGGATTTGGNGCTCAGTGGTNCTGGATAGTGGGTCACAAGCGACCATAGT 1622 rnd-4_family- 1313 ATTTCAGTCATTCTACCAACAAATGCTT-AGGCACCTGCCTATACAGCCA 1361 ? ?v i-i ii i - v i v vv iv? MamGyp-int#LT 1623 NTTNAAGTCATTCTAT-GACAAACACCTGAGCCATCTCCCATTACAAANA 1671 rnd-4_family- 1362 CTGACTGGCGTTGGTCTGTGTGGCCTCAGCATGGATGAATACCCCTACCA 1411 i ? vv v ? ? i v i i? v vv ? ? v MamGyp-int#LT 1672 TTGANTGGACTGGGNCTNTGTGGCTTGAGTACNGAAGTCTNCCCNTACCT 1721 rnd-4_family- 1412 AGGGTATGTCATAGTGCACCTGGAATTCCCAGAGGAGGTTGCTGGGGTAA 1461 ? v v vi ?viv i v i i v iv v MamGyp-int#LT 1722 NGGTTATGTGATTATNAGGCTGGAATTTCCTGAAGGGGTGGTGGGGGTCA 1771 rnd-4_family- 1462 GAGAAGAGGTGGACACAGCTGCATTAATATGCCCTGACCCTAAAGGGACC 1511 ? i v i iv viii v vii viiv MamGyp-int#LT 1772 GNGAGGAGGTGGACACTGCCGCGGTTGCGTGCCCGGACCCGGGAGGCGTG 1821 rnd-4_family- 1512 TCTGATGTGTCTGTGCTGATAGGGACCAACTCCAGTCTCTTCAAGGTGCT 1561 ivv iv vi? ii ? ? ii ? i i MamGyp-int#LT 1822 CAGGGAGTGGTNGCACTGATNGGGACNAACTCCAACCTNTTTAAAGTGCT 1871 rnd-4_family- 1562 CGCGGATTACTGCAGACGACGGGCTGGGGAC-CAGTACCTGAATACCCTG 1610 v vviv iv i ii iv - i v -v ii iii v MamGyp-int#LT 1872 AGCCCGGTACTGTCGGCAGCATG-TAGGCACAGAGTACCTAGATGTTCTT 1920 rnd-4_family- 1611 ATGATCCATACGCTTTGTGCTGAAGCCTATAGGAAGATTGAGG 1653 viv i iiiv v ? ? i i v MamGyp-int#LT 1921 CCTATTCACGTCCTGTGTGCNGANGCCTACAAGAAGATGGAGG 1963 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.22 CpG sites = 73, Kimura (unadjusted) = 43.12 Transitions / transversions = 1.22 (73/60) Gap_init rate = 0.01 (6 / 440), avg. gap size = 1.00 (6 / 6) 787 29.25 0.00 0.00 rnd-4_family-1385#LTR/Gypsy 2008 2260 (4) MamGyp-int#LTR/Gypsy 2027 2279 (2823) m_b14s551i2 rnd-4_family- 2008 TAGACCCTGCAAAGTTTGACTTTGGAGATTCACCGTTGTCCGAGGAGTGG 2057 i i ? vi iv i i i i v iv ii MamGyp-int#LT 2027 TAAATCCNGAGAGCTTTGATTTCGGGGACTCCCCAGTACCCGAGGAGTGG 2076 rnd-4_family- 2058 AAAGATCGCCTGAGGAGGAAACTTTGTGAAAGATCCAAGGTGTTCTCATT 2107 i vv v i iiiv vv ivvi ? v vi MamGyp-int#LT 2077 AAGGAGAGACTGAGAAGGAAACTCCAAGCCAGGAGTAANGTTTTCTCTCT 2126 rnd-4_family- 2108 GCATGAGTGGGATGTGGGATGTGCAAAAGGAGTAGAGCACAACATCAGAC 2157 v i i v vv i ? viv i v viii MamGyp-int#LT 2127 CCATGAATGGGACGTGGGCTGTGCTCAGGGNGAGCAGCATAAAATAGAGC 2176 rnd-4_family- 2158 TACATGACTCTCGACCTTTCAGGGAGAGATCTAGGAGGATTGCCCTCTCC 2207 i? ? i i iv ? i i v i MamGyp-int#LT 2177 TGNANGACCCTCGACCTTTTAGGGAACGNTCTAGAAGGATTGCTCTGTCT 2226 rnd-4_family- 2208 GAGATGGAAGATGTGCGACAACATCTTCAGGAGCTGGCTGCGAATGGCAT 2257 vi v v iv v ? v v i ?viviiv MamGyp-int#LT 2227 GAGATCAATGATTTAAGAGANCATATTAAAGAGCTNCTAATTAATGGCAT 2276 rnd-4_family- 2258 CAT 2260 ? MamGyp-int#LT 2277 NAT 2279 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.28 CpG sites = 40, Kimura (unadjusted) = 39.65 Transitions / transversions = 1.18 (40/34) Gap_init rate = 0.00 (0 / 252), avg. gap size = 0.0 (0 / 0) 15 8.91 4.17 0.00 rnd-4_family-1499#Unknown 573 596 (394) (GT)n#Simple_repeat 1 25 (0) m_b14s252i10 rnd-4_family- 573 GTGTGTGTGTGTGTGT-TGATTGTG 596 - vv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTG 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 747 17.13 2.17 1.62 rnd-4_family-1561#DNA 4 187 (0) UCON78#DNA 246 430 (13) m_b14s502i3 rnd-4_family- 4 GCATTATGACTTCACTGCAGGATCAAGTAGGANGGGANAGGAGGNTGGGA 53 i ? i ?iivi ? v UCON78#DNA 246 GCATTATGACTTCACTGCAGGATCAAGCAGGAGGAGAAGATGGGCTGTGA 295 rnd-4_family- 54 CC-AGGAAGCCCTTGTTTAAACACAAACGTCTTTGATAATTAGCAAAAGT 102 vv- i ii i ? UCON78#DNA 296 GGGAGAAAGCCCTTGTTTAAACACAAATATCTTCGATAATTAGCAAANGT 345 rnd-4_family- 103 GGCAATGAGGAAACATG-ATTCCAAGTGANAAG-GGATAAA-TTNNNTTT 149 - ii vi - vvv v ? i -ii ii - ??? UCON78#DNA 346 GGCAA-GAAAAATTATGAAAAACACGTGAAAGGTAAATGGATTTATGTTT 394 rnd-4_family- 150 AAANGTGTTACGTATNTNAAAGTTTTCCCCTTTNTGAA 187 i?v -- i? ? ? vv ? UCON78#DNA 395 AAGTCTG--ATNTATTTGAAAGTTTTCCCCGGTGTGAA 430 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.76 CpG sites = 19, Kimura (unadjusted) = 21.52 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.04 (7 / 183), avg. gap size = 1.00 (7 / 7) 318 19.06 8.63 5.59 rnd-4_family-2017#DNA 1 139 (289) Eulor9A#DNA 32 174 (127) m_b14s502i4 rnd-4_family- 1 ACGTTAAGGTTGCACAGTTAAAANTTCACAAAAGTCAGGAAATGCAAAAA 50 v i viv v v?-- v - i Eulor9A#DNA 32 ACGTTATGGCTGAGAATTTAAACG--CACAAAAGTCAGGAAATTC-AAAG 78 rnd-4_family- 51 TTA--GTTCCAACAGCAGCGTTAACTCNG-----TTGC-----GTCGTAC 88 -- v i vv ? ----- ----- ?v i Eulor9A#DNA 79 TTACGGTTCCCACAGCAACCGTAACTCGGCCCCCTTGCGCATAGNAGTAT 128 rnd-4_family- 89 TTTATATTCCTGTTTTCTTTTTGTTAAATATGTANCNTCTTAATATTATT 138 i v v --v v? v i ---?i i v Eulor9A#DNA 129 TTTGTATTACTGTAT--ATGNTGTTAAATTTAT---GCCTTAATATCAGT 173 rnd-4_family- 139 A 139 Eulor9A#DNA 174 A 174 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.05 CpG sites = 9, Kimura (unadjusted) = 23.05 Transitions / transversions = 0.56 (9/16) Gap_init rate = 0.08 (11 / 138), avg. gap size = 1.82 (20 / 11) 603 12.47 2.87 7.83 rnd-4_family-2017#DNA 135 308 (120) Eulor9A#DNA 133 298 (3) m_b14s502i5 rnd-4_family- 135 TATTACTGTTTATACGTCGTTAAACGCTATACCATAAAACATACAGGANN 184 -- i ?i i-i i v --i - ---? Eulor9A#DNA 133 TATTACTGT--ATATGNTGTTAAAT-TTATGCCTTAA--TAT-CAG---T 173 rnd-4_family- 185 ATGATGCAATGTGGCAGAGTTAGCGTTGCTGCTGGAACC-TAACTTTTGC 233 - v vv iv - - v Eulor9A#DNA 174 ATG-TGCAATGTGGCCGAGTTACGGTTGCTGTGGGAACCGTAAC-TTTGA 221 rnd-4_family- 234 ATTTCCTGGACTTTTGTGATTTTTAACTGTGCAACCTTAACGTTGCATTA 283 - vv v v v - v Eulor9A#DNA 222 ATTTCCT-GACTTTTGTGCGTTTAAAATCT-CAACCGTAACGTTGCATTA 269 rnd-4_family- 284 ACGTA---NTTTTTGCA-TTTAATTTCCT 308 ---? - v Eulor9A#DNA 270 ACGTAGGNTTTTTTGCATTTTACTTTCCT 298 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.86 CpG sites = 7, Kimura (unadjusted) = 13.86 Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.09 (16 / 173), avg. gap size = 1.12 (18 / 16) 252 28.79 0.00 0.00 rnd-4_family-2017#DNA 362 427 (1) C UCON69#DNA/hAT (187) 299 234 m_b14s502i6 rnd-4_family- 362 TTAATGATGTTAGCATTTAAATTGTCCCGATTAGNCTTTGAAGTTCACAA 411 ii ii viv ? iii v v C UCON69#DNA/hA 299 TTAACAATGTTGACATTTAAATTGTCATCATTAGGCTTCAGAGTTAACAC 250 rnd-4_family- 412 TTTGTTGAGGCGAGTG 427 iiii ii i C UCON69#DNA/hA 249 CCCATTGAGATGAATG 234 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 15, Kimura (unadjusted) = 40.30 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 1672 11.06 0.00 1.58 rnd-4_family-2136#LINE/CR1 46 302 (498) CR1-L3A_Croc#LINE/CR1 587 839 (3449) m_b14s551i3 rnd-4_family- 46 CACCAGACAGAAGAGGACCAGGAGGAATTCCACACAGCTAGAAGTTTCGA 95 v v v CR1-L3A_Croc# 587 CACCAGAGAGAAGAGGACCAGGAGGAATTCCACACAGCTAGAAGTATCCA 636 rnd-4_family- 96 ATCGCATCGCGAGGTTCTCAGTGTNNAAACTGTGGAAGATATCTCTTAAG 145 -- ii v i ?? ii i v CR1-L3A_Croc# 637 ATCG--TTACCAGGTTCTCAGCGTGGAAACTGCAGAAAATATCTCTGAAG 684 rnd-4_family- 146 ATCCAGCTGGTCCAAGGGAACAGAGAGATGTATGGGACACACNTGTGGAT 195 v v i v i i ? CR1-L3A_Croc# 685 ATCCAGCTGGTCGAATGGAACGGAGAGCTGTACGGGACATACCTGTGGAT 734 rnd-4_family- 196 GGCAGCTCGGCCCAACCTGTAAGAAAAATCAAGCTTGCCCACAAAGAGAT 245 v i i i - vi v CR1-L3A_Croc# 735 GGCTGCTCAGCCCAACCCGCAAG-ACGATCAAGCGTGCCCACAAAGAGAT 783 rnd-4_family- 246 CTCCAACCGTCCAAGGAAGACAGACGATCCTTGTTGGGGATTCAATACTC 295 i i v - CR1-L3A_Croc# 784 CTCCAACCATCCAAGGAAGACAGACGATCCTTGTCGGGGATTCTATACT- 832 rnd-4_family- 296 AAGAGGA 302 i CR1-L3A_Croc# 833 AAGAAGA 839 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.65 CpG sites = 16, Kimura (unadjusted) = 12.20 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.02 (4 / 256), avg. gap size = 1.00 (4 / 4) 3233 9.09 9.68 0.00 rnd-4_family-2136#LINE/CR1 295 800 (0) CR1-L3A_Croc#LINE/CR1 872 1426 (2862) m_b14s551i4 rnd-4_family- 295 CAAGAGGACAGTGTGCTGTCTTCCCGGAGCCAAGACATGAGATGTCACTC 344 v i i iv CR1-L3A_Croc# 872 CAACAGGACGGTGTGCTGTCTTCCCGGAGCCAAGACACGAGATGCGACTC 921 rnd-4_family- 345 TAAGATGGGA-AGCCTTCTGAAGTCCGTAGGTAAGGATCCACTGGTGNTG 393 iv - v v ii i ? CR1-L3A_Croc# 922 TAAGACTGGATAGGCTTCTGAAGTCGGCGGGCAAGGATCCACTGGTGATG 971 rnd-4_family- 394 GTNCANACTGGCACTAGTGACACTGCGTCACGGGATATCTCACANACNGT 443 ? ? ii i v i ? i ? i?i CR1-L3A_Croc# 972 GTGCATATCGGCACTAATGACACTGCTTCGCGNGATACCTCACAGATTAT 1021 rnd-4_family- 444 AGACGACTTCANGGAACGCAGAAGNGTGCTGAAGAANAANAATGCCCAAG 493 ? v i ? i ? ? i CR1-L3A_Croc# 1022 AGACGACTTCAGGGAACTCGGAAGGGTGCTGAAGGAGAAGAATGTCCAAG 1071 rnd-4_family- 494 CGATCTTCTCGGAGATCCTTCCTGTCCCGCGAGCGAAGGAAGAT-GAAGG 542 i i i- CR1-L3A_Croc# 1072 TGATCTTCTCGGAGATCCTTCCTGTCCCACGAGCGAAGGAAGACAGAAGG 1121 rnd-4_family- 543 -AGAAGATTCTGGAAGTGAACCGCTGGCTAGGTAAGTGGTGT-------A 584 - ------- CR1-L3A_Croc# 1122 CAGAAGATTCTGGAAGTGAACCGCTGGCTAGGTAAGTGGTGTAAGGTAGA 1171 rnd-4_family- 585 GGGTTTTGGTTTTGTGGAACATTGGTCCACCTTCTATAGGGAGAGGGGGC 634 i i i CR1-L3A_Croc# 1172 GGGTTTTGGTTTTGTGGAACACTGGTCCACCTTCTATGGGGAGAAGGGGC 1221 rnd-4_family- 635 TGTATAGTTTGGATGGCTTCCATCTCAGTAGAAGGGGGACCAATCTCCTC 684 i i i i i v CR1-L3A_Croc# 1222 TGTACAGTTTGGATGGCCTCCATCTCAGTAGAAGGGGAACCAGTCTTCTA 1271 rnd-4_family- 685 GGGGACAGGCTGGCTAGAGTAGTCAGGAGGGCGTTAAGCNAATAGCAAAA 734 v i ? i i CR1-L3A_Croc# 1272 GGGGACAGGCTGGCTAGACTAGTCAGGAGGGCGTTAAACTAACAACAAAA 1321 rnd-4_family- 735 --AGGGA-------AGGTAA--AAATG--------CTNAGAACAA----- 760 -- ------- v -- --------i ? v ----- CR1-L3A_Croc# 1322 GGAGGGAGTGAAAGAGGGAAACAAATGAGCACTCATTTAGCACAAAATCA 1371 rnd-4_family- 761 ---------------AATTAANCAAGGAACCAAAGGACATGAAGAGAAGA 795 --------------- ? v i i CR1-L3A_Croc# 1372 AGATGTCGAGAACAAAATTAATCAAGGCACCAAGGGACGTGAAGAGAAGA 1421 rnd-4_family- 796 AATTC 800 CR1-L3A_Croc# 1422 AATTC 1426 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.36 CpG sites = 34, Kimura (unadjusted) = 10.10 Transitions / transversions = 2.83 (34/12) Gap_init rate = 0.02 (9 / 505), avg. gap size = 5.44 (49 / 9) 311 30.11 4.15 3.44 rnd-4_family-2721#LINE/L2 55 343 (334) UCON86#LINE/L2 13 303 (379) m_b14s502i7 rnd-4_family- 55 TTATCCACGCCTTTGTTACTTCCAGACCGGATTACTGTAATGCGCT-CTG 103 i ? ii iv i iv v iv i i i ?iv v - v UCON86#LINE/L 13 TCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGCANCTCCCTTCTC 62 rnd-4_family- 104 TATGGGGCTACCNCTCAAAA--CCA-CTCGGAAG-CTNCAGCTAGTACAG 149 ----- ? i v i-- - vvv - ? vv i UCON86#LINE/L 63 TATGG-----CCTCCCCAAGTCCCAGCTCTCCAGACTCCAGCACGTGCAG 107 rnd-4_family- 150 AATGCGGCTGCCCGCTTNCTTAGTGGTGCTTNTGGCATGGACGTATNCTN 199 v i ? i v--ii vi?vi v - vi vvi? v? UCON86#LINE/L 108 AATGCTGCTGCCCGCCTTCTCAC--ACGCACAAAGAA-GTGCGACCACAT 154 rnd-4_family- 200 NACACCTGTGCTCCGCAGACTGCACTGGCTTCCNGTTCGTTTCTGGGTGC 249 ? v ii v vivvi v i ?i i v i v UCON86#LINE/L 155 CACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAGGATCC 204 rnd-4_family- 250 AGTTCAAGG-TGTTGATTTTGATCTATAAAGCCCTNNATGG-TTTGNGTC 297 ii- iivvii - i v i ?? -i ?- UCON86#LINE/L 205 AGTTCAAAATTGCCCTCCTTG-TTTTTAAAACCCTCCATGGACTTGC-TC 252 rnd-4_family- 298 TTGGCTACCTTAGANAAC----CTCNCTTTTCTCCCCT-CGTGCTCCANC 342 iv v i vi? v ---- ? i v - vi v? UCON86#LINE/L 253 CAGCCTACCTCACGGACCTTGTCTCTCTCTGCTCCCCTCCCCGCTCCCTC 302 rnd-4_family- 343 C 343 UCON86#LINE/L 303 C 303 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.45 CpG sites = 44, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.10 (44/40) Gap_init rate = 0.06 (18 / 288), avg. gap size = 1.22 (22 / 18) 13 7.81 0.00 10.00 rnd-4_family-3902#Unknown 75 107 (206) (CGCC)n#Simple_repeat 1 30 (0) m_b14s252i9 rnd-4_family- 75 CGCCCCCGCGCCCCGACCCGCTCCGCCCGCCCG 107 v v - - - (CGCC)n#Simpl 1 CGCCCGCCCG-CCCG-CCCGC-CCGCCCGCCCG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 14 4.70 0.00 4.35 rnd-4_family-4011#Unknown 118 141 (257) (GCA)n#Simple_repeat 1 23 (0) m_b14s252i8 rnd-4_family- 118 GCAGCAGCAGACAGCAGGAGCAGC 141 - v (GCA)n#Simple 1 GCAGCAGCAG-CAGCAGCAGCAGC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 435 25.41 3.76 2.66 rnd-4_family-408#Unknown 173 358 (118) UCON60#Unknown 99 286 (14) m_b14s502i8 rnd-4_family- 173 ACTTTC--TCCTCAGCGAGGGCTATTTCCGTGCCAAATTTCAGCTTTCTG 220 i -- ?i i ivvi v i v iv v i UCON60#Unknow 99 ATTTTCCTTCCTCANTGAGGACTACAATCCTGCCAAGTTTGAAGTTTATA 148 rnd-4_family- 221 CCCCCAGCTATTTC--GGCTGTA-GAGCGTTCAANGAAAGGTCGCAAGAN 267 v ii ii i--i i i - ii-v ?i vi iv i v ? UCON60#Unknow 149 GCTTCAGCCGTTTTTGAGTTATACGAGCAC-AAAAAAAACATTTCGATAT 197 rnd-4_family- 268 TTTTTANAA-TGGGAAAGTATGTACTTTCTTTACTCTCTCTCATN-CTTA 315 ? - i -- i ii i - - v ?- i UCON60#Unknow 198 TTTTTAGAANTGGAAAAGT--GTATTTCTTCTA-TC-CTCGCATAACTCA 243 rnd-4_family- 316 AAAATGTCTGAANCGTTTTTNCTCAAACTTCCCAAAAAAATTC 358 i v ? v ?? i v i UCON60#Unknow 244 AAAACGGCTGAACCGATTTNGCTCAAACTTTCAAAAGAAATTC 286 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 31, Kimura (unadjusted) = 34.21 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.05 (10 / 185), avg. gap size = 1.20 (12 / 10) 233 21.25 3.61 3.61 rnd-4_family-408#Unknown 394 476 (0) C MER131#DNA (129) 86 4 m_b14s601i1 rnd-4_family- 394 AGTTACGAGCGACTGAAA-TAGGGGCTNAGAATGGAAACCCGTGGAC--A 440 ii i vv - i ? v -- iv -- C MER131#DNA 86 AGTTATAAACCCCTGAAAATAGGGGTTTATAATGGAAA--CGCTGACAGA 39 rnd-4_family- 441 NCCTTNACTATAGCTGTCACTANTGCTTTCGCTATA 476 ? - v i v ?i vivi C MER131#DNA 38 NCCTTAACTATAGC-GGCGCGAACGGCGCCGCTATA 4 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.72 CpG sites = 9, Kimura (unadjusted) = 26.85 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.06 (5 / 82), avg. gap size = 1.20 (6 / 5) 13 21.81 2.70 0.00 rnd-4_family-449#DNA/Academ-1 1888 1924 (357) (GAT)n#Simple_repeat 1 38 (0) m_b14s252i7 rnd-4_family- 1888 GATCATAATGA-GAACAAGATGATGATAATGATGTTGA 1924 v i - vv v i v (GAT)n#Simple 1 GATGATGATGATGATGATGATGATGATGATGATGATGA 38 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 180 23.81 0.00 0.00 rnd-4_family-4663#LINE/RTE-BovB 1044 1085 (73) MamRTE1#LINE/RTE-BovB 3702 3743 (69) m_b14s601i2 rnd-4_family- 1044 TGTGGCAAGGACTGTCGCTCGAGAATTGGACTTTTTAGCTAC 1085 v i v iv v i v i i MamRTE1#LINE/ 3702 TGTGGAAAGGACTGTTGGTCACGCATCGGTCTTTTCAGCCAC 3743 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.66 CpG sites = 5, Kimura (unadjusted) = 28.89 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 21 16.37 0.00 6.78 rnd-4_family-4716#Unknown 41 103 (138) (CCCCGC)n#Simple_repeat 1 59 (0) m_b14s252i6 rnd-4_family- 41 CCCCGCCCCCTCCGCCCGCGCCCCTGCCCCGAGGCCCCGCCCCTGNACCG 90 v - - - -v v i ?v v (CCCCGC)n#Sim 1 CCCCGCCCCCGCC-CCCGC-CCCC-GCCCC-CGCCCCCGCCCCCGCCCCC 46 rnd-4_family- 91 GGCCCCACCCCCG 103 v i (CCCCGC)n#Sim 47 GCCCCCGCCCCCG 59 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 16 5.00 8.51 6.25 rnd-4_family-4926#Unknown 28 74 (476) (TCCCGC)n#Simple_repeat 1 48 (0) m_b14s252i5 rnd-4_family- 28 TCCCGCTCCCG-TCCCGC-CCCGCAATACCCACT-CC-CACCCGCTCCCG 73 - - -- - i - - v (TCCCGC)n#Sim 1 TCCCGCTCCCGCTCCCGCTCCCGC--T-CCCGCTCCCGCTCCCGCTCCCG 47 rnd-4_family- 74 C 74 (TCCCGC)n#Sim 48 C 48 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.15 (7 / 46), avg. gap size = 1.00 (7 / 7) 14 7.79 3.45 3.45 rnd-4_family-6193#LINE/RTE-BovB 2983 3011 (157) (GAA)n#Simple_repeat 1 29 (0) m_b14s252i3 rnd-4_family- 2983 GAAG-AGAAGAAGAGGTAGACAGAAGAAGA 3011 - i v - (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGA-AGAAGAAGA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 13 0.00 0.00 0.00 rnd-4_family-6193#LINE/RTE-BovB 3152 3168 (0) (TGA)n#Simple_repeat 1 17 (0) m_b14s252i4 rnd-4_family- 3152 TGATGATGATGATGATG 3168 (TGA)n#Simple 1 TGATGATGATGATGATG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 282 20.36 1.94 14.13 rnd-4_family-6208#DNA/hAT-Blackjack 1 103 (497) BLACKJACK#DNA/hAT-Blackjack 1 92 (2877) m_b14s502i9 rnd-4_family- 1 TAGGGTGACCACCCGTCCCTAATTGGGCGGGACAGTCCCGAAATGTACAT 50 iv viv vv --i v ii BLACKJACK#DNA 1 TAGGGTGACCATACGTCCCGGTTTGCCCGGGACAGTCCCG--GTTTACGC 48 rnd-4_family- 51 TTCAAGTCCCG--GTCCCGGGCTGAATGACTCCGGGACAGCATTTGTCCC 98 i vvv -- ----------- vvi BLACKJACK#DNA 49 CTGTTGTCCCGGCGTCCCG-----------TCCGGTTTAGCATTTGTCCC 87 rnd-4_family- 99 GGATT 103 BLACKJACK#DNA 88 GGATT 92 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.91 CpG sites = 7, Kimura (unadjusted) = 23.28 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.14 (14 / 102), avg. gap size = 1.07 (15 / 14) 25 25.16 2.17 4.44 rnd-4_family-734#LTR/Gypsy 391 482 (1492) (AG)n#Simple_repeat 1 90 (0) m_b14s252i2 rnd-4_family- 391 AGAGTTAGAAAGAGAGAGAGAGAAAGAGGCTGCTGAGAGAGAGAAAGA-A 439 vv i i ivv -v i - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGA 49 rnd-4_family- 440 GCTGATCAAAGAAAGAAGGAGGCTGATGAGAGAGA-AGAGAGAG 482 -v -v i i ii ivv - - (AG)n#Simple_ 50 G-AGA-GAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAG 90 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.00 (6 / 6) 773 7.48 0.67 10.29 rnd-4_family-86#DNA 1 149 (42) MER131#DNA 2 137 (78) m_b14s601i3 rnd-4_family- 1 ATTATAGCGGCGCCCGCTAGCACCGNTGTAGTTAAGGGTCTGTCAGTGTT 50 - i v i ? i ? i MER131#DNA 2 ATTATAGCGGCGCC-GTTCGCGCCGCTATAGTTAAGGNTCTGTCAGCGTT 50 rnd-4_family- 51 TCCATTATAAACCCCNNTTC-CAGGGGTTTCTATTTCAGTTTATAACTCA 99 ?? i- ------------ i MER131#DNA 51 TCCATTATAAACCCCTATTTTCAGGGGTTT------------ATAACTCG 88 rnd-4_family- 100 GCCGTAAAAATTTGCTCCGGGCTGAAACTTGGCATAGANGGCACTCAGCC 149 i v ? i- MER131#DNA 89 GCCGTAAAAATTCGCTCCGGGCTGAAACTTGGCATACAAGGT-CTCAGCC 137 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 5.12 CpG sites = 8, Kimura (unadjusted) = 8.23 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.10 (15 / 148), avg. gap size = 1.00 (15 / 15) 17 13.72 0.00 0.00 rnd-4_family-9989#DNA/hAT 192 223 (278) (CCCCG)n#Simple_repeat 1 32 (0) m_b14s252i0 rnd-4_family- 192 CCCGGCCCCAGCCCGCCCCGCTCCGCCCCGCC 223 v iv i (CCCCG)n#Simp 1 CCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCC 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 33 18.25 2.13 4.35 rnd-4_family-9989#DNA/hAT 267 360 (141) (GGCGG)n#Simple_repeat 1 92 (0) m_b14s252i1 rnd-4_family- 267 GGCGGGGAGGGGCGGGGGCTTGG-GGGAAGGGGTGGAATGGGGGCGGGGC 315 v - vv - iv i -ivv (GGCGG)n#Simp 1 GGCGGGGCGGGGC-GGGGCGGGGCGGGGCGGGGCGG-GGCGGGGCGGGGC 48 rnd-4_family- 316 AGGGGGCGGAGCGGGAAGGGGCGGGGCGGGG-GGAGCGGGGCCGGG 360 -- i iv - i v (GGCGG)n#Simp 49 --GGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGG 92 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.06 (6 / 93), avg. gap size = 1.00 (6 / 6) 1717 4.49 4.60 11.07 rnd-5_family-274#LINE/CR1 18 343 (148) CR1-16_AMi#LINE/CR1 537 843 (8) m_b14s551i5 rnd-5_family- 18 TTAATGATCTGGAAGAGGGAGTAAACAGCACGTTAATGAAATTCGCAGAT 67 CR1-16_AMi#LI 537 TTAATGATCTGGAAGAGGGAGTAAACAGCACGTTAATGAAATTCGCAGAT 586 rnd-5_family- 68 GATACTAAATTGGGAGGAGTTGCGAACACCAGTGAGG-------AATAAT 110 i ------- CR1-16_AMi#LI 587 GATACTAAATTGGGAGGAGTTGCAAACACCAGTGAGGACAGAGAAATAAT 636 rnd-5_family- 111 ACAAAGGGACCTAGAGAGATTAGAAACATGGGCAGAAAATAAACAAAA-G 159 -------- i - - CR1-16_AMi#LI 637 ACAAAGGGACCTAGAGAGATTAGAA--------AGGAAAT-AACAAAATG 677 rnd-5_family- 160 AGATCANCTTGGAAAAATGCAAGCTAATA--CATCTGGGGGAAAATAATC 207 i ? - -- - i ------- CR1-16_AMi#LI 678 AGATTAACTTGGAAAAATGC-AGCTAATATTCA-CTGGGGAAA------- 718 rnd-5_family- 208 CGAAACACAGATATTCAATGGGAGGGGAAACCTGGAAAGCAGTAATGCTA 257 ------------ i i i ? v? CR1-16_AMi#LI 719 ------------ATCCAATGGAAGAGGAAACNTGGAAAGCAGTAATGANA 756 rnd-5_family- 258 GAGAACCTATAGG-GAGAG----CAGCAAATTAGACATGAGTTTGCAATG 302 - ?v - v ---- i - CR1-16_AMi#LI 757 GAG-ACCTNGAGGCGATAGCGGACAGCAAATTAGATATGAG-TTGCAATG 804 rnd-5_family- 303 CGATATGGCAGCAAAAAAGGCCAATGCAATTTTGGGCTGCA 343 i -- i CR1-16_AMi#LI 805 TGATATGGCAGC--AAAAGGCCAGTGCAATTTTGGGCTGCA 843 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.69 CpG sites = 10, Kimura (unadjusted) = 4.69 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.12 (39 / 325), avg. gap size = 1.26 (49 / 39) 816 27.35 9.89 4.07 rnd-5_family-274#LINE/CR1 18 482 (9) CR1-3_Croc#LINE/CR1 2158 2648 (957) m_b14s551i6 rnd-5_family- 18 TTAATGATCTGGAAGAGGGAGTAAACAGCACGTTAATGAAATTCGCAGAT 67 i v vv vi i v viv i vv i i i CR1-3_Croc#LI 2158 TTAATGATTTGGATGCTGGCATAGAAAGCTTCTTGAGCAAGTTTGCAGAC 2207 rnd-5_family- 68 GATACTAAATTGGGAGGAGTTGCGAACACCAGT--GAGGA-------ATA 108 i v i i ii -- -- -------ii CR1-3_Croc#LI 2208 GACACGAAACTGGGAAGGATTGCGAACAC--GTTGGAGGACGNGAGCGCA 2255 rnd-5_family- 109 ATACAAAGGGACCTAGAGAGATTAGAAACATGGGCAGAAAATAAACAAAA 158 v i i i v v i vv -v i iiv ii CR1-3_Croc#LI 2256 ATTCAGAAGGATCTCGACAGATTGGAAAGCTGGGC-TAGAGCTAACAGGA 2304 rnd-5_family- 159 --GAGATCANCTTGGAAAAATGCAAGCTAATACATCTGGGGGAAAATAAT 206 --i v ?ivi v v iv i v iii CR1-3_Croc#LI 2305 TGAAGTTCAATGCGGACAAATGCAAGGTGCTACACCTCGGGAGGAATAAT 2354 rnd-5_family- 207 CCGAAACACAGATATTCAATGGGAGGGGAAAC----CTGGAAAGCAGTA- 251 vi i ivv --- v v ---- vi i - CR1-3_Croc#LI 2355 CAAAAACACAAATACAAAATG---GGTGACACCTGGCTGGATGGCAGCAC 2401 rnd-5_family- 252 -ATGCTAGAGAACCTA------TAGGGAGAGCAGCAAATTAGACATGAGT 294 - vv i i i------ v v v - i i vi i CR1-3_Croc#LI 2402 TATGGAAAAGGACCTGGGAGTCTTGGTAGATCA-CAGACTCAATATGAGT 2450 rnd-5_family- 295 TTGCAATGCGATATGGCAGCAAAAAAGGCCAATGCAATTTTGGGCTGC-- 342 i i i iii v v v ii v -- CR1-3_Croc#LI 2451 CTGCAGTGTGATGCAGCCGCACAAAAGGCGAATGCGGTTTTGGGATGCAT 2500 rnd-5_family- 343 ----AGA--CATCACGT------CACGGAGCAGAGGCATTACT--CTCTC 378 ---- -- i v ------ ---- iiv v -- CR1-3_Croc#LI 2501 CAATAGAAGCATTAGGTGCAAGACACGG----GAGGTGATAGTGCCTCTC 2546 rnd-5_family- 379 TGT------CTGGTGCGACCGCACCTGGAATATTGCGTTCGGTTCTGGGC 422 ii------ vv i v i i i i v i CR1-3_Croc#LI 2547 TACTCGGCACTGGTTAGGCCTCATCTGGAGTACTGTGTGCAGTTCTGGGC 2596 rnd-5_family- 423 ACCTCATTACCAGAAAGATACTGACAAACTGGAGGCGNNA-AGAGNANTC 471 v v -ii i ----- i--- iv ?? - ?i?i CR1-3_Croc#LI 2597 TCCACATT-TTAAAAAG-----GACG---TGGAGAAGTTAGAGAGGGTCC 2637 rnd-5_family- 472 AGAAGAGGACA 482 i v i CR1-3_Croc#LI 2638 AGAGGCGGGCA 2648 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.72 CpG sites = 72, Kimura (unadjusted) = 35.52 Transitions / transversions = 1.44 (72/50) Gap_init rate = 0.07 (34 / 464), avg. gap size = 1.94 (66 / 34) 2123 7.57 8.13 0.56 rnd-5_family-663#DNA/TcMar-Tigger 7 338 (12) MER127#DNA/TcMar-Tigger 8 364 (0) m_b14s502i10 rnd-5_family- 7 ACTTCGCTAATCCGCACTTCGCTAATCTG--------ATAATTCACACAA 48 i i v i -------- v v MER127#DNA/Tc 8 ACCTCGCTAATTCTCACTTCGCTAATCCGCAAACCCGATAATTCTCACCA 57 rnd-5_family- 49 TA--------GACTCTCCCCACTTCTCAGCAAAGATTTAATAGCAGAGTG 90 v -------- v v v MER127#DNA/Tc 58 AAACCCGGCGGTCTCACCCCACTTCTCAGCAAAGATTTAATAGCAGAGAG 107 rnd-5_family- 91 CTGTAGTGAGGT-TCCTCTG--TAAGACTTCATTATTTTTACAAAATATA 137 i - v v v-- i MER127#DNA/Tc 108 CTGTAGCGAGGTCTCATATTACTAAGACTTCATTACTTTTACAAAATATA 157 rnd-5_family- 138 CTACAGTACATTTACTAGTATACTATGAANTGTATAATCATAA----TTA 183 ? i -- v ---- MER127#DNA/Tc 158 CTACAGNACATTTACTAGTGTACTATGAA--GTATTATCATAAATAATTA 205 rnd-5_family- 184 AAACTAAACTACACTTGTCAAAATAAATGAACAAAGTACATTTTGTGATG 233 MER127#DNA/Tc 206 AAACTAAACTACACTTGTCAAAATAAATGAACAAAGTACATTTTGTGATG 255 rnd-5_family- 234 CANTATCCTTGATTTTTGTTGT-CATGTTTC---ACTTGCTAATTCGCAA 279 ? ? i i -iv ?--- i MER127#DNA/Tc 256 CAGTANCCTTGATTTTTATCGTGTTTGTTTNCTTACTCGCTAATTCGCAA 305 rnd-5_family- 280 AATTCAGTAATTCGCAATGGGTCTCCCAGTCATTAGTGCGAATTAGCGAG 329 i i ? MER127#DNA/Tc 306 AATTCGGTAATCCGCAATGGGTCTCCCNGTCATTAGTGCGAATTAGCGAG 355 rnd-5_family- 330 GTTCTGCTG 338 i MER127#DNA/Tc 356 GTTCTACTG 364 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.59 CpG sites = 13, Kimura (unadjusted) = 8.14 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (9 / 331), avg. gap size = 3.22 (29 / 9) 251 23.68 2.63 0.00 rnd-5_family-9#DNA/PIF-Harbinger 1 76 (1) MER133B#DNA/PIF-Harbinger 24 101 (14) m_b14s502i11 rnd-5_family- 1 TTCAGCCCTGGCGTAAGCGGGTGCAACT-CCACTGANTTCAAT-GGAGTT 48 v v vi v v i - i ?v - MER133B#DNA/P 24 TTCTGCCCTCGGATACGCGCGCGCAACTCCCATTGAAGTCAATGGGAGTT 73 rnd-5_family- 49 GCACCTGCTTACACCAGGGCTGAATTTG 76 ii v v iviv v MER133B#DNA/P 74 GTGCGTGCGTATCTGAGGGCAGAATTTG 101 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.18 CpG sites = 7, Kimura (unadjusted) = 28.95 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 1214 21.55 6.14 3.53 rnd-5_family-1005#LINE/RTE-BovB 452 1086 (55) MamRTE1#LINE/RTE-BovB 302 952 (2860) m_b15s601i0 rnd-5_family- 452 TGCACGCAGGCGGCGGNNGCGNGATGGTCGTCCGGCTCNCGGACTGAGGC 501 iv i vv?? -i?iv iiii - ? v ?- MamRTE1#LINE/ 302 TGCGAGTAGGCGGCCCAGG-ATATTGGTCGCTTAG-TCGCTGAN-GAGGC 348 rnd-5_family- 502 AGCAGTGGAGCANCTCGGCAGCTNCNNNNGCGACTGAGCAGCCCTCTTTA 551 ii--- v?i v ???? i v v MamRTE1#LINE/ 349 AGCAGCA---CCGTTCGGCAGCGNCCTGGGTGTCTGAGCAGCCCTGTTTA 395 rnd-5_family- 552 GGATCCACTCTGCTCACCCCGCATGGGGAGGGGGCTAGAAAAGGTGCCCT 601 ? -i v i v i ? MamRTE1#LINE/ 396 GGANC-GCGCTGCTCACTCCGAATGGGGAAGGGNCTAGAAAAGGTGCCCT 444 rnd-5_family- 602 AAACATNGCCTGCCTCNNC---NNC--NCCTGG----CCGGANNGCCGCG 642 i ? ?? --- ? --?? ---- i ??ii MamRTE1#LINE/ 445 AAACGTTGCCTGCCTCGCCAAANTCAAANCTGGCTCACCAGATTATCGCG 494 rnd-5_family- 643 NCCGGCGGGATCAACCCAATCTCAGCGGT-CGAAANNANA-AGAAACGTT 690 ? i i v ----ii ? i- - i ? ? - vv v MamRTE1#LINE/ 495 TCTGGTGGGTT----TTANTCTT-GCGGTGCAAAANCAAATAGAAAACTA 539 rnd-5_family- 691 TCAACT----------------TTGGNACATGGAATGTNCGCACCCTNAT 724 i ? ??---------------- v?v ii ?v v v - MamRTE1#LINE/ 540 CCNANNACAAAGAAAATAACCATTGCGTCATGGAACATCAGGACGCT-AT 588 rnd-5_family- 725 G-GACAACACAANCGNCGAANGACCGGAGAGAAGAACAGCNATCGTCGCT 773 - ii ivi ? i? iiv? v i i i ?v v MamRTE1#LINE/ 589 GCGATGACGAGAACAGCAGTCGTCCAGAAAGAAGAACGGCACTCGTCGCA 638 rnd-5_family- 774 NGAGAACTCGCNCGNTACAACATCGACATTGCNGCCCTNAGCGAAACNAG 823 ? v vv ?v ? iivi i ? v ? ? MamRTE1#LINE/ 639 CGTGAACTGTCCAGATACGGAGTCGACATCGCCGCACTGAGCGAAACCAG 688 rnd-5_family- 824 ACGNGCTGATGAAGGNCAGCTGAGNGAGGAAGGNGGTGGCTACACCTTCT 873 v?v ? v v? iv ? vi ? i MamRTE1#LINE/ 689 ACTTCCTGATGAAGGACAGCTCACGGAGACAGGTGCCGGNTACGCCTTCT 738 rnd-5_family- 874 TCTGGAAGGG---AAAATCTGCAGATGAGCCGCGAATCAT-GGAGTTGGC 919 ii ---vvvv v --- vi iv vi- v ii MamRTE1#LINE/ 739 TCTGGAGAGGTCTTCCCTCTTCA---GAGCGACGGCTCTCAGGCGTCAGC 785 rnd-5_family- 920 TTTGCCATCAAGAACAA--NCTCGTCAGNCGACTTNCNGAGCTCCCCGTG 967 v --i i--? i vv?v ? i? ?i vi v ivi MamRTE1#LINE/ 786 TTTGCAATCA--GACAGTCACTTGTCTCAAGNCTCCCAAATTTGCCCAGA 833 rnd-5_family- 968 GGNATCAATGAGCGGCTCATGACNCTNCGGCTTANG-CTCACCAAAAACC 1016 ? ? i v v v ? ? - i ??- v vvv v MamRTE1#LINE/ 834 GGCATNAGTGACCGTCTGATGACCCTAC-GCCTACNTCTGAAACAAAAGC 882 rnd-5_family- 1017 AACANGCCACTNTCGTCAGCGCATATGCNCCNACACTGGACG----CCGA 1062 ivi?? i? i ? ? vv - ---- MamRTE1#LINE/ 883 GCTNTGCCACCGTCATCAGCGCATATGCCCCCACCAT-GACGAATACCGA 931 rnd-5_family- 1063 NGAGGATGTNAAGGAANAATTCTA 1086 ? ---? i ?i MamRTE1#LINE/ 932 TGAGGA---GAAAGAAAGATTCTA 952 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.71 CpG sites = 68, Kimura (unadjusted) = 29.49 Transitions / transversions = 1.06 (68/64) Gap_init rate = 0.06 (35 / 634), avg. gap size = 1.77 (62 / 35) 25 12.93 0.00 0.00 rnd-5_family-1073#Unknown 49 91 (1364) (CTG)n#Simple_repeat 1 43 (0) m_b15s252i7 rnd-5_family- 49 CTGCTGCTGCTGTTGCTGCTTTCGCTGCCGCTGCTGCTGCTGC 91 i vii i (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 43 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 17 26.35 0.00 0.00 rnd-5_family-1073#Unknown 215 264 (1191) (CCTG)n#Simple_repeat 1 50 (0) m_b15s252i8 rnd-5_family- 215 CCTGCCTGCTTGCTTGCCTGCCTGGCCGGTTGCCCGGCCGGCTGACTGCC 264 i i v i vi i v i v v (CCTG)n#Simpl 1 CCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCC 50 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 14 11.18 0.00 6.45 rnd-5_family-1073#Unknown 255 287 (1168) (GCT)n#Simple_repeat 1 31 (0) m_b15s252i9 rnd-5_family- 255 GCTGACTGCCGCTCGCTGCTGCTGCTGTTCCTG 287 - i - i v (GCT)n#Simple 1 GCTG-CTGCTGCT-GCTGCTGCTGCTGCTGCTG 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 13 23.57 1.82 5.66 rnd-5_family-1073#Unknown 599 653 (802) (CCA)n#Simple_repeat 1 53 (0) m_b15s252i10 rnd-5_family- 599 CCCCCCCTACCACCACCCCCACCGCCGACACACCGCTGCCCACC-CCTCC 647 v v i v i - - i -vv - v (CCA)n#Simple 1 CCACCACCACCACCACCACCACCACC-AC-CACCAC-CACCACCACCACC 47 rnd-5_family- 648 ACCGCC 653 i (CCA)n#Simple 48 ACCACC 53 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 33 0.00 0.00 0.00 rnd-5_family-1073#Unknown 1427 1457 (28) (CTGCCC)n#Simple_repeat 1 31 (0) c_b15s251i0 rnd-5_family- 1427 CTGCCCCTGCCCCTGCCCCTGCCCCTGCCCC 1457 (CTGCCC)n#Sim 1 CTGCCCCTGCCCCTGCCCCTGCCCCTGCCCC 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 15 13.16 0.00 5.71 rnd-5_family-1367#Unknown 34 70 (601) (CGGCAG)n#Simple_repeat 1 35 (0) m_b15s252i6 rnd-5_family- 34 CGGCAGCCAGGCAGCGGCATAGACAGCTGCAGCGGCA 70 - - vv i v (CGGCAG)n#Sim 1 CGGCAG-C-GGCAGCGGCAGCGGCAGCGGCAGCGGCA 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 2136 5.04 4.18 3.10 rnd-5_family-1464#DNA/Crypton 1 287 (0) Eulor6D#DNA/Crypton 7 296 (6) m_b15s502i0 rnd-5_family- 1 AGCAATAAGACACGACAGGCAGTGCATTTCTGGGCGATTATNGCACGCCT 50 ? Eulor6D#DNA/C 7 AGCAATAAGACACGACAGGCAGTGCATTTCTGGGCGATTATAGCACGCCT 56 rnd-5_family- 51 CGGGTGGTGTTATAAGGCACGAGGCCGAAGGCCGAGTGACTTTAACCACC 100 i Eulor6D#DNA/C 57 CGGGTGGCGTTATAAGGCACGAGGCCGAAGGCCGAGTGACTTTAACCACC 106 rnd-5_family- 101 CGAGAAGTGCAATAATCCCCCAGAAATGCACTGCCTGGAGTGTCTTATTG 150 v ? Eulor6D#DNA/C 107 CGAGAAGTGCAATAATCGCCCNGAAATGCACTGCCTGGAGTGTCTTATTG 156 rnd-5_family- 151 CTATTATGAAATGGAATTTATGAAACAAAAATAAGGGAAAAGATCAGACT 200 - v i i ---- --- Eulor6D#DNA/C 157 CTATTATGAAATGGAATTTAT-ACATAAAAATAAGGAAAA----CAG--- 198 rnd-5_family- 201 ATTAGACCTGTGCATTTACTGGGCATTATTGACACGGGTATGACATCACT 250 - i i i ii i Eulor6D#DNA/C 199 -TCAGACCCGTGCATTTACTGGGCATTATTGACATGGGCGTGACATCACC 247 rnd-5_family- 251 GACAG------------CTCCATTTGCGTCCAGCGTTCTAAAGCCATTT 287 ------------ i? i ? i Eulor6D#DNA/C 248 GACAGCCAATCAGAAANCTCCGNTTGCGTCCGGNGTTCTAAAGCCGTTT 296 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.84 CpG sites = 12, Kimura (unadjusted) = 5.35 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.03 (10 / 286), avg. gap size = 2.10 (21 / 10) 14 11.42 7.50 2.38 rnd-5_family-1553#Unknown 486 525 (270) (GCACCG)n#Simple_repeat 1 42 (0) m_b15s252i5 rnd-5_family- 486 GCCCCGGCACCGGTCCCCGGCACCGG---CGGGAACGGCACCG 525 v - v --- v v (GCACCG)n#Sim 1 GCACCGGCACCGG-CACCGGCACCGGCACCGGCACCGGCACCG 42 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 2.00 (4 / 2) 752 10.71 0.89 0.00 rnd-5_family-1822#DNA/hAT-Charlie 197 308 (1) Charlie11#DNA/hAT-Charlie 2084 2196 (0) m_b15s502i1 rnd-5_family- 197 ATATATCT-AGGTTTAAAGAACTGACCTACTTCAACGATTTTTGATAAGG 245 - i i i ? iii i Charlie11#DNA 2084 ATATATCTTAAGTTTAAAGAACTAATCTNCTTCAGTAATTTTTGATAAGA 2133 rnd-5_family- 246 GGTGCGAGAACATATTTTGAGAACCAAAGGGGTGCAGGCTGCAGTAAAGG 295 i ? v i i i ? Charlie11#DNA 2134 GGTGTGAGAANATATTTTGAGAACAAAAGGGATGCAAGCCGCAGNAAAGG 2183 rnd-5_family- 296 TTAAGAACCACTG 308 ? Charlie11#DNA 2184 TTAAGNACCACTG 2196 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.39 CpG sites = 11, Kimura (unadjusted) = 12.44 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.01 (1 / 111), avg. gap size = 1.00 (1 / 1) 298 32.56 0.76 1.54 rnd-5_family-1861#LTR/Gypsy 2575 2705 (1896) MamGypsy2-I#LTR/Gypsy 2426 2555 (1611) m_b15s551i0 rnd-5_family- 2575 ATGGCATGGAGAAACCAATTGCCTTTGCNTCACGAACACTCACCA-CTCC 2623 iv iv i vivv? v v -ii - v MamGypsy2-I#L 2426 ATGGCACTGAGGCACCAATTGCTTACTACTCAAGAACAAT-GTCATCTAC 2474 rnd-5_family- 2624 TGAGAAGAACTATGCGCAAAATAGAGCGAGAAGCTCTCAGCATTATCTTC 2673 v ivi i i v - vvi i iivii viv MamGypsy2-I#L 2475 AGAATGGAACTACGCACAAATT-GACAAAGAAGCCCTTGCTGTTATCGCG 2523 rnd-5_family- 2674 GGAATTCGGAAGTTCCATACCTATCTGTATGG 2705 i ivi i v i v i MamGypsy2-I#L 2524 GGAGTCAAGAAGTTCCACAACTACCTCTACGG 2555 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 23, Kimura (unadjusted) = 44.25 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.00 (3 / 3) 476 34.28 2.52 1.95 rnd-5_family-1861#LTR/Gypsy 3088 3444 (1157) MamGypsy2-I#LTR/Gypsy 2938 3296 (870) m_b15s551i1 rnd-5_family- 3088 CGTCAACGTGAATTATCTGTGAATCANGGTTGCATCTTATGGGGAATGCG 3137 i i i ivv v ? v v i vv MamGypsy2-I#L 2938 CATCAACATGAGTTATCTGCCCATAAAGGATGCCTTTTATGGGGAAATCG 2987 rnd-5_family- 3138 AGTGATCATTCC-GAAATCACTTCAATCTCAGGTT---TTGGAAGCTCTT 3183 vi vi i - iv iv - --- v --- vvi v v MamGypsy2-I#L 2988 CATTGTTATTCCAGAAGGCGGT-CA---TCACGTTATCTTGGCCACACTA 3033 rnd-5_family- 3184 CACGAAGGTCATTTTGGCATTGTACGGATGAAGGCCATAGCCCGGAGTCA 3233 i v vv iiv v v v i vv i iv i ii MamGypsy2-I#L 3034 CATGCAGCACATCCGGGAATTGTTCGCATGAAAGCATTGGCTAGAAGCTA 3083 rnd-5_family- 3234 TGTCTGGTGGCCGGGGATCGACAAAGACATTGAGAGGAAGGCGAAGTGCT 3283 v i i ivvv i i i vv ii viv MamGypsy2-I#L 3084 TGTCTGGTGGCCTGGAATTGATTCTGATATTGAAAAGACTGTAAAGGAGT 3133 rnd-5_family- 3284 GTACTAC--GTCAGCAAATTCAGCATGATCCTGGCCCAGCTCGTCTAC-- 3329 vi -- i vvv i i i i -- v ivv ii -- MamGypsy2-I#L 3134 GTAGCACATGCCAGGCTACTCGGCATAACCC--GCCAAAGGCACCTACTT 3181 rnd-5_family- 3330 -ACCCTTGGTCGTGGCCTCAGACTCCTTGGACACGTATTCACGTGGACTT 3378 -v v v ivv i -v vv v v v i ii v i MamGypsy2-I#L 3182 TTCCATGGAAAGTGACC-AAGAAGCCTTGGTCAAGAATCCATATTGATTT 3230 rnd-5_family- 3379 TGCCGGACCTTTAGAAGGTTATATGTTTTTGGTCGTAGTCGATGCCCATT 3428 v v vv i vv v vv i i i i v iv ivi MamGypsy2-I#L 3231 TGCAGGACCATTCCAGGGGAAGAACTTCTTGATTGTGGTAGACTCCTTCT 3280 rnd-5_family- 3429 CGAAATGGCCAGAAGT 3444 i iv MamGypsy2-I#L 3281 CAAAATGGCTCGAAGT 3296 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.87 CpG sites = 54, Kimura (unadjusted) = 46.39 Transitions / transversions = 0.82 (54/66) Gap_init rate = 0.03 (12 / 356), avg. gap size = 1.33 (16 / 12) 801 8.77 10.60 1.83 rnd-5_family-2140#SINE/5S-Deu-L2 2 152 (2) AmnSINE1#SINE/5S-Deu-L2 397 560 (15) m_b15s502i2 rnd-5_family- 2 CTTCCTCCACTCACACTGTTGTGTCAGTGT-GCTGTGT--TG-------G 41 viv v - - - i-- ------- AmnSINE1#SINE 397 CTTCCTGTCCTAA-ACTGTTGTGT-AGTGTTGCTGTGCGCTGTTAAACAG 444 rnd-5_family- 42 CTGCCGCCCTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGNNNT--GTA 89 vi ???v-- i AmnSINE1#SINE 445 CTGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTG 494 rnd-5_family- 90 AT----GTATATAGTTTTGTAAAGTGCTTTGGGATCCTTCGGGATGAAAG 135 ---- i i - i AmnSINE1#SINE 495 ATCCCTGTATGTAGCTT-GTAAAGCGCTTTGGGATCCTTCGGGATGAAAG 543 rnd-5_family- 136 GCGCTATATAAATGTAA 152 i AmnSINE1#SINE 544 GCGCTATATAAATGCAA 560 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.18 CpG sites = 8, Kimura (unadjusted) = 9.61 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.05 (8 / 150), avg. gap size = 2.38 (19 / 8) 17 13.72 0.00 0.00 rnd-5_family-2194#Unknown 978 1009 (10) (GAACT)n#Simple_repeat 1 32 (0) m_b15s252i4 rnd-5_family- 978 GAGCTGAACTGAATTGATCTGAACAGAACTGA 1009 i i v v (GAACT)n#Simp 1 GAACTGAACTGAACTGAACTGAACTGAACTGA 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 12 9.71 0.00 0.00 rnd-5_family-2482#Unknown 111 132 (621) (CTCC)n#Simple_repeat 1 22 (0) m_b15s252i3 rnd-5_family- 111 CTCCCTCCCTCCTGCCCTCCCT 132 iv (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 230 19.51 0.00 0.00 rnd-5_family-2773#Unknown 47 87 (46) C UCON97#DNA (220) 90 50 m_b15s502i3 rnd-5_family- 47 TGATCTTTACCCGCTGCTGTAAATTGGCTCTGAGCACACCT 87 iv v iii v i C UCON97#DNA 90 TGATCTTTGGCCCCTGCTGTAAATTGATCCTGCGCACGCCT 50 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.91 CpG sites = 5, Kimura (unadjusted) = 23.02 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 273 21.92 3.95 3.95 rnd-5_family-3118#DNA/PIF-Harbinger 3 78 (20) MER133B#DNA/PIF-Harbinger 6 81 (34) m_b15s502i4 rnd-5_family- 3 TGAAATCGACGGGCCAAATCCTGAG---AGGTGCTGAGCACCTGCAACTC 49 i ? ? i i i vv---i i i --- i vi MER133B#DNA/P 6 TAANANCAATGGGCCAAATTCTGCCCTCGGATAC---GCGCGCGCAACTC 52 rnd-5_family- 50 CCACTGAAGTCAATGGGAGTTGCAGGTGC 78 i iiv MER133B#DNA/P 53 CCATTGAAGTCAATGGGAGTTGTGCGTGC 81 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.15 CpG sites = 12, Kimura (unadjusted) = 28.06 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.50 (6 / 4) 16 9.78 0.00 0.00 rnd-5_family-3568#LTR/Gypsy 67 88 (4389) (A)n#Simple_repeat 1 22 (0) m_b15s252i2 rnd-5_family- 67 AAAAAAAAACAAAAAAACAAAA 88 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 349 32.89 6.10 5.73 rnd-5_family-3568#LTR/Gypsy 1360 1933 (2544) MamGypsy2-I#LTR/Gypsy 1414 1989 (2177) m_b15s551i2 rnd-5_family- 1360 GAGGATCTGGGAAGT-ATGA-AGGGAATCACTGTGACATTGAACATTAAA 1407 v iv - ii - ii v -- vv iv vi v MamGypsy2-I#L 1414 GAGGAACTGGGAGCTTACAAGAGGGAGCCAGTGT--CATTCCATCTGGAT 1461 rnd-5_family- 1408 CCTGACAGTCAACCAAAATATCTGAAAGCCAGAACTGTGCCATATGCCAT 1457 v v v vv vvi ii i v i v v iv MamGypsy2-I#L 1462 CCAGCCATTGCACCAATTCACTTGAAAGCTAGAAATGTACCTTTTGCTCT 1511 rnd-5_family- 1458 CAGGCCGAAAGTTGAAGCGGACCTGGAGCGCCTGGTCACAAATGGAGTCC 1507 v vvi i? vi v v ii ii v v v v i MamGypsy2-I#L 1512 AAGGAAAAAAANTGAAGAAGAGCTTGAGCATCTAATCAAACAAGGTGCCC 1561 rnd-5_family- 1508 TAATACCAGTTACCCATAGCCCATGGGCAACTCCTATCGTTCCAATAGTG 1557 viv v v vi v iv v i iv ii v i MamGypsy2-I#L 1562 TCGAACCAGTTACACATACCCGGTGGGCTATACCAATTGCGCCGGTACTA 1611 rnd-5_family- 1558 AAGAAAGATGGCTCCCTCCGGATTTGCGGTGATTTTAAAGTCACTGTCAA 1607 vvvi ivvvv vv iv i v i vi ivv v MamGypsy2-I#L 1612 AAGCCTAATGGTAAGGTGAGACTTTGTGGAGACTACAAGTGCACTGTGAA 1661 rnd-5_family- 1608 CCCGGTGTTGTGTGCAG-AGCAATACCCGCTTCCCCGCA-TCGATGACCT 1655 ivv iii - iv - v v i i-v v i - i v v MamGypsy2-I#L 1662 TAAGGCACT-TAAGCAGCACCCATATCCA-GTGCCTGCAGTCAATCAACT 1709 rnd-5_family- 1656 CTTCGCGGGCCTGGCTGGGGGACAAAAGTTCAGTAAGA---TTGATCTGA 1702 i i v vi v --- v vv iv --- i vi MamGypsy2-I#L 1710 CCTTGCTGTTCTTGCTGGGG---AAAAGGTCTTTGCGAAACTTGACCTTG 1756 rnd-5_family- 1703 GTCAAGCGTATTTACAGATGCACGTCGATGA---------AAAGTCCCAA 1743 vi v iv v vv ii --------- i vv MamGypsy2-I#L 1757 CCCAAGCTTATCAACAGCTGATCGTCAGTGATGCTACTGCAGACGCCCAA 1806 rnd-5_family- 1744 GAGCTGTTGACTATTGTGACGCAT-AAGGGGCTTTATCGA--TACTGTCG 1790 --------- v ii v v -i v -i -- --iv MamGypsy2-I#L 1807 ---------ACAATCATCACTCATCGAGGGGCATT-CCGAGTTA--AGCG 1844 rnd-5_family- 1791 CCTACCCTTCGGAATAACGTCTGCTCCCGCCCTG-----TTCCAGAGGGC 1835 v vv ---v i v -- ----- v vvi MamGypsy2-I#L 1845 CCTTCAGTTCGGAAT---TTCTGTTGC--CCCTGGAATTTTCCAGTGCTT 1889 rnd-5_family- 1836 TATGGACCAGATCTTGTGTGGCTTGCCAGGAGTCCA-GTGC-------TA 1877 i --- i i ----- v i v - i------- MamGypsy2-I#L 1890 CATGG---AGACCCT-----GCTTTCTAGGATTCCAGGTGTGGTACCATA 1931 rnd-5_family- 1878 TCTGGACGACATCCTGGTCACTGGAAGGAAT-GAGGAGGA--TCACCTAA 1924 i v i ii i - i vv i- v -- i vv MamGypsy2-I#L 1932 TTTCGATGATGTCCTGATCA-TGGGATCAACAGAGGATGAACTCGCGGAA 1980 rnd-5_family- 1925 AGAATTTAG 1933 v i MamGypsy2-I#L 1981 AGACTTCAG 1989 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.11 CpG sites = 77, Kimura (unadjusted) = 43.67 Transitions / transversions = 0.76 (77/101) Gap_init rate = 0.08 (46 / 573), avg. gap size = 1.48 (68 / 46) 250 27.42 0.00 0.00 rnd-5_family-3568#LTR/Gypsy 2119 2180 (2297) X1_LR#LTR/Gypsy 27 88 (74) m_b15s502i5 rnd-5_family- 2119 TTTCTAGGACTATTGAACTATTATGGAAAGTTCATCTCACAGTTAGCCAC 2168 i i v i v i i i i iiv iv i X1_LR#LTR/Gyp 27 TTCCTGGCATTAGTAAACTACTATGGAAAATTCATTTCATGCTTGTCTAC 76 rnd-5_family- 2169 ACTGCTAAAACC 2180 v v X1_LR#LTR/Gyp 77 TCTGGTAAAACC 88 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.42 CpG sites = 11, Kimura (unadjusted) = 35.42 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 402 32.79 1.61 1.61 rnd-5_family-3568#LTR/Gypsy 2998 3245 (1232) MamGypsy2-I#LTR/Gypsy 3049 3296 (870) m_b15s551i3 rnd-5_family- 2998 GGAATAGTGCGCATGAAGGAAATTGCACGAAGCTATTTTTGGTGGCCTGG 3047 v v i v v v vv v i MamGypsy2-I#L 3049 GGAATTGTTCGCATGAAAGCATTGGCTAGAAGCTATGTCTGGTGGCCTGG 3098 rnd-5_family- 3048 ATTGGACAGTGCTATTGAAGAGAAGGCAAGAGCTTGTATGTCATGTCAGG 3097 v v ivv v i vv i ii vv vvv i MamGypsy2-I#L 3099 AATTGATTCTGATATTGAAAAGACTGTAAAGGAGTGTAGCACATGCCAGG 3148 rnd-5_family- 3098 GTGTGAGGAATGCACC--CCAGTGGGCACCCCTAC--ACCCATGGGACTG 3143 v iivv v i- -- i-i -- --vi i vvv MamGypsy2-I#L 3149 CTACTCGGCATA-ACCCGCCAA-AGGCA--CCTACTTTTCCATGGAAAGT 3194 rnd-5_family- 3144 GCCTGAAAACCCGTGGCAACGTATTCACGTTGACTTCGCTGGCCCCCTTG 3193 v ii i v v iv v v i ii i i v v vi iv MamGypsy2-I#L 3195 GACCAAGAAGCCTTGGTCAAGAATCCATATTGATTTTGCAGGACCATTCC 3244 rnd-5_family- 3194 AAGGAAGCATGTTCTTGGTGGTGGTAGATGCCCATTCTAAATGGCCAGAA 3243 i i iv vv i v iv ivi v iv MamGypsy2-I#L 3245 AGGGGAAGAACTTCTTGATTGTGGTAGACTCCTTCTCAAAATGGCTCGAA 3294 rnd-5_family- 3244 GT 3245 MamGypsy2-I#L 3295 GT 3296 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.31 CpG sites = 34, Kimura (unadjusted) = 43.31 Transitions / transversions = 0.74 (34/46) Gap_init rate = 0.02 (6 / 247), avg. gap size = 1.33 (8 / 6) 332 30.71 1.55 1.55 rnd-5_family-3568#LTR/Gypsy 3724 3852 (625) MamGypsy2-I#LTR/Gypsy 3769 3897 (269) m_b15s551i4 rnd-5_family- 3724 GTTTTGGCTCGGAATTATACTTCTGGAGCTAAATGGGTCCCTGCCACTGT 3773 i v v i ivvv v v ii i i MamGypsy2-I#L 3769 GTCTTTGCTAGGAACTATGGAGCTGGACCAAGGTGGGTTCCTGCCACTAT 3818 rnd-5_family- 3774 CATC--GCTCAAACAGGACCTGTTTCCTACACAGTCCGGACTGCAGAGGA 3821 v i-- v -- i i v v vi i v v i MamGypsy2-I#L 3819 AATTGAGGTC--ACGGGGCCTGTGTCATACAAGGTCCAGAGTGCAGATGG 3866 rnd-5_family- 3822 TCTCACCTGGCGGCGACATGTAGATCAGCTG 3852 v iviiv iv v i v i MamGypsy2-I#L 3867 GCCGGTGTGGCATCGCCGTGTTGATCAACTG 3897 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 19, Kimura (unadjusted) = 39.96 Transitions / transversions = 0.95 (19/20) Gap_init rate = 0.02 (3 / 128), avg. gap size = 1.33 (4 / 3) 22 10.66 7.58 4.41 rnd-5_family-3583#Unknown 243 308 (200) (CTGGGAG)n#Simple_repeat 1 68 (0) m_b15s252i1 rnd-5_family- 243 CTGGGAGCTGGCTGC--GGAG--GGAAGGCTGGGCAGCAGGCAGCCTGGG 288 vv -- -- i - - v v - (CTGGGAG)n#Si 1 CTGGGAGCTGGGAGCTGGGAGCTGGGA-GCTGGG-AGCTGGGAG-CTGGG 47 rnd-5_family- 289 AGCTGGGA-CTGAGAGCTGGG 308 - i (CTGGGAG)n#Si 48 AGCTGGGAGCTGGGAGCTGGG 68 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.33 (8 / 6) 13 24.52 0.00 2.27 rnd-5_family-368#Unknown 294 338 (79) (CCCCCTG)n#Simple_repeat 1 44 (0) m_b15s252i0 rnd-5_family- 294 CCCCCCACCCCATGCCCCGCTGTGCTCTTGCCCCTGGCCCCTGCC 338 ii v - iv i vv v (CCCCCTG)n#Si 1 CCCCCTGCCCCCTGCCCC-CTGCCCCCTGCCCCCTGCCCCCTGCC 44 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 494 31.88 4.81 6.14 rnd-5_family-3946#DNA/hAT-Charlie 976 1453 (671) Charlie12#DNA/hAT-Charlie 1491 1962 (908) m_b15s502i6 rnd-5_family- 976 AAAATATTTTGTGTGACAACAGATGGTGCTCCTGCCATGGTCGG-AAAAC 1024 v iv v i ii v ? ? i v v v? - v Charlie12#DNA 1491 AACATACGTGGTATAGCTACNGATGNTGCCCCGGCGATGGTANGTAAAAG 1540 rnd-5_family- 1025 AGAAGGGATTTGTAAAGTTACTTGAAGATCA---AATTGGCCGCCCGACA 1071 - ? ? i v v i v --- i - ? v Charlie12#DNA 1541 AGA-GGGANTTGTANAATTAATAGAAAATGATGCAGTTG-CCGCNCGAAA 1588 rnd-5_family- 1072 GTCAAATTT----------CACTGTATCATCCATCAAGAAAACCTGTGTG 1111 v v? ---------- i i vi v ii i i Charlie12#DNA 1589 CTCACNTTTGATGANGTGTCATTGCATAGTACATCAAGAAAATTTATGTA 1638 rnd-5_family- 1112 CTAAAATTTCTAATTCAGAGCTTAATAATGTGATGAATACAGTGGTGCGA 1161 v ii - ----- iv vi i v v v iv vi vvii Charlie12#DNA 1639 CAAAAGCTT-TAA-----AAATGGATAACGTCATGCAAATTGTCATCAAG 1682 rnd-5_family- 1162 ATTGTGAATTTCCTTGTTGCTCGATCTGCTTTGACTCACAGACAGTTTCA 1211 ii viv vv i?ii--- vv v iv v i Charlie12#DNA 1683 GCTGTGAATTTCACAGGGGCCNAG---GGATTGAATCATCGCCAGTTCCA 1729 rnd-5_family- 1212 AGCACTGCTAGAAGAGATGGACAGTGCTTATAACGACATC--CCACTTCA 1259 i v i v vi iiv iiv vi ? i i i --i -- Charlie12#DNA 1730 GGAATTCCTTAAAAGTATGGATGCTGACTNTAGCAACGTCATTCACTT-- 1777 rnd-5_family- 1260 CAGCAACATTCGGTGGCTAAGTCGTGGCAAGGTTTTGGTGCGCTTTGTAA 1309 -------- vi iv v - i v iviv v - - Charlie12#DNA 1778 --------TTCGGAAGTAAAGTCGAGGC-AGATGTTGAAAAGATTT-TA- 1816 rnd-5_family- 1310 ACTGTTTTG----ATGCAATCAAGGCCTTTTTGTCGGAAAAAGGACAAAA 1355 -- ? ----i v i -- v i v v vv ii Charlie12#DNA 1817 --TGNTTTGCGACGTGAAATCGAG--CTGTTTATGGTATCAAAAACAAAA 1862 rnd-5_family- 1356 CTA--CCCCGAACTGGATGATGACAAATGGCTGTGTAAGCTCA-TGTTTC 1402 i ?--v v v i i v v - ii iii i -ii i Charlie12#DNA 1863 TTNGTGCCAGAACTTGACGACGAAAACTGGCT-TACAGATTTAGCATTTT 1911 rnd-5_family- 1403 TAACTGACATCACCGCTCACCTAAACGAACTCAACCTCTGTCTCCAGGGT 1452 iiv iiv v i ii ii ii v ? v? i i ? Charlie12#DNA 1912 TAGTGGGTTTGACCGCCCATTTAAGTGAGTTAAACNTGNGTCTTCAAGNT 1961 rnd-5_family- 1453 G 1453 Charlie12#DNA 1962 G 1962 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.54 CpG sites = 79, Kimura (unadjusted) = 44.42 Transitions / transversions = 1.23 (79/64) Gap_init rate = 0.08 (36 / 477), avg. gap size = 1.44 (52 / 36) 227 23.08 0.00 0.00 rnd-5_family-3946#DNA/hAT-Charlie 1933 1984 (140) Cheshire#DNA/hAT-Charlie 2037 2088 (332) m_b15s502i7 rnd-5_family- 1933 TCAGCATTTGGATCCACATACCTGTGTGAACAGGTATTTTCACACATGAA 1982 i vvvi v i v ii v v Cheshire#DNA/ 2037 TCAGTATTTGGCAGTACCTATCTGTGTGAAAAGACATTTTCAAAGATGAA 2086 rnd-5_family- 1983 AT 1984 Cheshire#DNA/ 2087 AT 2088 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.64 CpG sites = 5, Kimura (unadjusted) = 27.64 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 249 16.67 16.67 0.00 rnd-5_family-4270#SINE/MIR 5 58 (0) AmnSINE1#SINE/5S-Deu-L2 508 570 (5) m_b15s502i8 rnd-5_family- 5 GTTTGTACAGCGCTTTGAA---------GATGTAAAGCGCTATATAAGTG 45 i v ii--------- v i i AmnSINE1#SINE 508 GCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATG 557 rnd-5_family- 46 CTAAGTATTATTA 58 v i AmnSINE1#SINE 558 CAAGGTATTATTA 570 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.22 CpG sites = 6, Kimura (unadjusted) = 19.22 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 53), avg. gap size = 9.00 (9 / 1) 1180 14.73 2.21 0.87 rnd-5_family-4628#DNA 5 230 (394) Eulor1#DNA 119 347 (10) m_b15s502i9 rnd-5_family- 5 TAGTGGTGATTATCGAATTTCTATATTTATAGAAGAACGGCANTTCATAN 54 i i i i v ? ? Eulor1#DNA 119 TAGTGATAATTACCGAATTTCTATATTTATAGAAAACCGGCACTTCATAA 168 rnd-5_family- 55 ATATCGAATNTGTGCTATTATTTCCATNCGGGCCAGTCTTTCTATCGATA 104 - i v ?i v i - vi Eulor1#DNA 169 ATATCGAAT-TGTGCTATTATCTACATATGTGCCGGT-TTTCTATAAATA 216 rnd-5_family- 105 TGGAAATCTGGTAATTATCACTAGAACTATTCATTAAAATTCAGAAGNAG 154 i ii i ii ? Eulor1#DNA 217 TAGAAATTCGGTAATTATCACTAGAACTATTCGTTAAAATTCGAAAGTAG 266 rnd-5_family- 155 ATAAATCANGAATAGGAATGTTACTTATTTCTTAANATTCTAAAAGAAAG 204 v ? ii i iv ? v i ? i Eulor1#DNA 267 ATAAATAACGAATAGGAATGCCATTTATTCGTTAAAATTCTACAAAANAA 316 rnd-5_family- 205 GA----CTACNTATT-TTCCTTTAAAGAATT 230 i ---- ? ?ii - i i v Eulor1#DNA 317 AAATATCTNCCCGTTATCCCTTTGATGAATT 347 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.27 CpG sites = 25, Kimura (unadjusted) = 17.65 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.02 (4 / 225), avg. gap size = 1.75 (7 / 4) 2041 9.57 7.45 0.00 rnd-5_family-4628#DNA 230 511 (113) Eulor2A#DNA 4 306 (0) m_b15s502i10 rnd-5_family- 230 TTAAGAGATAATGTCAATGGAATAGAATATTGTCACAGGATAATGGTCTC 279 ii i Eulor2A#DNA 4 TTAAGAGATAATGTCAATGGAATAGAACGTTGTCACGGGATAATGGTCTC 53 rnd-5_family- 280 CTGCTGCTAGATAAATGCCGAGGCGAAGCCGAGGCATTTATCGAAAATAA 329 i Eulor2A#DNA 54 CCGCTGCTAGATAAATGCCGAGGCGAAGCCGAGGCATTTATCGAAAATAA 103 rnd-5_family- 330 ACGTTGAAGC---------------------AAAGCGGGAGACATTGATC 358 i i --------------------- Eulor2A#DNA 104 ACGTCGAGGCGAAGCCGAGACGTTTATTTTCAAAGCGGGAGACATTGATC 153 rnd-5_family- 359 CTGTGACAATGTTCTATTACAATGACTTTATTTCTGTTATACCAAATGAC 408 i i Eulor2A#DNA 154 CTGTGACAACGTTCTATTACAATGACTTTATTTCTGTTATACCAAATGAT 203 rnd-5_family- 409 TGATGTAGATGCAATCATTTTGTCTGATGGATGCTGGTGCAGTAGAGTGA 458 vi i i ii i Eulor2A#DNA 204 TGATGTAGATTTAATCACTTTGTCTGATGGATGTTGGTGCAGCGGAATGA 253 rnd-5_family- 459 CAGTTGCTCACTGTACCATTACTGAATAGCTGCATTCTGATTGGCTTTAG 508 i i i i ?i i ?i? i i vi Eulor2A#DNA 254 CAGTCGCTCGCCGTACCGTTNTTAANCNGCTGCGTTCTGATCGGCTTAGG 303 rnd-5_family- 509 AGA 511 i Eulor2A#DNA 304 GGA 306 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.05 CpG sites = 25, Kimura (unadjusted) = 10.67 Transitions / transversions = 12.50 (25/2) Gap_init rate = 0.00 (1 / 281), avg. gap size = 21.00 (21 / 1) 464 3.39 1.69 0.00 rnd-5_family-496#DNA/hAT 12 70 (965) UCON69#DNA/hAT 195 254 (232) m_b15s502i11 rnd-5_family- 12 ACAGCCTGAAACAATAGCTCTGAGACGTGTGAANTGNCCCATTCATCTCA 61 v ? ? UCON69#DNA/hA 195 ACAGCCTGAAACAATAGCTCTGAGAGGTGTGAACTGCCCCATTCATCTCA 244 rnd-5_family- 62 GT-GGGTGTT 70 i - UCON69#DNA/hA 245 ATGGGGTGTT 254 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.60 CpG sites = 1, Kimura (unadjusted) = 3.60 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 1705 8.20 7.32 2.33 rnd-5_family-508#DNA 8 294 (32) C UCON78#DNA (108) 335 35 m_b15s502i12 rnd-5_family- 8 ATTTTCAAATCTATTTGTGTTTAAACAGAGGTTCTCTCCCTCNCAGCCCA 57 v i vv ii i i ? C UCON78#DNA 335 ATTATCGAAGATATTTGTGTTTAAACAAGGGCTTTCTCCCTCACAGCCCA 286 rnd-5_family- 58 TTTTTT--TTCT-CCTGATCCTGCAGTGAAGTCATAATGCTGAATTTGTG 104 i i -- i - i C UCON78#DNA 285 TCTTCTCCTCCTGCTTGATCCTGCAGTGAAGTCATAATGCTGAATTTGTG 236 rnd-5_family- 105 ACATCACANTCATTTCCATGGCAACAGACTGT-ATGTCACAAACACAGGA 153 ? - C UCON78#DNA 235 ACATCACAATCATTTCCATGGCAACAGACTGTGATGTCACAAACACAGGA 186 rnd-5_family- 154 TTATGACTTCACTGCAGGATCAAGCAGAAGGAGAAGCTGGGCTGTGAAGG 203 - C UCON78#DNA 185 TTATGACTTCACTGCAGGATCAAGCAGAAGGAGAAGCTGGGCTGTG-AGG 137 rnd-5_family- 204 GAGAAAACTAGCCCTTACTAAGANATAA----CT---------GC--AGA 238 i ---- i v i ? i ---- --------- -- i C UCON78#DNA 136 GAGAAAGCT----CTTATTCAAACACAAATATCTTCAATAATAGCAAAGG 91 rnd-5_family- 239 GAANNNGG--TANNACTGGCAAAGTAAATGGCTTTTTGTATAAATGAAGT 286 ???i --v ?? v --v C UCON78#DNA 90 GAATACAGAAAATTACTGGCAAAGTAAATTGCTTTTTGTATAAATG--TT 43 rnd-5_family- 287 CCNTTTTT 294 i? C UCON78#DNA 42 CTCTTTTT 35 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.71 CpG sites = 16, Kimura (unadjusted) = 9.10 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.05 (14 / 286), avg. gap size = 2.00 (28 / 14) 261 20.83 0.00 0.00 rnd-5_family-6781#DNA/hAT-Tip100 3 50 (3545) C MamRep4096#DNA/hAT-Tip100 (32) 394 347 m_b15s502i13 rnd-5_family- 3 TTTGGCCTGGGCCTCAAGCTCAAAGGGGGCCTCAAATTTAGACACTTG 50 i vii viii vi C MamRep4096#DN 394 TTTGGCCCGGGCCTCACATTCACGAAGGGCCTCAAATTTAGACTTTTG 347 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.71 CpG sites = 7, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 302 17.86 0.00 0.00 rnd-5_family-6781#DNA/hAT-Tip100 2240 2295 (1300) Zaphod#DNA/hAT-Tip100 2465 2520 (1559) m_b15s502i14 rnd-5_family- 2240 GGTCAAGCCTATGACAATGGATCTAATATGGCTGGGAAGTACAAAGGTGT 2289 v i vv i i v iv v Zaphod#DNA/hA 2465 GGGCAAGCCTATGATAATGGCGCTAACATGGTTGGTAAAGAAAAAGGTGT 2514 rnd-5_family- 2290 ACAAGC 2295 Zaphod#DNA/hA 2515 ACAAGC 2520 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.41 CpG sites = 4, Kimura (unadjusted) = 20.41 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 458 19.40 2.58 13.57 rnd-5_family-6781#DNA/hAT-Tip100 3439 3593 (2) C MamRep4096#DNA/hAT-Tip100 (281) 145 6 m_b15s502i15 rnd-5_family- 3439 AAAAGC----ATTTGTTAAATAAAAAATATTCAAATTATGTCTCACTCTT 3484 ---- iv -i i v ii v v --- C MamRep4096#DN 145 AAAAGCGTTAATTTGTTAAATGTAAA-CATTTAAAATATACCACAAT--- 100 rnd-5_family- 3485 TTTTTTTGGTGCCTTATTTTGTTTTCATGTGTCGTCATTTTTTATTTTTA 3534 --- ----- v iii viii v v ----- C MamRep4096#DN 99 ---TTTTG-----TAACCCTGTTTTGGCATTTCTTCATTTTTTA-----A 63 rnd-5_family- 3535 TTATGGCTAGGGGCCTCAAAAGCTGGAAGTGGCCCGGGCCTCTCTGGACC 3584 - i- ii i iv v C MamRep4096#DN 62 T-ATA-CCGGGAGCCTCAAAAAATGGAAGTGGCCCGGGCCTCTCTCGACC 15 rnd-5_family- 3585 TCTGAGAGG 3593 C MamRep4096#DN 14 TCTGAGAGG 6 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.39 CpG sites = 16, Kimura (unadjusted) = 22.44 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.13 (20 / 154), avg. gap size = 1.15 (23 / 20) 399 22.59 11.92 3.49 rnd-5_family-1028#LINE/L2 16 359 (307) L2-1_AMi#LINE/L2 349 720 (515) m_b16s551i0 rnd-5_family- 16 CTCATCTGCTTCCATGGTTTCAGCTACCACCTCTATGCNGATGATTCCCA 65 i vvv iiiv i -- i ----- i v L2-1_AMi#LINE 349 CTCATCCGCAAACACAAATTCAACTACCA--TCTGT-----TGACTCACA 391 rnd-5_family- 66 AATCTACCTC----CT---GACCT------------CCAN-CTTACATCT 95 i ---- --- ------------ ?- v v L2-1_AMi#LINE 392 GATCTACCTCTCTACTCCAGACCTGTCTCCTTCTGTCCAAACTAAAATCT 441 rnd-5_family- 96 C---CAGN-TCTTCGACATCTCCTCTTGGATA-CTGACCNNC---TTGCA 137 --- v ?- ii v i- ii ?? --- iivi L2-1_AMi#LINE 442 CGGCCTGTCTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTCAAG 491 rnd-5_family- 138 CTCAACATNTTC-AACACTGAACTTCTCATCTTTCCTCCTAATCCTTCTC 186 ?vi - v v i ii v i i - v ? L2-1_AMi#LINE 492 CTCAACATGGCCTAAAACAGAGCTCTTAATCTTCCCCCC-AAGCCTNCTC 540 rnd-5_family- 187 TACCACCTCCCTTCTCT--ATCGCCACTGANAACTCCACTNTCCT-CCTG 233 i- i- i -- i iiiv ? v i? - L2-1_AMi#LINE 541 C-CCAT-TCCCTTTTCTCGATCACTGTGGACAACACCACCATCCTGCCTG 588 rnd-5_family- 234 TCTCCCAGGCTCACAACCTCGGTGTCATCTTTGACT----CCTCTCTCCC 279 v i i ii v i i ---- -- L2-1_AMi#LINE 589 TCACTCAGGCCCGTAACCTGGGCGTCATCTTCGACTCGGACCTCTCTC-- 636 rnd-5_family- 280 TTCTCTCCCCACATCCAGNCTCTCACTAAATCCTGTCACTTCTTTCTT-- 327 - vvv i ? v vv i iviv v-- L2-1_AMi#LINE 637 -TAGGTCCTCACATCCAGGCTATGTCTAAATCTTGCAGATTCTTTCTGCA 685 rnd-5_family- 328 TAAC-TCAACAAAATCCGCCCTTTCC--TCCGTCC 359 - vvi i v v -- i L2-1_AMi#LINE 686 TAACATCTCTAAGATACGGCCTTTCCTATCCATCC 720 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.63 CpG sites = 43, Kimura (unadjusted) = 28.36 Transitions / transversions = 1.34 (43/32) Gap_init rate = 0.08 (27 / 343), avg. gap size = 2.00 (54 / 27) 260 27.77 8.19 5.19 rnd-5_family-1028#LINE/L2 366 646 (20) UCON86#LINE/L2 3 291 (391) m_b16s502i0 rnd-5_family- 366 GCTAAAACTCTTTGTCCACGCCTTGGTCATCTCTCGCCTCGACTACTGCA 415 i - i ii ? vi vi i i UCON86#LINE/L 3 GCTGAAA-TCCTCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGCA 51 rnd-5_family- 416 ACCTCCTCCTCTCTGGTCTTCCCACCTCC--ATTCTCC---CTCCATAGT 460 ? ii i v i i vv --ii --- -- i UCON86#LINE/L 52 NCTCCCTTCTCTATGGCCTCCCCAAGTCCCAGCTCTCCAGACTCC--AGC 99 rnd-5_family- 461 CCATCCAAAATACTGCTGCTAAAGTCATCTTCCCTTCCACTGC------- 503 v i v i i -----i ii -- iv - ------- UCON86#LINE/L 100 ACGTGCAGAATGCTGCTGC-----CCGCCTT--CTCACAC-GCACAAAGA 141 rnd-5_family- 504 --TCCGAACATGTCACTCC---TCTCGAATCCCTCCACTGGCTTCCNTNT 548 -- v v ii i ---i i ivv i ?v? UCON86#LINE/L 142 AGTGCGACCACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATT 191 rnd-5_family- 549 CTCTTACCGCATCAAATTCAAG------CTCCTCGTCCTCANNNNCCTGC 592 vi - v v v i i------ i ii i ???? v UCON86#LINE/L 192 CATTT-CAGGATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAAACCCTCC 240 rnd-5_family- 593 ATAATCTTNTTGCCCCCGCCTNCATCTCTGCTCTTATTTCCTCCCACTCT 642 iiv --- i v ? v v v vi i i iii ii i UCON86#LINE/L 241 ATGGAC---TTGCTCCAGCCTACCTCACGGACCTTGTCTCTCTCTGCTCC 287 rnd-5_family- 643 TCTC 646 i UCON86#LINE/L 288 CCTC 291 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.77 CpG sites = 50, Kimura (unadjusted) = 38.10 Transitions / transversions = 2.08 (50/24) Gap_init rate = 0.07 (21 / 280), avg. gap size = 1.81 (38 / 21) 15 4.53 4.00 4.00 rnd-5_family-10464#Unknown 516 540 (982) (GT)n#Simple_repeat 1 25 (0) m_b16s252i6 rnd-5_family- 516 GTGTGTGCTGTGTGTGCG-GTGTGTG 540 - i - (GT)n#Simple_ 1 GTGTGTG-TGTGTGTGTGTGTGTGTG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 247 17.31 0.00 1.92 rnd-5_family-1427#LINE/CR1 3 55 (523) Charlie32a#DNA/hAT-Charlie 20 71 (265) m_b16s502i1 rnd-5_family- 3 GTCTGTGGACCACTGGTGGTCTGCGGAGCACTTCCAGGTGGTCCGCGGAG 52 i v i i ii vv i - Charlie32a#DN 20 GTCCGGGGACCGCTGGTGGTCCGCGAGGGTCCTCCAGGTGGTCCGCGG-G 68 rnd-5_family- 53 CTG 55 Charlie32a#DN 69 CTG 71 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.27 CpG sites = 6, Kimura (unadjusted) = 20.08 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 305 24.44 1.11 0.00 rnd-5_family-1427#LINE/CR1 264 353 (225) CR1-16_AMi#LINE/CR1 570 660 (191) m_b16s551i1 rnd-5_family- 264 TGATCAAATTTGCGGACGACACCAAAACTGGAGGGGTAGCAAACACACG- 312 i v i i i i i viv i v vv - CR1-16_AMi#LI 570 TAATGAAATTCGCAGATGATACTAAATTGGGAGGAGTTGCAAACACCAGT 619 rnd-5_family- 313 GAGGACAGAACCAAACTGCAAAGTGACCTGGAGAGATTAGA 353 ivv v v i v i CR1-16_AMi#LI 620 GAGGACAGAGAAATAATACAAAGGGACCTAGAGAGATTAGA 660 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.29 CpG sites = 11, Kimura (unadjusted) = 29.85 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1) 289 31.51 1.34 2.03 rnd-5_family-1427#LINE/CR1 264 412 (166) CR1-3_Croc#LINE/CR1 2191 2338 (1267) m_b16s551i2 rnd-5_family- 264 TGATCAAATTTGCGGACGACACCAAAACT-GGAGGGGTAGCAAACACA-C 311 v i i - i - i i v i i-i CR1-3_Croc#LI 2191 TGAGCAAGTTTGCAGACGACA-CGAAACTGGGAAGGATTGCGAACACGTT 2239 rnd-5_family- 312 GGAGGACAGAACCAAACTGCAAAGTGACCTGGAGAGATTAGAGCAGTGGG 361 i?i v iv v v i iv i v v i i- i-v CR1-3_Croc#LI 2240 GGAGGACGNGAGCGCAATTCAGAAGGATCTCGACAGATTGGAA-AGC-TG 2287 rnd-5_family- 362 GGCTGCAGGCAACGAGGGGAGATTCGGTACTAATAAATGTAAAGNCCTAC 411 iv vi ii iv ii ii i vi i i i ?v CR1-3_Croc#LI 2288 GGCTAGAGCTAACAGGATGAAGTTCAATGCGGACAAATGCAAGGTGCTAC 2337 rnd-5_family- 412 A 412 CR1-3_Croc#LI 2338 A 2338 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 31, Kimura (unadjusted) = 44.10 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.03 (5 / 148), avg. gap size = 1.00 (5 / 5) 11 22.78 3.92 3.92 rnd-5_family-1641#Unknown 19 69 (346) (CAGCGAG)n#Simple_repeat 1 51 (0) m_b16s252i5 rnd-5_family- 19 CAACGAACAGC-AGTGGCCAG-AGCGAACAGTGAGCAGCTGGAGGAACGA 66 i i - ii v - i i -- v i (CAGCGAG)n#Si 1 CAGCGAGCAGCGAGCAGCGAGCAGCGAGCAGCGAGCAGC--GAGCAGCGA 48 rnd-5_family- 67 GCA 69 (CAGCGAG)n#Si 49 GCA 51 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 314 13.75 0.00 3.92 rnd-5_family-1801#SINE/5S-Deu-L2 1 53 (155) AmnSINE2#SINE/tRNA-Deu 214 264 (94) m_b16s502i2 rnd-5_family- 1 GGCACTTTATGTAAGGGCAGGGGTTTGCCCCGGTGTCCTTGGCCAAAAGT 50 i vi i i i i -- AmnSINE2#SINE 214 GGCGCTTTTCGTAAGAGTAGGGGTTTGCCCCGGTGCCCTTGGCCGAA--T 261 rnd-5_family- 51 TTC 53 AmnSINE2#SINE 262 TTC 264 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.07 CpG sites = 6, Kimura (unadjusted) = 15.71 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 395 14.47 9.21 0.00 rnd-5_family-1801#SINE/5S-Deu-L2 101 176 (32) AmnSINE1#SINE/5S-Deu-L2 446 528 (47) m_b16s502i3 rnd-5_family- 101 TGCTGCCCTCCACCCCAGAGGTGGCTGCATTTCAGTGGT-GCTG------ 143 i vi - v ------ AmnSINE1#SINE 446 TGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTGA 495 rnd-5_family- 144 TACATGTGTACAGTTTGTGAAGCGCTTTGGGAT 176 v v i ii i i AmnSINE1#SINE 496 TCCCTGTATGTAGCTTGTAAAGCGCTTTGGGAT 528 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.77 CpG sites = 7, Kimura (unadjusted) = 16.30 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.03 (2 / 75), avg. gap size = 3.50 (7 / 2) 1008 5.45 6.86 5.65 rnd-5_family-1802#DNA/Kolobok 6 180 (1) UCON29#DNA/Kolobok 263 439 (0) m_b16s502i4 rnd-5_family- 6 AAGAACCCAGCTTGACTTTCAGATCCCAGGTTGAGTTTTTGGCAGGGCTG 55 v i --- ? UCON29#DNA/Ko 263 AAGAACACAGCTTGATTTTCAGATCCCAGGTTGAGTTT---GCAGNGCTG 309 rnd-5_family- 56 GCAGTTAGAAAAAAANNNATCTTTTTACTTGTAAACTGAGCAAATTTGAT 105 ---?? v UCON29#DNA/Ko 310 GCAGTTAGAAAAA---TCATCTTTTGACTTGTAAACTGAGCAAATTTGAT 356 rnd-5_family- 106 NTGGAAGTCAC----AGAGAA-AAACATGGAACATC-------CATTTTT 143 i---- - i vi ------- UCON29#DNA/Ko 357 NTGGAAGTCATTGAGAGAGAATAAATATGGAACCCCACGATGTCATTTTT 406 rnd-5_family- 144 ACACAGTCACTTTTTCGNGAATATAACTGCACTTTAA 180 -- i? ? -- i UCON29#DNA/Ko 407 --ACAGTCACTTTTCNGAG--TATAACCGCACTTTAA 439 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.30 CpG sites = 6, Kimura (unadjusted) = 5.92 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.07 (13 / 174), avg. gap size = 1.69 (22 / 13) 232 20.00 0.00 0.00 rnd-5_family-1833#DNA 140 179 (25) UCON59#DNA 40 79 (178) m_b16s502i5 rnd-5_family- 140 CGCCCACAATTAACTGCAGGTGCAAAATTGCAGGTGCAAA 179 ii ?ii i iv i UCON59#DNA 40 CGCCTGCAATTANTCGCGGGTGCAAAATTGCGCGCGCAAA 79 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.47 CpG sites = 7, Kimura (unadjusted) = 25.59 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 2749 8.40 0.99 2.77 rnd-5_family-2217#Unknown 1 404 (0) UCON6#Unknown 14 410 (27) m_b16s502i6 rnd-5_family- 1 GGCAAGAGCCGACAGGNCTGCCTTTGNTTTTTTTTTGACCTTTATTTTAT 50 i i ? ?i vi? v v --- UCON6#Unknown 14 GGCAAGAGCCAACGGGTCTGCNCTGATTTTTTTTTTTAACTTT---TTAT 60 rnd-5_family- 51 TTATTAAAATGCTCTGGATACAGATTAACTTTCTTTGCTCAATATTTATT 100 UCON6#Unknown 61 TTATTAAAATGCTCTGGATACAGATTAACTTTCTTTGCTCAATATTTATT 110 rnd-5_family- 101 ATTGTTTCACCTGCCTTGAAATGGGAACTGCAAGCACTTTGATAAATGGA 150 i i UCON6#Unknown 111 ATTGTTTCACCTGCCTTGAAACGGGAACTGCAAGCGCTTTGATAAATGGA 160 rnd-5_family- 151 CTGAAAGGTTGTCTAGTTTCACTGTAGCTTCTGTAAGTACCTCTGTATCC 200 i UCON6#Unknown 161 TTGAAAGGTTGTCTAGTTTCACTGTAGCTTCTGTAAGTACCTCTGTATCC 210 rnd-5_family- 201 TCTGCTGAAATGCTATTTTGTAACTTCTTACAGCAATANTCCTCAGTGAA 250 i ? UCON6#Unknown 211 TCTGCTGAAATGCTATTTTGTAACTTCCTACAGCAATACTCCTCAGTGAA 260 rnd-5_family- 251 TCACAACAGATATCCCTTACACCTCCTNCAGCAACAGTACACTAANGGGA 300 i - ? i ? i? UCON6#Unknown 261 TCACAACAGACATCCC-TNCGCCTCCTACAGCAACAGTACACTAGGGGGA 309 rnd-5_family- 301 CTGTTATTC--TTTCCTCCACCAGCGGAAGAACACCACTGTCACAAA--G 346 i v --i i ? i ? -- UCON6#Unknown 310 CTATTTTTCCTCTTTCTCCANCAGCGAAAGNACACCACTGTCACAAAAGG 359 rnd-5_family- 347 TTGTGCTAAGTCGGAGCANAAGACCTTTTCCANTCTAACGATGAAGCCAA 396 ??i ?i i i?vi ? i -------i vv vi UCON6#Unknown 360 TTGTNNCANATCAGAGCGCCGGNCCTTTCC-------GCGCGGACACCAA 402 rnd-5_family- 397 CGGGCTCT 404 i i UCON6#Unknown 403 CAGGCCCT 410 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.46 CpG sites = 25, Kimura (unadjusted) = 9.38 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.03 (13 / 403), avg. gap size = 1.15 (15 / 13) 275 16.00 0.00 0.00 rnd-5_family-229#DNA/hAT-Charlie 1 50 (16) Charlie29b#DNA/hAT-Charlie 1 50 (1144) m_b16s502i7 rnd-5_family- 1 CAGCGTTTCTCAAACTGGGGTCCGCGAGGGTACTCCAGGGGGTCCGCGGG 50 i iiv i iv i Charlie29b#DN 1 CAGTGTTTCTCAAACTGGGGTCCGCGGACGTATTCTCGGGGGTCCGCGAG 50 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.51 CpG sites = 6, Kimura (unadjusted) = 18.51 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 12 7.52 6.67 3.23 rnd-5_family-3203#LTR/Gypsy 38 67 (1197) (GTT)n#Simple_repeat 1 31 (0) m_b16s252i4 rnd-5_family- 38 GTTGTTG-TCTTGTATGTTGTT-ATGTTGTTG 67 - v - -v (GTT)n#Simple 1 GTTGTTGTTGTTGT-TGTTGTTGTTGTTGTTG 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.10 (3 / 29), avg. gap size = 1.00 (3 / 3) 13 0.00 0.00 0.00 rnd-5_family-3209#Unknown 1496 1512 (824) (CCT)n#Simple_repeat 1 17 (0) m_b16s252i3 rnd-5_family- 1496 CCTCCTCCTCCTCCTCC 1512 (CCT)n#Simple 1 CCTCCTCCTCCTCCTCC 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 267 32.25 5.59 2.72 rnd-5_family-398#LINE/CR1 35 356 (50) CR1-3_Croc#LINE/CR1 1073 1403 (2202) m_b16s551i3 rnd-5_family- 35 ATGGAAGAAACAGAAGATACAAGAAGCGGCCAATGTGGCTTCANGAGGGG 84 v vv - iiiv v i v ?i i CR1-3_Croc#LI 1073 ATGGAAGCACAAGAAGA-ATGGCAAGAGACCAATGTGGCTGCACAAGGAG 1121 rnd-5_family- 85 CTGCTCAAAGATCTGAGGTTNAAAANAANTCTGTACTGGAAATGGAGAAG 134 v v vii v ii v? ?i ?vvii v v ---- CR1-3_Croc#LI 1122 CTTCTAAAATGCCTCAAATGCAAAAGGAAAGCATACAGGCAATGGA---- 1167 rnd-5_family- 135 AGAA-GGGAAGGAAACCAAACAAGAATATCA-NAGTCAGTTAAGGCTTGC 182 - v vv iv vi i -? ivi iv iii i CR1-3_Croc#LI 1168 AGAATGGGCAGGTCACCAAGGAAGCGTACCAGGAAATAGCAAGAACCTGC 1217 rnd-5_family- 183 AGGGAAAAGATAAG---GGCAGAAAAAGCAGAATGAGTTAATGCTGCCAG 229 v i v --- i i v i- i i ivvv v ii CR1-3_Croc#LI 1218 AGGGACAAAATCAGGAAGGCAAAGATAA-AGAACGAGCTGCACCTGGCGA 1266 rnd-5_family- 230 AGG-GATT---------AAGAAGGGCTTTTACAAATATATCAGGGGGAAA 269 - i --------- i v i i i i ii vvi CR1-3_Croc#LI 1267 AGGAGGTTAAGGACAACAAGAAGAGGTTCTATAAGTATGTTGGCCAGAAA 1316 rnd-5_family- 270 AGAAGTACTAGAGAGAAAGTAGGCCCA---TTAATAAATGAGGAGGGGGA 316 v i ii iivv i i ?--- i iiv i iivv CR1-3_Croc#LI 1317 AGAAGGACCAAGGAAGCTGTGGGTCCNCTGTTAACAAGCCAGGGGGAACT 1366 rnd-5_family- 317 TNAAATTAATGATGACTCNAAAATGGCTGAGNTACTGAAC 356 i?v i?i v --- ? i v v ? v CR1-3_Croc#LI 1367 CCTAACNGAAGATG---CAAAGAAGGCGGAGCTACTCAAC 1403 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.70 CpG sites = 58, Kimura (unadjusted) = 45.54 Transitions / transversions = 1.35 (58/43) Gap_init rate = 0.05 (15 / 321), avg. gap size = 1.80 (27 / 15) 1309 12.81 4.08 4.44 rnd-5_family-398#LINE/CR1 106 399 (7) CR1-12_AMi#LINE/CR1 3 295 (319) m_b16s551i4 rnd-5_family- 106 AAAANAANTCTGTACTGGAAATGGAGAAGAGAAGGGAAGGAAACCAAACA 155 ?i ?? - ?i i ?vv --- ? iiv ? iiv CR1-12_AMi#LI 3 AAAAGGAANCT-TACNAGAAATGGAAANTTG---GGNAAACAANCAGGGA 48 rnd-5_family- 156 AGAATATCANAGTCA--GTTAAGGCTTGCAGGGAAAAGATAAGGGCAGAA 203 i i v ?i - -- i i ii -- v iv CR1-12_AMi#LI 49 GGAGTATAAGGG-CATTGCTAAGGCTTGCAGGGAGAAAGTA--GGAAGGC 95 rnd-5_family- 204 AAAGCAGAATGAGTTAATGCT-GCCAGAGGGATTAAG---------AAGG 243 i iv - i i --------- CR1-12_AMi#LI 96 AAAACGCAATGAGTTAATGCTAGCCAAAGGGGTTAAGGGGAATAAGAAGG 145 rnd-5_family- 244 GCTTTTACAAATATATCAGGGGGAAAAGAAGTACTAGAGAGAAAGTAGGC 293 i i CR1-12_AMi#LI 146 GCTTTTACAAATATATCAGGGGGAAAAGAAATACTAGAGAGAAAGTAGGT 195 rnd-5_family- 294 CCATTAATAAATGAGGAGGGGGATNAAATTAATGATGACTCNAAAATGGC 343 ii i ? i-- ? CR1-12_AMi#LI 196 CCATTAATAAATGAGGGAGGGAATTAG--TAATGATGACTCTAAAATGGC 243 rnd-5_family- 344 TGAGNTACTGAACTCCTTTTTAAAAATCTGTCTTTAACAAGAAATAAGGG 393 ? v -- -- i i CR1-12_AMi#LI 244 TGAGATACTGAACTGCTTTTT--AAATCTGTCTTTAACAAGAA--AAAGA 289 rnd-5_family- 394 AAAGAA 399 CR1-12_AMi#LI 290 AAAGAA 295 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.58 CpG sites = 27, Kimura (unadjusted) = 15.01 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.05 (16 / 293), avg. gap size = 1.56 (25 / 16) 18 8.71 12.24 0.00 rnd-5_family-4155#Unknown 15 63 (423) (GCCTAG)n#Simple_repeat 1 55 (0) m_b16s252i2 rnd-5_family- 15 GCCTAGGCC---GACAAGGCCTAGGCCTAGGCC---GACAAGGCCTAGGC 58 --- v v --- v v (GCCTAG)n#Sim 1 GCCTAGGCCTAGGCCTAGGCCTAGGCCTAGGCCTAGGCCTAGGCCTAGGC 50 rnd-5_family- 59 CTAGG 63 (GCCTAG)n#Sim 51 CTAGG 55 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.04 (2 / 48), avg. gap size = 3.00 (6 / 2) 354 26.78 5.13 1.86 rnd-5_family-4262#LINE/CR1 562 717 (1836) CR1-13_AMi#LINE/CR1 563 723 (1) m_b16s551i5 rnd-5_family- 562 GNATTAGGAAGAAACTTCCCC-------AGGTTAGTCCAGAAAGGGCCAN 604 ?i ------- v v -vv ? CR1-13_AMi#LI 563 GGGTTAGGAAGAAACTTCCCCTATGGGCAGGTTATTCCATAA-TTGCCAT 611 rnd-5_family- 605 TTCGGTGGTCTTCTACTTTATTCTGAAGCGGCTGTTACTCCTCGCTACTG 654 vi v ? i vi i vi iv v vvi i iiii CR1-13_AMi#LI 612 TATGGGGNTTTTGCACCTTCCTCTGAAGCATCTGGTACTGGCCACTGTCA 661 rnd-5_family- 655 GAGACACGAGAATGGATNAAGCTGACAAGTGGTGTGNTCCAGTCTAGC-A 703 v v v i? iiiv v v -ii? v v ? - CR1-13_AMi#LI 662 GAGACAGGATACTGGACTAGATGGACCACTGGT-CATTCCACTATNGCGA 710 rnd-5_family- 704 ATTCCTATGTTCTT 717 vv - CR1-13_AMi#LI 711 ATTAAT-TGTTCTT 723 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.12 CpG sites = 19, Kimura (unadjusted) = 35.12 Transitions / transversions = 0.86 (19/22) Gap_init rate = 0.03 (5 / 155), avg. gap size = 2.20 (11 / 5) 988 13.26 3.00 9.56 rnd-5_family-444#SINE/tRNA 8 274 (1) LFSINE_Vert#SINE/tRNA 186 436 (23) m_b16s601i0 rnd-5_family- 8 TCACAAAACCACCGCGAATAATTTAACGCGNTTCGGCACA---GTTGGCC 54 iiv -i -ii i v?v i v--- v LFSINE_Vert#S 186 TCACAAAACCACCATCA-CAATT-GGCACTAATTGGCACCCTTGTTGGCA 233 rnd-5_family- 55 GTCTCTGCTCAGGAAAGGCAGCTGAGCCCANGACTAAGTTAGCGTG-AG- 102 v ---i i -------- v ? i i vi i - - LFSINE_Vert#S 234 GTCTCAGC---AGAGAGGC--------CAAGGACTGAATGGGCATGGAGA 272 rnd-5_family- 103 CTTAATCACC-TCTAACTCATGAGAGAGAGTGGTCCCTCCAGGTCAGGAG 151 v ii - v iiv --- - - LFSINE_Vert#S 273 CTGAACTACCCTCTCACCTCT---AGAG-GTGGTCCCTCCAGGTCAGG-G 317 rnd-5_family- 152 CTGAGGCACANNTGGCGGGGCAGTGTGGGGAAGCTTGCACTGCCGCTGCC 201 i ?- LFSINE_Vert#S 318 TTGAGGCACAT-TGGCGGGGCAGTGTGGGGAAGCTTGCACTGCCGCTGCC 366 rnd-5_family- 202 CGCGCTGTACCTGTTCTGTGGATAAATAGAGGACTTCAGTCTCCAGGNCT 251 i i ? LFSINE_Vert#S 367 CGTGCTGTACCTGTTCTGTGGATAAACAGAGGACTTCAGTCTCCAGGGCT 416 rnd-5_family- 252 GTCTAATCAATNTG--ACCTTTCAC 274 ----- ?i -- LFSINE_Vert#S 417 G-----TCAATCCGGCACCTTTCAC 436 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.54 CpG sites = 21, Kimura (unadjusted) = 15.02 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.11 (29 / 266), avg. gap size = 1.10 (32 / 29) 1874 14.28 3.21 2.02 rnd-5_family-5823#Unknown 5 347 (0) UCON1#Unknown 50 396 (990) m_b16s502i8 rnd-5_family- 5 CTACCCA--GGTACAACCAAAACACNCCCGAGTAATCGGGTAAACTCGAC 52 i-- vi i ? v i - i UCON1#Unknown 50 CTACCCGCGGGTACCGCCAAAATACCCGCGGGTAATCGGGTAA-CCCGAC 98 rnd-5_family- 53 CTACTTGGCACCTGAAAAAGCGTGAGTCGGGTGTTTGGTACCCGAAGAAA 102 i i i i ii i i i ?v UCON1#Unknown 99 CTGCCTGGTACCCGAAAAAATGCGGGTCGGGTGTTCGGTACCCGAANTAA 148 rnd-5_family- 103 TTACCTGAAAAATGACTGCCTGGGGTTGCACCAAGTATTGTCTCATCAGC 152 i - v UCON1#Unknown 149 TTACCCGAAAA-TGACTGCCTGGGGTTGGACCAAGTATTGTCTCATCAGC 197 rnd-5_family- 153 ATTCAGCACCACTGCCATAGCATGAAGGAGAA-AGAAAANCACAGAAACG 201 i ii- i ?--- v UCON1#Unknown 198 ATTCAGCACCACTGCCACAGCATGAAGGAGGGCAGAGAAA---AGAAAAG 244 rnd-5_family- 202 CAGA-GAAGGAGGAGATAAAAGG--AGAGCAGTGAGAAGAAAAA-GTTTC 247 vi - i i i v ? --i v v i i ? iv- UCON1#Unknown 245 CCAATGGAAGAGAAGAGANAAGGTAGGAGAAGGGGGAAAANAGCTGTTTC 294 rnd-5_family- 248 TTAACTGTGCTGTGANCTTTCTCTCT----GATCCCTCTCCCCCAACCCA 293 i i i? ---- i -- UCON1#Unknown 295 TTAATTGCGCTGTGGACTTTCTCTCTAACGGATCCCCCT--CCCAACCCA 342 rnd-5_family- 294 TCAACAATAAAGNAACTGGCACGTGGCATGTNCTGCAGATGGATCAGCAG 343 i vvv i ? i i ? UCON1#Unknown 343 CCCTAAGTAAAGCAACTGGCATGTGGCGTGTTCTGCAGATGGATCAGCAG 392 rnd-5_family- 344 TGGC 347 UCON1#Unknown 393 TGGC 396 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.80 CpG sites = 35, Kimura (unadjusted) = 16.65 Transitions / transversions = 2.69 (35/13) Gap_init rate = 0.04 (13 / 342), avg. gap size = 1.38 (18 / 13) 444 17.58 0.00 9.17 rnd-5_family-756#SINE/MIR 1 119 (71) MIR3#SINE/MIR 33 141 (67) m_b16s601i1 rnd-5_family- 1 CTAGGAGCCAAGAGGGAGATCTTGGGNTCTTGCTTAATCCAGGCTGAGCC 50 i i ---- i - ? ----- i v vv MIR3#SINE/MIR 33 CTGGGAGTCA----GGAGACCT-GGGTTCT-----AGTCCCGGCTCTGCC 72 rnd-5_family- 51 ACTGACTCACTGTGTGACCTTGGGCAAGTCACTTGACCTCCTTGTGCCTC 100 i ?i v ii v MIR3#SINE/MIR 73 ACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTC 122 rnd-5_family- 101 AGTCAACCCAGCTGGAAAA 119 ivv i v v MIR3#SINE/MIR 123 AGTTTCCTCATCTGTAAAA 141 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.41 CpG sites = 10, Kimura (unadjusted) = 20.41 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (10 / 118), avg. gap size = 1.00 (10 / 10) 457 15.67 0.00 6.42 rnd-5_family-756#SINE/MIR 14 129 (61) MIR1_Amn#SINE/MIR 47 155 (75) m_b16s601i2 rnd-5_family- 14 GGGAGATCTTGGGNTCTTGCTTAATCCAGGCTGAGCCACTGACTCACTGT 63 i - ? ?----- ? v vv ?i i?i ? MIR1_Amn#SINE 47 GGGAGACCT-GGGTTCN-----ANTCCCGGCTCTGCCACTNGCCNGCTGN 90 rnd-5_family- 64 GTGACCTTGGGCAAGTCACTTGACCTCCTTGTGCCTCAGTCAACCCAGCT 113 ? ii ? ivv i v MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCT 140 rnd-5_family- 114 GGAAAACTGGAGGTAA 129 v - i i MIR1_Amn#SINE 141 GTAAAA-TGGGGATAA 155 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.28 CpG sites = 10, Kimura (unadjusted) = 19.28 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.06 (7 / 115), avg. gap size = 1.00 (7 / 7) 13 26.56 6.35 0.00 rnd-5_family-958#Unknown 54 116 (74) (CCCT)n#Simple_repeat 1 67 (0) m_b16s252i1 rnd-5_family- 54 CCCGCCCCCGTTCACT-CCTCTTTCCC-CCCTCCC-CCGTCGCTCGCTGC 100 v i vi v - ii - - v v v v (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 50 rnd-5_family- 101 TTTTC-CCCTCCCTCCC 116 i ii - (CCCT)n#Simpl 51 CTCCCTCCCTCCCTCCC 67 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 17 8.08 4.65 2.27 rnd-5_family-99#LTR/DIRS 2 44 (1341) (TTAG)n#Simple_repeat 1 44 (0) m_b16s252i0 rnd-5_family- 2 TTAGTT-GTT-GTTAGTATAGTTAATTAGTTNGATAGNTAGTGAG 44 - - - i ? v ? v (TTAG)n#Simpl 1 TTAGTTAGTTAGTTAGT-TAGTTAGTTAGTTAGTTAGTTAGTTAG 44 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 507 24.86 15.47 0.00 rnd-5_family-10481#SINE/tRNA 73 253 (727) LFSINE_Vert#SINE/tRNA 213 421 (38) m_b17s601i0 rnd-5_family- 73 TAATTAGCTCCTTTGGTGGCTGTCTCAGTAGAATGACTGCAGTTTGAGAA 122 i v i v v i iv i iivi vi ivi LFSINE_Vert#S 213 TAATTGGCACCCTTGTTGGCAGTCTCAGCAGAGAGGCCAAGGACTGAATG 262 rnd-5_family- 123 GGC-TTTATACTGAACTACCATCTAATCTG-AGAATTGGGCTCTCCACCT 170 - vv v v v i v- iv v i vv LFSINE_Vert#S 263 GGCATGGAGACTGAACTACCCTCTCACCTCTAGAGGTGGTCCCTCCAGGT 312 rnd-5_family- 171 CTAGGCTGAGTCACATTGGCAGGAAAA----------------------- 197 vi i v i iv i----------------------- LFSINE_Vert#S 313 CAGGGTTGAGGCACATTGGCGGGGCAGTGTGGGGAAGCTTGCACTGCCGC 362 rnd-5_family- 198 TGCCCATG-TGCACCTGTTCTGAGGATAATT--AGGACATCAGTCTCCAG 244 i - i v vi-- v LFSINE_Vert#S 363 TGCCCGTGCTGTACCTGTTCTGTGGATAAACAGAGGACTTCAGTCTCCAG 412 rnd-5_family- 245 GGCTGTCAA 253 LFSINE_Vert#S 413 GGCTGTCAA 421 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.89 CpG sites = 22, Kimura (unadjusted) = 30.45 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.03 (5 / 180), avg. gap size = 5.60 (28 / 5) 13 28.33 0.00 0.00 rnd-5_family-10481#SINE/tRNA 313 355 (625) (TTTT)n#Simple_repeat 1 43 (0) m_b17s252i5 rnd-5_family- 313 TTTTTGTTTGGTGTTTTTTTATTTATTTTTGTCTGTTTGTTTT 355 v vv v v v v i v v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 653 32.19 5.46 6.10 rnd-5_family-1279#DNA/hAT-Charlie 922 1910 (725) Charlie3#DNA/hAT-Charlie 757 1739 (967) m_b17s502i0 rnd-5_family- 922 AAAAGAAAATATGACGATGATTATATAAAATATGGCTTTACATGC-ATTG 970 iv v vvvi iv v i v i i- - iv Charlie3#DNA/ 757 AAAAGAAAATACCAAGAGTCCTACTTAAATTACGGGTTCAT-TGCAACAG 805 rnd-5_family- 971 GTGATCAAGAACGTCCAAAACCACTGTGTGTGATTTGTGGTGATGTTCTA 1020 iv v viv iv i v i i v i ivvv Charlie3#DNA/ 806 GTGATTCACATTCTCCAAGCCCGCTTTGTATAATATGTGGCGACCGGCTA 855 rnd-5_family- 1021 GCAAACAGCAGCC-TCAAACCTTCTCTACTTCGGCGCCATTTAGAAACTA 1069 v v - v - v vvv v vv iv i i i Charlie3#DNA/ 856 TCCAAC-GAAGCCATGAAACCTTCAAAACTGCTTCGCCACATGGAGACCA 904 rnd-5_family- 1070 GGCATCCTGCACAACTCGACAAGCCTGTTGATTTTTTCAAGCGAAAATTA 1119 i i iv vvv v v v iv vv Charlie3#DNA/ 905 AGCACCCTGCATTAAAAGACAAGCCTTTGGAGTTTTTCAAAAGAAAAAAA 954 rnd-5_family- 1120 GCTGAG-AGGAAAAGTGACATTACCAGTTTTATATCCAAAGCAAGTAC-T 1167 vv i- v i --- vv v i ---- iv i v vi - Charlie3#DNA/ 955 CGTGAACACGAAGA---ACAGAAGCAAT----TATTGAAGGCCACCACTT 997 rnd-5_family- 1168 GAT--AATGAAAATGCACTTGAAGCGTCATACCGCGTGAGCT-ACCGAGT 1214 v -- vivv vii i v ivv - - vi Charlie3#DNA/ 998 CATCAAATGTGTCTGCACTGAGAGCATCATTCTTAGTG-GCTAACCGCAT 1046 rnd-5_family- 1215 AGCAAAAGCATCAGAAGCCC-ATACCA-TAGCAGAGAGCTTGATTGGTCC 1262 v v - v -v i - i iii - ivvv Charlie3#DNA/ 1047 TGCTAAAGC-TAAGAAGCCCTTTACTATTGGTGAAGAG-TTGATCCTGCC 1094 rnd-5_family- 1263 ATG-TATAAAAGACGTAGTTCATTGCATGCTCGGAGAAAAGGCTGCA--- 1308 - - iiv i ---i ii i iivi ivv i i --- Charlie3#DNA/ 1095 -TGCTGCTAAGGAC---ATTTGTCGTGAACTTTTAGGAGAGGCTGCAGTT 1140 rnd-5_family- 1309 -AAAAGGATTGACATG-GTACCTTTGTCCAATAATACGTTGTCACGAAGA 1356 - -- i i - v i v viv ii vv iv vv v Charlie3#DNA/ 1141 CAAAAGG--TGGCACGTGTTCCTCTTTCGGCTAGCACCATAACTAGACGA 1188 rnd-5_family- 1357 ATTAATGACATGTCAAATAATGTAGAGACCACAATTGTACAGAGAGTGAA 1406 i v iv i vi i v i- -i - v Charlie3#DNA/ 1189 ATTGATGAAATAGCAGAGGATATTGAGG-CACAATTGT-TAGAGAG-GAT 1235 rnd-5_family- 1407 AAAT-AGT--CCATATTATGCTATGCAGTTGGATGAATCAACTGATGTAG 1453 v - -- i iv i v v v v i i v i v Charlie3#DNA/ 1236 TAATGAGTCACCGTGGTACGCAATCCAGGTTGACGAGTCTACCGATGTTG 1285 rnd-5_family- 1454 CTAATCTAGCTATTTTGCTACTGTTTGTACG-----TT----------AT 1488 vi ivvi v ivv vv v i ----- ---------- Charlie3#DNA/ 1286 ACAACAAGGCAACAATGCTTGTTTTTGTGCGATATATTTTTCAGGAGGAT 1335 rnd-5_family- 1489 GTGAATGAAGGTATGGTTGAAGAAGACTTGTTGTTTTGCCGACCATTGGA 1538 v i i -- v v viv - -- i ----- Charlie3#DNA/ 1336 GTGCATGAGGATATG--TTATGTGCACTT-TTG--TTGCCAACC-----A 1375 rnd-5_family- 1539 AGAACGTACAACTGGAGAAGATATCTTCAA---TCTGACTAA-TGCATAT 1584 v v -- i v ---v v --- i v i - i - Charlie3#DNA/ 1376 ACACC--ACAGCTGCAGAA---CTATTCAAGTCTTTGAATGATTACATA- 1419 rnd-5_family- 1585 TTTCAAGAAAAGGAAATAGATTGGTCTCGTTGCCTAGGCATTTGCACTGA 1634 -- i ---- v ii viv iv v i v v Charlie3#DNA/ 1420 --TCAGGAA----AACTGAATTGGTCATTTTGTGTCGGTATATGCACGGA 1463 rnd-5_family- 1635 TGGGGCCACATCAATGACGGGGAAGTATACTGGATTTGTAGCTCGAACAA 1684 i i vi vv v v ivi iv v v iiivi iiiv Charlie3#DNA/ 1464 CGGAGCGGCTGCCATGACTGGACGGCTTTCTGGTTTCACTACTCGGGTCA 1513 rnd-5_family- 1685 AAAAGGTTGCATC--AA---AAGTCTCTTGGACTCATTGCAGCATCCATA 1729 i i v -- ---i ----- v i iiv Charlie3#DNA/ 1514 AAGAGGTCGCTTCTGAATGTGAGTCT-----ACGCACTGTGTCATCCATA 1558 rnd-5_family- 1730 GACAAGCCCTCGC-AAC---AAAACG-CATGCCTGAGGGACTGAAGGAAG 1774 v iiv v - i --- i - -- --- v vi v Charlie3#DNA/ 1559 GAGAAATGCTGGCTAGCCGAAAAATGTCA--CCTGA---ACTTAACAACG 1603 rnd-5_family- 1775 TGCTGGACAATGCAGTGAAAATGGTGAATTTCA-TAAAAT-CACGGCCAA 1822 vi v vi iii v vi v iiv - i - i v -- Charlie3#DNA/ 1604 TTTTGCAGGATGTGATTAAAATTATCAACCACATTAAAGTACATGCCC-- 1651 rnd-5_family- 1823 CAAATTCCAGAATATTTCACGTA-CTTTGTGAAGAAATGGGT----AGTA 1867 iv i vv vv i- i i - i i i ii---- i Charlie3#DNA/ 1652 TTAACTCACGTCTG-TTCGCGCAGCTCTGTGAGGAGATGGACGCAGAGCA 1700 rnd-5_family- 1868 TACACGACTGTCTGTTGACCCATACTGAAGTTAGATGGCTCTC 1910 i v - v i---i i v v i Charlie3#DNA/ 1701 CACACGTCT-TCTCTTA---TACACAGAAGTGAGATGGCTTTC 1739 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.00 CpG sites = 143, Kimura (unadjusted) = 42.52 Transitions / transversions = 0.92 (143/156) Gap_init rate = 0.09 (86 / 988), avg. gap size = 1.33 (114 / 86) 890 35.81 2.19 2.86 rnd-5_family-1279#DNA/hAT-Charlie 1171 2084 (551) Charlie1#DNA/hAT-Charlie 1006 1913 (868) m_b17s502i1 rnd-5_family- 1171 AATGAAAATGCACTTGAAGCGTCATACCGCGTGAGCTACCGAGTAGCAAA 1220 v vvi i v v v i i i vi v vv Charlie1#DNA/ 1006 AATGAAAAAGCCACTGAAGCATCTTACAGGGTAAGTTATCGTATTGCATT 1055 rnd-5_family- 1221 AGCATCAGAAGCCCATACCATAGCAGAGAGCTTGATTGGTCCATGTATAA 1270 i vvv v i v v vi i viiv v i i Charlie1#DNA/ 1056 GGCTGGAGAAGCGCACACAATAGCTGAGAGACTAATAAAGCCTTGTACAG 1105 rnd-5_family- 1271 AAGACGTAGTTCATTGCATGCTCGGAGAAAAGGCTGCAAAAAGGATTGAC 1320 vv i v i v v v v iv v v i iii --- Charlie1#DNA/ 1106 TTGACATTGCTGAATGCCTGCTGGATGAAAAGTCAGTAAAAGAAAT---C 1152 rnd-5_family- 1321 ATGGTAC---CTTTGTCCAATAATACGTTGTCACGAAGAATTAATGACAT 1367 i i --- vi v i iv iv v vv v iv Charlie1#DNA/ 1153 ACGGCACTGCCACTTTCCAATGATACAGTAACTCGTCGAATTAAAGATTT 1202 rnd-5_family- 1368 GTCAAATAATGTAGAGACCACAATTG-TACAGAGAGTGAAAAATAGTCCA 1416 iv vivv ii ii ii- i i- ivvv vv v i v v - Charlie1#DNA/ 1203 AGCTGCAAACATGAAGACTG-AGTTAATATCTCGTCTGCAGAATTGTAC- 1250 rnd-5_family- 1417 TATTATGCTATGCAGTTGGATGAATCAACTGATGTAGCTAATCTAGCTAT 1466 -- v iv i iv i v v i i iiv v i Charlie1#DNA/ 1251 --TTTTGCCTTACAAATGGACGAATCTACAGACGTGGCTGGACTTGCTGT 1298 rnd-5_family- 1467 TTTGCTACTGTTTGTACGTTATGTGAATGAAGGTATGGTTGAAGAAGACT 1516 vv i i v v vv v iv vvv vi i ii Charlie1#DNA/ 1299 TTTGCTTGTATTCGTCCGGTATCAGCACCAACTAATCATCGAAGAAGATC 1348 rnd-5_family- 1517 TGTTGTTT---TGCCGACCATTGGAAGAACGTACAACTGGAGAAGATATC 1563 v i v --- ------ v iv vii v v vv v v Charlie1#DNA/ 1349 TTTTATGTGAATGC------TTGGCAACAAACACAAGTGGTGCTGAAATA 1392 rnd-5_family- 1564 TTCAATCTGACTAATGCATATTTTCAAGAAAAGGAAATAGATTGGTCTCG 1613 vv viv ivv v v vvvv v ivv vvi vvivi Charlie1#DNA/ 1393 TTCAAAGTGTTGAATAACTTTTTTGAATCTCATGGTTTATCCTGGAACAA 1442 rnd-5_family- 1614 TTGCCTAGGCATTTGCACTGATGGGGCCACATCAATGACGGGGAAGTATA 1663 i iv v i v v v v ii v ivv i Charlie1#DNA/ 1443 CTGTGTTGACATTTGCACTGATGGTGCAAAAGCAATGGTGGGTAAAACTG 1492 rnd-5_family- 1664 CTGGATTTGTAGCTCGAACAAAAAAGGTTGCATCAAAAGTCT---CTTGG 1710 vviiv v iv iivi v i --- --- v v Charlie1#DNA/ 1493 CTGGCGCCTTAGCACGAATCAAGGCAGTGGCACCAAA---CTGTACTAGT 1539 rnd-5_family- 1711 ACTCATTGCAGCATCCATAGACAAGCCCTCGCAACAAAACGCATGCCTGA 1760 v i viv i iv v v v ii? viv v v v Charlie1#DNA/ 1540 AGTCATTGTATTCTTCACCGCCACGCACTCGCAGTNAAAAAAAAGCCAGT 1589 rnd-5_family- 1761 GGGACTGAAGGAAGTGCTGGACAATGCAGTGAAAATGGTGAATTTCATAA 1810 vvv v i v v v ii v i vi v i v Charlie1#DNA/ 1590 TTCACTTAAGAATGTCCTTGATGAAGCAGTAAAAATTATTAATTTTATTA 1639 rnd-5_family- 1811 AATCACGGCCAACAAATTCCAGAATATTTCACGTACTTTGTGAAGAAATG 1860 v i vvii i v vv vv v v ii v v v Charlie1#DNA/ 1640 AATCTCGACCCTTGAGTACACGTCTTTTTAATATTCTGTGTGACGAAATG 1689 rnd-5_family- 1861 GGTAGTATACACG----ACTGTCTGTTGACCCATACTGAAGTTAGATGGC 1906 v ii ii---- - i --- i vv i Charlie1#DNA/ 1690 GGAAGTACGCATAAAGCACT-TCTGCTG---CATACCGAAGTACGATGGT 1735 rnd-5_family- 1907 TCTCACGGGGCAAAATCCTTGTGCGCTTGTTTGAGCTTAGAACGGAAATC 1956 v v i v iiv v i vv i v v v Charlie1#DNA/ 1736 TGTCTCGAGGAAAAGCACTTGTGCGATTGTTTGAGTTGCGAGCTGAACTA 1785 rnd-5_family- 1957 CTAGTTTTTTTCAACAGCCACCCTTTCCACCTTGCCAG-----CTGTATG 2001 viv i vviiv v ii - vv ----- - ii Charlie1#DNA/ 1786 GCCGCTTTTTTCATGGAACACCATTTTTA-CTTGAAAGAACGACTG-ACA 1833 rnd-5_family- 2002 GA-AAATAATGTCTGGCTCCAGAGCCTAGCTTATTTAGCAGATATTTTCT 2050 - iv vi i-- i -- v vv i i Charlie1#DNA/ 1834 GACAAACTATGGTTA--TTCAGA--CTTGGGTATTTGGCAGACATTTTCT 1879 rnd-5_family- 2051 CAAGAATTAATGACCTAAATTTATCTCTTCAAGG 2084 i i v i vv i iii i v Charlie1#DNA/ 1880 CGAAAATGAACGAAGTGAGCCTGTCACTTCAAGG 1913 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.16 CpG sites = 133, Kimura (unadjusted) = 49.01 Transitions / transversions = 0.72 (133/185) Gap_init rate = 0.04 (33 / 913), avg. gap size = 1.39 (46 / 33) 233 33.07 0.78 0.78 rnd-5_family-1279#DNA/hAT-Charlie 2014 2141 (494) Charlie16#DNA/hAT-Charlie 2118 2245 (806) m_b17s502i2 rnd-5_family- 2014 TGGCTC-CAGAGCCTAGCTTATTTAGCAGATATTTTCTCAAGAATTAATG 2062 - i i- i i iv v ii Charlie16#DNA 2118 TGGCTCACAAAGT-TGGCTTATTTAGCAGATATTTTTTCAAGGCTGAACA 2166 rnd-5_family- 2063 ACCTAAATTTATCTCTTCAAGGNCTCAATATAACAGTTTTCAATGTGCAA 2112 vi v iv ivv v ?vvv v i i vv i v ii v Charlie16#DNA 2167 CTCTCAATCAACAACTGCAAGGCAAAACTGTGAATGTTTTTACTGCACAT 2216 rnd-5_family- 2113 GACCGAGTTGAATCCATGATAAAGAAGTT 2141 viii i vvv v v v Charlie16#DNA 2217 GACAAGATCGCTGCAATGAAAATGAAGTT 2245 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.09 CpG sites = 19, Kimura (unadjusted) = 44.45 Transitions / transversions = 0.83 (19/23) Gap_init rate = 0.02 (2 / 127), avg. gap size = 1.00 (2 / 2) 498 30.06 0.57 0.57 rnd-5_family-1279#DNA/hAT-Charlie 2455 2628 (7) Charlie29b#DNA/hAT-Charlie 722 895 (299) m_b17s502i3 rnd-5_family- 2455 TTTTGGCTGAGTTTAAGAAACGAGTACCCCCTTCTGGCAGAAAAAGCTGC 2504 i i v i ivvi v i ivvv i i v i-i Charlie29b#DN 722 TTTTGGTTAAGTATGAGGTCTGATTATCCTGAACTAGCAAACAAAGCC-T 770 rnd-5_family- 2505 TGCAGTT-TTGTTACCATTTTCAACAACATACTTATGCGAGAAAGCGTTT 2553 v - iv vv iv i i i Charlie29b#DN 771 TGAAGTTATTAATACCATTTTGTACAACATACTTATGCGAACAGGCATTC 820 rnd-5_family- 2554 TCCTCGTATGCACATCTGAAAACCAAATACAGAAACAGACTTGATGCCGA 2603 iv i vv i ivvi iv v i vi iiv Charlie29b#DN 821 TCTGCATTAGTATTATTGAAGTCAAAATACAGAAACAGATTAAATATAGA 870 rnd-5_family- 2604 ACCAGACCTGAGACTTTATCTTTCT 2628 i i vi Charlie29b#DN 871 ACCGGACCTGAGGCTACATCTTTCT 895 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 29, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.01 (2 / 173), avg. gap size = 1.00 (2 / 2) 2445 7.82 2.45 2.45 rnd-5_family-128#RC/Helitron 47 413 (0) UCON99#RC/Helitron 1 367 (4) m_b17s502i4 rnd-5_family- 47 TATCTGATCCAAAACATTTCACATGATAAAAAAATGCAAGTTAGAAAAA- 95 ? i - vv - UCON99#RC/Hel 1 TATCTGATCNAAAACGTTTCACATG-TAAAAAAAGCCAAGTTAGAAAAAG 49 rnd-5_family- 96 --TAGTTCAGCCATATAAAGATGTGATATCTATAAAAACAGCCACGTTAG 143 --i i ? UCON99#RC/Hel 50 AACAGTTCAGCCGTATAAAGATGTGATATCTNTAAAAACAGCCACGTTAG 99 rnd-5_family- 144 AAAAGGGTTAGCCGTTTAAATGGTCAAGTTAAACAAGACACAATTAGGGC 193 i i UCON99#RC/Hel 100 AAAAGGGTTAGCCATTTAAATGGCCAAGTTAAACAAGACACAATTAGGGC 149 rnd-5_family- 194 TAATTT-GCTCCCCCT----AATTCAGAGCTCCCATGTGTGGGTTTATGA 238 ?i - i ---- i i i UCON99#RC/Hel 150 TANCTTGGTTCCCCCTCCCCAGTTCAGAGCTCCCACGCGTGGGTTTATGA 199 rnd-5_family- 239 AGCCCTGNAGGAATGGGGCCAAGTTAGCCCTAATTGCGTCTTGTTTAACN 288 - -- iv ii i ? UCON99#RC/Hel 200 A-CCCT--AGGAGGGGAACCAAGTTAGCCCTAATTGTGTCTTGTTTAACT 246 rnd-5_family- 289 TGACCATTATTAAACGGCTAACCCTTTTCTAACGTGGCTGTTTTTATAGA 338 i i i -- ? UCON99#RC/Hel 247 CGGCCGT--TTAAACGGCTAACCCTTTTCTAACGTGGCTGTTTTTNTAGA 294 rnd-5_family- 339 TNTCACATCTTTGTATGGATCTGNACGGTTCTTTCCCTAACTTGGCTTTT 388 ? i i -- ? v ii - UCON99#RC/Hel 295 TATCACATCTTCGCATGG--CTGAACTGTTCTTTTTCTAACTTGGC-TTT 341 rnd-5_family- 389 TTGTATATGTGAANTGTTTT-GATCA 413 ? ii i ? - UCON99#RC/Hel 342 TNGTGCATATGAAATGTTTTGGATCA 367 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.57 CpG sites = 24, Kimura (unadjusted) = 8.65 Transitions / transversions = 6.00 (24/4) Gap_init rate = 0.04 (14 / 366), avg. gap size = 1.29 (18 / 14) 2116 5.89 8.77 0.90 rnd-5_family-1533#LTR 30 337 (41) MER129#LTR 52 383 (86) m_b17s502i5 rnd-5_family- 30 ATCCGAATGATCACTACATGCAGATCCATAAAACAGTGAGCTTCCCAAAT 79 ? ii? MER129#LTR 52 ATCCGAATGATCACNACGCNCAGATCCATAAAACAGTGAGCTTCCCAAAT 101 rnd-5_family- 80 CAGACGCGTGCACAGAAGCAAAATCTCCATCTTGCAAGGACAGAGCGAGT 129 ? i i i MER129#LTR 102 CAGACGCGTGCANAGAAGCAAAATCTCCATTTTGCGAGGACGGAGCGAGT 151 rnd-5_family- 130 TCTACTAGGCATTTTAATGCCAAGGCAGGTCAGTCAGGTTATAATTGGCT 179 ? i v i MER129#LTR 152 TCTNCTAGGCATTTTAGTGCCACGGCAGGTCAGTCAAGTTATAATTGGCT 201 rnd-5_family- 180 CTAATTGGCACT-------G----AACATTTCTTTACCTGCAGCCGAGTG 218 i ------- ---- - MER129#LTR 202 CTAATTAGCACTCCCACAAGCTGTAACA-TTCTTTACCTGCAGCCGAGTG 250 rnd-5_family- 219 GCACTCAAAAAGGTGCGAAATTCTTTCCTGCCTTTGAAAA--------AA 260 v i -------- MER129#LTR 251 GCACTCAAAAAGGTGAGAAATTCTTTCCTACCTTTGAAAACATCAAAGAA 300 rnd-5_family- 261 CATCAAAGAAATCGTTTCCAATCTGATCCTTGACAACCGAAAGTNCCCAC 310 v i - v -? i MER129#LTR 301 AATCAAAGAAATCGCTTCCAATCTGATCCTT-ACAACCGAATG-CCCCGC 348 rnd-5_family- 311 TGATCAGTATA----AGGGGTA----CAGCAGCAC 337 i ---- i ---- v MER129#LTR 349 TGATCAGCATAAGCGAGGGGCAAACGCATCAGCAC 383 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.98 CpG sites = 13, Kimura (unadjusted) = 6.30 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.03 (8 / 307), avg. gap size = 3.75 (30 / 8) 2048 8.60 2.17 2.80 rnd-5_family-1673#DNA/Kolobok 49 371 (0) UCON29#DNA/Kolobok 90 410 (29) m_b17s502i6 rnd-5_family- 49 TATCTNGTAACTTCTCTGATGTAAACACCAGTTNTTACGTC-ATTAATNC 97 ?v v iv iiv -- ? v? -i ii? UCON29#DNA/Ko 90 TATCTGCTTACTTTACTGACAAAAACA--AGTTTTTACTNCTGTTAGCAC 137 rnd-5_family- 98 T-CATGAGCCAGTACAGCTATGGGAGAGTGAGCTGGATTCTGTTCTGCCT 146 - - i i i i i UCON29#DNA/Ko 138 TGCA-GAGCCAATACAGCTACGGAAGAGCGAGCTGGATTCTATTCTGCCT 186 rnd-5_family- 147 CACGCATCATCGACAAAATTGTCAGCTAAGTTCTGACTGCAGAATCTTTA 196 i i i i UCON29#DNA/Ko 187 CATGCATCATCAACAAAATTGTCAGCTAAGTTCCGATTGCAGAATCTTTA 236 rnd-5_family- 197 TTACTGGTGATGATGCAAGAGGCAGA---AACACAGCTTGATTTTCAGAT 243 i ? --- UCON29#DNA/Ko 237 TTACTGGTGATGATGTANGAGGCAGAAAGAACACAGCTTGATTTTCAGAT 286 rnd-5_family- 244 CCCAGGTGGAGTTTGCAGCGCTGGCAGTTTAGAAAAATCACCTTGTTTTT 293 v ? - i ---- UCON29#DNA/Ko 287 CCCAGGTTGAGTTTGCAGNGCTGGCAG-TTAGAAAAATCATC----TTTT 331 rnd-5_family- 294 GACTTGTAAACTGAGCAAATTTGATCATGGAAGTCACTGAGAGGGAATAA 343 -? i i UCON29#DNA/Ko 332 GACTTGTAAACTGAGCAAATTTGAT-NTGGAAGTCATTGAGAGAGAATAA 380 rnd-5_family- 344 ATATGGAA-CCTGC-ATGTCATTTTTACAG 371 - ii - UCON29#DNA/Ko 381 ATATGGAACCCCACGATGTCATTTTTACAG 410 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.47 CpG sites = 21, Kimura (unadjusted) = 9.50 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.04 (14 / 322), avg. gap size = 1.14 (16 / 14) 240 9.52 0.00 0.00 rnd-5_family-1872#DNA/hAT-Charlie 2 43 (36) MER58A#DNA/hAT-Charlie 3 44 (180) m_b17s502i7 rnd-5_family- 2 GGGGTGGGCAAACTACGGCCCGCGGGCCGGATCCGGCCCNTC 43 v ii ?i MER58A#DNA/hA 3 GGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCC 44 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.61 CpG sites = 3, Kimura (unadjusted) = 10.61 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 211 18.73 9.23 1.43 rnd-5_family-1938#LINE/L2 395 459 (373) L2c_3end#LINE/L2 341 410 (68) m_b17s601i1 rnd-5_family- 395 TAATT-TCTGT----ATGTTCGTCTAGTCAGTTTAGATTGTAAGCTCTTC 439 - ----? ii vv vii - i i i i L2c_3end#LINE 341 TAATTGTCTGTTTACNTGTCTGTCTCCTCCACT-AGACTGTGAGCTCCTT 389 rnd-5_family- 440 G-GGGCAGGGACCGTGTTTTA 459 - i L2c_3end#LINE 390 GAGGGCAGGGACCGTGTCTTA 410 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.78 CpG sites = 9, Kimura (unadjusted) = 22.78 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.75 (7 / 4) 230 17.46 4.69 1.52 rnd-5_family-1938#LINE/L2 404 467 (365) L2d2_3end#LINE/L2 416 481 (74) m_b17s601i2 rnd-5_family- 404 TATGT-TCGTCTAGTCAGTTTAGATTGTAAGCTCTTCG-GGGCAGGGACC 451 - i vvi ii - i i - L2d2_3end#LIN 416 TATGTCTTGTCTCCCCAACT-AGATTGTAAGCTCCTTGAGGGCAGGGACC 464 rnd-5_family- 452 GTGTTTTA-ACTTGTTT 467 i i - v L2d2_3end#LIN 465 ATGTCTTATACTTCTTT 481 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.45 CpG sites = 8, Kimura (unadjusted) = 20.45 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.00 (4 / 4) 1020 13.63 11.43 4.20 rnd-5_family-1960#LINE/CR1 17 261 (80) CR1-13_AMi#LINE/CR1 323 584 (140) m_b17s551i0 rnd-5_family- 17 TGAATTTAAAAGGCAACANACTGAATAATTTAAAAC--ATAAGTGNAAAT 64 v i --------- -- iv ? CR1-13_AMi#LI 323 TGAAATTGAAAGGCAACA---------ATTTAAAACTGATAAAAGGAAAT 363 rnd-5_family- 65 ACTTTTTAAAATNCAATGTATAATTAAC-TGTGGAACTCACTGCTGCAGG 113 vv -i? i - ii i CR1-13_AMi#LI 364 ACTTTTTTTA-CACAATGCATAATTAACCTGTGGAACTCACTGCCACAAG 412 rnd-5_family- 114 ATA---CTGAGGCAAATAGCTCAG--------------GATTAGACATTT 146 --- v v i -------------- CR1-13_AMi#LI 413 ATATCACTGAGGCCAAGAGCTTAGCAGGATTCAAAAAGGATTAGACATTT 462 rnd-5_family- 147 ATATGAAGAAT---AGCATCTGCAGTTACACTAGCTAGGATAAAAT-TAC 192 i v i--- i i i v v- i CR1-13_AMi#LI 463 ATATGGATAACGAGAACATCCGCAGTTACATTAGATAGGATAAAAAATAT 512 rnd-5_family- 193 AAGGGCTATCAGTCCTCATGCTTCAGGGCATAAANTGATCACCAGCT--- 239 v - i? i?ii i i i --- CR1-13_AMi#LI 513 AAGGGATAT-AANCCTCATGCTTCAGGGCATAAGCCAACCACTAACTGAC 561 rnd-5_family- 240 GGGGTCAGGAAGAAA-TTCCCCT 261 i - CR1-13_AMi#LI 562 GGGGTTAGGAAGAAACTTCCCCT 584 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.64 CpG sites = 22, Kimura (unadjusted) = 15.65 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.08 (19 / 244), avg. gap size = 2.05 (39 / 19) 311 19.53 0.00 3.66 rnd-5_family-2154#Unknown 93 177 (593) C UCON69#DNA/hAT (330) 156 75 m_b17s502i8 rnd-5_family- 93 TCNGTTTACACTGTGATGGCTGTATNTTCGCAATGGGAAAGAGATAGAAG 142 ? i i v v i v --? iviv i - v i C UCON69#DNA/hA 156 TCGGTTCACATTTTGAAGGTTTT--CTTCGCAACCATAAGG-GCTAGAAA 110 rnd-5_family- 143 CTTNATTTTTTTAAATGAAAGCTTAGAATTTGCAG 177 ?? v i v C UCON69#DNA/hA 109 CTTANTTTTTTTAAATGAAAGCTTAGATTCTGGAG 75 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.13 CpG sites = 8, Kimura (unadjusted) = 24.13 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.00 (3 / 3) 379 19.56 4.83 4.83 rnd-5_family-2154#Unknown 557 701 (69) UCON60#Unknown 140 284 (16) m_b17s502i9 rnd-5_family- 557 AAGTTTCAAGCTTCAGCCATTTTTGCTGTAGCCCTGT-CNAAAATGGTAA 605 vv i vvv vv vv i- ? ---- UCON60#Unknow 140 AAGTTTATAGCTTCAGCCGTTTTTGAGTTATACGAGCACAAAAA----AA 185 rnd-5_family- 606 GTATGGTTAGA-ATTATTTTACAATGGGAAAAGTATTTTTCCCC-ACTCT 653 ii -- v - - v ?v i v ii - ii UCON60#Unknow 186 ACAT--TTCGATATT-TTTTAGAANTGGAAAAGTGTATTTCTTCTATCCT 232 rnd-5_family- 654 CCCATAACTCAAAA-TNGCTGAAGGGATTTTGCTCAAACGTT---AAGAA 699 v -i? vv ? v --- UCON60#Unknow 233 CGCATAACTCAAAAACGGCTGAACCGATTTNGCTCAAACTTTCAAAAGAA 282 rnd-5_family- 700 AT 701 UCON60#Unknow 283 AT 284 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.65 CpG sites = 10, Kimura (unadjusted) = 23.47 Transitions / transversions = 0.59 (10/17) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.17 (14 / 12) 13 17.22 4.88 2.38 rnd-5_family-2430#LINE/L1 149 189 (1203) (CAAGA)n#Simple_repeat 1 42 (0) m_b17s252i4 rnd-5_family- 149 CAAGACCAGACAATACAAAACCAGAC--GACACTACATAGACA 189 v v i v -- vv - (CAAGA)n#Simp 1 CAAGACAAGACAAGACAAGACAAGACAAGACAAGACA-AGACA 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.50 (3 / 2) 284 29.00 0.00 16.90 rnd-5_family-2451#SINE/MIR 4 169 (244) MIRc#SINE/MIR 41 182 (86) m_b17s601i3 rnd-5_family- 4 GCCAGGAAAACCAGGGTTAGGTCCCAGGCCTGGCTATCAGATCTGCTGTT 53 i i v v ----- v i ------- iii MIRc#SINE/MIR 41 GTCAGGAAGACCTGGGTTCG-----AGTCCCGGCT-------CTGCCACT 78 rnd-5_family- 54 TTCTATTCCTGGCTTTGGGACCATGAGCGAGTCTCTGCACCGCTGGGTGC 103 v ------ v v v i i v vv v vv v MIRc#SINE/MIR 79 TACTA------GCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 rnd-5_family- 104 CTCGGTTTCCCCAGCTATCAAATGGAGCTAATCAAGGTTTTGTTTGTTCT 153 i i v i v i v v ------ iii ii MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAA------TACCTGCCCT 166 rnd-5_family- 154 CCCCATTTTACAGGGT 169 v i ii i MIRc#SINE/MIR 167 GCCTACCTCACAGGGT 182 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.76 CpG sites = 21, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.15 (24 / 165), avg. gap size = 1.00 (24 / 24) 202 20.00 0.00 0.00 rnd-5_family-2451#SINE/MIR 147 186 (227) C MIR#SINE/MIR (110) 152 113 m_b17s601i4 rnd-5_family- 147 TTGTTCTCCCCATTTTACAGGGTGGGAAACCGAGACACAG 186 i v ivvi i i C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.72 CpG sites = 5, Kimura (unadjusted) = 23.72 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 480 20.31 8.29 2.08 rnd-5_family-259#DNA/hAT 18 198 (61) MER121B#DNA/hAT 2 193 (214) m_b17s502i10 rnd-5_family- 18 GGATACGNGAACCTCATGGAGTTCGAGGTTTTGCGAA-CCTCTC--ACTN 64 i v ? i vi i v ? ivi?? i? ? - v-- ? MER121B#DNA/h 2 GGGTAGGGGAGCCTGGTAGTGNTTTGNNTTTCNCNAAACCTCTANAACTT 51 rnd-5_family- 65 TGTTTT-----GGGTTCGCAGTTTGCAAAACTAGTTCGAGTT---CGNAN 106 v -----i v i viv i i vv i --- ? ? MER121B#DNA/h 52 TTTTTTTTNAAAGCTTTGGGTTTCGCGAAACTTTTTCAAGTTTCGCGAAA 101 rnd-5_family- 107 --TTTTTTNCCTGTAATT-ACACGTGTACTTGTTTTCAAGGGTGATTCAA 153 -- ? - - v ---i i vv vi i MER121B#DNA/h 102 CGTTTTTTCCCT-TAATTTAAAC---CATTGTTTTTCAAGGGAAATTTAA 147 rnd-5_family- 154 TTTTAAAAA-ACGTTTTTCTAGCTAAAGGGAAGCCTGTGCTATGTA 198 ? - i i v i MER121B#DNA/h 148 TTTNAAAAACATGTTTTTCTAACTAAATGGAAGCCTGTGCTATGCA 193 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.32 CpG sites = 20, Kimura (unadjusted) = 25.93 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.06 (11 / 180), avg. gap size = 1.73 (19 / 11) 1809 24.87 0.86 1.38 rnd-5_family-2686#LINE/RTE-BovB 1 583 (1) MamRTE2#LINE/RTE-BovB 379 958 (594) m_b17s551i1 rnd-5_family- 1 CATCGCTCCAACCNTGTTTGCGNTTTTTATTGC--CGTCATTCTTTACCT 48 v? v iv ? v v v -- -- v vi i MamRTE2#LINE/ 379 CATCGCTCCAACACTCTTCTCGATATTTCTTTCTACGT--TGCTACATCT 426 rnd-5_family- 49 NATCGCTGANAAGNTCCCCGCTGGCGTTGACATCGANTACAGAATGGATG 98 ? i i i ? i? vv i v v vv vi ? v i MamRTE2#LINE/ 427 GACCACCGATAAACTCCCACCCGGAGTAGAATTAAATTACCGAACGGATG 476 rnd-5_family- 99 GNAAGCTNTTCAANCTTAGCCGNCTCCGANCCAAGACTAAGATCTCCACG 148 ? v ? ? i ? i ? i i i i v i MamRTE2#LINE/ 477 GAAATCTGTTCAATCTCAGCCGGCTTCGAGCTAAAACTAGGACCTCCTCA 526 rnd-5_family- 149 ACATCNATCGCTGANCTTCAGTATGCNGATGACNGCGCNATCCTCGCNCA 198 iiv ? ii ? i i ? i?v i?i vivi ? MamRTE2#LINE/ 527 GTCTCAATCATTGAACTTCAATACGCTGATGATGCCGTAGTGTGTGCTCA 576 rnd-5_family- 199 CTCNGAGAAAGATCTTCAAACNATC-CTGAACGTNTTTGCCGATGCTTAC 247 ? iiv i i ? - - ? i v v i MamRTE2#LINE/ 577 CTCAGAAGCAGATCTCCAAGCAATCGCTGA-CGTCTTTACCGAGGCATAT 625 rnd-5_family- 248 NNANGNCTNGG--TCTCACTCAATATCGAGAAAGACTAAAGTGCTCTATC 295 ?? ?i?v ? -- v i i i v - i i ii MamRTE2#LINE/ 626 GAAAAAATGGGATTGTCGCTTAACATCCA-AAAGACTAAGGTACTTCATC 674 rnd-5_family- 296 AGCCCGCTCCAAACCNTGCATCACGNTCCGGCCCCATCAATCAANATCGA 345 ivvv v --- - v ii? ii iv iv ? iv MamRTE2#LINE/ 675 AAAAAGCTCCTAA---TG-AGCATACTCCAACCCCGGCAATTCAGATTCA 720 rnd-5_family- 346 CGGAGAGACNCTGGAGAACGTCGAGCATTTCCGCTACCTCGGNAGCCANC 395 i v ? v ii vv v ? ? MamRTE2#LINE/ 721 TGGTGAGACGCTGGAGAACGTGGAATATTTCCCGTACCTAGGAAGCCATC 770 rnd-5_family- 396 TTTCNCAAAAGGCAGACATCGACGCGGAAATTCAGCACAGGATCCGGTGC 445 i ? i i v i i vi i iv vv vii i MamRTE2#LINE/ 771 TCTCACAGAAAGCTGACATTGATGAAGAAATTCAACATCGCCTCAAATGT 820 rnd-5_family- 446 GCCAGCGCANCTTTTGGACGACTGCTNAAACGNGTCTTCGAAGATCGCGA 495 v ? i i v vv? ? v i ii MamRTE2#LINE/ 821 GCAAGCGCAGCCTTCGGACGCCTGAAGAAACGGGTGTTCGAGGACTGCGA 870 rnd-5_family- 496 CNTNCGGAANGACACCAAGNTTCTNGTCTACAAGGCNGTTGTTATCCCCG 545 ? ?v ivv? v i? v ? i v ? i v i MamRTE2#LINE/ 871 CATTAGATCTGAAACCAAACTTATGGTTTACCAGGCAGCTGTGATCCCCA 920 rnd-5_family- 546 CNCTCCTGTATGGGTCCGAAACCTGGGTNACNTACAGA 583 ?i v i iv i i v ii? ? MamRTE2#LINE/ 921 CCTTGCTGTACGGAGCTGAGACGTGGACAACATACAGA 958 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.68 CpG sites = 81, Kimura (unadjusted) = 33.96 Transitions / transversions = 1.31 (81/62) Gap_init rate = 0.02 (11 / 582), avg. gap size = 1.18 (13 / 11) 255 28.20 7.30 4.37 rnd-5_family-3134#LINE/L2 897 1074 (11) AmnL2-1#LINE/L2 1316 1498 (1115) m_b17s601i5 rnd-5_family- 897 GTTAAGTGATCTCCTCTCATCTGACT--------CTCATTCTCTTTTTTT 938 -i i iiv - -------- v i ii - AmnL2-1#LINE/ 1316 GTTAA-CGACCTCCTCCTTTCTG-CTGATGANGGCTCTTTCTCCTTCCT- 1362 rnd-5_family- 939 CATCCTTCCTGACCTCTGTGCTGCTTTTCATGCTGTCAACCATGACATCC 988 i i i v v i iv ii vi vv AmnL2-1#LINE/ 1363 CATTCTCCTTGACCTCAGTGCAGCCTTCGACACTGTGGACCATTCCATCC 1412 rnd-5_family- 989 TTCCCAATCGCCTGGGACCGTT-TGCTGGAGTCTCAGAGAACTGGCCNCC 1037 i ivi i -vv ?v i - v v v i---- vv ? AmnL2-1#LINE/ 1413 TCCTGGACCGCCT-CCANAGCTATGCAGGCGTCTCTGG----TTCCCTCC 1457 rnd-5_family- 1038 T----TGGTTTTGCTCCCATCTATCAGAGTCCTCTTTTTTT 1074 ---- ii i i i viv i i AmnL2-1#LINE/ 1458 TGTCATGGTTCCGCTCCTACCTATCAAACCGCTCTTTCTCT 1498 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.26 CpG sites = 29, Kimura (unadjusted) = 37.07 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.06 (11 / 177), avg. gap size = 1.91 (21 / 11) 413 10.29 0.00 0.00 rnd-5_family-3500#DNA/hAT-Charlie 1 68 (416) Charlie30a#DNA/hAT-Charlie 1 68 (723) m_b17s502i11 rnd-5_family- 1 CAGGGGTGGGGAACCTACGGCCCGCGGGCCGGATCCGGCCCGCTGCTTAA 50 v i v v i Charlie30a#DN 1 CAGGGGTGGGGAACCTCCGGCCCGCGGGCCGGACCCGGCCCTCGGCTTGA 50 rnd-5_family- 51 TTTCATCCGGCCCGCGGG 68 vi Charlie30a#DN 51 TTTCATCCGGCCCCTGGG 68 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.08 CpG sites = 3, Kimura (unadjusted) = 11.08 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 11 25.49 0.00 6.12 rnd-5_family-3500#DNA/hAT-Charlie 235 286 (198) (AGCCCCG)n#Simple_repeat 1 49 (0) m_b17s252i3 rnd-5_family- 235 AGCCCCGAGCCTCGGCGCCCCCCACCCCGCGGGGCTGGAGCCGCGAGCGC 284 - v v - v v - i v iv v v (AGCCCCG)n#Si 1 AGCCCCGAGCC-CCGAG-CCCCGAGCCC-CGAGCCCCGAGCCCCGAGCCC 47 rnd-5_family- 285 CG 286 (AGCCCCG)n#Si 48 CG 49 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 509 8.57 2.86 0.00 rnd-5_family-3500#DNA/hAT-Charlie 415 484 (0) Charlie30a#DNA/hAT-Charlie 719 790 (1) m_b17s502i12 rnd-5_family- 415 TGTGTGTGGCCCGCGACTGATTTT--TTCTGTGGGTCAATGGCCCCTGAT 462 i v i -- i ii Charlie30a#DN 719 TGTATGTGGCCCTCGATTGATTTTTTTTCTGTGGGTCAGTGGCCCTCGAT 768 rnd-5_family- 463 AGAAAAAAGGTTCCCCACCCCT 484 Charlie30a#DN 769 AGAAAAAAGGTTCCCCACCCCT 790 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.77 CpG sites = 5, Kimura (unadjusted) = 9.27 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.01 (1 / 69), avg. gap size = 2.00 (2 / 1) 13 21.67 2.63 0.00 rnd-5_family-3724#SINE/tRNA 766 803 (4485) (GTTTT)n#Simple_repeat 1 39 (0) m_b17s252i0 rnd-5_family- 766 GTTTTGGTTTGTTTTCTTAT-TTTATTTGTGTTTTCTTT 803 v v v - vv v v (GTTTT)n#Simp 1 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 248 33.09 2.54 5.22 rnd-5_family-3724#SINE/tRNA 1984 2101 (3187) LFSINE_Vert#SINE/tRNA 80 194 (265) m_b17s601i6 rnd-5_family- 1984 CCAGAGCAGCAGTAGTCAAA---TATGTCCAGCTTGTGTCCGTTTGGCGC 2030 iv i iii i ---i vv v vii v i i i v LFSINE_Vert#S 80 CCAGGTCAGTAGTGACCGAAAGTCATTACCATCTGACGGCTGTTCGGTGG 129 rnd-5_family- 2031 CCTGCGTGAGGTGATTTGGGGTTAGTGGTCTCCATCCATTTCTGACTGGG 2080 ii ii ------ i vi v iv v i LFSINE_Vert#S 130 CCTATGTGAAATGA------GTTGGTGGTCTCAGTCCAGTTCCTAGTGGA 173 rnd-5_family- 2081 CAGGTGTGCACGCTAAAAAGC 2101 v iii v i LFSINE_Vert#S 174 CAGGTGTCCACATCACAAAAC 194 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.91 CpG sites = 24, Kimura (unadjusted) = 45.94 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.29 (9 / 7) 496 25.34 1.72 4.73 rnd-5_family-3724#SINE/tRNA 2148 2321 (2967) LFSINE_Vert#SINE/tRNA 289 457 (2) m_b17s601i7 rnd-5_family- 2148 CCCCTCGATGTCGTCTCTCNCCAGGTCATGCTGGAAACAAACTGG---GC 2194 i v v v i -- v v v ii v i --- v LFSINE_Vert#S 289 CCTCTAGAGGTGGTCCCTC--CAGGTCAGGGTTGAGGCACATTGGCGGGG 336 rnd-5_family- 2195 CGCTGTGGGTGAAGCTTGCGCTGCCATTGCCTGAGCNGTACCTGCTCTGA 2244 iv - i ii i v ? i - LFSINE_Vert#S 337 CAGTGTGGG-GAAGCTTGCACTGCCGCTGCCCGTGCTGTACCTGTTCTG- 384 rnd-5_family- 2245 GGCCGGGATACATAGAGCAATCCAGCCTCCAGGCCCCGCAGTCCAGCAGC 2294 ----v v i v v i i v ivv i i v LFSINE_Vert#S 385 ----TGGATAAACAGAGGACTTCAGTCTCCAGGGCTGTCAATCCGGCACC 430 rnd-5_family- 2295 TTTCACTGGCATGAAATTCATCTGAAA 2321 vi iv ii i LFSINE_Vert#S 431 TTTCACGAGCACTAAATTCACTTAAAA 457 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.88 CpG sites = 22, Kimura (unadjusted) = 31.48 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.05 (9 / 173), avg. gap size = 1.22 (11 / 9) 13 7.99 3.45 3.45 rnd-5_family-3724#SINE/tRNA 3782 3810 (1478) (CTGCC)n#Simple_repeat 1 29 (0) m_b17s252i1 rnd-5_family- 3782 CTG-CCTGCCCCGCCCCGCCCTGTCCCTGC 3810 - i i - (CTGCC)n#Simp 1 CTGCCCTGCCCTGCCCTGCCCTG-CCCTGC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 12 13.69 6.25 0.00 rnd-5_family-3724#SINE/tRNA 4738 4769 (519) (CCAA)n#Simple_repeat 1 34 (0) m_b17s252i2 rnd-5_family- 4738 CCAAAAAACCAACCAGCCAA--AACCACCCAACC 4769 vv i -- v (CCAA)n#Simpl 1 CCAACCAACCAACCAACCAACCAACCAACCAACC 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 2.00 (2 / 1) 808 7.57 0.00 5.66 rnd-5_family-3825#SINE/5S-Deu-L2 1 112 (29) AmnSINE1#SINE/5S-Deu-L2 446 551 (24) m_b17s502i13 rnd-5_family- 1 TGCCGTATTCCACCCCAGAGGTGGCTGCATTTCAGTGGTAGGTGAAATGA 50 ii i i AmnSINE1#SINE 446 TGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTGA 495 rnd-5_family- 51 TTCCTATATCTGTATGCAGTTTGTAAAGCGCTTTGGGATCCTTCTGGATG 100 i ------ i i v AmnSINE1#SINE 496 TCC------CTGTATGTAGCTTGTAAAGCGCTTTGGGATCCTTCGGGATG 539 rnd-5_family- 101 AAAGGCGCTATA 112 AmnSINE1#SINE 540 AAAGGCGCTATA 551 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.02 CpG sites = 7, Kimura (unadjusted) = 8.11 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.00 (6 / 6) 365 23.68 0.00 0.00 rnd-5_family-4255#DNA/PIF-Harbinger 42 117 (43) MER133A#DNA/PIF-Harbinger 13 88 (16) m_b17s502i14 rnd-5_family- 42 TATTCTGCTCTCCCTACATGCGCGGAATTCCCATTGACGTCAATGGGAGN 91 v vv i ii v i i i ? MER133A#DNA/P 13 TATTCTCCTCTCGATGCGCGCGCGTAACTCCCATTAACGTTAATGGGAGT 62 rnd-5_family- 92 TCCGTGCATGTAGGGAGAGCAGAATA 117 v i i i vv i v MER133A#DNA/P 63 TACGCGCGTGCATCGAGGGGAGAATA 88 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.24 CpG sites = 10, Kimura (unadjusted) = 29.37 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 335 31.31 4.42 5.50 rnd-5_family-4979#LTR/ERV1 73 366 (1667) HERV17#LTR/ERV1 1970 2260 (6366) m_b17s701i0 rnd-5_family- 73 CAGGGCAAGGTGTACGCCCTTAGAATGCATTCTGGTGAACTGGAAAGTGT 122 i ii--- i ii i v i i vvvi HERV17#LTR/ER 1970 CAAGGCAAAA---ACGCCCCTAAGATGTATTCTGGAGAATTGGGACCAAT 2016 rnd-5_family- 123 TTGGA--TCGGATCCGTTGATTAAAAGTAA--ATTGAAAAGGTTCTGTAC 168 iv-- i -- i i --i v -- i v v vvv -- HERV17#LTR/ER 2017 TTGACCCTCAGA--CGCTAA--GAAAGAAACGACTTATATTCTTCTG--C 2060 rnd-5_family- 169 AGTA--GACTGGCCTCAATATCAGCT---AGAGGACCAGGAAAGGTGGCC 213 -- v v i vv --- i i---i vv HERV17#LTR/ER 2061 AGTACCGCCTGGCCACGATATCCTCTTCAAGGGGG---AGAAACCTGGCC 2107 rnd-5_family- 214 ACCGGAAGGATCACTTAATTATAACACGATCCTTCAATTGCTTCTGTTTT 263 v v i vvvv v v i v ii ivvi v HERV17#LTR/ER 2108 TCCTGAGGGAAGTATAAATTATAACACCATCTTACAGCTAGACCTCTTTT 2157 rnd-5_family- 264 GTCAGCGAACGGGTAAATGGAATGAACATATG---TATGTACAGTCGTTT 310 viivi ivi i i ---i --- iv v i HERV17#LTR/ER 2158 GTAGAAAAGAAGGCAAATGGAGTGAA---GTGCCATATGTACAAACTTTC 2204 rnd-5_family- 311 ATGTTGTTAAGAGATAGGTCAGATATTTTGC-ANAAGTGTAATTTGACTC 359 v v ii i iv iv - v i- ? i ivvi HERV17#LTR/ER 2205 TTTTCATTAAGAGACAACTCGCA-ATTATGTAAAAAGTGTGATTTATGCC 2253 rnd-5_family- 360 CGACAGG 366 v HERV17#LTR/ER 2254 CTACAGG 2260 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.17 CpG sites = 45, Kimura (unadjusted) = 41.40 Transitions / transversions = 1.07 (45/42) Gap_init rate = 0.08 (22 / 293), avg. gap size = 1.32 (29 / 22) 336 27.60 4.76 4.31 rnd-5_family-4979#LTR/ERV1 88 318 (1715) PABL_B-int#LTR/ERV1 491 722 (6400) m_b17s701i1 rnd-5_family- 88 GCCCT-TAGAATGCATTCTGGTGAACTGGAAAGTGTTTGGATCGGATCCG 136 - i iiv ? i vi i i vvv ? ? --- PABL_B-int#LT 491 GCCCTCTGGGGAGNATCCTGTCGGATTGGAAACACTNTGGNT---ATCCG 537 rnd-5_family- 137 T---TGATTAAAAGTAAATTGAAAAGGTTCTGT-ACAGTA--GACTGGCC 180 i--- i v ? --- vv v i -i i -- vi PABL_B-int#LT 538 CCCATGACTAAAAGAAAANT---AATCTACTATTGCAATACGGTTTGGCC 584 rnd-5_family- 181 TCAATATCAGCTAGAGGACC--AGGAAAGGTGGCCACCGGAAGGATCACT 228 -- i vv i vv i i -- ivivvv? i vi PABL_B-int#LT 585 --AATGTACGTTTTAGAATCTGAGGAAAGGTGGCCGATTTTNGGGTCCTT 632 rnd-5_family- 229 TAATTATAACACGATCCTTCAATT-GCTTCTGTTTTGTCAGCGAACGGGT 277 v ii vvi v iv i - vv - v iv v PABL_B-int#LT 633 GAGCTATTCTACCATCTATCAGTTAGAATC-GTTTTGTCAGAGGTCGGGA 681 rnd-5_family- 278 AAATGGAATGAACATA-TGTATGTACAGTCGTTTATGTTGTT 318 i ? - -i? v v ? i PABL_B-int#LT 682 AAATGGGANGAA-ATACCNTATGTCCAGGCNTTTATGTTGCT 722 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 30, Kimura (unadjusted) = 36.46 Transitions / transversions = 0.97 (30/31) Gap_init rate = 0.07 (17 / 230), avg. gap size = 1.24 (21 / 17) 348 28.36 2.90 2.90 rnd-5_family-4979#LTR/ERV1 176 313 (1720) HERV4_I#LTR/ERV1 1112 1249 (5290) m_b17s701i2 rnd-5_family- 176 TGGCCTCAATATCAGCTAGAGGACCAGGAA----AGGTGGCCACCGGAAG 221 i ? ? i??vii ----i i i vi v HERV4_I#LTR/E 1112 TGGCCCCANTATNAGCTGNNCAGCCAGGAACAATGGGCGGTCAATGGTAG 1161 rnd-5_family- 222 GATCACTTAATTATAACACGATCCTTCAATTGCTTCTGTTTTGTCAGCGA 271 --- - i v v ivvi i iv v i HERV4_I#LTR/E 1162 ---C-CTTAATTATGACACCATCCTGCAATTAGACCTATTTTGCAAGAGG 1207 rnd-5_family- 272 ACGGGTAAATGGAATGAACATATGTATGTACAGTCGTTTATG 313 vv i vvv vvivii v v i HERV4_I#LTR/E 1208 CAGGGCAAATGGTCAGAAATCCCATATGTACAGGCCTTCATG 1249 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 19, Kimura (unadjusted) = 37.50 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.04 (5 / 137), avg. gap size = 1.60 (8 / 5) 286 24.62 0.00 0.00 rnd-5_family-4979#LTR/ERV1 1078 1142 (891) MER52-int#LTR/ERV1 2600 2664 (4427) m_b17s701i3 rnd-5_family- 1078 AATTATAAAGGGTATCTTTACCAGCCGTGCNGCCCCTGATATTAAAAGGA 1127 iv i vv ii vi iv ? i ii MER52-int#LTR 2600 AATCCTAAAGGATAAGTTTATTACTCAGGCAGCCCCTGATATCAGGAGGA 2649 rnd-5_family- 1128 AACTGCAGAAAAAGG 1142 i v MER52-int#LTR 2650 AGCTGCAGAAACAGG 2664 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.26 CpG sites = 10, Kimura (unadjusted) = 31.26 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 264 15.07 3.95 3.95 rnd-5_family-4979#LTR/ERV1 1106 1181 (852) HERVS71#LTR/ERV1 3018 3093 (5885) m_b17s701i4 rnd-5_family- 1106 GCNGCCCCTGATATTAAAAGGAAACTGCAGAAAAAGG-AGGATTTGATGG 1154 ? v v i vv - v i HERVS71#LTR/E 3018 GCAGCCCCGGATATTAAAAGGAAACTCCAAAAACTGGAAGGATTTGCTAG 3067 rnd-5_family- 1155 GCATGACNATGGCA--CAGATTTTGGAAA 1181 i- v? -- -- v i HERVS71#LTR/E 3068 A-ATGAATAT--CAGTCAGCTTTTAGAAA 3093 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.36 CpG sites = 4, Kimura (unadjusted) = 17.36 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.20 (6 / 5) 257 23.33 0.00 0.00 rnd-5_family-4979#LTR/ERV1 1358 1417 (616) HERV15#LTR/ERV1 2485 2544 (6207) m_b17s701i5 rnd-5_family- 1358 AACCAGTGTGCCATATGCCGAAAGGAGGGACATTGGAAAAATGAGTGCCC 1407 i v vi v iv iiv v i i HERV15#LTR/ER 2485 AACCAATGTGCAAGGTGCAGGCAAATGGGCCACTGGAAAGATGAGTGCCC 2534 rnd-5_family- 1408 CGAAAGGGAA 1417 i HERV15#LTR/ER 2535 CGAAAAGGAA 2544 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 8, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 261 10.53 0.00 0.00 rnd-5_family-671#DNA/hAT-Tip100 114 151 (0) EuthAT-N1a#DNA/hAT-Tip100 219 256 (2) m_b17s502i15 rnd-5_family- 114 TGCTCGCCCCGGGCGCTAAAATGCCTAGTTACGGCTCT 151 i i vv EuthAT-N1a#DN 219 TGCTTGCCCCGGGCGCCAAAATTGCTAGTTACGGCTCT 256 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 11.37 CpG sites = 2, Kimura (unadjusted) = 11.37 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 780 20.29 8.21 1.44 rnd-5_family-726#SINE/tRNA 342 536 (0) LFSINE_Vert#SINE/tRNA 4 211 (248) m_b17s601i8 rnd-5_family- 342 GGGGNACTGGATGCCTCAGGGCATTGCTAATGAGCTACAGAGCCTTTCAC 391 ? v v v i v i LFSINE_Vert#S 4 GGGGGACTGGATGGCTCAGGGGATTGGTAATGGGATACGGAGCCTTTCAC 53 rnd-5_family- 392 CTGTAGGTCACCAGTTTGAATCCTGCCCAGCTCAGCAGGGATTAAAAGTT 441 v ii i v v i v iii i LFSINE_Vert#S 54 CTCTAGGTCACTGGTTCGAATCCAGCCCAGGTCAGTAGTGACCGAAAGTC 103 rnd-5_family- 442 GTTCCCATCTAACGGATGTTTGGTGGCCACTCTATGAGAT-AGTTTGGAG 490 i v i v i -- v i i - v vi LFSINE_Vert#S 104 ATTACCATCTGACGGCTGTTCGGTGGCC--TATGTGAAATGAGTTGGTGG 151 rnd-5_family- 491 TCCCAGTTCCAGCTCC---------------CACGTCACAAACTCACCAC 525 i - i --------------- i vi i LFSINE_Vert#S 152 TCTCAGT-CCAGTTCCTAGTGGACAGGTGTCCACATCACAAAACCACCAT 200 rnd-5_family- 526 CATGCTTTGCA 536 iiv v LFSINE_Vert#S 201 CACAATTGGCA 211 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.42 CpG sites = 23, Kimura (unadjusted) = 24.21 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.03 (5 / 194), avg. gap size = 3.80 (19 / 5) 315 26.21 2.83 2.83 rnd-5_family-936#LTR/ERVK 1058 1163 (794) HERVK22#LTR/ERVK 1138 1243 (5594) m_b17s701i6 rnd-5_family- 1058 AGGCAGTCCAGAGGCAGATTGATAACCCGCAAGCCCAGACTGA---ACTA 1104 i iv i i ii v v v i ---i ---vi HERVK22#LTR/E 1138 AGGCAATTAAGAGACAAATTAGTCACGCCCAGGCC---GCTGATATCTTA 1184 rnd-5_family- 1105 ATGATAAAATTGGCTTACGAAAATGCCAATGCAGACTGCCGCCGTGCCAT 1154 v v iv i i i? iv iv v HERVK22#LTR/E 1185 TTGTTGCAATTGGCTTATGAAAATGCTAATGTNGACTGCCAGCAAGCAAT 1234 rnd-5_family- 1155 GCAGGCAGT 1163 i HERVK22#LTR/E 1235 GCAGGCAAT 1243 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 16, Kimura (unadjusted) = 33.45 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.50 (6 / 4) 21 25.47 4.67 5.37 rnd-5_family-1227#LTR/DIRS 166 315 (748) (GCCGGT)n#Simple_repeat 1 149 (0) m_b18s252i12 rnd-5_family- 166 GCCGGTGNCGG-G--GGTGCCCCGGTGCCGACGTCGGCGCCGGGGCC-GT 211 ? - -- -- ii i i v - (GCCGGT)n#Sim 1 GCCGGTGCCGGTGCCGGTG--CCGGTGCCGGTGCCGGTGCCGGTGCCGGT 48 rnd-5_family- 212 --AGGTGCCTGCGCCGANGTCGGCGTCGACGACGGTGCCGGCGTCGGAGA 259 --v v i i? i i i ii v i i v - (GCCGGT)n#Sim 49 GCCGGTGCCGGTGCCGGTGCCGGTGCCGGTGCCGGTGCCGGTGCCGGTG- 97 rnd-5_family- 260 CGGGTGCGTCGACGCCGTAAGGNCGGTGCCGAAGTCGGCGCC-GAGCACG 308 v -- ii --iv ? iv i i - v - (GCCGGT)n#Sim 98 CCGGTGC--CGGTGCCG--GTGCCGGTGCCGGTGCCGGTGCCGGTGC-CG 142 rnd-5_family- 309 GTGCCGG 315 (GCCGGT)n#Sim 143 GTGCCGG 149 Matrix = Unknown Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.09 (13 / 149), avg. gap size = 1.15 (15 / 13) 3083 7.85 0.88 2.44 rnd-5_family-1237#Unknown 1 457 (1) UCON28c#Unknown 17 466 (102) m_b18s502i0 rnd-5_family- 1 ATACATCATGTTCTGAAACAGTTAAATAAAATGAAGA-TATTTTCAANTT 49 ii vi i - ii ? UCON28c#Unkno 17 ACGCATGGTGTTCTGAAACAGTTAAGTAAAATGAAGAATATTTCTAACTT 66 rnd-5_family- 50 ATATTAGTAACTTGCACTGAATTATACTTGGATNACTTATTAAAT-AAGA 98 i i ? - UCON28c#Unkno 67 ATATTAGTAACTTGTATTGAATTATACTTGGATTACTTATTAAATGAAGA 116 rnd-5_family- 99 ATATTATTCAAATTACATCTGTCACAGATGAAAAAAACACTACATAGCAT 148 i v i --- ?--- UCON28c#Unkno 117 ATATTATCCATATTATATCTGTCACAGATGAAAAAA---CTACATN---T 160 rnd-5_family- 149 ATGGATGAGTGTAATCCATTCATTGNTTTATGGACCCANAGTCCTCCAGG 198 ? ? UCON28c#Unkno 161 ATGGATGAGTGTAATCCATTCATTGGTTTATGGACCCAAAGTCCTCCAGG 210 rnd-5_family- 199 GAGTGTCACAAATCCACATGATGTCCCTGAGTGCTGGA-TTTGCATTTGG 247 - UCON28c#Unkno 211 GAGTGTCACAAATCCACATGATGTCCCTGAGTGCTGGATTTTGCATTTGG 260 rnd-5_family- 248 ATCTCTGAGTTAGCTGAAAGATGTGTAAAATCACACGTAGGC-GAGAGNT 296 i - v ? UCON28c#Unkno 261 ATCTCTGAGTTAGCTGAAAGATGTGTAAAATCACATGTAGGCAGACAGCT 310 rnd-5_family- 297 CCCTACTGACTACGCATCTGAGGAGGCTCCTGTGCGTTGTTTATTCCAGC 346 i v UCON28c#Unkno 311 CCCTATTGACTACGCATCTGAGGAGGCTCATGTGCGTTGTTTATTCCAGC 360 rnd-5_family- 347 AAGTNCAGCTGAAATATCTTGCGCTCATGAAATGTGNCACNGNTACGCTC 396 --? iv? i ?v vv ?iv ? ii UCON28c#Unkno 361 AA--ACGTNTGGAATANATTGCGCTCATGAAATTGGCTCCNGATACGCCT 408 rnd-5_family- 397 GTTTTTTCNGGCAGGAATACGCGAATAACTGATGCGCAGGGNTGAAACCT 446 --- ? i i ? i ii i i ? ? ? i ? UCON28c#Unkno 409 G---TTTCAGACGGNAGTATACGAATAACTGGTGCACNGNGCTAAANCCT 455 rnd-5_family- 447 CCCACTTTTGG 457 i UCON28c#Unkno 456 CCCACTTTCGG 466 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.76 CpG sites = 26, Kimura (unadjusted) = 8.76 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.03 (15 / 456), avg. gap size = 1.00 (15 / 15) 865 16.53 6.99 6.59 rnd-5_family-14266#Unknown 8 279 (150) UCON60#Unknown 9 281 (19) m_b18s502i1 rnd-5_family- 8 AGAAAAATTCTACTGCGCATGC------GTGAAATTNCCCTTAAGTGCTC 51 v i ------ iv ---- iivi UCON60#Unknow 9 AGAAAATTTCTACTGCGTATGCTCAGACGTATAATT----TTAAACCTTC 54 rnd-5_family- 52 ATAACCTTNAAAACTACTGAACCGATTTTCTTCAAACTTGGCTTGNTTTT 101 i i ? - ? v i ? UCON60#Unknow 55 GTAACTTTAAAAA-TACTNAACCGTTTTTCTTCAAATTTGGCTTGATTTT 103 rnd-5_family- 102 TAAANNTCTCAGTGAGATCTACAAAACAAGCCAAGTTTGANGTTTCTGNC 151 iv--??i ? iv vv v- ? v i? UCON60#Unknow 104 CC--TTCCTCANTGAGGACTACAATCCT-GCCAAGTTTGAAGTTTATAGC 150 rnd-5_family- 152 TTCAGCCATTNTTGAGTTATCCGNGCGCAAA------ATTTCTGA----- 190 i ? v ? i ------ - ----- UCON60#Unknow 151 TTCAGCCGTTTTTGAGTTATACGAGCACAAAAAAAACATTTC-GATATTT 199 rnd-5_family- 191 -TCGGAACATATGGGGAAATGGTGAGTATTTTTTCTTTACTGAAAATAAC 239 - ii ---? ii i ----- i v v -viv UCON60#Unknow 200 TTTAGAA---NTGGAAAAGT-----GTATTTCTTCTATCCT-CGCATAAC 240 rnd-5_family- 240 TNAAAAACGGAC-AACAGATTTTGCTCAAATTTTCCAAAAA 279 ? vi- v ? i v i UCON60#Unknow 241 TCAAAAACGGCTGAACCGATTTNGCTCAAACTTTCAAAAGA 281 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.53 CpG sites = 24, Kimura (unadjusted) = 20.05 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.08 (23 / 271), avg. gap size = 1.61 (37 / 23) 261 28.57 0.00 0.00 rnd-5_family-14266#Unknown 284 374 (55) C MER131#DNA (75) 140 50 m_b18s601i0 rnd-5_family- 284 CTGGGCTGAGACNAAGCATGGAAAATTTCAGCCCAAAAGGAATTTGTTTG 333 i ?vv i vv i ii iv v vi C MER131#DNA 140 CCGGGCTGAGACCTTGTATGCCAAGTTTCAGCCCGGAGCGAATTTTTACG 91 rnd-5_family- 334 AGAAAGTTATGAGCAACTGAAAAAGGGGGGTTAGAATGGAA 374 ivvi i i vv vi v v C MER131#DNA 90 GCCGAGTTATAAACCCCTGAAAATAGGGGTTTATAATGGAA 50 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 12, Kimura (unadjusted) = 36.75 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0) 12 11.26 6.90 0.00 rnd-5_family-1517#Unknown 18 46 (487) (GGAG)n#Simple_repeat 1 31 (0) m_b18s252i11 rnd-5_family- 18 GGA-GGAGGGAGGGAGCGAGCGAGCG-GGGA 46 - v v v - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 459 6.78 1.69 0.00 rnd-5_family-1907#DNA/hAT 137 195 (1057) UCON69#DNA/hAT 195 254 (232) m_b18s502i2 rnd-5_family- 137 ACAACCTGAAACAATAGCTCTGAGATGTGTGAACTGCTCCATTCATCTCA 186 i v i UCON69#DNA/hA 195 ACAGCCTGAAACAATAGCTCTGAGAGGTGTGAACTGCCCCATTCATCTCA 244 rnd-5_family- 187 GT-GGGTGTT 195 i - UCON69#DNA/hA 245 ATGGGGTGTT 254 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.18 CpG sites = 3, Kimura (unadjusted) = 7.18 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 22 30.03 1.55 4.80 rnd-5_family-1907#DNA/hAT 740 868 (384) (CTCCC)n#Simple_repeat 1 125 (0) m_b18s252i10 rnd-5_family- 740 CTCCCNCCCCCTCCCCT-ACCTCCCCTCCTGGTCCCCCATCCTATCCCCA 788 ?i -v -vv - - iv - (CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCTCCCCTCCCCTCC-CCT-CCCC-TCCCCTCCCC- 46 rnd-5_family- 789 TAATCACCCCTCCCCT-CGCTACACCCCAAACCCCTCTCCCTATTCCCAC 837 vvi v - v v v i vvv - vii i v (CTCCC)n#Simp 47 TCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC-CCCTCCCCTCCC 95 rnd-5_family- 838 CTACTCTTCACCCCAATCACCCTCCCCTCCC 868 v i i v i vv - (CTCCC)n#Simp 96 CTCCCCTCCCCTCCCCTC-CCCTCCCCTCCC 125 Matrix = Unknown Transitions / transversions = 0.53 (10/19) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.00 (8 / 8) 21 23.34 4.82 1.16 rnd-5_family-2018#Unknown 894 976 (1467) (CTCCCT)n#Simple_repeat 1 86 (0) m_b18s252i8 rnd-5_family- 894 CTCCCTC-CCCACTNATTGCTCCCGCTGCCCCTTCCAGT--CTCTCCTTC 940 - v ?vi - v v i i vv -- i (CTCCCT)n#Sim 1 CTCCCTCTCCCTCTCCCT-CTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC 49 rnd-5_family- 941 CCCTTCT-CCTCTCCCGCCCCCTCTCCCTGCCCCTCT 976 i i - v i vi (CTCCCT)n#Sim 50 TCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCT 86 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.25 (5 / 4) 12 18.17 0.00 7.50 rnd-5_family-2018#Unknown 1875 1917 (526) (CAGCCCC)n#Simple_repeat 1 40 (0) m_b18s252i9 rnd-5_family- 1875 CAGCCGCCGGAGCCCCAGACACCCCCGGACCCAGCCCCCAGCC 1917 v i -v - - v vv (CAGCCCC)n#Si 1 CAGCCCCCAG-CCCCCAG-C-CCCCAGCCCCCAGCCCCCAGCC 40 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 195 31.13 2.34 6.06 rnd-5_family-2071#Unknown 1436 1606 (31) C MER131#DNA (43) 172 8 m_b18s601i1 rnd-5_family- 1436 TTTTTTCCCGAGCTTCCCAGAAAAATTCTACCCNGGGATGAGATGCGGCA 1485 i vi vi viv i vvi ? v iviv i C MER131#DNA 172 TTTTTTTCAAATTTTGTAAAAAAAATTCGCTCCCGGGCTGAGACCTTGTA 123 rnd-5_family- 1486 TGCGAAATTTCAG-AGGGATTGGTTTCTTTTTGGGGAAGTTGTGGAAGAG 1534 v i -vv vi iv - vi vvi i ----- i C MER131#DNA 122 TGCCAAGTTTCAGCCCGGAGCGAATT-TTTACGGCCGAGTTAT-----AA 79 rnd-5_family- 1535 AGGTTTGAAAACTA--GGCTTATAATGGGAA-GCTAGCTTCAACCTTAAC 1581 vvii - -- i i - ii -vv ? C MER131#DNA 78 ACCCCTGAAAA-TAGGGGTTTATAATGGAAACGCTGAC-AGANCCTTAAC 31 rnd-5_family- 1582 TCTGGAGCGGCTAACACCGCTCCGC 1606 v -- vviv v v C MER131#DNA 30 TAT--AGCGGCGCGAACGGCGCCGC 8 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 23, Kimura (unadjusted) = 41.10 Transitions / transversions = 0.85 (23/27) Gap_init rate = 0.08 (13 / 170), avg. gap size = 1.08 (14 / 13) 384 26.47 0.00 0.00 rnd-5_family-2251#DNA/hAT-Charlie 622 723 (23) UCON71#Unknown 99 200 (91) m_b18s502i3 rnd-5_family- 622 AAATTAAATGTAGACTATAATTTGGCATTTGAGAAGTGAAAGGGATGGTA 671 vi v i v i vi iv vi iiv UCON71#Unknow 99 AAATTAAATGTCAAATATAATTTGGCACTGGAAACATGAAGTGTGTGACT 148 rnd-5_family- 672 GCCCTAAGGGAAAAGATAACAGCTTGGCTCNTTGTGTTAAATAGCTGTCT 721 vi i ?v i i ?vi i v v i UCON71#Unknow 149 GCCCTTGGAGAAAANCTGACAGCTCGGCTCTGCGTGTCAAATTGGTATCT 198 rnd-5_family- 722 GC 723 UCON71#Unknow 199 GC 200 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.09 CpG sites = 15, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.0 (0 / 0) 15 40.15 0.64 5.33 rnd-5_family-3253#Unknown 23 179 (38) (GCC)n#Simple_repeat 1 150 (0) m_b18s252i6 rnd-5_family- 23 GCCTCTGCTGCTGCCGCCGCCTCTGCAACTGGCTCACTGCTGCCGCTGTC 72 v i i i v i vi -v - i i i i i (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCGC-CGC-CGCCGCCGCCGCCGCC 48 rnd-5_family- 73 TCTGCCACCGCTCGCCGCTGCTGCTGCTTTCTCCGCCTCTCTGCC-ACGT 121 v i i - i i i ivi v v - - -v i (GCC)n#Simple 49 GCCGCCGCCGC-CGCCGCCGCCGCCGCCGCCGCCGCCGC-C-GCCGCCGC 95 rnd-5_family- 122 TGCTTCTGCCGCTGCCACGCTCTGCCGCTATCNCTGCCGCTGCTTGCCGC 171 i iv i i i - v i iii ? i i -i (GCC)n#Simple 96 CGCCGCCGCCGCCGCCGC-CGCCGCCGCCGCCGCCGCCGCCGC-CGCCGC 143 rnd-5_family- 172 TCGCTGCC 179 - i (GCC)n#Simple 144 -CGCCGCC 150 Matrix = Unknown Transitions / transversions = 2.82 (31/11) Gap_init rate = 0.06 (9 / 156), avg. gap size = 1.00 (9 / 9) 33 27.22 4.14 4.14 rnd-5_family-3253#Unknown 27 195 (22) (CTGCTG)n#Simple_repeat 1 169 (0) m_b18s252i7 rnd-5_family- 27 CTGCTGCTGCCGCCGCCTCTGCAACTGGCTCACTGCTGCCGCTGTCT-CT 75 i i iv vi - -i i - - (CTGCTG)n#Sim 1 CTGCTGCTGCTGCTGCTGCTGCTGCT-GCT-GCTGCTGCTGCTG-CTGCT 47 rnd-5_family- 76 GCCACCGCTCGCCGCTGCTGCTGCTTTCT-CCGCCTCT-CTGCCAC-GTT 122 ii i - i - v - i iv - ii - i (CTGCTG)n#Sim 48 GCTGCTGCT-GCTGCTGCTGCTGC-TGCTGCTGCTGCTGCTGCTGCTGCT 95 rnd-5_family- 123 GCTTCTGCCGCTGCCAC-GCT-CTGCCGCTATCNCTGCCGCTGCTTGCCG 170 v i ii - - i iii? i - i (CTGCTG)n#Sim 96 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TGCTG 144 rnd-5_family- 171 CTCGCTGCCACTTCTGC-GATGCCGC 195 - ii v - v i (CTGCTG)n#Sim 145 CT-GCTGCTGCTGCTGCTGCTGCTGC 169 Matrix = Unknown Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.08 (14 / 168), avg. gap size = 1.00 (14 / 14) 304 4.45 4.26 4.26 rnd-5_family-3354#DNA/Kolobok 5 51 (319) UCON4#DNA/Kolobok 3 49 (429) m_b18s502i4 rnd-5_family- 5 AAAGGGACACTGTCAAG--GTTGGTAGNCCCAAAATTTGACCTACCTTT 51 -- -- ? i i UCON4#DNA/Kol 3 AAAGGGACACTGTCAAGTAGTT--TAGGCTCAAAATTTGACCTACTTTT 49 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.77 CpG sites = 2, Kimura (unadjusted) = 4.77 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.33 (4 / 3) 277 17.77 8.22 7.48 rnd-5_family-3354#DNA/Kolobok 183 328 (42) UCON4#DNA/Kolobok 332 478 (0) m_b18s502i5 rnd-5_family- 183 AACAAACCAGTGTGTGCAGCGCAAGATGGAGG-GGAGAAANATTTTGNTA 231 v i i v ---- - ii- v ?--- i ? UCON4#DNA/Kol 332 AAAAAATCAATGTTTGC----CAA-ATGGAAAAGGACAAAA---TCGGTA 373 rnd-5_family- 232 AGGAAACAGATTTCANTTTCAAGCTTCC-AGAGGGTTATCATA---GATG 277 i v i i ? i- - i i ---i UCON4#DNA/Kol 374 GGGAAAGAAATTTTATTTTCAAGCTTCTAAGAGGG-TATTACAAACAATG 422 rnd-5_family- 278 ------AAAAACGTATTTAAAACANNATGAAAAA-TACCTTGATAGTGTG 320 ------ ?iv vv ? v ?? i - - i - UCON4#DNA/Kol 423 GAGAGTAAAAANAAAAATNAAAAACTATAAAAAAGTA-CTTGACAGTGT- 470 rnd-5_family- 321 TCCTTTAA 328 i UCON4#DNA/Kol 471 CCCTTTAA 478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.06 CpG sites = 16, Kimura (unadjusted) = 22.07 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.11 (16 / 145), avg. gap size = 1.44 (23 / 16) 303 27.30 0.00 3.41 rnd-5_family-350#LINE/L2 43 133 (192) AmnL2-1#LINE/L2 1124 1211 (1402) m_b18s601i2 rnd-5_family- 43 AAGAAACCATCTCTTGACGCTGANAATCTCGCCGATTATCGTCCTGTCCC 92 i v i v i ? v v ii i i i i i AmnL2-1#LINE/ 1124 AAAAAACCCTCCCTTGACCCCGACACTCTCTCTAACTACCGCCCTATCTC 1173 rnd-5_family- 93 TGAATCTCCCNTTTTTTAGGGAAAGGTTATTGAGAAGGTNG 133 - i i ? i i vi iv i-- i ? AmnL2-1#LINE/ 1174 T-AACCTTCCCTTTCTCAGCAAAGTGC--TTGAGAAAGTAG 1211 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.83 CpG sites = 18, Kimura (unadjusted) = 37.88 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 238 37.12 0.60 0.60 rnd-5_family-4145#LINE/L1 743 910 (520) L1P1_orf2#LINE/L1 2296 2463 (831) m_b18s551i0 rnd-5_family- 743 ATAAGATACCTGGGAATTCAAATCTCAAACAACCTAGAAGAGCTCTACGA 792 i i i v iv ivi iv ii i v v i L1P1_orf2#LIN 2296 ATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAA 2345 rnd-5_family- 793 TTTAAATGTCAAACCACTACTTCAGCAAATGAAAAAAGATCTGGAGTGCT 842 vvvi ivv i iv ?v i i i viii vviv L1P1_orf2#LIN 2346 GGAGAACTACAAACCACTGCTCAANGAAATAAAAGAGGATACAAACAAAT 2395 rnd-5_family- 843 GGGGGAAGTATGCAAT-TTCTTGGTTGGGAAGAATAGCCACAGTCAAAAT 891 ii -i v v -i v v i vivi iv v L1P1_orf2#LIN 2396 GGAAGAA-CATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2444 rnd-5_family- 892 GAATATTCTGCCAAGGATA 910 ivi v v i i L1P1_orf2#LIN 2445 GGCCATACTGCCCAAGGTA 2463 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 53.46 CpG sites = 34, Kimura (unadjusted) = 53.46 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.01 (2 / 167), avg. gap size = 1.00 (2 / 2) 13 9.08 0.00 4.00 rnd-5_family-4639#Unknown 111 136 (51) (TTTG)n#Simple_repeat 1 25 (0) m_b18s252i4 rnd-5_family- 111 TTTATTTATTTGTTTGTTTGTTGTGT 136 i i - (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTT-TGT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 20 0.00 0.00 0.00 rnd-5_family-4639#Unknown 161 182 (5) (CA)n#Simple_repeat 1 22 (0) m_b18s252i5 rnd-5_family- 161 CACACACACACACACACACACA 182 (CA)n#Simple_ 1 CACACACACACACACACACACA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 262 38.51 1.06 1.06 rnd-5_family-485#LINE/RTE-BovB 753 941 (1002) MamRTE1#LINE/RTE-BovB 2343 2531 (1281) m_b18s601i3 rnd-5_family- 753 GGATTTAGACCAGGACGAAGTACAATAGATCAGCTATTTGTGATAAGACA 802 v i ivii vi ? iii ivv v v i?ii v v MamRTE1#LINE/ 2343 GGCTTTAGGCCGCAGCGCGGTANAGCGGACGTGATCTTTGCNGCATGTCA 2392 rnd-5_family- 803 GATATCAGAGAAGTACATAGAAC-ACAACCGAACCTGTTACAACAACTTT 851 ivi i ii vi - v vii -i i viivv i MamRTE1#LINE/ 2393 GATACAGGAAAAGCGCAGGGAACAACATCAAGACCT-CTGCACTGTATTC 2441 rnd-5_family- 852 ATAGACTTCAAACAGGCTTTTGATAGCATTTGGCAGAAA-GGGTTATGGC 900 v i i v v i v iiv - ii i vv- i v MamRTE1#LINE/ 2442 ATCGACCTTACAAAAGCATTTGACGCCA-TCAGTAGACCTGGGCTCTGGC 2490 rnd-5_family- 901 AAGTCTTGAGAATGTATGGCATCCCCGAGAAATTGATCAAG 941 iv vi i v v v vv i i v i MamRTE1#LINE/ 2491 AGCTACTAAGCAAGTTTGGCTGCCCTGAGAAGTTCACCAAG 2531 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.85 CpG sites = 40, Kimura (unadjusted) = 57.11 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.02 (4 / 188), avg. gap size = 1.00 (4 / 4) 246 25.00 0.00 0.00 rnd-5_family-485#LINE/RTE-BovB 1022 1077 (866) L1M3_orf2#LINE/L1 1959 2014 (1274) m_b18s551i1 rnd-5_family- 1022 AGGAGTGAGACAAGGATGCACGCTATCGCCAGATTTGTTCAGCTTGGTAC 1071 iii i v i v vv i i i v i L1M3_orf2#LIN 1959 AGGAACAAGGCAAGGATGCCCACTCTCGCCACTTCTATTCAACATAGTAC 2008 rnd-5_family- 1072 TGGAAG 1077 L1M3_orf2#LIN 2009 TGGAAG 2014 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.36 CpG sites = 9, Kimura (unadjusted) = 31.36 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 12 21.55 0.00 5.00 rnd-5_family-485#LINE/RTE-BovB 1283 1324 (619) (AAGACA)n#Simple_repeat 1 40 (0) m_b18s252i3 rnd-5_family- 1283 AAGACAAGAGGAAGAGGTAAAGATCAAAGTCAGAGACAAAGA 1324 - iv i ii - v i (AAGACA)n#Sim 1 AAGACAA-AGACAAAGACAAAGA-CAAAGACAAAGACAAAGA 40 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 1896 6.61 1.90 2.29 rnd-5_family-5341#DNA/Crypton-A 3 265 (0) Eulor5A#DNA/Crypton-A 8 269 (47) m_b18s502i6 rnd-5_family- 3 AAGCAATAATGATCGAGGCGCAGGGCATTTCCTGGGGATTAATGACCGGC 52 i Eulor5A#DNA/C 8 AAGCAATAACGATCGAGGCGCAGGGCATTTCCTGGGGATTAATGACCGGC 57 rnd-5_family- 53 TGGGAGGAGTTGATGTGGCCCAAGNTGCAGC-GAGGGCCATTAACCCCAG 101 -- i ?ii? - Eulor5A#DNA/C 58 TGGGAGGAGTTGATG--GCCCGAGGCANAGCCGAGGGCCATTAACCCCAG 105 rnd-5_family- 102 CCGGTCATTAATCCCCAGGAAATGCCCTGCGCTGAGGTCGTTATTGCTAT 151 i Eulor5A#DNA/C 106 CCGGTCATTAATCCCCAGGAAATGCCCTGCGCCGAGGTCGTTATTGCTAT 155 rnd-5_family- 152 TATAAGCTGAAAAGGAAG-CATGGAC---TGTGTAGATTTTGTTTTTAAA 197 v ? -v i i ---i i i v ---- Eulor5A#DNA/C 156 TATAAGCTGAAAACGNAGAAACGAACAGGCGTATGGATTTTTTTT----A 201 rnd-5_family- 198 TGGGTGATGCNGTTTCAGTTGGTACGTACAGGGCATTTCTAGAGAATTAA 247 ? i i ii Eulor5A#DNA/C 202 TGGGTGATGCAGTTTCAATTGGTATGTACAGGGCATTTCCGGAGAATTAA 251 rnd-5_family- 248 TGCCCTGTACATTAGCCA 265 Eulor5A#DNA/C 252 TGCCCTGTACATTAGCCA 269 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.72 CpG sites = 14, Kimura (unadjusted) = 7.14 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.03 (9 / 262), avg. gap size = 1.22 (11 / 9) 13 6.28 2.38 10.26 rnd-5_family-5391#Unknown 547 588 (1876) (TGGGAGC)n#Simple_repeat 1 39 (0) m_b18s252i2 rnd-5_family- 547 TGGG-GCTGGTGGAGNTGGGAAGCAGGGGAGCTGGGTGCTGGG 588 - - - ? - -v v (TGGGAGC)n#Si 1 TGGGAGCT-G-GGAGCTGGG-AGC-TGGGAGCTGGGAGCTGGG 39 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5) 519 23.09 0.54 6.86 rnd-5_family-5987#LINE/L2 3 188 (13) L2-1_AMi#LINE/L2 608 782 (453) m_b18s551i2 rnd-5_family- 3 GGGAGTCATCTTCGACTCCTCCCTCTCCTTCTCC-CCCACACATCCAGGC 51 v vvv -- vv-i v L2-1_AMi#LINE 608 GGGCGTCATCTTCGACTCGGACCTCTC--TCTAGGTCCTCACATCCAGGC 655 rnd-5_family- 52 TGTCACCAAATCTTGCCGCTTCTTCCTCCACAACATTTCGAAAATCCAAC 101 i vv i v v i v i i v i v ii L2-1_AMi#LINE 656 TATGTCTAAATCTTGCAGATTCTTTCTGCATAACATCTCTAAGATACGGC 705 rnd-5_family- 102 CCTTCCTTTCTGTCCCGACGGCCAAAACNCTTGTCCANGCCCTNGTCATC 151 i v ii vv i i ? i ?---------- L2-1_AMi#LINE 706 CTTTCCTATCCATCCACACAGCTAAAACTCTCGTCCAG----------TC 745 rnd-5_family- 152 TCCTGTCTTGATTACTGTAACCTCCTCCTCTCTGGCC 188 vii i i v ii L2-1_AMi#LINE 746 TCACATCTCGATTACTGCAACATCCTTTTCTCTGGCC 782 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.76 CpG sites = 21, Kimura (unadjusted) = 28.14 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.07 (13 / 185), avg. gap size = 1.00 (13 / 13) 1116 8.70 7.39 3.81 rnd-5_family-660#SINE/tRNA 10 212 (15) LFSINE_Vert#SINE/tRNA 5 214 (245) m_b18s601i4 rnd-5_family- 10 GGGAACTGGATGGCTCAGGGGACTGGTAATGGGATATGGAGCCTTTCACC 59 i i i LFSINE_Vert#S 5 GGGGACTGGATGGCTCAGGGGATTGGTAATGGGATACGGAGCCTTTCACC 54 rnd-5_family- 60 TCTAGGTCACTGG-TCGANTTTGACCGNGGTCAAT----------AGTCA 98 - ? iiii v? i ---------- LFSINE_Vert#S 55 TCTAGGTCACTGGTTCGAATCCAGCCCAGGTCAGTAGTGACCGAAAGTCA 104 rnd-5_family- 99 TTACCATCTGATGGCTGTTCGGTGGCCTATGCGAAATGAGTTGAC-GTCT 147 i i ii- LFSINE_Vert#S 105 TTACCATCTGACGGCTGTTCGGTGGCCTATGTGAAATGAGTTGGTGGTCT 154 rnd-5_family- 148 CATTCGGTCCAG--CCCAGTGGACAAGTGTCCACATAACACACAAAA-CA 194 ---- -- i i ---- - LFSINE_Vert#S 155 CA----GTCCAGTTCCTAGTGGACAGGTGTCCACAT----CACAAAACCA 196 rnd-5_family- 195 CCATCACGATTGGCACCA 212 i i LFSINE_Vert#S 197 CCATCACAATTGGCACTA 214 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 8.52 CpG sites = 16, Kimura (unadjusted) = 9.64 Transitions / transversions = 16.00 (16/1) Gap_init rate = 0.06 (13 / 202), avg. gap size = 1.77 (23 / 13) 16 0.00 0.00 0.00 rnd-5_family-675#Unknown 21 37 (553) (G)n#Simple_repeat 1 17 (0) m_b18s252i1 rnd-5_family- 21 GGGGGGGGGGGGGGGGG 37 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 189 28.57 0.00 0.00 rnd-5_family-6856#LINE/RTE-BovB 1270 1311 (181) MamRTE1#LINE/RTE-BovB 3350 3391 (421) m_b18s601i5 rnd-5_family- 1270 AGCGCGACTTCGCTGGTTCGGACACATGCAGAGGATGAATGA 1311 i ii i vii ii i i i MamRTE1#LINE/ 3350 AACGCAGCTCCGCTGGGCTGGACATGTGCGGAGAATGGATGA 3391 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.36 CpG sites = 11, Kimura (unadjusted) = 40.88 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 331 18.96 1.04 6.59 rnd-5_family-6942#LINE/CR1 275 370 (465) CR1-3_Croc#LINE/CR1 3240 3330 (275) m_b18s551i3 rnd-5_family- 275 GGGCTAGGCTGATCGCCAGTTTTGGGGTCTGGAAGGGATTTTCCCNTATG 324 ii i i vv v i v ?i CR1-3_Croc#LI 3240 GGGTCAGACCGATCGCCATATTTGGGGTCAGGAAGGAATTTTACCCCATG 3289 rnd-5_family- 325 GCAAAATTGGCAAACTG-CTGTGTGGGTTTTTTTCACCTTCCATCTG 370 iv i i-- v - v ---i - CR1-3_Croc#LI 3290 GTCAGATTGGT--ACGGACTGTGGGGGTTTTT---GCCTTCC-TCTG 3330 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 10, Kimura (unadjusted) = 22.35 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.07 (7 / 95), avg. gap size = 1.00 (7 / 7) 598 5.63 0.00 0.00 rnd-5_family-7069#SINE/ID 4 74 (0) tRNA-Ala-GCY#tRNA 1 71 (3) c_b18s355i0 rnd-5_family- 4 GGGGAATTAGCTCAAGTGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGC 53 i i tRNA-Ala-GCY# 1 GGGGAATTAGCTCAAGCGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGC 50 rnd-5_family- 54 GGGATCGATACCCGCATTCTC 74 ii tRNA-Ala-GCY# 51 GGGATCGACGCCCGCATTCTC 71 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 1.72 CpG sites = 4, Kimura (unadjusted) = 5.98 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 712 2.25 3.37 0.00 rnd-5_family-7733#DNA 74 162 (0) UCON2#DNA 87 178 (407) m_b18s502i7 rnd-5_family- 74 TGAAANGTATTTAAAAA---AGTTTTTAATTACAATTGGCATTTCTGAGC 120 ? i --- ? UCON2#DNA 87 TGAAATGTATTTGAAAATAAAGTTTTTAATTANAATTGGCATTTCTGAGC 136 rnd-5_family- 121 CTACTGCTGGNGGCGGCCATCTTGCTGAAAAGTGACGTCATT 162 ? ? i UCON2#DNA 137 CTNCTGCTGGCGGCGGCCATCTTGCTGAAAAGTGACATCATT 178 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.41 CpG sites = 2, Kimura (unadjusted) = 2.41 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.01 (1 / 88), avg. gap size = 3.00 (3 / 1) 12 19.15 4.44 2.17 rnd-5_family-8254#Unknown 109 153 (314) (CGCGC)n#Simple_repeat 1 46 (0) m_b18s252i0 rnd-5_family- 109 CGC-CCCCGCNGCGAAGCGCAGCCCCTGC-CGGCGCCGCTCCGCGCC 153 - v ? vv v v - - v v (CGCGC)n#Simp 1 CGCGCCGCGCCGCGCCGCGCCGCGCC-GCGCCGCGCCGCGCCGCGCC 46 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 396 18.08 10.61 4.21 rnd-5_family-9327#LINE/L2 1 179 (284) AmnL2-1#LINE/L2 1808 1997 (616) m_b18s601i6 rnd-5_family- 1 CTCAAGCATAATTCCAGCTCTCCTATC-CCCACCTCCAGACCCAGAAGCG 49 i i i v ii - v -- i vviv AmnL2-1#LINE/ 1808 CTCAAACACAACTCCATCTCCTCTATCTCCCTCCTC--GACTCAGACCTC 1855 rnd-5_family- 50 CNATTCACCTCCTTACCGTCTGTAANCTTTGGCATNATCCTTGNCCCTGN 99 ? ii --i i i ? - i ? ? ? AmnL2-1#LINE/ 1856 CCATTTGCCTCC--GCTGTCCGTAACCTT-GGCGTCATCCTTGACCCTGA 1902 rnd-5_family- 100 ACTCTGTTCCTNCCCC----TCGCCC---TCCGTANATCTTGTGTCTATC 142 vi i ? i ---- v i--- i i ? --- i AmnL2-1#LINE/ 1903 ACTCTCCTTCTCCTCCCACATCTCCTGTGTCTGCAAATC---TGCCTATC 1949 rnd-5_family- 143 ACCACCCNCG---CACTNCCCAT--------CTGCCTTGACTCCACCT 179 i? --- i ? i -------- i AmnL2-1#LINE/ 1950 ACCACCTCCGCAACATTGCCCGTGTATGCCACTGCCTCGACTCCACCT 1997 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.96 CpG sites = 24, Kimura (unadjusted) = 23.00 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.07 (13 / 178), avg. gap size = 2.08 (27 / 13) 1872 10.95 1.06 0.00 rnd-5_family-9327#LINE/L2 180 462 (1) UCON86#LINE/L2 1 286 (396) m_b18s502i8 rnd-5_family- 180 CCGCNGAAATCNTNATCCANGCCTTCATCCCTTCTCGTCTCGACTACTGT 229 i ? ? ? i i i i i i UCON86#LINE/L 1 CTGCTGAAATCCTCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGC 50 rnd-5_family- 230 AATTCTCTTCTCTATGGCTTCCCAAGATCCCAGCTCTCCAGACTCCAGCA 279 ?i i i v ii UCON86#LINE/L 51 ANCTCCCTTCTCTATGGCCTCCCCAAGTCCCAGCTCTCCAGACTCCAGCA 100 rnd-5_family- 280 TATGCAGAAT-CTGCTGCCTNCCTTCTCACATATACAAAGAAGCATGACC 328 ii - i? iii iii UCON86#LINE/L 101 CGTGCAGAATGCTGCTGCCCGCCTTCTCACACGCACAAAGAAGTGCGACC 150 rnd-5_family- 329 NCATCACCCCCATCCTCGAACANCTCCACTGGCTCCCCGTTCATTTCAGG 378 ? i ? i UCON86#LINE/L 151 ACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAGG 200 rnd-5_family- 379 ATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAANCCTTCCATGGACTTGC 428 ? i UCON86#LINE/L 201 ATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAAACCCTCCATGGACTTGC 250 rnd-5_family- 429 TCCAGCCTACTTCGTGGA-CTTGCCACT-TTTGCTC 462 i ii - i v - i UCON86#LINE/L 251 TCCAGCCTACCTCACGGACCTTGTCTCTCTCTGCTC 286 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.58 CpG sites = 29, Kimura (unadjusted) = 12.73 Transitions / transversions = 14.50 (29/2) Gap_init rate = 0.01 (3 / 282), avg. gap size = 1.00 (3 / 3) 1779 6.83 4.02 0.00 rnd-5_family-9371#Unknown 5 253 (0) UCON22#Unknown 61 319 (15) m_b18s502i9 rnd-5_family- 5 AAATNAATGAGTTCTACTAATTGAGTTTATCCTTGTAAATTAATA----- 49 ? i ?ii ----- UCON22#Unknow 61 AAATTAATGAGCTNCGCTAATTGAGTTTATCCTTGTAAATTAATAAAATT 110 rnd-5_family- 50 ---GCAAATCTAC--AAATAATCGTAATGTTGTTTGCCTGTATANTACCC 94 --- ?-- ? v vvv i ? UCON22#Unknow 111 CTAGCAAATCTANNAAAANAAGCGTACGTTTGTTTGCCTGTGTATTACCC 160 rnd-5_family- 95 GTACGGAGATCATTAATACCTTGTGACATCGAGGTCATAGGTCAAATCCG 144 ? i i UCON22#Unknow 161 GNATGGAGATCATTAATACCTCGTGACATCGAGGTCATAGGTCAAATCCG 210 rnd-5_family- 145 AGACCTTATTGCAAATCTAGGGGAAATTACCTTTCNAATGACATATGGCA 194 i i UCON22#Unknow 211 AGACCTTACTGCAAATCTAGGGAAAATTACCTTTCNAATGACATATGGCA 260 rnd-5_family- 195 CGACCTTCAACTCCTAATAGTCTAGGAGGAGTTCGCGGCTGANCGTTCAT 244 ? i ?? v v i ? UCON22#Unknow 261 CGACCTTCAACTCCTAATAGTCNAGAAGNNGTTCGGGTCCGANCNTTCAT 310 rnd-5_family- 245 ACATTCAGA 253 i UCON22#Unknow 311 ATATTCAGA 319 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.26 CpG sites = 11, Kimura (unadjusted) = 7.59 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.01 (3 / 248), avg. gap size = 3.33 (10 / 3) 278 21.96 0.00 6.25 rnd-5_family-1077#Unknown 707 774 (1532) DNM1r#Unknown 2476 2539 (2123) m_b19s502i0 rnd-5_family- 707 ATGTGTACGTCTGTACATATGTGTATGTGTACATGTGCGTATGTATGTGT 756 i i v i ---- i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATG----TGTGTATATGTGTGTATGTGTGTAT 2521 rnd-5_family- 757 GTACGTGTATGTGCACAT 774 i i i ii i DNM1r#Unknown 2522 ATATGTGTATATATACGT 2539 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.55 CpG sites = 13, Kimura (unadjusted) = 28.19 Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4) 268 23.95 2.70 4.11 rnd-5_family-1077#Unknown 731 804 (1502) HSAT5v1#Satellite 5208 5280 (618) m_b19s502i1 rnd-5_family- 731 ATGTGTACATGTGCGTATGTATGTGTGTACGTGTATGTGCACATGAGTGT 780 i i ii--- i i i ii i i i v HSAT5v1#Satel 5208 ATGCGTGCATGCA---ATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGT 5254 rnd-5_family- 781 GTG--CACATGTGAGTGTGCGTGTGT 804 --? ii v i HSAT5v1#Satel 5255 GTGTGNACGCGTGTGTGCGCGTGTGT 5280 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.08 CpG sites = 15, Kimura (unadjusted) = 32.02 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.25 (5 / 4) 270 24.19 0.00 0.00 rnd-5_family-1077#Unknown 759 820 (1486) DNM1r#Unknown 2476 2537 (2125) m_b19s502i2 rnd-5_family- 759 ACGTGTATGTGCACATGAGTGTGTGCACATGTGAGTGTGCGTGTGTATGT 808 iii ivi i i v i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATAT 2525 rnd-5_family- 809 GTGTACATGTAC 820 i i DNM1r#Unknown 2526 GTGTATATATAC 2537 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.71 CpG sites = 13, Kimura (unadjusted) = 31.71 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 15 7.56 3.57 0.00 rnd-5_family-1077#Unknown 997 1024 (1282) (GCCCT)n#Simple_repeat 1 29 (0) m_b19s252i10 rnd-5_family- 997 GCCGTGCCCTGCCCTGCCCTG-GCTGCCC 1024 v -v (GCCCT)n#Simp 1 GCCCTGCCCTGCCCTGCCCTGCCCTGCCC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 13 21.67 2.63 0.00 rnd-5_family-1077#Unknown 1852 1889 (417) (GGCCGA)n#Simple_repeat 1 39 (0) m_b19s252i11 rnd-5_family- 1852 GGCCCAGGCC-CTTCCTAGCCGGAGGCCGAGGCCGAGGC 1889 v -vvv v v v (GGCCGA)n#Sim 1 GGCCGAGGCCGAGGCCGAGGCCGAGGCCGAGGCCGAGGC 39 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 484 21.41 1.95 9.03 rnd-5_family-10821#LINE/L2 3 156 (268) L2-1_AMi#LINE/L2 1078 1221 (14) m_b19s551i0 rnd-5_family- 3 ACGCTGC--CCCTTATGCATGGGAAAATCTCCCCGATAAA-ATCCANACG 49 i -- i v ii v - - i? v- L2-1_AMi#LINE 1078 ATGCTGCTCCCCTCATGCTTGGGAGGAGCTCCCCG-TAAACATCCGCAA- 1125 rnd-5_family- 50 GCCACTGCCTTATCCTCCTTCAAATCCCTCCTTAAGACTCACCTCTGCCA 99 --- iii v i - v i i L2-1_AMi#LINE 1126 ---ATCACATTATTCTCCTTCAAATCCCTCCTTAA-ACTCTCCTTTGCCG 1171 rnd-5_family- 100 TGATGCCTACAAACCCAGCCTGCTGATCATGGCTAGGCGGGTGACAAGCT 149 v-------i iv i i v v iiiv L2-1_AMi#LINE 1172 TGATGCCTACAAAA-------ACTGACAACGGTTAGGCTGCTGGTGTGCT 1214 rnd-5_family- 150 GTGACTA 156 v i L2-1_AMi#LINE 1215 GAGACCA 1221 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.93 CpG sites = 19, Kimura (unadjusted) = 25.81 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.10 (15 / 153), avg. gap size = 1.07 (16 / 15) 13 17.24 3.03 0.00 rnd-5_family-1093#Unknown 8 40 (66) (AACAA)n#Simple_repeat 1 34 (0) m_b19s252i9 rnd-5_family- 8 AAAAAAAC-AAACAAACCCTACCAAAACAAAACA 40 v - v vv v (AACAA)n#Simp 1 AACAAAACAAAACAAAACAAAACAAAACAAAACA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 23 22.51 0.00 0.00 rnd-5_family-11615#Unknown 747 799 (456) (GT)n#Simple_repeat 1 53 (0) m_b19s252i8 rnd-5_family- 747 GTGTGTGTGTGTGTGTTGGGGGGGGGGAGTGTGTGTGTGCCTGNGTGAGT 796 vv v v v v v iv ? v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 rnd-5_family- 797 GTG 799 (GT)n#Simple_ 51 GTG 53 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 298 20.41 13.27 0.00 rnd-5_family-143#DNA/hAT-Ac 69 166 (120) C UCON26#DNA/hAT-Ac (103) 295 185 m_b19s502i3 rnd-5_family- 69 ATGGGGCTG-AAATAACGCGAGATCTGGTCTTCTCACGGTATTTCAG--- 114 v - vv v v ii i iv v --- C UCON26#DNA/hA 295 ATTGGGCTGGAAATCTCGCGAGAACAGGCTTTCTCGCGAGATTTCCGGTA 246 rnd-5_family- 115 -TTCCTG-----GAT--GGT-GGAAATACCACGAGAAGACCAGATCTCGC 155 - ----- i -- i- i v v vvv C UCON26#DNA/hA 245 CTTCCTGCTTCCGGTCGGGCCGGAAATACCGCGAGAACAGCCTTTCTCGC 196 rnd-5_family- 156 GTTATTTCGGC 166 v C UCON26#DNA/hA 195 GGTATTTCGGC 185 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.35 CpG sites = 7, Kimura (unadjusted) = 23.82 Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.06 (6 / 97), avg. gap size = 2.17 (13 / 6) 385 18.28 22.56 1.24 rnd-5_family-1508#SINE/5S-Deu-L2 3 135 (232) AmnSINE1#SINE/5S-Deu-L2 414 574 (1) m_b19s502i4 rnd-5_family- 3 TTGTGCAGCATGCTGTNNNNTGCCGTTG----GCTGCTGCCCTCCACCCC 48 i -- i i????i i i---- i vi AmnSINE1#SINE 414 TTGTGTAG--TGTTGCTGTGCGCTGTTAAACAGCTGCCGCGTTCCACCCC 461 rnd-5_family- 49 AGAGGTTGCT-----TCCATGGTG-----------CTNTGTATGCAATGT 82 v ----- vi ----------- i? i iiv AmnSINE1#SINE 462 AGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTGATCCCTGTATGTAGCTT 511 rnd-5_family- 83 GTAAAGTG-TTTGTG---------GATGAAAGGTGCTATATAAATGTAAA 122 i - v --------- i i i AmnSINE1#SINE 512 GTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATGCAAG 561 rnd-5_family- 123 TTATTNTTACNAT 135 v ? i? AmnSINE1#SINE 562 GTATTATTATTAT 574 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.01 CpG sites = 18, Kimura (unadjusted) = 23.22 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.05 (7 / 132), avg. gap size = 4.57 (32 / 7) 15 15.68 6.98 0.00 rnd-5_family-15603#LTR/DIRS 481 523 (535) (CCGGCA)n#Simple_repeat 1 46 (0) m_b19s252i7 rnd-5_family- 481 CCGACATCGGTACCGCCAGCGGCATCGGC-CC-GC-CCGGCACCGG 523 i i i v v i - - - (CCGGCA)n#Sim 1 CCGGCACCGGCACCGGCACCGGCACCGGCACCGGCACCGGCACCGG 46 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 213 18.25 0.00 6.49 rnd-5_family-1617#SINE/tRNA 138 219 (471) LFSINE_Vert#SINE/tRNA 5 81 (378) m_b19s601i0 rnd-5_family- 138 GGGGACTGGCTGGCTCAGGGNGGGNCGGGGAATGGGACACGGGGCCTTTC 187 v --- ?iv v i i LFSINE_Vert#S 5 GGGGACTGGATGGCTCAGGG---GATTGGTAATGGGATACGGAGCCTTTC 51 rnd-5_family- 188 CCCTCTAGGGGGCGCCGGCTCCGATCCGGCCC 219 v -- v i i i vi i LFSINE_Vert#S 52 ACCTCTA--GGTCACTGGTTCGAATCCAGCCC 81 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 8, Kimura (unadjusted) = 21.38 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.00 (5 / 5) 210 19.78 0.00 3.70 rnd-5_family-1617#SINE/tRNA 226 309 (381) LFSINE_Vert#SINE/tRNA 4 84 (375) m_b19s601i1 rnd-5_family- 226 GGGGGACTGGCTGGCTCAGGGGGGCGGGGAATGGGACACGGGGCCTTTCC 275 v ivi v- i i v LFSINE_Vert#S 4 GGGGGACTGGATGGCTCAGGGGATTGGT-AATGGGATACGGAGCCTTTCA 52 rnd-5_family- 276 CCTCTAGGGGGCGCCGGCTCCGATCCGGCCCCGG 309 -- v i i i vi i v LFSINE_Vert#S 53 CCTCTA--GGTCACTGGTTCGAATCCAGCCCAGG 84 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.20 CpG sites = 9, Kimura (unadjusted) = 23.20 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.00 (3 / 3) 319 10.87 0.00 0.00 rnd-5_family-17561#DNA/hAT-Charlie 12 57 (80) MER113A#DNA/hAT-Charlie 1 46 (268) m_b19s502i5 rnd-5_family- 12 CAGGGGTTCCCAAACTGTGGTACGTGTACCACTGGTGGTACGTGAG 57 v v v i i MER113A#DNA/h 1 CAGTGTTTCCCAAAGTGTGGTACGCGTACCACTGGTGGTACGCGAG 46 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.33 CpG sites = 2, Kimura (unadjusted) = 11.75 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 341 21.21 1.98 1.98 rnd-5_family-192#SINE/MIR 1 101 (0) MIR1_Amn#SINE/MIR 1 101 (129) m_b19s601i2 rnd-5_family- 1 TAGGAAGAAGTGTTGTAGCCTAGTGGTTAGAGCAGGGGANTGGGAGCCAG 50 i -- iiv i i v vv ? vi i MIR1_Amn#SINE 1 TAGGGAG--GCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGG 48 rnd-5_family- 51 GACTCCTGGGTTCTATTCCCAGCTCTGCCACT-GTTGACT-TGCCACCCT 98 vv ? ? i - ii?i -? iv i MIR1_Amn#SINE 49 GAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTT 98 rnd-5_family- 99 GGG 101 MIR1_Amn#SINE 99 GGG 101 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.20 CpG sites = 13, Kimura (unadjusted) = 27.11 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.00 (4 / 4) 15 24.52 2.08 0.00 rnd-5_family-1943#Unknown 417 464 (29) (GCGGA)n#Simple_repeat 1 49 (0) m_b19s252i6 rnd-5_family- 417 GCGGCGGGAAGCGGAGCGCCGCGGCTGGGAGCTG-GCGGAGTGGAGCGG 464 v v i vv vvv v - i (GCGGA)n#Simp 1 GCGGAGCGGAGCGGAGCGGAGCGGAGCGGAGCGGAGCGGAGCGGAGCGG 49 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 204 24.39 0.00 0.00 rnd-5_family-2126#LINE/L2 94 134 (742) C MamRTE1#LINE/RTE-BovB (2777) 1035 995 m_b19s601i3 rnd-5_family- 94 TGTCGACATGNATGTTGAAATCTCCCAGGACGACAAGTCTG 134 i i ?ii iv iv ii C MamRTE1#LINE/ 1035 TGCCGACACGTGCGTTGAAATCTCCCGTGACGATCAGCTTG 995 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.55 CpG sites = 8, Kimura (unadjusted) = 32.53 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 462 9.65 0.00 8.22 rnd-5_family-2186#LINE/CR1 1348 1426 (714) Plat_L3#LINE/CR1 3499 3571 (2) m_b19s551i1 rnd-5_family- 1348 CCTGCCATGAGTGCAGGGGACCGGACTAGATGACCTCTCGAGGTCCCTTC 1397 vv - i i i Plat_L3#LINE/ 3499 CCTGCCTGGAG-GCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTTC 3547 rnd-5_family- 1398 CAGTCCTATGATTCTGTTCTATGATTCTA 1426 ii ? ----- Plat_L3#LINE/ 3548 CAGCTCTANGA-----TTCTATGATTCTA 3571 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.55 CpG sites = 5, Kimura (unadjusted) = 10.55 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.00 (6 / 6) 226 18.78 23.26 0.95 rnd-5_family-2536#LINE/L2 6 91 (30) L2b_3end#LINE/L2 315 419 (47) m_b19s601i4 rnd-5_family- 6 ATTGCCTAC---CATGTCTGTTT--------AGATTGTAAGCTCT-TCAG 43 i i?--- i -------- i i i- v L2b_3end#LINE 315 ATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAG 364 rnd-5_family- 44 GGCAGGGAC------TGTCTC--TTACTATATGTNTGTACAGCGCCTAGC 85 ------ i-- i iii- ? viv L2b_3end#LINE 365 GGCAGGGACCGNGTCTGTCTTGTTCACCGC-TGTATCCCCAGCGCCTAGC 413 rnd-5_family- 86 ACAANG 91 i L2b_3end#LINE 414 ACAGNG 419 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.26 CpG sites = 13, Kimura (unadjusted) = 23.72 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.07 (6 / 85), avg. gap size = 3.50 (21 / 6) 292 10.45 11.94 0.00 rnd-5_family-2536#LINE/L2 25 91 (30) L2d_3end#LINE/L2 393 467 (49) m_b19s601i5 rnd-5_family- 25 TAGATTGTAAGCTC-TTCAGGGCAGGGAC--TGTCTCTTACTATATGTNT 71 - v -- iv ? v v??i L2d_3end#LINE 393 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTC 442 rnd-5_family- 72 GT-----ACAGCGCCTAGCACAANG 91 ----- i? L2d_3end#LINE 443 GTTCCCCACAGCGCCTAGCACAGTG 467 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 10.37 CpG sites = 3, Kimura (unadjusted) = 12.04 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (3 / 66), avg. gap size = 2.67 (8 / 3) 432 13.48 3.26 3.26 rnd-5_family-255#DNA/hAT 14 105 (582) UCON69#DNA/hAT 108 199 (287) m_b19s502i6 rnd-5_family- 14 AGTTTCTAGCCCTCATTG--GTGAAGATNGCCTTCCCACGTGGGAACC-A 60 i v -- i v?i vv -i v - UCON69#DNA/hA 108 AGTTTCTAGCCCTTATGGTTGCGAAGAAAACCTTCAAA-ATGTGAACCGA 156 rnd-5_family- 61 GTGTAAGCTGATGCAGTGTGTTGTCTTCCTGAGTCTGCAGACAGC 105 i i ?-- v UCON69#DNA/hA 157 GTGTAAACCGATGCAGTGN--TGTCTGCCTGAGTCTGCAGACAGC 199 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.76 CpG sites = 6, Kimura (unadjusted) = 15.30 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.20 (6 / 5) 322 36.99 2.46 1.83 rnd-5_family-25713#LINE/I-Jockey 156 480 (4) X12_LINE#LINE/I-Jockey 35 361 (10) m_b19s601i6 rnd-5_family- 156 CGCG-TGGCGAGCTTCATGGTCCGCAGAGAAAGTGACAAATAATTATCTT 204 - vvvv iv vviiviiii i v vi i X12_LINE#LINE 35 CGCGCTGGCGAGAGGAATGGTCTTCATCAGCGACAACAAACAAGTTCCTC 84 rnd-5_family- 205 GTCTCGGACCCCACTCAAC-GTCAACCCGGGTTTGATTTACCGCGAAGGC 253 v v ii - v - vv i v iv ii i vv vv X12_LINE#LINE 85 GTCGCCGACCCTGC-CATCTGTCCTCCTGGTTTCCACCTACCACGCCGTA 133 rnd-5_family- 254 AATGGAGCCTTCTGAACCGGTTTCGTACCGGACATGGAATTTGTGCTGCA 303 v ivi v v v i v v -- ivv - X12_LINE#LINE 134 TATGGGCTCTGCTGAACAGGTTTCGGACTGGCCAAGG--TCACTGC-GCA 180 rnd-5_family- 304 GCAGAATTTC---GGTGGCGTTTTAGAGACAGTCCACTATGTCAATGTGG 350 vi vi i--- i v ivvv v vvi vvv iviv X12_LINE#LINE 181 GCCAACCTTTACAGATGGGGTCAGCGCGAACATCCAAATTGCAGCTGTGG 230 rnd-5_family- 351 GCAGCCACAAACCATGACACACATTGTTGAGGACTGCAAAATGACTCAAC 400 v iv i i v i i v v vvvv v ivi X12_LINE#LINE 231 CCAAACGCAGACGATGACGCACACTGTTGACGAGTGCCCTTTGTCCAGAC 280 rnd-5_family- 401 TTCCTGGAGGTCTTCG-TG-CCTTGAACATCGTTGATAAGAACGCTGTGG 448 vvi v -- - - vi i ?v ivi i ii v iv X12_LINE#LINE 281 TTGACGGTGGTC--CGATGACACTGAATANAGCAAATGAAGAAGCTGCTG 328 rnd-5_family- 449 CTTGGCTTGACCGGAT-TGCATACGCCAAATAA 480 i i vi i -i i v i v X12_LINE#LINE 329 CCTGGCTTGGCAAGGTACGCGTTCGCTAAAGAA 361 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.56 CpG sites = 52, Kimura (unadjusted) = 51.65 Transitions / transversions = 0.79 (52/66) Gap_init rate = 0.04 (12 / 324), avg. gap size = 1.17 (14 / 12) 225 28.79 6.15 7.47 rnd-5_family-2862#LINE/L1 983 1226 (534) L1M1_orf2#LINE/L1 1973 2213 (1081) m_b19s551i2 rnd-5_family- 983 GACAGGGTTGCCCNTTATCCCCCCTGTTGTTTGCTTTGGCAATGGAG--- 1029 i v ?i v v v i iiviv i i v i--- L1M1_orf2#LIN 1973 GACAAGGATGCCCACTTTCACCACTGTTATTCAACATAGTACTGGAAGTC 2022 rnd-5_family- 1030 CCATTT---GCAAT-AAATGTGAGAAACAGCCCCTTGGTAAAGGGCATCA 1075 i vi --- - i iiv v i-------i v L1M1_orf2#LIN 2023 CTAGCTAGAGCAATCAGACAAGAGAAAGAA-------ATAAAGGGCATCC 2065 rnd-5_family- 1076 AAATGTCTTCTGGATTAGAACA---CAAAATAGCTTTGTATGCTGACGAT 1122 ------ vvi v --- v v i v v i L1M1_orf2#LIN 2066 AAAT------TGGAAAGGAAGAAGTCAAATTATCCTTGTTTGCAGATGAT 2109 rnd-5_family- 1123 GTCTTGTTATATTTGCAGGATCCAGAAGCCT-CATT-AAAAATTA-TAGA 1169 i vv v v ii v vi v - i?- i - L1M1_orf2#LIN 2110 ATGATCTTATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTAGA 2159 rnd-5_family- 1170 AC-AATTGACTTTGGAATTTGGGCAGGTATCAGGCTTCAAAATAAAC-TA 1217 -i vi ----i ii vv i vv v v v - L1M1_orf2#LIN 2160 ACTGATAAAC----AAATTCAGTAAAGTTGCAGGATACAAAATCAACATA 2205 rnd-5_family- 1218 CGATAAATC 1226 i - L1M1_orf2#LIN 2206 CAA-AAATC 2213 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.10 CpG sites = 32, Kimura (unadjusted) = 37.10 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.11 (27 / 243), avg. gap size = 1.22 (33 / 27) 238 15.71 4.17 2.74 rnd-5_family-30671#DNA/TcMar-Tigger 2 73 (564) Tigger8#DNA/TcMar-Tigger 1 73 (594) m_b19s502i7 rnd-5_family- 2 CAGGCAGTCCTCGACTTTACG-ACGTCCGACTTACG-ACGAACGGCACTT 49 i - - i v - i v v Tigger8#DNA/T 1 CAGGCGGTCCTCGACTTT-CGTACGTTCGACTTTCGNACAACCCGCACTT 49 rnd-5_family- 50 ACG-ACGCTTCTGAATTGACNNCCC 73 v - i- v iv ?? Tigger8#DNA/T 50 TCGTACA-TTATACATTGACACCCC 73 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.57 CpG sites = 5, Kimura (unadjusted) = 18.27 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 567 27.81 1.58 1.58 rnd-5_family-30671#DNA/TcMar-Tigger 447 636 (1) Tigger22N1#DNA/TcMar-Tigger 1385 1574 (0) m_b19s502i8 rnd-5_family- 447 TCATCTATAATTCATTTAGTACAAAAATCTG-GGTTATTGTGGTGAAAA- 494 i i v v i iiivi- i - i vivi i - Tigger22N1#DN 1385 TCATTTATAGTTGATTAAATATGGTG-TTTGTGGTCATTTCTATAAAAAG 1433 rnd-5_family- 495 TAGTGTATCAAGCCTTGGTTCAGGAACCAATCCCCCCTTCATACCATTGA 544 v v i i i v v vv v iv i v - Tigger22N1#DN 1434 TTGGGCATCAGGCCCTTGGTCAGGAACGTAACCCCCTATTATAACATTG- 1482 rnd-5_family- 545 TTCCTATGGGAAAAGCGGTTCCGAGTTACGACGTTTCGACTTACGACGCA 594 i v i v i v iv i ii i v Tigger22N1#DN 1483 TTTCTATGGGAAAATCAGATTCGACTTACATCATTTCGACTTACAGCACC 1532 rnd-5_family- 595 ATTTTCAGGAAC-CAATTGTGTCGTAAGTCCGAGGACTGCCTG 636 v i -i ii-i i v Tigger22N1#DN 1533 TTTTCCAGGAACGTAACC-CGCCGTAAGTGCGAGGACTGCCTG 1574 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.84 CpG sites = 31, Kimura (unadjusted) = 35.70 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.03 (6 / 189), avg. gap size = 1.00 (6 / 6) 12 3.33 12.50 0.00 rnd-5_family-3219#Unknown 22 53 (58) (GTTTT)n#Simple_repeat 1 36 (0) m_b19s252i5 rnd-5_family- 22 GTTTT-NTTTGTTTTG--TTGTTTT-TTTTGCTTTG 53 -? -- - i (GTTTT)n#Simp 1 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.33 (4 / 3) 1540 4.28 0.53 0.53 rnd-5_family-3761#Unknown 1 188 (0) UCON16#Unknown 51 238 (23) m_b19s502i9 rnd-5_family- 1 TTTGTTTAGAAGCCGCCTTCGTTTAGTAGCTGCCCACCTTCCAGTNG-TG 49 i? ? i v v -i ? -i UCON16#Unknow 51 TTCNTTTAGAAGCCGCCTTCGTTTAGNAGCCGCCCTCATT-TAGTAGCCG 99 rnd-5_family- 50 CACCTTTACCATGCAAGCCGCAGGGGAAAGTAATTAAATTTAATAGAAGC 99 UCON16#Unknow 100 CACCTTTACCATGCAAGCCGCAGGGGAAAGTAATTAAATTTAATAGAAGC 149 rnd-5_family- 100 TGCCCTCGTTTTGAAGCCGCCCTCGATTTAAAGCCGCAGGGGGAAGTAAT 149 i UCON16#Unknow 150 CGCCCTCGTTTTGAAGCCGCCCTCGATTTAAAGCCGCAGGGGGAAGTAAT 199 rnd-5_family- 150 TAAATTTAATAGAAGCCGCGGCTTCTAAACGAAGATATA 188 i UCON16#Unknow 200 TAAATTTAATAGAAGCCGCGGCTTCTAAACGAAGATACA 238 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.94 CpG sites = 6, Kimura (unadjusted) = 4.51 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.01 (2 / 187), avg. gap size = 1.00 (2 / 2) 13 16.31 0.00 5.56 rnd-5_family-4166#Unknown 506 543 (503) (TAACCA)n#Simple_repeat 1 36 (0) m_b19s252i4 rnd-5_family- 506 TAGCCTTAAGCCTTATCCATAACCCTAACCCATAACCA 543 i v - v v v - (TAACCA)n#Sim 1 TAACCATAA-CCATAACCATAACCATAA-CCATAACCA 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 239 28.01 0.79 1.59 rnd-5_family-4341#LINE/L2 4 130 (98) L2b_3end#LINE/L2 115 240 (226) m_b19s601i7 rnd-5_family- 4 TCCCATCTCTGTGCCTTTTCCCATGCTGCCCCCTATGCATGGAATACCC- 52 ii v v v v ? ii v v ii - L2b_3end#LINE 115 TCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCT 164 rnd-5_family- 53 TCCCAATCCCGGTTCGCCAAGCCACCACCCTCTCCTCATTCAGATCCCTC 102 v i i -- vi v v iv v v i i vv L2b_3end#LINE 165 TCCCCACCTC--TTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAG 212 rnd-5_family- 103 CTGAAGACTCACTTCTTCCGCGATGCCC 130 v ivv i i v v L2b_3end#LINE 213 CTCAAATGTCACCTCCTCCGGGAAGCCC 240 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 15, Kimura (unadjusted) = 35.55 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.02 (3 / 126), avg. gap size = 1.00 (3 / 3) 19 21.73 2.00 2.00 rnd-5_family-4567#Unknown 115 164 (26) (GA)n#Simple_repeat 1 50 (0) m_b19s252i3 rnd-5_family- 115 GAGCGTGAGAGAGGTATCGAGCGTGAGCAG-GAGACAGAGAGAGAGAGAG 163 v v iv vv v v - - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAG 49 rnd-5_family- 164 A 164 (GA)n#Simple_ 50 A 50 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 577 8.37 0.00 5.95 rnd-5_family-5611#DNA/PIF-Harbinger 1 89 (2) MER133A#DNA/PIF-Harbinger 9 92 (12) m_b19s502i10 rnd-5_family- 1 GGGCTATTCTCCCCTTCTCCATGCGCGCTTGCATAACTCCCATTAACGTT 50 v --- v -- i MER133A#DNA/P 9 GGTCTATTCTCC---TCTCGATGCGCGC--GCGTAACTCCCATTAACGTT 53 rnd-5_family- 51 AACGGGAGTTACGCGCACGCATCAAGGGGAGAATAGACC 89 i ii i MER133A#DNA/P 54 AATGGGAGTTACGCGCGTGCATCGAGGGGAGAATAGACC 92 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.31 CpG sites = 5, Kimura (unadjusted) = 8.93 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.06 (5 / 88), avg. gap size = 1.00 (5 / 5) 267 20.54 0.00 3.85 rnd-5_family-6957#SINE/MIR 18 98 (564) MIR1_Amn#SINE/MIR 72 149 (81) m_b19s601i8 rnd-5_family- 18 TCTGCTACGAACTCTGTCTTATATANCTTTTGGCAAGTCACTTANACTCT 67 i v?i - ? i-- i?i i? i v ??v MIR1_Amn#SINE 72 TCTGCCACTNGC-CNGC--TGNGTGACCTTGGGCAAGTCACTTNACCTCT 118 rnd-5_family- 68 CTGTTCCTCCGTTACCCCGTCTGGAAAATGG 98 ?v v v i i v MIR1_Amn#SINE 119 CTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.19 CpG sites = 9, Kimura (unadjusted) = 27.19 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 277 20.97 0.00 0.00 rnd-5_family-6957#SINE/MIR 37 98 (564) MIR#SINE/MIR 82 143 (119) m_b19s601i9 rnd-5_family- 37 TATATANCTTTTGGCAAGTCACTTANACTCTCTGTTCCTCCGTTACCCCG 86 i i i? i v i ?v v v v i i MIR#SINE/MIR 82 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCA 131 rnd-5_family- 87 TCTGGAAAATGG 98 v MIR#SINE/MIR 132 TCTGTAAAATGG 143 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.85 CpG sites = 7, Kimura (unadjusted) = 25.85 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 229 22.27 6.25 19.30 rnd-5_family-729#SINE/5S-Deu-L2 42 169 (224) AmnSINE2#SINE/tRNA-Deu 149 262 (96) m_b19s502i11 rnd-5_family- 42 GTCCTTCAGATGAGATGTTAAAN-CGAGGGTCCCTTCTGCCTGTCTCTGG 90 i i iv ?- v ii i ---- i - - AmnSINE2#SINE 149 GTCTTTCGGATGAGACCTTAAAAACCAAAGCCC----TGTCTG-CTCTG- 192 rnd-5_family- 91 TGGCTGTCCAGGTGGAAGTTAAAGATCCCATGGCACTTTTTTTTTCGGAA 140 -------- -- vi i i iv ------ AmnSINE2#SINE 193 --------C--GTGGACATTAAAGATCCCGTGGCGCTTTTCGT------A 226 rnd-5_family- 141 AGAGTA-------ACTCCAGCGTCCTAGTCGGAATT 169 -------i i i i i v v v AmnSINE2#SINE 227 AGAGTAGGGGTTTGCCCCGGTGCCCTTGGCCGAATT 262 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.40 CpG sites = 16, Kimura (unadjusted) = 26.79 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.19 (24 / 127), avg. gap size = 1.25 (30 / 24) 298 20.31 0.00 0.00 rnd-5_family-729#SINE/5S-Deu-L2 285 348 (45) UCON86#LINE/L2 616 679 (3) m_b19s502i12 rnd-5_family- 285 CTTTGTAAAGCACTTTGGGATATCTTGAGTATGAAAGGCNCTATATAAAA 334 i ii ivv vv i ? i UCON86#LINE/L 616 CTCTGTAAAGCGTTTTGGGATACAGTTTGTATGAAAGACGCTATACAAAA 665 rnd-5_family- 335 NNAAATTCTATTAT 348 ?? i v i UCON86#LINE/L 666 TAAAGTTGTATTGT 679 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 8, Kimura (unadjusted) = 25.58 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 2160 10.73 0.00 1.26 rnd-5_family-806#DNA 1 321 (203) UCON8#DNA 668 984 (129) m_b19s502i13 rnd-5_family- 1 GGGGCATATGGGAAACTCAAACACTAATGGAGAGTGGGATTTTCCTTGCG 50 i - i iv i i i UCON8#DNA 668 GGGACATA-GGGGAACTCAAACATAAACGGAGAGCGGGATTTTCCTTGCA 716 rnd-5_family- 51 ATGGCCACAATAAATATGTTTGTTAAGGGAAGAAAAANAGAGGAAAGAAG 100 ? i i ii i v ?v i i i UCON8#DNA 717 NTGGCCACAATAAATATGTTTGTTGAAGAGAAAATAAGTGGGAAGAGAAG 766 rnd-5_family- 101 ACACGCATGCCTGATGCTGAAGAAAAGCNTGTTTGTGCCTAATACATTGG 150 i i ? UCON8#DNA 767 ACATGCATGCCTGATGTTGAAGAAAAGCCTGTTTGTGCCTAATACATTGG 816 rnd-5_family- 151 AGAAATTGTTCAAGAACAGTTCATCCGTGTGAAAATATNACCCCCGTAAT 200 ? ? i UCON8#DNA 817 AGAAATTGTTCAAGAACAGTTCATCCNTGTGAAAATATGACCCCTGTAAT 866 rnd-5_family- 201 GCTGCCAAGGTCAGTGAGACCTGGGGTGATCTGCTGAGTAAGTGCTGGCT 250 ? ? i ii UCON8#DNA 867 GCTGCCAAGGTCAGTGAGACCTNGGGTGATCTGCTGNGTAAGTGCCGGTC 916 rnd-5_family- 251 GGGCAAGTTAAAGCTGCCTGTGAGGCCACTTTAACCCAGCACGCCAGATT 300 v - i vi ii - i i v UCON8#DNA 917 GCGCAAGTTAAAGCTGCCTG-GGGGCAGCTTTAACTTA-CGCACCCGATT 964 rnd-5_family- 301 TTNCTCAAGATTTTCAAAAAT 321 ? - iv UCON8#DNA 965 TTTC-CAAGATTTCAAAAAAT 984 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.37 CpG sites = 27, Kimura (unadjusted) = 12.15 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.01 (4 / 320), avg. gap size = 1.00 (4 / 4) 2573 9.13 1.74 2.24 rnd-5_family-8435#DNA/hAT 24 426 (5) MER121B#DNA/hAT 1 401 (6) m_b19s502i14 rnd-5_family- 24 GGGATGGGAGAACCCG-TGGTGNTTGTGGGGTTTGCAAAACCTCTAGAAC 72 i i i i i - i - ??v i? ? ? MER121B#DNA/h 1 GGGGTAGGGGAGCCTGGTAGTGNTT-TGNNTTTCNCNAAACCTCTANAAC 49 rnd-5_family- 73 TTTNTTNTTT--AAGTATTGAAGTTTCGCGAAACTTTTTCGAGTTTCCGA 120 ? ? -- iv i- i vvi MER121B#DNA/h 50 TTTTTTTTTTNAAAGCTTTGG-GTTTCGCGAAACTTTTTCAAGTTTCGCG 98 rnd-5_family- 121 AAACATTTTTCCCTTTAATTTAAACCGTTGTTTTTCAAGGGAAATTTAAT 170 i i i i MER121B#DNA/h 99 AAACGTTTTTTCCCTTAATTTAAACCATTGTTTTTCAAGGGAAATTTAAT 148 rnd-5_family- 171 TTAAAAACAAATATGCTTATTTCTAACTAAATGGAAGCCTGTGCTATGCA 220 ? --- i i -- MER121B#DNA/h 149 TTNAAAA---ACATGTTT--TTCTAACTAAATGGAAGCCTGTGCTATGCA 193 rnd-5_family- 221 AACAATAAAGATTCTTGTTTGAAAGTAATTCTTGCCCTGCTTCTAGGACT 270 MER121B#DNA/h 194 AACAATAAAGATTCTTGTTTGAAAGTAATTCTTGCCCTGCTTCTAGGACT 243 rnd-5_family- 271 ACCAGGGGAA-AACATAGTTTAAAAC--GCAGCAGCCCAGAACTCGCATT 317 - v vivvv -- ? ii MER121B#DNA/h 244 ACCAGGGGAATAAAATTAAAAAAAACATGCAGCAGCCCAGANCTCGTGTT 293 rnd-5_family- 318 TTGCCAGAGCCAAATGGAACTCGAACCTCAAAAGTTTCGAGTTCTGTTCT 367 i v v MER121B#DNA/h 294 TTGCCAGAGCCAAACGGAACTCGAAGCTCAAAAGTTTCGAGTTCGGTTCT 343 rnd-5_family- 368 AAATCTAGAACCCACGATTTTCNTGAGT-GGTTCGAAATTTGGCAAAACA 416 i i -- - v i MER121B#DNA/h 344 AAATTTAGAACCCGCGATTTTC--GAGTGGGTTCTAAATTTGGCAAAACG 391 rnd-5_family- 417 AGTTCTCCCA 426 MER121B#DNA/h 392 AGTTCTCCCA 401 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.74 CpG sites = 24, Kimura (unadjusted) = 10.11 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.03 (14 / 402), avg. gap size = 1.14 (16 / 14) 17 20.40 5.26 0.00 rnd-5_family-92#Unknown 84 140 (738) (GCTGCC)n#Simple_repeat 1 60 (0) m_b19s252i1 rnd-5_family- 84 GCGGCCGGCGCCGCTCTCCCTTGC-CTGCTGCTGCCGCTGCCG--GCAGC 130 v vi vi v vv - i -- v (GCTGCC)n#Sim 1 GCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGC 50 rnd-5_family- 131 TGCCNCTGCC 140 ? (GCTGCC)n#Sim 51 TGCCGCTGCC 60 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.50 (3 / 2) 13 28.49 1.33 4.11 rnd-5_family-92#Unknown 108 182 (696) (CTG)n#Simple_repeat 1 73 (0) m_b19s252i2 rnd-5_family- 108 CTGCTGCTGCCGCTGCCGGCAGCTGCCNCTGCCTAAGGCTACAGGGAGCA 157 i - v v i? - ivv i -v vv v (CTG)n#Simple 1 CTGCTGCTGCTGCTG-CTGCTGCTGCTGCTG-CTGCTGCTGC-TGCTGCT 47 rnd-5_family- 158 GCGGCTGAGGCAG-NGCTGCTGCTGC 182 v vv v -? (CTG)n#Simple 48 GCTGCTGCTGCTGCTGCTGCTGCTGC 73 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.00 (4 / 4) 16 22.70 1.82 3.70 rnd-5_family-9510#Unknown 151 205 (121) (CCGC)n#Simple_repeat 1 54 (0) m_b19s252i0 rnd-5_family- 151 CCGCCCGCGTTCGCCGCGCTCCCG-CCACCCGCACCGCCCGCCTGCTCCC 199 viv - v v - i - i i v (CCGC)n#Simpl 1 CCGCCCGCCCGC-CCGCCCGCCCGCCCGCCCGC-CCGCCCGCCCGCCCGC 48 rnd-5_family- 200 CTGCCC 205 i (CCGC)n#Simpl 49 CCGCCC 54 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 330 25.00 0.00 0.00 rnd-5_family-1161#LTR/DIRS 1545 1612 (3) C MER133A#DNA/PIF-Harbinger (21) 83 16 m_b20s502i0 rnd-5_family- 1545 TTCCCCCAGTGCTTGCATGTAACTTGCATTANCATTAANAGNANTTATGC 1594 i i ii vi ii iv ? i ?i ? ? i C MER133A#DNA/P 83 TCCCCTCGATGCACGCGCGTAACTCCCATTAACGTTAATGGGAGTTACGC 34 rnd-5_family- 1595 ACTTGCATCAAGAGGAGA 1612 i vi i C MER133A#DNA/P 33 GCGCGCATCGAGAGGAGA 16 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.61 CpG sites = 14, Kimura (unadjusted) = 35.58 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 695 26.33 2.02 1.61 rnd-5_family-1194#LINE/L2 33 279 (247) AmnL2-1#LINE/L2 1755 2002 (611) m_b20s601i0 rnd-5_family- 33 TCCAG-TGAATGCTTNCAAATACTNAAGTCTCTCTTCTGGGTAANAAG-G 80 i - i - i? v v? vii ii i ? i - AmnL2-1#LINE/ 1755 TTCAGCTAAATG-TCTCAAAGACAGAAGTGCTTCTCTTGGGCAAGAGGAG 1803 rnd-5_family- 81 CTTCTTTGCCCCATATCTCCGACTCCGCTATCACTCTCCTTAACTCAGAC 130 v i iivv - i v iv v v i ii AmnL2-1#LINE/ 1804 CATCCTCAAAC-ACAACTCCATCTCCTCTATCTCCCTCCTCGACTCAGAC 1852 rnd-5_family- 131 GTTAACTTTGCTCCCAAGGCCAGAAATCTTGGACGTCATCCTTGACCCCA 180 v ivvv ii ivv i v v i - ii AmnL2-1#LINE/ 1853 CTCCCATTTGCCTCCGCTGTCCGTAACCTTGG-CGTCATCCTTGACCCTG 1901 rnd-5_family- 181 AGATTACTTTTCTCCTCCCACATCTCCCTTGTCTGTAAGTCTGCCTATCA 230 - i viii iv i i AmnL2-1#LINE/ 1902 A-ACTCTCCTTCTCCTCCCACATCTCCTGTGTCTGCAAATCTGCCTATCA 1950 rnd-5_family- 231 CCACCTCCGGAACATTGCCAGAATTTGTCCTTACCATG--TCC-TCTCTG 277 v v vi v i vi i vi -- -i AmnL2-1#LINE/ 1951 CCACCTCCGCAACATTGCCCGTGTATGCCACTGCCTCGACTCCACCTCTG 2000 rnd-5_family- 278 CT 279 AmnL2-1#LINE/ 2001 CT 2002 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 38, Kimura (unadjusted) = 33.77 Transitions / transversions = 1.46 (38/26) Gap_init rate = 0.03 (8 / 246), avg. gap size = 1.12 (9 / 8) 893 21.50 7.41 2.35 rnd-5_family-1194#LINE/L2 282 524 (2) UCON86#LINE/L2 2 256 (426) m_b20s502i1 rnd-5_family- 282 TGCTGAAATCCTTATTCGTGCCTTNATCACTTCCCGTCTCGACTACTGCA 331 i i i? ? v i i i i i UCON86#LINE/L 2 TGCTGAAATCCTCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGCA 51 rnd-5_family- 332 ATTCCTTCTTTTTATAGTCTTCCTAAATCCCTACTCTCTAAACTTCAG-- 379 ?i i - i i i i i i i vi i i i -- UCON86#LINE/L 52 NCTCCCT-TCTCTATGGCCTCCCCAAGTCCCAGCTCTCCAGACTCCAGCA 100 rnd-5_family- 380 ----------GCTGCCTGACTGCNCTTTCACTC-C---AGGAAGCGGGGC 415 ---------- - v i ?i i v - --- i i v i UCON86#LINE/L 101 CGTGCAGAATGCTG-CTGCCCGCCTTCTCACACGCACAAAGAAGTGCGAC 149 rnd-5_family- 416 TATATCACCTCCATCTTCCGTCACCTTCGCTGGCTTCCTATCCATTACCC 465 i i i i viv v i i i i i ---- UCON86#LINE/L 150 CACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATT---- 195 rnd-5_family- 466 TC--GATCCAATTCAAAANTACCCTNCTGGTTTTCAAAATNCTCCGTGGA 513 -- i ? i ? v i i? i UCON86#LINE/L 196 TCAGGATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAAACCCTCCATGGA 245 rnd-5_family- 514 CTTNCTCCAGC 524 ? UCON86#LINE/L 246 CTTGCTCCAGC 256 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.44 CpG sites = 42, Kimura (unadjusted) = 28.10 Transitions / transversions = 4.67 (42/9) Gap_init rate = 0.05 (11 / 242), avg. gap size = 2.18 (24 / 11) 14 0.00 0.00 4.76 rnd-5_family-12727#Unknown 426 447 (535) (AGA)n#Simple_repeat 1 21 (0) m_b20s252i14 rnd-5_family- 426 AGAAGGAAGAAGAAGAAGAAGA 447 - (AGA)n#Simple 1 AGAA-GAAGAAGAAGAAGAAGA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 18 28.62 1.32 4.05 rnd-5_family-12727#Unknown 734 809 (173) (AAAGG)n#Simple_repeat 1 74 (0) m_b20s252i15 rnd-5_family- 734 AAAAGAACAGAAAGGTAAAGGAATGGGAGGGGAGGGAAAGGAAGGGAGGA 783 i vi - v i i i i i -- (AAAGG)n#Simp 1 AAAGGAAAGGAAAGG-AAAGGAAAGGAAAGGAAAGGAAAGGAAAGGA--A 47 rnd-5_family- 784 AGG-GGGGCAGGGAGGGGAAAGGAGAG 809 -ii v i ii i (AAAGG)n#Simp 48 AGGAAAGGAAAGGAAAGGAAAGGAAAG 74 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 17 12.14 0.00 7.69 rnd-5_family-12727#Unknown 758 799 (183) (GGGA)n#Simple_repeat 1 39 (0) m_b20s252i16 rnd-5_family- 758 GGGAGGGGAGGGAAAGGAAGGGAGGAAGGGGGGCAGGGAGGG 799 - -- i i i v (GGGA)n#Simpl 1 GGGA-GGGAGGG--AGGGAGGGAGGGAGGGAGGGAGGGAGGG 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 14 25.59 5.00 0.00 rnd-5_family-12747#LTR/Gypsy 372 431 (378) (CAGCCCC)n#Simple_repeat 1 63 (0) m_b20s252i13 rnd-5_family- 372 CAGCCCCC-CCTCCCCG-CTACTGCCCCCTGCCCGCAGCCTCC-CCTCCC 418 -v i v - iv v v v i -v i (CAGCCCC)n#Si 1 CAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCC 50 rnd-5_family- 419 AGCCCGCAGCTCC 431 v i (CAGCCCC)n#Si 51 AGCCCCCAGCCCC 63 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 12 16.34 2.78 2.78 rnd-5_family-1486#Unknown 106 141 (249) (GAGCCG)n#Simple_repeat 1 36 (0) m_b20s252i12 rnd-5_family- 106 GAGCAGCAGCCGGAGCCCG-GCTCACAGCCGGAGCCG 141 v v v - - iv (GAGCCG)n#Sim 1 GAGCCGGAGCCGGAGCCGGAGC-CGGAGCCGGAGCCG 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 19 19.41 2.44 0.00 rnd-5_family-15227#Unknown 490 530 (1477) (AG)n#Simple_repeat 1 42 (0) m_b20s252i11 rnd-5_family- 490 AGAGAGAGAGAGAGAGAGAAAGGCAGTGGTAGAG-GAGTGAG 530 i iv v iv - v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 379 25.12 2.63 8.33 rnd-5_family-1525#DNA/TcMar 8 159 (4) X22_DNA#DNA/TcMar 11 154 (0) m_b20s502i2 rnd-5_family- 8 CATTAAAAAATGGACGTTTACCGCACCGCGGTATTTACCTTTACCGCGGT 57 i vi i i vi i iii - ii X22_DNA#DNA/T 11 CATTAAAAAGTTAACATTTATCTTATCGTAATATTTAC-TTTATTGCGGT 59 rnd-5_family- 58 A-TTTGCGGTATTC-CCTATACTTAGAATGGGAAATACCGCAAATACCGC 105 -v i i i- v i vv ----------- i i i X22_DNA#DNA/T 60 AAGTCGCGATATTTTCCTATTCCTTCAATG-----------AGATATCGT 98 rnd-5_family- 106 GGTAAATTTAACT-ACTGCGG-GTGGTAAATGTCCAGTTTTTAATGGCAN 153 iv v - i -iv i v v iv ? X22_DNA#DNA/T 99 GGTAAGATAAACTCACCGCGGTAAGATAAATGTCAACTTTTTAATGAAAA 148 rnd-5_family- 154 CCACTG 159 X22_DNA#DNA/T 149 CCACTG 154 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.57 CpG sites = 23, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.11 (16 / 151), avg. gap size = 1.00 (16 / 16) 268 25.92 3.60 2.86 rnd-5_family-1548#Unknown 91 229 (114) UCON60#Unknown 155 294 (6) m_b20s502i3 rnd-5_family- 91 GCCGTTTTGGAGNTATGACAAGN-CAAAAAA--CTTCTAGGAAAATGTTC 137 v ? - i ?- -- v i v -- v v i UCON60#Unknow 155 GCCGTTTTTGAGTTAT-ACGAGCACAAAAAAAACATTTCG--ATATTTTT 201 rnd-5_family- 138 AAGAAGTGAGATCACCTCATTTTTTGAACCNTCATAT--CTCCCAAACGC 185 v ? - vv vivi i vv i ? ii -- vv v UCON60#Unknow 202 TAGAANTG-GAAAAGTGTATTTCTTCTATCCTCGCATAACTCAAAAACGG 250 rnd-5_family- 186 CTTGTCCGATTTGCCTCAAACTTTCCAGAAAAATTCTACCCTGG 229 viv ?v v i i i i i i UCON60#Unknow 251 CTGAACCGATTTNGCTCAAACTTTCAAAAGAAATTCCATCTTAG 294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 16, Kimura (unadjusted) = 33.55 Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.29 (9 / 7) 1480 9.36 0.00 0.00 rnd-5_family-2015#LINE/CR1 1 203 (0) CR1-L3A_Croc#LINE/CR1 224 426 (3862) m_b20s551i0 rnd-5_family- 1 GGCCAGCGATGGAACAGTGGTGGTGACCTGCAACGGATGTGCCATGTTTT 50 ? v i i CR1-L3A_Croc# 224 GGCCAGCGATGGANCAGTGGTTGTGACCTGCAACGGATGCGCCACGTTTT 273 rnd-5_family- 51 CTTTCCTGCCTGAAGCCAGAAGGGACTTCCTGTGCATGAAGTGCAAGTTG 100 i CR1-L3A_Croc# 274 CTTTCCTGCCTGAAGCCAGAAGGGACTTCCTGTGTATGAAGTGCAAGTTG 323 rnd-5_family- 101 GTGGCTGTGCTGGAGGAAAAGATTCTTGGATTGGAGGGGCAAGTAGAGAC 150 i v v i i vv CR1-L3A_Croc# 324 GTGGCTGTGCTGGAAGAAAAGATTCGTGGTTTGGAAGGACAAGTACTGAC 373 rnd-5_family- 151 GCTACTGAGAATCAGAGAAGCTGAGGAGTTCCTAGACAGCCAGGTTCGGG 200 i v v i i i i i CR1-L3A_Croc# 374 GCTGCGGAGCATCAGAGAGGCTGAGGAGTTCTTGGACAACCAGATTCGGG 423 rnd-5_family- 201 AAG 203 CR1-L3A_Croc# 424 AAG 426 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.08 CpG sites = 12, Kimura (unadjusted) = 10.13 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 202), avg. gap size = 0.0 (0 / 0) 351 23.81 12.93 0.00 rnd-5_family-2205#LINE/CR1 1707 1853 (661) CR1-L3B_Croc#LINE/CR1 420 585 (2692) m_b20s551i1 rnd-5_family- 1707 GGAATCTGGGCAATAAGGAAGAGGAGATGGAAATTCTCCCTGGGGAGGGG 1756 i i i v iv vi iv ii CR1-L3B_Croc# 420 GGAGTCTGGGTAACAAGCAAGAGGAACTGGAAATTCTCATTGATGAGAAG 469 rnd-5_family- 1757 AAAT--G--------GG-------GAAACCCGGGGGGACGATGGGTATGA 1789 -- -------- ------- i v i vv i CR1-L3B_Croc# 470 AAATTTGATATAATTGGCATTACTGAAACCTGGTGGGATGATTCGCATGA 519 rnd-5_family- 1790 CTGGAATGTT--TGTCGCTGGTTACAGCCCACTGAGGTAGGGGAGAGAGG 1837 --vi ? i i iii v v iv v CR1-L3B_Croc# 520 CTGGAATGTTAAAATCNCTGGTTATAACCTGTTTAGGAAGGACAGAGCGG 569 rnd-5_family- 1838 GTACAAAAAGTGGTGG 1853 v i i i v CR1-L3B_Croc# 570 GTAAAAGAGGCGGGGG 585 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.52 CpG sites = 21, Kimura (unadjusted) = 29.51 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.03 (4 / 146), avg. gap size = 4.75 (19 / 4) 1104 23.55 1.44 0.36 rnd-5_family-2205#LINE/CR1 2231 2507 (7) CR1-L3B_Croc#LINE/CR1 593 872 (2405) m_b20s551i2 rnd-5_family- 2231 CCCTGCATTAGACACATCATTACCTGTTTTAC-GTTCTTGGTTATTGAGA 2279 i i i v i v- v i v i v CR1-L3B_Croc# 593 CTCTACATTAAAGACACCATTACCTGTTTTAGAGTTATTGATAACTCAGA 642 rnd-5_family- 2280 ACCCCAGGACCTCGAATGGACAGGGATCAATCTGCTAACTGACACAGCCC 2329 v i i v i v v i v CR1-L3B_Croc# 643 ACCGCAGGATCTTGAATGCATATGGATCAATGTGCTAACTAACAAAGCCC 692 rnd-5_family- 2330 AGCAGATGA-ACCGGTGGGGGGCTGGCACAGTTCACTGAATCCAAACCAG 2378 v iv i- i v vi vi i - CR1-L3B_Croc# 693 AGGAGGGGGTACTGGTGGGGGTCTGTTACAGACCACCGAATC-AAACCAG 741 rnd-5_family- 2379 AGAGCAGGAAATGTTTCTCCTTTTGCACCTGTCTGTGACTTGTGGGAAG- 2427 i viv v vv i iv i - CR1-L3B_Croc# 742 AGAACAGGATGAGTTACTCCTTAAGCACCTGTCTGTAATGTGTGGAAAGA 791 rnd-5_family- 2428 -AAATTAGGTTAGCCCGGGGGACTTCCTACTGGGAGACAGACGGGGGCGG 2476 - i iv iviv vvvi v i vv v CR1-L3B_Croc# 792 AAAACTGTGTTGTTACGGGGGACTTCAGTTTGGGAGACATATGCTGGAGG 841 rnd-5_family- 2477 TCTCACGTAGCCAGGAGTAAATCGTCCTTGG 2507 i i v v i v i CR1-L3B_Croc# 842 TCTCATGCAGCCAGTAGTAAAACATCATTAG 872 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.95 CpG sites = 31, Kimura (unadjusted) = 28.44 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.02 (5 / 276), avg. gap size = 1.00 (5 / 5) 256 18.74 3.08 1.52 rnd-5_family-2703#DNA/hAT-Charlie 68 132 (1) Charlie23a#DNA/hAT-Charlie 274 339 (0) m_b20s502i4 rnd-5_family- 68 GGGGGTC-GTGAAAATNTTTGACTTCGAATAAGGGGTCGCCA-ACCTGAA 115 i - i v ? v ii - vi - ii Charlie23a#DN 274 GGGGATCCGCGAAATTTTTTGACGTTAAA-AAGGGGTCCTCATACTCGAA 322 rnd-5_family- 116 AAGGTTGAGAAACACTG 132 i v Charlie23a#DN 323 AAGGTTGGGAACCACTG 339 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.47 CpG sites = 8, Kimura (unadjusted) = 22.49 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 210 21.67 5.00 0.00 rnd-5_family-3087#Unknown 17 76 (335) C L2c_3end#LINE/L2 (27) 451 389 m_b20s601i1 rnd-5_family- 17 AGCGCCCANNATGTGCTAGGCGCTTTCCAAACACAGAGG---AAGACACA 63 i ?? i vvvv v v v --- i C L2c_3end#LINE 451 AGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACG 402 rnd-5_family- 64 GTCCCTGCTTCCA 76 iii C L2c_3end#LINE 401 GTCCCTGCCCTCA 389 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.49 CpG sites = 6, Kimura (unadjusted) = 26.75 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.02 (1 / 59), avg. gap size = 3.00 (3 / 1) 12 8.66 0.00 7.41 rnd-5_family-3087#Unknown 306 334 (77) (ATAA)n#Simple_repeat 1 27 (0) m_b20s252i10 rnd-5_family- 306 ATAAGATAAATAAATGAAATAGATAAGTA 334 - - i i (ATAA)n#Simpl 1 ATAA-ATAAATAAAT-AAATAAATAAATA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 958 8.21 0.00 0.75 rnd-5_family-3304#DNA/Merlin 1 135 (0) MER125#DNA/Merlin 34 167 (9) m_b20s502i5 rnd-5_family- 1 ATGAATTCATTTGGTATTCATTGTAATAACACTGATCATAATGAATTCAT 50 v v i i i i MER125#DNA/Me 34 ATTAATTCCTTTGGTATTCATTGTAATAACATTAATCATGATGAACTCAT 83 rnd-5_family- 51 TTGGTATTCATGTGGATGTCACATGTACTTCCATAGGAATTTTCACTGTA 100 v i ? - i MER125#DNA/Me 84 TTGGTATTAATGTGGATGTCATATGTANTTCCATAGGAA-TTCCACTGTA 132 rnd-5_family- 101 ATTCAGCATTAGTTAACTGGACCATTATTTTAAAG 135 i i MER125#DNA/Me 133 ATTTAGCATTAATTAACTGGACCATTATTTTAAAG 167 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.86 CpG sites = 8, Kimura (unadjusted) = 8.86 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1) 377 8.33 0.00 0.00 rnd-5_family-3501#DNA/hAT-Charlie 1 60 (137) Charlie30a#DNA/hAT-Charlie 4 63 (728) m_b20s502i6 rnd-5_family- 1 GGGTGGGGAACCTACGGCCCGCGGGCCGGATCCGGCCCGCTGCTTCATTT 50 v i v v v Charlie30a#DN 4 GGGTGGGGAACCTCCGGCCCGCGGGCCGGACCCGGCCCTCGGCTTGATTT 53 rnd-5_family- 51 CATCCGGCCC 60 Charlie30a#DN 54 CATCCGGCCC 63 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.85 CpG sites = 1, Kimura (unadjusted) = 8.85 Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 12 21.12 6.00 0.00 rnd-5_family-4921#Unknown 1 50 (334) (TTATATTA)n#Simple_repeat 1 53 (0) m_b20s252i9 rnd-5_family- 1 TTATATNATTATATTA-TAAATTGTCA-GTTAATACAATA-TATAATATA 47 ? - v i i -i v i v - v v (TTATATTA)n#S 1 TTATATTATTATATTATTATATTATTATATTATTATATTATTATATTATT 50 rnd-5_family- 48 ATA 50 (TTATATTA)n#S 51 ATA 53 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 440 20.37 0.91 1.83 rnd-5_family-4921#Unknown 106 215 (169) C UCON60#Unknown (158) 142 34 m_b20s502i7 rnd-5_family- 106 CTTCAGACTTGGCTTGATTTTTAAGTC-TCAGTGAGATCTACAAAACAAG 154 i vv v -- - ? ivvviv v C UCON60#Unknow 142 CTTCAAACTTGGCAGGATTGT--AGTCCTCANTGAGGAAGGAAAATCAAG 95 rnd-5_family- 155 CCAAGTTTGAAGAAAATCAGTTCAGTAGTTTTAAAGTTATGAACATTTAA 204 i v i ? v i vi C UCON60#Unknow 94 CCAAATTTGAAGAAAAACGGTTNAGTATTTTTAAAGTTACGAAGGTTTAA 45 rnd-5_family- 205 AGCTGAACGNC 215 ii iv ? C UCON60#Unknow 44 AATTATACGTC 34 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.26 CpG sites = 10, Kimura (unadjusted) = 24.66 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.03 (3 / 109), avg. gap size = 1.00 (3 / 3) 14 24.43 0.00 2.27 rnd-5_family-5194#Unknown 119 163 (71) (TCTCTG)n#Simple_repeat 1 44 (0) m_b20s252i8 rnd-5_family- 119 TCTCTGTCTCAGTCTCTGCAACTGGTTCCTGTCTCTGAGTCAGTC 163 v ivv - ii vv v (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTC 44 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 12 0.00 0.00 12.50 rnd-5_family-7211#LINE/RTE-BovB 1265 1291 (61) (AAG)n#Simple_repeat 1 24 (0) m_b20s252i7 rnd-5_family- 1265 AAGATAGAAGATAGAAAGAAGAAGAAG 1291 - - - (AAG)n#Simple 1 AAGA-AGAAGA-AG-AAGAAGAAGAAG 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (3 / 26), avg. gap size = 1.00 (3 / 3) 570 5.56 0.00 0.00 rnd-5_family-7299#tRNA 168 239 (1169) tRNA-Arg-CGA#tRNA 1 72 (1) c_b20s355i0 rnd-5_family- 168 GACCGCGTGGCCTAATGGATAAGGCGTCTGACTTCGGATCAGGNGATTGA 217 i i? tRNA-Arg-CGA# 1 GACCACGTGGCCTAATGGATAAGGCGTCTGACTTCGGATCAGAAGATTGA 50 rnd-5_family- 218 GGGTTCGAGTCCCTTCGCGGTT 239 i i tRNA-Arg-CGA# 51 GGGTTCGAATCCCTTCGTGGTT 72 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 5.98 CpG sites = 4, Kimura (unadjusted) = 5.98 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 564 8.33 0.00 0.00 rnd-5_family-7299#tRNA 1288 1359 (49) C tRNA-Gln-CAA#tRNA (3) 72 1 c_b20s355i1 rnd-5_family- 1288 AGGTCCCACTGAGATTTGAACTCAGATTGCAGGATTCAGAGTCCTGAGTG 1337 i i i v v C tRNA-Gln-CAA# 72 AGGTCCCACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAGAGTG 23 rnd-5_family- 1338 CTGACCATTACACCATGGGACC 1359 i C tRNA-Gln-CAA# 22 CTAACCATTACACCATGGGACC 1 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 4.73 CpG sites = 4, Kimura (unadjusted) = 8.91 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 12 22.84 10.45 0.00 rnd-5_family-7455#Unknown 249 315 (179) (TGCCT)n#Simple_repeat 1 74 (0) m_b20s252i6 rnd-5_family- 249 TGCCTGGAC-TGCCTTGCC-CGCC--GCCTCGCC-TGACCCGACCTGCCT 293 v v - -i -- i - v ii v i (TGCCT)n#Simp 1 TGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCT 50 rnd-5_family- 294 TGCC--GCCTCGCCTGACCTCGCC 315 -- i vi i (TGCCT)n#Simp 51 TGCCTTGCCTTGCCTTGCCTTGCC 74 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.40 (7 / 5) 13 21.67 2.63 0.00 rnd-5_family-7522#Unknown 401 438 (2998) (GCCTCG)n#Simple_repeat 1 39 (0) m_b20s252i3 rnd-5_family- 401 GCCTCGGCCTCGGCCTCCGGCTAGG-AAGGGCCTGGGCC 438 v v v -vvv v (GCCTCG)n#Sim 1 GCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCC 39 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 15 7.56 3.57 0.00 rnd-5_family-7522#Unknown 1265 1292 (2144) (GGGCA)n#Simple_repeat 1 29 (0) m_b20s252i4 rnd-5_family- 1265 GGGCA-GCCAGGGCAGGGCAGGGCACGGC 1292 - v v (GGGCA)n#Simp 1 GGGCAGGGCAGGGCAGGGCAGGGCAGGGC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 14 31.60 0.00 0.00 rnd-5_family-7522#Unknown 1959 2009 (1427) (CAGG)n#Simple_repeat 1 51 (0) m_b20s252i5 rnd-5_family- 1959 CAGCCTGTCAAGCAGGTGGGCAGGCGGGCGAGCTGGCAGGGAGCCAAGCA 2008 v v v i ii i ii v v v i (CAGG)n#Simpl 1 CAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCA 50 rnd-5_family- 2009 G 2009 (CAGG)n#Simpl 51 G 51 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 18 16.07 3.77 3.77 rnd-5_family-7881#Unknown 94 146 (1769) (GGGAC)n#Simple_repeat 1 53 (0) m_b20s252i0 rnd-5_family- 94 GGGACAGGACTGGGACGGG-GGGGGCGGG-GGGGATGGGACAGGACTGGG 141 i - -v i -v i i - (GGGAC)n#Simp 1 GGGACGGGAC-GGGACGGGACGGGACGGGACGGGACGGGACGGGAC-GGG 48 rnd-5_family- 142 ATGGG 146 i (GGGAC)n#Simp 49 ACGGG 53 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 14 0.00 4.76 0.00 rnd-5_family-7881#Unknown 975 995 (920) (TATT)n#Simple_repeat 1 22 (0) m_b20s252i1 rnd-5_family- 975 TATTTATTTATTTATTT-TTTA 995 - (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 20), avg. gap size = 1.00 (1 / 1) 13 17.83 5.36 5.36 rnd-5_family-7881#Unknown 1820 1875 (40) (GCCGG)n#Simple_repeat 1 56 (0) m_b20s252i2 rnd-5_family- 1820 GCC-GGCCGGGCGGGGCCGGGCCCCCCCCAGGAGCGGGCTGGCGCC--GC 1866 - v - vvv - iv i - -- (GCCGG)n#Simp 1 GCCGGGCCGGGCCGGGCCGGG-CCGGGCC-GGGCCGGGCCGG-GCCGGGC 47 rnd-5_family- 1867 CGCGCCGGG 1875 v (GCCGG)n#Simp 48 CGGGCCGGG 56 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.09 (5 / 55), avg. gap size = 1.20 (6 / 5) 1608 24.53 2.06 3.34 rnd-5_family-8773#LTR/Gypsy 7 491 (19) MamGyp-int#LTR/Gypsy 2617 3095 (2007) m_b20s551i3 rnd-5_family- 7 GGAGACATGAATTTACTGCAAGTGTTAGTTTATTTGGATGACCTGGTTGT 56 i i vv v i i v ii MamGyp-int#LT 2617 GGGGATATGAATTATCTGGAAGTGCTAGTTTATTTAGATGACATAATTGT 2666 rnd-5_family- 57 GTTTGGAAGAACCTTGGAGGAGCATGAAGAAAGACTTCTTAAAGTGCTTG 106 ? i v i i iv v i i v MamGyp-int#LT 2667 NTTCGGCAGGACTTTGGAGGAGCATGAGCAACGACTCCTTAAGGTGCTGG 2716 rnd-5_family- 107 ATAGGTTGGAGGATTATGGTTTGAAGCTTTCAATTGACAAATGCCAGTTC 156 iv vi i vvvv ? ii v vv i MamGyp-int#LT 2717 ACCGCCTGGAAGAGGCAGGNTTGAAATTGTCCCTTGACAAATGCCAATTC 2766 rnd-5_family- 157 TGCAGGACCTCAGTGAAGTATGTGGGTCACATCGTGTCCCAAGAGGGTGT 206 v ? ? i ? v i v ? v v MamGyp-int#LT 2767 TGCCGNACCTCNGTGAAATATGTNGGGCATATAGTNTCCCAACAGGGAGT 2816 rnd-5_family- 207 GAGTACTGATCCCGATAAAATAGAAGCNCTCACTACATGGCCACGTCCAA 256 i v i i v i ?vvv ?v i vv v v MamGyp-int#LT 2817 GAGCACAGACCCTGAAAAGATNTCTGCCATCACCAATTGGCCCCGTCCCA 2866 rnd-5_family- 257 GTAACTACAGAGAACTCAAGACCTTTCTTGGGTTTAGTGGCTACTACCGC 306 vi i i i v ? ii v i ? i iv v MamGyp-int#LT 2867 CCAATTATAGAGAATTAAAGACNTTCTTGGGGTTCAGTGGNTATTATAGG 2916 rnd-5_family- 307 AGATTTGTGAAGAACTATGCTACGATTGTAAAACCTCTGAATGATCTTAC 356 i v i ? i? i ? v i v MamGyp-int#LT 2917 AGGTTTGTGAAGAACTATTCCANGATTGCNAAGCCNCTCAATGACCTAAC 2966 rnd-5_family- 357 CAGGGGATACCAGTCCA--GCAGGAACAAATCTAAGACCAAGAATAAGGG 404 v v i vi -- v ii ---? i ---? -- MamGyp-int#LT 2967 CCGGGGTTATCAGGTCAGGGCTGGGGC---NCCAA---NAAGA--AAGGG 3008 rnd-5_family- 405 GAGGTCCCCAAAGCCTCCTGTGCAGA-GACACTATGG-------CCCCTT 446 vi i v iii --------v - v? i v ------- MamGyp-int#LT 3009 GCAGCCCACAGGAC--------AAGAGGAANCCAGGGTCCCCCACCCCTT 3050 rnd-5_family- 447 CGAACCATTTGGGCCACGGTGGGATGAGAGATGTGAAAGGGCTTT 491 i v i vvi ? ivi ivv ivi v MamGyp-int#LT 3051 TGAACCCTTCGGGGAGCGNTGGGGGAAGGCCTGTGAGCAGGCGTT 3095 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.75 CpG sites = 58, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.02 (58/57) Gap_init rate = 0.04 (19 / 484), avg. gap size = 1.37 (26 / 19) 259 11.11 0.00 0.00 rnd-5_family-1921#DNA/PIF-Harbinger 43 78 (82) MER133B#DNA/PIF-Harbinger 43 78 (37) m_b21s502i0 rnd-5_family- 43 CGCGCGACTCCCATTAAAGTCAATGGGAGTCGCGCG 78 i i i i MER133B#DNA/P 43 CGCGCAACTCCCATTGAAGTCAATGGGAGTTGTGCG 78 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.57 CpG sites = 4, Kimura (unadjusted) = 12.57 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 334 18.46 3.08 0.00 rnd-5_family-2347#LINE/L2 266 330 (10) UCON86#LINE/L2 616 682 (0) m_b21s502i1 rnd-5_family- 266 CTCTGCAAAGCATTTTGTGATAC--TTTGTATGAAGGATGCTATATAAAA 313 i i v -- i i i UCON86#LINE/L 616 CTCTGTAAAGCGTTTTGGGATACAGTTTGTATGAAAGACGCTATACAAAA 665 rnd-5_family- 314 ATAAATTGCATTGCACT 330 vv i i i i UCON86#LINE/L 666 TAAAGTTGTATTGTATT 682 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.00 CpG sites = 9, Kimura (unadjusted) = 21.93 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1) 1343 1.75 12.87 0.00 rnd-5_family-2782#LINE/CR1 1 171 (0) CR1-L3A_Croc#LINE/CR1 1424 1616 (2672) m_b21s551i0 rnd-5_family- 1 TTCTTTAATTGCCTATACACCAATGCTAGGAGCCTGGGTAACAAACAAGA 50 i CR1-L3A_Croc# 1424 TTCTTTAATTGCCTATACACCAATGCTAGGAGCCTGGGTAATAAACAAGA 1473 rnd-5_family- 51 GGAATTGGAATTGCTCATTTATGAGCATAAATTCGATCTAGTTGGTATTA 100 i CR1-L3A_Croc# 1474 GGAATTGGAATTGCTCATTTATGAGCATAAATTCGACCTAGTTGGTATTA 1523 rnd-5_family- 101 CTGAAACCTGGT------------ATGAAT----------AATCAATGGT 128 ------------ v ---------- CR1-L3A_Croc# 1524 CTGAAACCTGGTGGGAAGATTCGCATGACTGGAATGTTAAAATCAATGGT 1573 rnd-5_family- 129 TATAACCTATTTAGGAAGGATCGAGTGGGCAAAAGGGGAGGGG 171 CR1-L3A_Croc# 1574 TATAACCTATTTAGGAAGGATCGAGTGGGCAAAAGGGGAGGGG 1616 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 1.78 CpG sites = 2, Kimura (unadjusted) = 1.78 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.01 (2 / 170), avg. gap size = 11.00 (22 / 2) 18 12.03 0.00 0.00 rnd-5_family-29#Unknown 58 84 (432) (A)n#Simple_repeat 1 27 (0) m_b21s252i8 rnd-5_family- 58 AAAAAATAAAAAACAAGAAAAAAAAAA 84 v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 661 12.93 1.69 1.69 rnd-5_family-3352#SINE/tRNA 2 119 (19) LFSINE_Vert#SINE/tRNA 333 450 (9) m_b21s601i0 rnd-5_family- 2 GGGGCAGCGTGGGGAAGCTTGCACTGCCGCTGCCTACGCTGTACCTGTCC 51 i iii i LFSINE_Vert#S 333 GGGGCAGTGTGGGGAAGCTTGCACTGCCGCTGCCCGTGCTGTACCTGTTC 382 rnd-5_family- 52 TGTGGNTAAACA-AAGACTTCGGTTCCCAAAGC-GTTAGTCCCGGCACCT 99 ? - i i ii ii - i i - LFSINE_Vert#S 383 TGTGGATAAACAGAGGACTTCAGTCTCCAGGGCTGTCAAT-CCGGCACCT 431 rnd-5_family- 100 TTCACAAGCACCATAATTCA 119 i i - LFSINE_Vert#S 432 TTCACGAGCACTA-AATTCA 450 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 12.93 CpG sites = 15, Kimura (unadjusted) = 15.11 Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.00 (4 / 4) 305 33.60 4.48 4.48 rnd-5_family-3505#LTR/ERV1 187 588 (2012) HERVE#LTR/ERV1 4840 5241 (2572) m_b21s701i0 rnd-5_family- 187 GCTGCTCCATTTCAACATCTTCAAATTGACTTTGCAGATATGCCAAAGGC 236 v i v v v i ii v ii v vv HERVE#LTR/ERV 4840 GCAGCCCCCTTTGAAGATCTCCAGGTGGACTTCACAGAGATGCCAAAGTG 4889 rnd-5_family- 237 TTTTGGGAAAAAGCACCTCCTTGTTTT--GGTTTGCC--CTCTGACTTCC 282 vvv v v i ii v v i -- iv i -- iv --- HERVE#LTR/ERV 4890 TGGAGGTAACAAGTATTTACTAGTTCTTGGGCGTACCTACTCTGGGT--- 4936 rnd-5_family- 283 TGGGTCGAAGCTTTTCCTACTGCTAATTG-TACTGCTGCCACAGTGGCGA 331 - v i i v v -i v i -v vv vviiv ii vv HERVE#LTR/ERV 4937 -GGGTGGAGGCCTATCCAAC-ACGAACTGAGAAAGCTCGTGAAGTAACCC 4984 rnd-5_family- 332 AGATTCTCCTTAGAGACATTGTACCCCGTTTTGGCAT-CCCTCTCGTGCT 380 ivi v i v iv vi v iv v vv - iv - v HERVE#LTR/ERV 4985 GTGTGCTTCTTCGAGATCTGATTCCTAGATTTGGACTGCCCTTACG-GAT 5033 rnd-5_family- 381 TGACTCAGATCGCGGACCTCACTTTACTGGTCATGTCCTTGGCCGTTTAG 430 i i vi i -i v v? i-- ? - --- vi HERVE#LTR/ERV 5034 CGGCTCAGATAACGGGCCT-GCGTTTNTGGC--TGNC-TTGG---TACAG 5076 rnd-5_family- 431 AA-----CAAGG--ACTGGGCATTTCACACTCCTTTCATACACCCTACCA 473 ----- i -- i v iv ivvvvi v i vv v i HERVE#LTR/ERV 5077 AAGACGGCAAAGGTATTGGGGATCACACGGAAACTGCATGCCGCCTCCCG 5126 rnd-5_family- 474 CCCCCAGTCTAGCGGGAAAGTTGAGCGTATGAATAGGGAGCTTAA----- 518 v i vv vv i i v v v ivvv i ----- HERVE#LTR/ERV 5127 GCCTCAGAGTTCCGGAAAGGTGGAGCGGATGAATCGGACTATCAAAAATA 5176 rnd-5_family- 519 GTTTACATTGGCTAAATACTGTCAGGAAACAGGGTTAAAGTGGCCTCAGG 568 ---- vv i - i i viv HERVE#LTR/ERV 5177 GTTTA----GGGAAAGTA-TGTCAGGAAACAGGATTAAAATGGATACAGG 5221 rnd-5_family- 569 TACTTCCCTTGGTCCTGTTT 588 iv i iv vi i HERVE#LTR/ERV 5222 CTCTCCCTATGGTATTATTT 5241 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 56, Kimura (unadjusted) = 45.15 Transitions / transversions = 0.77 (56/73) Gap_init rate = 0.06 (25 / 401), avg. gap size = 1.44 (36 / 25) 333 31.94 6.07 4.95 rnd-5_family-3505#LTR/ERV1 305 584 (2016) MER34-int#LTR/ERV1 5551 5833 (2374) m_b21s701i1 rnd-5_family- 305 CTAATTGTACTGCTGCCAC---AGTGGCGAAGATTCTCCTTAGAGACATT 351 ivi i v --- ii vvi vv v vv v MER34-int#LTR 5551 CTAGACGTGCTGATGCCACGACAGTGGTAAAGAAATTAATAACTGAGATT 5600 rnd-5_family- 352 GTACCCCGTTTTGGCATCCCTCTCGTGCTTGACTCAGATCGCGGACCTCA 401 i v i i i vvv v v i iv v MER34-int#LTR 5601 ATTCCTCGTTTTGGCATTCCTTTATGGATTGAATCAGACCAAGGAACTCA 5650 rnd-5_family- 402 CTTTACTG---------GTCATGTCCTTGGCCGTTTAGAACAAGGACT-- 440 i v ---------ii iv v ----------- ii -- MER34-int#LTR 5651 TTTTACAGCAGAAATAAACCACTTGCTTG-----------CAAAAACTCT 5689 rnd-5_family- 441 -GGGCATTTCACACT--CCTTTCATACACCCTACCACCCCCAGTCTAGCG 487 - i i --- i --vv v v i i ivvv MER34-int#LTR 5690 GGGGTACT---CATTAAAATTTCATACCCCATACCATCCCCAATCCTCAG 5736 rnd-5_family- 488 GGAAAGTTGAGCGTATGAATAGGGAGCTTAAGTTTACATTGGCTAAATAC 537 v v i vi vvi vv v i?vv v vv vv MER34-int#LTR 5737 GGCAAGTGGAACGTAAAAATCTAGACATAAAANGGACTTTGGGAAAAGTC 5786 rnd-5_family- 538 TGTCAGGAAACAGGGTTAAAGTGGCCTCAGGTACTTCCCTTGGTCCT 584 i ? v ii v i vv i i i v i i MER34-int#LTR 5787 TGTCAAGANACTGGACTTAAATGGCCAGAAGCATTACCCCTGGCCCT 5833 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 37, Kimura (unadjusted) = 42.31 Transitions / transversions = 0.77 (37/48) Gap_init rate = 0.07 (19 / 279), avg. gap size = 1.63 (31 / 19) 334 26.61 3.88 3.88 rnd-5_family-3505#LTR/ERV1 460 588 (2012) HERVE_a#LTR/ERV1 5136 5264 (2583) m_b21s701i2 rnd-5_family- 460 CATACACCCTACCACCCCCAGTCTAGCGGGAAAGTTGAGCGTATGAATAG 509 i vv iv i vv vv i i v v v HERVE_a#LTR/E 5136 CATGCCGCCTACCGACCTCAGAGTTCCGGAAAGGTGGAGCGAATGAATCG 5185 rnd-5_family- 510 GGAGCTTAA-----GTTTACATTGGCTAAATACTGTCAGGAAACAGGGTT 554 ivvv i ----- ---- vv i - i HERVE_a#LTR/E 5186 GACTATCAAAAATAGTTTA----GGGAAAGTA-TGTCAGGAAACAGGATT 5230 rnd-5_family- 555 AAAGTGGCCTCAGGTACTTCCCTTGGTCCTGTTT 588 viv iv iv vi HERVE_a#LTR/E 5231 AAAGTGGATACAGGCCCTTCCTATGGTATTGTTT 5264 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 13, Kimura (unadjusted) = 32.92 Transitions / transversions = 0.65 (13/20) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.67 (10 / 6) 420 17.30 2.80 2.80 rnd-5_family-3505#LTR/ERV1 2118 2224 (376) PABL_B-int#LTR/ERV1 6551 6657 (465) m_b21s701i3 rnd-5_family- 2118 GAAATGTCCCAGCTGCGCCAG-TTAGCTTTGCAAAACCGAATGGCTTTAG 2166 v vv vv -i v - ? ii PABL_B-int#LT 6551 GAAATGTACCATATGCGGAAGGCTATCTT-GCAAAACCGNATGGCCCTAG 6599 rnd-5_family- 2167 ACATAATGTTAGCAGCCCAGGGAGGAACTTGCGCCCTCATAAATGAA--G 2214 vv ?viv ? i i ? ? v -- -- PABL_B-int#LT 6600 ACATCCTNACTGCNGCCCAGGGGGGAACCTGCGCCNTNATTAA--AACTG 6647 rnd-5_family- 2215 AATGCTGTGT 2224 i PABL_B-int#LT 6648 AATGTTGTGT 6657 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.84 CpG sites = 7, Kimura (unadjusted) = 20.84 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.20 (6 / 5) 325 30.11 0.00 0.00 rnd-5_family-3505#LTR/ERV1 2146 2238 (362) HERVL18#LTR/ERVL 5693 5785 (262) m_b21s701i4 rnd-5_family- 2146 TGCAAAACCGAATGGCTTTAGACATAATGTTAGCAGCCCAGGGAGGAACT 2195 i i i iviv v i ? v i HERVL18#LTR/E 5693 TGCAAAACCGGATGGCCTTAGACATAGTAACTGCTGCCCAAGGNGGCACC 5742 rnd-5_family- 2196 TGCGCCCTCATAAATGAAGAATGCTGTGTTTTTGTAAATGACA 2238 i iv iiviv v i iii i vvv HERVL18#LTR/E 5743 TGTGCCCTTTTAGGAACACAATGTTGTACCTTTATCCCTGACA 5785 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.41 CpG sites = 17, Kimura (unadjusted) = 40.41 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 28 0.00 0.00 0.00 rnd-5_family-3527#SINE/tRNA 736 762 (2079) (TATC)n#Simple_repeat 1 27 (0) c_b21s251i0 rnd-5_family- 736 TATCTATCTATCTATCTATCTATCTAT 762 (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTAT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 290 27.48 9.21 1.84 rnd-5_family-3527#SINE/tRNA 855 1006 (1835) LFSINE_Vert#SINE/tRNA 141 303 (156) m_b21s601i1 rnd-5_family- 855 TGAGTTGCTGGGTCTCTCTGCAGTTCCTAGCAGACAGGGATCTACTCCAC 904 v - vv v ii vi i vi LFSINE_Vert#S 141 TGAGTTGGTGG-TCTCAGTCCAGTTCCTAGTGGACAGGTGTCCACATCAC 189 rnd-5_family- 905 AGA-------------TGGGCGCTCCCTGCTCCCCTCCTTGGGCGGGCTT 941 i ------------- v i vvi viv iv - i v i LFSINE_Vert#S 190 AAAACCACCATCACAATTGGCACTAATTGGCACCCTTGTTGG-CAGTCTC 238 rnd-5_family- 942 GGCTGAGAGGTGATGGACTAAATGGG-ATGAGGGACTGAAAGCCTCTCCC 990 i v iv v i - - i vvv i i LFSINE_Vert#S 239 AGCAGAGAGGCCAAGGACTGAATGGGCATG-GAGACTGAACTACCCTCTC 287 rnd-5_family- 991 AGCTCTAGAGAGGGCC 1006 v iv i LFSINE_Vert#S 288 ACCTCTAGAGGTGGTC 303 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 20, Kimura (unadjusted) = 34.61 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.03 (5 / 151), avg. gap size = 3.40 (17 / 5) 351 6.67 0.00 0.00 rnd-5_family-3527#SINE/tRNA 2556 2600 (241) C UCON69#DNA/hAT (246) 240 196 m_b21s502i2 rnd-5_family- 2556 ACGAGTGGAGCAGTTCACACCTCTCNGAGCNATTGTTTCAGGCTG 2600 i i i ? ? C UCON69#DNA/hA 240 ATGAATGGGGCAGTTCACACCTCTCAGAGCTATTGTTTCAGGCTG 196 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.51 CpG sites = 3, Kimura (unadjusted) = 7.51 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 18 18.65 1.61 6.78 rnd-5_family-373#Unknown 1605 1666 (323) (TTTAT)n#Simple_repeat 1 59 (0) m_b21s252i7 rnd-5_family- 1605 TTTATTCTAATTTGATTT-GTTTATATGATTATTATTTTATGTTTTTGCT 1653 i v iv -v v v - - v -i (TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATT-TTATTTTAT-TTTAT-TT 47 rnd-5_family- 1654 TAGTTTTATTTTA 1666 - (TTTAT)n#Simp 48 TA-TTTTATTTTA 59 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 701 30.74 3.11 4.25 rnd-5_family-4131#LTR/ERV1 271 817 (62) MER110-int#LTR/ERV1 2017 2557 (2090) m_b21s701i5 rnd-5_family- 271 ATGTGTGATTTGTCAGCAGCATAACATTGGTAAAGCTGTTAAAGTTAGGC 320 v v ii ? ivi i i v i vi i MER110-int#LT 2017 ATGTCTCACCTGTCANCAGCATAATCCTGGCAAAACTGTAAAGGTGGGAC 2066 rnd-5_family- 321 AGGCAGCTCACCCTCCCCCTTGGGGACCTTTTGTAAATATTCAGATTGAT 370 v v --- vvvv ?vvv i i v i v v iv i i v MER110-int#LT 2067 ATGGA---CAAGAGCCNAAATAGAGCCCCTTTGAACACCTCCAAATGGAT 2113 rnd-5_family- 371 TTTATTCAACTGTCT--AAATGTTGTGGCTATGAATATGTGTTGGTTTTG 418 i v v v i--v ---- i v vi viv MER110-int#LT 2114 TTCATACATCTCTCCTGCAATG----GGTTTTGAATATGTTCTGTCATTG 2159 rnd-5_family- 419 GTGGATGTATTTTCAAATTGGGTTGAAGCTTTTCCCTGCAGGAAAGCAGA 468 v v v - i iiiv i i i v i viv MER110-int#LT 2160 TTTGCT-TATTCTCGGGATGGATTGAAGCCTTTCCTTGCCGGAGAGCTAC 2208 rnd-5_family- 469 TGCCAGGACTGTTGT-GAAACTTCTGCTTAAAGATTTTGTAC-CACGATT 516 v ivvi v v i- v ?i i --- ?i- v i ii MER110-int#LT 2209 GGCTCTAACGGTAGCAGAAAATNTTACTT---GATTTTGTNTTCCCAACC 2255 rnd-5_family- 517 TGGC--ATCCCTGTGAGTATCAA--CAGTGACCGTGGAACTCATTTTACT 562 v-- i i-i v vv-- v v ? i MER110-int#LT 2256 TGGGGAATTCCTA-AACTATCTCTCCAGTGACAGAGGNACCCATTTTACT 2304 rnd-5_family- 563 -GGACAGATTGTAAAGGAGTTATGTGCAGCTTCGCAG---ACTCAACACA 608 - v - i v i i v iiv i v?--- i--- MER110-int#LT 2305 GGGACTG-TTATTAAAGAGCTTTGCAAAGCTTTGCCNCTTACTCAG---A 2350 rnd-5_family- 609 ACCTTCACTGTCCCCACCATCCGCAGTCTGCTGGGACAGTGGAACGCCAG 658 v ?i i - i v - i v ?i v vvv? MER110-int#LT 2351 AACTTCACTGTCCNTATCATCC-CAATCTTC-GGAAAAGNAGAAAGAACN 2398 rnd-5_family- 659 AATGGAATTCTGAAAAATAAACTGGCCAAGATTTGTGCTGAAA----CAA 704 i vvv i i v v i --- v i ---- i MER110-int#LT 2399 AATGGAATTCTAAAACTAAAATTAGCAAAGCTCT---CAGAGACCCTCGA 2445 rnd-5_family- 705 ACTTGAAGTGGCCAGATGCCCTTCCTCTGGCACTAATGAGTATGAGGGCC 754 vv - vi v ivi ? vi vi vv i iv v MER110-int#LT 2446 ACTTCCA-TGGCCTAAGGTATTNCCATTGGCTTTAATGACAATAAGATCA 2494 rnd-5_family- 755 ACTCCCAATCGAA-AGACCGGACTCAGCCCTCATGAGATTCTGACAGGGC 803 ivv v i -vv - ?vv i v vv i v MER110-int#LT 2495 ACTCCTTCTGGGATTCACC-GACTNTCCCCTTATGAGTTAGTAACAGGCC 2543 rnd-5_family- 804 GCCCGATGCGACTA 817 ? v iv MER110-int#LT 2544 GNCCCATGCATCTA 2557 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 72, Kimura (unadjusted) = 41.04 Transitions / transversions = 0.81 (72/89) Gap_init rate = 0.06 (32 / 546), avg. gap size = 1.25 (40 / 32) 788 28.90 3.66 2.51 rnd-5_family-4131#LTR/ERV1 334 688 (191) PRIMA4-int#LTR/ERV1 5454 5812 (2458) m_b21s701i6 rnd-5_family- 334 TCCCCCTT--GG--GGACCTTTTGTAAATATT-CAGATTGATTTTATTCA 378 i -- -- - ii v- v i PRIMA4-int#LT 5454 TTCCCCTTCCGGCTGGACCTTTTG-AGGTATGGCAGCTTGATTTTATCCA 5502 rnd-5_family- 379 ACTGTCTAAATGTTGTGGCTATGAATATGTGTTGGTTTTGGTGGATGTAT 428 i i vvv v iiv i ii i v i vv vviii i PRIMA4-int#LT 5503 GCTGCCATCATCTCAAGGTTACAAGTATGTTTTAGTAATGGTCTGCATGT 5552 rnd-5_family- 429 TTTCAAATTGGGTTGAAGCTTTTCCCTGCAGGAAAGCAGATGCCAGGACT 478 vv v ivv v i v PRIMA4-int#LT 5553 TTTCCCATTGGGTTGAAGCTTTTCCCTGCAGGCAAGCAACAGCCATGGCA 5602 rnd-5_family- 479 GTTGTGAAACTTCTGCTTAAAGATTTTGTACCACGATTTGGCAT-CCCTG 527 vi v i i vi i vv i v vi vv vi - PRIMA4-int#LT 5603 GTTGGAAAAATCCTACTAGAAAAAATTATCCCACTGTGGGGAGTCCCCTG 5652 rnd-5_family- 528 TGAGTATCAACAGTGACCGTGGAACTCATTTTACTGGACAGATTGT--AA 575 iiv - v v i v i i -- PRIMA4-int#LT 5653 TGAACTTC-ACAGTGACAGGGGAACTCACTTTACTGGCCAGGTTATTCAA 5701 rnd-5_family- 576 AGGAGTTATGTGCAGCTTCGCAGA---CTCAACACAACCTTCACTGTCCC 622 iv v -- iv ii v vv ---i --- ii i i v PRIMA4-int#LT 5702 AATATT--TGTAAAATTTGGCCCATATTTCAAC---ATTTCCATTGTGCC 5746 rnd-5_family- 623 CACCATCCGCAGTCTGCTGGGACAGTGGAACG--CCAGAATGGAATTCTG 670 i v iv v vvii iv -- -- vv v PRIMA4-int#LT 5747 TACCATCCCCAGTCCTCAGGCCTGGTGGAGAGGACC--AATGGAATAATT 5794 rnd-5_family- 671 AAAAATAAACTGGCCAAG 688 vvv i i PRIMA4-int#LT 5795 AAAACACAATTGGCTAAG 5812 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 48, Kimura (unadjusted) = 36.85 Transitions / transversions = 0.92 (48/52) Gap_init rate = 0.05 (16 / 354), avg. gap size = 1.38 (22 / 16) 16 23.51 1.54 4.76 rnd-5_family-4414#Unknown 114 178 (119) (GCGACAG)n#Simple_repeat 1 63 (0) m_b21s252i6 rnd-5_family- 114 GCGACAGGCGACAGCAGCGACAGGCAACAGGGGGCCCCCTGCAAGGTTCC 163 -- i v i vvv - vv ivv (GCGACAG)n#Si 1 GCGACAGGCGACAG--GCGACAGGCGACAGGCGACAGGC-GACAGGCGAC 47 rnd-5_family- 164 A-GCGACAGGTGACAG 178 - i (GCGACAG)n#Si 48 AGGCGACAGGCGACAG 63 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 954 4.24 0.00 1.69 rnd-5_family-4654#DNA/hAT 1 120 (0) UCON89#DNA/hAT 123 240 (2) m_b21s502i3 rnd-5_family- 1 TTTCTGTGGTTTGCATTATCATTTGCTAAATATATTACGACGCGCTATTT 50 i i UCON89#DNA/hA 123 TTTCTGTGGTTTGCATTATCGTTTGCTAAATATATTACGACACGCTATTT 172 rnd-5_family- 51 ACCTCGGTCCGCAGCTTCGAGACCTTTGTGTGGCTTCTTCCCGCTCCAGG 100 ii - i UCON89#DNA/hA 173 ACCTCGGTCCGCAGCTTCGAGACCTTTGTGTGGCTTCCCCCC-CTCTAGG 221 rnd-5_family- 101 AAATTTCACAAATAAATCAC 120 - UCON89#DNA/hA 222 -AATTTCACAAATAAATCAC 240 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.60 CpG sites = 5, Kimura (unadjusted) = 4.43 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.00 (2 / 2) 492 30.73 1.46 0.48 rnd-5_family-4712#LINE/L2 23 228 (119) L2-2_Mam#LINE/L2 6 213 (159) m_b21s601i2 rnd-5_family- 23 TCAGAGACCGCCTCTCACCATAAAC-CCACTCACGGCAGTTAAGATCAGC 71 i i v v vi - - ii i i L2-2_Mam#LINE 6 TTAGAGATCGCCTCTCTCCCTATGCGCCA-TCGTGGCAATTGAGATCAGC 54 rnd-5_family- 72 TGGGAGGCTCTTGCTGTCAGTTCCCGGGNTNAAACNCTCCGGGGCTGGCG 121 i iv i v i iii? ?v v ?vivv i v iv L2-2_Mam#LINE 55 CGGGGCGCTCCTGCTGACGGTTCCCAAATTCCATCCGCAGGGAGCGGAAG 104 rnd-5_family- 122 GCAGGGCTTTCTCAGTTGAGGGCCCCCGNCTTTGGAATTCGCTCCCCTTG 171 i i i v i v iv i ?i v v v viv L2-2_Mam#LINE 105 ACGGGACGTTTTCCGCGGAGGGCCCTCGTTTGTGGAATTCCCTGCCCGCC 154 rnd-5_family- 172 GCAGTCTGCCAGAGCCCGAGTCTAGCGACC-TGAGGGCAAGATGC-AGAC 219 vii ii v v i ivi - v v i - L2-2_Mam#LINE 155 CTGGTTCGGCAGAGCCCCAGTTTGCTGACCTTCAGGGCACGGTGCAAGAC 204 rnd-5_family- 220 TTATTTATT 228 vi i v L2-2_Mam#LINE 205 GCATCTTTT 213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.61 CpG sites = 35, Kimura (unadjusted) = 41.59 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.02 (4 / 205), avg. gap size = 1.00 (4 / 4) 279 12.78 0.00 4.26 rnd-5_family-4731#DNA/PIF-Harbinger 30 78 (1) Chompy-6_Croc#DNA/PIF-Harbinger 926 972 (8) m_b21s502i4 rnd-5_family- 30 TAGGCGCCTAAAAGNTCAGCGCATTGCAACGCCTAAGTCCCTTTGTGGA 78 ivv v ? -- ii Chompy-6_Croc 926 TAGGCGCTGCAACGCTCAGCG--TTGCGGCGCCTAAGTCCCTTTGTGGA 972 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.01 CpG sites = 3, Kimura (unadjusted) = 14.38 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 2608 8.17 0.00 0.27 rnd-5_family-526#DNA 138 505 (1) MER130#DNA 936 1302 (284) m_b21s502i5 rnd-5_family- 138 CAAGTGTCAACAGGTGTGATCANGTGTAAAGAGGCATGTGGCGCCAATGT 187 ? i MER130#DNA 936 CAAGTGTCAACAGGTGTGATCAAGTGTAAAGAGGCATGTGGCGCCAATGC 985 rnd-5_family- 188 GGCAGTGCTGNCAGAGAGGAGGGACTTCCTGCAGAAGAGATGGCACTTGC 237 vv i ? v ii i MER130#DNA 986 TTCAGCGCTGTCACAGGAGAAGGACTTCCTGCAGAAGAGATGGCACTTGC 1035 rnd-5_family- 238 AGTATTATGCAGGCTGCCCATCTAAACCCATCGTCGCTTGGCACCTGTGC 287 ii i MER130#DNA 1036 AGCGTTATGCAGGCTGCCCATCTAAACCCATCGTTGCTTGGCACCTGTGC 1085 rnd-5_family- 288 CCTAGGGCAAGGGTCCGACCAACTTGTGAGCGGGCACCATGCCATCCNAA 337 ? v ? ? ? MER130#DNA 1086 CCTAGNGAAANGGTCCGACCAACTTGTGAGCGGGCACNATGCCATCCTAA 1135 rnd-5_family- 338 CAGATGGGCACGAGTGTAGGCAGCCAAGAGACAATGTATGTGCATCGNNT 387 i i v i?? MER130#DNA 1136 CAGATGGGCATGAGCGTAGGCAGCCAAGAGACCATGTATGTGCATCAAGT 1185 rnd-5_family- 388 GTGTGTACTGAGGGCANGATTCCTAGCCGGGAACGTCCAAGCGGCTGTTC 437 ?? i ? i ? i i MER130#DNA 1186 GTGNNTGCTGAGGGCAGGATTCCCAGCCGGGAACGTCNAAACGGCTGTCC 1235 rnd-5_family- 438 GTCCTNAGCTTACGTGCCTNTGGTTAAGGGNNGTGNGNTNTGGATTACAA 487 ? ? i ? ??- ? ?i? v v v ivv MER130#DNA 1236 GTCCTGAGCTTNCGCGCCTATGGTTAAGGGGA-TGTGCCATCGCTAATCC 1284 rnd-5_family- 488 ATCTCTGAGATGGATTAA 505 v v MER130#DNA 1285 AGCTCTGAGCTGGATTAA 1302 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.01 CpG sites = 18, Kimura (unadjusted) = 9.24 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.00 (1 / 367), avg. gap size = 1.00 (1 / 1) 1753 7.41 0.82 0.41 rnd-5_family-559#DNA 1 244 (3) UCON2#DNA 21 265 (320) m_b21s502i6 rnd-5_family- 1 ATCTTGCTCAGCGCAGCGTTCTGAAAGTTCACATGGCGAG--GCATTCCT 48 i ? iv ? ii -- i i UCON2#DNA 21 ATTTTGCTCAGCNCAGCAGTCTGAAAGTTCACANGGTAAGAAGCACTTCT 70 rnd-5_family- 49 CATCCTGGTTAAAACTCTGCAATGTGATTNCAAATGAAGNTTTTAATTAC 98 i v ?v - v v iv ?v i ? ? UCON2#DNA 71 CACCATGNATAAA-CTGTGAAATGTATTTGAAAATAAAGTTTTTAATTAN 119 rnd-5_family- 99 AATTGGCATTTCTGAGCCTNCTGCTGGCGGCGGCCATCTTGCTGAAAAGT 148 UCON2#DNA 120 AATTGGCATTTCTGAGCCTNCTGCTGGCGGCGGCCATCTTGCTGAAAAGT 169 rnd-5_family- 149 GACATCATTTGTGACNCCGGCAGTATGGGAGCCCAATGNAAGAGACTGTA 198 ? i UCON2#DNA 170 GACATCATTTGTGACACCGGCAGTATGGGAGCCCAGTGNAAGAGACTGTA 219 rnd-5_family- 199 AANCAGTTTCCATCCTGCTTTAATANTGGTTCAACAATCAGAAGAA 244 ? ? i UCON2#DNA 220 AACCAGTTTCCATCCTGCTTTAATACTGGTTTAACAATCAGAAGAA 265 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.23 CpG sites = 11, Kimura (unadjusted) = 8.23 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (2 / 243), avg. gap size = 1.50 (3 / 2) 1627 4.06 0.86 4.46 rnd-5_family-563#DNA 91 322 (1) UCON2#DNA 355 578 (7) m_b21s502i7 rnd-5_family- 91 TGNNAACCGGTTATTGAAACATTCTCTTACATNGGGCTCCCGCACTGCCG 140 ?? i -- --- v ? i UCON2#DNA 355 TGGAAACTGGTT--T---ACAATCTCTTACATTGGGCTCCCGTACTGCCG 399 rnd-5_family- 141 TAGTGTCACAAATGACGTCACTTTTCAGCAAGATGGCCGCCTCCAGCANT 190 -- i v ?? UCON2#DNA 400 --GTGTCACAAATGATGTCACTTTTCAGCAAGATGGCCGCCGCCAGCAGN 447 rnd-5_family- 191 AGGCTCAGAAATGCCAATTGTAATTAAAANCT--ATTTTAAAATAAATCA 238 ? ? -- v --- UCON2#DNA 448 AGGCTCAGAAATGCCAATTNTAATTAAAAACTTTATTTTCAAATA---CA 494 rnd-5_family- 239 TTTCACAGTTTATTCATGATGAGAAGTGCTTCTTACCTTGTGAACTTTCA 288 ? i i ? UCON2#DNA 495 TTTCACAGTTTATNCATGGTGAGAAGTGCTTCTCACCNTGTGAACTTTCA 544 rnd-5_family- 289 GACTGCTGGGCTGAGCAAAATGGGTGCAGTTTTC 322 ? i UCON2#DNA 545 GACTGCTGNGCTGAGCAAAATGGGTGCAGCTTTC 578 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 4.39 CpG sites = 6, Kimura (unadjusted) = 4.39 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.05 (11 / 231), avg. gap size = 1.09 (12 / 11) 12 21.14 0.00 0.00 rnd-5_family-5994#DNA/hAT 1 29 (157) (TCTT)n#Simple_repeat 1 29 (0) m_b21s252i5 rnd-5_family- 1 TCTTTCTCTCTCTTTTTCTTTTTTTTTTT 29 i i i i i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 320 13.21 0.00 0.00 rnd-5_family-5994#DNA/hAT 31 83 (103) UCON69#DNA/hAT 102 154 (332) m_b21s502i8 rnd-5_family- 31 AAAGTAAGTTTCTAGCCCTCATGGTCGCGGAGAAAAGCTGGAAAACGTGA 80 ? i i i v vv i UCON69#DNA/hA 102 AAANTAAGTTTCTAGCCCTTATGGTTGCGAAGAAAACCTTCAAAATGTGA 151 rnd-5_family- 81 ANC 83 ? UCON69#DNA/hA 152 ACC 154 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.28 CpG sites = 4, Kimura (unadjusted) = 15.28 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 12 11.98 7.89 2.50 rnd-5_family-678#Unknown 108 145 (416) (AGCCGC)n#Simple_repeat 1 40 (0) m_b21s252i4 rnd-5_family- 108 AGCCCCAGCCCGCAGCCGC-GGTGGAGCCG-AGCC-CAGCC 145 v - - vi v - - (AGCCGC)n#Sim 1 AGCCGCAG-CCGCAGCCGCAGCCGCAGCCGCAGCCGCAGCC 40 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 379 15.58 2.60 0.00 rnd-5_family-7207#DNA/PIF-Harbinger 16 92 (64) MER133B#DNA/PIF-Harbinger 23 101 (14) m_b21s502i9 rnd-5_family- 16 ATTCTGCACTCGT-TCCGCGCGCGGAACTCCCATTGACGTCAATGGGAGT 64 v v- v v v MER133B#DNA/P 23 ATTCTGCCCTCGGATACGCGCGCGCAACTCCCATTGAAGTCAATGGGAGT 72 rnd-5_family- 65 TCTGCATGAGGANC-AAGTGCAGAATATG 92 v i v v ? -i v v MER133B#DNA/P 73 TGTGCGTGCGTATCTGAGGGCAGAATTTG 101 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.38 CpG sites = 2, Kimura (unadjusted) = 17.81 Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 364 12.73 0.00 0.00 rnd-5_family-7272#DNA/hAT 426 480 (1006) UCON69#DNA/hAT 195 249 (237) m_b21s502i10 rnd-5_family- 426 ATAGTCTNACACAGTAGCTCTGGGNGATGTGAANTGACCCATTCATCTCA 475 i i ? v i i ? i ? v UCON69#DNA/hA 195 ACAGCCTGAAACAATAGCTCTGAGAGGTGTGAACTGCCCCATTCATCTCA 244 rnd-5_family- 476 ATGGG 480 UCON69#DNA/hA 245 ATGGG 249 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.12 CpG sites = 5, Kimura (unadjusted) = 15.12 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 16 3.96 3.85 0.00 rnd-5_family-7272#DNA/hAT 929 954 (532) (TTGTT)n#Simple_repeat 1 27 (0) m_b21s252i2 rnd-5_family- 929 TTTTTTTGTTTTGTTTTGTTTT-TTTT 954 v - (TTGTT)n#Simp 1 TTGTTTTGTTTTGTTTTGTTTTGTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 17 12.69 0.00 0.00 rnd-5_family-7272#DNA/hAT 929 954 (532) (T)n#Simple_repeat 1 26 (0) m_b21s252i3 rnd-5_family- 929 TTTTTTTGTTTTGTTTTGTTTTTTTT 954 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 242 28.79 2.38 0.78 rnd-5_family-7410#LINE/CR1 2 127 (254) CR1-L3B_Croc#LINE/CR1 2471 2598 (679) m_b21s551i1 rnd-5_family- 2 AAATGCAA-GCTAAATATCTNGGGGGAAATAATCCGAANCACAGGTATTC 50 - i v i ? iiv iv v iii? i vv ivv CR1-L3B_Croc# 2471 AAATGCAAAGTTATACATCTAGGAACAAGGAATGCAGGCCATACCTACAG 2520 rnd-5_family- 51 AGTGGGAGGGAGANACCTGGAAAGCAGTAATGCCG-AAAGAGTCNCGGGG 99 i i ivv v?v i iv i - ii i?v CR1-L3B_Croc# 2521 AATGGGGGACTGTATCCTGGAAAGCAGTGACTCTGAAAAGGATTTAGGGG 2570 rnd-5_family- 100 TGATAGTGGAC-AGCAAATCAGACATAAG 127 v - v - i CR1-L3B_Croc# 2571 TCATAGTGGACAAGCAACTCA-ACATGAG 2598 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.75 CpG sites = 20, Kimura (unadjusted) = 38.75 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.00 (4 / 4) 345 14.31 1.23 5.13 rnd-5_family-7410#LINE/CR1 47 127 (254) CR1-16_AMi#LINE/CR1 719 796 (55) m_b21s551i2 rnd-5_family- 47 ATTCAGTGGGAGGGAGANACCTGGAAAGCAGTAATGCCGAAAGAG-TCNC 95 i i i i - ? ? --- ? -i ?? CR1-16_AMi#LI 719 ATCCAATGGAAGAG-GAAACNTGGAAAGCAGTAATG---ANAGAGACCTN 764 rnd-5_family- 96 GGGGTGATAGTGGACAGCAAATCAGACATAAG 127 i i i i i i CR1-16_AMi#LI 765 GAGGCGATAGCGGACAGCAAATTAGATATGAG 796 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.76 CpG sites = 11, Kimura (unadjusted) = 18.23 Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.06 (5 / 80), avg. gap size = 1.00 (5 / 5) 446 29.53 1.99 1.32 rnd-5_family-7410#LINE/CR1 220 370 (11) CR1-3_Croc#LINE/CR1 2448 2599 (1006) m_b21s551i3 rnd-5_family- 220 AGTTTGCAATGTGCTATGGCAGCAGAAAAGGCCAATGTAGTTTTGGGCTG 269 i i v iii v v v ii v CR1-3_Croc#LI 2448 AGTCTGCAGTGTGATGCAGCCGCACAAAAGGCGAATGCGGTTTTGGGATG 2497 rnd-5_family- 270 CATACGCAGAGGCATCACGTCACGGAGCA-GGGGGGTAACGGT--CTCTC 316 vvii i i v -i iiii - i i ii -- CR1-3_Croc#LI 2498 CATCAATAGAAGCATTAGGT-GCAAGACACGGGAGGTGATAGTGCCTCTC 2546 rnd-5_family- 317 TTCTATGGCACTGGTGTGACTGTACCTAGAATATTGCCTTCAGTTCTGGG 366 v -i vv i ivi i i i i iv v CR1-3_Croc#LI 2547 TACT-CGGCACTGGTTAGGCCTCATCTGGAGTACTGTGTGCAGTTCTGGG 2595 rnd-5_family- 367 CACC 370 v CR1-3_Croc#LI 2596 CTCC 2599 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 29, Kimura (unadjusted) = 39.28 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.03 (4 / 150), avg. gap size = 1.25 (5 / 4) 249 21.41 0.00 5.62 rnd-5_family-84#LINE/CR1 384 477 (211) CR1-3_Croc#LINE/CR1 3240 3328 (277) m_b21s551i4 rnd-5_family- 384 GGGTCTGACCGATCGCCAGTTTTNGGGATNGGGGAGGAATTTTTCCCTTC 433 v - v ? i ?i i v ivi CR1-3_Croc#LI 3240 GGGTCAGACCGATCGCCA-TATTTGGGGTCAGGAAGGAATTTTACCCCAT 3288 rnd-5_family- 434 GGGAAGTATTCACAAGGTGCCTAGTGGNCTTTTTCGCCTTCCTC 477 vv - vii v -- v - ?vv i CR1-3_Croc#LI 3289 GGTCAG-ATTGGTACG--GACT-GTGGGGGTTTTTGCCTTCCTC 3328 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 8, Kimura (unadjusted) = 26.23 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.00 (5 / 5) 2470 8.85 6.77 0.95 rnd-5_family-884#DNA 1 399 (27) Eulor11#DNA 59 480 (72) m_b21s502i11 rnd-5_family- 1 ATAANTGCAGAAACAAAGACATGCGCA------GNTGAANAAGC-CAGGG 43 ? v iii ------i? i ? - v Eulor11#DNA 59 ATAAATGCAGAAACAAAGAAATATACATTGATAAGTAAAGAAGCACAGGT 108 rnd-5_family- 44 ATGCATCGCTTCCTGTAGAGAGTAAAGTGNCTTTAAGAGGTCTTGAACCA 93 i i v i vvv v v i i- -? Eulor11#DNA 109 GTACCTTGCAGGCAGTATAAAA-AAAGT-CCTTTAAGAGGTCTTGAACCA 156 rnd-5_family- 94 GCATCTTTA-------TACGCTGCAGCCTAATGTGCAACCACTAGACCAC 136 ii ii ------- ii i i Eulor11#DNA 157 GTGTCCCTACGTGCTTTATACTGCAGCCCAATGTGCAGCCACTAGACCAC 206 rnd-5_family- 137 CCCACCACAGGTNAGAAATGAGAAATTNTGAGGGCTATTGAACNGCTCGT 186 ? ? ?- - i Eulor11#DNA 207 CCCACCACAGGTAAGAAATGAGAAATTTTGAGGGCTATTGAACA-CT-GC 254 rnd-5_family- 187 GAATTTTCACAGTGGATCAGCACAAAGTTATTTAGCACAGGTGTTTCTGT 236 Eulor11#DNA 255 GAATTTTCACAGTGGATCAGCACAAAGTTATTTAGCACAGGTGTTTCTGT 304 rnd-5_family- 237 AATTGTGATACATTGGGAAAATTCACAGTGTTCAATGGCCCTCAA----- 281 ----- Eulor11#DNA 305 AATTGTGATACATTGGGAAAATTCACAGTGTTCAATGGCCCTCAAACTCA 354 rnd-5_family- 282 -ACTTCCACCTGTNTGGNGTGGTGGTCTAGTGTTANTACACTGGGCTGTA 330 - i? ? i ? Eulor11#DNA 355 CACTTCCACCTGCGTGGTGCGGTGGTCTAGTGTTAGTACACTGGGCTGTA 404 rnd-5_family- 331 ATATAAAACATGTANGAATNCAGGCTGGCTCAAGACCGG--GANG--TNT 376 ? ? v v --i ? -- ? Eulor11#DNA 405 ATATAAAACATGTAGGAATACTGGCTGGCTCAAGACCTGCTAAAGGTTTT 454 rnd-5_family- 377 TCCTNACACTGTC---GTTTCTTTGT 399 ? i i --- i Eulor11#DNA 455 TCCTTATACCGTCCGTGCTTCTTTGT 480 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.83 CpG sites = 25, Kimura (unadjusted) = 9.94 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.03 (12 / 398), avg. gap size = 2.58 (31 / 12) 14 22.07 2.00 2.00 rnd-5_family-9079#Unknown 900 949 (169) (CGCCCC)n#Simple_repeat 1 50 (0) m_b21s252i0 rnd-5_family- 900 CGCCTCC-CCCCCGCCCCCGGCTTAACCCCGGCTCCCACCCCCCGCCNCC 948 i - v iivi v - vv ? (CGCCCC)n#Sim 1 CGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGC-CCCCGCCCCCGCCCCC 49 rnd-5_family- 949 G 949 (CGCCCC)n#Sim 50 G 50 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 12 15.21 0.00 7.50 rnd-5_family-9079#Unknown 906 948 (170) (CCCCCCG)n#Simple_repeat 1 40 (0) m_b21s252i1 rnd-5_family- 906 CCCCCCGCCCCCGGCTTAACCCCGGCTCCCACCCCCCGCCNCC 948 v ---v v i i ? (CCCCCCG)n#Si 1 CCCCCCGCCCCCCGC---CCCCCGCCCCCCGCCCCCCGCCCCC 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 1096 17.18 7.04 11.58 rnd-5_family-12333#DNA/TcMar-Tigger 43 312 (253) Tigger10#DNA/TcMar-Tigger 1666 1924 (173) m_b22s502i0 rnd-5_family- 43 TATACTGCCCAGGAGGTTATGCAATTGCACATTCTGCACTCTACTTTTAT 92 i i ii ? v i Tigger10#DNA/ 1666 TACACTGCCCAGGAGGTCATGCAGCTGCACATNCTTCACTCTACCTTTAT 1715 rnd-5_family- 93 GCAAAAGAGGCAGAAGACAAGTAAGCAAGCTGATATCAGGGATTTATTCA 142 vi i v v iv i i v Tigger10#DNA/ 1716 GAGAAAGAGGCAAATGACCAAAAAGCAAGCTGACATCAGGGACTTTTTCA 1765 rnd-5_family- 143 AAAAAGCAGCTTCCAGGGTGTGTCATAGGGTCATTACAGATTCAGCCCAA 192 i iv ivvv vv i v vv v Tigger10#DNA/ 1766 AGAAAGCAAGTTCCAGGGCCACTGCTGGGGTCAGTACCCATTCAGCCCTA 1815 rnd-5_family- 193 TCTCCTACACCTTCTACATCTACA-------------------ATGATAA 223 v i v i ------------------- ii Tigger10#DNA/ 1816 TGTCCCACACCATCTACATCTGCATCTACATCTACAGCACAGCACAATAA 1865 rnd-5_family- 224 TTGATGTTGATAATGATGACCCTGAGGCACTGCAAGATCCTGAAGTGCCT 273 i v ------------------------ Tigger10#DNA/ 1866 CTGATGTTCATAATGATGACCCTGAG------------------------ 1891 rnd-5_family- 274 TCTGAATCATCAAAGAAAGATTAAATTATGTTCAGTATA 312 ------ ii i Tigger10#DNA/ 1892 ------TCATCAAGAAAAGGTTAAATTATGTTCAGTATA 1924 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.63 CpG sites = 22, Kimura (unadjusted) = 19.63 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.12 (31 / 269), avg. gap size = 1.58 (49 / 31) 1127 2.88 0.00 1.44 rnd-5_family-12333#DNA/TcMar-Tigger 194 334 (231) Tigger14a#DNA/TcMar-Tigger 57 195 (129) m_b22s502i1 rnd-5_family- 194 CTCCTACACCTTCTACATCTACAATGATAATTGATGTTGATAATGATGAC 243 i ? - v- i v Tigger14a#DNA 57 CTTCTACACNT-CTACAG-TACAGTGATAATTGATGTTCATAATGATGAC 104 rnd-5_family- 244 CCTGAGGCACTGCAAGATCCTGAAGTGCCTTCTGAATCATCAAAGAAAGA 293 Tigger14a#DNA 105 CCTGAGGCACTGCAAGATCCTGAAGTGCCTTCTGAATCATCAAAGAAAGA 154 rnd-5_family- 294 TTAAATTATGTTCAGTATAGTTTTAGTGTTAAGTGTATTTT 334 Tigger14a#DNA 155 TTAAATTATGTTCAGTATAGTTTTAGTGTTAAGTGTATTTT 195 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.96 CpG sites = 2, Kimura (unadjusted) = 2.96 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.00 (2 / 2) 308 5.45 10.91 0.00 rnd-5_family-12333#DNA/TcMar-Tigger 511 565 (0) Tigger14a#DNA/TcMar-Tigger 191 251 (73) m_b22s502i2 rnd-5_family- 511 ATTTTATTGTATTCTAATTCTTTGAAAATTGGTATTCCAT---TGGTAAG 557 v --- vi Tigger14a#DNA 191 ATTTTATTGTATTCTAATTCTTTGAAAATTGGTAATCCATGTATGGTATA 240 rnd-5_family- 558 TA---TAACTC 565 --- Tigger14a#DNA 241 TATGGTAACTC 251 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.66 CpG sites = 1, Kimura (unadjusted) = 5.66 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (2 / 54), avg. gap size = 3.00 (6 / 2) 553 35.59 1.48 1.48 rnd-5_family-13230#LINE/RTE-BovB 14 418 (218) MamRTE2#LINE/RTE-BovB 883 1287 (265) m_b22s551i0 rnd-5_family- 14 AACAAAACTGACGATATACAATGCAGCAGTGATAGCATCCCTTTTATAAT 63 v v i i v v v v vv vv i vi i -i MamRTE2#LINE/ 883 AACCAAACTTATGGTTTACCAGGCAGCTGTGATCCCCACCTTGCTGTA-C 931 rnd-5_family- 64 GGATGTGAAACATGGACAGTTTACCACAGACACATTAAGCAACTTGAAAA 113 vv i i iiv viv iv vvi v MamRTE2#LINE/ 932 GGAGCTGAGACGTGGACAACATACAGAAGACATCTTAAGGTGCTGGAAAA 981 rnd-5_family- 114 ATTTCACATGTGCTGTCTCCGTTCTAT--TCGGAAGGTCCACTGGCAAGA 161 vi ivvii i v vvvv -- v -- v v v i MamRTE2#LINE/ 982 ATACCATCAACGCTGCCTGCGGAAGATCCTCCGA--GTCAAATGGGAGGA 1029 rnd-5_family- 162 CAAAGTCTCAAACATTAACATCCT---GAAAGAGCAAAAACAACCAGCAT 208 i vv v v ii v i --- v i -- i ivi v v i MamRTE2#LINE/ 1030 CAGACGCACTAATGTGAGCATCCTCTCGCAGG--CGAGCGCTACAAGTAT 1077 rnd-5_family- 209 CGAGGCAATGATCATCAAAGCTCAGCTTAGATGGACAGGTCATGTTATCA 258 ii vvi v v v v i v MamRTE2#LINE/ 1078 CGAGGCAATGATTGTCAAACACCAGCTTCGCTGGACTGGACACGTGATCA 1127 rnd-5_family- 259 GAATGGGCGATGACAGACTCCCGAAAAAAGTCCTCTATGGTGAGCTGAAA 308 vvi vv i i iv v v ivviv ii i iv MamRTE2#LINE/ 1128 GAATGTCTGATTCCAGGCTCCCAAAGCAAGTGCTGTACTCCCAATTAAGC 1177 rnd-5_family- 309 CTCGGAAAGCGCAGGAGGGGCGGTCAACGAAAACGCTTCAGAGACACCCT 358 vv i ii vvi i v v iv i i i iii MamRTE2#LINE/ 1178 CAAGGGAGACGCCTAAGAGGAGGGCAGAGAAAACGTTTTAAAGATGTCCT 1227 rnd-5_family- 359 TAAGCAGAATCTCACCTCATGCGGCATAAATATCGATAACTTCGAAGACA 408 i ivv i i?vvvv iiv - iii v v i v MamRTE2#LINE/ 1228 CAAGTCTAATTTTNAAAAATGCAAAATAAATA-CAGCATCTTGGGAGACC 1276 rnd-5_family- 409 -CAGCCAAGGA 418 -ii MamRTE2#LINE/ 1277 TTGGCCAAGGA 1287 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 46.24 CpG sites = 66, Kimura (unadjusted) = 49.00 Transitions / transversions = 0.87 (66/76) Gap_init rate = 0.02 (9 / 404), avg. gap size = 1.33 (12 / 9) 16 22.11 0.00 0.00 rnd-5_family-13318#Unknown 442 490 (365) (CCCCC)n#Simple_repeat 1 49 (0) m_b22s252i4 rnd-5_family- 442 CCCCTCCTCCCCCCCCGCTCGNCCCGGCCCCCNCCCCCACCCCGCCCCC 490 i i v i v? vv ? v v (CCCCC)n#Simp 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 49 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 225 26.55 1.15 4.76 rnd-5_family-2013#SINE/5S-Deu-L2 1298 1384 (1187) AmnSINE1#SINE/5S-Deu-L2 454 537 (38) m_b22s502i3 rnd-5_family- 1298 TCCACCCCAGAGGCGGCTGCATCTTAGCACTGCGGGAAGCAACCCCT-CA 1346 i i i iiv v v ii i -i AmnSINE1#SINE 454 TCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTGATCCCTGTA 503 rnd-5_family- 1347 CGGAGACCATTCGTCATGGGGTTTGGGANACTTCTGGA 1384 i v ----i i v v v v ?v v AmnSINE1#SINE 504 TGTAG----CTTGTAAAGCGCTTTGGGATCCTTCGGGA 537 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 12, Kimura (unadjusted) = 33.77 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.00 (5 / 5) 302 36.02 1.40 1.87 rnd-5_family-221#DNA/TcMar-Tc2 1179 1393 (1179) Kanga11a#DNA/TcMar-Tc2 528 741 (229) m_b22s502i4 rnd-5_family- 1179 TAGTTTCCATCGATACGTAATACAACAGCGCACTAAACATGGCTATGCGT 1228 ii v v iviv v vv ivii i v Kanga11a#DNA/ 528 TAACTTCCAGCGATACGTAATTCAATTAAGGAAAAAACGAAACTACGAGT 577 rnd-5_family- 1229 TAAGTAGTATTGGAAATATGGATGAAACTCCAATGAATTTTGATATGGTT 1278 v iiviv v iii i i ii ivvi i vi Kanga11a#DNA/ 578 TTAACCAAATAGGAAATGCAGACGAAACCCCGGTATTCTTCGATATGCCT 627 rnd-5_family- 1279 GGAAATAAAACTGTCCATCAAAAAGGTGAAAAAACAATTTTAATTAAAAC 1328 v v v v vv vv ivii ivvi i vi v Kanga11a#DNA/ 628 CGAAATTATACTGTCAATCCTAAAGGTGCTAAAGAGGTCAAGATCACGAG 677 rnd-5_family- 1329 AACAGGACATGAGAAGTCCAGTTTTACAGTGGTACTAGGATGCACA---G 1375 v i vi i ivvv v i v i i --- i --- Kanga11a#DNA/ 678 CACGGGTTATGAAAAGCAGCGTGTCACCGTGATGCT---ATGCATAACTG 724 rnd-5_family- 1376 CTGATGGCGCCAAACTGA 1393 i - v v Kanga11a#DNA/ 725 CCGATGGC-CAAAAGTGA 741 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.10 CpG sites = 38, Kimura (unadjusted) = 50.02 Transitions / transversions = 1.00 (38/38) Gap_init rate = 0.02 (5 / 214), avg. gap size = 1.40 (7 / 5) 274 31.19 1.80 1.80 rnd-5_family-221#DNA/TcMar-Tc2 1624 1734 (838) Kanga2_a#DNA/TcMar-Tc2 253 363 (524) m_b22s502i5 rnd-5_family- 1624 AACACAGATGCGGCAGTTATTCCTGCAGGATTGACATCGTTGGTACAGCC 1673 vii i i vi vv v iiviv i ivi Kanga2_a#DNA/ 253 AACACAGATTTAGTAATTATTCCTGGGGGTATGACCTCACAATTGCAAGT 302 rnd-5_family- 1674 ACTGGATGTG--TGCCTAAACAAGCCATTTAAAGATCGCATTCAAGAACA 1721 ii v-- -- v i v v i i Kanga2_a#DNA/ 303 GTTGGATGTCATTG--TAAACAAGCCTTTTAAAGATCACTTTAAAAAGCA 350 rnd-5_family- 1722 GTGGAATGAATGG 1734 i iv i i i Kanga2_a#DNA/ 351 ATACAGTAAGTGG 363 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.93 CpG sites = 21, Kimura (unadjusted) = 41.93 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.03 (3 / 110), avg. gap size = 1.33 (4 / 3) 305 35.72 4.57 4.42 rnd-5_family-2685#LINE/RTE-BovB 247 946 (0) MamRTE1#LINE/RTE-BovB 1557 2257 (1555) m_b22s601i0 rnd-5_family- 247 CGNCACCAAGACTGGTTTGATGAGAACGACGAGGAAATCCTAGCACTNAT 296 ? ii i vvi i ivviivi ?v MamRTE1#LINE/ 1557 CGCCACCAGAACTGGTTTGATGAGAATGACTCAGAGATTAAGAAGCTACT 1606 rnd-5_family- 297 T-CANCAGAA-GAGAAGCGCATTCT--GCACTTGGCAAAATGANCCCTC- 341 - ? i i-i ? ii ? v --i i v i-----?i - MamRTE1#LINE/ 1607 TGCAGCAAAGCAAGNAATGCNTTGTCAACACCTTGCAG-----CTCCTCA 1651 rnd-5_family- 342 TAA-CCAG-CAAAANCAGAGNCTTATCACCGGCTCAAAGC-TGAAGTCCA 388 i - - i ?- v? - vvi iiiv v - vi v MamRTE1#LINE/ 1652 TGATCCAGACGAAAG-AGACGCTTA-CAGAAGCCTGTATCGTGACATGCA 1699 rnd-5_family- 389 AAGGAGGCTNCGTGACATCAAAAATAAGTGGTGGCGAGAAAAGGCCGCGG 438 i vv i i ?v vi iiv? vi iv viv vv i vi MamRTE1#LINE/ 1700 GATCAAGTTAAGAAACGCGNATGACCAGTGGTGGGATGCCAAGGCTGAAG 1749 rnd-5_family- 439 AGATCCAGAGCTTCGCTGATCAGCATGACATGAGAAGCTTCTTTCAAGCA 488 ii vi v i i? iv v iv iiii v vvi? v MamRTE1#LINE/ 1750 AGATCCAGGACTATGCAGACCGNCACCAAACCAAGGACTTCTATGCGNCC 1799 rnd-5_family- 489 ACAAAAGCCATNTATGGGCCANGCTCCAANGGCCCNACCCCNCTNCGATC 538 vi iiivv ? ? ?vviv iv?iv v ?i v ? ?v ivv MamRTE1#LINE/ 1800 CTAAAGATGTTATATGGNCCAACACACGCCATCACGGCACCGCTGAGGAG 1849 rnd-5_family- 539 CCAGGACGGNTCCACCCTCCTTAAGGACAACGNAGCCATCAAGCNACGNT 588 iv?i i ? i v i vi iivi?i vv vvi ?iv ? MamRTE1#LINE/ 1850 TGNAGATGGCTCCGCCCTCATCACAGACGGGAAGGGAATCCTACGGAGAT 1899 rnd-5_family- 589 GGAAGGAGCACTTTGAGANNCTACTGAACCGCGAATCNACGGTCTCTGAN 638 v v i ii vi?? v ? --------- vii --- MamRTE1#LINE/ 1900 GGCAGCAACACTTCAACGATCTTCTNAAC---------ACGCCTTCT--- 1937 rnd-5_family- 639 GNCACCATCGAG--TCCATTCCTCAACGNTCAGCA-ATAGAACCT-CT-- 682 --- -- vv v --i ?-- i- v - i-- MamRTE1#LINE/ 1938 ---ACCATCGAGGATGAAGTCCT--GCGA--AGCGTAGAGAACCTGCCAA 1980 rnd-5_family- 683 --TGC-------TGA---TCCCCCCATCTTCTGAGGAAGTCCGGCA-TGC 719 -- ------- i--- v i v i i - i? -i MamRTE1#LINE/ 1981 GATGCGATAACNTGGCCTTCGCTCCAACTTTTGAAGAAGT-CANCACCGC 2029 rnd-5_family- 720 CATCACNCAGACAAGAAACAACAAGGCACCAGGCCCAGACGGCATCCCCG 769 ii v?vvv ii ii iiii i v iv v v i v i MamRTE1#LINE/ 2030 TGTCAGAGCCATGAAGAATGGTAAAGCTCTCGGACCTGATGGCATACCTG 2079 rnd-5_family- 770 CGGAGGTCTTCAAAGCTGGTAGAATAGCGCTCGTTGCAAAAACA-ATGCA 818 v i i - v v iiv v--- i vv i i-v MamRTE1#LINE/ 2080 CTGAGATTTTC-AAGCAGGAAGGGGAGA---CGCTGCTTAGACGTCTGCA 2125 rnd-5_family- 819 TCAACTTCTTGTTAGAATTTGGGTTAACGAAGAAATTCCATCCGACCTAA 868 vii i iv i v v iv v i v iivv ii v MamRTE1#LINE/ 2126 TAGGCTTTTCTTCAGCATATGGAGTACCGAGGAAATGCCGCAGGATTTCA 2175 rnd-5_family- 869 AGAATTCCA-NATTGTNACAATNCTTAGGNAAGGGGACAAGTCAA-TG-- 914 ii v -? ii ? v ?i i i ? iiii i i vv i- -- MamRTE1#LINE/ 2176 AAGATGCCACTATCATCACCATCTTCAAGAAGAAAGGCGAGAAAGCTGAC 2225 rnd-5_family- 915 TGCGGGAGTTACCGAGGCATTGCCTTCCTCTC 946 v ii i v iv ?i v MamRTE1#LINE/ 2226 TGCGGCAACTATCGCGGCATCTCNCTGCTCTC 2257 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.88 CpG sites = 135, Kimura (unadjusted) = 54.51 Transitions / transversions = 1.30 (135/104) Gap_init rate = 0.07 (49 / 699), avg. gap size = 1.29 (63 / 49) 400 30.12 2.69 5.85 rnd-5_family-2779#LTR/ERV1 278 612 (1756) HERVP71A#LTR/ERV1 4691 5015 (2575) m_b22s701i0 rnd-5_family- 278 CACAGGNTNCAAATTGATTTTATTGGTCNATTGCCAAAGAGCAAGGAAGG 327 v v? ? i v i iv ---? v v - i - - HERVP71A#LTR/ 4691 CAAAGCATTCAAGTAGATTTCACAG---AAATGCCCAA-AGTA-GGAAG- 4734 rnd-5_family- 328 ANNCCAGTATTTNTTGGTAATAATNGATCCCTTTNCTAGATGGGTGGAGG 377 ??vv ?i i vi ? v i ? ii v i HERVP71A#LTR/ 4735 ACTAAAGTATTTACTGGTGATCGTAGATCACCTTTCCGGCTGGGTGGAAG 4784 rnd-5_family- 378 CATT-CCCCACTAAAGATAACAGC-ACCACGGNTA--GTGGCCAAAAGGT 423 v - v i-----i - i v ?v -- i viv HERVP71A#LTR/ 4785 CCTTTCCCCTCC-----CAACAGCCACCGCCGGGAATGTGGTCAAAATAA 4829 rnd-5_family- 424 TCTTTAATGAGGTAGTACGTAGATAGGGCACCCCC-----AAAATAATAG 468 v vi vv i v v vv ---- i----- v - HERVP71A#LTR/ 4830 TATTAGAACAGATTGTACCTAGATTTGGC----CTGGTGGAAAATATT-G 4874 rnd-5_family- 469 ATTCTGACAATGGGGGAGCCACTTTGTAGGAGAAATCTTTACAGCAATGA 518 v -- iivvv iiii v v vi v v HERVP71A#LTR/ 4875 ATTCAGACAATGGG--AGCCACTTTACCTCAAGGGTGTTAAGGGGAATTA 4922 rnd-5_family- 519 TACAAGCCTTGGGNATTAAACAAAAGCTCCATATACCATACCGNCCTCAG 568 iv vi ivi? i iiii vivi i iv v iv i? i vv HERVP71A#LTR/ 4923 TGGAAGGTTTACAAATTAGATGGGATTATCACACCCCTTGGCATCCCCCT 4972 rnd-5_family- 569 NCCTCAGGNCAGGTAGAGNGCATGAATNGCACTATTAAAGAAGC 612 ? v ?v i? v ?iv v i - HERVP71A#LTR/ 4973 TCCTCTGGAAAGGTAGAAAGAATGAATCAAACTCTCAAA-AAGC 5015 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.67 CpG sites = 45, Kimura (unadjusted) = 41.38 Transitions / transversions = 0.90 (45/50) Gap_init rate = 0.07 (23 / 334), avg. gap size = 1.22 (28 / 23) 781 17.67 8.43 1.12 rnd-5_family-3965#DNA/Crypton-A 66 231 (118) Eulor5A#DNA/Crypton-A 3 180 (136) m_b22s502i6 rnd-5_family- 66 TATTTAAGCAATAATGACCAATGCGGAGGGCATTTCCTGGCGGTTAATGA 115 v i i i v v v i Eulor5A#DNA/C 3 TAATTAAGCAATAACGATCGAGGCGCAGGGCATTTCCTGGGGATTAATGA 52 rnd-5_family- 116 CCGGCTAGGAGG---TGA-GG-CCAAGGTGCAGTT--------TTAA-CT 151 i --- - - i ii? ii-------- - i Eulor5A#DNA/C 53 CCGGCTGGGAGGAGTTGATGGCCCGAGGCANAGCCGAGGGCCATTAACCC 102 rnd-5_family- 152 CAGCCGGTCATTAACTGCCAGGAAATGCCCGACCCGGAGGTCATTATTGC 201 iiv vi v v i Eulor5A#DNA/C 103 CAGCCGGTCATTAATCCCCAGGAAATGCCCTGCGCCGAGGTCGTTATTGC 152 rnd-5_family- 202 TATTATAAACCGTGAAAATATAAAAATAAA 231 i -- ii? i ii Eulor5A#DNA/C 153 TATTATAAGC--TGAAAACGNAGAAACGAA 180 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.56 CpG sites = 21, Kimura (unadjusted) = 21.05 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.04 (7 / 165), avg. gap size = 2.29 (16 / 7) 2276 12.98 3.42 7.72 rnd-5_family-4371#LINE/CR1 15 540 (17) CR1-16_AMi#LINE/CR1 132 636 (215) m_b22s551i1 rnd-5_family- 15 AAGTCT-AACTTCTATCCCCAGTAAAATAATGGAACAAATATTGAGAGCC 63 - i i -- CR1-16_AMi#LI 132 AAGTCTTAACTTCTATCCCTAGTAAAATAATGGAACAAATATTAAGAG-- 179 rnd-5_family- 64 TCCTAAGAGAAAAAA--CNATAAACANCTAGAGGATAATGGCGCCATTAG 111 -----i i -- ?v ? i vi v CR1-16_AMi#LI 180 -----GGAGGAAAAAATCACTAAACATCTAGAGGATAACGGAACCATGAG 224 rnd-5_family- 112 CAATAGNCANCATGGGTTNATAGAANAANAATTTTGCCAG-CAACATTTG 160 i? ? ? i i? v? i - - i CR1-16_AMi#LI 225 CAATAAGCAGCATGGGTTTATAAAGAACAAATCTTGCCAGACAA-ACTTG 273 rnd-5_family- 161 ATTGCAGGATATTTTTTCTGATAGAATTACAAAATTAGTGGATGAAGGGA 210 ------- i -- CR1-16_AMi#LI 274 ATTGC-------TTTTTTTGATAGAATTACAAAATTAGTGGATGAAGG-- 314 rnd-5_family- 211 ACGCAGTAGATGTAATATGTTTGGATTTTAGTA---CA-TTGAT--AGTG 254 -------- i i --- - -- CR1-16_AMi#LI 315 --------GATGCAATATATTTGGATTTTAGTAAAGCATTTGATACAGTG 356 rnd-5_family- 255 TCTCAAAAATATTTCTACATTAATTCAAATTGGCTTGGATATGAACACTG 304 -- v i iv v i CR1-16_AMi#LI 357 TCTC--ACATATCTTAAAATTAATTCAAATTGGCTTGGATATGAGCACTG 404 rnd-5_family- 305 TCACAAATGGATTGAAAACTTGAGGTGAAGGG-CATAAACAAAGGGTGA- 352 --i i --i v i- i i - CR1-16_AMi#LI 405 TCAC--GTGGACTGAAAACT--GGCTGAAGGACCGTAAACAAAGGGTAAT 450 rnd-5_family- 353 GACAAACAGCAACGTATCGCAGTTAGGGAGAAAGGTGTCNAGCGGGGTGC 402 i i i - i i -- ? -- i CR1-16_AMi#LI 451 GATAAACGGCAATGTATCG-AGTTGGGGGG--AGGTGTCTA--GGGGTAC 495 rnd-5_family- 403 CGCAGGGATCGGCTTTAGATCCGGTCTTNNTTAATATCTTCATAAAC-AT 451 i - iv i i ?? i v i- CR1-16_AMi#LI 496 TGCAGGGAT-GGTGTTAGGTCTGGTCTTATTTAACATCTTCATTAATGAT 544 rnd-5_family- 452 CTAGAAGAGGGAGTAAAGATAACATTAATTACATTCANAGATTATACTAA 501 i v vv i v v i? v CR1-16_AMi#LI 545 CTGGAAGAGGGAGTAAACAGCACGTTAATGAAATTCGCAGATGATACTAA 594 rnd-5_family- 502 A----GAAATGTTGCGAACG-CGGGNAGAACAAAAAGAAATAAT 540 ---- iiv i i- i v? i -- i CR1-16_AMi#LI 595 ATTGGGAGGAGTTGCAAACACCAGTGAGGAC--AGAGAAATAAT 636 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.42 CpG sites = 45, Kimura (unadjusted) = 14.87 Transitions / transversions = 2.50 (45/18) Gap_init rate = 0.10 (50 / 525), avg. gap size = 1.14 (57 / 50) 191 16.80 1.27 9.59 rnd-5_family-4430#Unknown 693 771 (193) C MIR1_Amn#SINE/MIR (155) 75 3 m_b22s601i1 rnd-5_family- 693 CAGAGCTTGGAAGGGAACCCAGGAGTCCTGACTCCCAGTTCGCCCCCTGC 742 iv ?v? vv i v ---- vv C MIR1_Amn#SINE 75 CAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGT----CCAGTGC 30 rnd-5_family- 743 TCTAACCCACTAAATGCAACAC-GCCTCCC 771 - i i -- v - C MIR1_Amn#SINE 29 TCT-ATCCACTAGA--CCACACTGCCTCCC 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.24 CpG sites = 4, Kimura (unadjusted) = 19.46 Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.10 (8 / 78), avg. gap size = 1.00 (8 / 8) 191 18.62 6.56 3.17 rnd-5_family-4430#Unknown 693 753 (211) C MIR3#SINE/MIR (138) 70 8 m_b22s601i2 rnd-5_family- 693 CAGAGCTTGGAAGGGAACCCAGGAGTCCTGACTCCCAGTTCG----CCCC 738 iv vvi vv i ---- i i C MIR3#SINE/MIR 70 CAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCT 21 rnd-5_family- 739 CTGCTCTAACCCACT 753 -- v C MIR3#SINE/MIR 20 CTGCTC--AGCCACT 8 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.45 CpG sites = 5, Kimura (unadjusted) = 21.50 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.05 (3 / 60), avg. gap size = 2.00 (6 / 3) 197 28.77 0.00 0.00 rnd-5_family-4430#Unknown 829 901 (63) C MIR1_Amn#SINE/MIR (155) 75 3 m_b22s601i3 rnd-5_family- 829 CAGAGCTGGGAACACAAGTGAGGTGTCATGACTCCCAGTCCCCTCCTCTA 878 i ?i?v viv v vi v vv v C MIR1_Amn#SINE 75 CAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTA 26 rnd-5_family- 879 ACGACTACGTCAGACTGCATCTC 901 v v vii v v i C MIR1_Amn#SINE 25 TCCACTAGACCACACTGCCTCCC 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.59 CpG sites = 7, Kimura (unadjusted) = 37.61 Transitions / transversions = 0.50 (7/14) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 32 10.76 2.06 8.79 rnd-5_family-4629#Unknown 550 646 (951) (TTAACAT)n#Simple_repeat 1 91 (0) m_b22s252i3 rnd-5_family- 550 TTCACATTCATANATTAANACATTTATAACA-TTAACA-TAACCACTTAA 597 v i - ? v - - - - - v v i (TTAACAT)n#Si 1 TTAACATTTA-ACATTTA-ACA-TT-TAACATTTAACATTTAACATTTAA 46 rnd-5_family- 598 CACTTTAAACATTTAGACCATTTAACATTAANCACTTAACATTTAACAT 646 - - - - v ? i (TTAACAT)n#Si 47 CA-TTT-AACATTTA-A-CATTTAACATTTAACATTTAACATTTAACAT 91 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.10 (10 / 96), avg. gap size = 1.00 (10 / 10) 911 15.87 7.32 7.84 rnd-5_family-4664#LINE/L2 1 205 (0) AmnSINE1#SINE/5S-Deu-L2 371 574 (1) m_b22s502i7 rnd-5_family- 1 GTTTCATTTGT-TATAGAATCCTTCNCTTCTTACC----------GTGTA 39 v v- ii v i ? i ii ---------- AmnSINE1#SINE 371 GTTTCAATTGGATACGGTATTCTTCACTTCCTGTCCTAAACTGTTGTGTA 420 rnd-5_family- 40 GTGTTGCTGTACGCTGTTAAACAGCTGCCACGTTTCACCCCAGAGG---- 85 i i i ---- AmnSINE1#SINE 421 GTGTTGCTGTGCGCTGTTAAACAGCTGCCGCGTTCCACCCCAGAGGTGGC 470 rnd-5_family- 86 TGCCTTGTAGCTGTGGACGAAGTGATTCTTGTGTGTAGTTTGTGTGGTTT 135 v vi iv ii i i i i ---------- AmnSINE1#SINE 471 TGCATTTCAGTGGTGGGTGAAGTGATCCCTGTATGTAGCT---------- 510 rnd-5_family- 136 AAATCTGTAAAGTGCTTTGGGATCCTTCTGGATGAAAGGCGCTATATAAA 185 ----- i v AmnSINE1#SINE 511 -----TGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAA 555 rnd-5_family- 186 TATAAGTTAGCTATTATCAT 205 ii v -i i AmnSINE1#SINE 556 TGCAAGGTA-TTATTATTAT 574 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.40 CpG sites = 22, Kimura (unadjusted) = 18.41 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.09 (19 / 204), avg. gap size = 1.63 (31 / 19) 671 13.86 0.00 0.00 rnd-5_family-5336#Unknown 82 182 (114) UCON70#Unknown 7 107 (149) m_b22s502i8 rnd-5_family- 82 AAAAATAGAATTTACCTCGCAGCAACTTTGAAAGTCCCTGCTTTCTCATG 131 ? i i ii i i i v i ? UCON70#Unknow 7 AANAACAGAACTTACCTTACAACGACTTTGAAAGTCTCTGATTTCCCNTG 56 rnd-5_family- 132 CATTCAAACGGGAGCTGCATTCCCTGAGTCCTANTCTACGTCATCAGACT 181 i i v v i UCON70#Unknow 57 CGTTCAAATGGGAGCTGAATTCCCTCAGTCCTANTCTGCGTCATCAGACT 106 rnd-5_family- 182 G 182 UCON70#Unknow 107 G 107 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.90 CpG sites = 11, Kimura (unadjusted) = 16.30 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0) 425 18.00 0.00 6.60 rnd-5_family-5589#DNA/Crypton 36 148 (795) Eulor6E#DNA/Crypton 56 161 (131) m_b22s502i9 rnd-5_family- 36 TNGGGTGCACGTTGCAGCGGGATGGGTGCATCCAAAGGTCGAGTGCCTTC 85 ? -- - v v i i - --- i i v Eulor6E#DNA/C 56 TCGGGTGC--GTTGC-GAGGCACGAG-GC---CGAAGGCCGAGTGACTTC 98 rnd-5_family- 86 AGCCACCCGAGAAGTNCANCAATAGCCTATTAATGCACACCCTGAAGTGG 135 i ? ?i vv ii vv vv i v Eulor6E#DNA/C 99 AACCACCCGAGAAGTGCAATAATCCCTCAGAAATGCACCGCCTGGAGTGT 148 rnd-5_family- 136 CTTATTGCTATTA 148 ? Eulor6E#DNA/C 149 CTTATTGNTATTA 161 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.13 CpG sites = 9, Kimura (unadjusted) = 21.50 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 457 17.07 0.00 0.00 rnd-5_family-5589#DNA/Crypton 67 148 (795) Eulor6D#DNA/Crypton 81 162 (140) m_b22s502i10 rnd-5_family- 67 CCAAAGGTCGAGTGCCTTCAGCCACCCGAGAAGTNCANCAATAGCCTATT 116 i i v i i ? ?i v i?vv Eulor6D#DNA/C 81 CCGAAGGCCGAGTGACTTTAACCACCCGAGAAGTGCAATAATCGCCCNGA 130 rnd-5_family- 117 AATGCACACCCTGAAGTGGCTTATTGCTATTA 148 vv i v Eulor6D#DNA/C 131 AATGCACTGCCTGGAGTGTCTTATTGCTATTA 162 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.80 CpG sites = 7, Kimura (unadjusted) = 20.33 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 22 19.69 1.61 3.28 rnd-5_family-5780#Unknown 29 90 (35) (GGGGC)n#Simple_repeat 1 61 (0) m_b22s252i2 rnd-5_family- 29 GGGGC-GGGAGGGGCGGGGCAGGGGTGGAGTCGGGGCGGGGCTGCGGGGG 77 - v - i - v v v v (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGC-GGGGCGG-GGCGGGGCGGGGCGGGGCGGG 48 rnd-5_family- 78 TAGGGGGGGGTCG 90 vv v v (GGGGC)n#Simp 49 GCGGGGCGGGGCG 61 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 450 10.61 0.00 1.52 rnd-5_family-8786#SINE/5S-Deu-L2 96 162 (6) AmnSINE1#SINE/5S-Deu-L2 508 573 (2) m_b22s502i11 rnd-5_family- 96 GTTTGCAAAGCGCTTTGGGATCCTTCGGGATGAAAGGTGCTATATAAATG 145 i i i AmnSINE1#SINE 508 GCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATG 557 rnd-5_family- 146 TTAGCCTATTATCATTA 162 iv -v i AmnSINE1#SINE 558 CAAG-GTATTATTATTA 573 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.96 CpG sites = 5, Kimura (unadjusted) = 11.60 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 1535 6.17 0.00 2.37 rnd-5_family-892#Unknown 13 228 (0) UCON12#Unknown 300 510 (2) m_b22s502i12 rnd-5_family- 13 CTNNTTTTCTTTGTGTTAANGGTNTGTACTGACTTTGTGGAATCACTGCA 62 ?? ? i ? i ? UCON12#Unknow 300 CTTCTTTNCTTTGCGTTAAGGATATGTACTGACTTTGTGGAATCACTGCA 349 rnd-5_family- 63 GCAAGTTGTGAATGATGTATGAAATGAAAAATCCCTGCCCAGTGCACAGA 112 i UCON12#Unknow 350 GCAAGTTGTAAATGATGTATGAAATGAAAAATCCCTGCCCAGTGCACAGA 399 rnd-5_family- 113 GAGAATACAGACAGTGCTNTGCAATCACTGCTATCGTGTGCTGTGTGNTG 162 ? i vv i v ? UCON12#Unknow 400 GAGAATACAGACAGTGCTGTGCAATCACTGCTGTGCTGTGCTATTTGCTG 449 rnd-5_family- 163 TAGTACACTATTCCGCTCAGACGCAGNCAGAAANCNNCACCGAGCNCAGA 212 i----- v ? ?v?? i ? UCON12#Unknow 450 TAA-----TATTCAGCTCAGACGCAGCCAGAAAAGCCCACCAAGCCCAGA 494 rnd-5_family- 213 AGTCTCAGACAAAAAA 228 ? i ? UCON12#Unknow 495 AGTNTCGGACAANAAA 510 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.93 CpG sites = 8, Kimura (unadjusted) = 6.94 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (5 / 215), avg. gap size = 1.00 (5 / 5) 11 21.40 4.44 2.17 rnd-5_family-8997#Unknown 299 343 (145) (GCTGCC)n#Simple_repeat 1 46 (0) m_b22s252i1 rnd-5_family- 299 GCTGCCAC-GCTGCGTGTCTC-GCAGCTGCCCCTGCCGCTGGCACTG 343 i - i - i v - v v v i (GCTGCC)n#Sim 1 GCTGCCGCTGCCGC-TGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTG 46 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 19 10.92 1.64 10.71 rnd-5_family-9394#LTR/Gypsy 1994 2054 (215) (TTCCTG)n#Simple_repeat 1 56 (0) m_b22s252i0 rnd-5_family- 1994 TTCCTGCTCCTGTT-CTGTTTCCTGGTTCCTGCTCCCTGAACTCAGTGTT 2042 i - - - - i --i -v (TTCCTG)n#Sim 1 TTCCTGTTCCTGTTCCTG-TTCCT-GTTCCTG-TTCCTG--TTC-CTGTT 44 rnd-5_family- 2043 CCAGTTCCTGTT 2054 v (TTCCTG)n#Sim 45 CCTGTTCCTGTT 56 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.12 (7 / 60), avg. gap size = 1.00 (7 / 7) 1024 17.18 3.54 2.18 rnd-5_family-9692#SINE/tRNA 1 226 (13) LFSINE_Vert#SINE/tRNA 225 453 (6) m_b22s601i4 rnd-5_family- 1 TTGTTGGCCANCCCAGGTGGAGAGAGGCCAAGGTCTGAACCGGC--GGAT 48 vi? i v--- v iv -- v LFSINE_Vert#S 225 TTGTTGGCAGTCTCAGC---AGAGAGGCCAAGGACTGAATGGGCATGGAG 271 rnd-5_family- 49 NTTTA--TATT-TCTCGCTTTTAGAGATTGCCCTCCTGAGTCAAGTT--A 93 ?i v -- ii- i i i i v i ii iii i v -- LFSINE_Vert#S 272 ACTGAACTACCCTCTCACCTCTAGAGGTGGTCCCTCCAGGTCAGGGTTGA 321 rnd-5_family- 94 CTTATGNTGGTGGGGCAGTGTGGGGAAGCTTGCACTGCTACTGCCCATGT 143 vvi ii? i ii -- LFSINE_Vert#S 322 GGCACATTGGCGGGGCAGTGTGGGGAAGCTTGCACTGCCGCTGCCC--GT 369 rnd-5_family- 144 GCTGTACCTGTTCTGTGGATAAAC-GAGGACTTNAATCTCCAGGGTTGTC 192 - ? i i LFSINE_Vert#S 370 GCTGTACCTGTTCTGTGGATAAACAGAGGACTTCAGTCTCCAGGGCTGTC 419 rnd-5_family- 193 AGTCTGGCACCTTTCACCAGCACTANATTCACTT 226 i i v ? LFSINE_Vert#S 420 AATCCGGCACCTTTCACGAGCACTAAATTCACTT 453 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.76 CpG sites = 27, Kimura (unadjusted) = 20.59 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.04 (10 / 225), avg. gap size = 1.30 (13 / 10) 308 20.40 4.90 3.88 rnd-5_family-10296#LINE/L1 337 438 (414) L1MA1_3end#LINE/L1 194 296 (753) m_b23s551i0 rnd-5_family- 337 ACCTCACTCCATTTAAGCTAAGGAAATATATNTANAAAA--GGGAGT--C 382 i i v --- v ivv ?i ? i -- v i -- L1MA1_3end#LI 194 ATCTCACCCCAGTTAA---AATGGCTTATATCCAAAAGACAGGCAATAAC 240 rnd-5_family- 383 AAATGCTGNAGAGGATGTGGAGGAATAGGGACCTTTCTGCA-TATATGGT 431 ?v i vi i i v i - i - L1MA1_3end#LI 241 AAATGCTGGCGAGGATGTGGAGAAAAGGGAACCCTTGTACACTGT-TGGT 289 rnd-5_family- 432 GGGAATG 438 L1MA1_3end#LI 290 GGGAATG 296 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.15 CpG sites = 12, Kimura (unadjusted) = 25.15 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.07 (7 / 101), avg. gap size = 1.29 (9 / 7) 317 26.12 4.85 4.85 rnd-5_family-10296#LINE/L1 382 546 (306) L1PA6_3end#LINE/L1 240 404 (497) m_b23s551i1 rnd-5_family- 382 CAAATGCTGNAGAGGATGTGGAGGAATAGGGACCTTTCTGCA-TATATGG 430 i ? i i vi i i - i - L1PA6_3end#LI 240 CAGATGCTGGAGAGGATGTGGAGAAATAGGAACGCTTTTACACTGT-TGG 288 rnd-5_family- 431 TGGGAATGCCCTAAGATAAT---AGTATTTTGGAAGAAAATAAATAGAAT 477 i --- iv i --- vi v v i ivivv v L1PA6_3end#LI 289 TGGGAGTG---TAAACTAGTTCAACCATTGTGGAAGACAGTGTGGCGATT 335 rnd-5_family- 478 TTTCAAGGTAACTAAAGTTAG-GCTACCCACAGAACCCATAGTGATTCTA 526 ii - v i ii -iv - ivvi -- i i i L1PA6_3end#LI 336 CCTCAAGG-ATCTAGAACTAGAAATA-CCATTTGACCC--AGCGATCCCA 381 rnd-5_family- 527 TTA--GGTTACA-GNCCAAAGGA 546 -- v i -i? L1PA6_3end#LI 382 TTACTGGGTATATACCCAAAGGA 404 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 27, Kimura (unadjusted) = 33.86 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.08 (13 / 164), avg. gap size = 1.23 (16 / 13) 229 22.03 1.69 0.00 rnd-5_family-11947#LINE/CR1 1 59 (12) CR1-13_AMi#LINE/CR1 630 689 (35) m_b23s551i2 rnd-5_family- 1 TCCTCTGAAGCATCAGGGA-TGGCCACGGCTGGAGACGGGACATTGGACG 49 v v - v iii i i i v CR1-13_AMi#LI 630 TCCTCTGAAGCATCTGGTACTGGCCACTGTCAGAGACAGGATACTGGACT 679 rnd-5_family- 50 GGGTGGGCCA 59 i i i CR1-13_AMi#LI 680 AGATGGACCA 689 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.97 CpG sites = 9, Kimura (unadjusted) = 26.97 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 299 33.17 2.80 1.38 rnd-5_family-12153#LINE/RTE-BovB 652 865 (1012) MamRTE1#LINE/RTE-BovB 883 1099 (2713) m_b23s601i0 rnd-5_family- 652 GCTTTGCCAACATCATCAGTACATATGCCCCAACGCTTTCCTCCGTCTCT 701 ? v i ii v vv vv vvviii vv MamRTE1#LINE/ 883 GCTNTGCCACCGTCATCAGCGCATATGCCCCCACCATGACGAATACCGAT 932 rnd-5_family- 702 GAAGAGAAGGACTTGTTCTATCAGCAACTCGACAGCGTCATCNGTAA-GC 750 i i vvvi iv v v v vv - i i- v MamRTE1#LINE/ 933 GAGGAGAAAGAAAGATTCTACAAGGATCTGGACAGACTCATC-GCAGCGG 981 rnd-5_family- 751 TACCACCGGTTGAGCAACTCTATCTNC-TGGGAGACTTCAACGCTAGAGT 799 v ivi - viiv v? -i i vv v MamRTE1#LINE/ 982 TACCAACATCTGA-CAAGCTGATCGTCACGGGAGATTTCAACGCACGTGT 1030 rnd-5_family- 800 CGGCTCAGATCACGAGATGTGGCTGCTGCGT----GGCCACCATGGAGTG 845 vvv vv i i v- vviv ---- v v? i ii v MamRTE1#LINE/ 1031 CGGCAGCGATGCCGAAACGTGGA-GAAAAGTCATCGGACCNCACGGGATT 1079 rnd-5_family- 846 GGAAAAATGAATGACAATGG 865 iv ? iii MamRTE1#LINE/ 1080 GGAAAGCTNAACAGCAATGG 1099 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 28, Kimura (unadjusted) = 45.08 Transitions / transversions = 0.67 (28/42) Gap_init rate = 0.03 (6 / 213), avg. gap size = 1.50 (9 / 6) 17 11.25 0.00 0.00 rnd-5_family-1224#Unknown 1 29 (49) (TCC)n#Simple_repeat 1 29 (0) m_b23s252i7 rnd-5_family- 1 TCCTCTTCCCCGTCCTCCTCCTCCTCCTC 29 i i v (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTC 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 284 25.00 11.03 0.00 rnd-5_family-1317#LINE/L2 36 171 (261) L2-1_AMi#LINE/L2 577 727 (508) m_b23s551i3 rnd-5_family- 36 CCATCCTACAGATCACTCAGGCCTNCACTCTGGGGGTTATTTTTGACT-- 83 i vvi i?i vi v i i i -- L2-1_AMi#LINE 577 CCATCCTGCCTGTCACTCAGGCCCGTAACCTGGGCGTCATCTTCGACTCG 626 rnd-5_family- 84 --CCTCCCTCT---CCCTTGC-CCCA-------TCCAAATCCTGCCGCTN 120 -- i ---i ii -i ------- i i v v ? L2-1_AMi#LINE 627 GACCTCTCTCTAGGTCCTCACATCCAGGCTATGTCTAAATCTTGCAGATT 676 rnd-5_family- 121 CTTCCTCCTCAGCATCTCCAAGATCCGTCCTTTTCTTTCCGCCCCCACAG 170 i v vi i i v v i v ii v L2-1_AMi#LINE 677 CTTTCTGCATAACATCTCTAAGATACGGCCTTTCCTATCCATCCACACAG 726 rnd-5_family- 171 C 171 L2-1_AMi#LINE 727 C 727 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.73 CpG sites = 22, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.04 (5 / 135), avg. gap size = 3.00 (15 / 5) 239 31.14 2.13 4.35 rnd-5_family-1317#LINE/L2 173 360 (72) UCON86#LINE/L2 7 190 (492) m_b23s502i0 rnd-5_family- 173 AAATCTCTCGTCCAGGCCCTCGTTATATCCCGCCTCGNCTACTGCAACAC 222 - i ? i i iviv i i ? i ? v UCON86#LINE/L 7 AAATC-CTCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGCANCTC 55 rnd-5_family- 223 CCTCCTCTCTGGCTTCCCAAACACACATCCAATTGCCCC--TCTTCAGTC 270 i v i ----- vi v viv i --v i iv UCON86#LINE/L 56 CCTTCTCTATGGCCTCCC-----CAAGTCCCAGCTCTCCAGACTCCAGCA 100 rnd-5_family- 271 CATACAAAATACAGCCGCTAAAGTCATCTTCCTTGCCCGCCGA--TCTGA 318 i i i i v i i--v i v iv vi v ivv -- vi UCON86#LINE/L 101 CGTGCAGAATGCTGCTGCC--CGCCTTCTCACACGCACAAAGAAGTGCGA 148 rnd-5_family- 319 TCGTGTCACTCCCCTCTTCNAATCCCTCCGCTGGCTCCCCAT 360 i iii i v i ? ivv i UCON86#LINE/L 149 CCACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCAT 190 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 34, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.55 (34/22) Gap_init rate = 0.05 (10 / 187), avg. gap size = 1.20 (12 / 10) 284 15.25 0.00 0.00 rnd-5_family-150#SINE/MIR 1 59 (0) MIR1_Amn#SINE/MIR 14 72 (158) m_b23s601i1 rnd-5_family- 1 TGGTCTTGTGGTTAGAGCACGGGACTAGGAGTCAGGACTCCTGGGTTCCA 50 v v v i v i vv ? MIR1_Amn#SINE 14 TGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNA 63 rnd-5_family- 51 TTCCTGNCT 59 ? i ? MIR1_Amn#SINE 64 NTCCCGGCT 72 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.15 CpG sites = 3, Kimura (unadjusted) = 18.09 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 14 14.42 2.44 2.44 rnd-5_family-1558#Unknown 74 114 (263) (CCACCCC)n#Simple_repeat 1 41 (0) m_b23s252i6 rnd-5_family- 74 CCA-CCCCTTCCCCCAACGCCCCCTCTCCCCNCCCCCCACCC 114 - iv v - v i ? (CCACCCC)n#Si 1 CCACCCCCCACCCCCCAC-CCCCCACCCCCCACCCCCCACCC 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 17 26.26 8.11 1.69 rnd-5_family-19706#Unknown 92 202 (289) (GA)n#Simple_repeat 1 118 (0) m_b23s252i5 rnd-5_family- 92 GAGA-AGAAAG-GAGAGAGA-AAATATAG-GGGAGAGAGATTGNAGA-AN 136 - i - - i v v - i vv - - ? (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAG 49 rnd-5_family- 137 ACAGTGTAGGGAAAGAAAG-GAG-GAGATAAAGGGGTTGAGGGGGAGAGA 184 v v - i i i - - v i i ivv i i (GA)n#Simple_ 50 AGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 98 rnd-5_family- 185 -AGGAAAAGAGA-ANAGAGA 202 - ii i - ? (GA)n#Simple_ 99 GAGAGAGAGAGAGAGAGAGA 118 Matrix = Unknown Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.10 (11 / 110), avg. gap size = 1.00 (11 / 11) 263 33.52 3.91 3.33 rnd-5_family-225#LINE/L2 346 524 (336) X24_LINE#LINE/L2 43 222 (92) m_b23s601i2 rnd-5_family- 346 CAGCTTGTTCAGAATGCAGCAGCACGATTGCTCATGGGTTCGAGCTATTG 395 v v i v vi v v? vi? i iv? X24_LINE#LINE 43 CAGCTGGTGCAGAATGCAGCGGCTCGTCTGCTGAANGGTGTNAGCCACAN 92 rnd-5_family- 396 TGATCATATTCAGCCCGCTTTGTGTTCTTTACATTGGCTGCCCATT---- 441 v v i vvi i ivi vi ivv i i i i ? ---- X24_LINE#LINE 93 GGAGCACATTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCT 142 rnd-5_family- 442 ---AAGTGGAATTTATTTAACTAGCTTTAATGGTTTATAAAGCCTCTGAT 488 ---i v i vvvvii ii --- i iivv X24_LINE#LINE 143 TCCGAGTGCAATTCAAGGTGTTGACTTTAA---TCTATAAAGCCCTATAT 189 rnd-5_family- 489 GGGGCTGGCCCTAGCGGTGNTATTCGAGACCTCCTC 524 vviv --- v?iv v i v X24_LINE#LINE 190 GGTTTGGGCCCT---GGTTACCTTAGAGATCGCCTC 222 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 28, Kimura (unadjusted) = 46.91 Transitions / transversions = 0.93 (28/30) Gap_init rate = 0.04 (8 / 178), avg. gap size = 1.62 (13 / 8) 95 24.15 3.95 2.22 rnd-5_family-2425#DNA/hAT-Tip100 61 414 (227) (CCGC)n#Simple_repeat 1 360 (0) m_b23s252i4 rnd-5_family- 61 CCGTCCGCCCGGCGCGCCCGCCCGCCCGGCCG-CCGCTCGCCTCCTCACC 109 i - v v - i iv i i (CCGC)n#Simpl 1 CCGCCCGCCC-GCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCC 49 rnd-5_family- 110 CTCCCCGCCCGCCCGCCCG-CCGCTCGCCTCCTCACCCACCCGCCCG-CC 157 -v - i iv i i i - (CCGC)n#Simpl 50 C-GCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCC 98 rnd-5_family- 158 GCTCGCCTCCCCGCTAGTCTCCTCG-CCGTCCGTCCGGCGCGCCC-CNC- 204 i iv iv i iv i - i - v v - ? - (CCGC)n#Simpl 99 GCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCG-CCCGCCCGCCCGCCCG 147 rnd-5_family- 205 CCCGTCCGCCCGNCCG-CCGCTCTCCTCCTCG-CCGTCCGCCCGCCTGCC 252 i ? - i v iv i - i i (CCGC)n#Simpl 148 CCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCC 197 rnd-5_family- 253 TG-CCTCCCTCCTCACACCCCCGCCCGCCTG-CCGCTCGCCTCCCCGTTC 300 i - v v - i v v i - i iv ii (CCGC)n#Simpl 198 CGCCCGCCCGCC-CGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCC 246 rnd-5_family- 301 GCCTCCTCACCCCGCTCGCCCGCCCG-CCTCCCGCCTCACCTCCCCGCCC 349 - vi vv i - v - i iv (CCGC)n#Simpl 247 GCC-CGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCC-CGCCCGCCCGCCC 294 rnd-5_family- 350 G-CCTCCTCACCGTCCACTCGCCNGNCTG-CCGCTCNNCTCCTCAC-CCC 396 - v ivv i i i ? ? i - - ?? - v v - (CCGC)n#Simpl 295 GCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGC-CCGC-CCGCCCGCCC 342 rnd-5_family- 397 GCCCACCCGCCGGCCCGC 414 i v (CCGC)n#Simpl 343 GCCCGCCCGCCCGCCCGC 360 Matrix = Unknown Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.06 (22 / 353), avg. gap size = 1.00 (22 / 22) 1278 3.06 0.00 7.32 rnd-5_family-24574#DNA/hAT-Tip100 1 176 (2778) MamTip1#DNA/hAT-Tip100 1 164 (103) m_b23s502i1 rnd-5_family- 1 CAGGGCTGGATTACCCAATAGGCAGACTAAGCACGTGCTTAGGGCACCAG 50 v i MamTip1#DNA/h 1 CAGTGCTGGATTACCCAACAGGCAGACTAAGCACGTGCTTAGGGCACCAG 50 rnd-5_family- 51 CAAAGCAGGGGGCACCAAAAAAAAATGGATTTTTTTTTGGAAAAAANTTG 100 - ------ v ----- i ? MamTip1#DNA/h 51 CAAAGCAGGGG-CACCAAAA------GCATTTTT-----GAAAGAATTTG 88 rnd-5_family- 101 ATATTTGATATTTCAAAAAAAGCATCGAAGTAGTCATCATGGGAAAAATC 150 MamTip1#DNA/h 89 ATATTTGATATTTCAAAAAAAGCATCGAAGTAGTCATCATGGGAAAAATC 138 rnd-5_family- 151 AGAACTTTGTTAGACTTCCTTACACT 176 i MamTip1#DNA/h 139 AGAACTTTGTTGGACTTCCTTACACT 164 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.14 CpG sites = 3, Kimura (unadjusted) = 3.14 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (12 / 175), avg. gap size = 1.00 (12 / 12) 23 14.60 0.00 0.00 rnd-5_family-24574#DNA/hAT-Tip100 372 409 (2545) (TA)n#Simple_repeat 1 38 (0) m_b23s252i3 rnd-5_family- 372 TATATATATATATATATATATATACACACATAAAAATA 409 i i i v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATA 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 306 29.18 8.12 8.67 rnd-5_family-24574#DNA/hAT-Tip100 1231 1624 (1330) Arthur1#DNA/hAT-Tip100 1978 2369 (1578) m_b23s502i2 rnd-5_family- 1231 GCCGTTATTCAAACATTAGCTGAACGCGGNCTGCCTTTCCGGGG-----A 1275 v v viv ivi v v ?i i v i ----- Arthur1#DNA/h 1978 GCGGTTATTAAATTTTTAAGCGAAAGAGGTTTGCCCTTCAGAGGTCACGA 2027 rnd-5_family- 1276 TCAAATGACGCATTTGGATCATTGCAGAATGGAAATTTCTTGGGATTGTT 1325 v v vv ----- v iiv v v v vv Arthur1#DNA/h 2028 TGAAAAGTGGCATT-----CTTCAAATAATGGAAATTTCATGGGAATCAT 2072 rnd-5_family- 1326 GGAGCTTGTGGCTCAGTTTGACCCATTTTT-----AGCA---GGCCATAT 1367 vi i vi v v i i ----- --- vv v Arthur1#DNA/h 2073 CAAACTAATTGCTGAATTTGATCCATTTTTGCACGAGCACTTGGAAAAAT 2122 rnd-5_family- 1368 CTCAAAATATGGGAATGCTGGCAAAGGTAANCCATCATACTTATCCAAGA 1417 ? iviii ------ v i ----- v i i Arthur1#DNA/h 2123 NTCAAAATGAAAAAA------CAAATGTGA-----CTTATTTATCCAAAA 2161 rnd-5_family- 1418 CAATATGTGATGAACTCATTGGTCTAACGAGTGACAAAGTTCGTTCA--- 1464 i v i v i v i ivv i i ---- iivi v --- Arthur1#DNA/h 2162 CAGTTTATGAAGAATTAATCGAAATAATGGG----AAAACGTGTACAAAA 2207 rnd-5_family- 1465 -GCTATTGTGGACGAAATAAGTACTGCCGGG----------TACTTCAGT 1503 - vvi v ii iv i v-i i i---------- i -- Arthur1#DNA/h 2208 TGAAGTGGTAAATCAAATAAATAA-ACCAGACACCAAATACTACTCCA-- 2254 rnd-5_family- 1504 TTATCTGTCGACTCTACACCCGATCTTTCACATATTGATCAATT---GAG 1550 - v i v v vv v i i --- v Arthur1#DNA/h 2255 TTAT-TGTAGATTCTACACCGGATGTGACAAATACTGATCAGTTGGCGAT 2303 rnd-5_family- 1551 TATTGTACTAAGATATGTGTCTCCCACAGATGGAAAACCAGTTGAACGAT 1600 i --- v i- ----i i - i vvv i Arthur1#DNA/h 2304 TATTGTGC---GCTAC-TGT----TATA-ACGGAAAACCCTATGAGCGAT 2344 rnd-5_family- 1601 TTATAAC--ATTCCTCAATTTGAAAA 1624 v --v vi -i Arthur1#DNA/h 2345 TTTTAACTTTTTCGCCAA-CTGAAAA 2369 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.80 CpG sites = 50, Kimura (unadjusted) = 37.54 Transitions / transversions = 0.91 (50/55) Gap_init rate = 0.11 (42 / 393), avg. gap size = 1.57 (66 / 42) 256 32.82 0.78 0.78 rnd-5_family-24574#DNA/hAT-Tip100 2729 2857 (97) Zaphod#DNA/hAT-Tip100 3499 3627 (452) m_b23s502i3 rnd-5_family- 2729 ATTTCCAAACGTAGAGATCGCACTACGTATTTTTCTAACATTGATGATTA 2778 i iv iiv i vi v v vi i v vviii i Zaphod#DNA/hA 3499 ATTTCCGAATCTAAGTATTGCTTTAAGAATTTTATTGACAATTCCAGTTG 3548 rnd-5_family- 2779 CTAACTGC-TCCGCAGAACGCTCTTTTTCTCAGCTGAAAAGAATAAAAAA 2827 - - v i vvv i iv ii vv Zaphod#DNA/hA 3549 CTA-CTGCCTCAGCAGAGCGAAGTTTCTCCAAATTGAAATTAATAAAAAA 3597 rnd-5_family- 2828 CCCTCAGAGAACAACAATGTGTCAGGACAG 2857 iv vi v vv i v Zaphod#DNA/hA 3598 CTATCTAAGAACTACAATGACTCAAGAAAG 3627 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 20, Kimura (unadjusted) = 43.65 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.02 (2 / 128), avg. gap size = 1.00 (2 / 2) 431 0.00 0.00 0.00 rnd-5_family-24574#DNA/hAT-Tip100 2908 2954 (0) MamTip1b#DNA/hAT-Tip100 82 128 (141) m_b23s502i4 rnd-5_family- 2908 TCAGCTTCGATGAACTTATCCAGAATTTTGCAATCAGAAAATCTAGA 2954 MamTip1b#DNA/ 82 TCAGCTTCGATGAACTTATCCAGAATTTTGCAATCAGAAAATCTAGA 128 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.00 CpG sites = 0, Kimura (unadjusted) = 0.00 Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 444 29.60 5.78 4.77 rnd-5_family-2582#LINE/L1 79 493 (1943) L1MC_orf2#LINE/L1 1405 1823 (1471) m_b23s551i4 rnd-5_family- 79 AAGACCCCCGGCCCTGATGGCCT-ACCGATAGAATTCTATCAAA-GTTTC 126 ii v v v vi - i i - i -i v L1MC_orf2#LIN 1405 AAAGCACCAGGCCCAGATGGGTTCACTGGT-GAATTCTACCAAACATTTA 1453 rnd-5_family- 127 A--AAGAAATTCTGGCCCCTAAGCTGTTATACA----TTTAC-GAAGATG 169 -- v i---- i -- vi v ----i v - i L1MC_orf2#LIN 1454 AGGAAGAAATTATA----CCAA--TTCTCTACAATCTCTTCCAGAAGATA 1497 rnd-5_family- 170 CCTTNAAG-AAAGG---TACGT--TACCTCCTACTATGAGGGAAGCCCTA 213 ----? - i --- v -- v v v vv ---- L1MC_orf2#LIN 1498 ----GAAGCAGAGGGAATACTTCCTAACTCATTCTATGAGGCCAGC---- 1539 rnd-5_family- 214 ATTACCGTACTACTTAAACCGGGTAAGGATG-CGCAAAAGTGTAATAGCT 262 v v iv i ii i ii-ii i iviv - i L1MC_orf2#LIN 1540 ATTACCCTAATACCAAAACCAGACAAAGACATTACAAGAAAAGAA-AACT 1588 rnd-5_family- 263 ATAGACCCATCTCTTTAATCAATGCTGATNTAAAAATACTTTCAAAAATA 312 i v v i v v iiiv ?i v ivvv L1MC_orf2#LIN 1589 ACAGACCAATATCTCTCATGAACATAGATGCAAAAATCCTCAACAAAATA 1638 rnd-5_family- 313 TTGGCTAAGAGGCNTGAAAAA-GTAATAAGTGATATGATTCACC-CCACC 360 i v vv iv?iv v - vv iv - v v - v L1MC_orf2#LIN 1639 TTAGCAAATCGAATCCAACAATGTATAAAAAGA-ATTATACACCACGACC 1687 rnd-5_family- 361 AGGTGGGATTTATTNNAAAAAGGCACGGTTCAGATAACACACGTCAGCTG 410 i i?? iiv v v i vivvi iv vv iiii L1MC_orf2#LIN 1688 AAGTGGGATTTATCCCAGGTATGCAAGGCTGGTTCAACATTCGAAAATCA 1737 rnd-5_family- 411 ATCAATGTTATGGCATTCCACCAACATTCTA------GAAATTCCCATGC 454 i v -v iv i vv ------i v v - L1MC_orf2#LIN 1738 ATTAATGTAAT-CCATCACATCAACAGGCTAAAGAAGAAAAATCACATG- 1785 rnd-5_family- 455 AATCATTTCACTCGATGCAGAGAAAGCCTTTGACAGAGT 493 - v v v i v i i L1MC_orf2#LIN 1786 -ATCATATCAATAGATGCAGAAAAAGCATTTGACAAAAT 1823 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 56, Kimura (unadjusted) = 38.69 Transitions / transversions = 0.92 (56/61) Gap_init rate = 0.08 (32 / 414), avg. gap size = 1.38 (44 / 32) 294 34.98 1.18 3.21 rnd-5_family-2582#LINE/L1 608 861 (1575) L1P1_orf2#LINE/L1 1972 2220 (1074) m_b23s551i5 rnd-5_family- 608 AGACAGGGATGCTCCCTCCCCTCCCCTCACCCTTGTTCAATTTGGCATTA 657 ----- i i vi i i i iv i ii i L1P1_orf2#LIN 1972 AGACAGGGATGC-----CCTCTCTCACCACTCCTATTCAACATAGTGTTG 2016 rnd-5_family- 658 GAACCACTTGCAATACTAATTAGGGAACACCAAGGTATTCAAGGG-ATCA 706 viv v v vivi i v iv v- v v v - iv L1P1_orf2#LIN 2017 GAAGTTCTGGCCAGGGCAATCAGGCAGGAG-AAGGAAATAAAGGGTATTC 2065 rnd-5_family- 707 AATCAGGGTCTCAGGAGACAAAAATCCTTCTANATGCAGACGACATCCTC 756 i ivvvv iiiv v viii i?v vv i L1P1_orf2#LIN 2066 AATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAGACGACATGATT 2115 rnd-5_family- 757 CTATTTATTAAAAATCCAGATCAGTCCATTCC-AAATATCCTACAAAC-A 804 v v -i i v vv ivii vi - v -i i -i L1P1_orf2#LIN 2116 GTATAT-CTAGAAAACCCCATCGTCTCAGCCCAAAATCTCCT-TAAGCTG 2163 rnd-5_family- 805 ATAGATAACNTTGGCAAATTCTCTGGCTACAACATAAATTGGGATAAGTC 854 iii ? ii v v v v v vv v v i L1P1_orf2#LIN 2164 ATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATC 2213 rnd-5_family- 855 GGAAGCA 861 iv L1P1_orf2#LIN 2214 ACAAGCA 2220 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.70 CpG sites = 43, Kimura (unadjusted) = 48.48 Transitions / transversions = 1.00 (43/43) Gap_init rate = 0.04 (11 / 253), avg. gap size = 1.00 (11 / 11) 1213 6.00 0.00 0.00 rnd-5_family-25840#SINE/U 2 151 (2614) U2#snRNA 38 187 (1) m_b23s502i5 rnd-5_family- 2 ATCTGTTCTTATCAGTTTAATATCTGATATGTCCTCNATNTGAGAACTNT 51 i ? ?i i v? U2#snRNA 38 ATCTGTTCTTATCAGTTTAATATCTGATACGTCCTCTATCCGAGGACAAT 87 rnd-5_family- 52 ATATTAAATGGANTTTTGGAACAGGGAGATGGAATAGGAGCTTGCTCCGT 101 ? i U2#snRNA 88 ATATTAAATGGATTTTTGGAGCAGGGAGATGGAATAGGAGCTTGCTCCGT 137 rnd-5_family- 102 CCACTCCACGCATCGGCCTGGTATTGCAGTACTTCCAGGNGCGGTGCGCC 151 i i ?i i U2#snRNA 138 CCACTCCACGCATCGACCTGGTATTGCAGTACCTCCAGGAACGGTGCACC 187 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 5.20 CpG sites = 8, Kimura (unadjusted) = 6.58 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0) 238 0.00 0.00 0.00 rnd-5_family-25840#SINE/U 606 632 (2133) CR1-3_Croc#LINE/CR1 3542 3568 (37) m_b23s551i6 rnd-5_family- 606 GCAGGGGGTTGGACTAGATGACCTCTG 632 CR1-3_Croc#LI 3542 GCAGGGGGTTGGACTAGATGACCTCTG 3568 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.00 CpG sites = 0, Kimura (unadjusted) = 0.00 Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 359 32.91 3.59 3.17 rnd-5_family-2845#DNA/hAT-Tip100 244 494 (1105) Zaphod#DNA/hAT-Tip100 2456 2707 (1372) m_b23s502i6 rnd-5_family- 244 GATTGCAGGGGACAAAGCTATGACAATGGAGCTAACATGGCTGCAGCATA 293 iv i i iv i v i vviv v Zaphod#DNA/hA 2456 GATTGTCGAGGGCAAGCCTATGATAATGGCGCTAACATGGTTGGTAAAGA 2505 rnd-5_family- 294 CAAAGGTGTTCAAAATCGAA-TTCAGCAGGTAAATCAGTACGTGTCTTTC 342 v v iviv - ii v iv vi - v ii ii i Zaphod#DNA/hA 2506 AAAAGGTGTACAAGCCAGAATTTTGGCCGAAAATCCAG-AAGCATTCTTT 2554 rnd-5_family- 343 ATCCCATGTGCTGCCCACTCACTGAATCTTGTT----GGAGAAGCTGCTG 388 i v i v v ivvvi - ---- v iv iv Zaphod#DNA/hA 2555 GTGCCATGTACGGCGCATAGTTTGAAT-TTGTTACTAGGAGACGTGGCCT 2603 rnd-5_family- 389 CAATGGTNGTTCCCCAAGTTGTTCTG---TTTTTTGGAATTGTTCAAAGA 435 iv ?----- - v ivv --- i ivi Zaphod#DNA/hA 2604 CAACTGTG-----CCAA-TAGCGATGACATTCTTTGGAACAATTCAAAGA 2647 rnd-5_family- 436 TTGTATACCCTGTTTTCCGCTTCTACTAGTCGTTGGGATGTGTTGA-AAA 484 i vv i i vv i ivivv v i ii v -i Zaphod#DNA/hA 2648 TTATATACGATATTTTCTGGATCTGCCCAAAGATGGAACATCTTGATGAA 2697 rnd-5_family- 485 AAACGTATTA 494 v i i Zaphod#DNA/hA 2698 ACACATATCA 2707 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.65 CpG sites = 41, Kimura (unadjusted) = 44.38 Transitions / transversions = 1.05 (41/39) Gap_init rate = 0.05 (12 / 250), avg. gap size = 1.42 (17 / 12) 249 34.57 4.76 2.06 rnd-5_family-2845#DNA/hAT-Tip100 346 534 (1065) Arthur1#DNA/hAT-Tip100 2539 2732 (1215) m_b23s502i7 rnd-5_family- 346 CCATGTGCTGCCCACTCACTGAATCTTGTTGGAGAA---GCTGCTGCAAT 392 i i v i i v v i i --- iv v i Arthur1#DNA/h 2539 CCGTGCGCAGCTCATTCCCTTAATCTCGTCGGAGAAAAAGCTGCCTCCAC 2588 rnd-5_family- 393 GGTNGTTCCCCAAGTTGTTCTGTTTTTTGGAATTGTTCAAAGATTGTATA 442 i ?--- iv vvv vi i v v v vii i i Arthur1#DNA/h 2589 AGTA---CCTGAAGTTGTTGACTACTTCGGTATTTTGCAACAGTTATATG 2635 rnd-5_family- 443 CCCTGTTTTCCGCTTCTACTAGTCGTTGGGATGTGTTGAAAAAAACGTAT 492 iii v v v vv v v v ii i - v v v i ii Arthur1#DNA/h 2636 TTTTCTTTTCGGGTTCGTCTCGTAGATGGAGTAT-TTTAAACACACATGC 2684 rnd-5_family- 493 TAGC----A--TTACATTAAAATGCCAAAGCACGACAAGATGGTCAGC 534 i i ---- -- v v iv i v iiii i v Arthur1#DNA/h 2685 CAACTTGGATTTTTCTTTAAAGAGTCTAAGTGTAACGAGATGGTCTGC 2732 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 34, Kimura (unadjusted) = 47.90 Transitions / transversions = 1.13 (34/30) Gap_init rate = 0.04 (7 / 188), avg. gap size = 1.86 (13 / 7) 263 26.44 1.14 1.14 rnd-5_family-2845#DNA/hAT-Tip100 1355 1442 (157) Zaphod#DNA/hAT-Tip100 3570 3657 (422) m_b23s502i8 rnd-5_family- 1355 GTTTCAGCAAGCTAAAATTAATCAAGACCTATCTAAGAACGTCCATGGGG 1404 vv ii i v i v vv v ivv Zaphod#DNA/hA 3570 GTTTCTCCAAATTGAAATTAATAAAAAACTATCTAAGAACTACAATGACT 3619 rnd-5_family- 1405 CAGGAAAGGTTAAGCGATCTGGCAGTTATT-TCTATAGA 1442 i ivvii i - i - v Zaphod#DNA/hA 3620 CAAGAAAGGTTGTCTAATTTGGCA-TTACTGTCAATAGA 3657 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 11, Kimura (unadjusted) = 32.85 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.00 (2 / 2) 251 23.29 4.11 0.00 rnd-5_family-3672#LINE/CR1 51 123 (123) CR1-L3B_Croc#LINE/CR1 2793 2868 (409) m_b23s551i7 rnd-5_family- 51 GAGCAACAAAAATGA---GGGGGCTGGAGGGATTGACTTATGAGGAAAGA 97 v --- i ii v v iiiv i CR1-L3B_Croc# 2793 GAGCCACAAAAATGATTCGAGGGCTGGAGAAAATGCCTTACAGTGAGAGA 2842 rnd-5_family- 98 TTAAAAGAGCTAAATATGTACAGCTT 123 i v v v vi CR1-L3B_Croc# 2843 CTTAAAGAGCTCAATCTGTTTAGCTT 2868 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.20 CpG sites = 9, Kimura (unadjusted) = 28.20 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.01 (1 / 72), avg. gap size = 3.00 (3 / 1) 247 27.99 2.91 2.91 rnd-5_family-3672#LINE/CR1 51 153 (93) X21_LINE#LINE/CR1 15 117 (167) m_b23s551i8 rnd-5_family- 51 GAGCAACAAAAATGA---GGGGGCTGGAGGGATTGACTTATGAGGAAAGA 97 i --- i iii ivvv ? i X21_LINE#LINE 15 GGGCAACAAAAATGATACGAGGATCGGAGGATAAGACNTATGAGGAGAGA 64 rnd-5_family- 98 TTAAAAGAGCTAAATATGTACAGCTTGGCTAAGCAACGGCNAGGGATGGG 147 i i ii v i i ii i vv vi v ?vi --- X21_LINE#LINE 65 CTGAGGGAGCTAAATTTATATAGTCTAGAAAAGAGAAGGCTCAG---GGG 111 rnd-5_family- 148 GAACAT 153 i X21_LINE#LINE 112 GGACAT 117 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.00 CpG sites = 19, Kimura (unadjusted) = 37.73 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.50 (6 / 4) 495 4.41 0.00 23.61 rnd-5_family-38929#SINE? 1 89 (17) tRNA-Tyr-TAC#tRNA 2 73 (1) c_b23s355i0 rnd-5_family- 1 CTTCGATAGCTCAGTTGGTAGAGCGGAGGACTGTAGGCTTAATTCTCGGG 50 i -------------- tRNA-Tyr-TAC# 2 CTTCGATAGCTCAGCTGGTAGAGCGGAGGACTGTAG-------------- 37 rnd-5_family- 51 GGAATCCTTAGGTCGCTGGTTCAACTCCGGCTCGAAGGA 89 --- i i tRNA-Tyr-TAC# 38 ---ATCCTTAGGTCGCTGGTTCGATTCCGGCTCGAAGGA 73 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 3.01 CpG sites = 3, Kimura (unadjusted) = 4.35 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.19 (17 / 88), avg. gap size = 1.00 (17 / 17) 13 22.55 0.00 0.00 rnd-5_family-6022#Unknown 246 281 (60) (CCCCCTC)n#Simple_repeat 1 36 (0) m_b23s252i2 rnd-5_family- 246 CCCCCTCCCCGATCCCTCCTGCCCCCCCCACCCCCC 281 vv i v i v i (CCCCCTC)n#Si 1 CCCCCTCCCCCCTCCCCCCTCCCCCCTCCCCCCTCC 36 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 2771 0.97 3.87 0.00 rnd-5_family-9166#DNA/TcMar-Tigger 6 315 (1823) MamRep137#DNA/TcMar-Tigger 90 411 (99) m_b23s502i9 rnd-5_family- 6 TAAATAGTGCAGGCGATTC------------CACCCAATGAGCGTATGCC 43 i ------------ i MamRep137#DNA 90 TAAATAGTGCGGGCGATTCTGCCCGCCATTCCACTCAATGAGCGTATGCC 139 rnd-5_family- 44 CCGGAGTGAGCGTGAGATGGGAGACGTGAATCTGCTGTTCCCTCAGTCGG 93 MamRep137#DNA 140 CCGGAGTGAGCGTGAGATGGGAGACGTGAATCTGCTGTTCCCTCAGTCGG 189 rnd-5_family- 94 TCTCAGTTCCCGCGTGCCTCTCATAGTGTGAGCATCTCGCCGCGCTGAGT 143 MamRep137#DNA 190 TCTCAGTTCCCGCGTGCCTCTCATAGTGTGAGCATCTCGCCGCGCTGAGT 239 rnd-5_family- 144 GTGATTCTAGTGTTTAAAGATACGTATTTTTCGTACAACATGGCCCCTAA 193 MamRep137#DNA 240 GTGATTCTAGTGTTTAAAGATACGTATTTTTCGTACAACATGGCCCCTAA 289 rnd-5_family- 194 ACGCAAGCCAACTACTTCATCTGGTGCTCAACCGAAGAAACAGCGATCTG 243 MamRep137#DNA 290 ACGCAAGCCAACTACTTCATCTGGTGCTCAACCGAAGAAACAGCGATCTG 339 rnd-5_family- 244 TTCCAACGCTGGAGGAAAAACTGGCTGTGTTGGACTTATTGAGAGACGGT 293 i MamRep137#DNA 340 TTCCAACGCTGGAGGAAAAACTGGCTGTGTTGGACTTACTGAGAGACGGT 389 rnd-5_family- 294 ATGTCGGTCTCCAACGTGGCGC 315 MamRep137#DNA 390 ATGTCGGTCTCCAACGTGGCGC 411 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.68 CpG sites = 3, Kimura (unadjusted) = 0.98 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (1 / 309), avg. gap size = 12.00 (12 / 1) 2415 31.93 2.82 3.57 rnd-5_family-9166#DNA/TcMar-Tigger 170 1692 (446) Tigger12#DNA/TcMar-Tigger 269 1780 (695) m_b23s502i10 rnd-5_family- 170 TTTTTCGTACAACATGGCCCCTAAACGCAAGCCAACTACTTCATCTGGTG 219 i i iv v v v v i vvvv Tigger12#DNA/ 269 TTCTTTGTGAAAAATGGCCCCGAAAAGAAAGCCAACTGCTAGTGCTGGTG 318 rnd-5_family- 220 CTC-AACCGAAGAAACAGCGA-----TCTGTTCCAACGCTGG-----AGG 258 v v- vi i v i ----- ivvvv ii v ----- v Tigger12#DNA/ 319 ATGGAAGTGAAGAGAAAGTGAAGAAGTCTAAGAAAGTGATGGTTCTTAGC 368 rnd-5_family- 259 -AAAAACTGGCTGTGTTGGACTTATTGAGAGACGGTATGTCGGTCTCCAA 307 - i v i vv v ivv i iiiii v ivi viv Tigger12#DNA/ 369 CAGAAAATAGAAGTTTTGGATAAATTAAAGAGTGGAATGTCGAATTCGGC 418 rnd-5_family- 308 CGTGGCGCGTAAATATGGCCGCAACGAATCTAGCATCCGTGCCATCAAGA 357 v v v vv iivvv i i v v iv i vvi Tigger12#DNA/ 419 GGTGGCTCGGATCTATGATGTGAACGAGTCCACCATACGCTCTATACGGA 468 rnd-5_family- 358 TTCGAGAGAGAGAAATTCGTCAAGCCGTGGCATCAAGTGCTCCAATAACT 407 vv i i i vi v i i vv v i iiv v Tigger12#DNA/ 469 AACAAGAAAAAGCGATTCGTGAAACTGTTTCAGCGAGTGCTCCAGCCAGT 518 rnd-5_family- 408 GCTAAGGTGACGAGCCAGGTGCGTGATAAGACTTTAGTGAAGACTGAAAA 457 v ii vi vvii i v v i iii Tigger12#DNA/ 519 GCAAAAATTGCTCATCAAGTGAGAGATAAAACTTTAGTGAAAGTTGAAAA 568 rnd-5_family- 458 GGCATTAAACTTATGGCTGGAAGACATGAACCGTAAACGTGTGCCTATCG 507 iv v i ivv i i v v v ii v v Tigger12#DNA/ 569 GGCGGTTAACTTGTGGTGTGAGGATATGCACAGGAAACACGTGACTCTCG 618 rnd-5_family- 508 ATGGCAACACGTTGCGAGAAAAGGCTCTTAGCCTCTACGCGCTGTTC--- 554 i v iii v v i i i ivvv v ivi vv --- Tigger12#DNA/ 619 ACGGAAATGTGATTCGGGAGAAAGCCAGGAGCCTGTACAAACATTTCCGT 668 rnd-5_family- 555 AAACCTCCCGCCGAAGAGGG-AC-AGC-CTTCTGATGAGAAGGAATTCAA 601 i v vv v vi iv i - - i- vv iv ivv ivv i v Tigger12#DNA/ 669 GAAGCAACAGGTGGTGAAGGCACTAGTGCGGCTACTGAACCGACCTTTAC 718 rnd-5_family- 602 AGCCAGCCAAGGTTGGCTTAACAGTTTTAGGAACCGCTTCAACCTCAAAA 651 v v iv i ii v i i v i ivvii vv v Tigger12#DNA/ 719 CGCGAGTAAAGGTTGGTTCGAGAATTTTAAGAAGCGTTTTTCTTTGCATA 768 rnd-5_family- 652 ACGTGCAGACTACTGGTGAAGCTGCATCTGCCAATGAAGAGGCAGCAAAA 701 i v viv v v i v v ii iv v vv v ii Tigger12#DNA/ 769 ATGTGAAGTTAACAGGAGAGGCGGCATCAGCTGACCACGTTGCCGCGGAA 818 rnd-5_family- 702 GC--CTAC-CCCGAACAATTAAAGAAAATCATAGAAGAAAAGGGCTATCT 748 --i v - i --- i iv i i i vv Tigger12#DNA/ 819 GCATTTCCTCCCGAGC---TGAAGAAGCTCATAGAGGAGAAGGGTTATAG 865 rnd-5_family- 749 TCCGGAACAAGTTTTTAATGCTGACGAGACTGGGCTCTTCTGGAAAAAAA 798 v v i i v i i v v vi i Tigger12#DNA/ 866 GCCGGAACAAGTGTTCAACGCAGACGAAACCGGCCTATATTGGAAGAAAA 915 rnd-5_family- 799 TGCCCAACCGCACTTACATTTCGAAATCAGAAAGACAAGCCCCTGGCTTC 848 ivvv v v v v ivvi i ii i vi v v i Tigger12#DNA/ 916 TGCCTTCGCGAACATACATATCCAAGGAGGAGAAGCGAGCATCAGGGTTT 965 rnd-5_family- 849 AAAGCAGCTAAAGACCGTGTGACTGTGTTGTTTTGTGGCAATGCGGCTGG 898 i i i i v vv v vi ii -i Tigger12#DNA/ 966 AAGGCGGCCAAGGACAGACTGACTCTTCTACTTTGTGGCAATGCGGC-AG 1014 rnd-5_family- 899 GCATT-TAATAAAGCCGGGCTTGCTCTACAGGGCTGCAAATCCCCGTGCC 947 v - i v v vv i i v v v Tigger12#DNA/ 1015 GCTTTATGATTAAGCCGGGCTTGCTCTACCGTTCTGCGAACCCCAGGGCA 1064 rnd-5_family- 948 CTAAAAGGCAAGAACAAAAATCTCCTGCCTGTGTTCTGGCAATCAAATAA 997 i ii i i i i i i vi i v Tigger12#DNA/ 1065 TTAAGGGGCAAGAATAAGAACCTCTTGCCCGTATATTGGCAGTCCAATAA 1114 rnd-5_family- 998 AAAGGCTTGGGTGACGGCAGCATTATTTCTGGATTGGTTCCACAAGTGTT 1047 i v ivv i v i i i i i Tigger12#DNA/ 1115 AAAAGCTTGGGTCACGGCGCAACTCTTTTTGGACTGGTTTCATAAGTGCT 1164 rnd-5_family- 1048 TCATTCCGGAGGTCAAGCGGTACCTCGAAGAGAAAGGACTTGACTTTAAA 1097 ii v ii i vi vii ?? i vvvv v iiiv v i Tigger12#DNA/ 1165 TTGTGCTAGAAGTGGAGAAATANNTTGCTTTGCAGAACCTTGAATTTAAG 1214 rnd-5_family- 1098 GTGTTGCTGATCGTAGACAATGCTCCTGGCCACCCTGCGGCA-CTCCGGT 1146 vi i v ?? ? vi v -i i ?i??- v v Tigger12#DNA/ 1215 GTTCTACTCATNNTAGACANTGCGTCGGGCCA-TCTACNANNTCTGCCGT 1263 rnd-5_family- 1147 TTGCGCA--TAACGACGTTGAAGTCGTCTTTCTCCCCCCCAATACCACCT 1194 ? i i-- -- i i ? ? ivi i i i i i v Tigger12#DNA/ 1264 TTNCACGTCTAA--ATGTCGANGTNGCGCTCCTTCCCCCTAATACTATCA 1311 rnd-5_family- 1195 CCATCCTCCAACCTCTCGACCAAGGCGTGATTCGCTG--TTTCAAGGCCA 1242 vv i?i ii ii?i ?i -- ?i--? i---- Tigger12#DNA/ 1312 CGCTCTNTCGGCCTCTCGACCAGANTGNAA--CGCNAGCNTTCAAA---- 1355 rnd-5_family- 1243 CGTACACGA----GGCTTACGTTC-TCACGGATACGTAGCGCTATGGATG 1287 - i ?? ---- ? v v - ii vivi iiv i i i Tigger12#DNA/ 1356 -GTATANNATNTTGNCATACTTTCGTTGCCATCATAAAACGCCATGGATA 1404 rnd-5_family- 1288 CTGATCCCAATCTTAATGTGATGGAGTGTTGGAAGTCCTTCAACATTGCC 1337 vv i? i? i v vvvii i i vvv v --- Tigger12#DNA/ 1405 AAGATCTNAACNTTGATGTCAGCCGATGCTAGAAGAAGTACAACATT--- 1451 rnd-5_family- 1338 GATTGCATCACTTATATTAAACAGGC----AATGGATGCAATCAAGCCTG 1383 i i i v ?vv i v iv ---- ? vii ivi -i Tigger12#DNA/ 1452 GGTTACGTAANGAACATTAAAAAATCCCTTANTGGAGATAGGTAA-TCTG 1500 rnd-5_family- 1384 AAACAGTCAATGCATGTTGGCGAAACC-TATGGAAAGAATGT-GTGAATG 1431 ii v v ? -i i - i - v i- Tigger12#DNA/ 1501 AAATGGTGAATGCTTNTTGG-AAAGCCGTACGG-AAGAAGGCAGTGAATG 1548 rnd-5_family- 1432 ATTTTAAGGGTTTCCCGACCATTGACAAAGAAGTGAAACGCATTGTTCAG 1481 i i ii-- ?v i v i i - i Tigger12#DNA/ 1549 ATTTCAAGGGTTCCTT--CCANAGACGATGAAGTGAAATGCATCGTT-AA 1595 rnd-5_family- 1482 GTGGCCAGGCAAGTGGGTGGTGATGGCTTCGTCGACAT-CCTTGAGGAAG 1530 i? ?v v i i vv i- v i -v? Tigger12#DNA/ 1596 ANGGCNCGGCAAGTGGGTGGTGAAGGTTTTGAGGACACGCATTGAAG-TN 1644 rnd-5_family- 1531 AAATTGAAGAATTAATTGAGAGCCATAGAGAAACATTGACTAACGAAGAG 1580 v ?v v ii ii i i? i ---- v ---- -- i - Tigger12#DNA/ 1645 ATANGGACGAGCTGGTTAAANGTC----AGTAA----GACT--CGGAGA- 1683 rnd-5_family- 1581 TTAGAGGAACTGATAAAATCGTCTACAGAA-GACGAAGATGATGACGACG 1629 ---------- ---- i v - v - i ?v ii i vi Tigger12#DNA/ 1684 ----------TG----AGTCGGC-AAAGAATGGCGAAGNAGACAATGTTG 1718 rnd-5_family- 1630 AACAGGAAGAGCCAGCAAGT-TGGAA--TCTTCATAAATTTGCTGAAGTG 1676 -- i ?v -- i - ?i -- i iv i Tigger12#DNA/ 1719 A--AGAANTAG--AACAAGTCTGNGAGNTCTTCGTAAATTTAGTGAAGCG 1764 rnd-5_family- 1677 TTCCAAGCAGCGAAAC 1692 ?vvv Tigger12#DNA/ 1765 TTCCANTATGCGAAAC 1780 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 250, Kimura (unadjusted) = 43.87 Transitions / transversions = 1.14 (250/219) Gap_init rate = 0.05 (77 / 1522), avg. gap size = 1.26 (97 / 77) 3861 29.87 2.18 2.59 rnd-5_family-9166#DNA/TcMar-Tigger 330 1841 (297) Tigger7#DNA/TcMar-Tigger 473 1978 (514) m_b23s502i11 rnd-5_family- 330 AACGAATCTAGCATCCGTGCCATC---AAGATTCGAGAGAGAGAAATTCG 376 vvi vv i--- ---ii i i Tigger7#DNA/T 473 AACGAATCTTCTATCCGTGAAATTGTGAAGA---AGGAAAAAGAAATTCG 519 rnd-5_family- 377 T-CAAGCCGTGGCATCAAGTGCTCCAATAACTGCTAAGGTGACGAGCCA- 424 - v iiv vii -- ii ii -- v i v - - Tigger7#DNA/T 520 TGCTAGTTTTGCTGTC--GCACCTCAA--ACTGCAAAAGTTACG-GCCAC 564 rnd-5_family- 425 GGTGCGTGATAAGACTTTAGTGAAGACTGAAAAGGCATTAAACTTATGGC 474 i vvi v iv i i v Tigger7#DNA/T 565 AGTGCGTGATAAGTGCTTAGTTAAGATGGAAAAGGCATTAAATTTGTGGG 614 rnd-5_family- 475 TGGAAGACATGAACCGTAAACGTGTGCCTATCGATGGCAACACGTTGCGA 524 v v v v i i ii v Tigger7#DNA/T 615 TGGAAGACATGAACAGAAAACGTGTTCCGATTGACGGCAACGTGTTGCGC 664 rnd-5_family- 525 GAAAAGGCTCTTAGCCTCTACGCGCTGTTCAAACCTCCCGCCGAAGAGGG 574 v i i vi v v -------- iv i v ----i Tigger7#DNA/T 665 CAGAAAGCATTGAGCCTATACG--------AAGACTTCAGC----AAGGG 702 rnd-5_family- 575 ACAGCCTTCTGA--TGAG-------AAGGAATTCAAAGCCAGCCAAGGTT 615 i--- ii --i ------- vv i vv v iv i v Tigger7#DNA/T 703 AT---CCCCTGAAACGAGTGACACCAAGCCATTTACTGCAAGTAAGGGAT 749 rnd-5_family- 616 GGCTTAACAGTTTTAGGAACCGCTTCAACCTCAAAAACGTGCAGACTACT 665 i vv v i iv v iiiv v ii iv i i Tigger7#DNA/T 750 GGTTACACAGATTCAGGAATAGGTTTGGACTGAAAAATATAAAAATTACT 799 rnd-5_family- 666 GGTGAAGCTGCATCTGCCAATGAAGAGGCAGCAAAAGCCTACCCCGAACA 715 v i i i i v vivvi v vi v v v Tigger7#DNA/T 800 GGAGAGGCTGCGTCTGCCGATGAAGAAGCTGCTGCCACATTTCCGGCAGA 849 rnd-5_family- 716 ATTAAAGAAAATCATAGAAGAAAAGGGCTATCTTCCGGAACAAGTTTTTA 765 i i iv v vi i i i v i v ii i i i Tigger7#DNA/T 850 GTTGAAGAAGTTGATTAAGGAGAAAGGATACCATCCAAAGCAAGTCTTCA 899 rnd-5_family- 766 ATGCTGACGAGACTGGGCTCTTCTGGAAAAAAATGCCCAACCGCACTTAC 815 vvi i i i i i iv v i Tigger7#DNA/T 900 ATTGCGATGAAACCGGGCTCTTCTGGAAGAAGATGCCCAATAGAACCTAC 949 rnd-5_family- 816 ATTT-CGAAATCAGAAAGACAAGCCCCTGGCTTCAAAGCAGCTAAAGACC 864 i-ii viiv i- i v v vivi i vvv i v Tigger7#DNA/T 950 ATTCATAAAAGTGCAAAGG-AGGCACCAGGGCATAAAACATGGAAGGACA 998 rnd-5_family- 865 GTGTGACTGTGTTGTTTTGTGGCAATGCGGCTGGGCATTTAATAAAGCCG 914 vv i v v ii v i v v v i i Tigger7#DNA/T 999 GATTAACTCTGGTACTATGTGGCAACGCTGCAGGGCATATGATAAAGCCA 1048 rnd-5_family- 915 GGCTTGCTCTACAGGGCTGCAAATCCCCGTGCCCTAAAAGGCAAGAACAA 964 v iv v i vivi i v i i v ii i Tigger7#DNA/T 1049 GGCGTAGTGTACAGAGCGAAGAACCCACGCGCTCTCAAAAACAAAAACAA 1098 rnd-5_family- 965 AAATCTCCTGCCTGTGTTCTGGCAATCAAATAAAAAGGCTTGGGTGACGG 1014 ivi i ivv v i i v i Tigger7#DNA/T 1099 AAATTATCTGCCCGTGTTCTGGCAACATAATCAGAAAGCGTGGGTGACAG 1148 rnd-5_family- 1015 CAGCATTATTTCTGGATTGGTTCCACAAGTGTTTCATTCCGGAGGTCAAG 1064 viiv i v v v i i i i i v i Tigger7#DNA/T 1149 CCATCTTGTTTATGGAATGGTTCCACCAATGCTTCATCCCAGAAGTGAAA 1198 rnd-5_family- 1065 CGGTACCTCGAAGAGAAAGGACTTGACTTTAAAGTGTTGCTGATCGTAGA 1114 vii i v i ii v v vi ii i vi Tigger7#DNA/T 1199 AAATACTTGGAAGAGGAAGGGTTGGAATTTAAAGTCCTATTAATAATAGA 1248 rnd-5_family- 1115 CAATGCTCCTGGCCACCCTGCGGCACTCCGGTTTGC-----GCATAACGA 1159 v i ---- v i- -----iv i vi Tigger7#DNA/T 1249 CAATGCACCTGGCCATCCTG----AATCT-GTTTGCTATGAAAATGAAAA 1293 rnd-5_family- 1160 CGTTGAAGTCGTCTTTCTCCCCCCCAATACCACCTCCATCCTCCAACCTC 1209 i i i i v i v i v v vv v i i i Tigger7#DNA/T 1294 TGTCGAGGTTGTATTTTTACCTCCAAATACAACCTCATTGCTTCAGCCCC 1343 rnd-5_family- 1210 TCGACCAAGGCGTGATTCGCTGTTTCAAGGCCACGTACACGAGGCTTACG 1259 i i i v v v v i vv v viii Tigger7#DNA/T 1344 TTGACCAGGGCATCATTCGGTTTGTCAAGGCCACATACACCCGCCTGGTA 1393 rnd-5_family- 1260 TTCTCACGGATACGTAGC-GCTATGGATGCTGATCCCAATCTTAATGTGA 1308 ivvv v v - v - v v v i i vi ii i Tigger7#DNA/T 1394 TTTGATCGCATTCG-ATCAGCAATTGATGCAGACCCTAATCTGGACATAA 1442 rnd-5_family- 1309 TGGAGTGTTGGAAGTCCTTCAACATTGCCGATTGC-ATCACTTATATTAA 1357 v i i v vi i - - v v vi i Tigger7#DNA/T 1443 TGCAGTGCTGGAAATCATTCACTATTGCTGA-TGCAATAACATTCATCAA 1491 rnd-5_family- 1358 ACAGGCAATGGATGCAATCAAGCCTGAAACAGTCAATGCATGTTGGCGAA 1407 vvv v v v i v v v v i vii Tigger7#DNA/T 1492 AGCTGCAATGGATGAATTAAAACCAGAAACTGTAAATGCCTGCTGGAAGA 1541 rnd-5_family- 1408 ACCTATGGAAAGAATGTGTGAATGATTTTAAGGGTTTCCCGACCATTGAC 1457 i iv vvi i i ivv i i Tigger7#DNA/T 1542 ACTTATGGAGTGAAGTCGTGAATGATTTTAAAGGCTTCCCGGGGATCGAT 1591 rnd-5_family- 1458 AAAGAAGT---GAAACGCATTGTTCAGGTGGCCAGGCAAGTGGGTGGTGA 1504 ii --- --- ii v ii v i v v Tigger7#DNA/T 1592 GGAGAAGTTAGGAAA---ATCATTCATGCAGCAAGACAAGTTGGTGGAGA 1638 rnd-5_family- 1505 TGGCTTCGTCGACATCCTTGAGGAAGAAATTGAAGAATTAATTGAGAGCC 1554 v v i i v v i v ivv ii Tigger7#DNA/T 1639 AGGATTTGCCGACATGCTTGATGAAGAAGTGGAAGAACATATTGAAGGCC 1688 rnd-5_family- 1555 ATAGAGAAACATTGACTAACGAAGAGTTAGAGGAACTGATAAAATCGTCT 1604 v iii i v i i i i i vi vi i i Tigger7#DNA/T 1689 ATCGAGAAGTGTTAACAAATGAGGAATTGGAAGAACTTGTTGAGTCATCT 1738 rnd-5_family- 1605 ACAGAAGACGAAGATGATGACGACG-AAC--AGGAAGAGCCAGCAAGTTG 1651 i v i v v v - -- i v i vv Tigger7#DNA/T 1739 ACAGAGGAAGAGGAAGATGAAGAAGAAACTGAAGCAGAACCAGCAATGTG 1788 rnd-5_family- 1652 GA-ATCTTCATAAATTTGCTGAAGTGTTCCAAGCAGCG-AAACACTTGAA 1699 - ivi i- i i iiv i- i - i Tigger7#DNA/T 1789 GACATTACCG-AAATTTGCCGAAGTGTTTCAAATTGCACAGACA-TTAAA 1836 rnd-5_family- 1700 TGATTTAATTTCTGAATACGATCCCTCTATGGAACGAAGCCTCAAAATCA 1749 v ivv viv iivv v v i i Tigger7#DNA/T 1837 GGACAAAATTATGGAATACGATCCTCGGATGGAACGCAGCATTAAAGTCA 1886 rnd-5_family- 1750 CACGTAGTATTACGGACGATTTGAGACC---GTATCAAGAAATGTTTGAG 1796 v i vv i v v iv ivi --- i v v ---v v Tigger7#DNA/T 1887 CCCATATGATCACCGAAGGATTACAACCTCTGCAGCAACA---CTTTGAT 1933 rnd-5_family- 1797 CAGCTCAAGAGACAACAGCGACAGTTGCCGATCACCATGTTTTTC 1841 v i v i v ivii i ii v i v i Tigger7#DNA/T 1934 GAGTTAAAAAGAAAGAGACAACAACTTCCGATTACAATGTTCTTC 1978 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.07 CpG sites = 238, Kimura (unadjusted) = 38.85 Transitions / transversions = 1.18 (238/202) Gap_init rate = 0.04 (54 / 1511), avg. gap size = 1.33 (72 / 54) 12 22.59 6.85 4.00 rnd-5_family-9166#DNA/TcMar-Tigger 2030 2102 (36) (ATTACAT)n#Simple_repeat 1 75 (0) m_b23s252i0 rnd-5_family- 2030 ATTATATTTTGCATATGTAC-TCTT---TATTATATACTGTACATTAC-T 2074 i v i - - v --- i i ii i - (ATTACAT)n#Si 1 ATTACATATTACATAT-TACATATTACATATTACATATTACATATTACAT 49 rnd-5_family- 2075 GTATACATTATACATTTATACATATTAC 2102 i - vv v - (ATTACAT)n#Si 50 AT-TACATATTACATAT-TACATATTAC 75 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.33 (8 / 6) 16 13.37 4.65 2.27 rnd-5_family-9166#DNA/TcMar-Tigger 2055 2097 (41) (ATTATAC)n#Simple_repeat 1 44 (0) m_b23s252i1 rnd-5_family- 2055 ATTATATACTGTACA-T-TACTGTATACATTATACATTTATACAT 2097 i i i - - vv - (ATTATAC)n#Si 1 ATTATACATTATACATTATACATTATACATTATACA-TTATACAT 44 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 429 33.70 2.88 2.88 rnd-5_family-10470#LINE/RTE-BovB 21 298 (243) MamRTE1#LINE/RTE-BovB 3271 3548 (264) m_b24s601i0 rnd-5_family- 21 TCAAANGGTGGGACAAGATTCCCANTATCAAAATCCTTAATCGTTGTCGG 70 i ? iii i iv ?i v i ii vi v iv i i MamRTE1#LINE/ 3271 TTAAATGGCAAGACAGGATCACCAACAACGAGGTCCTGGAACGCAGCCAG 3320 rnd-5_family- 71 ATGTCTGGCATTCAAAGC-ATGCTCGTAAAAGCTCAGCTGCGTTGATCTG 119 vivv ii i -i - iviv i v v i iv MamRTE1#LINE/ 3321 TCTACCAGCACT-GAAGCGATGCTCGCCGCAACGCAGCTCCGCTGGGCTG 3369 rnd-5_family- 120 GGCATCTTGTTCGTA---TGGCCGACTCGAGAATACCCAAG--GCCATAT 164 i --- v v --- vi vvv i -- -- ii MamRTE1#LINE/ 3370 GACAT---GTGCGGAGAATGGATGACAGCAGGATACCCAAGCAGC--TGC 3414 rnd-5_family- 165 TTTATGGTCAGCTAAAGCAAGGCACCCGTTCTCATGGTGGCCGGTACAAA 214 v i v i iii v ivvv v v v i v v MamRTE1#LINE/ 3415 TGTACGGTGAGCTGAAGTGGGGCAACCGCAAGCAGGGAGGGCAGAAGAAA 3464 rnd-5_family- 215 CGATATAAAGACACACTGAAGTCAAACTTGAAAGCATGTCAGGTTGACCC 264 v v i i? ivv i v vv - i vv ii iv MamRTE1#LINE/ 3465 CGCTTTAAGGATNCACTGAAGCACAGCTTCAAACAATG-CGGCATAGCTG 3513 rnd-5_family- 265 CAG-CAACTGGGAAGCAACAGC-CCACGACAGAGCA 298 ii - vi i -v - v MamRTE1#LINE/ 3514 TGGACTGCTGGGAAACAACAGCAGCA-GACAGACCA 3548 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 48, Kimura (unadjusted) = 46.48 Transitions / transversions = 1.12 (48/43) Gap_init rate = 0.05 (13 / 277), avg. gap size = 1.23 (16 / 13) 23 20.30 0.00 0.00 rnd-5_family-10967#Unknown 143 187 (2041) (A)n#Simple_repeat 1 45 (0) m_b24s252i8 rnd-5_family- 143 AAAAAATAACAAAACAAAACAAAAAGAACAAAAGAAAAAGAAAAA 187 v v v v i v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 307 22.76 8.75 1.16 rnd-5_family-11495#DNA/PIF-Harbinger 1 80 (0) MER133B#DNA/PIF-Harbinger 17 102 (13) m_b24s502i0 rnd-5_family- 1 GGCCAAATTCTGCTCTCGGTTACACCGGTGCAACCTCCC-------TCAG 43 i v i vv i - ------- i MER133B#DNA/P 17 GGCCAAATTCTGCCCTCGGATACGCGCGCGCAA-CTCCCATTGAAGTCAA 65 rnd-5_family- 44 TAGGGGTTGCACCGGTGTAACTGAAAGGAGAATTTGG 80 i i ii vv i v ii v MER133B#DNA/P 66 TGGGAGTTGTGCGTGCGTATCTGAGGGCAGAATTTGG 102 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.62 CpG sites = 11, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (2 / 79), avg. gap size = 4.00 (8 / 2) 16 19.24 3.39 5.17 rnd-5_family-1150#Unknown 294 352 (150) (CCGCCT)n#Simple_repeat 1 58 (0) m_b24s252i7 rnd-5_family- 294 CCG-CTCCAGCC-CCTCCTCCGGGTCCCGCTCTCGCCTCCGCCCTCCGCC 341 - - - v vv vv - - (CCGCCT)n#Sim 1 CCGCCTCC-GCCTCCGCCTCCGCCTCCGCCTC-CGCCTCCG-CCTCCGCC 47 rnd-5_family- 342 CACGCATGCGC 352 iv v v (CCGCCT)n#Sim 48 TCCGCCTCCGC 58 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 25 7.92 5.17 3.39 rnd-5_family-1158#LTR/DIRS 1407 1464 (71) (AAAT)n#Simple_repeat 1 59 (0) m_b24s252i6 rnd-5_family- 1407 AAATAAAGTAAATAACT-AA-AAATAAAGAAA-AAATAAATAAAGTAAAT 1453 - v - - v - - (AAAT)n#Simpl 1 AAATAAA-TAAATAAATAAATAAATAAATAAATAAATAAATAAA-TAAAT 48 rnd-5_family- 1454 AANGAAGTAAA 1464 ?v i (AAAT)n#Simpl 49 AAATAAATAAA 59 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 270 28.57 3.90 0.00 rnd-5_family-13353#DNA/TcMar-Tc2 1432 1508 (360) Kanga1d#DNA/TcMar-Tc2 207 286 (323) m_b24s502i1 rnd-5_family- 1432 CTCGGA---AATGGTAGAAAAATCATTTAGGAAATGCTGTATCAGCAATG 1478 i --- i i iv v v i i v i Kanga1d#DNA/T 207 CCCGGAGACAATAGTGGAGCACTCTTTTAAGAAATGCTGCATCACCAACG 256 rnd-5_family- 1479 CACTCGACGGGTCAGAAGATGATGCCATAT 1508 v i i vv i i i ii i Kanga1d#DNA/T 257 CTCTTGATGGCACAGAGGACGATACTGTGT 286 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.45 CpG sites = 15, Kimura (unadjusted) = 37.76 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.01 (1 / 76), avg. gap size = 3.00 (3 / 1) 286 26.36 0.89 1.80 rnd-5_family-161#LINE/L2 33 144 (0) L2-2_Mam#LINE/L2 96 206 (166) m_b24s601i1 rnd-5_family- 33 GNNCGGGAG-CAGGGCGTTCTCTGCGAGGGCTCCGGGACTCTGGAACTTG 81 ?? i - i i i i ii vi vv vi v i iv L2-2_Mam#LINE 96 GAGCGGAAGACGGGACGTTTTCCGCGGAGGGCCCTCGTTTGTGGAATTCC 145 rnd-5_family- 82 CTCCCCTCCCTTGGTCCGAAATAGCCCGAATTTGGTGACCTTCCGGGCAC 131 v v - i iv v v i v v L2-2_Mam#LINE 146 CTGCCCGCCCT-GGTTCGGCAGAGCCCCAGTTTGCTGACCTTCAGGGCAC 194 rnd-5_family- 132 GCTGCAAAGACAC 144 v - i L2-2_Mam#LINE 195 GGTGC-AAGACGC 206 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 15, Kimura (unadjusted) = 33.67 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.00 (3 / 3) 572 1.56 0.00 0.00 rnd-5_family-17663#SINE/tRNA 1 64 (0) tRNA-Lys-AAA#tRNA 5 68 (8) m_b24s502i2 rnd-5_family- 1 GGCTAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGGGTCCAGGGT 50 v tRNA-Lys-AAA# 5 GGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGGGTCCAGGGT 54 rnd-5_family- 51 TCAAGTCCCTGTTC 64 tRNA-Lys-AAA# 55 TCAAGTCCCTGTTC 68 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 1.58 CpG sites = 0, Kimura (unadjusted) = 1.58 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 273 28.49 6.74 7.89 rnd-5_family-2410#LINE/RTE-BovB 1486 1767 (79) MamRTE1#LINE/RTE-BovB 1967 2245 (1567) m_b24s601i2 rnd-5_family- 1486 AGAGAACCATGCCGTATGATAAAACCAAACCGGGTCTGGTGGCACCAGTC 1535 - -- v ivi i-- ?v i -- v v iii MamRTE1#LINE/ 1967 AGAGAACC-TGCC--AAGATGCGAT--AACNTGGCCT--TCGCTCCAACT 2009 rnd-5_family- 1536 CTAGAAGAAGNAGTTACAGAAG-CATTGAGCAACATGAAAAATAAGAAAG 1584 i v ?vi?i v vv - -- -- i iiv MamRTE1#LINE/ 2010 TTTGAAGAAGTCANCACCGCTGTCA--GAGC--CATGAAGAATGGTAAAG 2055 rnd-5_family- 1585 CTCTCGGCCCCGATGGCATACCAGCAGAAGTATGGAAGTGCCTGGGGCAA 1634 v i v v ii v vv --------- i MamRTE1#LINE/ 2056 CTCTCGGACCTGATGGCATACCTGCTGAGATTTTCAA---------GCAG 2096 rnd-5_family- 1635 GCAGGCGTGAACATATTGANACAACTGTTTAA------TTTCATCAT--- 1675 v v v vvv ii v ? iv iv i------i v --- MamRTE1#LINE/ 2097 GAAGGGGAGACGCTGCTTAGACGTCTGCATAGGCTTTTCTTCAGCATATG 2146 rnd-5_family- 1676 GAGGACTGAGAAGATGCCTGGAG------AAAGA-GCACATTGGTACCA- 1717 v i i i - v ------ - - i ivi i - MamRTE1#LINE/ 2147 GAGTACCGAGGAAATGCC-GCAGGATTTCAAAGATGC-CACTATCATCAC 2194 rnd-5_family- 1718 -ATATTTAAGAGAAAAGGAGACGTACAAGACTGTGGTAACTACCGCGGCA 1766 - v i ii v viv vvv i i i MamRTE1#LINE/ 2195 CATCTTCAAGAAGAAAGGCGAGAAAGCTGACTGCGGCAACTATCGCGGCA 2244 rnd-5_family- 1767 T 1767 MamRTE1#LINE/ 2245 T 2245 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 37, Kimura (unadjusted) = 36.95 Transitions / transversions = 1.00 (37/37) Gap_init rate = 0.10 (29 / 281), avg. gap size = 1.41 (41 / 29) 2046 8.49 6.85 9.57 rnd-5_family-3363#LINE/CR1 1 482 (122) CR1-16_AMi#LINE/CR1 289 758 (93) m_b24s551i0 rnd-5_family- 1 AGAATTGCAAAANGAGTGGAGATGTGAAGAGTTGAAAT---TTTGA--TT 45 i ?v ---- i v v --- i-- CR1-16_AMi#LI 289 AGAATTACAAAATTAGTGGA----TGAAGGGATGCAATATATTTGGATTT 334 rnd-5_family- 46 TAGTAAAGCATTTGNTACAGTGNCTCAANANANCTTACTCNCAAAATTAA 95 ? ? -? ? ? ------ CR1-16_AMi#LI 335 TAGTAAAGCATTTGATACAGTGTCTCA-CATATCTTA------AAATTAA 377 rnd-5_family- 96 TTGAAACTGNCCCTGGAAACGAG----------TGGATTGAAAACTGGCT 135 v i ? i- v i ---------- i CR1-16_AMi#LI 378 TTCAAATTGGCT-TGGATATGAGCACTGTCACGTGGACTGAAAACTGGCT 426 rnd-5_family- 136 GAAGGACCATAAACAAAGGNGAATGATAAATGGCAANGTATTGAGTT-GG 184 i ?v i ? i - CR1-16_AMi#LI 427 GAAGGACCGTAAACAAAGGGTAATGATAAACGGCAATGTATCGAGTTGGG 476 rnd-5_family- 185 GGGAGGTGTCTAGTGGATGCCGCAGGGATCGGNGTTAGGTCCGGTCTTAT 234 - i i i - ? i CR1-16_AMi#LI 477 GGGAGGTGTCTAG-GGGTACTGCAGGGAT-GGTGTTAGGTCTGGTCTTAT 524 rnd-5_family- 235 TTAACATCTTCATTAATGATCTGGAAGAGGGGGGGAAGACCTCCANGTTA 284 i vi v ---v ? CR1-16_AMi#LI 525 TTAACATCTTCATTAATGATCTGGAAGAGGGAGTAAACA---GCACGTTA 571 rnd-5_family- 285 ATAAAATTCGCAGAAGAT---------------GTTGCAAACACCAGTGA 319 i v --------------- CR1-16_AMi#LI 572 ATGAAATTCGCAGATGATACTAAATTGGGAGGAGTTGCAAACACCAGTGA 621 rnd-5_family- 320 GGACAGAGAAATAATACAAAGGGACCTAGAGAGGTTAGAAATACGGAAAG 369 i --- - CR1-16_AMi#LI 622 GGACAGAGAAATAATACAAAGGGACCTAGAGAGATTAGAAA---GGAAA- 667 rnd-5_family- 370 TAGCAAAACGAAAGATTCANCTTGGAAAAATGCAAGCTAATA--CATCTG 417 i i -- - ? - -- - CR1-16_AMi#LI 668 TAACAAAATG--AGATT-AACTTGGAAAAATGC-AGCTAATATTCA-CTG 712 rnd-5_family- 418 AGGGAGACAGNAAACCNAGACAGATGGTGGAAGGAGGCGGGAACCTGGGA 467 i i ------ v ? --------- i---- i ? i CR1-16_AMi#LI 713 GGGAA------AATCCAA---------TGGAAGA----GGAAACNTGGAA 743 rnd-5_family- 468 AGNAGTAATGCCAGA 482 ? v? CR1-16_AMi#LI 744 AGCAGTAATGANAGA 758 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.69 CpG sites = 25, Kimura (unadjusted) = 9.43 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.11 (51 / 481), avg. gap size = 1.53 (78 / 51) 358 16.13 3.23 0.00 rnd-5_family-3436#SINE/5S-Deu-L2 15 76 (112) AmnSINE2#SINE/tRNA-Deu 182 245 (113) m_b24s502i3 rnd-5_family- 15 TGGCTGTTC--CGTAGCCATTAAANATCTCATGGNACTTTTCNTAAGAGC 62 v i -- i v ? i i ?i ? i AmnSINE2#SINE 182 TGTCTGCTCTGCGTGGACATTAAAGATCCCGTGGCGCTTTTCGTAAGAGT 231 rnd-5_family- 63 AGAGATTTGCCCCG 76 i i AmnSINE2#SINE 232 AGGGGTTTGCCCCG 245 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.75 CpG sites = 8, Kimura (unadjusted) = 19.95 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 61), avg. gap size = 2.00 (2 / 1) 349 15.09 1.15 8.64 rnd-5_family-3436#SINE/5S-Deu-L2 98 184 (4) AmnSINE1#SINE/5S-Deu-L2 411 491 (84) m_b24s502i4 rnd-5_family- 98 CTCTTGTGCAGCGT-GCCGTGTGCCAGTTATCCACCGGCTGCTGCCCTCC 146 v i i - i i i- --- v i i vi AmnSINE1#SINE 411 CTGTTGTGTAGTGTTGCTGTGCGCT-GTTA---AACAGCTGCCGCGTTCC 456 rnd-5_family- 147 ACCCCAGAGGTGGCTGCATTTCAGTGGTGCTGGATGAA 184 --- i AmnSINE1#SINE 457 ACCCCAGAGGTGGCTGCATTTCAGTGG---TGGGTGAA 491 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.21 CpG sites = 9, Kimura (unadjusted) = 17.17 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.09 (8 / 86), avg. gap size = 1.00 (8 / 8) 13 14.69 0.00 0.00 rnd-5_family-597#DNA/PIF-Harbinger 859 889 (193) (AGAAAA)n#Simple_repeat 1 31 (0) m_b24s252i5 rnd-5_family- 859 AGATACAGAAAGAGAAAAAGNAATAGAAAAA 889 v v i ? v (AGAAAA)n#Sim 1 AGAAAAAGAAAAAGAAAAAGAAAAAGAAAAA 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 13 20.15 0.00 2.86 rnd-5_family-6353#Unknown 131 166 (922) (CAG)n#Simple_repeat 1 35 (0) m_b24s252i4 rnd-5_family- 131 CAGCAGCTGCAGCAGCAAAACCTGGAGTCAGCAGCA 166 v iv v v v - (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGCAG-CAGCAGCA 35 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 14 17.72 0.00 0.00 rnd-5_family-6604#Unknown 224 255 (328) (GGCGGT)n#Simple_repeat 1 32 (0) m_b24s252i3 rnd-5_family- 224 GGCGGTGCCGGTGGCGGTGGCATTAGCGGCGG 255 v iv i i (GGCGGT)n#Sim 1 GGCGGTGGCGGTGGCGGTGGCGGTGGCGGTGG 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 11 26.92 0.00 2.04 rnd-5_family-67#LTR/DIRS 372 421 (1733) (GCTCCG)n#Simple_repeat 1 49 (0) m_b24s252i2 rnd-5_family- 372 GCTCCGACTGTCGATTCCTGCTCCGGTTTCGGNTCCATCTTCGGNTCCGG 421 i -i ii v i i ? iv i ? (GCTCCG)n#Sim 1 GCTCCGGCT-CCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGG 49 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 229 10.00 0.00 0.00 rnd-5_family-6779#Unknown 3 32 (172) Chompy-6_Croc#DNA/PIF-Harbinger 951 980 (0) m_b24s502i5 rnd-5_family- 3 GGTGCCTAAGTCCCCTTGTGAATCTAGCCC 32 i i i Chompy-6_Croc 951 GGCGCCTAAGTCCCTTTGTGGATCTAGCCC 980 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 7.54 CpG sites = 3, Kimura (unadjusted) = 11.16 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 262 24.19 4.17 5.26 rnd-5_family-703#DNA/PIF-Harbinger 989 1084 (979) C MIR1_Amn#SINE/MIR (45) 185 91 m_b24s601i3 rnd-5_family- 989 CAAAGTACTTTAGAACACAAAGGA----ACTAGCATAAACCATGTTTTAA 1034 i ----- ---- v v v v vii v C MIR1_Amn#SINE 185 CAAAGCACTTTA-----CAAAGGAGGTCAGTATCATTATCCCCATTTTAC 141 rnd-5_family- 1035 AAATGGGGAAACTGAGGTATGGTGCAGTGTAATGAGTTTTCCAAGGTCAC 1084 i i i?ii v vi ?v i v vi C MIR1_Amn#SINE 140 AGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCAC 91 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 11, Kimura (unadjusted) = 30.26 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.50 (9 / 6) 278 24.57 16.08 4.23 rnd-5_family-703#DNA/PIF-Harbinger 1347 1601 (462) UCON9B#DNA/PIF-Harbinger 639 922 (437) m_b24s502i6 rnd-5_family- 1347 AGATTGCTGGCAGCGTGT-CACAGTTACTTGGGCTGTGACATTGTCTGAA 1395 -- v v - i v i i v --- v i UCON9B#DNA/PI 639 AGATT--TGGCAGCCTTTTCATATTTACTTGGACTGCGAGA---TATAAA 683 rnd-5_family- 1396 --GAATTTGGGGTCCAGGCAGCTCCAAAAAGAAGGTGTTTCCAA--TGAA 1441 -- ii ---ivv i v v i viv -- UCON9B#DNA/PI 684 TCGAATTTGGGGCTC---TCTCTCCAAGAATAAGTTATTTGTTATCTGAA 730 rnd-5_family- 1442 -----ATCTGTCTGNGGATCATGTCTGGGCAAAGTGTTTCCATTGCAGCA 1486 ----- v iv ? viivi ii i i ii i v UCON9B#DNA/PI 731 TAAGTATGTGTTAGTGGATCAGACACGGATAAGGTGTTTCTATTATAACT 780 rnd-5_family- 1487 GTGTGT-TTCGGTGTGTCGTTTACACGG--------TGTTCT---CTCTC 1524 v - v i --i iv -------- i --- iv i UCON9B#DNA/PI 781 GTGTTTGTTAGGTATG--ATTTACATTGTTCTATATTGTTTTATACCGTT 828 rnd-5_family- 1525 TCTC--TCTC---TAATTCATTTG---CACGTT---TGTA-----TCACG 1558 i -- i --- v v --- vi --- ----- UCON9B#DNA/PI 829 TTTCATTTTCGATTACTTAATTTGTTTCTTGTTTTGTGTATTTTGTCACG 878 rnd-5_family- 1559 GTCACTTGTGGGGTTAGTTGTG---GACTTTCTAACTTTGCAACAC 1601 iivi v -- --- i i UCON9B#DNA/PI 879 GTTGGCTGTGGGTTT--TTGTGGTTGACTTTTTAACTTTGTAACAC 922 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.91 CpG sites = 35, Kimura (unadjusted) = 30.71 Transitions / transversions = 1.40 (35/25) Gap_init rate = 0.10 (25 / 254), avg. gap size = 2.12 (53 / 25) 15 13.67 0.00 0.00 rnd-5_family-703#DNA/PIF-Harbinger 1915 1938 (125) (G)n#Simple_repeat 1 24 (0) m_b24s252i1 rnd-5_family- 1915 GGGGGTGGGGGGGAGGGCGGGGGG 1938 v i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 412 12.34 15.56 0.97 rnd-5_family-7118#SINE/U 1 90 (38) U2#snRNA 18 120 (68) m_b24s502i7 rnd-5_family- 1 TGGCTAAGATCAAGTGTAGNACC-------A-CAGTTTAATATCTGATAC 42 ? i ------- - U2#snRNA 18 TGGCTAAGATCAAGTGTAGTATCTGTTCTTATCAGTTTAATATCTGATAC 67 rnd-5_family- 43 GTCCTCTATNCGGGGGACTATATCCT------GCCCTTGCAGCAGGGGGA 86 ? - i v vi ------iiii v i U2#snRNA 68 GTCCTCTATCC-GAGGACAATATATTAAATGGATTTTTGGAGCAGGGAGA 116 rnd-5_family- 87 TGGA 90 U2#snRNA 117 TGGA 120 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.11 CpG sites = 8, Kimura (unadjusted) = 14.11 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (4 / 89), avg. gap size = 3.75 (15 / 4) 1563 12.77 1.43 1.80 rnd-5_family-887#DNA 2 280 (3) UCON8#DNA 658 935 (178) m_b24s502i8 rnd-5_family- 2 TACTATGAAAGGNAT-TAGGGANACTGAAAGNATANATAGAAAACAGNAG 50 ii i ? i- i? v -? ? ii i i i ? v UCON8#DNA 658 TACTGCGAGAGGGACATAGGGGAACTCAAA-CATAAACGGAGAGCGGGAT 706 rnd-5_family- 51 TT-CCTTGCAGTGGCCATATTTGAATACATTTGTTCAAGATAAAAAAGAA 99 - ? i v -i ii v --i v UCON8#DNA 707 TTTCCTTGCANTGGCCACAAT-AAATATGTTTGTTGAAGA--GAAAATAA 753 rnd-5_family- 100 AGGGGAACAGGAAGACATGCATGCCTGTTG--AAAGGAAAGCNTGTTTGT 147 iv v - v --i i ? UCON8#DNA 754 GTGGGAAGAG-AAGACATGCATGCCTGATGTTGAAGAAAAGCCTGTTTGT 802 rnd-5_family- 148 GCCCAATACACTGGAGAAATTGTTCAAGAACAGTTCATCCTTGTGNAAAN 197 i i ? ? ? UCON8#DNA 803 GCCTAATACATTGGAGAAATTGTTCAAGAACAGTTCATCCNTGTGAAAAT 852 rnd-5_family- 198 ATTACCCCTGTAATGCTGCCAAGGTCAGCGNNAGCCTGGGTTATCTGCCG 247 v i ?? v i? v i UCON8#DNA 853 ATGACCCCTGTAATGCTGCCAAGGTCAGTGAGACCTNGGGTGATCTGCTG 902 rnd-5_family- 248 TGTAAGTGCCGGTCACGCAAGTTAAAGCTGCCT 280 ? i UCON8#DNA 903 NGTAAGTGCCGGTCGCGCAAGTTAAAGCTGCCT 935 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.27 CpG sites = 24, Kimura (unadjusted) = 15.08 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.03 (8 / 278), avg. gap size = 1.12 (9 / 8) 268 28.24 9.68 0.99 rnd-5_family-90#DNA/hAT-Charlie 468 653 (208) Charlie7#DNA/hAT-Charlie 571 772 (1843) m_b24s502i9 rnd-5_family- 468 GGNAAGAAAAANGGGAAAT-ACGANGNCAAATATATGATGTATGGTTTTA 516 ?v i ?vv - iv ? ?vi v v vi v Charlie7#DNA/ 571 GGCCAAAAAAATTCGAAATTATCAAGAAGACTATTTGAAATATGGATTTA 620 rnd-5_family- 517 CATCGATTG--ATT--CGA--AACC-------AATTG--TACTGTGTTCT 551 v i i--i -- -- ------- v -- i iii Charlie7#DNA/ 621 CATCCACTATCGTTAACGATGAACCTCGCCCTAAGTGTATATTGTGCCTT 670 rnd-5_family- 552 GAAGTGCTGGCTGCCGAGAGTATGAAGCCTTCGATG-TTGTTGCGACATT 600 ii ii i ivi v v - i - iviiv Charlie7#DNA/ 671 GAGATATTAGCTAATGATAGTATGAAGCCATC-ACGATTAGCAAGACATT 719 rnd-5_family- 601 TAGAAACCAAACATCCGTCACTGAAAGATAAACC-CGAGGATTTTCTTCA 649 i i i ivv vvi i - v vi - Charlie7#DNA/ 720 TAAAAACTAAGCATCCAGAACATGAAGACAAACCTCTACAATTTT-TTCA 768 rnd-5_family- 650 GAGA 653 v Charlie7#DNA/ 769 GCGA 772 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 29, Kimura (unadjusted) = 37.27 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.05 (10 / 185), avg. gap size = 2.00 (20 / 10) 288 36.21 0.43 0.43 rnd-5_family-9054#LTR/ERV 54 286 (2350) HERVIP10F#LTR/ERV1 5116 5348 (2389) m_b24s701i0 rnd-5_family- 54 AACAGGTGTCCCAGGCACTCGGTATACAATGGAAGTTGCATACACCCTGG 103 v v i? i v ii ?vi i i vv v HERVIP10F#LTR 5116 AAAAGCTANCCCAAGCACTAGACATNAGATGGGAATACCATACTCCCTGG 5165 rnd-5_family- 104 AGGCCGCAAAGCTCGGGNCAGGTGGAAAGAATGAATAGAACTCTCAAGGA 153 viv i vvvvv i ?vii i ivii v i HERVIP10F#LTR 5166 CACCCACCTTCATCAGGGAGAGTAGAAAGAATGAACCAGACTCTAAAGAA 5215 rnd-5_family- 154 TACCCTCACTAAACTATGCACAGAGTCTAGTTTAAAGTGG-CTTGATGCG 202 ivv i v i i vv vi v v v ivvi - ivi v HERVIP10F#LTR 5216 CCACTTAACCAAATTAGTCTTAGAGACTCGGTTGCCATGGACCAAATGCC 5265 rnd-5_family- 203 TTACCGCTCGCCCTTACCCGCATTCGAAGGGCCCCACGTAAGGGTCTTAA 252 - vv i vvivv v i vv ? v i i v ii HERVIP10F#LTR 5266 TT-CCTATTGCCCTGTTGAGAATCCGAACTGCCCCNCGGAAAGATATTGG 5314 rnd-5_family- 253 GCTTTCACCATTTGAACTGGTCTTTGGGTTCCCT 286 v ? v v v iv v v i v HERVIP10F#LTR 5315 CCTNTCCCCTTATGAGATGCTCTATGGATTGCCT 5348 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 51.27 CpG sites = 35, Kimura (unadjusted) = 51.27 Transitions / transversions = 0.71 (35/49) Gap_init rate = 0.01 (2 / 232), avg. gap size = 1.00 (2 / 2) 290 27.47 1.09 1.09 rnd-5_family-9054#LTR/ERV 59 150 (2486) HERV17#LTR/ERV1 6298 6389 (2237) m_b24s701i1 rnd-5_family- 59 GTGTCCCAGGCACTCGGTATACAATGGAAGTTGCA-TACACCCTGGAGGC 107 i ii v i ivv v i - i i - HERV17#LTR/ER 6298 GTATCCCAGGCGTTAGGCATACAATATCACTTACACTGCGCC-TGGAGGC 6346 rnd-5_family- 108 CGCAAAGCTCGGGNCAGGTGGAAAGAATGAATAGAACTCTCAA 150 i vv i ?v i v i i iii v HERV17#LTR/ER 6347 CACAATCCTCAGGAAAAGTCGAGAAAATGAACGAAACACTCAA 6389 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 16, Kimura (unadjusted) = 35.98 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.00 (2 / 2) 313 24.00 0.00 0.00 rnd-5_family-9054#LTR/ERV 77 151 (2485) HERV3#LTR/ERV1 5418 5492 (2934) m_b24s701i2 rnd-5_family- 77 ATACAATGGAAGTTGCATACACCCTGGAGGCCGCAAAGCTCGGGNCAGGT 126 v i i v ivv i i ?v i HERV3#LTR/ERV 5418 ATAAAATGGAAGTTACACACAGCCTACCGGCCGCAGAGCTCAGGAAAAGT 5467 rnd-5_family- 127 GGAAAGAATGAATAGAACTCTCAAG 151 iv v iv i v HERV3#LTR/ERV 5468 GGAGCGCATGAACCGGACACTCAAG 5492 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 9, Kimura (unadjusted) = 29.66 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 1004 26.37 1.95 2.81 rnd-5_family-9054#LTR/ERV 1830 2188 (448) HERVE#LTR/ERV1 7160 7515 (298) m_b24s701i3 rnd-5_family- 1830 GAGTGGCCCCCTGAGAGAATTATAAAGCATTATGGTCCAGCTACATGGAA 1879 i i i ?v i v v i i- HERVE#LTR/ERV 7160 GAGTGGCCCCCTGAAAGGATCATNCAGTATTATGGGCCTGCCACATGGG- 7208 rnd-5_family- 1880 TCCTAATGAGTGGATCTCAGGGGCA-AGGGAGCCC--ATTTACAACTTGA 1926 - vi - -i -- v v - vv i -- i vvi v HERVE#LTR/ERV 7209 -CACAA-GA-CGG--CTCATGGGGATACCGAACCCCCATCTACATGCTCA 7253 rnd-5_family- 1927 ATCGGATAATTAGGCTGCAAGCCATCTTAGAAATAATAACTAATCAGAC- 1975 v vv i i i v v i - HERVE#LTR/ERV 7254 ATCGGATCATACGGTTGCAGGCCGTCTTAGAAATAATTACTAATGAAACT 7303 rnd-5_family- 1976 GGCTGCAGCTCTTGA-TCTTTTGGCCGATCAGTCCACTCAGATGAGGAAT 2024 v - - - v i iviv ivvv i i HERVE#LTR/ERV 7304 GGCAG-AGCT-TTGACTGTTTTAGCTTGGCAAGAAACCCAAATGAGGAAT 7351 rnd-5_family- 2025 GTGCTCTACCAGCACCATCTAGTTCTTGATTATTTGCTGGCAGAGGAAGG 2074 ivv i v iviv i iii v i i i i vv HERVE#LTR/ERV 7352 GCTATCTATCAGAATAGACTGGCCTTAGACTACTTGCTAGTAGCTGAAGG 7401 rnd-5_family- 2075 GGGAATNTGTGCAAAATTAAACNAATCTAATTGCTGTTTACAAATAGATG 2124 i i ? v v ?v v i ii i HERVE#LTR/ERV 7402 AGGAGTTTGTGGAAAATTTAACTTAACCAATTGCTGCCTACAAATAAATG 7451 rnd-5_family- 2125 ATAATGGAAAGGCGGT--AAAACAGCTAACAAAAGAAATGAGGAAGCTAG 2172 v v v i -- -- iiv ii v vi v i HERVE#LTR/ERV 7452 ATCAAGGACAGGTGGTTAAAAACA--TAGTCAGGGACATGACAAAGGTGG 7499 rnd-5_family- 2173 CCCATGTCCCGGTCCA 2188 v v v v HERVE#LTR/ERV 7500 CACATGTGCCTGTACA 7515 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.31 CpG sites = 46, Kimura (unadjusted) = 33.17 Transitions / transversions = 1.00 (46/46) Gap_init rate = 0.04 (15 / 358), avg. gap size = 1.13 (17 / 15) 722 11.71 0.00 0.00 rnd-5_family-915#SINE/tRNA 1 111 (48) LFSINE_Vert#SINE/tRNA 270 380 (79) m_b24s601i4 rnd-5_family- 1 AGACTGAACTACCCTTTCATCCCTAGAGGTGGTCCCTCCAGANCAGGGCT 50 i i i i? i LFSINE_Vert#S 270 AGACTGAACTACCCTCTCACCTCTAGAGGTGGTCCCTCCAGGTCAGGGTT 319 rnd-5_family- 51 GAAGCACGTTGGCGGGGCAGTGTGGGGAAGCTTGCACTGCTGCTGTCCGT 100 i i i i LFSINE_Vert#S 320 GAGGCACATTGGCGGGGCAGTGTGGGGAAGCTTGCACTGCCGCTGCCCGT 369 rnd-5_family- 101 GCTAGGCCCGT 111 ivi i LFSINE_Vert#S 370 GCTGTACCTGT 380 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 12.30 CpG sites = 12, Kimura (unadjusted) = 13.35 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.0 (0 / 0) 1215 12.55 4.23 15.77 rnd-5_family-9419#DNA/Kolobok 4 334 (5) UCON4#DNA/Kolobok 181 478 (0) m_b24s502i10 rnd-5_family- 4 TTTTA-GCTCCCTTTGCTGGCTCTGCGGCAGCAGTTAATTGA-GCACGCC 51 i- ii i i i - v i i UCON4#DNA/Kol 181 TTTTGTGCTCCCCCTGCTGGCTCTGCAGCAGCAGTTAACTAACGAACACT 230 rnd-5_family- 52 CAGTTCCCAGAGCTGTGCTGACATCATCCGTGATGCTGGTGCACAAACAA 101 --i vi ---- UCON4#DNA/Kol 231 --ATTCCCAGAGCTGTGCTGACATCATCGATGATGCTGGTGC----ACAA 274 rnd-5_family- 102 AGATGTTCTTGGCATGATGCNCTGCTANAGAAGTTGAAGCTGTTGTAAAA 151 ------------------------i ?i ------------- UCON4#DNA/Kol 275 A------------------------CAAGGAAGT-------------AAA 287 rnd-5_family- 152 CAACAAAGCAGNCATGTTAATTTCAGCTCCATT-CAAANNCAGAGAGAAA 200 v -- ? -v ?? i - UCON4#DNA/Kol 288 CAAAAAA--AGCCATGTTAATTTCAGCTCCATTAGAAACACAGGGA-AAA 334 rnd-5_family- 201 ANATCANCGTTTGCCAAATGGGAACAGACGAAATCAGTA-GGAAAGAAA- 248 ? ?i i vi i i - - UCON4#DNA/Kol 335 AAATCAATGTTTGCCAAATGGAAAAGGACAAAATCGGTAGGGAAAGAAAT 384 rnd-5_family- 249 TGTATTTTCAAGCTTCTAAGAGGGTATTACAAACAAAGGAGGGGAAAA-- 296 v v i v -- UCON4#DNA/Kol 385 TTTATTTTCAAGCTTCTAAGAGGGTATTACAAACAATGGAGAGTAAAAAN 434 rnd-5_family- 297 ------TGAACACCATACCAAATTATTTTGACAGTG-CCTTTTAA 334 ------?i v i vv v -i - i UCON4#DNA/Kol 435 AAAAATNAAAAACTATAAAAAAGTA-CTTGACAGTGTCCCTTTAA 478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.60 CpG sites = 23, Kimura (unadjusted) = 14.01 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.17 (55 / 330), avg. gap size = 1.11 (61 / 55) 258 31.31 0.00 1.74 rnd-5_family-9864#LINE/CR1 618 734 (2733) C X6B_LINE#LINE/CR1 (17) 1055 941 m_b24s601i5 rnd-5_family- 618 GACCCAGCCAGGTGACCATCTTATGCAGAAAAGAATGAAATTTGAAAGGC 667 vvv i i v vvvi v i vviv C X6B_LINE#LINE 1055 GACCCCTGCAGGCGATCAGCTTATGCCCTGAAGCATGAGATTTGATTACC 1006 rnd-5_family- 668 CTTACAGTTAGACCCCAGTGTTGGAAATGTTACTGCTGGTCATACAGTTN 717 iv- viiv vvii iv i i? v i ? C X6B_LINE#LINE 1005 CTTATC-TTAGCTTGCATAACTACAAATGTTATTANTGGTCATAAAATTA 957 rnd-5_family- 718 CCCAATCTCCTTTTAAA 734 i i- i i C X6B_LINE#LINE 956 TCCAG-CCCTTTTTAAA 941 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 18, Kimura (unadjusted) = 42.08 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 29 15.63 1.75 10.48 rnd-5_family-9864#LINE/CR1 922 1035 (2432) (TATTT)n#Simple_repeat 1 105 (0) m_b24s252i0 rnd-5_family- 922 TATTNTTAATTTTATTTCTAGGTTATTTTTATTTTAGATTA-CTTATGTT 970 - - - vv - vv -i v (TATTT)n#Simp 1 TATT-TT-ATTTTATTT-TATTTTA-TTTTATTTTATTTTATTTTATTTT 46 rnd-5_family- 971 -TTTTATTGTTTATTGTATTNTATGTGTGCATTTTAAAATTATTTAAATT 1019 - - - v ? - - -i - vv -v (TATTT)n#Simp 47 ATTTTA-T-TTTATTTTATTTTAT-T-T-TATTTT-ATTTTATTT-TATT 89 rnd-5_family- 1020 TTATTGTATTTCATTT 1035 v i (TATTT)n#Simp 90 TTATTTTATTTTATTT 105 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.12 (13 / 113), avg. gap size = 1.00 (13 / 13) 419 31.17 0.00 0.00 rnd-5_family-9864#LINE/CR1 1272 1425 (2042) Plat_L3#LINE/CR1 1215 1368 (2205) m_b24s551i1 rnd-5_family- 1272 ATTGGAGGCAATTTCTAATTTCAGAAGGTGGAGAAAGCTACTGGGGGAGA 1321 i i iv v v i i i v v i v Plat_L3#LINE/ 1215 ATTGGGGACAATTTCCTAGTGCAGAAAGTAGAGGAATCAACTAGGGCAGA 1264 rnd-5_family- 1322 GGCTGTTGCAGATTTGATTTTGATAAATAGGGAGGAACGGGTTGAGAATC 1371 v iv viv i v iv ii i ivi i i Plat_L3#LINE/ 1265 TGCCCTTCTTGATTTGATTCTTACTAACGGGGAAGAATTAGTCGAGGATC 1314 rnd-5_family- 1372 TGAAAGTGGAAGGCAGCTTGGGTGAAAGTGATCATGAAATTATGGAGTTC 1421 i i v v i i v i i ii i v v vi Plat_L3#LINE/ 1315 TAAAGGTGGATGGAAACCTTGGTGGAAGCGATCACAAGATGATCGTATTC 1364 rnd-5_family- 1422 ATGA 1425 v Plat_L3#LINE/ 1365 AAGA 1368 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 28, Kimura (unadjusted) = 41.53 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.00 (0 / 153), avg. gap size = 0.0 (0 / 0) 192 20.90 13.43 0.00 rnd-5_family-9864#LINE/CR1 2501 2567 (900) MIR#SINE/MIR 109 184 (78) m_b24s601i6 rnd-5_family- 2501 CCCTCTGTGCGTCAGGTCCC-CGTCTGNAAAGCAGGGATAATAG------ 2543 i v v i - i ? iii i------ MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTAC 158 rnd-5_family- 2544 -CATCTCATGGGG-TGGTGGGAGGAT 2567 -i i i - v v MIR#SINE/MIR 159 CTACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.83 CpG sites = 10, Kimura (unadjusted) = 25.83 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.06 (4 / 66), avg. gap size = 2.25 (9 / 4) 15 22.58 0.00 4.17 rnd-5_family-17356#LINE/L1 433 482 (2994) (TTTTATA)n#Simple_repeat 1 48 (0) m_b25s252i10 rnd-5_family- 433 TTTTATGTTGTATTTTTCATATTTAGATTTTGTACTAATTTATATTTGAT 482 i v v i -v v v - v v (TTTTATA)n#Si 1 TTTTATATTTTATATTTTATATTT-TATATTTTA-TATTTTATATTTTAT 48 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 713 3.70 0.00 0.00 rnd-5_family-18011#tRNA 644 724 (74) tRNA-Ser-TCY#tRNA 1 81 (4) c_b25s355i0 rnd-5_family- 644 GTAGTTGTGGCCGAGTGGTTAAGGCGATGGACTAGAAATCCATTGGGGTC 693 i tRNA-Ser-TCY# 1 GTAGTCGTGGCCGAGTGGTTAAGGCGATGGACTAGAAATCCATTGGGGTC 50 rnd-5_family- 694 TCCCCGCGCAGGTTCAAATCCTGCCAACTAC 724 i i tRNA-Ser-TCY# 51 TCCCCGCGCAGGTTCGAATCCTGCCGACTAC 81 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 0.37 CpG sites = 3, Kimura (unadjusted) = 3.85 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 412 22.70 6.33 2.44 rnd-5_family-18826#SINE/MIR 4 161 (1) MIRc#SINE/MIR 86 249 (19) m_b25s601i0 rnd-5_family- 4 TGCANGGCCTGGGGCAAGCCAGTGTAAC---TCTG--CCTTTGTTTCAAC 48 ii? i v i v - --- -- iv vv MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACT-TAACCTCTCTGAGCCTCAGTTTCCTC 134 rnd-5_family- 49 ATCTAGAAAACGGGGATAATAATATATTACTTANCCACCTCGCAACAGGN 98 iv i iv vv i i? i --- ? MIRc#SINE/MIR 135 ATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTC---ACAGGG 181 rnd-5_family- 99 ATGTT-CATGGA--AGATTAGTTAATGTTTGT-ANAGTGCTTTG-AAGAT 143 v -iiv -- i v v v - ? i - iv MIRc#SINE/MIR 182 TTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACT 231 rnd-5_family- 144 GTAAAGCACTATATAAGT 161 ii i i MIRc#SINE/MIR 232 GTAAAGTGCTATACAAAT 249 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.48 CpG sites = 20, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.06 (10 / 157), avg. gap size = 1.40 (14 / 10) 1773 8.95 3.50 0.00 rnd-5_family-194#Unknown 71 327 (25) UCON31#Unknown 86 351 (102) m_b25s502i0 rnd-5_family- 71 GGCCATCACAGGACCCAGATGCCAAGCTGTGGAAGATATTCTTCCAGCAG 120 v UCON31#Unknow 86 GGCAATCACAGGACCCAGATGCCAAGCTGTGGAAGATATTCTTCCAGCAG 135 rnd-5_family- 121 CAGCATCTGGCTCCTTGGCAGACTCCNCAGGCAGTTGTGCTGGCGGCTCT 170 i ? i UCON31#Unknow 136 CAGCATCTGGCTCCTTGGCAGGCTCCGCAGGCAGTTGTGCTGGCGGCTTT 185 rnd-5_family- 171 GAAGTTGCCTCTGGGTCTGTCACGTGGTTAGGCTGCTAG--------CTG 212 i ii-------- UCON31#Unknow 186 GGAGTTGCCTCTGGGTCTGTCACGTGGTTAGGCTGCTGATGGGCTGTCTG 235 rnd-5_family- 213 GGCTGNCTTGTCCTNCTCGATGCCATTTTTCTTTGACTCACCTTTGATCC 262 ? ? v i i i UCON31#Unknow 236 GGCTGCCTTGTCCTCCTGGACGCCATTTTCCTTTGACTCACCTTTGATTC 285 rnd-5_family- 263 TGAGANATTTGCGCACTGTTATGTGCTTG-GAAAAAGNTCCTGCGCAAAT 311 i? i v vi i - v ?? i i UCON31#Unknow 286 TGAGGAATTTGCGCATTTTTATCCGTTTGAGAATAAGGNCCCGTGCAAAT 335 rnd-5_family- 312 CCCTCTTGAGCTCTCT 327 v vi v ? UCON31#Unknow 336 GCCTCACGAGATCTNT 351 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.23 CpG sites = 15, Kimura (unadjusted) = 9.90 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (2 / 256), avg. gap size = 4.50 (9 / 2) 2520 9.39 0.75 3.62 rnd-5_family-1972#DNA/TcMar-Tigger 1 398 (6) UCON11#DNA/TcMar-Tigger 1 387 (51) m_b25s502i1 rnd-5_family- 1 TACAGTG-AATCCTTCTGTAGGGAATGCCCTNANATATNATAAGCATCGC 49 -? i vi ii v i v ? ? --iii i i iv UCON11#DNA/Tc 1 TACAGTGGNACCCTGTTACAGCGAGTCCCCTGANANA--GCGAACGTTTC 48 rnd-5_family- 50 GTAAAGTCCNTAAGT--CTTTCCANTGTGTTTCAGCGGAGCAAAAANNCG 97 v i ?--- -- ? i ? ii ? - UCON11#DNA/Tc 49 CTGAAGTCCC---GTTNCTTTCCAATGTATTTNAGTAGAGCAAAAACNC- 94 rnd-5_family- 98 CTTGCGTTATAGTGAACAAACTCCCTGTTANAGTGAACAATCACTTGGCA 147 ---- i ii ? i UCON11#DNA/Tc 95 ----CGTTATAGTGAACGAATCCCCTGTTACAGTGAACAATCACTCGGCA 140 rnd-5_family- 148 GCGTAGGTTATTTTAATGGACACATCACTTTAAACTAAGCCTTCACCATC 197 UCON11#DNA/Tc 141 GCGTAGGTTATTTTAATGGACACATCACTTTAAACTAAGCCTTCACCATC 190 rnd-5_family- 198 TGTTCTGCCCTCTAATTACAAATGCAAAAAGAACATAATTCACAATTGCA 247 i UCON11#DNA/Tc 191 TGTTCCGCCCTCTAATTACAAATGCAAAAAGAACATAATTCACAATTGCA 240 rnd-5_family- 248 TCATAANAAAGCTAAGATATAATGCGTGATTTAAATGCATGCGTATGTTC 297 ? - --- i? UCON11#DNA/Tc 241 TCATAAAAAAG-TAAGATATAA---GTGATTTAAATGCATGTNTATGTTC 286 rnd-5_family- 298 TTTATTCAATGCAGCATGCATCTGTTATGTTNTTTTCATGTTTCAGACAC 347 ? i i UCON11#DNA/Tc 287 TTTATTCAATGCAGCATGCATCTGTTATGTTTTTCTCATGTTTCAGGCAC 336 rnd-5_family- 348 AAATCAGGGACGAAACTGCTCTCCCCTGATANANTGAATTCCCTCANACA 397 iiv i i? ? i v ? i UCON11#DNA/Tc 337 AAATCAGGAGGGAAACTGCTCTTCCCTGATGGAGTGAATTTCCTGACATA 386 rnd-5_family- 398 G 398 UCON11#DNA/Tc 387 G 387 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.19 CpG sites = 29, Kimura (unadjusted) = 10.69 Transitions / transversions = 4.14 (29/7) Gap_init rate = 0.04 (16 / 397), avg. gap size = 1.06 (17 / 16) 271 25.67 0.00 7.45 rnd-5_family-2070#Unknown 90 190 (211) UCON5#Unknown 173 266 (169) m_b25s502i2 rnd-5_family- 90 TGCACAGCGGTTTATAAAATTTTAAAGCTAATGGTATAACAAACTCAAAT 139 v v v i v v vi i v i v v v ii UCON5#Unknown 173 TGCTCACCTGCTTAAATATCTCTAAAGCTACTAGTAAAAAATACCTAAAT 222 rnd-5_family- 140 AATGATATTGCAGATGTATCGTAAGTGCATCCTGGGATGAATAAATTATG 189 ---- vi i i--- i i iv UCON5#Unknown 223 A----TATAACAGATGCAC---AAGTGCACCTTGGGATGAATGCATTATG 265 rnd-5_family- 190 G 190 UCON5#Unknown 266 G 266 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 12, Kimura (unadjusted) = 31.51 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7) 538 29.48 5.66 5.44 rnd-5_family-2124#LINE/L2 67 543 (53) UCON86#LINE/L2 9 486 (196) m_b25s502i3 rnd-5_family- 67 ATCCGTATCCTTGACTTTATCTNTTNCGGAACCTTGATCTATNTCCTGTT 116 vi v? v i ?i ?iv -- -------- i UCON86#LINE/L 9 ATCCTCATCCANGCCTTCATCTCCTCTCG--CCTTGA--------CTATT 48 rnd-5_family- 117 GCAATTCCCTCTTC-ATGGTCTTCCTAAATCCCTACTNTCTAAACTTCAG 165 ?i ii - i i i i vi ? i i i UCON86#LINE/L 49 GCANCTCCCTTCTCTATGGCCTCCCCAAGTCCCAGCTCTCCAGACTCCAG 98 rnd-5_family- 166 GGGGCCCAGAATGCTGCAGTCCCTGGTAAATTCTTTCTCTCCAGGAAACG 215 viv iv -- v i ------- i v vv v v vi UCON86#LINE/L 99 CACGTGCAGAATGCTGC--TGCCCG-------CCTTCTCACACGCACAAA 139 rnd-5_family- 216 GAAGC----CCATATACCCTCNCATCCTTNATCACCTTCACTGGCTTCCT 261 i---- i - v i ? i? v v i i i UCON86#LINE/L 140 GAAGTGCGACCACAT-CACCCCCATCCTCAAACAACTCCACTGGCTCCCC 188 rnd-5_family- 262 ATCCATCTCCGAATCTAATTCAAAATTGCNTTCTTTTTCCCCAAAAAACT 311 i i v i i i ?i i v iiii vv UCON86#LINE/L 189 ATTCATTTCAGGATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAAACCCT 238 rnd-5_family- 312 CCCAATNGGCTCACTCTACCTAACTTCCCTGA-CTCATCATCCACCTATT 360 -- ? i ii i v iv i v v - ii - ivi ii UCON86#LINE/L 239 CC--ATGGACTTGCTCCAGCCTACCTCACGGACCTTGTC-TCTCTCTGCT 285 rnd-5_family- 361 CCCTTGTGCA-TTCCTCCAATC-TCTGG--------NCCTCT---TCCCT 397 i viv i- i iv - i --------? --- UCON86#LINE/L 286 CCCCTCCCCGCTCCCTCCGCTCGTCTAGCACCGGCCTCCTCTCTGTCCCT 335 rnd-5_family- 398 ---CATGTTCTCCACGGCTGGGGGTCGC----TCTTTCACTTGTGCTGTC 440 --- iiv - i v vv - ----v i v i v v ii UCON86#LINE/L 336 TCACACAATCT-CGCCGCTGTTGG-CGCGAGAGCCTTCTCCTCTGCAGCT 383 rnd-5_family- 441 CCATCTATCTGGAACTCCCTCTCCTCTCCCTCTAAGCCAC-TTGAGTCGC 489 vv i vv - v vi vv v - i v v UCON86#LINE/L 384 CCTGCCATCTGGAACAGCCT-TCCTGTATCTCTCCGCCTCATCGACTCTC 432 rnd-5_family- 490 TTCCCCTCTTTAAATCTCATCTTAAAACCTTCCTTTTCTCTTTAGTTTAT 539 ivi i i i ? ivivi ii v ii UCON86#LINE/L 433 CATCTCTTTTCAAATCTCATCTNAAAATACATCTTTTCTCCCTTGCCTAT 482 rnd-5_family- 540 GACT 543 v UCON86#LINE/L 483 GCCT 486 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 79, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.46 (79/54) Gap_init rate = 0.08 (36 / 476), avg. gap size = 1.47 (53 / 36) 269 15.69 3.92 0.00 rnd-5_family-2124#LINE/L2 543 593 (3) UCON86#LINE/L2 613 665 (17) m_b25s502i4 rnd-5_family- 543 TGACTCTCTGGAGCGTTTTGTGATACNG--TGTCTGAAGGACGCTATATA 590 i v ii v ? -- v i i UCON86#LINE/L 613 TAACTCTGTAAAGCGTTTTGGGATACAGTTTGTATGAAAGACGCTATACA 662 rnd-5_family- 591 AAA 593 UCON86#LINE/L 663 AAA 665 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.25 CpG sites = 5, Kimura (unadjusted) = 18.25 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 50), avg. gap size = 2.00 (2 / 1) 12 25.14 1.75 5.45 rnd-5_family-21621#LINE/Dong-R4 775 831 (426) (AGA)n#Simple_repeat 1 55 (0) m_b25s252i9 rnd-5_family- 775 AGCAGACAGAAACATAAAAAAAAGAAACAAGAAG-AGAAGATGGCGAAGT 823 v - iv v i i - v - v iv - (AGA)n#Simple 1 AGAAGA-AGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAGAAGAAG- 47 rnd-5_family- 824 ATGAAGAA 831 v (AGA)n#Simple 48 AAGAAGAA 55 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 11 17.44 0.00 5.88 rnd-5_family-25670#Unknown 133 168 (165) (GGGGGA)n#Simple_repeat 1 34 (0) m_b25s252i8 rnd-5_family- 133 GGGTGAGGTGGAGCGGGGCGGAGGCAGGGGGAAGGG 168 v v - v - v i (GGGGGA)n#Sim 1 GGGGGAGGGGGAG-GGGGAGG-GGGAGGGGGAGGGG 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 22 21.37 3.70 3.70 rnd-5_family-2679#LTR/DIRS 1143 1223 (32) (TAAAAC)n#Simple_repeat 1 81 (0) m_b25s252i6 rnd-5_family- 1143 TAAAACTAAAGCTGATACTACTACT-AAACTAACTCT-ACACTAATACTA 1190 i i v vv - vv - v v (TAAAAC)n#Sim 1 TAAAACTAAAACTAAAACTAAAACTAAAACTAAAACTAAAACTAAAACTA 50 rnd-5_family- 1191 AGAACTACTAAAAT-AAACTACTATAAAAACTAA 1223 - -- v - vv iv (TAAAAC)n#Sim 51 A-AACTA--AAACTAAAACTAAAACTAAAACTAA 81 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.07 (6 / 80), avg. gap size = 1.00 (6 / 6) 15 14.95 8.93 3.39 rnd-5_family-2679#LTR/DIRS 1158 1213 (42) (TAC)n#Simple_repeat 1 59 (0) m_b25s252i7 rnd-5_family- 1158 TACTACTACTA-AACTAACT-CTAC-ACTAATACTAAGAACTACTA-AAA 1203 -v - - - v - vv -v v (TAC)n#Simple 1 TACTACTACTACTACT-ACTACTACTACTACTACT-ACTACTACTACTAC 48 rnd-5_family- 1204 TA-AACTACTA 1213 -v (TAC)n#Simple 49 TACTACTACTA 59 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.13 (7 / 55), avg. gap size = 1.00 (7 / 7) 13 26.50 1.59 3.23 rnd-5_family-290#Unknown 89 151 (635) (TCTTT)n#Simple_repeat 1 62 (0) m_b25s252i4 rnd-5_family- 89 TCTNTGCTTTTGTTGGTTTTTAGTTTTGTNTATCTGTCTTTTTCTTTGCT 138 ? v v -v i vv v - v v ii v (TCTTT)n#Simp 1 TCTTTTCTTTTCTT-TTCTTTTCTTTTCT-TTTCTTTTCTTTTCTTTTCT 48 rnd-5_family- 139 TTTC-TTTATTTTC 151 - v (TCTTT)n#Simp 49 TTTCTTTTCTTTTC 62 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 13 13.96 3.03 0.00 rnd-5_family-290#Unknown 466 498 (288) (TCTTC)n#Simple_repeat 1 34 (0) m_b25s252i5 rnd-5_family- 466 TCTCCTNTTCT-TTCCCTTCTCCTGTCTTCTCTT 498 i ? - i i v (TCTTC)n#Simp 1 TCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT 34 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 2434 12.36 3.80 4.46 rnd-5_family-3882#LINE/L2 5 478 (4) X13_LINE#LINE/L2 976 1446 (0) m_b25s551i0 rnd-5_family- 5 CAGCGACGTTGGTTTACCGCATTGTATAAATGTGTTCATAGCTTGGCACC 54 i ii ? ? X13_LINE#LINE 976 CAGCGACATTGGTTTACTACATTGNATAAATGTGTTCANAGCTTGGCACC 1025 rnd-5_family- 55 AGCATATTTATTTTCANTTTTATCCAAGACNGANAGCAAGATGTNCTTCT 104 v ? vi ? ?v - i ? iii X13_LINE#LINE 1026 AGCATATTTATGTTCACTTTTATCCAATGCAGACTGCAA-ATATGCCCTT 1074 rnd-5_family- 105 TGCTCAANCCAGTCTATTAATTTTTAAAGTGCCTGGAGCTAAAACNNACT 154 i i ? - i i ?? X13_LINE#LINE 1075 CGCTCGACCCAGTCTATTAA-TTTTAAAGTGCCTAGAGCCAAAACTGACT 1123 rnd-5_family- 155 AANATGTGGAGGCCAGC-TTGGGGGCCTCACGGGTCCCCAANAGCCGGAA 203 ---? - vi - v iiv --- i v ? i X13_LINE#LINE 1124 ---NTG-GGAGGCAGGCTTTTGGGGTTGCA---GCCCCAAACAGCTGGAA 1166 rnd-5_family- 204 TAAGCACTGTACCTGGCTTCTTTAAAATAGGCACCATGCCTGGTTTGGTT 253 ---- - i i v i -?i v v i X13_LINE#LINE 1167 TAAGC----TACCT-GTTCCATTAAAACAGGCACC-NACATTGTCTGGTT 1210 rnd-5_family- 254 TTAAGAAACTTTTGATCCCTCATCTTAAGAAGCCTTGTCAGTGTAAAGAG 303 i i i i? X13_LINE#LINE 1211 TTAAGAAACTTTTAATCCCTTACCTTAAGAAGCCTTGTCAGTGTAAAANG 1260 rnd-5_family- 304 AACTGAAATTGTGACTGCTCAGTGCTGTCTGCTATTTTAGTGAC-GAGTG 352 i i i -- - X13_LINE#LINE 1261 AACCGAAATTGTGACTGCTCGGTGTTGTCTGCTATTTTA--GACTGAGTG 1308 rnd-5_family- 353 TCCTGCANTATATCGTTTGT----------ATTGCGCTGGAGCATGACAG 392 i? i ---------- v ?i i v? iv X13_LINE#LINE 1309 TCCTGCGTTATATTGTTTGTGCGGTACTGAAGTNTGCTGGAGTAANATTG 1358 rnd-5_family- 393 TCTTAT-----TCTAGCTGGGACCCTTCAC-AAAACGAGACGTGCATCTC 436 v v i----- ivv - - i ?i X13_LINE#LINE 1359 TATGACTGCTGTCCCCCTGGGACCC-TCACGAAAACGAGATGTNTATCTC 1407 rnd-5_family- 437 ATGAGGCTATCCCAGTGAGCAAAATTTTTGTAAATAAATAAA 478 i --- X13_LINE#LINE 1408 ATGAGGCTATCCCAGCGAGCAAAATTT---TAAATAAATAAA 1446 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.76 CpG sites = 39, Kimura (unadjusted) = 14.32 Transitions / transversions = 2.29 (39/17) Gap_init rate = 0.05 (26 / 473), avg. gap size = 1.50 (39 / 26) 187 18.17 7.46 1.41 rnd-5_family-3984#Unknown 130 196 (20) AmnSINE1#SINE/5S-Deu-L2 417 487 (88) m_b25s601i1 rnd-5_family- 130 TGCGGTGTTACGCTGCGGCTGTTNCCCAGCTGCC-----CCGCCCCAGAG 174 ii i vv - ?vv ----- i AmnSINE1#SINE 417 TGTAGTGTTGCTGTGCG-CTGTTAAACAGCTGCCGCGTTCCACCCCAGAG 465 rnd-5_family- 175 CTGGCTGCATTTCAGCGCCGGG 196 v i vi AmnSINE1#SINE 466 GTGGCTGCATTTCAGTGGTGGG 487 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.31 CpG sites = 6, Kimura (unadjusted) = 21.31 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.03 (2 / 66), avg. gap size = 3.00 (6 / 2) 251 20.03 1.37 4.23 rnd-5_family-4055#SINE/5S-Deu-L2 64 136 (222) AmnSINE2#SINE/tRNA-Deu 189 259 (99) m_b25s502i5 rnd-5_family- 64 TCCGGGTGGAAGTTAAAGATCCCANGGCGATTTTTGAAAAGAGTAGGGGG 113 i v vi i? v i -v v AmnSINE2#SINE 189 TCTGCGTGGACATTAAAGATCCCGTGGCGCTTTTCG-TAAGAGTAGGGGT 237 rnd-5_family- 114 ATAACTCCGGGTGTCC-TGGCCAA 136 - vi i - i - i AmnSINE2#SINE 238 -TTGCCCC-GGTGCCCTTGGCCGA 259 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.54 CpG sites = 8, Kimura (unadjusted) = 23.97 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 359 9.39 1.49 4.62 rnd-5_family-4055#SINE/5S-Deu-L2 76 142 (216) AmnSINE1#SINE/5S-Deu-L2 264 328 (247) m_b25s502i6 rnd-5_family- 76 TTAAAGATCCCANGGCGATTTTTGAAAAGAGTAGGGG-GATAACTCCGGG 124 ? - i viv - v i - AmnSINE1#SINE 264 TTAAAGATCCCATGGC-ACTTTTCGCAAGAGTAGGGGTGTTAACCCC-GG 311 rnd-5_family- 125 TGTCCTGGCCAACATTCC 142 - AmnSINE1#SINE 312 TGTCCTGGCCAA-ATTCC 328 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.57 CpG sites = 3, Kimura (unadjusted) = 10.21 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 205 13.70 9.43 3.57 rnd-5_family-4259#Unknown 65 117 (37) C L2d2_3end#LINE/L2 (84) 471 416 m_b25s601i2 rnd-5_family- 65 AAGACACAGTCGCTGCCC-CGAAGAGCTTACAATCTA----AGAAGACAA 109 ii v - i i ----i i C L2d2_3end#LIN 471 AAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAA 422 rnd-5_family- 110 GCAACATA 117 -- C L2d2_3end#LIN 421 G--ACATA 416 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.71 CpG sites = 6, Kimura (unadjusted) = 15.71 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.75 (7 / 4) 12 21.77 0.00 9.62 rnd-5_family-4531#Unknown 40 96 (491) (CCCCT)n#Simple_repeat 1 52 (0) m_b25s252i3 rnd-5_family- 40 CCCCCCACCCCACCTGACCCTCCTCTTCCCCTCTCAGGCACCCCTCCCCT 89 i v i v -v - i - --v v (CCCCT)n#Simp 1 CCCCTCCCCTCCCCT-CCCCTCC-CCTCCCCTC-C--CCTCCCCTCCCCT 45 rnd-5_family- 90 CCCCACC 96 v (CCCCT)n#Simp 46 CCCCTCC 52 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 1109 32.74 4.68 2.73 rnd-5_family-4636#LINE/RTE-BovB 572 1469 (6) MamRTE1#LINE/RTE-BovB 299 1213 (2599) m_b25s601i3 rnd-5_family- 572 CTCTGCACACAGGCGGCCTTAGGGTGATGGTCG-TTCTCCACAGACCAGG 620 ? ivii i- i iv - vvi i v ?v MamRTE1#LINE/ 299 CTNTGCGAGTAGGCGGCCC-AGGATATTGGTCGCTTAGTCGCTGANGAGG 347 rnd-5_family- 621 GCAGATATGGAGCTCG-TATCCTCCTGAGGTGACAGAGCAGGCCTTTTTA 669 - vviiivv i -i v v? - v v v v MamRTE1#LINE/ 348 -CAGCAGCACCGTTCGGCAGCGNCCTG-GGTGTCTGAGCAGCCCTGTTTA 395 rnd-5_family- 670 GGCACAGCGCTGCTCTCCCC-AGTCCGGGGAAAGGGGACT-GAAAAGGAA 717 v? - v i - i -- -- ? - vi MamRTE1#LINE/ 396 GGANC-GCGCTGCTCACTCCGAAT--GGGGAA--GGGNCTAGAAAAGGTG 440 rnd-5_family- 718 CCCTAAACACAGCCTGCCCTTTC-----CGTACCTG-----TCAGGCTAC 757 iiv iivi ----- iv ? -----i ii i MamRTE1#LINE/ 441 CCCTAAACGTTGCCTGCCTCGCCAAANTCAAANCTGGCTCACCAGATTAT 490 rnd-5_family- 758 TGCTCCTGGCTGGTCATCCAACTCAGCGGT-CGAAATAAAACAAAGATTC 806 i vi iv -- ii ?iiiv - i ?v i i i vii MamRTE1#LINE/ 491 CGCGTCTGGTGGGT--TTTANTCTTGCGGTGCAAAANCAAATAGAAAACT 538 rnd-5_family- 807 AC-----------AGACTGACNTTTGGGTCATGGAATGTCAGAACTCTTC 845 ----------- i v i ?v v ii i v vi MamRTE1#LINE/ 539 ACCNANNACAAAGAAAATAACCATTGCGTCATGGAACATCAGGACGCTAT 588 rnd-5_family- 846 TTGACAATGACCAAAGA------CCGGAACGAAGAACAGCCCTTATTGCC 889 vi ii i vv v v------ i v i v ii i - MamRTE1#LINE/ 589 GCGATGACGAGAACAGCAGTCGTCCAGAAAGAAGAACGGCACTCGTCGC- 637 rnd-5_family- 890 AAAACACNGAANANGTATA-ANANGCATATAGACATCGCTGCCCTCAGTG 938 --- i-? ?-? vi - ? ? v -i v i v v i MamRTE1#LINE/ 638 ---ACG-TGAAC-TGTCCAGATACGGA-GTCGACATCGCCGCACTGAGCG 681 rnd-5_family- 939 AAACCAGACTCGCTGATGAGTCCCACCTTGAGGACGTGGGAGCAGGCTAC 988 iv ivvv v iiv viii v v ? MamRTE1#LINE/ 682 AAACCAGACTTCCTGATGAAGGACAGCTCACGGAGACAGGTGCCGGNTAC 731 rnd-5_family- 989 ACCTACTACTGGATTGGCAAGGCCAAGGACGAGCCGAGACAGTCAGGGGT 1038 i v v vv ivvvv vvvvvv viv i vv v MamRTE1#LINE/ 732 GCCTTCTTCTGGAGAGGTCTTCCCTCTTCAGAGCGACGGCTCTCAGGCGT 781 rnd-5_family- 1039 AGGGTTCGC---CATACGGTCTGACGTTGCCCGCAAGCTTGACTCG---C 1082 vi v i --- v i -- - i i- ?i -- i i---i MamRTE1#LINE/ 782 CAGCTTTGCAATCAGACAGTC--AC-TTGTCT-CAAGNCT--CCCAAATT 825 rnd-5_family- 1083 TCCCCAAGGGAGTCAATGACCGACTTACGGTGCTCTGCGTAAACTTGTCC 1132 v ii vi ? i v v i iiv vi v v?ii vvv MamRTE1#LINE/ 826 TGCCCAGAGGCATNAGTGACCGTCTGATGACCCTACGCCTACNTCTGAAA 875 rnd-5_family- 1133 AGAGACCAGTACGCCACCATTATCAGCGCCTACGCGCCGACAGTGACTCG 1182 vi i v iv ?i i i v i v v vi vvi MamRTE1#LINE/ 876 CAAAAGCGCTNTGCCACCGTCATCAGCGCATATGCCCCCACCATGACGAA 925 rnd-5_family- 1183 TACAGATGAGATCAAGGAGGCGTTTTATGAAGATCTCAGCAGGGTCATCA 1232 v ivv i iivi i ii i vii iv i MamRTE1#LINE/ 926 TACCGATGAGGAGAAAGAAAGATTCTACAAGGATCTGGACAGACTCATCG 975 rnd-5_family- 1233 GAGGGGTGCCA-CACCAGGACAAACTCATTGTCCTTGGAGACTTTAATGC 1281 v v i - i -v i v i viv i i i MamRTE1#LINE/ 976 CAGCGGTACCAACATC-TGACAAGCTGATCGTCACGGGAGATTTCAACGC 1024 rnd-5_family- 1282 TCGTGTGGGAGCCGACTCTGACATGTGGAGCAGAGTGCTAGGCCATCACA 1331 v v viv iv i v i v i vv v v v? i MamRTE1#LINE/ 1025 ACGTGTCGGCAGCGATGCCGAAACGTGGAGAAAAGTCATCGGACCNCACG 1074 rnd-5_family- 1332 GCACTGGAAGGTCAAACTCCAACAGCCAACTACTTCTCTCCAAGTGTGCC 1381 v i i ii? vv ii i v v v vv i i MamRTE1#LINE/ 1075 GGATTGGAAAGCTNAACAGCAATGGTCTACTCCTGCTCAGCGAATGTGCC 1124 rnd-5_family- 1382 GAGT-TCAATCTCACTATTACCAACACGGTCTTCCAACAGGCCAACAAAA 1430 i i- i- iiv i vi iv viv v i i MamRTE1#LINE/ 1125 AAGCATCAG-CTCGTAATCACCAACACCATCTTCCGCCTACCGAATAAGA 1173 rnd-5_family- 1431 TAA-GACAACATGGATGCATCCCAGNTCAAAACAGTGGTA 1469 v - v i v ? v i i MamRTE1#LINE/ 1174 GAAAGACATCATGGATGCACCCAAGGTCTAAGCAGTGGCA 1213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 149, Kimura (unadjusted) = 45.50 Transitions / transversions = 1.09 (149/137) Gap_init rate = 0.04 (40 / 897), avg. gap size = 1.68 (67 / 40) 403 23.22 0.69 13.28 rnd-5_family-4721#LINE/L2 2 145 (172) L2-1_AMi#LINE/L2 1093 1220 (15) m_b25s551i1 rnd-5_family- 2 TGCATGGGAAGANTCCCTGATAAAAATCTATACAGC-CNTTACTCATATC 50 v i ?ii ivi v iii v v - ? i ----- L2-1_AMi#LINE 1093 TGCTTGGGAGGAGCTCCCCGTAAACATCCGCAAATCACATTATTC----- 1137 rnd-5_family- 51 CTCCTTCAAATCCCTCCTTAGGCTCACCTCTGCCGTGATGCCTNCCTACA 100 - ii v i ---- L2-1_AMi#LINE 1138 -TCCTTCAAATCCCTCCTTAAACTCTCCTTTGCCGTGATG----CCTACA 1182 rnd-5_family- 101 AAACCCAGCTTCTGATCATGGCTAGGCAGATGACGAGCTGTGACC 145 v------- iv i i v v ii v v L2-1_AMi#LINE 1183 AAAA-------CTGACAACGGTTAGGCTGCTGGTGTGCTGAGACC 1220 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.85 CpG sites = 17, Kimura (unadjusted) = 28.27 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.13 (18 / 143), avg. gap size = 1.00 (18 / 18) 419 27.43 0.00 0.00 rnd-5_family-4801#LINE/L2 14 126 (18) L2-2_Mam#LINE/L2 101 213 (159) m_b25s601i4 rnd-5_family- 14 GGAGGCAGGGCATTCTCGGTGGAGGGTCCTTGACTGTGGAACTCGCTCCC 63 i i i i i i v i i i vi i v v L2-2_Mam#LINE 101 GAAGACGGGACGTTTTCCGCGGAGGGCCCTCGTTTGTGGAATTCCCTGCC 150 rnd-5_family- 64 TCTGNTGGTCCGTCAGAGCCCGAGTTTGTTAGCTTTCGGAGCGCGGTGCA 113 iviv? i v v i ii i i i i L2-2_Mam#LINE 151 CGCCCTGGTTCGGCAGAGCCCCAGTTTGCTGACCTTCAGGGCACGGTGCA 200 rnd-5_family- 114 AGGCTCATCTTTT 126 i v L2-2_Mam#LINE 201 AGACGCATCTTTT 213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.33 CpG sites = 22, Kimura (unadjusted) = 36.43 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.0 (0 / 0) 1077 15.21 4.69 5.07 rnd-5_family-4827#DNA/Kolobok 55 331 (268) UCON4#DNA/Kolobok 145 420 (58) m_b25s502i7 rnd-5_family- 55 AGCCATTGTTTNTGTAGTGCCTGGGCAAAAATGATGCTTTGT-TTCGCCC 103 i i v? iiviv ii? i -i v UCON4#DNA/Kol 145 AGCCACTATTTNTGTAGGNCCCACAAAAAAACANTGTTTTGTGCTCCCCC 194 rnd-5_family- 104 TGC-AGTT----ANTTACA---AACCAA-AAAC-CTGTTCCCAGAGCTGT 143 -i i ---- ?ivi --- i -i - i UCON4#DNA/Kol 195 TGCTGGCTCTGCAGCAGCAGTTAACTAACGAACACTATTCCCAGAGCTGT 244 rnd-5_family- 144 NCTGACAATNCTCAGGCCGATGCTGGTGCACAAACAAGGAAGTAAACAAN 193 ? - ?v -- vi ? UCON4#DNA/Kol 245 GCTGACA-TCATC--GATGATGCTGGTGCACAAACAAGGAAGTAAACAAA 291 rnd-5_family- 194 AAACAGCACCATGTTAATTTCAAGCTCCGTTAGAAACGCAGAGGGAGAAA 243 - -- - i i -- i UCON4#DNA/Kol 292 AAA-AG--CCATGTTAATTTC-AGCTCCATTAGAAACAC--AGGGAAAAA 335 rnd-5_family- 244 AATCAATGTTTGCCAAATGGAAAAAGCAGAACAACAT-GGTAGGGAAAGA 292 ---- i v - UCON4#DNA/Kol 336 AATCAATGTTTGCCAAATGGAAA----AGGACAAAATCGGTAGGGAAAGA 381 rnd-5_family- 293 AATGCGTTTTATAAGCTTTCTGAGA-GGCAATGTAAACAA 331 vivv vi - i - i v ii UCON4#DNA/Kol 382 AATTTTATTTTCAAGC-TTCTAAGAGGGTATTACAAACAA 420 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.38 CpG sites = 27, Kimura (unadjusted) = 17.85 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.08 (22 / 276), avg. gap size = 1.23 (27 / 22) 381 31.25 2.22 2.22 rnd-5_family-5408#LTR/Gypsy 1388 1567 (623) MamGypsy2-I#LTR/Gypsy 2376 2555 (1611) m_b25s551i2 rnd-5_family- 1388 TGACGCTTCCCCNTATGGAATAGGAGCAGTAATT--TCACATGTGATGGA 1435 v ? i viiv v iv --i --vi vv MamGypsy2-I#L 2376 TGACGCTTCACCTTACGGTGCTGGAGCTGTGCTTAGCCACA--AAATGCC 2423 rnd-5_family- 1436 AGATCATACTGAAAGGCCTATTGCCTTTGCT--TCTAGATCTCTTACCTC 1483 vii iivi v -- i -- v v vv vv v MamGypsy2-I#L 2424 AGATGGCACTGAGGCACCAATTGC--TTACTACTCAAGAACAATGTCATC 2471 rnd-5_family- 1484 TGCAGAACGNAACTATGCTCAAATTGATAGNGAAGCTCTGAGTTTAGTCT 1533 i i ? i v i i? i viv v vi v MamGypsy2-I#L 2472 TACAGAATGGAACTACGCACAAATTGACAAAGAAGCCCTTGCTGTTATCG 2521 rnd-5_family- 1534 GGGGAGTTAAAGAGTTTTACCAATATCTGTATGG 1567 v i ii ii v v i v i MamGypsy2-I#L 2522 CGGGAGTCAAGAAGTTCCACAACTACCTCTACGG 2555 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 27, Kimura (unadjusted) = 41.90 Transitions / transversions = 0.96 (27/28) Gap_init rate = 0.03 (6 / 179), avg. gap size = 1.33 (8 / 6) 39 29.75 2.70 4.59 rnd-5_family-5452#Unknown 506 727 (316) (CCAGCCC)n#Simple_repeat 1 218 (0) m_b25s252i2 rnd-5_family- 506 CCAGCCCCAAGCCCCC-GCCCCC--CCCCCAG-GACTTCCCCCCTACACA 551 v - -- -vv ivv vi v v (CCAGCCC)n#Si 1 CCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCC 50 rnd-5_family- 552 CACACCCCAACCCCCTGCCCTGAGCCCCTCACGCCACCCAACCCTGACTC 601 vv i v iv - - - i iv -v (CCAGCCC)n#Si 51 CAGCCCCCAGCCCCCAGCCCCCAGCCCC-CA-GCC-CCCAGCCCCCA-GC 96 rnd-5_family- 602 CTGCACCCCCCATGCTCCCAGCCCTGACTCCTGCATCATCCACATCCCCA 651 iv v - i iv -v iv v vi -ii (CCAGCCC)n#Si 97 CCCCAGCCCCCA-GCCCCCAGCCCCCA-GCCCCCAGCCCCCA-GCCCCCA 143 rnd-5_family- 652 -CCCCCTGCCCTGAGCCCCCCGCACCCCAACCCCCTGCCCTGAGTGCTC- 699 - v iv v - i v iv iv i - (CCAGCCC)n#Si 144 GCCCCCAGCCCCCAGCCCCCAGC-CCCCAGCCCCCAGCCCCCAGCCCCCA 192 rnd-5_family- 700 CCCCCCACACCCACACATCCCCAGCCCC 727 v -i v -ii (CCAGCCC)n#Si 193 GCCCCCA-GCCCCCA-GCCCCCAGCCCC 218 Matrix = Unknown Transitions / transversions = 0.72 (21/29) Gap_init rate = 0.06 (14 / 221), avg. gap size = 1.14 (16 / 14) 827 8.48 7.69 1.82 rnd-5_family-6373#Unknown 1 156 (0) UCON70#Unknown 86 250 (6) m_b25s502i8 rnd-5_family- 1 CCTACTCTGCATAATAATGGCTGTCAAGATGGCAGCTTCCTGTTTGATTG 50 ? i v v - i UCON70#Unknow 86 CCTANTCTGCGTCATCA-GACTGTCAAGATGGCAGCTTCCTGTTTGATTG 134 rnd-5_family- 51 TTA-------TTTCATATTAGCACTTNAGAC--TTTAA---TTTTCAGTA 88 ------- iv -i i ? -- ---? ivv UCON70#Unknow 135 TTAATTATTCTTTTTTATTA-TATTTAAGACACTTTAAAAANTTTTTTTA 183 rnd-5_family- 89 CGTGATTTACTCTTCTTTGTAATTAGATGCAGTGATTAGAATATCTTTTA 138 - i UCON70#Unknow 184 -GTGATTTACTCTTCTTTGTAATTAGATGTAGTGATTAGAATATCTTTTA 232 rnd-5_family- 139 TATTACACTGAAGTTTTC 156 v UCON70#Unknow 233 TATTACACTGCAGTTTTC 250 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.55 CpG sites = 7, Kimura (unadjusted) = 9.24 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.04 (6 / 155), avg. gap size = 2.50 (15 / 6) 1656 28.68 2.40 0.73 rnd-5_family-669#LINE/RTE-BovB 4 544 (2) MamRTE1#LINE/RTE-BovB 3258 3807 (5) m_b25s601i5 rnd-5_family- 4 GCCATACTCCGCANCAAANGGCAGGATAAAGTTA--AATAATGAGGTTCT 51 ivi ?i ? i i iii i -- i i i MamRTE1#LINE/ 3258 GCCATACTTAACATTAAATGGCAAGACAGGATCACCAACAACGAGGTCCT 3307 rnd-5_family- 52 GGAACGTAGTCACTCCACAGGGATTGAAGCCATGCTTATCGCATCACAGT 101 i i v i vi v i v iii v i i MamRTE1#LINE/ 3308 GGAACGCAGCCAGTCTACCAGCACTGAAGCGATGCTCGCCGCAACGCAGC 3357 rnd-5_family- 102 TACGCTGGGCTGGTCATGTGTTGAGGATGGACGACACCAGAACGCCAAAG 151 v v iv i i v i ii v MamRTE1#LINE/ 3358 TCCGCTGGGCTGGACATGTGCGGAGAATGGATGACAGCAGGATACCCAAG 3407 rnd-5_family- 152 CGGCTGCGGNATGGCAAACTGAAAGCGGGCAACCGCACAGGAGGCGGCCA 201 i v ? i ii i ivv vivii v v MamRTE1#LINE/ 3408 CAGCTGCTGTACGGTGAGCTGAAGTGGGGCAACCGCAAGCAGGGAGGGCA 3457 rnd-5_family- 202 GAAGAAACGCTTCAAGGACACACTGAAGCATAACTTGAAACAGTGCGACA 251 i i? i i v i i MamRTE1#LINE/ 3458 GAAGAAACGCTTTAAGGATNCACTGAAGCACAGCTTCAAACAATGCGGCA 3507 rnd-5_family- 252 ------TTGACAGCTGGGAGTCGTCAGCAACAGATAGATCACGCTGGCGA 295 ------ v v iv iv i i i vv iv MamRTE1#LINE/ 3508 TAGCTGTGGACTGCTGGGAAACAACAGCAGCAGACAGACCAGCCTGGCAT 3557 rnd-5_family- 296 GCAGTAGTCAACGATGGGGTTACCCAGTTCGAGATTAACCGCCGTATGGA 345 i i ivi i vi i vv i vvv iv vi viiv MamRTE1#LINE/ 3558 GCAGCAATCAGGAACGGGGTGGCTCTTTTTGAGCAAAGGCTTCGGGCCGA 3607 rnd-5_family- 346 TCTTGAGGCACAGAGGCTGAGTCGTAAACAGCGGCAGACTCAGCAGGCAC 395 i vi v vv v i i i v iii v MamRTE1#LINE/ 3608 CCGCGAGTCTAAGAGGCAGAGTCGCAAACAGCGACAGGCTCTGCAAATAG 3657 rnd-5_family- 396 AGACTGTAATCCC--TTCCTCGG-CA-TCGAGCTACCTATGCACTTCATG 441 v i i ii v --v vvv - - --vii v i --vi MamRTE1#LINE/ 3658 CGGCTGCAGCCGCAAATCAAAGGACAGTC--TTCACGTGTGCAC--AGTG 3703 rnd-5_family- 442 CGGAAAGGACTGCCACTCGCGCATCGGCCTTTTTAGCCACAACCGTACTC 491 i iiiv i i i v i v MamRTE1#LINE/ 3704 TGGAAAGGACTGTTGGTCACGCATCGGTCTTTTCAGCCACACCCGCACAC 3753 rnd-5_family- 492 ACAAGACGTAA-NACCGTCATCAGCGTCATCTTCGGTCACGAAGGACAAC 540 i iivv i -? vi ivi MamRTE1#LINE/ 3754 ATAGATAGCAATCACCGTCAGTAGCGTCATCTTCGAATACGAAGGACAAC 3803 rnd-5_family- 541 AACA 544 i i MamRTE1#LINE/ 3804 GATA 3807 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 94, Kimura (unadjusted) = 37.77 Transitions / transversions = 1.57 (94/60) Gap_init rate = 0.02 (10 / 540), avg. gap size = 1.70 (17 / 10) 1072 15.06 12.70 10.32 rnd-5_family-6758#DNA/Crypton 2 371 (129) MER134#DNA/Crypton 10 387 (126) m_b25s502i9 rnd-5_family- 2 AAGCANATATTGANTTCTGTTGGGNNAGAATATTATGGTCTACCAATTCA 51 ? ? i ??- i i v i i iii ii i MER134#DNA/Cr 10 AAGCAGATATTGACTTCTGTTGAGGT-GAACATCAAGATTTATTGACCCG 58 rnd-5_family- 52 AGAGGTTNATAATGACCAAGGGGAANTTTCTTTCCTNAGGTCAATATTTA 101 v? v i v ?-------- i? MER134#DNA/Cr 59 AGAGGTAAATATTGACCGAGGCGAAG--------CCGAGGTCAATATTTA 100 rnd-5_family- 102 ACTAAAAGGACAAGAA-------TGTTTACCGCAACG-GAAGTCAACGTA 143 v vi i v ------- i v i- -- MER134#DNA/Cr 101 CCTCGAGGGACAATAAATCTTGATGTTCACCGAAACACGAAGTCAA--TA 148 rnd-5_family- 144 TATATAATAATAACAATAGTAATATAGTATGTTGTTACATACGTTCTGAA 193 i i ------------------------- i MER134#DNA/Cr 149 TGTGTA-------------------------TTGTTACATACATTCTGAA 173 rnd-5_family- 194 TATCT---TCAGAAATATCTGGAAATCTCT-CACTATGGCCATGAATT-- 237 i --- - ii -- MER134#DNA/Cr 174 TGTCTTCATCAGAAATATCTGGAAATCTCTCCGTTATGGCCATGAATTTC 223 rnd-5_family- 238 AAGNNTGNAACGTTATTTTTTCCTTTTAAACTGACATNCTAAGGGNAGGA 287 i i?? ? ---v? v i ? i ??i ? MER134#DNA/Cr 224 GAAAGTGTAACG---GNTTTTCCTTTGAAACTAACATTCTAAAGGGNAGN 270 rnd-5_family- 288 T-AAGTTAGAGGTCCAG-----------------------------GAAT 307 - ? i ----------------------------- MER134#DNA/Cr 271 TGAANTTAGGGGTCCAGAAAAAGCTNTTGCGCGGCTCTGAGGAGGCGAAT 320 rnd-5_family- 308 AAAANTATT--CCGACCTCTGATG-AGCCAGTCAGGAAGCAGANATTTGC 354 v ? v -- i v v v - i v ?v? MER134#DNA/Cr 321 AATAGTTTTCGCTGAACTCAGCTGCAGCCAATCAGGATGCANTCATTTGC 370 rnd-5_family- 355 ATATGCTATCTGATTGG 371 v i MER134#DNA/Cr 371 ATATGCGACCTGATTGG 387 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.02 CpG sites = 32, Kimura (unadjusted) = 18.31 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.13 (48 / 369), avg. gap size = 1.79 (86 / 48) 244 2.86 0.00 5.71 rnd-5_family-6758#DNA/Crypton 364 400 (100) C MER134#DNA/Crypton (158) 355 321 m_b25s502i10 rnd-5_family- 364 CTGATTGGCTGCAGCATGAGTTCAGGAGAAAACTATT 400 - - v C MER134#DNA/Cr 355 CTGATTGGCTGCAGC-TGAGTTCA-GCGAAAACTATT 321 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 2.92 CpG sites = 0, Kimura (unadjusted) = 2.92 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 671 7.87 0.00 0.00 rnd-5_family-6758#DNA/Crypton 409 497 (3) MER134#DNA/Crypton 346 434 (79) m_b25s502i11 rnd-5_family- 409 AGCCAATCAGGATGCGNTNATTTGCATATGCGATCTGATTGGTTAACATT 458 i ? i ? MER134#DNA/Cr 346 AGCCAATCAGGATGCANTCATTTGCATATGCGACCTGATTGGTNAACATT 395 rnd-5_family- 459 GTTCCAGATCTCAGTACTGTTGACCTCTGAGGAGGTAAA 497 i ? i i ii ? ? MER134#DNA/Cr 396 GCTCNAGACCTCGGTATCGTTNACCTCTGAGGAGGNAAA 434 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 6.69 CpG sites = 7, Kimura (unadjusted) = 9.24 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 16 2.93 10.81 2.50 rnd-5_family-6970#Unknown 103 139 (348) (GCCT)n#Simple_repeat 1 40 (0) m_b25s252i1 rnd-5_family- 103 GCCTG-CT-CCTG-CTGCCTGCCTGCCTGCCATGTCT-CCT 139 - - - - i - (GCCT)n#Simpl 1 GCCTGCCTGCCTGCCTGCCTGCCTGCCTGCC-TGCCTGCCT 40 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.14 (5 / 36), avg. gap size = 1.00 (5 / 5) 471 22.66 2.42 9.03 rnd-5_family-74#LINE/L2 111 275 (47) L2-1_AMi#LINE/L2 1081 1235 (0) m_b25s551i3 rnd-5_family- 111 CTGNGCTNTCCACGCTTCTGAGAAACCCATCG---AAATTCGTAAAGCCG 157 ?v i?ii i vv i i i vi --- v i i ---- L2-1_AMi#LINE 1081 CTGCTCCCCTCATGCTTGGGAGGAGCTCCCCGTAAACATCCGCAAA---- 1126 rnd-5_family- 158 TCACCTTATCCTCTTTTAAAATCCCTCCTTAAAACCTACCTCTGCCGTGA 207 v i i i - vi - i L2-1_AMi#LINE 1127 TCACATTATTCTCCTTCAAA-TCCCTCCTTAAACTCT-CCTTTGCCGTGA 1174 rnd-5_family- 208 TGCCTACAAATCGCTNCCGTCTGGCACTGGTTAGGCAAGTGGNGAGCTGA 257 --------iv i vi viv ? v L2-1_AMi#LINE 1175 TGCCTACAAA--------AACTGACAACGGTTAGGCTGCTGGTGTGCTGA 1216 rnd-5_family- 258 GACTTCTGCTT-TTCTGCT 275 iv i - ? L2-1_AMi#LINE 1217 GACCACTGCCTATTNTGCT 1235 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.33 CpG sites = 21, Kimura (unadjusted) = 28.30 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.10 (16 / 164), avg. gap size = 1.12 (18 / 16) 460 26.83 2.83 3.32 rnd-5_family-7421#DNA/hAT-Tip100 842 1053 (240) Zaphod#DNA/hAT-Tip100 3527 3737 (342) m_b25s502i12 rnd-5_family- 842 ATTCTACCGACAATTCCTGTAACAGCAGCATCAGGAGAACGGAGTTTCTC 891 i ii v vi vi v v v i i Zaphod#DNA/hA 3527 ATTTTATTGACAATTCCAGTTGCTACTGCCTCAGCAGAGCGAAGTTTCTC 3576 rnd-5_family- 892 AAAACTAAAGCTCATTAAAAACTATCTCCGTTCTACAATGAGTCAGGAAT 941 v i i ii v v vv vv v i v Zaphod#DNA/hA 3577 CAAATTGAAATTAATAAAAAACTATCTAAGAACTACAATGACTCAAGAAA 3626 rnd-5_family- 942 GCTTGACTGGTCTTGCTATTCCTG-CAATCGAACAAGACATCACTTTG-- 988 v v ii - vi v - v vi - i - v -- Zaphod#DNA/hA 3627 GGTTGTCTAAT-TTGGCATTACTGTCAATAGAACACAA-ATTA-TGTGAA 3673 rnd-5_family- 989 --TCTTTGTCATACAATGACATTATTACTGCTTTTGCAGCCAAA-AAAAG 1035 -- vi -- i ii v v v v -- -i i Zaphod#DNA/hA 3674 AATCTTGAT--TATAACAACATAATTAGTGATTTTGCTG--AAATGAAGG 3719 rnd-5_family- 1036 CCAGAAAGATTGCTTTTA 1053 v i viv Zaphod#DNA/hA 3720 CAAGAAAAATAAATTTTA 3737 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 25, Kimura (unadjusted) = 33.39 Transitions / transversions = 0.83 (25/30) Gap_init rate = 0.05 (11 / 211), avg. gap size = 1.18 (13 / 11) 282 20.00 0.00 0.00 rnd-5_family-7660#DNA/hAT 534 588 (119) UCON69#DNA/hAT 211 265 (221) m_b25s502i13 rnd-5_family- 534 GCTCNGAGAGGTGTTAAGCGGCCCGTTCATCTCAATGAGATGTTCTCACT 583 ? v vi v i i i vv v UCON69#DNA/hA 211 GCTCTGAGAGGTGTGAACTGCCCCATTCATCTCAATGGGGTGTTAACTCT 260 rnd-5_family- 584 GAAAC 588 i UCON69#DNA/hA 261 GAAGC 265 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.85 CpG sites = 5, Kimura (unadjusted) = 23.85 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 392 8.62 3.45 0.00 rnd-5_family-7660#DNA/hAT 605 662 (45) UCON69#DNA/hAT 195 254 (232) m_b25s502i14 rnd-5_family- 605 ACAGCCTGAAACAACAGCTCTGAGACGCGTGAACTGCTCCATTCA-CTCA 653 i v i i - UCON69#DNA/hA 195 ACAGCCTGAAACAATAGCTCTGAGAGGTGTGAACTGCCCCATTCATCTCA 244 rnd-5_family- 654 GT-GGGTGTT 662 i - UCON69#DNA/hA 245 ATGGGGTGTT 254 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 9.31 CpG sites = 4, Kimura (unadjusted) = 9.31 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 639 19.42 15.96 1.40 rnd-5_family-9261#DNA/Kolobok 59 246 (7) UCON29#DNA/Kolobok 203 417 (22) m_b25s502i15 rnd-5_family- 59 AACTGTAGGCAGAATTTGGCCTGCAGAATCTTTATTACTGGTGATGATGC 108 i vi vi i iv vi i UCON29#DNA/Ko 203 AATTGTCAGCTAAGTTCCGATTGCAGAATCTTTATTACTGGTGATGATGT 252 rnd-5_family- 109 GTGATACGGAAAGAG-------------TCA------AGAGTGAGGCTGT 139 i? vi i i------------- ------ iv vi i UCON29#DNA/Ko 253 ANGAGGCAGAAAGAACACAGCTTGATTTTCAGATCCCAGGTTGAGTTTGC 302 rnd-5_family- 140 GGAGCCT-CAGTTAGGAAAAATCGTCTTTTGACTTGTAAACCGAGCAAAA 188 i ? iv- - i i v UCON29#DNA/Ko 303 AGNGCTGGCAGTTAG-AAAAATCATCTTTTGACTTGTAAACTGAGCAAAT 351 rnd-5_family- 189 TTGATACGGAAATCANTGAGACACAACGAA----------CACGAAGCCA 228 ?i i ? v v ii ---------- v i UCON29#DNA/Ko 352 TTGATNTGGAAGTCATTGAGAGAGAATAAATATGGAACCCCACGATGTCA 401 rnd-5_family- 229 TTTTNATACACTCACTTT 246 -- v UCON29#DNA/Ko 402 TTTT--TACAGTCACTTT 417 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.60 CpG sites = 23, Kimura (unadjusted) = 23.60 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.04 (7 / 187), avg. gap size = 4.71 (33 / 7) 12 24.30 0.00 0.00 rnd-5_family-9705#Unknown 106 139 (710) (CCCAG)n#Simple_repeat 1 34 (0) m_b25s252i0 rnd-5_family- 106 CCCTGCCCAGCCCAGTGGCGCCCTGCACAGCCCA 139 v ivvv v v (CCCAG)n#Simp 1 CCCAGCCCAGCCCAGCCCAGCCCAGCCCAGCCCA 34 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 217 6.45 0.00 0.00 rnd-5_family-9796#Unknown 3 33 (55) MIRc#SINE/MIR 80 110 (158) m_b25s601i6 rnd-5_family- 3 ACTCGCTGTGTGACCTTGGGCGAGTCACTTA 33 v i MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 6.76 CpG sites = 1, Kimura (unadjusted) = 6.76 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 1427 11.17 1.19 4.08 rnd-5_family-10092#LINE/CR1 1 252 (0) X2_LINE#LINE/CR1 1148 1392 (16) m_b26s551i0 rnd-5_family- 1 AGGAGACTAGGAGTAAATAGGGAACTCGGGCAGAATTGCTTCATGCAAAG 50 i i i ii i X2_LINE#LINE/ 1148 AGGAAACTAGGAGTAAATAGGGAACTCAGGCAGAACTATTTCACGCAAAG 1197 rnd-5_family- 51 GGTAATAAAAATATATGGAATAAGTTGCCGGGGAAGGCGACTGAAGCAAA 100 --i i i X2_LINE#LINE/ 1198 GGTAATAAA--CATATGGAATAAGTTACCGGGGAAGGCGATTGAAGCAAA 1245 rnd-5_family- 101 GAGTATAAATGAGTTCAAGAGACACCCGGATTTGTTTCTGG---AGGAGG 147 ii --- X2_LINE#LINE/ 1246 GAGTATAAATGAGTTCAAGAGACACCTAGATTTGTTTCTGGAGAAGGAGG 1295 rnd-5_family- 148 GGATTGAGGGGCATGGTGAAAAAGCCGGANGGTNGGATGAAGCGGGACGG 197 i i ? v ? ? vi vvii v? X2_LINE#LINE/ 1296 GGATTGAAGGGTATGGTGANAAAGCAGGAAGGTGGGATTGAGATAAACCN 1345 rnd-5_family- 198 ATTTTTCTTTAAAGGCGAGCGCGTTGGGCTCGGNTGGNCTTTTCCTGTTC 247 -------vv i ii i - ? ? X2_LINE#LINE/ 1346 A-------AAAAGGGCAGGCGTGTTGGGC-CGGATGGCCTTTTCCTGTTC 1387 rnd-5_family- 248 CTAAA 252 X2_LINE#LINE/ 1388 CTAAA 1392 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.16 CpG sites = 20, Kimura (unadjusted) = 12.63 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.04 (11 / 251), avg. gap size = 1.18 (13 / 11) 388 32.11 3.53 3.53 rnd-5_family-10158#LINE/CR1 30 284 (201) CR1-3_Croc#LINE/CR1 729 983 (2622) m_b26s551i1 rnd-5_family- 30 GAANAAAACCTTATGATCCAGAAAGCAGAGANTTCAACACCAAGGAGA-- 77 i? v i v v ii i? --- v v i -- CR1-3_Croc#LI 729 GAGGACAACTTTCTGTTCCAGAAAGTGGAGGAT---ACAACTAGGGGATC 775 rnd-5_family- 78 AGCCATCCTGGATCTGCTTCTTACCGATAGGGAGAAACTGACTGAGGATG 127 v i i vv i v i i ii iiv CR1-3_Croc#LI 776 ATCTATCTTGGATCTTGTCCTGACCAACAGGGAAGAACTGGTGGAGGATG 825 rnd-5_family- 128 TGAGAATAATAGGGAAGCTTGGAACCAGTGACCATGAGCNACTTGAATTC 177 iii i i v vi v ivv i i i vv?iv v CR1-3_Croc#LI 826 TGAAGGTGATGGGTAACTTGGGAGGAAGCGATCACGATATGATAGAATTC 875 rnd-5_family- 178 AGNATAGTAAGGAATGGGATCACAGAATG----CAGCAGTACAAGGGTAT 223 vi? vv i -- i i-- v v ---- iv iv iiii CR1-3_Croc#LI 876 CAGATCCTGAG--ACGGGG--AAAGCATGAGGTCAGCAAAATTAGGACGC 921 rnd-5_family- 224 TAGATTTCAGGAAAGCAAATTTGGGAGNAATTAAGAAATCCATAG---TG 270 ii i ii vivvv? v i i i iv --- CR1-3_Croc#LI 922 TAGATTTCAAAAAGGCGGATTTCATCCGACTCAAGGAGTTAATAGGCATG 971 rnd-5_family- 271 ACGTNCGATGGGAG 284 -- ? v CR1-3_Croc#LI 972 --GTGCCATGGGAG 983 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.98 CpG sites = 46, Kimura (unadjusted) = 44.82 Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.05 (12 / 254), avg. gap size = 1.50 (18 / 12) 399 34.19 0.51 1.02 rnd-5_family-10158#LINE/CR1 48 245 (240) Plat_L3#LINE/CR1 1236 1432 (2141) m_b26s551i2 rnd-5_family- 48 CAGAAAGCAGAGANTTCAACACCAAGG-AGAAGCCATCCTGGATCTGCTT 96 i i?v --i i - v v i v i v Plat_L3#LINE/ 1236 CAGAAAGTAGAGGAATCAAC--TAGGGCAGATGCCCTTCTTGATTTGATT 1283 rnd-5_family- 97 CTTACCGATAGGGAGAAACTGACTGAGGATGTGAGAATAATAGGGAAGCT 146 ii ii ii i iiii v i iii iivv i v Plat_L3#LINE/ 1284 CTTACTAACGGGGAAGAATTAGTCGAGGATCTAAAGGTGGATGGAAACCT 1333 rnd-5_family- 147 TGGAACCAGTGACCATGAGCNACTTGAATTCAGNATAGTAAGGAATGGGA 196 vivv i i ii v?iv i v i? vv i v Plat_L3#LINE/ 1334 TGGTGGAAGCGATCACAAGATGATCGTATTCAAGATCCTAAGGGAAGGGA 1383 rnd-5_family- 197 TCACAGAATGCAGCAGTACAAGGGTATTAGATTTCAGGAAAGCAAATTT 245 vv v vv iv i i iv v ii i i Plat_L3#LINE/ 1384 GGAGAGAAGTCAGCAAGATAAAGAAAATGAACTTTAGGAAAGCAAATTT 1432 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.68 CpG sites = 41, Kimura (unadjusted) = 48.85 Transitions / transversions = 1.58 (41/26) Gap_init rate = 0.02 (3 / 197), avg. gap size = 1.00 (3 / 3) 230 11.65 0.00 4.65 rnd-5_family-10436#LINE/CR1 74 118 (542) CR1-L3B_Croc#LINE/CR1 3213 3255 (22) m_b26s551i3 rnd-5_family- 74 ATACAAGGGGGTCAGAGGAGATGATCACAACGGTCCCTTCTGGCC 118 - i vv -i i CR1-L3B_Croc# 3213 ATACA-GGAGGTCAGACTAGATGATC-TAATGGTCCCTTCTGGCC 3255 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.73 CpG sites = 3, Kimura (unadjusted) = 12.73 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 257 22.81 0.00 0.00 rnd-5_family-1301#LINE/RTE-BovB 948 1004 (1287) Plat_L3#LINE/CR1 2138 2194 (1379) m_b26s551i4 rnd-5_family- 948 GGGTGAAGTCCCTGAAGACTGGCAATGCTCAGNCATTGTACCACTCTTTA 997 v i i v v vv i? i i vv Plat_L3#LINE/ 2138 GGGAGAAGTCCCTGAGGATTGGAAAAGGGCAAACGTTGTGCCCATCTTTA 2187 rnd-5_family- 998 AGAAAGG 1004 i Plat_L3#LINE/ 2188 AAAAAGG 2194 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.54 CpG sites = 6, Kimura (unadjusted) = 27.91 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 261 37.33 3.70 2.44 rnd-5_family-1301#LINE/RTE-BovB 1114 1275 (1016) MamRTE1#LINE/RTE-BovB 2325 2488 (1324) m_b26s601i0 rnd-5_family- 1114 CTTTCTGAGTCACAAGCTGGCTTTAGACCTGGACACTCCGCCGTAGATCA 1163 ii v i i vv i vvii i vvii?v ii ivv MamRTE1#LINE/ 2325 CTCCCGGAATCGCAATGTGGCTTTAGGCCGCAGCGCGGTANAGCGGACGT 2374 rnd-5_family- 1164 GATATTTGTTTTTCGTCAAATCTTGGAGAGACACACAGAGT----TCAAC 1209 v i?vivi i viv i ii i vi ii---- - MamRTE1#LINE/ 2375 GATCTTTGCNGCATGTCAGATACAGGAAAAGCGCAGGGAACAACATCAA- 2423 rnd-5_family- 1210 GAACCCCTGTTTTGCACATTCNTTGACTTTAAGAAAGCATTCGACTCCGT 1259 -i i ivi --i ? i i vi i v i MamRTE1#LINE/ 2424 -GACCTCTGCACTG--TATTCATCGACCTTACAAAAGCATTTGACGCCAT 2470 rnd-5_family- 1260 TAACAGA--GAGGCTCTG 1275 i ii --vi MamRTE1#LINE/ 2471 CAGTAGACCTGGGCTCTG 2488 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.66 CpG sites = 39, Kimura (unadjusted) = 57.48 Transitions / transversions = 1.95 (39/20) Gap_init rate = 0.04 (6 / 161), avg. gap size = 1.67 (10 / 6) 15 20.27 7.81 1.47 rnd-5_family-1570#Simple_repeat 1 64 (5) (CCCCACA)n#Simple_repeat 1 68 (0) m_b26s252i8 rnd-5_family- 1 CCCCACACCCCA-A-CCCTCTGCCC-CAGCCCTGAGCCC-C-TCCCACAC 45 - - v vv - v vv v - -i (CCCCACA)n#Si 1 CCCCACACCCCACACCCCACACCCCACACCCCACACCCCACACCCCACAC 50 rnd-5_family- 46 CCCGAACCCCTCATCCCCA 64 iv v - (CCCCACA)n#Si 51 CCCACACCCCACA-CCCCA 68 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 391 13.91 0.00 4.17 rnd-5_family-16702#DNA/hAT 249 323 (46) UCON69#DNA/hAT 85 156 (330) m_b26s502i0 rnd-5_family- 249 TAAGCTTTCATTTTGAAAAAATTAAGTCTCTAGCCCTTTTCCTTGCGGGG 298 -i ? i v vv -- i UCON69#DNA/hA 85 TAAGCTTTCATTT-AAAAAAANTAAGTTTCTAGCCCTTATGGTTGC--GA 131 rnd-5_family- 299 AGACAGCCTTCAAAATGTAAACTGA 323 v i i i UCON69#DNA/hA 132 AGAAAACCTTCAAAATGTGAACCGA 156 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.15 CpG sites = 6, Kimura (unadjusted) = 15.76 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.00 (3 / 3) 445 30.18 5.63 5.63 rnd-5_family-18879#LTR/ERV1 708 1009 (2972) HERVI#LTR/ERV1 5054 5355 (2429) m_b26s701i0 rnd-5_family- 708 AGTATTTATTAGTGATAGTAGATTCTTTTTCTGGATGGGTGGAGGCGATT 757 i i i ivii v iviv i v i HERVI#LTR/ERV 5054 AATACTTATTAGTAATAGTAGATCACCTTACCCACTGGGTAGAGGCTATC 5103 rnd-5_family- 758 CCCACCAGAAATCATACTGCAGAGACCACCGCCAAGAAGTTGTGG--GAA 805 vi ----- - v ------ iv -- i --i i HERVI#LTR/ERV 5104 CCCTTC-----TCA-AGTGCA------ACCGCCAGTAA--TGTAGTTAAG 5139 rnd-5_family- 806 GTAGTGTTTAGTAGATATGGAACTC----------CAAAAGTAA---TTG 842 i v iv - v i v v i ----------i v v --- HERVI#LTR/ERV 5140 GCATTAATT-GAAAATATCGTACCCAGGTTTGGACTAATAGAAAATATTG 5188 rnd-5_family- 843 ATTCAGATAATGGACCACATTTTGTAGGAGAAGTAATTAAAAGTTTATTA 892 v v iiiv v v v v ivi viv HERVI#LTR/ERV 5189 ATTCAGATAATGGAACCCATTTCACTGCACATGTCATTAAAAAGCTAGCC 5238 rnd-5_family- 893 AAAGCTTTAGGAATAAAGCAACAACTACATATCCCCTACCATCCTCAATC 942 v ivi i? iiiiv ivv i iv i vivv HERVI#LTR/ERV 5239 CAAGTACTAGANATAAAATGGGAATACCATACCCCCTGGCACCCATCCTC 5288 rnd-5_family- 943 GTCAGGGACAGTAGAAAGGATGAATCAAACTATTAAGCAAGC--TCTACG 990 ? i v i i v v -- --ii vv HERVI#LTR/ERV 5289 NTCAGGAAGAGTAGAAAGGATGAACCAGACTCTAAA--AAGCCACTTAAC 5336 rnd-5_family- 991 CAAAGTAGTGCAAGAAACT 1009 v v v i HERVI#LTR/ERV 5337 CAAATTAGTTCTAGAGACT 5355 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 44, Kimura (unadjusted) = 39.55 Transitions / transversions = 1.05 (44/42) Gap_init rate = 0.07 (21 / 301), avg. gap size = 1.62 (34 / 21) 13 10.07 5.88 2.86 rnd-5_family-18879#LTR/ERV1 1613 1646 (2335) (TGCTT)n#Simple_repeat 1 35 (0) m_b26s252i7 rnd-5_family- 1613 TGCTTATGC-TCGCTTTGCTTTGCATT-TTTTGCTT 1646 - - i v -i (TGCTT)n#Simp 1 TGCTT-TGCTTTGCTTTGCTTTGCTTTGCTTTGCTT 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 321 26.12 0.89 0.89 rnd-5_family-2603#DNA 2 113 (7) MER131#DNA 27 138 (77) m_b26s601i1 rnd-5_family- 2 TATAGTTATGGTTGAGAAGGCACTTCCATTNCACGCCCCTGTTTTCAGGC 51 v ? vv vvi ii ?i vi i v MER131#DNA 27 TATAGTTAAGGNTCTGTCAGCGTTTCCATTATAAACCCCTATTTTCAGGG 76 rnd-5_family- 52 GCTTATAACTTT-CGGAAAAAANTACCCTTTGGGCTGAAATTTCTCATGT 100 i iv- v v ? - v ii i vv ii MER131#DNA 77 GTTTATAACTCGGCCGTAAAAATT-CGCTCCGGGCTGAAACTTGGCATAC 125 rnd-5_family- 101 TTGTTCTCAGCCC 113 vv v MER131#DNA 126 AAGGTCTCAGCCC 138 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.48 CpG sites = 13, Kimura (unadjusted) = 33.41 Transitions / transversions = 0.81 (13/16) Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.00 (2 / 2) 564 11.76 4.85 0.93 rnd-5_family-2838#SINE/5S-Deu-L2 37 139 (9) AmnSINE1#SINE/5S-Deu-L2 444 550 (25) m_b26s502i1 rnd-5_family- 37 GCTGCTGCCCTCCTCCCCAGAGGTGGCTGCATTTC---GGTGGG-GCCGT 82 i vi v --- - vv AmnSINE1#SINE 444 GCTGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGT 493 rnd-5_family- 83 GATCGCCTATGTGTAGTTTGCAAGGCA-TTTGGGATCCTTCGGGATGAAA 131 - i i i i i i- AmnSINE1#SINE 494 GATC-CCTGTATGTAGCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAA 542 rnd-5_family- 132 GGCGCTAT 139 AmnSINE1#SINE 543 GGCGCTAT 550 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 10.81 CpG sites = 8, Kimura (unadjusted) = 12.95 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.50 (6 / 4) 455 15.30 0.00 2.35 rnd-5_family-3508#LINE/L2 1 87 (75) L2-1_AMi#LINE/L2 1151 1235 (0) m_b26s551i5 rnd-5_family- 1 TCCTTAAAACTCACCTCTGCTGCGATGCCTACGNAACANTGNCAATGGCT 50 - v i i i i? - ? ? i i L2-1_AMi#LINE 1151 TCCTTAAA-CTCTCCTTTGCCGTGATGCCTACAAAA-ACTGACAACGGTT 1198 rnd-5_family- 51 AGGCAGCTGGTGTGCTGTGACCGCTGCTTATTACACT 87 v v i i ?ii L2-1_AMi#LINE 1199 AGGCTGCTGGTGTGCTGAGACCACTGCCTATTNTGCT 1235 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.61 CpG sites = 10, Kimura (unadjusted) = 18.62 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 12 21.77 0.00 6.67 rnd-5_family-362#LTR/Gypsy 2700 2747 (101) (TAAATGT)n#Simple_repeat 1 45 (0) m_b26s252i6 rnd-5_family- 2700 TAGATGTGGAATGTTAAATATGTTAAATGTTCTTTTGATAATTGTTAA 2747 i vi - - -vvv v v (TAAATGT)n#Si 1 TAAATGTTAAATGTT-AA-ATGTTAAATGTT-AAATGTTAAATGTTAA 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 1657 7.86 0.00 6.09 rnd-5_family-4005#Unknown 4 247 (77) UCON5#Unknown 153 382 (53) m_b26s502i2 rnd-5_family- 4 TGTGGTCTTTTAGGTGTAGATGCTCACCTNCTTAAATATCTCTGAAAGTA 53 i ? i iv UCON5#Unknown 153 TATGGTCTTTTAGGTGTAGATGCTCACCTGCTTAAATATCTCTAAAGCTA 202 rnd-5_family- 54 CTAGTAAAAGAATAAAAAAATACCTAAATATATAACAGATGCGCAAGTGC 103 --------- i UCON5#Unknown 203 CTAGTAAAA---------AATACCTAAATATATAACAGATGCACAAGTGC 243 rnd-5_family- 104 ACCTTGGGATGAATGCACTNTGGACACAGAACCGTCATCACATCCTTCAC 153 i ? i i i i UCON5#Unknown 244 ACCTTGGGATGAATGCATTATGGACGCAGAACTGTCATCACACCCCTCAC 293 rnd-5_family- 154 AATCACGTTTTTTCATCTGCTCATGTGGTGTACACCTGTGGCATGTTGGC 203 i-- i v UCON5#Unknown 294 AATCACA--TTTTCACCTGCTCATGTGGTGTACACCTGTGGCTTGTTGGC 341 rnd-5_family- 204 AATGCTTTTGGTTGCAGCGCGGGAGACTTACCAGGTATTCAAAG 247 vi i i i- -- UCON5#Unknown 342 AATGCACTTGGTTGCAGTGTGGGAGACTC-CCAGG--TTCAAAG 382 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 8.02 CpG sites = 15, Kimura (unadjusted) = 8.48 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.06 (14 / 243), avg. gap size = 1.00 (14 / 14) 13 0.00 5.00 0.00 rnd-5_family-4188#Unknown 137 156 (221) (GCCT)n#Simple_repeat 1 21 (0) m_b26s252i5 rnd-5_family- 137 GCCTGCCTGCCTGCCT-CCTG 156 - (GCCT)n#Simpl 1 GCCTGCCTGCCTGCCTGCCTG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 19), avg. gap size = 1.00 (1 / 1) 184 11.63 4.65 0.00 rnd-5_family-4233#LINE/L2 35 77 (423) L2#LINE/L2 2046 2090 (992) m_b26s601i2 rnd-5_family- 35 CTCATGCTGCTGGACCTCT--GCAGCCTTTGACACAGNNGANCAC 77 vi i v ? -- v ?? ? L2#LINE/L2 2046 CTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGATCAC 2090 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.07 CpG sites = 2, Kimura (unadjusted) = 14.07 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 2.00 (2 / 1) 1412 13.28 2.63 3.80 rnd-5_family-4447#DNA/hAT-Ac 6 271 (3) C OldhAT1#DNA/hAT-Ac (922) 1920 1658 m_b26s601i3 rnd-5_family- 6 GAGGGGGAGGNGGAGGAATTGCATGGCCTGCAGCNCTTTGTTTATGAGAA 55 ii ? -iv v ? i C OldhAT1#DNA/h 1920 GAGAAGGAGGAGGAGGA-CGGCATGGCCTCCAGCACTTTGTTTACGAGAA 1872 rnd-5_family- 56 CGTCCTTCCAGTG-------TCTGAACCCGGCGGAAGTATGGTTTCAATT 98 i ------- v i C OldhAT1#DNA/h 1871 CATCCTTCCAGTGATCTATGTCTGCACCCGGTGGAAGTATGGTTTCAATT 1822 rnd-5_family- 99 TTCCCTTTGAAACGTGGATCAAGNAACGTTGCCAACACATATTTTTCTCT 148 i v i ? i i i C OldhAT1#DNA/h 1821 CTGCCCTTGAAACGTGGATCAAGCAATGTTGCCAACACATATTCTTCCCT 1772 rnd-5_family- 149 GTCAAACATTTCACTTATTCTGGAGTCTGTAGACGGTTTGAGAGCCATGT 198 v i i i i C OldhAT1#DNA/h 1771 GTCAAACATTTCACTGATTCTGGAGTCTGTAGACAGCTTAAAAGCCATGT 1722 rnd-5_family- 199 CTTCTGNCAGGGTTATTACAGCAGTGTCCCGTTTGTCATNTTCAGCTTTA 248 ? v i i i i i v i---------i i C OldhAT1#DNA/h 1721 CTTCTGCCAGCGTTACTGCAGCGGCGTCTCCTTTGC---------TTTCA 1681 rnd-5_family- 249 AATTGGANNCANATTTGTTCCAG 271 v i?? i? v C OldhAT1#DNA/h 1680 AATTCGGTTCGCATTTGTTCAAG 1658 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 13.08 CpG sites = 25, Kimura (unadjusted) = 15.40 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.04 (11 / 265), avg. gap size = 1.55 (17 / 11) 18 8.53 0.00 0.00 rnd-5_family-5011#Unknown 310 334 (2704) (CA)n#Simple_repeat 1 25 (0) m_b26s252i3 rnd-5_family- 310 CACACACACACACACAAAAACACAC 334 v v (CA)n#Simple_ 1 CACACACACACACACACACACACAC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 16 8.18 0.00 0.00 rnd-5_family-5011#Unknown 1339 1364 (1674) (TTTG)n#Simple_repeat 1 26 (0) m_b26s252i4 rnd-5_family- 1339 TTTCTTTGTTTGTTTGTTTGTTTTTT 1364 v v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 752 23.31 2.55 4.83 rnd-5_family-5355#LINE/L2 3 277 (13) L2-1_AMi#LINE/L2 607 875 (360) m_b26s551i6 rnd-5_family- 3 TGGGACTCATCTTTGACTCCTCCCTCTCCTTTGCCCCACACATCCAGGCC 52 vv i vvv ii v vi v i L2-1_AMi#LINE 607 TGGGCGTCATCTTCGACTCGGACCTCTCTCTAGGTCCTCACATCCAGGCT 656 rnd-5_family- 53 GTGTCCAAATNCTGCCGTTTCTTCCTCCATAACATTTCCAAGATCTGACC 102 i i ?i v v i v i i vi i L2-1_AMi#LINE 657 ATGTCTAAATCTTGCAGATTCTTTCTGCATAACATCTCTAAGATACGGCC 706 rnd-5_family- 103 TTTTCTTTCTGTCCACACCGCCAAAACTCTTGTCCAGGCCTTCATCATCT 152 i v ii v i i ---------- L2-1_AMi#LINE 707 TTTCCTATCCATCCACACAGCTAAAACTCTCGTCCAG----------TCT 746 rnd-5_family- 153 CCCATCTCG---ACTACGACCTCCTCTTCCTCTGCCTCCCTGAC--ACNC 197 v --- i i v - i --v i -- i? L2-1_AMi#LINE 747 CACATCTCGATTACTGCAACATCCT-TTTCTCTG--GCCTTGACAAATGC 793 rnd-5_family- 198 ACT-TCACCTTCTTCA-GTCCGTTCGAAACGCNGCTGCTAAGATCNTCTT 245 v - ii iivi -i i ii i ? v ? i L2-1_AMi#LINE 794 AATCTTGCCCCGCTCATATCCATTCAGAATGCTGCTGCAAAGATCATTTT 843 rnd-5_family- 246 CCTTGCCCATTGNTCNGATCACATCACCCCCC 277 v i i ? i? i i i L2-1_AMi#LINE 844 CCTAGCCCGTCGCTTTGACCACGTCACCCCTC 875 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.66 CpG sites = 40, Kimura (unadjusted) = 29.57 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.06 (17 / 274), avg. gap size = 1.18 (20 / 17) 307 2.70 0.00 0.00 rnd-5_family-5626#DNA/hAT-Tag1 1 37 (1) hAT-5_Mam#DNA/hAT-Tag1 3504 3540 (0) m_b26s502i3 rnd-5_family- 1 GATTTAAATCAATTTGATTTAAATCAAATCCACCCTG 37 i hAT-5_Mam#DNA 3504 GATTTAAATCGATTTGATTTAAATCAAATCCACCCTG 3540 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.27 CpG sites = 1, Kimura (unadjusted) = 2.78 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 182 24.65 0.00 4.92 rnd-5_family-5783#LINE/RTE-BovB 14 77 (623) MamRTE1#LINE/RTE-BovB 1252 1312 (2500) m_b26s601i4 rnd-5_family- 14 AAGATGTCCANATCACCNATGTCATGAGAGGAGCCGACGATTGCTGGACT 63 i ii ? i i?vv ii v v v - -- i MamRTE1#LINE/ 1252 AGGATGTTTAGATTACTGCAGCTATGCGTGGCGCCGA-G--TGCTGGACC 1298 rnd-5_family- 64 GACCACCGCCTGGT 77 i i MamRTE1#LINE/ 1299 GACCATCGCCTGAT 1312 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 10, Kimura (unadjusted) = 32.20 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 801 1.14 0.00 0.00 rnd-5_family-7944#SINE/U-L1 1 88 (0) U6#snRNA 10 97 (10) m_b26s502i4 rnd-5_family- 1 TCAGCAGCACATATACTAAAATTGGAACGATACAGAGAAGATTAGCATGG 50 i U6#snRNA 10 TCGGCAGCACATATACTAAAATTGGAACGATACAGAGAAGATTAGCATGG 59 rnd-5_family- 51 CCCCTGCGCAAGGATGACACGCAAATTCGTGAAGCGTT 88 U6#snRNA 60 CCCCTGCGCAAGGATGACACGCAAATTCGTGAAGCGTT 97 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 0.11 CpG sites = 1, Kimura (unadjusted) = 1.15 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 17 29.65 0.00 0.00 rnd-5_family-8247#Unknown 281 329 (161) (CC)n#Simple_repeat 1 49 (0) m_b26s252i2 rnd-5_family- 281 CCCCCCCCCCCCCCCGGCTTAACCCCGGCTCCCACCCCCCCCTGCCCCC 329 vv iivv vv i v iv (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 49 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 2246 12.45 2.85 8.58 rnd-5_family-9256#Unknown 165 656 (4) UCON1#Unknown 739 1204 (182) m_b26s502i5 rnd-5_family- 165 CTACAACAGCTCTTCTTGGTCTTTTNAACAGTCTTTTCAGTGGAGGCAAA 214 --- - iiv -- i UCON1#Unknown 739 CTACAACAGCTCTT---GGTCTTTT-AACAGTTCGTTCAGTGGAGG--AG 782 rnd-5_family- 215 GGGAAGAAAGGGACANGCNNCCATGCCCGATTGGTGNTGTTCAATAGTAT 264 i i i i - ? ??---- -- ? i UCON1#Unknown 783 GAGGAGGAAGAGA-AAGCGG----GCCC--TTGGTGTTGTTCAGTAGTAT 825 rnd-5_family- 265 GACTGTTTTTCTCAAGCTTGGCAGCCAGCACTGACACTATGCTGTTCTTC 314 v i - UCON1#Unknown 826 GACTGGTTTTCTCAGG-TTGGCAGCCAGCACTGACACTATGCTGTTCTTC 874 rnd-5_family- 315 AGGAGGTGTTCTTTTGATGGACGATAACTTCCCCAGNGACGTCGGCCAGA 364 i ---- ? iii v UCON1#Unknown 875 AGGAGGTGTTCTTTTGATGGACGGTA----CCCCAGTGACACTGGACAGA 920 rnd-5_family- 365 GCAGCAGTGGCAGCAGCAG-AGCACTGAGGTGGTAGCACGATTTTTAGTG 413 i i ii v i - - vvvivv i v - vv i v UCON1#Unknown 921 GCAACGGCAGCAGAAGCGGCAGCA-TGCCCCTCTAACTC-AGGTTTGGTT 968 rnd-5_family- 414 GATGAACCAGAAGAACCTACAGAGCCTGTGAGAGCGGGACCCACAGGAAT 463 i i i i ? i UCON1#Unknown 969 GATGAACCAGAAGAACCTGCAGAGCCTGTGGGAGTGGGACCCATAGNAGT 1018 rnd-5_family- 464 GGCTGTGGCC---AACTTTCTCNTTNTTTTGTGCTTTTCCTTTCTTTTTC 510 --- ---- v --i UCON1#Unknown 1019 GGCTGTGGCCATTAACTTTCTC----TTTTGTGATTTTCC--CCTTTTTC 1062 rnd-5_family- 511 ATTATGTTTGAA--TTTTGAGACTGAGCTTTGTTCCAGAATACTGNTAGC 558 v-- ? --- i? UCON1#Unknown 1063 ATTATGTTTGACATTTTTGAGACTGAGCTTTGTTNCAG---ACTAGTAGC 1109 rnd-5_family- 559 CTGTGGCAGTGAACTAGG--GGCGGGACTTCCAATGAGATCATAGAACAC 606 i ii i -- ii i - v - UCON1#Unknown 1110 CTATGGCAGTGGGCTGGGGAGATGAGACTT-CACTGAGAT-ATAGAACAC 1157 rnd-5_family- 607 ----AAAGAAA--GCGTGAAAAAGAACCTTGAAGTGACAGAGCTGAACAN 650 ---- -- i ----- ? i ii i ----? UCON1#Unknown 1158 AGAAAAAGAAAATGTGTGAAAAA-----TTGNAATGACAAGGTTG----T 1198 rnd-5_family- 651 GTTGGT 656 UCON1#Unknown 1199 GTTGGT 1204 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.35 CpG sites = 40, Kimura (unadjusted) = 14.12 Transitions / transversions = 2.50 (40/16) Gap_init rate = 0.09 (46 / 491), avg. gap size = 1.17 (54 / 46) 13 16.97 3.03 0.00 rnd-5_family-9471#Unknown 329 361 (1280) (CACCTC)n#Simple_repeat 1 34 (0) m_b26s252i0 rnd-5_family- 329 CACCTGCATCTCC-CCACCACCACCTCCTCCACC 361 v i - v v v (CACCTC)n#Sim 1 CACCTCCACCTCCACCTCCACCTCCACCTCCACC 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 13 26.97 1.61 3.28 rnd-5_family-9471#Unknown 836 897 (744) (CCCT)n#Simple_repeat 1 61 (0) m_b26s252i1 rnd-5_family- 836 CCCTCCCTCCCTCTGCCCCCTGCCACACCAACC-CCCCACCTTCAACCCA 884 -v i v v - vv - iv i vv v (CCCT)n#Simpl 1 CCCTCCCTCCCTC-CCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCT 48 rnd-5_family- 885 CCCTNCTTCCCTC 897 ? i (CCCT)n#Simpl 49 CCCTCCCTCCCTC 61 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 1144 13.87 1.63 15.79 rnd-5_family-9920#LINE/CR1 53 420 (343) CR1-16_AMi#LINE/CR1 529 851 (0) m_b26s551i7 rnd-5_family- 53 CAGCTTCANATTTAATA--CTGAAA-AGGGGTTAANAGGCACACTAATTA 99 v --- i-- i - iv ?vi ii v CR1-16_AMi#LI 529 CATCTTCA---TTAATGATCTGGAAGAGGGAGTAAACAGCACGTTAATGA 575 rnd-5_family- 100 AATTTTACAGNTGATACTAAATTGGGAGGAGCTGAAAATCCCAGTATGGA 149 i-i ? i v iv iv CR1-16_AMi#LI 576 AATTC-GCAGATGATACTAAATTGGGAGGAGTTGCAAACACCAGTGAGGA 624 rnd-5_family- 150 CAGAGANA-AATACAAAAGGANNTAGAGAGGTTAGAAACATGGGCAGAAA 198 ? - i ?? i -------- i CR1-16_AMi#LI 625 CAGAGAAATAATACAAAGGGACCTAGAGAGATTAGAA--------AGGAA 666 rnd-5_family- 199 ATAACCANACGTAAGATTCAGCTTGGGAAAATGCAANNGTGGATA--CAT 246 v ? -- i - i i i??---i -- - CR1-16_AMi#LI 667 ATAACAAAA--TGAGATT-AACTTGGAAAAATGCAGCT---AATATTCA- 709 rnd-5_family- 247 CTGAGGAAAAATAATCTAAATACAGATATTCAATGGGAGNGAGAAACCTG 296 i ------------------ i i ? - ? CR1-16_AMi#LI 710 CTGGGGAAA------------------ATCCAATGGAAGAG-GAAACNTG 740 rnd-5_family- 297 GAAAGCAGTAATGCTGAAANAGTCATAGGGGCCTGGATGANAGTGGACAG 346 --- ? ? v v ? i ------ ? i CR1-16_AMi#LI 741 GAAAGCAGTAA---TGANAGAGACCTNGAGGC------GATAGCGGACAG 781 rnd-5_family- 347 CAAATTAGACATGACGTTTGCAGTGTAATATGGCAGCAAAAATGNCCGAT 396 i - - i i -- ? ii CR1-16_AMi#LI 782 CAAATTAGATATGA-G-TTGCAATGTGATATGGCAGCAAAA--GGCCAGT 827 rnd-5_family- 397 GCAGTTTTGGGCTGCATACGCAAA 420 i i ii CR1-16_AMi#LI 828 GCAATTTTGGGCTGCATATGCGGA 851 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.60 CpG sites = 33, Kimura (unadjusted) = 16.21 Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.15 (55 / 367), avg. gap size = 1.04 (57 / 55) 372 33.05 5.20 6.09 rnd-5_family-9920#LINE/CR1 92 687 (76) CR1-L3A_Croc#LINE/CR1 3367 3957 (331) m_b26s551i8 rnd-5_family- 92 ACTAATTAAATTTTACAGNTGATACTAA-ATTGGGAGGAGCTGAAAATCC 140 i - v i ? i v - - iv v vv CR1-L3A_Croc# 3367 ACTGAT-AAAGTTTGCAGATGACACAAAGATTGGG-GGAGTGGTAAATAA 3414 rnd-5_family- 141 CAGTATGGACAGAG-ANAAATACAAAAGGANNTAGAGAGGTTAGAAACAT 189 iiiviv iv- ?vi i iv ?? i vv v i v vv CR1-L3A_Croc# 3415 TGAAGAGGACAGGTCACTGATACAGAGCGATCTGGATCGCTTGGTAAGCT 3464 rnd-5_family- 190 GGGC---AGAAAATAACCANACGTAAGATTCAGCTTGGGAAAATGCAANN 236 --- v i i- ?i ---- iivi vv i ?? CR1-L3A_Croc# 3465 GGGCGCAAGCAAACAAT-ATGCGT----TTCAATACGGCCAAATGTAAAG 3509 rnd-5_family- 237 GTGGATACATCTGAGGAA-AAATAATCTAAATACAG---ATATTCAATGG 282 vi-- - - ------i i --- i i vv CR1-L3A_Croc# 3510 TC--ATACATCT-AGGAACAAA------GAATGCAGGCCATACTTACAGG 3550 rnd-5_family- 283 GAGNGAGA----AACCTGGAAAGCAGTAATGCTGAAANAGTCATAGGGGC 328 iv ? i ---- v i ii iv ?i v v i i CR1-L3A_Croc# 3551 ATGGGGGACTCTATCCTGGGAAGCAGCGACTCTGAAAAGGACTTGGGGGT 3600 rnd-5_family- 329 CTGGATGANAGTGGACAGCAAATTAGACATGACGTTTGCAGTGTAATATG 378 ------ ?i i iiv ii ii - i iv ii iiiv CR1-L3A_Croc# 3601 C------ACGGTGGATAATCAGCTGAACATGA-GCTCCCAGTGCGACGCT 3643 rnd-5_family- 379 GCAGCAAAAATGNCCGATGCAGTTTTGGGCTGCATACGCAAAAGNNNGAC 428 ii v v ? ii ii ii v v i vi iii ????v CR1-L3A_Croc# 3644 GTGGCCAAAAGGGCTAATGCGATCCTTGGATGTATAAACAGGGGAATNTC 3693 rnd-5_family- 429 GGCTCATGACAGCAGGAAGGTAANAGTCCCTCTNTGTACGGCTNTGGTAC 478 i---i iiv i i v ? v v ? i vi v? i CR1-L3A_Croc# 3694 GA---GTAGGAGTAGGGAGGTTATATTACCTCTGTATTTGGCACTGGTGC 3740 rnd-5_family- 479 GACTGTATCTGGAATACTGCATTCGNTTCTGAGACCAANAC----AGAAA 524 i ivv ii i i? ivii v ? ?---- i CR1-L3A_Croc# 3741 GACCGCTACTGGAATACTGTGTCCAGTTCTGGTGTCCACANTTCAAGAAG 3790 rnd-5_family- 525 GACA--NACAAACTGAAGGTCGTT---AGAA-AATTAAGATTTTTATTTA 568 ii--? ? i i ivv --- - iii v vvv v v CR1-L3A_Croc# 3791 GATGTTGANAAATTGGAGAGGGTTCAGAGAAGAGCCACGAGAATGATTAA 3840 rnd-5_family- 569 AAGGTCAGTAAACAAGGAATTCATTGCTTTATGCAGAAATATTAGAAGAG 618 i iiii v ---------- i ivv i v i vi i CR1-L3A_Croc# 3841 AGGACTGGAAAACA----------TGCCTTATAGTGAGAGACTCAAGGAG 3880 rnd-5_family- 619 TTAAATATGTATAGTGTAGCTAAGACAA--CTAAGGGA------GAAAGA 660 i v v i v iv v v v --i i------ vv v CR1-L3A_Croc# 3881 CTCAATCTATTTAGCTTATCAAAGAGAAGGTTAAGGGGTGACTTGATCGC 3930 rnd-5_family- 661 AGTCTACAAATACATGAATGGTAAACA 687 i i v iv i vi CR1-L3A_Croc# 3931 AGTCTATAAGTACCTACACGGGGAACA 3957 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 45.10 CpG sites = 111, Kimura (unadjusted) = 48.12 Transitions / transversions = 1.50 (111/74) Gap_init rate = 0.08 (48 / 595), avg. gap size = 1.40 (67 / 48) 667 30.84 0.97 4.00 rnd-5_family-9920#LINE/CR1 100 511 (252) CR1-3_Croc#LINE/CR1 2196 2595 (1010) m_b26s551i9 rnd-5_family- 100 AATTTTACAGNTGATACTAAATTGGGAGGAGCTGAAAATCCCAGT--ATG 147 v i ?i i v i i iii vi iv -- --iv CR1-3_Croc#LI 2196 AAGTTTGCAGACGACACGAAACTGGGAAGGATTGCGAACAC--GTTGGAG 2243 rnd-5_family- 148 GAC-AGAGANAAATACAAAAGGANNTAGAGAGGTTAGAAACATGGGCAGA 196 -? v?v v i ?? v v i i vv vii CR1-3_Croc#LI 2244 GACGNGAGCGCAATTCAGAAGGATCTCGACAGATTGGAAAGCTGGGCTAG 2293 rnd-5_family- 197 AAATAACCANACGTAAGATTCAGCTTGGGAAAATGCAANNGTGGATACAT 246 iv vi? i - - iivi iv ?- v- i CR1-3_Croc#LI 2294 AGCTAACAGGATG-AAG-TTCAATGCGGACAAATGCAAG-GTGC-TACAC 2339 rnd-5_family- 247 CTGAGGAAAAATAATCTAAA-TACAGATATTCAATGGGAGNGAGAAACCT 295 vi ii v -i i ivv v ?v vvviv CR1-3_Croc#LI 2340 CTCGGGAGGAATAATCAAAAACACAAATACAAAATGGGTGACACCTGGCT 2389 rnd-5_family- 296 GGAAAGCAGTAATGCTGAAANAGTCATAGGGGCCTGGATGANAGTGGACA 345 vi i v iiv ?i v v i i i v ------ i iv CR1-3_Croc#LI 2390 GGATGGCAGCACTATGGAAAAGGACCTGGGAGTCTTG------GTAGATC 2433 rnd-5_family- 346 GCAAATTAGACATGACGTTTGCAGTGTAATATGGCAGCAAAAATGNCCGA 395 i i i vi i - i i iii v v v ? vi CR1-3_Croc#LI 2434 ACAGACTCAATATGA-GTCTGCAGTGTGATGCAGCCGCACAAAAGGCGAA 2482 rnd-5_family- 396 TGCAGTTTTGGGCTGCATACGCAAAAGNNNGACGGCTCATGACAGCAGGA 445 i v vvii i ???v - iv v - - i CR1-3_Croc#LI 2483 TGCGGTTTTGGGATGCATCAATAGAAGCATTA-GGTGCAAGACA-C-GGG 2529 rnd-5_family- 446 AGGTAANAGTCCCTCTNTGTACGGCTNTGGTACGACTGTATCTGGAATAC 495 i ? v ? iiv v? vv i ivi i CR1-3_Croc#LI 2530 AGGTGATAGTGCCTCTCTACTCGGCACTGGTTAGGCCTCATCTGGAGTAC 2579 rnd-5_family- 496 TGCATTCGNTTCTGAG 511 ii v i? i CR1-3_Croc#LI 2580 TGTGTGCAGTTCTGGG 2595 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.92 CpG sites = 69, Kimura (unadjusted) = 43.26 Transitions / transversions = 1.30 (69/53) Gap_init rate = 0.05 (19 / 411), avg. gap size = 1.05 (20 / 19) 17 8.91 0.00 0.00 rnd-5_family-10568#Unknown 126 149 (2784) (T)n#Simple_repeat 1 24 (0) m_b27s252i9 rnd-5_family- 126 TTTTTTGTTTTTTTTGTTTTTTTT 149 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 262 35.41 0.55 2.23 rnd-5_family-1067#LINE/RTE-BovB 11 192 (381) MamRTE1#LINE/RTE-BovB 3251 3429 (383) m_b27s601i0 rnd-5_family- 11 CCTAANATCCATCTGCANCATCAGGTGGCAGGACAGGAGGATCCCCAGCA 60 v? v vivi ? i ii i --- v i MamRTE1#LINE/ 3251 CCTACGAGCCATACTTAACATTAAATGGCAAGACAGGA---TCACCAACA 3297 rnd-5_family- 61 CTNAAGTCCTTGAGAGGTGCCAAATCNCTGGCATCAAGAGC-ATGCTCAT 109 vi? i v iv vv ivii? ii iii - - ii MamRTE1#LINE/ 3298 ACGAGGTCCTGGAACGCAGCCAGTCTACCAGCACTGA-AGCGATGCTCGC 3346 rnd-5_family- 110 CAGGGCTCAACTTCGCTGGGTCGGACACNTGGTCCGCATGGAGGTTTCCC 159 ivii v i i ii i? vvvv v v vivv v MamRTE1#LINE/ 3347 CGCAACGCAGCTCCGCTGGGCTGGACATGTGCGGAGAATGGATGACAGCA 3396 rnd-5_family- 160 GTATACCGAAAGCGGTGCTCTACCGCCAACTGA 192 v v ivv v v v iv i MamRTE1#LINE/ 3397 GGATACCCAAGCAGCTGCTGTACGGTGAGCTGA 3429 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.58 CpG sites = 32, Kimura (unadjusted) = 50.92 Transitions / transversions = 1.03 (32/31) Gap_init rate = 0.03 (5 / 181), avg. gap size = 1.00 (5 / 5) 202 14.65 0.00 2.44 rnd-5_family-13012#Unknown 42 83 (125) C AmnSINE1#SINE/5S-Deu-L2 (20) 555 515 m_b27s601i1 rnd-5_family- 42 TTTATATAGCACCTTTCATATTCNAGGTATCTCAAAGCNCTT 83 i -ii ? i v i ? C AmnSINE1#SINE 555 TTTATATAGCGCCTTTCAT-CCCGAAGGATCCCAAAGCGCTT 515 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.77 CpG sites = 5, Kimura (unadjusted) = 17.88 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 11 11.47 10.26 0.00 rnd-5_family-14144#Unknown 22 60 (224) (GCCCTCT)n#Simple_repeat 1 43 (0) m_b27s252i8 rnd-5_family- 22 GCCCTGTTNCCTCTGCCCTCT--CCTCTG--GTCTCCCCTCTG 60 v v? -- --v v (GCCCTCT)n#Si 1 GCCCTCTGCCCTCTGCCCTCTGCCCTCTGCCCTCTGCCCTCTG 43 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 2.00 (4 / 2) 183 27.51 1.61 3.28 rnd-5_family-15046#Unknown 68 191 (183) L2b_3end#LINE/L2 110 231 (235) m_b27s601i2 rnd-5_family- 68 CTCACANACGTCTCTGTGCCTTCTTCCATGCTGCCCCTTATGCNTGGAAC 117 ? v?v i v v iviv ? ii i v ? L2b_3end#LINE 110 CTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAAC 159 rnd-5_family- 118 GCCTTCCCAAACCTGTTCACCAAGCCACCTCC--CTCATTTCATTCNANT 165 i i vv v i vi v -- -- v ?i? L2b_3end#LINE 160 GCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCA--TCCTTCAGGT 207 rnd-5_family- 166 CCCCTCCTAAAANACTCACTTCTGCC 191 i vv ii v?-- i iv L2b_3end#LINE 208 CTCAGCTCAAATG--TCACCTCCTCC 231 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.99 CpG sites = 16, Kimura (unadjusted) = 37.37 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.04 (5 / 123), avg. gap size = 1.20 (6 / 5) 319 23.61 1.39 0.00 rnd-5_family-15365#DNA/Maverick 1496 1567 (835) UCON86#LINE/L2 593 665 (17) m_b27s502i0 rnd-5_family- 1496 GTCTACTGTTTCGTATTATTTAACGCTGTACAGCATCTAGGGTTACAGTT 1545 ii i i v v i i v v UCON86#LINE/L 593 GTCCGCTGTCTTGTATTATTTAACTCTGTAAAGCGTTTTGGGATACAGTT 642 rnd-5_family- 1546 TGCGTAAAAG-TGTTTTATAAAA 1567 ii i -i i v i UCON86#LINE/L 643 TGTATGAAAGACGCTATACAAAA 665 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.39 CpG sites = 12, Kimura (unadjusted) = 29.51 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 15 4.71 0.00 0.00 rnd-5_family-15365#DNA/Maverick 2342 2363 (39) (AACA)n#Simple_repeat 1 22 (0) m_b27s252i7 rnd-5_family- 2342 AAAAAACAAACAAACAAACAAA 2363 v (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 2897 12.18 2.82 2.82 rnd-5_family-2356#DNA/PIF-Harbinger 3 534 (8) AmnHarb1#DNA/PIF-Harbinger 122 653 (791) m_b27s502i1 rnd-5_family- 3 TGCAAACATATAAG--CTTGTCTGCACAACTNTTTCTGCAG-TCGCNAAA 49 i i v -- v vi ii ? v- i ? AmnHarb1#DNA/ 122 TGCAAATATGTACGTGCATGTACGCATGACTATTTCTGCACCTTGCAAAA 171 rnd-5_family- 50 ANTAGGGTGACGAAGAAGAGATGCTGTCACAATTATTGNATAGCATTT-- 97 ?-- --- i ivi i vv ii i v ?vvv -- AmnHarb1#DNA/ 172 AT--GGG---CGGAGAGTGGGTGGAGCTACGATTATAGTCGCGCATTTGT 216 rnd-5_family- 98 -----TCGAAGAAAAATTGTGNGGGCATCTTCCATTATNCCCGGGCAAAT 142 ----- i i ? v ? AmnHarb1#DNA/ 217 AATTTTCAAAGGAAAATTGTGTGGGCAGCTTCCATTATGCCCGGGCAAAT 266 rnd-5_family- 143 TTAGACGAATGAAAGCACNGACTAAGTAATTTTTGANATTGTACATATGT 192 ii? ? ? -- i AmnHarb1#DNA/ 267 TTAGACGAATGAAAGCGTCGACTAAGTAATTNTTGATAT--TATATATGT 314 rnd-5_family- 193 TTATAAATNAAAGCAGGAAAGCCTCTAATTCNTTCNTTTTAGCTGCTAAA 242 v ? i- ?i ? AmnHarb1#DNA/ 315 GTATAAATTAAAGCAGGAAAGCCTCTAG-TCACTCATTTTAGCTGCTAAA 363 rnd-5_family- 243 ATGCCTCTAGGGCTTTGGATTAGAAAGAGACAGAGG-CCCTTACAAGGAT 291 v i --- - ? AmnHarb1#DNA/ 364 ATGCCTCTAGGGGTTTGGATTAGAAGGAG---GAGGACCCTTANAAGGAT 410 rnd-5_family- 292 CAGAAGGCAATATCCCACAGGGAGGCAAATTGATACATAAGAATACAG-A 340 -- i i i - AmnHarb1#DNA/ 411 CAGAAGGCAATATCCCAC--GGGGGCAAATTGATACGTAGGAATACAGTA 458 rnd-5_family- 341 GA-ATTCCTTTTTTGACCTCACAGAGGAACANG-TTTAGATGAACATATG 388 v- v i ? - i ? i AmnHarb1#DNA/ 459 GCTATTCCTTTTTGGACCTCGCAGAGGAACAAGTTTTAGATAAANATACG 508 rnd-5_family- 389 ACAAACGGACCATTTTGGATCNCTNTGAGAAGATTTGANAAGTCGAACAC 438 i ? ? i ? i AmnHarb1#DNA/ 509 ACAAACAGACCATTTTGGATCTCTGTAAGAAGATTTGAAAAGTCAAACAC 558 rnd-5_family- 439 ACAGGAACGCTACTTTACCTGCAATGATGCAAATTACGTCATCT-TAGCC 487 i vv i i i iv i i- i AmnHarb1#DNA/ 559 ACAGGAGCCATGCTTTACCTGTAATGGTAAAAATTACATCATCCGTAACC 608 rnd-5_family- 488 TTTTAAGNAACAGGCTTATTTCACAAAAAGCAATGATTTANAGACNC 534 ? ? -- v i i i i ? i? AmnHarb1#DNA/ 609 TTTTNAGCAACAGGCTTATTT--CAAACAACAGTAACTTACAGATGC 653 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 12.56 CpG sites = 43, Kimura (unadjusted) = 14.16 Transitions / transversions = 2.15 (43/20) Gap_init rate = 0.05 (24 / 531), avg. gap size = 1.25 (30 / 24) 16 0.00 0.00 0.00 rnd-5_family-2673#DNA/hAT 112 128 (234) (A)n#Simple_repeat 1 17 (0) m_b27s252i6 rnd-5_family- 112 AAAAAAAAAAAAAAAAA 128 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 22.20 2.90 4.41 rnd-5_family-27926#DNA/hAT-Tip100 2970 3038 (65) (TTTAG)n#Simple_repeat 1 68 (0) m_b27s252i5 rnd-5_family- 2970 TTAAGTAAAGTTTAGTTGTTAATTTAAAAAAANTAAGTTTAGTTAAGTTT 3019 v vv - - i ivvv i? v v - (TTTAG)n#Simp 1 TTTAGTTTAGTTTAG-T-TTAGTTTAGTTTAGTTTAGTTTAGTTTAG-TT 47 rnd-5_family- 3020 TAGTTT-CTTTAGTTT-GTTT 3038 -v - (TTTAG)n#Simp 48 TAGTTTAGTTTAGTTTAGTTT 68 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5) 960 18.93 3.77 2.80 rnd-5_family-2857#DNA/hAT-Ac 3 214 (73) UCON26#DNA/hAT-Ac 5 218 (180) m_b27s502i2 rnd-5_family- 3 GATGGGCGAACCAGTTCGGATAAAATAAGAACCGACTCGAGCCTTTGACC 52 i ii i i v UCON26#DNA/hA 5 GATGGGCGAACCGGTTCGGATAAAATAAGAACCGACCTGAACCTTCGCCC 54 rnd-5_family- 53 CAAATTCGAACCGAACCCGATC--AAATCTTTTGGAGGTTTGAAAATGTT 100 v i v --i ii v i v UCON26#DNA/hA 55 AAAACTCGAACCGAACCCGAACCTGAACTTTTTTGAGGTTCGAAAAAGTT 104 rnd-5_family- 101 TTGTNAGNANTGTTGGCATACTATTAATGTTAATTTTCGTGCATTCTNCA 150 iv ? i?v? v v? i -- --- v v i i-i ?ii UCON26#DNA/hA 105 CGGTTAACTTTTTTTNCGT--TAT---TTTTCATTTTCGCGCG-CCTCTG 148 rnd-5_family- 151 CACTTCCTGGTTTCAGCCGGGACAGGAAGCGGAAATGCC--AATGAAGCG 198 i i v i -- ivv UCON26#DNA/hA 149 CACTTCCTGGTTCCGGCCGGGACCGGAAGCGGAAGTGCCGAAATACCGCG 198 rnd-5_family- 199 ----AGGCTGTTCTCATAGT 214 ---- iii UCON26#DNA/hA 199 AGAAAGGCTGTTCTCGCGGT 218 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.68 CpG sites = 25, Kimura (unadjusted) = 22.92 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.56 (14 / 9) 12 19.48 0.00 2.70 rnd-5_family-3579#Unknown 705 742 (983) (TTTTA)n#Simple_repeat 1 37 (0) m_b27s252i4 rnd-5_family- 705 TTTTATTTTNTTTAATTTATATATTTTACTATTTGATT 742 ? v - v v vi v (TTTTA)n#Simp 1 TTTTATTTTATTTTATTT-TATTTTATTTTATTTTATT 37 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 15 9.78 0.00 0.00 rnd-5_family-39154#Unknown 592 613 (123) (TG)n#Simple_repeat 1 22 (0) m_b27s252i3 rnd-5_family- 592 TGTTTGTGTGTGTGTGTGTCTG 613 v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTG 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 23 16.08 1.64 5.08 rnd-5_family-4673#DNA/hAT-Tip100 563 623 (1221) (CTC)n#Simple_repeat 1 59 (0) m_b27s252i2 rnd-5_family- 563 CTCCTCCTCGGCTTGTCC-CCGCCTCTGCCTCCTCCTCCTCCTCCTCTCT 611 -- iv - v iv - (CTC)n#Simple 1 CTCCTCCTC--CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CT 47 rnd-5_family- 612 GCGCCGCCTCCT 623 v v v (CTC)n#Simple 48 CCTCCTCCTCCT 59 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 654 22.09 5.69 4.95 rnd-5_family-4922#Unknown 13 293 (87) UCON60#Unknown 1 283 (17) m_b27s502i3 rnd-5_family- 13 AAACCTAACNNAAAATCCTACTGCGCATGCGTGAAA---AAANTGTCCAG 59 v v?? v i i - v i --- v ? v iv i UCON60#Unknow 1 AAACCAAAAGAAAATTTCTACTGCGTATGC-TCAGACGTATAATTTTAAA 49 rnd-5_family- 60 TGCTCATAACTTCAAAACTACTGAACCAATTTCCTTCAAACTTGGCTTG- 108 ivi i i v ? iv i i - UCON60#Unknow 50 CCTTCGTAACTTTAAAAATACTNAACCGTTTTTCTTCAAATTTGGCTTGA 99 rnd-5_family- 109 --TTCCTTAGATCTCAATGAGATCTACAAAACAAGCCAAGTCTGAACAAA 156 -- ---i ? iv - v vv i vvvv UCON60#Unknow 100 TTTTCCTT---CCTCANTGAGGACTAC-AATCCTGCCAAGTTTGAAGTTT 145 rnd-5_family- 157 ATCCGTTCAGTTCTGTTGTTGAGTTATGCATGCACAAA------ATTTCT 200 vvv -- i v i iv ------ - UCON60#Unknow 146 ATAGCTTCAG--CCGTTTTTGAGTTATACGAGCACAAAAAAAACATTTC- 192 rnd-5_family- 201 GATCACACCTAAG----GGGAATGTGCGTTTATTTTANTACACACGCCAG 246 - ivii v ---- i v ii v i ?i--- v - v UCON60#Unknow 193 GAT-ATTTTTTAGAANTGGAAAAGTGTATTTCTTCTATC---CTCG-CAT 237 rnd-5_family- 247 AACTCAAAAATGGCTGAACGGATTTTGCTGAANCTTTCTAAAACAAA 293 i v ? v ? - v UCON60#Unknow 238 AACTCAAAAACGGCTGAACCGATTTNGCTCAAACTTTC-AAAAGAAA 283 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.74 CpG sites = 27, Kimura (unadjusted) = 27.27 Transitions / transversions = 0.84 (27/32) Gap_init rate = 0.07 (19 / 280), avg. gap size = 1.58 (30 / 19) 295 30.38 5.56 7.04 rnd-5_family-5874#DNA/hAT-Charlie 292 507 (966) C Charlie8#DNA/hAT-Charlie (371) 2086 1874 m_b27s502i4 rnd-5_family- 292 GAACGTTGCTTGTTTTTATTCATGTTCATGATGGAAAATGTTTGTTCACA 341 i v ii iv vv i iivi C Charlie8#DNA/ 2086 GAGCGATATTTAGTTTTATTCAGTTTCATAATGGAAAACAGCTGTTCACA 2037 rnd-5_family- 342 TATGTAAGTGCTTCCAAAAATGCTGAACGTTTTCAGTGCAACTTCAATAA 391 v i i i i v vvv ivi i --- ---- -- C Charlie8#DNA/ 2036 AACGTAGGTACTTCCGAACATGGATAGAATCTT---TGCA----CAAT-- 1996 rnd-5_family- 392 GATTCTTGTATTT-------TTCATCGTCCAGACTTTTGTAGAAGTCCCG 434 i i i -------i vv -i v iv v iv C Charlie8#DNA/ 1995 GGTTTTTATATTTAGGGTAACTACTC-CCGAGATATTTGTAGAATTCTGG 1947 rnd-5_family- 435 CAAGCTGCTTTCTCTGTGCTTA--TTTCGGTAAACTGCCGAA---CACTG 479 i vv iiviv vii ii -- i ----- v --- C Charlie8#DNA/ 1946 TATTCCAACGTCGTCGTATTTAGTTTTCAGTA-----CCGTATTGCACTG 1902 rnd-5_family- 480 AAGTTCAATAACCTCCAACTGCAAATCT 507 v i vi i iv C Charlie8#DNA/ 1901 CAGTTCAATAACTTCCATTTGTAGCTCT 1874 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 35, Kimura (unadjusted) = 39.95 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.08 (18 / 215), avg. gap size = 1.50 (27 / 18) 541 34.36 5.21 2.25 rnd-5_family-5874#DNA/hAT-Charlie 922 1439 (34) C Charlie8#DNA/hAT-Charlie (986) 1471 939 m_b27s502i5 rnd-5_family- 922 TCTTTCAA-AG--CAACGAAACGCTGGAGCACTCTTCCTCGACTCAACCA 968 - -- vi v v vv iviv v v i C Charlie8#DNA/ 1471 TCTTTCAACAGTTCAAAAAATCTCTTCAGCACCACGCCACGACTAAGCCA 1422 rnd-5_family- 969 CCTCACTTCTGTATGGTAGATTAAGTCGTTGCACTCGGTGTCTACCCCTT 1018 v i i i i v vi iiiiiii i i vv ii i vii v C Charlie8#DNA/ 1421 CCTAACCTCCGTGTAGTACAGCAGACTACCGTATTGTGCATCCAATTCAT 1372 rnd-5_family- 1019 CAAGAAAGGC-TCGAAATGTCCTATGTTTTAGTCCTCTAGAACGGATGNA 1067 v i - i v - i v i iv v vi i v v? C Charlie8#DNA/ 1371 CAAGCAAAGCATTGAACTGTC-TGTGGTTCAAGCCACGGGAGCGTATCCA 1323 rnd-5_family- 1068 GTTTACAATGGAAACTACCACTGACATTACATGCTCAAATTTTAAGACTT 1117 i ii vv i i vvv v i i v v -- C Charlie8#DNA/ 1322 GTTCACGGTGTTAATTACTACGTCCATGACGTGTTCCATTTTTAA--CTT 1275 rnd-5_family- 1118 TGCTACACAAAAC--CTGCTGATGTATAATGCAGTGA-TG---TTTGGTT 1161 vivi i --i v i v i i -i --- vi C Charlie8#DNA/ 1274 TTTAGCACAAAGCGATTCCTGGTGAATGATGCAATGAACGGACTTAAGTT 1225 rnd-5_family- 1162 ATTTGTC-TCCCGATAAATT-----CTTCAAG--AAG---AGTAACTGCT 1200 viv - iv i v vi ----- vi v-- ---v viv C Charlie8#DNA/ 1224 CCGTGTCCTTGCAAAACGTTGCCACCTTGGATTTAAGTTTCGTAACAAGT 1175 rnd-5_family- 1201 CCAACATTTTTTCCGCACATAGCTGGAGCACCATCAGTACAAATGGCCAC 1250 i i vviv vv v v i v vvv i vii C Charlie8#DNA/ 1174 CCGACGTTAACACCGACCATCGCAGGAGCACCGTCTGTAGTCACGCTTAC 1125 rnd-5_family- 1251 CAAGTTTGTGAAATCTAATCCCGACTTATCATTCATGCACTTTATCACTT 1300 i v vvv i vviivi ---- v vvi v viv C Charlie8#DNA/ 1124 TAATTTTGACCAGTCTACATTAAACTT----TTCAAGACTTTTCTCAACA 1079 rnd-5_family- 1301 CACTGGAGAT---TTCTTTTCCG--GTTGTGCGACCCGTCATGGAGCAC- 1344 -ii i --- iv i i -- --- i - - C Charlie8#DNA/ 1078 CAC-AAAAATAAGTCATTTCCTGATGTTGTGC---CTGTCATGG-GCACC 1034 rnd-5_family- 1345 ATGCCAGCAAGTTCTTCAGTAATTTCAAAGTTTTTATCAATACCTCTAAT 1394 i viv i v iv i i i i i v v C Charlie8#DNA/ 1033 ATGTCCAAAAGTTCTTCGGTCACATCAAAATTCTCATCGACACCACGAAT 984 rnd-5_family- 1395 AAAAATAAGAAGTTGGGCGGTGTCTTTTAAATCGGTGCTTTCATC 1439 v ivv ii i i iv v v i C Charlie8#DNA/ 983 AAATATAGCTAACTGGGTGGTATTATTTATATCTGTGCTCTCATC 939 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.09 CpG sites = 89, Kimura (unadjusted) = 47.04 Transitions / transversions = 1.05 (89/85) Gap_init rate = 0.05 (25 / 517), avg. gap size = 1.56 (39 / 25) 322 27.50 0.00 0.00 rnd-5_family-5874#DNA/hAT-Charlie 1378 1457 (16) C Charlie12#DNA/hAT-Charlie (1541) 1329 1250 m_b27s502i6 rnd-5_family- 1378 TTATCAATACCTCTAATAAAAATAAGAAGTTGGGCGGTGTCTTTTAAATC 1427 i i iiv v v i ? v vivi C Charlie12#DNA 1329 TCATCAATGCCTCTAATAAAAATGGCAAGTTGTGCCGTATNTGTAGCGTC 1280 rnd-5_family- 1428 GGTGCTTTCATCCATAGCTAGGGAGTAAAA 1457 i i v i ii vii C Charlie12#DNA 1279 AGTGCCTTCATCCATCGCCAAAGCACAAAA 1250 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 14, Kimura (unadjusted) = 36.07 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0) 15 13.59 2.17 6.82 rnd-5_family-635#Unknown 317 362 (226) (GCGGG)n#Simple_repeat 1 44 (0) m_b27s252i1 rnd-5_family- 317 GCGCGGTCGGGTCGGGTCGAGG-GGGGCGGGGGCAGGGGCGGGGGGG 362 - v v v i - - - v (GCGGG)n#Simp 1 GCG-GGGCGGGGCGGGGCGGGGCGGGGC-GGGGC-GGGGCGGGGCGG 44 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 14 25.60 0.00 2.13 rnd-5_family-6480#DNA/hAT-Tip100 281 328 (311) (GGCGG)n#Simple_repeat 1 47 (0) m_b27s252i0 rnd-5_family- 281 GGCGGGGCGACGCCGGGAGCCGGCGGAGCGGAGCGGGCCGGGCTGGGG 328 iv v v -v i i v vi (GGCGG)n#Simp 1 GGCGGGGCGGGGCGGGGCG-GGGCGGGGCGGGGCGGGGCGGGGCGGGG 47 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 14 0.00 5.00 10.53 rnd-5_family-10982#LTR/DIRS 1369 1408 (266) (AACT)n#Simple_repeat 1 38 (0) m_b28s252i14 rnd-5_family- 1369 AACTANNCTAACTATACTACAGCTAA-T-ACTAACTAACTAA 1408 -? - - - - - (AACT)n#Simpl 1 AACTA-ACTAACTA-ACTA-A-CTAACTAACTAACTAACTAA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.15 (6 / 39), avg. gap size = 1.00 (6 / 6) 2710 15.98 12.16 3.40 rnd-5_family-11304#DNA/PIF-Harbinger 23 754 (5) UCON9B#DNA/PIF-Harbinger 156 949 (410) m_b28s502i0 rnd-5_family- 23 GCAGCCCATTGTTAGANTTTCCAAAANNTTCAAGGAGAAGTNTTTGTGCT 72 i i ii i ? - ?? i ? UCON9B#DNA/PI 156 GCAACCTATCATCAGATTTTC-AAAAAATTCAGGGAGAAGTTTTTGTGCT 204 rnd-5_family- 73 TACAGNTCCNCACTGATCAA-----------------GCATATGTGTCNC 105 ii i? v ? -----------------i iii ? UCON9B#DNA/PI 205 CGCAATTGCACACTGATCAACGCCCCCTTGCTCATTAACATACACGTCCC 254 rnd-5_family- 106 CTTCC-----TG-TCTCATTTGNACTATGTAAACAGTTTCTAACAGCTCC 149 i i----- - ? i UCON9B#DNA/PI 255 CTCCTATTTGTGCTCTCATTTGCACTATGTAAACAGCTTCTAACAGCTCC 304 rnd-5_family- 150 TTTCTCTTCTTCATTCAAACAA----TGGCCTTTGTAACCAAGAAGAAAA 195 i i i ---- UCON9B#DNA/PI 305 TTTCCCCTCTTCGTTCAAACAAACAATGGCCTTTGTAACCAAGAAGAAAA 354 rnd-5_family- 196 TTAGTAGCAGGCGAAAGCTTATTTTTNATAATGCTGAGACCAAANTGTTA 245 i ? i ? UCON9B#DNA/PI 355 TTAGTAGCAGGTGAAAGCTTATTTTTAATGATGCTGAGACCAAATTGTTA 404 rnd-5_family- 246 TT-AACTTGAAATA---GAACATGCACTTCCCCTTA---CCACCCTAANT 288 - i ---i vi- i i --- v ii ? UCON9B#DNA/PI 405 TTTAACTTAAAATATNAAAACATTT-CTTTCCCTCAAATCCCCTTTAATT 453 rnd-5_family- 289 CCTCTTTGATGTTTCCGGATAATATANTTT--CATGCCC-TACACTTTGA 335 viv i ----i -- ? -- i i- - i UCON9B#DNA/PI 454 CCTCACAGATATT----AAT--TATAGTTTGTCATACCTATAC-CTCTGA 496 rnd-5_family- 336 AATGTTTGCTCTTCCAGAAGAGNTCAAAANNCAGCCCTTTGCGGGCACGC 385 ii i ii ? ??i i vv i ii UCON9B#DNA/PI 497 AATACTTGCTCCTCCGAAAGAGTTCAAAAACTAACCCTTTGCCTGTATAC 546 rnd-5_family- 386 CAAAT-----GAGTAAAAA-GCCTC-------------ATTTTTCCANTG 416 vv ----- i - i------------- ? i UCON9B#DNA/PI 547 CCTATTAGCAGGGTAAAAACGCCTTCTCTCTTCTCACTATTTTTCCAATA 596 rnd-5_family- 417 CATACGATGAAAACACANGAGATNACCGTGCAGGATTTGTATAGNNAGAT 466 i i ? --- -ii i ?? UCON9B#DNA/PI 597 CATATGATGAAAACATATGAGAT---CGT-TGGGATTTATATAGGCAGAT 642 rnd-5_family- 467 TTGGCAACCTTTTCNTATTNACTTGGACTGTGAAATATAAATCGAATNTG 516 i ? ? i i ? UCON9B#DNA/PI 643 TTGGCAGCCTTTTCATATTTACTTGGACTGCGAGATATAAATCGAATTTG 692 rnd-5_family- 517 GGNTTCTTTC--CAAGAATAAGTTATTTGTTATCGGAATAAGTGTGTGTT 564 ?i i -- v i UCON9B#DNA/PI 693 GGGCTCTCTCTCCAAGAATAAGTTATTTGTTATCTGAATAAGTATGTGTT 742 rnd-5_family- 565 GCTGGGCAAGGTATCGATGAGGNATNNCTNT----------------AAG 598 iv iiv ii iv i ?i ?? ? ---------------- i UCON9B#DNA/PI 743 AGTGGATCAGACACGGATAAGGTGTTTCTATTATAACTGTGTTTGTTAGG 792 rnd-5_family- 599 TATAGTTTAATTTTTTCTCCACTNNTTAGAAACTACAATATTTTTCNTTT 648 ii vv v vi i ?? ------ i vii ? UCON9B#DNA/PI 793 TATGATTTACATTGTTCTATATTGTTT------TATACCGTTTTTCATTT 836 rnd-5_family- 649 TTGGC----------GTGNTCTTGTCCT----ATCTTTTC-CGNTTGGTA 683 i ii---------- -? ii ---- i v - ? i- UCON9B#DNA/PI 837 TCGATTACTTAATTTGT-TTCTTGTTTTGTGTATTTTGTCACGGTTGGC- 884 rnd-5_family- 684 NATGATGNCTCTATATNGTCATTANTTTTTAACTTTGACAANANTCTGGT 733 -- - ?v i v i ? -- v ? -i ? ? i ii UCON9B#DNA/PI 885 --TG-TGGGTTTTTGTGGT--TGACTTTTTAACTTTG-TAACACTTTAAT 928 rnd-5_family- 734 ACAAAGGAAATGTAAACAATA 754 i v v i UCON9B#DNA/PI 929 GCAAAGGAAATTTAAAAAACA 949 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.31 CpG sites = 89, Kimura (unadjusted) = 19.87 Transitions / transversions = 3.71 (89/24) Gap_init rate = 0.06 (44 / 731), avg. gap size = 2.64 (116 / 44) 1171 17.57 3.37 4.01 rnd-5_family-12789#LINE/L2 5 330 (306) AmnL2-1#LINE/L2 1674 1997 (616) m_b28s601i0 rnd-5_family- 5 TCAGCTCCTTTCTTAGCTTTNCCCTGCCCACTCTCTCNGNCTGCCTTGAT 54 ii v vv ii ii? i i ? ? i i AmnL2-1#LINE/ 1674 TCGACACCTTTAATGACTCCTCCCTGTCCACCCTCTCTGCCTGTCTTGAC 1723 rnd-5_family- 55 CAAGTAAACTTGTG-CTTTNTCTCGACGTCCTTCAGCTAAATGTCTNAGA 103 - i? ii v ? i AmnL2-1#LINE/ 1724 CAAGTAAACTTGTGGCTTCGTCTCAGCTTCCTTCAGCTAAATGTCTCAAA 1773 rnd-5_family- 104 ANC-GAAGTACTCCTCTTGCGAAAGAAG-GTTTCCTAAGACACCGTNTCT 151 i? - i i v v i - iv v i vi----- AmnL2-1#LINE/ 1774 GACAGAAGTGCTTCTCTTGGGCAAGAGGAGCATCCTCAAACACAA----- 1818 rnd-5_family- 152 CCTNCTTTTCCTCTCTCCCCTCCACTCAATTCAGACCTTCCATTTGCCTC 201 - ? v i v i ii - i i i AmnL2-1#LINE/ 1819 -CTCCATCTCCTCTATCTCCCTC-CTCGACTCAGACCTCCCATTTGCCTC 1866 rnd-5_family- 202 CTCCGNCCGTAACCTTGGTGTCACCCTTGACTCTGAACTCTCCT----CT 247 v i ? i i i ---- AmnL2-1#LINE/ 1867 CGCTGTCCGTAACCTTGGCGTCATCCTTGACCCTGAACTCTCCTTCTCCT 1916 rnd-5_family- 248 CCCAA--CTCTTATG--GGCAAATTTGCATATCCGCCACTTCCGCAANAT 293 v-- i i --v i v - i i ? AmnL2-1#LINE/ 1917 CCCACATCTCCTGTGTCTGCAAATCTGCCTAT-CACCACCTCCGCAACAT 1965 rnd-5_family- 294 TNCCTNTGTATGTGCCACTTCACTTGACTCAACACCT 330 ? i? -- v - i -- AmnL2-1#LINE/ 1966 TGCCCGTGTA--TGCCACTGC-CTCGACTC--CACCT 1997 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.91 CpG sites = 39, Kimura (unadjusted) = 21.44 Transitions / transversions = 2.44 (39/16) Gap_init rate = 0.06 (19 / 325), avg. gap size = 1.26 (24 / 19) 1298 14.80 6.95 1.57 rnd-5_family-12789#LINE/L2 331 632 (4) UCON86#LINE/L2 1 318 (364) m_b28s502i1 rnd-5_family- 331 CCGCTGAAATCCTCATCCGCGCCTTCATCTCGNCTCATCTCCACTATGGC 380 i i? v? ii iv v UCON86#LINE/L 1 CTGCTGAAATCCTCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGC 50 rnd-5_family- 381 AACTCCCTTCTCNTGGGTCTTCCCAAGTCCCANCTCCNCAGACTCCAGCA 430 ? ?vv i i ? i? UCON86#LINE/L 51 ANCTCCCTTCTCTATGGCCTCCCCAAGTCCCAGCTCTCCAGACTCCAGCA 100 rnd-5_family- 431 TGTGCAGAATGCTGCTGCCCGCCTT-TCTCCCGCANNTACAAGGGCG-CC 478 i - v v ??v v v - UCON86#LINE/L 101 CGTGCAGAATGCTGCTGCCCGCCTTCTCACACGCACAAAGAAGTGCGACC 150 rnd-5_family- 479 ACA-CACCTCCATCCTCAAACANCTCCACTGGCTCCCCATTCATTTCAGG 527 - i ? UCON86#LINE/L 151 ACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAGG 200 rnd-5_family- 528 ATCCAGTTCAAAATTGCCTCTCTTGTTTC--AAAT--------------C 561 iii i-- i-------------- UCON86#LINE/L 201 ATCCAGTTCAAAATTGCCCTCCTTGTTTTTAAAACCCTCCATGGACTTGC 250 rnd-5_family- 562 TCCACCCTTCATCAC--ACCTAGAACTGCCCGCCTCCACTTCCCTCTCTG 609 v v v -- ----- i ivi ii i i i UCON86#LINE/L 251 TCCAGCCTACCTCACGGACCT-----TGTCTCTCTCTGCTCCCCTCCCCG 295 rnd-5_family- 610 CCCTCCTCACTNATCTACCACCG 632 i i ii i ?i v UCON86#LINE/L 296 CTCCCTCCGCTCGTCTAGCACCG 318 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 15.38 CpG sites = 29, Kimura (unadjusted) = 17.44 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.04 (11 / 301), avg. gap size = 2.36 (26 / 11) 237 14.55 0.00 0.00 rnd-5_family-13155#DNA/hAT-Charlie 11 65 (214) Charlie13b#DNA/hAT-Charlie 11 65 (447) m_b28s502i2 rnd-5_family- 11 CAACATGCGGCCCGCGGGCCGCATGCGGCCCGCGTGGGCTCACTGTGCGG 60 iv v iv i vv Charlie13b#DN 11 CAACATGCGGCCCGCGGGCCAAATGCGGCCCGCCTGACCCCAGGGTGCGG 60 rnd-5_family- 61 CCCGC 65 Charlie13b#DN 61 CCCGC 65 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.17 CpG sites = 3, Kimura (unadjusted) = 16.17 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 19 18.88 0.00 0.00 rnd-5_family-13155#DNA/hAT-Charlie 132 173 (106) (GGCT)n#Simple_repeat 1 42 (0) m_b28s252i12 rnd-5_family- 132 GGCTGGCTGGCTGGCTGGCCGGCCGGCGGGTGGGCGGGGTGG 173 i i v iv v v (GGCT)n#Simpl 1 GGCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 13 10.36 6.45 0.00 rnd-5_family-13155#DNA/hAT-Charlie 218 248 (31) (CAGCGG)n#Simple_repeat 1 33 (0) m_b28s252i13 rnd-5_family- 218 CAGCGGCAG-GGCGGGGGC-GGGGCAGCGGCAG 248 - i v - v (CAGCGG)n#Sim 1 CAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAG 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 404 33.01 1.99 3.54 rnd-5_family-19757#LINE/RTE-X 28 228 (1607) L4_A_Mam#LINE/RTE-X 3218 3415 (1575) m_b28s551i0 rnd-5_family- 28 CGAGGAACAAGCCGGTTTCAGGAATGGCTGCTCTACCATTGATAATTGTT 77 i i v i i v i ii i i iv i L4_A_Mam#LINE 3218 CGAGGAGCAGGCGGGCTTTAGGCACGGCTATTCCACTATTGACCACTGTT 3267 rnd-5_family- 78 TTGTCCTCTCTCATTTGATTTATAAATATTGNTCCCCCAAGAGGGA---- 123 v iii i v ii vi vv v -i ?----- i ivi ---- L4_A_Mam#LINE 3268 ATACTCTTTATCACCTTGTGGAGAAAT-CTGT-----CAGGAACAACATA 3311 rnd-5_family- 124 AAATTNTATGCGGCCTTTNTTGATCTGAAATTGGCATTTGATTCCGTTGA 173 i ? v i ? i vvvv i v i i v L4_A_Mam#LINE 3312 AGATTGTTTGCGGCTTTTATTGACCTTTCCTCGGCCTTTGACTCTGTGGA 3361 rnd-5_family- 174 CANAGGTCGTCTCTGGGAGAAACTCGCGAGGGACTGGNATAGACCCTCGG 223 ?iii vi v vv i - iv i viiii? i L4_A_Mam#LINE 3362 CAGGAATCGGTTATGGGCTAAGCT-GCATGAGCTCAATATAGACCCCCGG 3410 rnd-5_family- 224 CTACT 228 i L4_A_Mam#LINE 3411 CTATT 3415 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 45.42 CpG sites = 41, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.04 (8 / 200), avg. gap size = 1.38 (11 / 8) 201 21.73 9.38 2.94 rnd-5_family-20212#SINE/MIR 335 462 (688) MIRc#SINE/MIR 27 162 (106) m_b28s601i1 rnd-5_family- 335 GCCCGGGGCTTGG-----GGGATNCCTNGGTTCTATTCCCAGCTGTGCCG 379 v v i ----- i v? ? v v i v i MIRc#SINE/MIR 27 GCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCA 76 rnd-5_family- 380 CTGACT--CC-TGTGAGCTTTGGCAGGTCCCCT--CCTGTCTGGGTGCCT 424 v -- i- v v i v i -- v i -- MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG--CCT 124 rnd-5_family- 425 CAGTTTGCCCTC-TCTCTAAGCCGGGG-CNATAACATTTG 462 -- - v ivi -i? i ii MIRc#SINE/MIR 125 CAGTTT--CCTCATCTGTAAAATGGGGATAATAATACCTG 162 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.62 CpG sites = 14, Kimura (unadjusted) = 26.74 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.60 (16 / 10) 228 17.60 5.26 5.26 rnd-5_family-20212#SINE/MIR 337 450 (700) MIR1_Amn#SINE/MIR 38 151 (79) m_b28s601i2 rnd-5_family- 337 CCGGGGCTTGGGGGATNCCTNGGTTCTATTCCCAGCTGTGCCGCTGACTC 386 i i i i -- ? ? ? i v i ?i i? MIR1_Amn#SINE 38 CTGGGACTCGGGAGA--CCTGGGTTCNANTCCCGGCTCTGCCACTNGCCN 85 rnd-5_family- 387 -CTG--TGAGCTTTGGCAGGTCCCCT--CCTGTCTGGGTGCCTCAGTTTG 431 - -- v v i v i -- v ? -- - MIR1_Amn#SINE 86 GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNG--CCTCAGTTT- 132 rnd-5_family- 432 CCCTC-TCTCTAAGCCGGGG 450 - - v ivi MIR1_Amn#SINE 133 -CCTCATCTGTAAAATGGGG 151 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.33 CpG sites = 12, Kimura (unadjusted) = 21.81 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.09 (10 / 113), avg. gap size = 1.20 (12 / 10) 246 14.27 6.32 4.12 rnd-5_family-20212#SINE/MIR 349 443 (707) MIR3#SINE/MIR 43 139 (69) m_b28s601i3 rnd-5_family- 349 GGATNCCTNGGTTCTATTCCCAGCTGTGCCGCTGACTC-C--TGTGAGCT 395 v? ? v i v i i ?- -- v MIR3#SINE/MIR 43 GGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCT 92 rnd-5_family- 396 TTGGCAGGTCCCCT--CCTGTCTGGGTGCCTCAGTTTGCCCTC-TCTCTA 442 v i v i -- v -- -- - v MIR3#SINE/MIR 93 TGGGCAAGTCACTTCACCTCTCTGG--GCCTCAGTTT--CCTCATCTGTA 138 rnd-5_family- 443 A 443 MIR3#SINE/MIR 139 A 139 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.19 CpG sites = 5, Kimura (unadjusted) = 16.46 Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.09 (8 / 94), avg. gap size = 1.25 (10 / 8) 225 21.76 6.15 4.55 rnd-5_family-20212#SINE/MIR 352 481 (669) MIR#SINE/MIR 45 176 (86) m_b28s601i4 rnd-5_family- 352 TNCCTNGGTTCTATTCCCAGCTGTGCCGCTGACT--CC-TGTGAGCTTTG 398 ? ? v v i v i v -- i- v v MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 rnd-5_family- 399 GCAGGTCCCCT--CCTGTCTGGGTGCCTCAGTTTGCCCTC-TCTCTAAGC 445 i iv i -- v -- -- - v iv MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTG--TGCCTCAGTTT--CCTCATCTGTAAAA 140 rnd-5_family- 446 CGGGGCNATAACATTTGTG--TGCTTCATACAGGTGTT 481 i -- i v v i-- i i vi v MIR#SINE/MIR 141 TGGGG--ATAATAATAGTACCTACCTCATAGGGTTGTT 176 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.30 CpG sites = 13, Kimura (unadjusted) = 26.38 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.09 (11 / 129), avg. gap size = 1.27 (14 / 11) 12 35.17 0.00 0.00 rnd-5_family-2067#Unknown 61 117 (417) (CCCC)n#Simple_repeat 1 57 (0) m_b28s252i10 rnd-5_family- 61 CCCCCCCCCCACCTCCCCCCGCGCGGGCCCCCTGCCCAGCCCTCCCTGCC 110 v i v v vvv iv vv i iv (CCCC)n#Simpl 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 rnd-5_family- 111 TCCCGCC 117 i v (CCCC)n#Simpl 51 CCCCCCC 57 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 15 25.47 1.67 3.39 rnd-5_family-2067#Unknown 392 451 (83) (GCCGG)n#Simple_repeat 1 59 (0) m_b28s252i11 rnd-5_family- 392 GCGGGGCCGGCCCGAGGCC-CCCCGCCGCCCGCCCGTGCGGGGCCGGCCC 440 v v - -vv -v v v v v v (GCCGG)n#Simp 1 GCCGGGCCGGGCCG-GGCCGGGCCG-GGCCGGGCCGGGCCGGGCCGGGCC 48 rnd-5_family- 441 GGCCCGAGCCG 451 v i (GCCGG)n#Simp 49 GGGCCGGGCCG 59 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 238 19.35 0.00 0.00 rnd-5_family-23493#DNA/Crypton 73 134 (677) Eulor6D#DNA/Crypton 101 162 (140) m_b28s502i3 rnd-5_family- 73 ACCANNGCAGAAGTGCACCAGTAGCCTACTAATGCACATCCNGGNGTGGN 122 ??vv vi i v i?vv vv ? ? v? Eulor6D#DNA/C 101 ACCACCCGAGAAGTGCAATAATCGCCCNGAAATGCACTGCCTGGAGTGTC 150 rnd-5_family- 123 TTATTGCTANTA 134 ? Eulor6D#DNA/C 151 TTATTGCTATTA 162 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.83 CpG sites = 3, Kimura (unadjusted) = 25.83 Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 353 24.83 7.03 4.21 rnd-5_family-2407#DNA/Kolobok 4 188 (0) UCON4#DNA/Kolobok 285 474 (4) m_b28s502i4 rnd-5_family- 4 AAACAAAAAAATGCC--GTCAGCAGCCCAGCACTCATGAGCAACCCTACA 51 - -- i -- vii v - v v v vivi UCON4#DNA/Kol 285 AAACAAAAAAA-GCCATGTTA--ATTTCAGCTC-CATTAGAAACACAGGG 330 rnd-5_family- 52 ATAACAAACCAACGTGCGCCG--CGGAAGGAGGGAAAAAATTGGTAAGGA 99 - v i i vi i--i -- i v i i UCON4#DNA/Kol 331 A-AAAAAATCAATGTTTGCCAAATGGAA--AAGGACAAAATCGGTAGGGA 377 rnd-5_family- 100 AACAGATTTCAGTTTCAAGCTTTCAAGGGATTATTATAAACAATAANGAG 149 v i i v ii i iv i ii? UCON4#DNA/Kol 378 AAGAAATTTTATTTTCAAGCTTCTAAGAGGGTATTACAAACAATGGAGAG 427 rnd-5_family- 150 --------GATTTTTTTAATTATGAAAAA-TACCTTGACAGTGTCCTT 188 --------i vv ?vvv i i - - i UCON4#DNA/Kol 428 TAAAAANAAAAATNAAAAACTATAAAAAAGTA-CTTGACAGTGTCCCT 474 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.45 CpG sites = 26, Kimura (unadjusted) = 31.30 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.07 (12 / 184), avg. gap size = 1.75 (21 / 12) 12 23.90 0.00 2.50 rnd-5_family-2561#SINE/tRNA 468 508 (3748) (GGGCAG)n#Simple_repeat 1 40 (0) m_b28s252i7 rnd-5_family- 468 GGGCAGGGGCTGGCTGGGGGGCAGGGAATGGGGCACGGGGC 508 v vvvi ivv - (GGGCAG)n#Sim 1 GGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCA-GGGGC 40 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 211 20.00 0.00 1.82 rnd-5_family-2561#SINE/tRNA 727 782 (3474) LFSINE_Vert#SINE/tRNA 6 60 (399) m_b28s601i5 rnd-5_family- 727 GAGACTGGTTGGCTCAGAGGGGCAAGGAATGGGGCACGGGGCCTTTCCCC 776 i v - iivi v ii i v LFSINE_Vert#S 6 GGGACTGGATGGCTCAG-GGGATTGGTAATGGGATACGGAGCCTTTCACC 54 rnd-5_family- 777 TCTAGG 782 LFSINE_Vert#S 55 TCTAGG 60 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.75 CpG sites = 7, Kimura (unadjusted) = 23.75 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 27 3.45 0.00 0.00 rnd-5_family-2561#SINE/tRNA 2238 2267 (2054) (GGAGCCC)n#Simple_repeat 1 30 (0) c_b28s251i0 rnd-5_family- 2238 GGAGCCCGGAGCCCGGAGCCCAGAGCCCGG 2267 i (GGAGCCC)n#Si 1 GGAGCCCGGAGCCCGGAGCCCGGAGCCCGG 30 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 18 10.96 4.05 11.59 rnd-5_family-2561#SINE/tRNA 2418 2491 (1794) (GCCCCA)n#Simple_repeat 1 69 (0) m_b28s252i8 rnd-5_family- 2418 GCCCCACCCCCAG---CGGCCCCAGCCCCAGGCCTCACGAGCACAGGCCC 2464 v --- i - - - - v vi (GCCCCA)n#Sim 1 GCCCCAGCCCCAGCCCCAGCCCCAGCCCCA-GCC-C-C-AGCCCCAGCCC 46 rnd-5_family- 2465 CAGCCTGCCTGCCCCAGCCTCTCAGCC 2491 -- v - - (GCCCCA)n#Sim 47 CAGCC--CCAGCCCCAGCC-C-CAGCC 69 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.12 (9 / 73), avg. gap size = 1.22 (11 / 9) 19 29.59 1.32 1.32 rnd-5_family-2561#SINE/tRNA 2889 2964 (1321) (TGGGTC)n#Simple_repeat 1 76 (0) m_b28s252i9 rnd-5_family- 2889 TGGGGCAGGGTCTGTGTCTCGCTCTGAGTCTGTGATCTCAG-CAGGGACA 2937 v v v v v i - i vi - v v v (TGGGTC)n#Sim 1 TGGGTCTGGGTCTGGGTCTGGGTCTGGGTCTG-GGTCTGGGTCTGGGTCT 49 rnd-5_family- 2938 GGGACTGTCTCTGGTTGTGTGTCTGGG 2964 v vv v v v (TGGGTC)n#Sim 50 GGGTCTGGGTCTGGGTCTGGGTCTGGG 76 Matrix = Unknown Transitions / transversions = 0.20 (3/15) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 43 0.00 0.00 0.00 rnd-5_family-2561#SINE/tRNA 3534 3570 (751) (TG)n#Simple_repeat 1 37 (0) c_b28s251i1 rnd-5_family- 3534 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 3570 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 4.30 4.00 0.00 rnd-5_family-304#Unknown 280 304 (155) (TTTTG)n#Simple_repeat 1 26 (0) m_b28s252i6 rnd-5_family- 280 TTTTGTTTTG-NTTGTTTTGTGTTGT 304 -? v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 235 26.80 3.00 3.00 rnd-5_family-3384#LINE/L2 1 100 (197) L2-2_Mam#LINE/L2 114 213 (159) m_b28s601i6 rnd-5_family- 1 TTTCTGGCAGAAGNTC-TCAGCTGTGGAACTCCCTA-CCGCTGGAGAGCA 48 i - i i ?i - ivi i i- ivvi vv i L2-2_Mam#LINE 114 TTTCCG-CGGAGGGCCCTCGTTTGTGGAATTCCCTGCCCGCCCTGGTTCG 162 rnd-5_family- 49 GGATGAGCCCNANTCTTGCC-NCCTTTAGGGTACAACGCAAGACTCACCT 97 v - ? ? - i-? i i iii v i L2-2_Mam#LINE 163 GCA-GAGCCCCAGT-TTGCTGACCTTCAGGGCACGGTGCAAGACGCATCT 210 rnd-5_family- 98 TCT 100 i L2-2_Mam#LINE 211 TTT 213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 19, Kimura (unadjusted) = 37.15 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.00 (6 / 6) 294 24.24 0.00 0.00 rnd-5_family-3660#SINE/B2 616 681 (716) tRNA-Thr-ACA#tRNA 7 72 (3) m_b28s502i5 rnd-5_family- 616 ATAGCTCAGTGGTTTGAGCATTGGCCTGCTAAACCCAGGGTTGTGAGTTT 665 v v i i vv vi i i i tRNA-Thr-ACA# 7 ATAGCTCAGGGGTTAGAGCACTGGTCTTGTAAACCAGGGGTCGCGAGTTC 56 rnd-5_family- 666 AATCCTTGAGGGGGCC 681 vi i vv tRNA-Thr-ACA# 57 AAATCTCGCTGGGGCC 72 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.49 CpG sites = 8, Kimura (unadjusted) = 29.54 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 359 16.69 0.00 3.33 rnd-5_family-3660#SINE/B2 715 776 (621) Plat_L3#LINE/CR1 3499 3558 (15) m_b28s551i1 rnd-5_family- 715 CCTGCTAGTGAAGGCAGCGGGCTGGACTCAATGACTTTTCAAGGTCCCTT 764 i-- i v ivi i i i Plat_L3#LINE/ 3499 CCTGCC--TGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTT 3546 rnd-5_family- 765 CCAGTTCTAGGA 776 i ? Plat_L3#LINE/ 3547 CCAGCTCTANGA 3558 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.81 CpG sites = 8, Kimura (unadjusted) = 19.95 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 12 29.56 2.78 2.78 rnd-5_family-4409#DNA/Kolobok 534 605 (739) (GGAGAGA)n#Simple_repeat 1 72 (0) m_b28s252i5 rnd-5_family- 534 GGAGGGAAGA-AGATGAAAAGGGAGAGAGGAGAGACTGGA-AGGGGCAGC 581 i i - v i ii vvi - i - - (GGAGAGA)n#Si 1 GGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAG-AG- 48 rnd-5_family- 582 AGGAGCAANAAGTGGGGAGGGAGG 605 vi ?i v i i (GGAGAGA)n#Si 49 AGGAGAGAGGAGAGAGGAGAGAGG 72 Matrix = Unknown Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 14 20.75 2.17 2.17 rnd-5_family-453#Unknown 252 297 (201) (GCTGGGA)n#Simple_repeat 1 46 (0) m_b28s252i4 rnd-5_family- 252 GCTGGGAGCCGGGGCCTGGGTGGGTGGGATCTGGCAGCTGTG-GCTG 297 i iv -i v v v v - (GCTGGGA)n#Si 1 GCTGGGAGCTGGGAGCTGGG-AGCTGGGAGCTGGGAGCTGGGAGCTG 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 17 15.73 7.55 3.64 rnd-5_family-6594#Unknown 733 785 (33) (TA)n#Simple_repeat 1 55 (0) m_b28s252i3 rnd-5_family- 733 TATA-ATACTATATATATA-ATATCTATTTCTCTA-ACAT-TATTTAGTA 778 - - - v v v v - i - v - (TA)n#Simple_ 1 TATATATA-TATATATATATATATATATATATATATATATATATATA-TA 48 rnd-5_family- 779 TACATAT 785 i (TA)n#Simple_ 49 TATATAT 55 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 14 25.31 1.47 6.15 rnd-5_family-6659#Unknown 376 443 (155) (CCAC)n#Simple_repeat 1 65 (0) m_b28s252i2 rnd-5_family- 376 CCACCCAACTACCACAGACACCTCTCAGCACCCACCAGCCCAGGCACCTC 425 v i - vv - v -v vi vv - (CCAC)n#Simpl 1 CCACCCACCCACC-CACCCACC-CAC-CCACCCACCCACCCACCCACC-C 46 rnd-5_family- 426 A-GAACCCACCCACCTACC 443 -vv i (CCAC)n#Simpl 47 ACCCACCCACCCACCCACC 65 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.00 (5 / 5) 1360 34.12 1.99 2.58 rnd-5_family-715#DNA/hAT-Charlie 139 1191 (746) Charlie8#DNA/hAT-Charlie 441 1487 (970) m_b28s502i6 rnd-5_family- 139 GTTTTCCAAGACAAATGGGAGAATTTATATTTTTTCGCAGAGGTAAAAGA 188 v i v ivvi i i ii i i ii Charlie8#DNA/ 441 GTGTTTCAAGAAAAATGGGAGAGAGCATATTTCTTTGTGGAAGTGAAGAA 490 rnd-5_family- 189 TAAAATTCA---ATGCCTTATTTGTCAGCAAACGATTGCTGTTCCCAAGG 235 --- v---i ii v v iv i vvi vv vi v i Charlie8#DNA/ 491 TA---TTCCTACGTGTTTAATATGCAAACAAAGTGTGTCTGTGTCGAAAG 537 rnd-5_family- 236 AGTATAACGTGCGTCGGCACTACGACACGATGCACCGTGAAAAATATGAT 285 i i v iv v v i i v i vv iv i i v i Charlie8#DNA/ 538 AATACAACTTAAGACGCCATTATGAAACAAACCATAGTAAGAACTATGAC 587 rnd-5_family- 286 GCATTCACCGGAAAAATCCGAGAGGAAAAAGTTCAGCAACTTAAAGCAGC 335 vvi vi v i i v v v v v vv v iv v Charlie8#DNA/ 588 CGGTATACGGAAAAGATGCGTGATGAAAAACTTAATGAACTGAAAAAAGG 637 rnd-5_family- 336 ATT----TGCCAAGCAAAGAAATTTCTTTTCGGAGATTAACAAGTCTAGC 381 i ---- vi - ii --- v i i viiv i iviv i Charlie8#DNA/ 638 ACTGAAATTTCAA-CAGGG---TTTGTTTTTGAATGCGAATAAAATAAGT 683 rnd-5_family- 382 GAAGATTCAGTAAGA-GCAAGTTTTGTGATAAGCGAAATGATAGCTAAAT 430 v v v v i i - - v iv i vi v iviiv Charlie8#DNA/ 684 GATGCTGCTGTGAAATGCA-GTTATGTATTAAGTGAAAAAATTGCCCGGG 732 rnd-5_family- 431 CATCGCGACCTTTTACAGAAGGCCTATTCGTAAAAGAATGTCTTGTGAAG 480 ivi v vvi ii i vv v Charlie8#DNA/ 733 CATCAAAACCTTTTACAGATGGCGAGTTTATAAAAGAGTGTCTATTGAAT 782 rnd-5_family- 481 GCCAGC-GAAATTTTATGTCCTGATAGGAAGAAAGTTTTTGAAGGCATAA 529 - - v i i vvi iv iv v iiii Charlie8#DNA/ 783 GC-AGCAGAAATTATGTGTCCCGAACAGAAACAAGCATTTGCAAATGTAA 831 rnd-5_family- 530 GCTTGTCTGCCAATACAGTTGC-CTGCAGGATAACGGATTTAGCNGATAA 578 ii iv i vv v - v iv v i -i vii ? v Charlie8#DNA/ 832 GTCTAACCGGAAATACTGTTGCTCAGCGTGTTGA-AGATACGGCTGAGAA 880 rnd-5_family- 579 TGTGCAAAAAAACAATTGATTCAAATGGCAAAAGACTTCGAAGCATTTTC 628 iv i ii v --i vv v vi iv vvv i vi i Charlie8#DNA/ 881 CTTACAGGACAA--GTTGCGTGAAAAAGTTAAATCATTTGTGGCGTTTTC 928 rnd-5_family- 629 AATTGCTCTTGATGAGAGTACAGATGTATCAGATACCGCACAGTGTGCAG 678 v vvi i i vvvi i v vv vi Charlie8#DNA/ 929 TATTGCAGCTGATGAGAGCACAGATATAAATAATACCACCCAGTTAGCTA 978 rnd-5_family- 679 TGTTCATTAGAGGTGTGGATTGNAATTTGAATATAACTGAAGAATTGCTA 728 i i v v v vi? vi i i i i vi i Charlie8#DNA/ 979 TATTTATTCGTGGTGTCGATGAGAATTTTGATGTGACCGAAGAACTTTTG 1028 rnd-5_family- 729 GACTTAATGCCACTGAAGGGTACCACAACGGGACGTGACATATTTCAAGG 778 v ii vv vi i v v i vi v iviv Charlie8#DNA/ 1029 GACATGGTGCCCATGACAGGCACAACATCAGGAAATGACTTATTTTTGTG 1078 rnd-5_family- 779 -ACTG-GAAGAGTGCATTGAAAAAGCTG-CGCTGCCATGGAACAAACTCG 825 -ii - i - - ivi i-i iv v - vvv i v Charlie8#DNA/ 1079 TGTTGAGAAAAGT-C-TTGAAAAGTTTAATGTAGAC-TGGTCAAAATTAG 1125 rnd-5_family- 826 TATCTTTGGCTACGGACGGTGCGCCATCAATGTGCTCTGAAAACGTTGGT 875 vviv i i v vv i vv vv vv i v Charlie8#DNA/ 1126 TAAGCGTGACTACAGACGGTGCTCCTGCGATGGTCGGTGTTAACGTCGGA 1175 rnd-5_family- 876 GTGGTTGGATTATTGAAGACCAAACTG--AACAGCCT-CAAT-ATACCAG 921 v v ivivv i v iv iv -- ivii - v- i -- Charlie8#DNA/ 1176 CTTGTTACGAAACTTAAATCCAAGGTGGCAACGTTTTGCAAGGACAC--G 1223 rnd-5_family- 922 GAA-TTAGCTTCACCAGTATACATTGCATTTTGCGCCAAGAAGCCCTGTG 970 - iv i i------ v iv v i i v v v Charlie8#DNA/ 1224 GAACTTAAGTCCG------TTCATTGCATCATTCACCAGGAATCGCTTTG 1267 rnd-5_family- 971 TAGTAAAAGTCTACAAATGAAGGAAGTTATGGACGTAGTTGTTAAAACCG 1020 iv ivi v i iv v i vi v Charlie8#DNA/ 1268 TGCTAAAAAGTTAAAAATGGAACACGTCATGGACGTAGTAATTAACACCG 1317 rnd-5_family- 1021 TTAATTTTATACGTGCACGAGGGCTGAATCACAGACAGTTCACTTCTTTT 1070 v i vv iv v v vi i v v v Charlie8#DNA/ 1318 TGAACTGGATACGCTCCCGTGGCTTGAACCACAGACAGTTCAATGCTTTG 1367 rnd-5_family- 1071 CTAG-CAAGTATGGACAGCG-AATATGGGGAACTTCTGTATCACACTGAA 1118 v -ii i - i- i- i viiv v ii v i Charlie8#DNA/ 1368 CTTGATGAAT-TGGAT-GCACAATACGGTAGTCTGCTGTACTACACGGAG 1415 rnd-5_family- 1119 GTTAGATGGCTGAGTCGTGGAGATGTTTTGAAGCGTTTTTTTTGCACT-T 1167 i v v vv vi v -v v - Charlie8#DNA/ 1416 GTTAGGTGGCTTAGTCGTGGCGTGGTGCTGAAGAG-ATTTTTTGAACTGT 1464 rnd-5_family- 1168 AGAGAGGAGATCGATTCCTTCATG 1191 v - i i i iv Charlie8#DNA/ 1465 TGA-AAGAAATCGACTTGTTCATG 1487 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.46 CpG sites = 169, Kimura (unadjusted) = 46.25 Transitions / transversions = 0.93 (169/181) Gap_init rate = 0.04 (42 / 1052), avg. gap size = 1.14 (48 / 42) 329 37.09 4.72 3.35 rnd-5_family-715#DNA/hAT-Charlie 934 1463 (474) Charlie13a#DNA/hAT-Charlie 269 805 (709) m_b28s502i7 rnd-5_family- 934 CCAGTATACATTGCATTTTGCGCCAAGAAGCCCTGTGTAGTAAAAGTCTA 983 iv v iv v ii i iivii iv i v- i i Charlie13a#DN 269 CCAGCTTCCATTGCATCATTCATCAGGAGAGTTTGTGCTGTGAAC-TTTG 317 rnd-5_family- 984 CAAATGAAG----------GAAGTTATGGACGTAGTTGTTAAAACCGTTA 1023 i v i ---------- v v v v vi i i ii v Charlie13a#DN 318 CAAGTCAGGTTCATTGCATGATGTGATGGAGGAAGTGATCAAGATTGTGA 367 rnd-5_family- 1024 ATTTTATACGTGCACGAGGGCTGAATCACAGACAGTTCACTTCTTTTCTA 1073 v v v v vv v i iv v i ivvvv v i i Charlie13a#DN 368 ATTTTCTTCGTGCTCGTGCCCTTAACCATCGCCAGTTTATGGGATATTTG 417 rnd-5_family- 1074 GCAAGTATGGACAGC-GAATATGGGGAACTTCTGTATCACACTGAAGTTA 1122 v iivi v - - i i vi vv v ivi v v i Charlie13a#DN 418 GAAGAAGTTGA-AGCAGAGTATGGAGATTTAGTTTATTTTAATGCAGTCA 466 rnd-5_family- 1123 GATGGCTGAGTCGTGGAGATGTTTTGAAGCGTTTTTTTTGCACTTAGAGA 1172 ii i iv v v v ------ -- v Charlie13a#DN 467 GATGGCTAGGTCGTGGAAACTTGTTGAAGAGATTT------ACT--GAGC 508 rnd-5_family- 1173 GG-------AGATCGATTCCTTCATGAAAATGAAAAACAAGGAGGTTCCA 1215 v ------- i vvv iv i v i iii vvv ivv - Charlie13a#DN 509 TGCTTCCTCAGATCAAGGACTTTTTGGAATTAAAGGGCTCTGAGAGACC- 557 rnd-5_family- 1216 CAGCTTGCTGATTCCACTTTNATCTGCAACCTTGC-TTTTCTAGCAGATG 1264 i ii ivi v vv ?iiiii vv i-i vi v Charlie13a#DN 558 CAACTTGTCGGACCCCCAGTGGCTCACAAGATTGTACTTTCTTACTGATG 607 rnd-5_family- 1265 TAACTGATCACCTGAACGCACTGAACTCGAAGCTTCAGGGTAGAAAACAG 1314 i viiv i i i i v - i i Charlie13a#DN 608 TGACAAGACATCTGAACACACTGAACTTGAAACTGCAGGG-AAAAAACAA 656 rnd-5_family- 1315 GTGATAACGCGGATGTAT----GACAGTGTTAAGTCATTCGAAGTCAAGC 1360 v -i vi v v i ---- iv -i i - ii v i Charlie13a#DN 657 GAG-CATTGCTGATTTGTTCAAGGAAGTG-CAGGT-ATTCAGACTCAAAC 703 rnd-5_family- 1361 TTACTTTGTGGGGGAAACAGCTGACTGCTGGCAATTTGGTCCATTTCTCG 1410 viviv ivvi i v i vi vi i vviii i i Charlie13a#DN 704 TGGACATGTGGATTGAGCAGATGGCAACTGGAGACTGCACTCATTTCCCA 753 rnd-5_family- 1411 ACTCTGAATT-CCTTAGGAAAAGTTGAACC-CAAATCCTTGAAAGAATAT 1458 viv i - i ii vvv i v i - i -- vi i- Charlie13a#DN 754 TTGCTGAACTGCCCTGAGCTCAATGGAATCACAGAT--TTTGAAGAAC-T 800 rnd-5_family- 1459 GCAGA 1463 Charlie13a#DN 801 GCAGA 805 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 52.51 CpG sites = 102, Kimura (unadjusted) = 52.92 Transitions / transversions = 1.16 (102/88) Gap_init rate = 0.05 (25 / 529), avg. gap size = 1.72 (43 / 25) 306 34.90 1.80 3.20 rnd-5_family-715#DNA/hAT-Charlie 1564 1785 (152) Charlie8#DNA/hAT-Charlie 1857 2075 (382) m_b28s502i8 rnd-5_family- 1564 ATTGACAATGTTGCAGAGGAAATGCAGATGGA-GTTAGTGGAGCTTCAGT 1612 i i vivv i iv i i - v i - v Charlie8#DNA/ 1857 ATTGATAGTGTGAATGAAGAGCTACAAATGGAAGTTATTGAA-CTGCAGT 1905 rnd-5_family- 1613 GCGACACCATTTTGAAGCGGAAGTATACAGATGTTGGAATTCCAGAATTC 1662 i i vi vi ivvv i iivv i v Charlie8#DNA/ 1906 GCAATACGGTACTGAAAACTAAATACGACGACGTTGGAATACCAGAATTC 1955 rnd-5_family- 1663 TACCGGTTTCTTTCACAAGAAAGATTTCCC---ATGTTATTCTCTGCTTC 1709 vii v ---- ii ivii v --- i v vvvi --v v Charlie8#DNA/ 1956 TACAAATATCT----CGGGAGTAGTTACCCTAAATATAAAAACC--ATTG 1999 rnd-5_family- 1710 CGCAAGGGTAATGGCAATGTTTGGAAGTACATATATATGTGAACAGTTTT 1759 i i i vv iv v i v ii v i v Charlie8#DNA/ 2000 TGCAAAGATTCTATCCATGTTCGGAAGTACCTACGTTTGTGAACAGCTGT 2049 rnd-5_family- 1760 TCTCTTCCATGAAGATTAACAAATCT 1785 i ivii iv v i v Charlie8#DNA/ 2050 TTTCCATTATGAAACTGAATAAAACT 2075 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.63 CpG sites = 40, Kimura (unadjusted) = 48.12 Transitions / transversions = 1.14 (40/35) Gap_init rate = 0.04 (9 / 221), avg. gap size = 1.22 (11 / 9) 18 23.45 4.00 4.00 rnd-5_family-7282#Unknown 154 228 (144) (CAG)n#Simple_repeat 1 75 (0) m_b28s252i1 rnd-5_family- 154 CAGCAGCAACAGGCCGC-GCAACAGCAGCAGCACCAGACA-CAGCTGCTA 201 i - v - i v - - v vi (CAG)n#Simple 1 CAGCAGCAGCA-GCAGCAGCAGCAGCAGCAGCAGCAG-CAGCAGCAGCAG 48 rnd-5_family- 202 CAACA-AATCATGGCCCAGCAGCAACAG 228 i -v v - vvv i (CAG)n#Simple 49 CAGCAGCAGCA-GCAGCAGCAGCAGCAG 75 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.08 (6 / 74), avg. gap size = 1.00 (6 / 6) 476 15.09 3.77 0.00 rnd-5_family-7635#SINE/MIR 8 113 (1) MIR1_Amn#SINE/MIR 2 111 (119) m_b28s601i7 rnd-5_family- 8 AGGGAGGGAGTGNTGTCTANTGGTTAGAGCAGGGGACTGGGAGTCAGGAC 57 v ?v ? v vv v i v MIR1_Amn#SINE 2 AGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAG 51 rnd-5_family- 58 TCCTGGGTTCTATTCCTGNCTCTGCCACTGACTCACTGAG----ATTCGA 103 v ? ? i ? ?i i?i ? ----v v i MIR1_Amn#SINE 52 ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 rnd-5_family- 104 CAAGTCACTT 113 MIR1_Amn#SINE 102 CAAGTCACTT 111 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.10 CpG sites = 6, Kimura (unadjusted) = 18.42 Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.01 (1 / 105), avg. gap size = 4.00 (4 / 1) 13 19.39 0.00 2.78 rnd-5_family-8036#Unknown 393 429 (176) (CCGGG)n#Simple_repeat 1 36 (0) m_b28s252i0 rnd-5_family- 393 CCAGGCAGGGCTCGGCGGGGCCGCGGCCGGGCCGCGC 429 i v iv v - v (CCGGG)n#Simp 1 CCGGGCCGGGCCGGGCCGGGCCG-GGCCGGGCCGGGC 36 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 230 26.23 0.00 0.00 rnd-5_family-9265#LTR/Gypsy 193 253 (733) MamGypsy2-I#LTR/Gypsy 3350 3410 (756) m_b28s551i2 rnd-5_family- 193 TATTTGCAAGANATGGAGTTCCTGAAGTCCTCATATCTGATAATGGGCCT 242 v ? i v v v viiiv i v i i MamGypsy2-I#L 3350 TATTTGCAACACACGGATTGCCAGACACTATCGTTTCTGACAATGGGTCT 3399 rnd-5_family- 243 CAATTTACCTC 253 vv MamGypsy2-I#L 3400 GCATTTACCTC 3410 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 7, Kimura (unadjusted) = 33.09 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 1323 3.41 2.26 0.56 rnd-5_family-9325#LINE/CR1 2 178 (35) X21_LINE#LINE/CR1 72 251 (33) m_b28s551i3 rnd-5_family- 2 AGCTAAATTTATGTAGTCTGGAAAAGAGAAGACTCAGGGG--ANATGATC 49 i i i -- ? X21_LINE#LINE 72 AGCTAAATTTATATAGTCTAGAAAAGAGAAGGCTCAGGGGGGACATGATC 121 rnd-5_family- 50 ACAGTCTATAAATACCTTCCAAGGTAACAATATAAATGAAGGAAGGGAAT 99 i - X21_LINE#LINE 122 ACGGTCTATAAATACCTT-CAAGGTAACAATATAAATGAAGGAAGGGAAT 170 rnd-5_family- 100 TA-TCACAGTCTCAGAAGATGGTAGGACAAGGAGCAATGGCCTGAAGCTA 148 - X21_LINE#LINE 171 TATTCACAGTCTCAGAAGATGGTAGGACAAGGAGCAATGGCCTGAAGCTA 220 rnd-5_family- 149 AGGAA-GAAAAATTTAGNCTAGACATTAAGA 178 - i ? i X21_LINE#LINE 221 AGGAAGGAAAAGTTTAGGCTAGATATTAAGA 251 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 3.02 CpG sites = 6, Kimura (unadjusted) = 3.57 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.02 (4 / 176), avg. gap size = 1.25 (5 / 4) 247 27.14 0.00 0.00 rnd-5_family-9919#DNA/hAT-Charlie 1 70 (96) Charlie32a#DNA/hAT-Charlie 6 75 (261) m_b28s502i9 rnd-5_family- 1 GTTCTCAAACTGTGGTACGTGTACCACTGGTGGTACGCGGGCCGCAGTCA 50 v v v v i v i vvv vvi Charlie32a#DN 6 GTTCTCAAAGTGTGGTCCGGGGACCGCTGGTGGTCCGCGAGGGTCCTCCA 55 rnd-5_family- 51 GGTGGTATGTGGATTGGTTT 70 vi i ii i Charlie32a#DN 56 GGTGGTCCGCGGGCTGGTCT 75 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.88 CpG sites = 8, Kimura (unadjusted) = 33.80 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 312 20.97 0.00 0.00 rnd-5_family-9919#DNA/hAT-Charlie 2 63 (103) MER113A#DNA/hAT-Charlie 7 68 (246) m_b28s502i10 rnd-5_family- 2 TTCTCAAACTGTGGTACGTGTACCACTGGTGGTACGCGGGCCGCAGTCAG 51 i v i i vi vvv i MER113A#DNA/h 7 TTCCCAAAGTGTGGTACGCGTACCACTGGTGGTACGCGAGATGATTTTAG 56 rnd-5_family- 52 GTGGTATGTGGA 63 iii MER113A#DNA/h 57 GTGGTACACGGA 68 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.87 CpG sites = 8, Kimura (unadjusted) = 25.08 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) ## Total Sequences: 2323 ## Total Length: 1373014 ## Total NonMask ( excluding >20bp runs of N/X bases ): 1373014 ## Total NonSub ( excluding all non ACGT bases ):1355163 RepeatMasker version 4.1.5 , default mode run with rmblastn version 2.13.0+ RM Library: CONS-Dfam_3.7