+ 657 13.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1101:22820:68799/1 1 92 (59) C AluSx SINE/Alu (220) 92 1 1
ANNOTATION EVIDENCE:
657 13.04 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:22820:68799/1 1 92 59 C AluSx SINE/Alu 1 92 220
657 13.04 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:22820:68799/1 1 92 (59) C AluSx#SINE/Alu (220) 92 1 m_b5s357i58
E00378:188:HV 1 CAGGCTGGTCCCAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTC 50
i i i i i i
C AluSx#SINE/Al 92 CAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTC 43
E00378:188:HV 51 CCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 92
i i vi i i
C AluSx#SINE/Al 42 CCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.46
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1101:26189:14863/2 13 44 (107) + (CA)n Simple_repeat 1 32 (0) 2
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:26189:14863/2 13 44 107 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:26189:14863/2 13 44 (107) (CA)n#Simple_repeat 1 32 (0) m_b4s252i80
E00378:188:HV 13 CATACATGCACACACATACACACACACACACA 44
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 672 4.9 0.0 0.0 E00378:188:HVMVNCCXX:1:1101:4706:24901/1 1 82 (69) + AluSx SINE/Alu 210 291 (21) 3
ANNOTATION EVIDENCE:
672 4.88 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:4706:24901/1 1 82 69 + AluSx SINE/Alu 210 291 21
672 4.88 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:4706:24901/1 1 82 (69) AluSx#SINE/Alu 210 291 (21) m_b4s357i17
E00378:188:HV 1 GAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGG 50
i i
AluSx#SINE/Al 210 GAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGG 259
E00378:188:HV 51 GCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 82
i i
AluSx#SINE/Al 260 GCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.93
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1101:4706:24901/1 110 141 (10) + (CA)n Simple_repeat 1 32 (0) 4
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:4706:24901/1 110 141 10 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1101:4706:24901/1 110 141 (10) (CA)n#Simple_repeat 1 32 (0) m_b4s252i79
E00378:188:HV 110 CATACATGCACACACATACACACACACACACA 141
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 250 30.8 1.3 0.0 E00378:188:HVMVNCCXX:1:1101:4706:24901/2 3 80 (71) C MIRb SINE/MIR (68) 200 122 5
ANNOTATION EVIDENCE:
250 30.77 1.26 0.00 E00378:188:HVMVNCCXX:1:1101:4706:24901/2 3 80 71 C MIRb SINE/MIR 122 200 68
250 30.77 1.26 0.00 E00378:188:HVMVNCCXX:1:1101:4706:24901/2 3 80 (71) C MIRb#SINE/MIR (68) 200 122 m_b4s601i26
E00378:188:HV 3 TTATTTTCTCTAATCCTCACAGTTATCTGGCCAGGTAAGTGATA-TATCT 51
i iv i iiv i iv v i iv - i
C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCC 151
E00378:188:HV 52 TCACTCTACTGATGAGGGTACGAAGGCCC 80
i i i v iv vi i
C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 41.70
Transitions / transversions = 2.00 (16/8)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1)
+ 1248 8.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1102:10429:7673/1 1 151 (0) + AluSx SINE/Alu 92 242 (70) 6
ANNOTATION EVIDENCE:
1248 7.95 0.00 0.00 E00378:188:HVMVNCCXX:1:1102:10429:7673/1 1 151 0 + AluSx SINE/Alu 92 242 70
1248 7.95 0.00 0.00 E00378:188:HVMVNCCXX:1:1102:10429:7673/1 1 151 (0) AluSx#SINE/Alu 92 242 (70) m_b4s356i18
E00378:188:HV 1 GGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCAG 50
i i i i i
AluSx#SINE/Al 92 GGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGG 141
E00378:188:HV 51 GGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGG 100
v iv i i
AluSx#SINE/Al 142 GCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGG 191
E00378:188:HV 101 AGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGC 150
i i
AluSx#SINE/Al 192 AGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGC 241
E00378:188:HV 151 C 151
AluSx#SINE/Al 242 C 242
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 183 34.9 8.0 3.1 E00378:188:HVMVNCCXX:1:1102:10429:7673/2 1 130 (21) C MIRb SINE/MIR (116) 152 16 7
ANNOTATION EVIDENCE:
183 34.93 8.03 3.08 E00378:188:HVMVNCCXX:1:1102:10429:7673/2 1 130 21 C MIRb SINE/MIR 16 152 116
183 34.93 8.03 3.08 E00378:188:HVMVNCCXX:1:1102:10429:7673/2 1 130 (21) C MIRb#SINE/MIR (116) 152 16 m_b4s601i38
E00378:188:HV 1 CTTCACTCTACTGATGAGGGTACGAAGGCCCTAGATGACATAAGGCAAGT 50
ii i i v iv vi i - - vi v i i v
C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTC-AGA-GAGGTTAAGTAACT 105
E00378:188:HV 51 TTTTTACCAGA----AAAGTTA--AGGCTGTGGTACTGGGATTTGAATTT 94
viii -- i---- v i -- i iv ii vi i i iii
C MIRb#SINE/MIR 104 TGCCCA--AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57
E00378:188:HV 95 ---TCTGTTTGACTTCAAAGCC--TTTTGTTTTTACTATAC 130
--- i i -- vi v ii ii
C MIRb#SINE/MIR 56 AGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCAC 16
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 48.02
Transitions / transversions = 2.67 (32/12)
Gap_init rate = 0.06 (8 / 129), avg. gap size = 1.88 (15 / 8)
+ 1253 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1102:5254:48107/2 1 151 (0) C L1P3 LINE/L1 (3045) 3101 2951 8
ANNOTATION EVIDENCE:
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1102:5254:48107/2 1 151 0 C L1P3_orf2 LINE/L1 842 992 2302
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1102:5254:48107/2 1 151 (0) C L1P3_orf2#LINE/L1 (2302) 992 842 m_b7s551i4
E00378:188:HV 1 TTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTT 50
i
C L1P3_orf2#LIN 992 TTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTC 943
E00378:188:HV 51 GATTTTAGATCTTTCCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATT 100
i v ?
C L1P3_orf2#LIN 942 GATTTTAGATCTTTCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATT 893
E00378:188:HV 101 TCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACATTGTG 150
i
C L1P3_orf2#LIN 892 TCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTG 843
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 842 T 842
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 522 21.9 7.0 0.8 E00378:188:HVMVNCCXX:1:1103:27651:8148/2 1 120 (31) + L1MC4 LINE/L1 7784 7911 (131) 9
ANNOTATION EVIDENCE:
522 21.85 7.03 0.83 E00378:188:HVMVNCCXX:1:1103:27651:8148/2 1 120 31 + L1MC4_3end LINE/L1 2531 2658 131
522 21.85 7.03 0.83 E00378:188:HVMVNCCXX:1:1103:27651:8148/2 1 120 (31) L1MC4_3end#LINE/L1 2531 2658 (131) m_b3s551i17
E00378:188:HV 1 TGATTATACTGTGGCTAAACAGAAGTGTATCCTTGTTTTTAGGAAATATA 50
i i i vii ii vi i i i
L1MC4_3end#LI 2531 TAATTGTACTGTGGTTATGTAAGAGAATGTCCTTGTTCTTAGGAAATACA 2580
E00378:188:HV 51 CACTGAAGTAT---------AAGGAGCATCACGTGTGCGATTTCATCTCA 91
--------- i ? i v i i vv
L1MC4_3end#LI 2581 CACTGAAGTATTTAGGGGTAAAGGGGCATNATGTCTGCAACTTACTCTCA 2630
E00378:188:HV 92 AAATGGTTCAGAGAAAATGATGTGTGTAT 120
- i vi i i
L1MC4_3end#LI 2631 AA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.01
Transitions / transversions = 3.17 (19/6)
Gap_init rate = 0.02 (2 / 119), avg. gap size = 5.00 (10 / 2)
+ 1348 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1104:22424:57424/1 1 151 (0) C L1P1 LINE/L1 (866) 5280 5130 10
ANNOTATION EVIDENCE:
1348 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1104:22424:57424/1 1 151 0 C L1P1_orf2 LINE/L1 3021 3171 123
1348 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1104:22424:57424/1 1 151 (0) C L1P1_orf2#LINE/L1 (123) 3171 3021 m_b1s551i113
E00378:188:HV 1 GAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTG 50
C L1P1_orf2#LIN 3171 GAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTG 3122
E00378:188:HV 51 CGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTT 100
i
C L1P1_orf2#LIN 3121 CGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTT 3072
E00378:188:HV 101 TCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAAT 150
C L1P1_orf2#LIN 3071 TCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAAT 3022
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 3021 T 3021
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1277 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1104:22424:57424/2 1 151 (0) + L1P1 LINE/L1 4939 5089 (1057) 11
ANNOTATION EVIDENCE:
1277 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1104:22424:57424/2 1 151 0 + L1P1_orf2 LINE/L1 2830 2980 314
1277 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1104:22424:57424/2 1 151 (0) L1P1_orf2#LINE/L1 2830 2980 (314) m_b1s551i31
E00378:188:HV 1 TGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTGATAGAAAAATCAA 50
v v i
L1P1_orf2#LIN 2830 TGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAA 2879
E00378:188:HV 51 TTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCC 100
i
L1P1_orf2#LIN 2880 TTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCC 2929
E00378:188:HV 101 TAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGAC 150
?
L1P1_orf2#LIN 2930 TAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGAC 2979
E00378:188:HV 151 T 151
L1P1_orf2#LIN 2980 T 2980
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 810 16.8 0.0 4.7 E00378:188:HVMVNCCXX:1:1105:13311:48318/1 1 150 (1) + AluSx SINE/Alu 132 274 (38) 12
ANNOTATION EVIDENCE:
810 16.78 0.00 4.67 E00378:188:HVMVNCCXX:1:1105:13311:48318/1 1 150 1 + AluSx SINE/Alu 132 274 38
810 16.78 0.00 4.67 E00378:188:HVMVNCCXX:1:1105:13311:48318/1 1 150 (1) AluSx#SINE/Alu 132 274 (38) m_b5s356i2
E00378:188:HV 1 AATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGG 50
i i v i v v vi i i
AluSx#SINE/Al 132 AATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGG 181
E00378:188:HV 51 CTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCA 100
v i iivv v
AluSx#SINE/Al 182 CTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCC 231
E00378:188:HV 101 GATATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGAC 150
v v i ------- i ii i
AluSx#SINE/Al 232 GAGATCGCGCCACTGCACTCCAGCCTG-------GGCGACAGAGCGAGAC 274
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 11.95
Transitions / transversions = 1.40 (14/10)
Gap_init rate = 0.05 (7 / 149), avg. gap size = 1.00 (7 / 7)
+ 185 34.9 7.9 3.0 E00378:188:HVMVNCCXX:1:1106:28219:26818/1 12 144 (7) + MIRb SINE/MIR 16 155 (113) 13
ANNOTATION EVIDENCE:
185 34.88 7.86 3.01 E00378:188:HVMVNCCXX:1:1106:28219:26818/1 12 144 7 + MIRb SINE/MIR 16 155 113
185 34.88 7.86 3.01 E00378:188:HVMVNCCXX:1:1106:28219:26818/1 12 144 (7) MIRb#SINE/MIR 16 155 (113) m_b4s601i34
E00378:188:HV 12 GTATAGTAAAAACAAAA--GGCTTTGAAGTCAAACAGA---AAATTCAAA 56
ii ii v iv -- i i ---iii i
MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA 65
E00378:188:HV 57 TCCCAGTACCACAGCCT--TAACTTT----TCTGGTAAAAAACTTGCCTT 100
i iv ii vi i -- i v ----i -- iiiv v i i v
MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCT--TGGGCAAGTTACTTA 113
E00378:188:HV 101 ATGTCATCTAGGGCCGTCGTACCCTCATCAGTAGAGTGAAGATA 144
iv - - i viv vi v i i ii
MIRb#SINE/MIR 114 ACCTC-TCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 47.71
Transitions / transversions = 2.46 (32/13)
Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.88 (15 / 8)
+ 1326 0.7 0.0 0.7 E00378:188:HVMVNCCXX:1:1106:4503:49373/1 1 151 (0) + L1PA3 LINE/L1 5711 5860 (295) 14
ANNOTATION EVIDENCE:
1326 0.66 0.00 0.66 E00378:188:HVMVNCCXX:1:1106:4503:49373/1 1 151 0 + L1PA3_3end LINE/L1 458 607 295
1326 0.66 0.00 0.66 E00378:188:HVMVNCCXX:1:1106:4503:49373/1 1 151 (0) L1PA3_3end#LINE/L1 458 607 (295) m_b1s551i341
E00378:188:HV 1 TATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATA 50
L1PA3_3end#LI 458 TATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATA 507
E00378:188:HV 51 GACTGGATTAAGAAACTGTGGCACATATACACCATGGAATACTATGCAGC 100
v
L1PA3_3end#LI 508 GACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGC 557
E00378:188:HV 101 CATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTG 150
-
L1PA3_3end#LI 558 CATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTG 606
E00378:188:HV 151 G 151
L1PA3_3end#LI 607 G 607
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1284 2.0 0.0 0.7 E00378:188:HVMVNCCXX:1:1106:4503:49373/2 1 151 (0) C L1PA2 LINE/L1 (192) 5963 5814 15
ANNOTATION EVIDENCE:
1284 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:1106:4503:49373/2 1 151 0 C L1PA2_3end LINE/L1 561 710 192
1284 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:1106:4503:49373/2 1 151 (0) C L1PA2_3end#LINE/L1 (192) 710 561 m_b1s551i380
E00378:188:HV 1 TTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAA 50
C L1PA2_3end#LI 710 TTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAA 661
E00378:188:HV 51 CATGCGGTGTTTGGTTTTTTCTTCTTGCGACAGTTTACTGAGAATGATGA 100
i v i
C L1PA2_3end#LI 660 TATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGA 611
E00378:188:HV 101 TTTCCAATTTCATCCATGTCCCTAACAAAGGACATGAACTCATCATTTTT 150
-
C L1PA2_3end#LI 610 TTTCCAATTTCATCCATGTCCCT-ACAAAGGACATGAACTCATCATTTTT 562
E00378:188:HV 151 T 151
C L1PA2_3end#LI 561 T 561
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1296 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1106:5101:50973/1 1 151 (0) + L1P1 LINE/L1 5163 5313 (833) 16
ANNOTATION EVIDENCE:
1296 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1106:5101:50973/1 1 151 0 + L1P1_orf2 LINE/L1 3054 3204 90
1296 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1106:5101:50973/1 1 151 (0) L1P1_orf2#LINE/L1 3054 3204 (90) m_b1s551i129
E00378:188:HV 1 CTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAA 50
i
L1P1_orf2#LIN 3054 CTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAG 3103
E00378:188:HV 51 AATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCC 100
L1P1_orf2#LIN 3104 AATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCC 3153
E00378:188:HV 101 AGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCC 150
L1P1_orf2#LIN 3154 AGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCC 3203
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3204 C 3204
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1348 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1106:5101:50973/2 1 151 (0) C L1P2 LINE/L1 (518) 5637 5487 17
ANNOTATION EVIDENCE:
1348 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1106:5101:50973/2 1 151 0 C L1PA4_3end LINE/L1 234 384 518
1348 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1106:5101:50973/2 1 151 (0) C L1PA4_3end#LINE/L1 (518) 384 234 m_b1s551i271
E00378:188:HV 1 TAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGA 50
i
C L1PA4_3end#LI 384 TAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGA 335
E00378:188:HV 51 ATCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAA 100
i
C L1PA4_3end#LI 334 ATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAA 285
E00378:188:HV 101 CAGTGTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTT 150
vi
C L1PA4_3end#LI 284 CAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTT 235
E00378:188:HV 151 T 151
C L1PA4_3end#LI 234 T 234
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1051 11.1 1.4 0.0 E00378:188:HVMVNCCXX:1:1109:18467:72754/2 1 144 (7) C AluSx SINE/Alu (166) 146 1 18
ANNOTATION EVIDENCE:
1051 11.11 1.37 0.00 E00378:188:HVMVNCCXX:1:1109:18467:72754/2 1 144 7 C AluSx SINE/Alu 1 146 166
1051 11.11 1.37 0.00 E00378:188:HVMVNCCXX:1:1109:18467:72754/2 1 144 (7) C AluSx#SINE/Alu (166) 146 1 m_b4s357i38
E00378:188:HV 1 CACCCCTGGCTAATTTTTGTGTTTTTAGTAGAGATGGAGTTTCACCATAT 50
v i i i i i
C AluSx#SINE/Al 146 CACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGT 97
E00378:188:HV 51 TGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCTTCAG 98
v i i-- i i i i
C AluSx#SINE/Al 96 TGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG 47
E00378:188:HV 99 CCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCC 144
i i i
C AluSx#SINE/Al 46 CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.74
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 2.00 (2 / 1)
+ 285 26.1 5.6 0.7 E00378:188:HVMVNCCXX:1:1110:24474:5985/1 5 139 (12) + L1ME4c LINE/L1 5696 5837 (246) 19
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:1:1110:24474:5985/1 5 139 12 + L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:1:1110:24474:5985/1 5 139 (12) L1ME4c_3end#LINE/L1 443 584 (246) m_b2s551i13
E00378:188:HV 5 AAATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCT 52
i v iiiv i vi --i v i v i
L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492
E00378:188:HV 53 AAATTTCTGACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT-- 96
v ii iii- - i -- i? i--
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
E00378:188:HV 97 GACAGAAAAATGGTGAAGCCATTAAAAAGTATGACTATCAAGA 139
ii v - vi v vv i i v
L1ME4c_3end#L 543 GATGGAATA-TTATGCAGCCATTAAAAATGATAATTATGAAGA 584
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 988 8.5 0.0 0.8 E00378:188:HVMVNCCXX:1:1110:24474:5985/2 1 130 (21) + AluY SINE/Alu 169 297 (14) 20
ANNOTATION EVIDENCE:
988 8.53 0.00 0.77 E00378:188:HVMVNCCXX:1:1110:24474:5985/2 1 130 21 + AluY SINE/Alu 169 297 14
988 8.53 0.00 0.77 E00378:188:HVMVNCCXX:1:1110:24474:5985/2 1 130 (21) AluY#SINE/Alu 169 297 (14) m_b2s356i94
E00378:188:HV 1 CTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAACCTGGGGAGGTGGAG 50
i i i i - i
AluY#SINE/Alu 169 CTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGG-AGGCGGAG 217
E00378:188:HV 51 GTTGCAGTGAGCCGAGATCATGCCACTGCATTCCAGCCTGGGCGACAGAG 100
v ii i
AluY#SINE/Alu 218 CTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAG 267
E00378:188:HV 101 CGAGACTCCGTCTCAAAAAAAGAAATAAAA 130
i v
AluY#SINE/Alu 268 CGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.24
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 129), avg. gap size = 1.00 (1 / 1)
+ 1084 12.1 0.0 0.0 E00378:188:HVMVNCCXX:1:1110:9810:10609/2 3 151 (0) + AluSx SINE/Alu 121 269 (43) 21
ANNOTATION EVIDENCE:
1084 12.08 0.00 0.00 E00378:188:HVMVNCCXX:1:1110:9810:10609/2 3 151 0 + AluSx SINE/Alu 121 269 43
1084 12.08 0.00 0.00 E00378:188:HVMVNCCXX:1:1110:9810:10609/2 3 151 (0) AluSx#SINE/Alu 121 269 (43) m_b6s356i10
E00378:188:HV 3 AAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTAATCCCAGC 52
v i i iv
AluSx#SINE/Al 121 AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGC 170
E00378:188:HV 53 TACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGAGGAGGTAGAGGC 102
i v i vi ii i
AluSx#SINE/Al 171 TACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGT 220
E00378:188:HV 103 TGAAGTGAACCGAGATCACACCACTGCACTCCAGCCTGGGTGACAGAGC 151
v i i i i
AluSx#SINE/Al 221 TGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGC 269
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.23
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1322 0.7 0.0 0.7 E00378:188:HVMVNCCXX:1:1111:13149:56545/1 1 151 (0) + L1PA3 LINE/L1 5712 5861 (294) 22
ANNOTATION EVIDENCE:
1322 0.66 0.00 0.66 E00378:188:HVMVNCCXX:1:1111:13149:56545/1 1 151 0 + L1PA3_3end LINE/L1 459 608 294
1322 0.66 0.00 0.66 E00378:188:HVMVNCCXX:1:1111:13149:56545/1 1 151 (0) L1PA3_3end#LINE/L1 459 608 (294) m_b1s551i342
E00378:188:HV 1 ATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAG 50
L1PA3_3end#LI 459 ATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAG 508
E00378:188:HV 51 ACTGGATTAAGAAACTGTGGCACATATACACCATGGAATACTATGCAGCC 100
v
L1PA3_3end#LI 509 ACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCC 558
E00378:188:HV 101 ATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGG 150
-
L1PA3_3end#LI 559 ATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGG 607
E00378:188:HV 151 A 151
L1PA3_3end#LI 608 A 608
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 257 26.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 1 85 (66) + L1ME4c LINE/L1 5743 5830 (253) 23 *
ANNOTATION EVIDENCE:
242 29.41 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 1 85 66 + L1ME4c_3end LINE/L1 493 577 253
242 29.41 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 1 85 (66) L1ME4c_3end#LINE/L1 493 577 (253) m_b1s551i455
E00378:188:HV 1 AAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTACAT 50
vii v vi vi i ii ii ? vi
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
E00378:188:HV 51 AACAAAATAATATGCAAACTTTAAAAATGATTATT 85
i iii v iv v v
L1ME4c_3end#L 543 GATGGAATATTATGCAGCCATTAAAAATGATAATT 577
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.06
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0)
257 25.76 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 1 66 85 + L1ME3A_3end LINE/L1 490 555 365
257 25.76 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 1 66 (85) L1ME3A_3end#LINE/L1 490 555 (365) m_b1s551i456
E00378:188:HV 1 AAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTACAT 50
v i i v vi ii i ii i
L1ME3A_3end#L 490 AAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCACAC 539
E00378:188:HV 51 AACAAAATAATATGCA 66
iii v i
L1ME3A_3end#L 540 AATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.54
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 567 2.8 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 81 151 (0) C L1PA2 LINE/L1 (2) 6153 6083 24
ANNOTATION EVIDENCE:
567 2.82 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 81 151 0 C L1PA2_3end LINE/L1 830 900 2
567 2.82 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:13149:56545/2 81 151 (0) C L1PA2_3end#LINE/L1 (2) 900 830 m_b1s551i457
E00378:188:HV 81 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 130
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 131 AGGTTAGTTACATATGTATAC 151
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATAC 830
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 593 11.2 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:15097:61714/1 72 151 (0) + AluY SINE/Alu 1 80 (231) 25
ANNOTATION EVIDENCE:
593 11.25 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:15097:61714/1 72 151 0 + AluY SINE/Alu 1 80 231
593 11.25 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:15097:61714/1 72 151 (0) AluY#SINE/Alu 1 80 (231) m_b2s357i66
E00378:188:HV 72 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 121
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 122 GGCGGGCTGATCATGAGGTCAGGAGATCAA 151
v i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGA 80
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.67
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 688 7.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:15097:61714/2 66 151 (0) C AluSx SINE/Alu (14) 298 213 26
ANNOTATION EVIDENCE:
688 6.98 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:15097:61714/2 66 151 0 C AluSx SINE/Alu 213 298 14
688 6.98 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:15097:61714/2 66 151 (0) C AluSx#SINE/Alu (14) 298 213 m_b2s357i104
E00378:188:HV 66 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 115
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 116 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCAC 151
ii i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGC 213
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.95
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)
+ 1301 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:21237:21403/1 1 151 (0) + L1P1 LINE/L1 5304 5454 (701) 27
ANNOTATION EVIDENCE:
1301 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21237:21403/1 1 151 0 + L1PA2_3end LINE/L1 51 201 701
1301 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21237:21403/1 1 151 (0) L1PA2_3end#LINE/L1 51 201 (701) m_b1s551i191
E00378:188:HV 1 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 50
L1PA2_3end#LI 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
E00378:188:HV 51 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 100
L1PA2_3end#LI 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 150
E00378:188:HV 101 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 150
L1PA2_3end#LI 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
E00378:188:HV 151 A 151
L1PA2_3end#LI 201 A 201
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1344 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:21237:21403/2 1 151 (0) C L1P2 LINE/L1 (511) 5644 5494 28
ANNOTATION EVIDENCE:
1344 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21237:21403/2 1 151 0 C L1PA4_3end LINE/L1 241 391 511
1344 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21237:21403/2 1 151 (0) C L1PA4_3end#LINE/L1 (511) 391 241 m_b1s551i273
E00378:188:HV 1 TACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCC 50
i
C L1PA4_3end#LI 391 TACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCC 342
E00378:188:HV 51 CTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTC 100
i
C L1PA4_3end#LI 341 CTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTC 292
E00378:188:HV 101 CCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACC 150
vi
C L1PA4_3end#LI 291 CCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACC 242
E00378:188:HV 151 T 151
C L1PA4_3end#LI 241 T 241
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1280 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:21765:52660/1 1 151 (0) + L1P1 LINE/L1 4945 5095 (1051) 29
ANNOTATION EVIDENCE:
1280 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21765:52660/1 1 151 0 + L1P1_orf2 LINE/L1 2836 2986 308
1280 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21765:52660/1 1 151 (0) L1P1_orf2#LINE/L1 2836 2986 (308) m_b1s551i35
E00378:188:HV 1 AAGCTGAAACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAG 50
v v i
L1P1_orf2#LIN 2836 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 2885
E00378:188:HV 51 ATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAG 100
i
L1P1_orf2#LIN 2886 ATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAG 2935
E00378:188:HV 101 AAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 150
?
L1P1_orf2#LIN 2936 AAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 2985
E00378:188:HV 151 T 151
L1P1_orf2#LIN 2986 T 2986
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1347 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:21765:52660/2 1 151 (0) C L1P1 LINE/L1 (856) 5290 5140 30
ANNOTATION EVIDENCE:
1347 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21765:52660/2 1 151 0 C L1P1_orf2 LINE/L1 3031 3181 113
1347 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:21765:52660/2 1 151 (0) C L1P1_orf2#LINE/L1 (113) 3181 3031 m_b1s551i115
E00378:188:HV 1 AAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGAT 50
C L1P1_orf2#LIN 3181 AAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGAT 3132
E00378:188:HV 51 GAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCT 100
i
C L1P1_orf2#LIN 3131 GAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCT 3082
E00378:188:HV 101 GATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCC 150
C L1P1_orf2#LIN 3081 GATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCC 3032
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 3031 A 3031
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1272 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:22252:27767/1 1 151 (0) + L1P LINE/L1 5255 5405 (750) 31
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:22252:27767/1 1 151 0 + L1PA2_3end LINE/L1 2 152 750
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:22252:27767/1 1 151 (0) L1PA2_3end#LINE/L1 2 152 (750) m_b1s551i164
E00378:188:HV 1 TAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACA 50
L1PA2_3end#LI 2 TAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACA 51
E00378:188:HV 51 AACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAA 100
L1PA2_3end#LI 52 AACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAA 101
E00378:188:HV 101 AGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCAC 150
L1PA2_3end#LI 102 AGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCAC 151
E00378:188:HV 151 T 151
L1PA2_3end#LI 152 T 152
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1338 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:22252:27767/2 1 151 (0) C L1P1 LINE/L1 (483) 5672 5522 32
ANNOTATION EVIDENCE:
1338 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:22252:27767/2 1 151 0 C L1PA3_3end LINE/L1 269 419 483
1338 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:22252:27767/2 1 151 (0) C L1PA3_3end#LINE/L1 (483) 419 269 m_b1s551i280
E00378:188:HV 1 CGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGG 50
i
C L1PA3_3end#LI 419 CAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGG 370
E00378:188:HV 51 GTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCACCACACTGACT 100
i i
C L1PA3_3end#LI 369 GTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACT 320
E00378:188:HV 101 TCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATT 150
vi
C L1PA3_3end#LI 319 TCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTT 270
E00378:188:HV 151 C 151
C L1PA3_3end#LI 269 C 269
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1297 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:23835:23970/1 1 151 (0) C L1P1 LINE/L1 (1120) 5026 4876 33
ANNOTATION EVIDENCE:
1297 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:23835:23970/1 1 151 0 C L1P1_orf2 LINE/L1 2767 2917 377
1297 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:23835:23970/1 1 151 (0) C L1P1_orf2#LINE/L1 (377) 2917 2767 m_b1s551i6
E00378:188:HV 1 TTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTA 50
i i v
C L1P1_orf2#LIN 2917 TTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTA 2868
E00378:188:HV 51 TCAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCA 100
v
C L1P1_orf2#LIN 2867 TAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCA 2818
E00378:188:HV 101 GTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGT 150
C L1P1_orf2#LIN 2817 GTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGT 2768
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2767 T 2767
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1325 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:27052:27785/1 1 151 (0) C L1P1 LINE/L1 (694) 5461 5311 34
ANNOTATION EVIDENCE:
1325 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:27052:27785/1 1 151 0 C L1PA2_3end LINE/L1 58 208 694
1325 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:27052:27785/1 1 151 (0) C L1PA2_3end#LINE/L1 (694) 208 58 m_b1s551i198
E00378:188:HV 1 TAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTG 50
C L1PA2_3end#LI 208 TAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTG 159
E00378:188:HV 51 ATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAAT 100
C L1PA2_3end#LI 158 ATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAAT 109
E00378:188:HV 101 GTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGG 150
C L1PA2_3end#LI 108 GTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGG 59
E00378:188:HV 151 G 151
C L1PA2_3end#LI 58 G 58
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1281 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1111:27052:27785/2 1 151 (0) + L1P1 LINE/L1 5033 5183 (963) 35
ANNOTATION EVIDENCE:
1281 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:27052:27785/2 1 151 0 + L1P1_orf2 LINE/L1 2924 3074 220
1281 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1111:27052:27785/2 1 151 (0) L1P1_orf2#LINE/L1 2924 3074 (220) m_b1s551i80
E00378:188:HV 1 AAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGC 50
?
L1P1_orf2#LIN 2924 AAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGC 2973
E00378:188:HV 51 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAAT 100
v i
L1P1_orf2#LIN 2974 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAAT 3023
E00378:188:HV 101 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 150
L1P1_orf2#LIN 3024 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 3073
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3074 C 3074
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1232 4.0 1.3 0.0 E00378:188:HVMVNCCXX:1:1112:10247:27503/1 1 151 (0) C L1P3 LINE/L1 (2427) 3719 3567 36
ANNOTATION EVIDENCE:
1232 3.97 1.30 0.00 E00378:188:HVMVNCCXX:1:1112:10247:27503/1 1 151 0 C L1P3_orf2 LINE/L1 1458 1610 1684
1232 3.97 1.30 0.00 E00378:188:HVMVNCCXX:1:1112:10247:27503/1 1 151 (0) C L1P3_orf2#LINE/L1 (1684) 1610 1458 m_b6s551i85
E00378:188:HV 1 TTCATCACGGATAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCC 48
v v i--
C L1P3_orf2#LIN 1610 TTCATCAGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCC 1561
E00378:188:HV 49 AGGTTTTGGAATCAGGATGATGCTGGCATCATAAAATGAGTTAGGGAAGA 98
v v i
C L1P3_orf2#LIN 1560 AGGTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGA 1511
E00378:188:HV 99 GTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGC 148
C L1P3_orf2#LIN 1510 GTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGC 1461
E00378:188:HV 149 TCC 151
C L1P3_orf2#LIN 1460 TCC 1458
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.08
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1024 5.3 7.4 0.0 E00378:188:HVMVNCCXX:1:1112:10247:27503/2 1 151 (0) + L1P3 LINE/L1 3207 3369 (2777) 37
ANNOTATION EVIDENCE:
1024 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1112:10247:27503/2 1 151 0 + L1P3_orf2 LINE/L1 1098 1260 2034
1024 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1112:10247:27503/2 1 151 (0) L1P3_orf2#LINE/L1 1098 1260 (2034) m_b6s551i191
E00378:188:HV 1 TTTTGAAAAGATTAACAAAACAGA----CCGCTAGCAAGACTAATAAAGA 46
i ---- v
L1P3_orf2#LIN 1098 TTTTGAAAAGATTAACAAAATAGATAGACCGCTAGCCAGACTAATAAAGA 1147
E00378:188:HV 47 --------GAGAAGAATCAAATAGACTCAATAAAAAATGATAAAGAGGAT 88
-------- v i
L1P3_orf2#LIN 1148 AGAAAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGAT 1197
E00378:188:HV 89 AATACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAA 138
vi
L1P3_orf2#LIN 1198 ATCACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAA 1247
E00378:188:HV 139 ATACCTCTATGCA 151
i i
L1P3_orf2#LIN 1248 ACACCTCTACGCA 1260
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1112:24474:10205/2 33 64 (87) + (CA)n Simple_repeat 1 32 (0) 38
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1112:24474:10205/2 33 64 87 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1112:24474:10205/2 33 64 (87) (CA)n#Simple_repeat 1 32 (0) m_b4s252i78
E00378:188:HV 33 CATACATGCACACACATACACACACACACACA 64
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1140 8.7 0.7 0.7 E00378:188:HVMVNCCXX:1:1113:29143:59182/1 1 151 (0) C AluY SINE/Alu (87) 224 74 39
ANNOTATION EVIDENCE:
1140 8.67 0.66 0.66 E00378:188:HVMVNCCXX:1:1113:29143:59182/1 1 151 0 C AluY SINE/Alu 74 224 87
1140 8.67 0.66 0.66 E00378:188:HVMVNCCXX:1:1113:29143:59182/1 1 151 (0) C AluY#SINE/Alu (87) 224 74 m_b2s356i64
E00378:188:HV 1 CTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCCTCC 50
v i - i i i i
C AluY#SINE/Alu 224 CTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCC 176
E00378:188:HV 51 CGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA-TTTTTG 99
iv -
C AluY#SINE/Alu 175 CGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTG 126
E00378:188:HV 100 TGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGAT 149
i i ii i
C AluY#SINE/Alu 125 TATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGAT 76
E00378:188:HV 150 CT 151
C AluY#SINE/Alu 75 CT 74
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1157 6.6 1.3 0.0 E00378:188:HVMVNCCXX:1:1113:7720:66584/1 1 151 (0) C L1P3 LINE/L1 (2388) 3758 3606 40
ANNOTATION EVIDENCE:
1157 6.62 1.30 0.00 E00378:188:HVMVNCCXX:1:1113:7720:66584/1 1 151 0 C L1P3_orf2 LINE/L1 1497 1649 1645
1157 6.62 1.30 0.00 E00378:188:HVMVNCCXX:1:1113:7720:66584/1 1 151 (0) C L1P3_orf2#LINE/L1 (1645) 1649 1497 m_b6s551i74
E00378:188:HV 1 CAGTTTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCATCACGGA 50
i i i v
C L1P3_orf2#LIN 1649 CGGTTTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATCAGGGA 1600
E00378:188:HV 51 TAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGGTTTGGAA 98
v i-- v v
C L1P3_orf2#LIN 1599 TATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTA 1550
E00378:188:HV 99 TCAGGATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTT 148
v i
C L1P3_orf2#LIN 1549 TCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTT 1500
E00378:188:HV 149 TCT 151
C L1P3_orf2#LIN 1499 TCT 1497
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.64
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1270 2.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1113:7720:66584/2 2 151 (0) + L1P3 LINE/L1 3429 3578 (2568) 41
ANNOTATION EVIDENCE:
1270 2.67 0.00 0.00 E00378:188:HVMVNCCXX:1:1113:7720:66584/2 2 151 0 + L1P3_orf2 LINE/L1 1320 1469 1825
1270 2.67 0.00 0.00 E00378:188:HVMVNCCXX:1:1113:7720:66584/2 2 151 (0) L1P3_orf2#LINE/L1 1320 1469 (1825) m_b6s551i130
E00378:188:HV 2 ACTAAAGCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTG 51
v
L1P3_orf2#LIN 1320 ACTAAACCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTG 1369
E00378:188:HV 52 AAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCA 101
L1P3_orf2#LIN 1370 AAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCA 1419
E00378:188:HV 102 GAGGGATTCACAGCCGAATTCTACCAGGGATACAAAGAGGAGCTGGTACC 151
v i i
L1P3_orf2#LIN 1420 GACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTACC 1469
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1257 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1114:22191:43413/1 1 151 (0) + L1P1 LINE/L1 4961 5111 (1035) 42
ANNOTATION EVIDENCE:
1257 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:22191:43413/1 1 151 0 + L1P1_orf2 LINE/L1 2852 3002 292
1257 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:22191:43413/1 1 151 (0) L1P1_orf2#LINE/L1 2852 3002 (292) m_b1s551i41
E00378:188:HV 1 CCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTA 50
v v i
L1P1_orf2#LIN 2852 CCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTA 2901
E00378:188:HV 51 AACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTAC 100
i ?
L1P1_orf2#LIN 2902 AACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTAC 2951
E00378:188:HV 101 CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAG 150
L1P1_orf2#LIN 2952 CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAG 3001
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3002 C 3002
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1283 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1114:22191:43413/2 1 151 (0) C L1P LINE/L1 (733) 5422 5272 43
ANNOTATION EVIDENCE:
1283 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:22191:43413/2 1 151 0 C L1PA2_3end LINE/L1 19 169 733
1283 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:22191:43413/2 1 151 (0) C L1PA2_3end#LINE/L1 (733) 169 19 m_b1s551i177
E00378:188:HV 1 GCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTG 50
C L1PA2_3end#LI 169 GCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTG 120
E00378:188:HV 51 GCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCA 100
C L1PA2_3end#LI 119 GCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCA 70
E00378:188:HV 101 CTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCAT 150
C L1PA2_3end#LI 69 CTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCAT 20
E00378:188:HV 151 T 151
C L1PA2_3end#LI 19 T 19
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 804 17.9 0.7 0.0 E00378:188:HVMVNCCXX:1:1114:25753:46349/2 1 151 (0) C AluY SINE/Alu (149) 162 11 44
ANNOTATION EVIDENCE:
804 17.88 0.66 0.00 E00378:188:HVMVNCCXX:1:1114:25753:46349/2 1 151 0 C AluY SINE/Alu 11 162 149
804 17.88 0.66 0.00 E00378:188:HVMVNCCXX:1:1114:25753:46349/2 1 151 (0) C AluY#SINE/Alu (149) 162 11 m_b2s356i55
E00378:188:HV 1 CTACAGGCGCCCGCCACCACGCCCATCTAATCTGTGGGGG-TTTAGGAGA 49
iv i v v viv- v
C AluY#SINE/Alu 162 CTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGA 113
E00378:188:HV 50 GATGGGGATTCACCACGCTAGCCAGGGTGGCCTTGATCTCCTGACCTCAT 99
i v ii i i i i i
C AluY#SINE/Alu 112 GACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGT 63
E00378:188:HV 100 GTTCAGCCCGCCTTGGCCTCCCAAAGCGCTGAGTGTACAAGCGAGAGCCA 149
v v i i i vv i v
C AluY#SINE/Alu 62 GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA 13
E00378:188:HV 150 CC 151
C AluY#SINE/Alu 12 CC 11
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 15.90
Transitions / transversions = 1.25 (15/12)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1225 8.0 0.7 0.0 E00378:188:HVMVNCCXX:1:1114:26210:45910/2 1 151 (0) C AluY SINE/Alu (149) 162 11 45
ANNOTATION EVIDENCE:
1225 7.95 0.66 0.00 E00378:188:HVMVNCCXX:1:1114:26210:45910/2 1 151 0 C AluY SINE/Alu 11 162 149
1225 7.95 0.66 0.00 E00378:188:HVMVNCCXX:1:1114:26210:45910/2 1 151 (0) C AluY#SINE/Alu (149) 162 11 m_b2s356i56
E00378:188:HV 1 CTACAGGCGCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGA 49
iv - i
C AluY#SINE/Alu 162 CTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGA 113
E00378:188:HV 50 GATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGATCTCCTGACCTCAT 99
i ii i i
C AluY#SINE/Alu 112 GACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGT 63
E00378:188:HV 100 GATCAGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTACAAGCGTGAGCCA 149
v i i i
C AluY#SINE/Alu 62 GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA 13
E00378:188:HV 150 CC 151
C AluY#SINE/Alu 12 CC 11
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.52
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1024 5.3 7.4 0.0 E00378:188:HVMVNCCXX:1:1114:28483:27486/1 1 151 (0) + L1P3 LINE/L1 3183 3345 (2801) 46
ANNOTATION EVIDENCE:
1024 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1114:28483:27486/1 1 151 0 + L1P3_orf2 LINE/L1 1074 1236 2058
1024 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1114:28483:27486/1 1 151 (0) L1P3_orf2#LINE/L1 1074 1236 (2058) m_b6s551i196
E00378:188:HV 1 AATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAACAGA-- 48
v i i --
L1P3_orf2#LIN 1074 AATCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAATAGATA 1123
E00378:188:HV 49 --CCGCTAGCAAGACTAATAAAGA--------GAGAAGAATCAAATAGAC 88
-- v --------
L1P3_orf2#LIN 1124 GACCGCTAGCCAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGAC 1173
E00378:188:HV 89 TCAATAAAAAATGATAAAGAGGATAATACCACTGATCCCACAGAAATACA 138
v i vi
L1P3_orf2#LIN 1174 ACAATAAAAAATGATAAAGGGGATATCACCACTGATCCCACAGAAATACA 1223
E00378:188:HV 139 AACTACCATCAGA 151
L1P3_orf2#LIN 1224 AACTACCATCAGA 1236
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.50
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 4.00 (12 / 3)
+ 1324 1.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1114:28483:27486/2 1 151 (0) C L1P3 LINE/L1 (2534) 3612 3462 47
ANNOTATION EVIDENCE:
1324 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:28483:27486/2 1 151 0 C L1P3_orf2 LINE/L1 1353 1503 1791
1324 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:28483:27486/2 1 151 (0) C L1P3_orf2#LINE/L1 (1791) 1503 1353 m_b6s551i118
E00378:188:HV 1 TTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTT 50
C L1P3_orf2#LIN 1503 TTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTT 1454
E00378:188:HV 51 TGTACCCCTGGTAGAATTCGGCTGTGAATCCCTCTGGTCCTGGGCTTTTT 100
i v
C L1P3_orf2#LIN 1453 TGTACCTCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTT 1404
E00378:188:HV 101 TTGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGG 150
C L1P3_orf2#LIN 1403 TTGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGG 1354
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 1353 T 1353
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1069 5.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1114:8684:50322/1 5 151 (0) + L1P3 LINE/L1 3260 3406 (2740) 48
ANNOTATION EVIDENCE:
1069 5.44 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:8684:50322/1 5 151 0 + L1P3_orf2 LINE/L1 1151 1297 1997
1069 5.44 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:8684:50322/1 5 151 (0) L1P3_orf2#LINE/L1 1151 1297 (1997) m_b6s551i178
E00378:188:HV 5 AAAGAGAGAAGAATCAAATAGACTCAATAAAAAATGATAAAGAGGATAAT 54
v i vi
L1P3_orf2#LIN 1151 AAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATC 1200
E00378:188:HV 55 ACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAATA 104
i
L1P3_orf2#LIN 1201 ACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAACA 1250
E00378:188:HV 105 CCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCC 151
i vv
L1P3_orf2#LIN 1251 CCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCC 1297
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.99
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 1272 4.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1114:8684:50322/2 1 151 (0) C L1P3 LINE/L1 (2462) 3684 3534 49
ANNOTATION EVIDENCE:
1272 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:8684:50322/2 1 151 0 C L1P3_orf2 LINE/L1 1425 1575 1719
1272 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:1114:8684:50322/2 1 151 (0) C L1P3_orf2#LINE/L1 (1719) 1575 1425 m_b6s551i100
E00378:188:HV 1 TGTTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATCATAAA 50
v v
C L1P3_orf2#LIN 1575 TGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCATAAA 1526
E00378:188:HV 51 ATGAGTTAGGGAAGAGTCCCTCTTTTTCTATGGTTTGGAATAGTTTCAGA 100
i v
C L1P3_orf2#LIN 1525 ATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGA 1476
E00378:188:HV 101 AGGAATGGTACCAGCTCCTCTTTGTGCCCCTGGTAGAATTCGGCTGTGAA 150
i i
C L1P3_orf2#LIN 1475 AGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTGAA 1426
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 1425 T 1425
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.09
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1341 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1115:19583:35871/1 1 151 (0) + L1P1 LINE/L1 5394 5544 (611) 50
ANNOTATION EVIDENCE:
1341 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1115:19583:35871/1 1 151 0 + L1PA2_3end LINE/L1 141 291 611
1341 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1115:19583:35871/1 1 151 (0) L1PA2_3end#LINE/L1 141 291 (611) m_b1s551i236
E00378:188:HV 1 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 50
L1PA2_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190
E00378:188:HV 51 ACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAAC 100
i
L1PA2_3end#LI 191 ACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAAC 240
E00378:188:HV 101 AGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTG 150
iv
L1PA2_3end#LI 241 AGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTG 290
E00378:188:HV 151 G 151
L1PA2_3end#LI 291 G 291
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1286 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1115:19583:35871/2 1 151 (0) C L1P1 LINE/L1 (353) 5802 5652 51
ANNOTATION EVIDENCE:
1286 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1115:19583:35871/2 1 151 0 C L1PA2_3end LINE/L1 399 549 353
1286 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1115:19583:35871/2 1 151 (0) C L1PA2_3end#LINE/L1 (353) 549 399 m_b1s551i319
E00378:188:HV 1 GTATATCATGGTGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTG 50
vi v
C L1PA2_3end#LI 549 GTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTG 500
E00378:188:HV 51 TTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACA 100
i
C L1PA2_3end#LI 499 TTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCA 450
E00378:188:HV 101 ATAAACATACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTT 150
i
C L1PA2_3end#LI 449 ATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTT 400
E00378:188:HV 151 T 151
C L1PA2_3end#LI 399 T 399
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.77
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1284 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1116:25134:16410/2 1 151 (0) C L1P1 LINE/L1 (974) 5172 5022 52
ANNOTATION EVIDENCE:
1284 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1116:25134:16410/2 1 151 0 C L1P1_orf2 LINE/L1 2913 3063 231
1284 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1116:25134:16410/2 1 151 (0) C L1P1_orf2#LINE/L1 (231) 3063 2913 m_b1s551i74
E00378:188:HV 1 TGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTCTGTCTT 50
i v
C L1P1_orf2#LIN 3063 TGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTT 3014
E00378:188:HV 51 TTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCT 100
C L1P1_orf2#LIN 3013 TTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCT 2964
E00378:188:HV 101 ATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTT 150
?
C L1P1_orf2#LIN 2963 ATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTT 2914
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2913 A 2913
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1348 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1116:2646:43343/1 1 151 (0) C L1P1 LINE/L1 (573) 5582 5432 53
ANNOTATION EVIDENCE:
1348 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1116:2646:43343/1 1 151 0 C L1PA3_3end LINE/L1 179 329 573
1348 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1116:2646:43343/1 1 151 (0) C L1PA3_3end#LINE/L1 (573) 329 179 m_b1s551i254
E00378:188:HV 1 CACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTG 50
C L1PA3_3end#LI 329 CACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTG 280
E00378:188:HV 51 TAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTG 100
vi
C L1PA3_3end#LI 279 TAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTG 230
E00378:188:HV 101 ACTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTG 150
i
C L1PA3_3end#LI 229 ACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTG 180
E00378:188:HV 151 G 151
C L1PA3_3end#LI 179 G 179
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1303 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1116:2646:43343/2 1 151 (0) + L1P1 LINE/L1 5329 5479 (676) 54
ANNOTATION EVIDENCE:
1303 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1116:2646:43343/2 1 151 0 + L1PA2_3end LINE/L1 76 226 676
1303 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1116:2646:43343/2 1 151 (0) L1PA2_3end#LINE/L1 76 226 (676) m_b1s551i210
E00378:188:HV 1 AAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA 50
L1PA2_3end#LI 76 AAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA 125
E00378:188:HV 51 ACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCA 100
L1PA2_3end#LI 126 ACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCA 175
E00378:188:HV 101 AAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAA 150
i
L1PA2_3end#LI 176 AAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAA 225
E00378:188:HV 151 A 151
L1PA2_3end#LI 226 A 226
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 858 15.4 0.0 4.7 E00378:188:HVMVNCCXX:1:1116:31081:49039/1 2 151 (0) C AluSx SINE/Alu (23) 289 147 55
ANNOTATION EVIDENCE:
858 15.39 0.00 4.67 E00378:188:HVMVNCCXX:1:1116:31081:49039/1 2 151 0 C AluSx SINE/Alu 147 289 23
858 15.39 0.00 4.67 E00378:188:HVMVNCCXX:1:1116:31081:49039/1 2 151 (0) C AluSx#SINE/Alu (23) 289 147 m_b5s356i0
E00378:188:HV 2 TTTTTTTGAGATGGAGTCTCACTCCATCACCCAGGCTGCAGGCTGGAGTG 51
i i ii i -------
C AluSx#SINE/Al 289 TTTTTTTGAGACGGAGTCTCGCTCTGTCGCC-------CAGGCTGGAGTG 247
E00378:188:HV 52 CAGTGGTGCTATATCTGCTCACTGCAACCTCCGCCTAGTAGGTTCAAGCA 101
i v v v vvii i
C AluSx#SINE/Al 246 CAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCG 197
E00378:188:HV 102 ATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACAGGCTCCCACCAC 151
v i i iv v v i
C AluSx#SINE/Al 196 ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCAC 147
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 11.06
Transitions / transversions = 1.44 (13/9)
Gap_init rate = 0.05 (7 / 149), avg. gap size = 1.00 (7 / 7)
+ 285 26.1 5.6 0.7 E00378:188:HVMVNCCXX:1:1119:18791:29507/1 9 143 (8) + L1ME4c LINE/L1 5696 5837 (246) 56
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:1:1119:18791:29507/1 9 143 8 + L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:1:1119:18791:29507/1 9 143 (8) L1ME4c_3end#LINE/L1 443 584 (246) m_b2s551i15
E00378:188:HV 9 AAATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCT 56
i v iiiv i vi --i v i v i
L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492
E00378:188:HV 57 AAATTTCTGACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT-- 100
v ii iii- - i -- i? i--
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
E00378:188:HV 101 GACAGAAAAATGGTGAAGCCATTAAAAAGTATGACTATCAAGA 143
ii v - vi v vv i i v
L1ME4c_3end#L 543 GATGGAATA-TTATGCAGCCATTAAAAATGATAATTATGAAGA 584
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 432 3.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 1 56 (95) + L1PA2 LINE/L1 6098 6153 (2) 57
ANNOTATION EVIDENCE:
432 3.57 0.00 0.00 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 1 56 95 + L1PA2_3end LINE/L1 845 900 2
432 3.57 0.00 0.00 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 1 56 (95) L1PA2_3end#LINE/L1 845 900 (2) m_b1s551i466
E00378:188:HV 1 TAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAA 50
i
L1PA2_3end#LI 845 TAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAA 894
E00378:188:HV 51 AAATAA 56
v
L1PA2_3end#LI 895 AAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.66
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 50 138 (13) C L1M5 LINE/L1 (293) 5831 5741 58 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 50 138 13 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 50 138 (13) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i467
E00378:188:HV 50 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 99
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 100 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 138
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 71 138 13 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:1119:23886:57600/1 71 138 (13) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i468
E00378:188:HV 71 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 120
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 121 CTATTGTTGGACATTTAG 138
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1185 11.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1119:23886:57600/2 1 151 (0) + AluSx SINE/Alu 75 225 (87) 59
ANNOTATION EVIDENCE:
1185 11.26 0.00 0.00 E00378:188:HVMVNCCXX:1:1119:23886:57600/2 1 151 0 + AluSx SINE/Alu 75 225 87
1185 11.26 0.00 0.00 E00378:188:HVMVNCCXX:1:1119:23886:57600/2 1 151 (0) AluSx#SINE/Alu 75 225 (87) m_b2s356i25
E00378:188:HV 1 GAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAA 50
i ii i v
AluSx#SINE/Al 75 GAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAA 124
E00378:188:HV 51 ATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTACT 100
i i i v i
AluSx#SINE/Al 125 ATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACT 174
E00378:188:HV 101 CAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGATTGCA 150
i i i i i i i
AluSx#SINE/Al 175 CGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCA 224
E00378:188:HV 151 G 151
AluSx#SINE/Al 225 G 225
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.20
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1345 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1120:10571:13052/1 1 151 (0) C L1P1 LINE/L1 (575) 5580 5430 60
ANNOTATION EVIDENCE:
1345 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1120:10571:13052/1 1 151 0 C L1PA3_3end LINE/L1 177 327 575
1345 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1120:10571:13052/1 1 151 (0) C L1PA3_3end#LINE/L1 (575) 327 177 m_b1s551i251
E00378:188:HV 1 CACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTA 50
C L1PA3_3end#LI 327 CACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTA 278
E00378:188:HV 51 AAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGAC 100
vi
C L1PA3_3end#LI 277 AAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGAC 228
E00378:188:HV 101 TTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGT 150
i
C L1PA3_3end#LI 227 TTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGT 178
E00378:188:HV 151 T 151
C L1PA3_3end#LI 177 T 177
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1308 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1120:10571:13052/2 1 151 (0) + L1P1 LINE/L1 5186 5336 (810) 61
ANNOTATION EVIDENCE:
1308 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1120:10571:13052/2 1 151 0 + L1P1_orf2 LINE/L1 3077 3227 67
1308 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:1120:10571:13052/2 1 151 (0) L1P1_orf2#LINE/L1 3077 3227 (67) m_b1s551i137
E00378:188:HV 1 CCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACC 50
i
L1P1_orf2#LIN 3077 CCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACC 3126
E00378:188:HV 51 TACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACA 100
L1P1_orf2#LIN 3127 TACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACA 3176
E00378:188:HV 101 AATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACA 150
L1P1_orf2#LIN 3177 AATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACA 3226
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3227 T 3227
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 951 10.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1120:15219:15197/2 1 125 (26) C AluY SINE/Alu (186) 125 1 62
ANNOTATION EVIDENCE:
951 10.40 0.00 0.00 E00378:188:HVMVNCCXX:1:1120:15219:15197/2 1 125 26 C AluY SINE/Alu 1 125 186
951 10.40 0.00 0.00 E00378:188:HVMVNCCXX:1:1120:15219:15197/2 1 125 (26) C AluY#SINE/Alu (186) 125 1 m_b2s357i76
E00378:188:HV 1 TGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGAT 50
i i ii i
C AluY#SINE/Alu 125 TATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGAT 76
E00378:188:HV 51 CTCCTGACCTCATGATCAGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTA 100
i v i i
C AluY#SINE/Alu 75 CTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA 26
E00378:188:HV 101 CAAGCGTGAGCCACCATGCCGGGCC 125
i ii v
C AluY#SINE/Alu 25 CAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.59
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.00 (0 / 124), avg. gap size = 0.0 (0 / 0)
+ 221 27.1 1.7 0.0 E00378:188:HVMVNCCXX:1:1120:5041:37225/2 93 151 (0) + MIRb SINE/MIR 67 126 (142) 63
ANNOTATION EVIDENCE:
221 27.12 1.66 0.00 E00378:188:HVMVNCCXX:1:1120:5041:37225/2 93 151 0 + MIRb SINE/MIR 67 126 142
221 27.12 1.66 0.00 E00378:188:HVMVNCCXX:1:1120:5041:37225/2 93 151 (0) MIRb#SINE/MIR 67 126 (142) m_b6s601i79
E00378:188:HV 93 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 141
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 142 TCACTAAGTC 151
v i i
MIRb#SINE/MIR 117 TCTCTGAGCC 126
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.74
Transitions / transversions = 1.67 (10/6)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)
+ 435 14.4 0.0 7.8 E00378:188:HVMVNCCXX:1:1122:23297:10064/1 1 90 (61) + AluSx SINE/Alu 222 304 (8) 64
ANNOTATION EVIDENCE:
435 14.45 0.00 7.78 E00378:188:HVMVNCCXX:1:1122:23297:10064/1 1 90 61 + AluSx SINE/Alu 222 304 8
435 14.45 0.00 7.78 E00378:188:HVMVNCCXX:1:1122:23297:10064/1 1 90 (61) AluSx#SINE/Alu 222 304 (8) m_b5s357i4
E00378:188:HV 1 GCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGAT 50
v v v i ------- i i
AluSx#SINE/Al 222 GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG-------GGCGAC 264
E00378:188:HV 51 GGAGTGAGACTCCATCTCAAAAAAACACAAAAACAAAAAA 90
i i i v v v
AluSx#SINE/Al 265 AGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.87
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.00 (7 / 7)
+ 1375 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1122:2717:41919/1 1 151 (0) + L1P1 LINE/L1 5527 5677 (478) 65
ANNOTATION EVIDENCE:
1375 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1122:2717:41919/1 1 151 0 + L1PA3_3end LINE/L1 274 424 478
1375 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1122:2717:41919/1 1 151 (0) L1PA3_3end#LINE/L1 274 424 (478) m_b1s551i283
E00378:188:HV 1 CTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTC 50
L1PA3_3end#LI 274 CTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTC 323
E00378:188:HV 51 AGTGTGGTGATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAG 100
i i
L1PA3_3end#LI 324 AGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAG 373
E00378:188:HV 101 CCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCGCTAT 150
i
L1PA3_3end#LI 374 CCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTAT 423
E00378:188:HV 151 A 151
L1PA3_3end#LI 424 A 424
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1306 1.3 0.0 0.7 E00378:188:HVMVNCCXX:1:1122:2717:41919/2 1 151 (0) C L1PA3 LINE/L1 (284) 5871 5722 66
ANNOTATION EVIDENCE:
1306 1.33 0.00 0.66 E00378:188:HVMVNCCXX:1:1122:2717:41919/2 1 151 0 C L1PA3_3end LINE/L1 469 618 284
1306 1.33 0.00 0.66 E00378:188:HVMVNCCXX:1:1122:2717:41919/2 1 151 (0) C L1PA3_3end#LINE/L1 (284) 618 469 m_b1s551i345
E00378:188:HV 1 AATGATGATTTCCAATTTCATCCATGTCCCTAACAAAGGACATGAACTCA 50
-
C L1PA3_3end#LI 618 AATGATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGACATGAACTCA 570
E00378:188:HV 51 TCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGTTT 100
v
C L1PA3_3end#LI 569 TCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTT 520
E00378:188:HV 101 CTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGGCTTTG 150
v
C L1PA3_3end#LI 519 CTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTG 470
E00378:188:HV 151 C 151
C L1PA3_3end#LI 469 C 469
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 774 14.4 0.0 5.0 E00378:188:HVMVNCCXX:1:1122:5183:18766/1 13 151 (0) C AluSx SINE/Alu (8) 304 173 67
ANNOTATION EVIDENCE:
774 14.40 0.00 5.04 E00378:188:HVMVNCCXX:1:1122:5183:18766/1 13 151 0 C AluSx SINE/Alu 173 304 8
774 14.40 0.00 5.04 E00378:188:HVMVNCCXX:1:1122:5183:18766/1 13 151 (0) C AluSx#SINE/Alu (8) 304 173 m_b5s357i28
E00378:188:HV 13 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 62
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 63 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 112
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 113 TAGTAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAG 151
vvii i v i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAG 173
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.21
Transitions / transversions = 1.11 (10/9)
Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.00 (7 / 7)
+ 1029 11.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1122:5183:18766/2 20 151 (0) + AluSx SINE/Alu 1 132 (180) 68
ANNOTATION EVIDENCE:
1029 11.36 0.00 0.00 E00378:188:HVMVNCCXX:1:1122:5183:18766/2 20 151 0 + AluSx SINE/Alu 1 132 180
1029 11.36 0.00 0.00 E00378:188:HVMVNCCXX:1:1122:5183:18766/2 20 151 (0) AluSx#SINE/Alu 1 132 (180) m_b5s356i32
E00378:188:HV 20 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 69
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 70 GGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACGT 119
i i i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 120 GTTGAAACCCCATCTCTACTAAAAATACAAAA 151
v i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAA 132
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.45
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 936 11.0 1.6 0.0 E00378:188:HVMVNCCXX:1:1124:10054:67955/1 1 127 (24) C AluSx SINE/Alu (183) 129 1 69
ANNOTATION EVIDENCE:
936 11.02 1.55 0.00 E00378:188:HVMVNCCXX:1:1124:10054:67955/1 1 127 24 C AluSx SINE/Alu 1 129 183
936 11.02 1.55 0.00 E00378:188:HVMVNCCXX:1:1124:10054:67955/1 1 127 (24) C AluSx#SINE/Alu (183) 129 1 m_b4s357i41
E00378:188:HV 1 TGTGTTTTTAGTAGAGATGGAGTTTCACCATATTGGCCAGGCTGTTCTCA 50
i i i i v i
C AluSx#SINE/Al 129 TGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCG 80
E00378:188:HV 51 AACTCCTGACCTT--GTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGG 98
i-- i i i i
C AluSx#SINE/Al 79 AACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGG 30
E00378:188:HV 99 ATTACAGGTGTGAGCCACTGCACCCGGCC 127
i i i
C AluSx#SINE/Al 29 ATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.62
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 126), avg. gap size = 2.00 (2 / 1)
+ 1298 2.0 0.0 0.7 E00378:188:HVMVNCCXX:1:1201:19015:70082/1 1 151 (0) + L1PA3 LINE/L1 5779 5928 (227) 70
ANNOTATION EVIDENCE:
1298 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:1201:19015:70082/1 1 151 0 + L1PA3_3end LINE/L1 526 675 227
1298 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:1201:19015:70082/1 1 151 (0) L1PA3_3end#LINE/L1 526 675 (227) m_b1s551i358
E00378:188:HV 1 TGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTT 50
L1PA3_3end#LI 526 TGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTT 575
E00378:188:HV 51 CATGTCCTTTGTTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGT 100
-
L1PA3_3end#LI 576 CATGTCCTTTGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGT 624
E00378:188:HV 101 AAACTGTCGCAAGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGG 150
i v i
L1PA3_3end#LI 625 AAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGG 674
E00378:188:HV 151 T 151
L1PA3_3end#LI 675 T 675
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 699 8.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1201:19015:70082/2 56 151 (0) C L1PA2 LINE/L1 (2) 6153 6058 71
ANNOTATION EVIDENCE:
699 8.33 0.00 0.00 E00378:188:HVMVNCCXX:1:1201:19015:70082/2 56 151 0 C L1PA2_3end LINE/L1 805 900 2
699 8.33 0.00 0.00 E00378:188:HVMVNCCXX:1:1201:19015:70082/2 56 151 (0) C L1PA2_3end#LINE/L1 (2) 900 805 m_b1s551i453
E00378:188:HV 56 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 105
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 106 AGGTTAGTTACATATGTATACATGGTCCATGCTGATGGGCGGCGCC 151
vv i v v i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACC 805
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.83
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 576 17.9 17.9 0.0 E00378:188:HVMVNCCXX:1:1201:25307:34641/1 1 151 (0) C L1MC4 LINE/L1 (398) 7644 7461 72
ANNOTATION EVIDENCE:
576 17.88 17.93 0.00 E00378:188:HVMVNCCXX:1:1201:25307:34641/1 1 151 0 C L1MC4_3end LINE/L1 2208 2391 398
576 17.88 17.93 0.00 E00378:188:HVMVNCCXX:1:1201:25307:34641/1 1 151 (0) C L1MC4_3end#LINE/L1 (398) 2391 2208 m_b3s551i101
E00378:188:HV 1 CATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGTTCT-- 48
v vvv v i i--
C L1MC4_3end#LI 2391 CATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGTTCCTC 2342
E00378:188:HV 49 ----TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACAG---- 90
---- i i i v ? v i v v ----
C L1MC4_3end#LI 2341 AGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACAGGCCA 2292
E00378:188:HV 91 ---------------GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTAT 125
--------------- iiv i i i
C L1MC4_3end#LI 2291 GTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCAT 2242
E00378:188:HV 126 GATTAAAT-----TTATAC---TTTGACGAGAAT 151
i ----- i --- i ii
C L1MC4_3end#LI 2241 GATTAGATTCAGGTTATGCATTTTTGGCAGGAAT 2208
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.00
Transitions / transversions = 1.60 (16/10)
Gap_init rate = 0.03 (5 / 150), avg. gap size = 6.60 (33 / 5)
+ 546 10.8 0.0 0.0 E00378:188:HVMVNCCXX:1:1202:10307:22932/1 78 151 (0) + AluY SINE/Alu 1 74 (237) 73
ANNOTATION EVIDENCE:
546 10.81 0.00 0.00 E00378:188:HVMVNCCXX:1:1202:10307:22932/1 78 151 0 + AluY SINE/Alu 1 74 237
546 10.81 0.00 0.00 E00378:188:HVMVNCCXX:1:1202:10307:22932/1 78 151 (0) AluY#SINE/Alu 1 74 (237) m_b2s357i61
E00378:188:HV 78 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 127
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 128 GGCGGGCTGATCATGAGGTCAGGA 151
v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGA 74
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.91
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 1104 9.3 0.0 0.7 E00378:188:HVMVNCCXX:1:1202:10307:22932/2 1 151 (0) C AluSx SINE/Alu (39) 273 124 74
ANNOTATION EVIDENCE:
1104 9.33 0.00 0.66 E00378:188:HVMVNCCXX:1:1202:10307:22932/2 1 151 0 C AluSx SINE/Alu 124 273 39
1104 9.33 0.00 0.66 E00378:188:HVMVNCCXX:1:1202:10307:22932/2 1 151 (0) C AluSx#SINE/Alu (39) 273 124 m_b2s356i78
E00378:188:HV 1 TCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATCTCGGCTCACT 50
i ii
C AluSx#SINE/Al 273 TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACT 224
E00378:188:HV 51 GCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCCTCCCG 100
i - i v vi i
C AluSx#SINE/Al 223 GCAACCTCCGCCT-CCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCG 175
E00378:188:HV 101 AGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAATTTTTGTGT 150
i v iv i
C AluSx#SINE/Al 174 AGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTAT 125
E00378:188:HV 151 T 151
C AluSx#SINE/Al 124 T 124
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.64
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1112 7.4 2.0 0.0 E00378:188:HVMVNCCXX:1:1202:8592:10187/1 1 149 (2) + L1P3 LINE/L1 3724 3875 (2271) 75
ANNOTATION EVIDENCE:
1112 7.38 1.97 0.00 E00378:188:HVMVNCCXX:1:1202:8592:10187/1 1 149 2 + L1P3_orf2 LINE/L1 1615 1766 1528
1112 7.38 1.97 0.00 E00378:188:HVMVNCCXX:1:1202:8592:10187/1 1 149 (2) L1P3_orf2#LINE/L1 1615 1766 (1528) m_b6s551i44
E00378:188:HV 1 GATGTGAAAATCCTCGATAAAATACTGGCAAACTGAATCCAGCA---CAT 47
i i i ---
L1P3_orf2#LIN 1615 GATGCGAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACAT 1664
E00378:188:HV 48 CAAAACGCTTATCCACCACTATCAAGTCAGCTTCATCCCTGGGACGCAAG 97
v v i i
L1P3_orf2#LIN 1665 CAAAAAGCTTATCCACCACGATCAAGTCGGCTTCATCCCTGGGATGCAAG 1714
E00378:188:HV 98 GCTGATTCAGCATACACAAATCAATAAACATAATCCATCACATAAACAGA 147
i i i i
L1P3_orf2#LIN 1715 GCTGGTTCAACATACGCAAATCAATAAACGTAATCCATCACATAAACAGA 1764
E00378:188:HV 148 AC 149
L1P3_orf2#LIN 1765 AC 1766
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 3.00 (3 / 1)
+ 415 24.2 0.0 0.8 E00378:188:HVMVNCCXX:1:1202:8592:10187/2 3 151 (0) C AluSx SINE/Alu (0) 312 162 76
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1202:8592:10187/2 3 30 121 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1202:8592:10187/2 3 30 (121) (T)n#Simple_repeat 1 28 (0) c_b6s251i20
E00378:188:HV 3 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 30
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
415 24.17 0.00 0.83 E00378:188:HVMVNCCXX:1:1202:8592:10187/2 31 151 0 C AluSx SINE/Alu 162 281 31
415 24.17 0.00 0.83 E00378:188:HVMVNCCXX:1:1202:8592:10187/2 31 151 (0) C AluSx#SINE/Alu (31) 281 162 m_b6s357i6
E00378:188:HV 31 AGGTGGGGTTTTGCTCATTTCTCCCAGGCTGGGGTGCAATGGTGTGTTCT 80
ii i i i - v v i i i i v
C AluSx#SINE/Al 281 AGACGGAGTCTCGCTC-TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
E00378:188:HV 81 CGGTTCTCTTCCGCCTCTTCCTCCCTGGTTCTAGCAATTTTTCTGCCTCC 130
i v v vi iv v v i i i v
C AluSx#SINE/Al 232 CGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCA 183
E00378:188:HV 131 TCCTCCTGGGTAGCTGGGGTT 151
v i i i
C AluSx#SINE/Al 182 GCCTCCCGAGTAGCTGGGATT 162
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 21.95
Transitions / transversions = 1.64 (18/11)
Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1)
+ 30 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1203:4432:33252/1 12 39 (112) + (T)n Simple_repeat 1 28 (0) 77
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1203:4432:33252/1 12 39 112 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1203:4432:33252/1 12 39 (112) (T)n#Simple_repeat 1 28 (0) c_b6s251i19
E00378:188:HV 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 1216 9.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1203:4432:33252/2 1 151 (0) + AluSx SINE/Alu 21 171 (141) 78
ANNOTATION EVIDENCE:
1216 9.27 0.00 0.00 E00378:188:HVMVNCCXX:1:1203:4432:33252/2 1 151 0 + AluSx SINE/Alu 21 171 141
1216 9.27 0.00 0.00 E00378:188:HVMVNCCXX:1:1203:4432:33252/2 1 151 (0) AluSx#SINE/Alu 21 171 (141) m_b6s356i17
E00378:188:HV 1 GCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCACCTGAGG 50
i v i i i
AluSx#SINE/Al 21 GCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGG 70
E00378:188:HV 51 TCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACG 100
i i i v
AluSx#SINE/Al 71 TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACT 120
E00378:188:HV 101 AAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTAATCCCAGC 150
v i i iv
AluSx#SINE/Al 121 AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGC 170
E00378:188:HV 151 T 151
AluSx#SINE/Al 171 T 171
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.65
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 996 7.5 0.0 0.0 E00378:188:HVMVNCCXX:1:1204:12652:43765/1 3 135 (16) + L1P3 LINE/L1 3766 3898 (2248) 79
ANNOTATION EVIDENCE:
996 7.52 0.00 0.00 E00378:188:HVMVNCCXX:1:1204:12652:43765/1 3 135 16 + L1P3_orf2 LINE/L1 1657 1789 1505
996 7.52 0.00 0.00 E00378:188:HVMVNCCXX:1:1204:12652:43765/1 3 135 (16) L1P3_orf2#LINE/L1 1657 1789 (1505) m_b6s551i33
E00378:188:HV 3 CAGCACATCAAAACGCTTATCCACCACTATCAAGTCAGCTTCATCCCTGG 52
v v i
L1P3_orf2#LIN 1657 CAGCACATCAAAAAGCTTATCCACCACGATCAAGTCGGCTTCATCCCTGG 1706
E00378:188:HV 53 GACGCAAGGCTGATTCAGCATACACAAATCAATAAACATAATCCATCACA 102
i i i i i
L1P3_orf2#LIN 1707 GATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAATCCATCACA 1756
E00378:188:HV 103 TAAACAGAACGAATGACAAAAACTACATGATTA 135
v i
L1P3_orf2#LIN 1757 TAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.72
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
+ 773 15.3 0.0 4.9 E00378:188:HVMVNCCXX:1:1205:20263:42956/2 2 145 (6) + AluSx SINE/Alu 168 304 (8) 80
ANNOTATION EVIDENCE:
773 15.32 0.00 4.86 E00378:188:HVMVNCCXX:1:1205:20263:42956/2 2 145 6 + AluSx SINE/Alu 168 304 8
773 15.32 0.00 4.86 E00378:188:HVMVNCCXX:1:1205:20263:42956/2 2 145 (6) AluSx#SINE/Alu 168 304 (8) m_b5s357i29
E00378:188:HV 2 AGCTGCTCAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGA 51
i i v i iivv
AluSx#SINE/Al 168 AGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGA 217
E00378:188:HV 52 GGTTGCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCAGCCTGGG 101
v v v i -------
AluSx#SINE/Al 218 GGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG-------GG 260
E00378:188:HV 102 TGATGGAGTGAGACTCCATCGCAAAAAAACACAAAAACAAAAAA 145
i ii i i v v v v
AluSx#SINE/Al 261 CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.49
Transitions / transversions = 1.10 (11/10)
Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.00 (7 / 7)
+ 1217 9.9 0.0 0.0 E00378:188:HVMVNCCXX:1:1206:5294:67586/1 1 151 (0) C AluSx SINE/Alu (107) 205 55 81
ANNOTATION EVIDENCE:
1217 9.93 0.00 0.00 E00378:188:HVMVNCCXX:1:1206:5294:67586/1 1 151 0 C AluSx SINE/Alu 55 205 107
1217 9.93 0.00 0.00 E00378:188:HVMVNCCXX:1:1206:5294:67586/1 1 151 (0) C AluSx#SINE/Alu (107) 205 55 c_b2s352i0
E00378:188:HV 1 GTTCAAGTGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGT 50
i i i i
C AluSx#SINE/Al 205 GTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGC 156
E00378:188:HV 51 GCCCACCACCACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTT 100
v i i i v i ii
C AluSx#SINE/Al 155 GCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTT 106
E00378:188:HV 101 TCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCAC 150
i i i
C AluSx#SINE/Al 105 TCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGC 56
E00378:188:HV 151 C 151
C AluSx#SINE/Al 55 C 55
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.39
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 678 19.6 6.1 0.7 E00378:188:HVMVNCCXX:1:1207:14661:4561/1 13 151 (0) C L1MC4 LINE/L1 (131) 7911 7765 82
ANNOTATION EVIDENCE:
678 19.56 6.12 0.72 E00378:188:HVMVNCCXX:1:1207:14661:4561/1 13 151 0 C L1MC4_3end LINE/L1 2512 2658 131
678 19.56 6.12 0.72 E00378:188:HVMVNCCXX:1:1207:14661:4561/1 13 151 (0) C L1MC4_3end#LINE/L1 (131) 2658 2512 m_b3s551i24
E00378:188:HV 13 ATACACACATCATTTTCTCTGAACCATTTTGAGATGAAATCGCACACGTG 62
i i iv i - vv i i v i ?
C L1MC4_3end#LI 2658 ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAGTTGCAGACATN 2610
E00378:188:HV 63 ATGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAACAAGGA 103
i --------- i i
C L1MC4_3end#LI 2609 ATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAACAAGGA 2560
E00378:188:HV 104 TACACTTCTGTTTAGCCACAGTATAATCATCAAAATCAGGAAGTTAAC 151
i iv ii iiv i i i i
C L1MC4_3end#LI 2559 CATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGAAATTAAC 2512
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.75
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 138), avg. gap size = 5.00 (10 / 2)
+ 327 22.6 12.5 0.0 E00378:188:HVMVNCCXX:1:1207:14661:4561/2 50 133 (18) + L1MC4 LINE/L1 7416 7529 (513) 83
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:1:1207:14661:4561/2 50 133 18 + L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:1:1207:14661:4561/2 50 133 (18) L1MC4a_3end#LINE/L1 2163 2258 (371) m_b3s551i125
E00378:188:HV 50 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 90
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
E00378:188:HV 91 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGGAC 133
--- i i i i i vii
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAATTGAGGGAC 2258
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.05 (4 / 83), avg. gap size = 3.00 (12 / 4)
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:1:1207:14661:4561/2 59 133 18 + L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:1:1207:14661:4561/2 59 133 (18) L1MC4_3end#LINE/L1 2194 2276 (513) m_b3s551i126
E00378:188:HV 59 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 100
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
E00378:188:HV 101 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC 133
i i i vii
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGAC 2276
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 463 18.4 5.8 0.0 E00378:188:HVMVNCCXX:1:1208:29396:35045/2 35 132 (19) C L1MC4 LINE/L1 (393) 7649 7546 84
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:1:1208:29396:35045/2 35 132 19 C L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:1:1208:29396:35045/2 35 132 (19) C L1MC4_3end#LINE/L1 (393) 2396 2293 m_b3s551i92
E00378:188:HV 35 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 84
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 85 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 128
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
E00378:188:HV 129 GGTC 132
i
C L1MC4_3end#LI 2296 GGCC 2293
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 6.00 (6 / 1)
+ 1016 5.3 5.1 0.0 E00378:188:HVMVNCCXX:1:1209:12023:33744/1 2 151 (0) C L1P3 LINE/L1 (2752) 3394 3237 85
ANNOTATION EVIDENCE:
1016 5.33 5.06 0.00 E00378:188:HVMVNCCXX:1:1209:12023:33744/1 2 151 0 C L1P3_orf2 LINE/L1 1128 1285 2009
1016 5.33 5.06 0.00 E00378:188:HVMVNCCXX:1:1209:12023:33744/1 2 151 (0) C L1P3_orf2#LINE/L1 (2009) 1285 1128 m_b6s551i182
E00378:188:HV 2 TTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTATTTATAGTATTCT 51
i i
C L1P3_orf2#LIN 1285 TTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCT 1236
E00378:188:HV 52 CTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATC 101
iv i
C L1P3_orf2#LIN 1235 CTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATC 1186
E00378:188:HV 102 ATTTTTTTTTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTC 143
v v --------
C L1P3_orf2#LIN 1185 ATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTC 1136
E00378:188:HV 144 TTGCTAGC 151
v
C L1P3_orf2#LIN 1135 TGGCTAGC 1128
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.89
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 8.00 (8 / 1)
+ 938 4.3 0.7 7.3 E00378:188:HVMVNCCXX:1:1209:12023:33744/2 1 151 (0) + L1P3 LINE/L1 3073 3213 (2933) 86
ANNOTATION EVIDENCE:
938 4.28 0.71 7.28 E00378:188:HVMVNCCXX:1:1209:12023:33744/2 1 151 0 + L1P3_orf2 LINE/L1 964 1104 2190
938 4.28 0.71 7.28 E00378:188:HVMVNCCXX:1:1209:12023:33744/2 1 151 (0) L1P3_orf2#LINE/L1 964 1104 (2190) m_b6s551i247
E00378:188:HV 1 AAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACA 50
L1P3_orf2#LIN 964 AAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACA 1013
E00378:188:HV 51 AGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAGACACACACAC 99
v i- ------
L1P3_orf2#LIN 1014 AGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGACAC------ 1057
E00378:188:HV 100 ACAAAAAAAACCTTTCAAAAAAATCAATTAATCCAGGAGCTGATTTTTTG 149
----i i - v i
L1P3_orf2#LIN 1058 ----GAAAAACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTG 1102
E00378:188:HV 150 AA 151
L1P3_orf2#LIN 1103 AA 1104
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 921 15.4 0.0 1.3 E00378:188:HVMVNCCXX:1:1209:28777:37418/1 1 151 (0) + AluSx SINE/Alu 97 245 (67) 87
ANNOTATION EVIDENCE:
921 15.43 0.00 1.32 E00378:188:HVMVNCCXX:1:1209:28777:37418/1 1 151 0 + AluSx SINE/Alu 97 245 67
921 15.43 0.00 1.32 E00378:188:HVMVNCCXX:1:1209:28777:37418/1 1 151 (0) AluSx#SINE/Alu 97 245 (67) m_b5s356i8
E00378:188:HV 1 ACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCA 50
i v i -- i i
AluSx#SINE/Al 97 ACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCG 144
E00378:188:HV 51 TTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGACA 100
v i v v vi i i v
AluSx#SINE/Al 145 TGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGA 194
E00378:188:HV 101 ATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGATATAGCACCAC 150
i iivv v v v i
AluSx#SINE/Al 195 ATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCAC 244
E00378:188:HV 151 T 151
AluSx#SINE/Al 245 T 245
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 11.36
Transitions / transversions = 1.09 (12/11)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 416 14.8 0.0 8.0 E00378:188:HVMVNCCXX:1:1209:28777:37418/2 64 151 (0) C AluSx SINE/Alu (8) 304 224 88
ANNOTATION EVIDENCE:
416 14.82 0.00 7.95 E00378:188:HVMVNCCXX:1:1209:28777:37418/2 64 151 0 C AluSx SINE/Alu 224 304 8
416 14.82 0.00 7.95 E00378:188:HVMVNCCXX:1:1209:28777:37418/2 64 151 (0) C AluSx#SINE/Alu (8) 304 224 m_b5s357i0
E00378:188:HV 64 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 113
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 114 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACT 151
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACT 224
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.16
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.08 (7 / 87), avg. gap size = 1.00 (7 / 7)
+ 23 10.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1210:2585:10855/1 116 148 (3) + (TG)n Simple_repeat 1 33 (0) 89
ANNOTATION EVIDENCE:
23 10.03 0.00 0.00 E00378:188:HVMVNCCXX:1:1210:2585:10855/1 116 148 3 + (TG)n Simple_repeat 1 33 0
23 10.03 0.00 0.00 E00378:188:HVMVNCCXX:1:1210:2585:10855/1 116 148 (3) (TG)n#Simple_repeat 1 33 (0) m_b4s252i77
E00378:188:HV 116 TGTGTGTGTGTGTGTATGTGTGTGTATGTATGT 148
i i i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 1114 11.9 1.3 0.0 E00378:188:HVMVNCCXX:1:1210:2585:10855/2 1 151 (0) + AluSx SINE/Alu 14 166 (146) 90
ANNOTATION EVIDENCE:
1114 11.92 1.30 0.00 E00378:188:HVMVNCCXX:1:1210:2585:10855/2 1 151 0 + AluSx SINE/Alu 14 166 146
1114 11.92 1.30 0.00 E00378:188:HVMVNCCXX:1:1210:2585:10855/2 1 151 (0) AluSx#SINE/Alu 14 166 (146) m_b4s356i42
E00378:188:HV 1 GGCTCACACTTGTAATCCCAGCACTTTGGGAGGCTGAAGCAGGCAGATCA 50
i i i i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 51 C--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCAT 98
--i i v i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
E00378:188:HV 99 CTCTACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAA 148
i i v iv i
AluSx#SINE/Al 114 CTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAA 163
E00378:188:HV 149 TCC 151
AluSx#SINE/Al 164 TCC 166
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.59
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1319 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1211:15057:31406/1 1 151 (0) C L1P1 LINE/L1 (1138) 5008 4858 91
ANNOTATION EVIDENCE:
1319 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:15057:31406/1 1 151 0 C L1P1_orf2 LINE/L1 2749 2899 395
1319 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:15057:31406/1 1 151 (0) C L1P1_orf2#LINE/L1 (395) 2899 2749 m_b1s551i0
E00378:188:HV 1 AGTCTTTAATCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGA 50
i v v
C L1P1_orf2#LIN 2899 AGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGA 2850
E00378:188:HV 51 TCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTT 100
C L1P1_orf2#LIN 2849 TCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTT 2800
E00378:188:HV 101 ATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAA 150
C L1P1_orf2#LIN 2799 ATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAA 2750
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2749 A 2749
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1059 9.9 0.0 0.0 E00378:188:HVMVNCCXX:1:1211:23115:49619/1 21 151 (0) + AluY SINE/Alu 1 131 (180) 92
ANNOTATION EVIDENCE:
1059 9.92 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:23115:49619/1 21 151 0 + AluY SINE/Alu 1 131 180
1059 9.92 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:23115:49619/1 21 151 (0) AluY#SINE/Alu 1 131 (180) m_b2s356i46
E00378:188:HV 21 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 70
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 71 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 120
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 121 TGAAACCCCATCTCTACTAAAAACACAAAAA 151
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAA 131
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.60
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 1076 10.0 0.7 0.7 E00378:188:HVMVNCCXX:1:1211:23115:49619/2 1 151 (0) C AluY SINE/Alu (67) 244 94 93
ANNOTATION EVIDENCE:
1076 10.00 0.66 0.66 E00378:188:HVMVNCCXX:1:1211:23115:49619/2 1 151 0 C AluY SINE/Alu 94 244 67
1076 10.00 0.66 0.66 E00378:188:HVMVNCCXX:1:1211:23115:49619/2 1 151 (0) C AluY#SINE/Alu (67) 244 94 m_b2s356i70
E00378:188:HV 1 AGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCATGCC 50
ii v i - i i
C AluY#SINE/Alu 244 AGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCC 196
E00378:188:HV 51 GTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCAC 100
i i
C AluY#SINE/Alu 195 ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCAC 146
E00378:188:HV 101 CACGCCCATCTAA-TTTTTGTGTGTTTAGTAGAGATGGGGTTTCACCCCG 149
iv - i v i vi
C AluY#SINE/Alu 145 CACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTG 96
E00378:188:HV 150 TT 151
C AluY#SINE/Alu 95 TT 94
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.05
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 445 6.9 0.0 0.0 E00378:188:HVMVNCCXX:1:1211:30675:57407/1 94 151 (0) C AluSx SINE/Alu (14) 298 241 94
ANNOTATION EVIDENCE:
445 6.90 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:30675:57407/1 94 151 0 C AluSx SINE/Alu 241 298 14
445 6.90 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:30675:57407/1 94 151 (0) C AluSx#SINE/Alu (14) 298 241 m_b2s357i115
E00378:188:HV 94 TTTTATTTCTTTTTTTGAGACGGAGTCCCGCTCTGTCGCCCAGGCTGGAA 143
v i i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 144 TGCAGTGG 151
C AluSx#SINE/Al 248 TGCAGTGG 241
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.31
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 804 11.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1211:30675:57407/2 42 150 (1) + AluY SINE/Alu 1 109 (202) 95
ANNOTATION EVIDENCE:
804 11.01 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:30675:57407/2 42 150 1 + AluY SINE/Alu 1 109 202
804 11.01 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:30675:57407/2 42 150 (1) AluY#SINE/Alu 1 109 (202) m_b2s357i74
E00378:188:HV 42 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTATGGGAGGCCAA 91
i ii i i v i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 92 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 141
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 142 TGAAACCCC 150
AluY#SINE/Alu 101 TGAAACCCC 109
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.44
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0)
+ 1286 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1211:6279:68553/1 1 146 (5) + L1PA2 LINE/L1 6008 6153 (2) 96
ANNOTATION EVIDENCE:
1286 2.05 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:6279:68553/1 1 146 5 + L1PA2_3end LINE/L1 755 900 2
1286 2.05 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:6279:68553/1 1 146 (5) L1PA2_3end#LINE/L1 755 900 (2) m_b1s551i414
E00378:188:HV 1 GGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTG 50
L1PA2_3end#LI 755 GGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTG 804
E00378:188:HV 51 GGTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAACCTGCAC 100
i
L1PA2_3end#LI 805 GGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCAC 854
E00378:188:HV 101 AATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 146
i v
L1PA2_3end#LI 855 AATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.45
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0)
+ 975 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1211:6279:68553/2 39 151 (0) C L1PA2 LINE/L1 (2) 6153 6041 97
ANNOTATION EVIDENCE:
975 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:6279:68553/2 39 151 0 C L1PA2_3end LINE/L1 788 900 2
975 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1211:6279:68553/2 39 151 (0) C L1PA2_3end#LINE/L1 (2) 900 788 m_b1s551i438
E00378:188:HV 39 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 88
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 89 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 138
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
E00378:188:HV 139 AACTCGTCATCTA 151
C L1PA2_3end#LI 800 AACTCGTCATCTA 788
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.88
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.0 (0 / 0)
+ 1234 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1212:10703:50375/1 1 151 (0) + L1P3 LINE/L1 2982 3132 (3014) 98
ANNOTATION EVIDENCE:
1234 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:10703:50375/1 1 151 0 + L1P3_orf2 LINE/L1 873 1023 2271
1234 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:10703:50375/1 1 151 (0) L1P3_orf2#LINE/L1 873 1023 (2271) m_b6s551i273
E00378:188:HV 1 TAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGACAA 50
? v
L1P3_orf2#LIN 873 TAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAGAA 922
E00378:188:HV 51 AGTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTA 100
i i
L1P3_orf2#LIN 923 AGCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTA 972
E00378:188:HV 101 GAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAAC 150
L1P3_orf2#LIN 973 GAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAAC 1022
E00378:188:HV 151 T 151
L1P3_orf2#LIN 1023 T 1023
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1033 5.3 7.4 0.0 E00378:188:HVMVNCCXX:1:1212:10703:50375/2 1 151 (0) C L1P3 LINE/L1 (2784) 3362 3200 99
ANNOTATION EVIDENCE:
1033 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1212:10703:50375/2 1 151 0 C L1P3_orf2 LINE/L1 1091 1253 2041
1033 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1212:10703:50375/2 1 151 (0) C L1P3_orf2#LINE/L1 (2041) 1253 1091 m_b6s551i193
E00378:188:HV 1 AGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGT 50
i
C L1P3_orf2#LIN 1253 AGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGT 1204
E00378:188:HV 51 GGTATTATCCTCTTTATCATTTTTTATTGAGTCTATTTGATTCTTCTC-- 98
iv i v --
C L1P3_orf2#LIN 1203 GGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTC 1154
E00378:188:HV 99 ------TCTTTATTAGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTT 138
------ v ---- i
C L1P3_orf2#LIN 1153 TTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTT 1104
E00378:188:HV 139 TCAAAAAATCAGC 151
i
C L1P3_orf2#LIN 1103 TCAAAAAACCAGC 1091
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.51
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 4.00 (12 / 3)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 10 98 (53) + L1M5 LINE/L1 5741 5831 (293) 100 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 10 98 53 + L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 10 98 (53) L1ME4a_3end#LINE/L1 491 578 (293) m_b1s551i463
E00378:188:HV 10 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 59
vii ? v v vi i ii ii i i
L1ME4a_3end#L 491 CTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCAT 540
E00378:188:HV 60 ATAACAAAATAATATGCAAACTTTAAAAATTATTATTTT 98
ii iii v iv v ? -i
L1ME4a_3end#L 541 ACGATGGAATATTATGCAGCCATTAAAAATNAT-GTTTT 578
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 10 77 74 + L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 10 77 (74) L1ME3A_3end#LINE/L1 488 555 (365) m_b1s551i464
E00378:188:HV 10 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 59
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
E00378:188:HV 60 ATAACAAAATAATATGCA 77
i iii v i
L1ME3A_3end#L 538 ACAATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 463 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 92 151 (0) C L1PA2 LINE/L1 (2) 6153 6094 101
ANNOTATION EVIDENCE:
463 3.33 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 92 151 0 C L1PA2_3end LINE/L1 841 900 2
463 3.33 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:11160:11963/1 92 151 (0) C L1PA2_3end#LINE/L1 (2) 900 841 m_b1s551i465
E00378:188:HV 92 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 141
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 142 AGGTTAGTTA 151
C L1PA2_3end#LI 850 AGGTTAGTTA 841
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.41
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 1298 2.0 0.0 0.7 E00378:188:HVMVNCCXX:1:1212:11160:11963/2 1 151 (0) + L1PA3 LINE/L1 5788 5937 (218) 102
ANNOTATION EVIDENCE:
1298 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:1212:11160:11963/2 1 151 0 + L1PA3_3end LINE/L1 535 684 218
1298 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:1212:11160:11963/2 1 151 (0) L1PA3_3end#LINE/L1 535 684 (218) m_b1s551i361
E00378:188:HV 1 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTT 50
L1PA3_3end#LI 535 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTT 584
E00378:188:HV 51 TGTTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCG 100
- i
L1PA3_3end#LI 585 TGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCG 633
E00378:188:HV 101 CAAGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTG 150
v i
L1PA3_3end#LI 634 CAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTG 683
E00378:188:HV 151 A 151
L1PA3_3end#LI 684 A 684
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1295 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1212:23186:71647/1 1 151 (0) C L1P1 LINE/L1 (1105) 5041 4891 103
ANNOTATION EVIDENCE:
1295 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:23186:71647/1 1 151 0 C L1P1_orf2 LINE/L1 2782 2932 362
1295 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1212:23186:71647/1 1 151 (0) C L1P1_orf2#LINE/L1 (362) 2932 2782 m_b1s551i12
E00378:188:HV 1 CTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTT 50
i
C L1P1_orf2#LIN 2932 CTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTT 2883
E00378:188:HV 51 GAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCT 100
i v v
C L1P1_orf2#LIN 2882 GAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCT 2833
E00378:188:HV 101 ACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCT 150
C L1P1_orf2#LIN 2832 ACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCT 2783
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2782 T 2782
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1005 5.3 7.4 0.0 E00378:188:HVMVNCCXX:1:1212:7172:36487/1 1 151 (0) + L1P3 LINE/L1 3215 3377 (2769) 104
ANNOTATION EVIDENCE:
1005 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1212:7172:36487/1 1 151 0 + L1P3_orf2 LINE/L1 1106 1268 2026
1005 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1212:7172:36487/1 1 151 (0) L1P3_orf2#LINE/L1 1106 1268 (2026) m_b6s551i189
E00378:188:HV 1 AGATTAACAAAACAGA----CCGCTAGCAAGACTAATAAAGA-------- 38
i ---- v --------
L1P3_orf2#LIN 1106 AGATTAACAAAATAGATAGACCGCTAGCCAGACTAATAAAGAAGAAAAGA 1155
E00378:188:HV 39 GAGAAGAATCAAATAGACTCAATAAAAAATGATAAAGAGGATAATACCAC 88
v i vi
L1P3_orf2#LIN 1156 GAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATCACCAC 1205
E00378:188:HV 89 TGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAATACCTCT 138
i
L1P3_orf2#LIN 1206 TGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAACACCTCT 1255
E00378:188:HV 139 ATGCAAATAAACT 151
i
L1P3_orf2#LIN 1256 ACGCAAATAAACT 1268
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1161 4.6 1.3 0.0 E00378:188:HVMVNCCXX:1:1212:7172:36487/2 1 151 (0) C L1P3 LINE/L1 (2650) 3496 3344 105
ANNOTATION EVIDENCE:
1161 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:1212:7172:36487/2 1 151 0 C L1P3_orf2 LINE/L1 1235 1387 1907
1161 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:1212:7172:36487/2 1 151 (0) C L1P3_orf2#LINE/L1 (1907) 1387 1235 m_b6s551i147
E00378:188:HV 1 TAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCG 50
C L1P3_orf2#LIN 1387 TAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCG 1338
E00378:188:HV 51 ACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAATTTATC 98
v -- v i
C L1P3_orf2#LIN 1337 ACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATC 1288
E00378:188:HV 99 ACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTATTTATAGTATT 148
vv i i
C L1P3_orf2#LIN 1287 CATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAGTATT 1238
E00378:188:HV 149 CTC 151
C L1P3_orf2#LIN 1237 CTC 1235
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1220 4.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1213:16559:62452/2 1 148 (3) C L1P3 LINE/L1 (3076) 3070 2923 106
ANNOTATION EVIDENCE:
1220 4.73 0.00 0.00 E00378:188:HVMVNCCXX:1:1213:16559:62452/2 1 148 3 C L1P3_orf2 LINE/L1 814 961 2333
1220 4.73 0.00 0.00 E00378:188:HVMVNCCXX:1:1213:16559:62452/2 1 148 (3) C L1P3_orf2#LINE/L1 (2333) 961 814 m_b7s551i21
E00378:188:HV 1 ATTGTGATGTTAGGGTGTTGATTTTAGATCTTTCCCACTTTGTCCTGTGG 50
i i v ?
C L1P3_orf2#LIN 961 ATTGTGATGTTAGGGTGTCGATTTTAGATCTTTCCCGCTTTCTCNTGTGG 912
E00378:188:HV 51 GCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCA 100
C L1P3_orf2#LIN 911 GCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCA 862
E00378:188:HV 101 GAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGGTTCAAAGAACTT 148
i i v
C L1P3_orf2#LIN 861 GAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTT 814
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.28
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 1104 6.0 1.3 0.0 E00378:188:HVMVNCCXX:1:1213:28493:65546/1 1 151 (0) C L1P3 LINE/L1 (2690) 3456 3304 107
ANNOTATION EVIDENCE:
1104 5.96 1.30 0.00 E00378:188:HVMVNCCXX:1:1213:28493:65546/1 1 151 0 C L1P3_orf2 LINE/L1 1195 1347 1947
1104 5.96 1.30 0.00 E00378:188:HVMVNCCXX:1:1213:28493:65546/1 1 151 (0) C L1P3_orf2#LINE/L1 (1947) 1347 1195 m_b6s551i161
E00378:188:HV 1 CAGGGATTCGACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTA 48
v -- v i
C L1P3_orf2#LIN 1347 CAGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCA 1298
E00378:188:HV 49 GGAATTTATCACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTAT 98
vv i i
C L1P3_orf2#LIN 1297 GGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGT 1248
E00378:188:HV 99 TTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATT 148
iv
C L1P3_orf2#LIN 1247 TTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGAT 1198
E00378:188:HV 149 ATC 151
C L1P3_orf2#LIN 1197 ATC 1195
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.57
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1253 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1213:28493:65546/2 1 151 (0) + L1P3 LINE/L1 2947 3097 (3049) 108
ANNOTATION EVIDENCE:
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1213:28493:65546/2 1 151 0 + L1P3_orf2 LINE/L1 838 988 2306
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1213:28493:65546/2 1 151 (0) L1P3_orf2#LINE/L1 838 988 (2306) m_b7s551i8
E00378:188:HV 1 AAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAG 50
i
L1P3_orf2#LIN 838 AAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAG 887
E00378:188:HV 51 AGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTA 100
? v i
L1P3_orf2#LIN 888 AGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTA 937
E00378:188:HV 101 AAATCAACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAA 150
i
L1P3_orf2#LIN 938 AAATCGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAA 987
E00378:188:HV 151 A 151
L1P3_orf2#LIN 988 A 988
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1027 12.7 0.0 0.7 E00378:188:HVMVNCCXX:1:1214:20567:41620/1 1 151 (0) + AluSx SINE/Alu 121 270 (42) 109
ANNOTATION EVIDENCE:
1027 12.66 0.00 0.66 E00378:188:HVMVNCCXX:1:1214:20567:41620/1 1 151 0 + AluSx SINE/Alu 121 270 42
1027 12.66 0.00 0.66 E00378:188:HVMVNCCXX:1:1214:20567:41620/1 1 151 (0) AluSx#SINE/Alu 121 270 (42) m_b6s356i8
E00378:188:HV 1 AAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTAATCCCAGC 50
v i i iv
AluSx#SINE/Al 121 AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGC 170
E00378:188:HV 51 TACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGAGGAGGTAGAGGC 100
i v i vi ii i
AluSx#SINE/Al 171 TACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGT 220
E00378:188:HV 101 TGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTGGGAGACATGAGC 150
v i i i i v -
AluSx#SINE/Al 221 TGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGC 269
E00378:188:HV 151 G 151
AluSx#SINE/Al 270 G 270
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.58
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1029 10.2 1.4 0.0 E00378:188:HVMVNCCXX:1:1215:10287:68465/1 14 150 (1) + AluSx SINE/Alu 1 139 (173) 110
ANNOTATION EVIDENCE:
1029 10.22 1.44 0.00 E00378:188:HVMVNCCXX:1:1215:10287:68465/1 14 150 1 + AluSx SINE/Alu 1 139 173
1029 10.22 1.44 0.00 E00378:188:HVMVNCCXX:1:1215:10287:68465/1 14 150 (1) AluSx#SINE/Alu 1 139 (173) m_b4s357i39
E00378:188:HV 14 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 63
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 64 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 111
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 112 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCC 150
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCC 139
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.19
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 136), avg. gap size = 2.00 (2 / 1)
+ 209 30.1 3.7 1.9 E00378:188:HVMVNCCXX:1:1215:10287:68465/2 7 111 (40) C MIRb SINE/MIR (58) 210 104 111
ANNOTATION EVIDENCE:
209 30.09 3.74 1.90 E00378:188:HVMVNCCXX:1:1215:10287:68465/2 7 111 40 C MIRb SINE/MIR 104 210 58
209 30.09 3.74 1.90 E00378:188:HVMVNCCXX:1:1215:10287:68465/2 7 111 (40) C MIRb#SINE/MIR (58) 210 104 m_b4s601i21
E00378:188:HV 7 TTTACGTTTATTTTCTC---TAATCCTCACAGGTATCGGGCCAGGTAAGT 53
i vi v --- ivv i vv v i
C MIRb#SINE/MIR 210 TTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT 161
E00378:188:HV 54 GATA-TATCTTCACTCTACTTATGAGGTTACGAAGGCCCTAGATGACATA 102
iv - ii i i vv vv vi i - - vi v
C MIRb#SINE/MIR 160 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC-AGA-GAGGTT 113
E00378:188:HV 103 AGGCAATTT 111
i i i
C MIRb#SINE/MIR 112 AAGTAACTT 104
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 39.08
Transitions / transversions = 1.07 (16/15)
Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.50 (6 / 4)
+ 581 8.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1215:11627:5317/1 69 149 (2) C L1P3 LINE/L1 (2559) 3587 3507 112
ANNOTATION EVIDENCE:
581 8.64 0.00 0.00 E00378:188:HVMVNCCXX:1:1215:11627:5317/1 69 149 2 C L1P3_orf2 LINE/L1 1398 1478 1816
581 8.64 0.00 0.00 E00378:188:HVMVNCCXX:1:1215:11627:5317/1 69 149 (2) C L1P3_orf2#LINE/L1 (1816) 1478 1398 m_b6s551i126
E00378:188:HV 69 AGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGT 118
i
C L1P3_orf2#LIN 1478 AGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGT 1429
E00378:188:HV 119 GAAGCTGTCTGGGCGTGGCCTTTTTTGGGTT 149
v i v v v v
C L1P3_orf2#LIN 1428 GAATCCGTCTGGTCCTGGGCTTTTTTTGGTT 1398
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.95
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0)
+ 1346 1.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1216:19309:2838/1 1 151 (0) C L1P3 LINE/L1 (2546) 3600 3450 113
ANNOTATION EVIDENCE:
1346 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:1216:19309:2838/1 1 151 0 C L1P3_orf2 LINE/L1 1341 1491 1803
1346 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:1216:19309:2838/1 1 151 (0) C L1P3_orf2#LINE/L1 (1803) 1491 1341 m_b6s551i121
E00378:188:HV 1 TTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGT 50
i
C L1P3_orf2#LIN 1491 TTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGT 1442
E00378:188:HV 51 AGAATTCGGCTGTGAATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGG 100
v
C L1P3_orf2#LIN 1441 AGAATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGG 1392
E00378:188:HV 101 CTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGA 150
C L1P3_orf2#LIN 1391 CTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGA 1342
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 1341 T 1341
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 958 6.7 7.4 0.7 E00378:188:HVMVNCCXX:1:1216:19309:2838/2 1 151 (0) + L1P3 LINE/L1 3173 3334 (2812) 114
ANNOTATION EVIDENCE:
958 6.66 7.41 0.66 E00378:188:HVMVNCCXX:1:1216:19309:2838/2 1 151 0 + L1P3_orf2 LINE/L1 1064 1225 2069
958 6.66 7.41 0.66 E00378:188:HVMVNCCXX:1:1216:19309:2838/2 1 151 (0) L1P3_orf2#LINE/L1 1064 1225 (2069) m_b6s551i202
E00378:188:HV 1 CCTTTCAAAAAAATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAA 50
i - v i
L1P3_orf2#LIN 1064 CCCTTCAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAA 1112
E00378:188:HV 51 CAAAACAGA----CCGCTAGCAAGACTAATAAAGA--------GAGAAGA 88
i ---- v --------
L1P3_orf2#LIN 1113 CAAAATAGATAGACCGCTAGCCAGACTAATAAAGAAGAAAAGAGAGAAGA 1162
E00378:188:HV 89 ATCAAATAGACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCC 138
v i vi
L1P3_orf2#LIN 1163 ATCAAATAGACACAATAAAAAATGATAAAGGGGATATCACCACTGATCCC 1212
E00378:188:HV 139 ACAGAGATACAAA 151
i
L1P3_orf2#LIN 1213 ACAGAAATACAAA 1225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.01
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 4.33 (13 / 3)
+ 468 17.4 6.9 14.8 E00378:188:HVMVNCCXX:1:1217:2980:34078/2 2 143 (8) C L1MC4 LINE/L1 (102) 7940 7811 115
ANNOTATION EVIDENCE:
468 17.36 6.93 14.79 E00378:188:HVMVNCCXX:1:1217:2980:34078/2 2 143 8 C L1MC4_3end LINE/L1 2558 2687 102
468 17.36 6.93 14.79 E00378:188:HVMVNCCXX:1:1217:2980:34078/2 2 143 (8) C L1MC4_3end#LINE/L1 (102) 2687 2558 m_b3s551i13
E00378:188:HV 2 CCATATTTGCTTAATCATTCCCTCTCTCCACACACACACTCATACGCAGA 51
i v i ? ? ------------------ --
C L1MC4_3end#LI 2687 CCACATTTGCTTTATCATTCTCTNTNT------------------GC--A 2658
E00378:188:HV 52 TACACACATCATTTTCTCTGAACCATTTTGAGATGAAATCGCACACGTGA 101
i i iv i - vv i i v i ?
C L1MC4_3end#LI 2657 TATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAGTTGCAGACATNA 2609
E00378:188:HV 102 TGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAACAAGGAT 142
i --------- i i i
C L1MC4_3end#LI 2608 TGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAACAAGGAC 2559
E00378:188:HV 143 A 143
C L1MC4_3end#LI 2558 A 2558
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.45
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.16 (22 / 141), avg. gap size = 1.36 (30 / 22)
+ 1136 4.6 1.3 0.0 E00378:188:HVMVNCCXX:1:1219:13636:62909/1 1 151 (0) + L1P3 LINE/L1 3310 3462 (2684) 116
ANNOTATION EVIDENCE:
1136 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:1219:13636:62909/1 1 151 0 + L1P3_orf2 LINE/L1 1201 1353 1941
1136 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:1219:13636:62909/1 1 151 (0) L1P3_orf2#LINE/L1 1201 1353 (1941) m_b6s551i157
E00378:188:HV 1 ACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAATA 50
i
L1P3_orf2#LIN 1201 ACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAACA 1250
E00378:188:HV 51 CCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAG 100
i vv i
L1P3_orf2#LIN 1251 CCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGG 1300
E00378:188:HV 101 ACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAAT 148
v -- v
L1P3_orf2#LIN 1301 ACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAAT 1350
E00378:188:HV 149 AGA 151
L1P3_orf2#LIN 1351 AGA 1353
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1120 6.0 3.2 0.0 E00378:188:HVMVNCCXX:1:1219:13636:62909/2 1 151 (0) C L1P3 LINE/L1 (2357) 3789 3634 117
ANNOTATION EVIDENCE:
1120 5.96 3.20 0.00 E00378:188:HVMVNCCXX:1:1219:13636:62909/2 1 151 0 C L1P3_orf2 LINE/L1 1525 1680 1614
1120 5.96 3.20 0.00 E00378:188:HVMVNCCXX:1:1219:13636:62909/2 1 151 (0) C L1P3_orf2#LINE/L1 (1614) 1680 1525 m_b6s551i65
E00378:188:HV 1 GTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTAT 47
v --- i
C L1P3_orf2#LIN 1680 GTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTAT 1631
E00378:188:HV 48 CGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCT 97
i i v v
C L1P3_orf2#LIN 1630 TGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCT 1581
E00378:188:HV 98 TTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATC 145
i-- v v
C L1P3_orf2#LIN 1580 TTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTC 1531
E00378:188:HV 146 ATAAAA 151
C L1P3_orf2#LIN 1530 ATAAAA 1525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1220:17990:39862/1 89 120 (31) + (TG)n Simple_repeat 1 32 (0) 118
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:17990:39862/1 89 120 31 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:17990:39862/1 89 120 (31) (TG)n#Simple_repeat 1 32 (0) m_b4s252i76
E00378:188:HV 89 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 120
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:1:1220:17990:39862/1 121 133 (18) + (TGTATG)n Simple_repeat 1 41 (0) 119
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:1:1220:17990:39862/1 89 133 18 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:1:1220:17990:39862/1 89 133 (18) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i75
E00378:188:HV 89 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 133
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 1235 7.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1220:17990:39862/2 1 151 (0) + AluSx SINE/Alu 119 269 (43) 120
ANNOTATION EVIDENCE:
1235 7.28 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:17990:39862/2 1 151 0 + AluSx SINE/Alu 119 269 43
1235 7.28 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:17990:39862/2 1 151 (0) AluSx#SINE/Alu 119 269 (43) m_b4s356i14
E00378:188:HV 1 CTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCCA 50
i i v iv i
AluSx#SINE/Al 119 CTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA 168
E00378:188:HV 51 GCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGAAG 100
i i i
AluSx#SINE/Al 169 GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAG 218
E00378:188:HV 101 GTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCAACAGAG 150
i i
AluSx#SINE/Al 219 GTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAG 268
E00378:188:HV 151 C 151
AluSx#SINE/Al 269 C 269
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1253 4.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1220:25773:68957/2 1 151 (0) C L1P1 LINE/L1 (1050) 5096 4946 121
ANNOTATION EVIDENCE:
1253 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:25773:68957/2 1 151 0 C L1P1_orf2 LINE/L1 2837 2987 307
1253 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:25773:68957/2 1 151 (0) C L1P1_orf2#LINE/L1 (307) 2987 2837 m_b1s551i36
E00378:188:HV 1 GACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTT 50
?
C L1P1_orf2#LIN 2987 GACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTT 2938
E00378:188:HV 51 TTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCC 100
i
C L1P1_orf2#LIN 2937 TTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCC 2888
E00378:188:HV 101 ATCTTGAATTGATTTTTCTATCAGGTGTTAGGAAGGGATCCAGTTTCAGC 150
i v v v
C L1P1_orf2#LIN 2887 ATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGC 2838
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2837 T 2837
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 812 5.8 3.5 8.0 E00378:188:HVMVNCCXX:1:1220:27702:45646/1 1 151 (0) C L1P3 LINE/L1 (2886) 3260 3117 122
ANNOTATION EVIDENCE:
812 5.76 3.47 7.95 E00378:188:HVMVNCCXX:1:1220:27702:45646/1 1 151 0 C L1P3_orf2 LINE/L1 1008 1151 2143
812 5.76 3.47 7.95 E00378:188:HVMVNCCXX:1:1220:27702:45646/1 1 151 (0) C L1P3_orf2#LINE/L1 (2143) 1151 1008 m_b6s551i223
E00378:188:HV 1 TTCTCTCTTTATTAGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTT 46
- v ---- i
C L1P3_orf2#LIN 1151 TTCT-TCTTTATTAGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTT 1103
E00378:188:HV 47 CAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGT 96
i v - i i----
C L1P3_orf2#LIN 1102 CAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC---- 1058
E00378:188:HV 97 GTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCT 145
------ -i v
C L1P3_orf2#LIN 1057 ------GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCT 1014
E00378:188:HV 146 TGTCTT 151
C L1P3_orf2#LIN 1013 TGTCTT 1008
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.30
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.21 (17 / 14)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:1:1220:3376:1080/1 45 137 (14) C MIRb SINE/MIR (49) 219 122 123
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:1:1220:3376:1080/1 45 137 14 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:1:1220:3376:1080/1 45 137 (14) C MIRb#SINE/MIR (49) 219 122 m_b4s601i8
E00378:188:HV 45 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 90
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 91 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 137
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1149 5.1 0.0 0.0 E00378:188:HVMVNCCXX:1:1220:3376:1080/2 3 140 (11) + AluSx SINE/Alu 154 291 (21) 124
ANNOTATION EVIDENCE:
1149 5.07 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:3376:1080/2 3 140 11 + AluSx SINE/Alu 154 291 21
1149 5.07 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:3376:1080/2 3 140 (11) AluSx#SINE/Alu 154 291 (21) m_b4s357i28
E00378:188:HV 3 GCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGA 52
i i
AluSx#SINE/Al 154 GCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGA 203
E00378:188:HV 53 ACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 102
i i
AluSx#SINE/Al 204 ACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 253
E00378:188:HV 103 GCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 140
i i i
AluSx#SINE/Al 254 GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.22
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 137), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:1:1220:3407:1028/1 45 137 (14) C MIRb SINE/MIR (49) 219 122 125
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:1:1220:3407:1028/1 45 137 14 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:1:1220:3407:1028/1 45 137 (14) C MIRb#SINE/MIR (49) 219 122 m_b4s601i9
E00378:188:HV 45 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 90
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 91 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 137
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1149 5.1 0.0 0.0 E00378:188:HVMVNCCXX:1:1220:3407:1028/2 3 140 (11) + AluSx SINE/Alu 154 291 (21) 126
ANNOTATION EVIDENCE:
1149 5.07 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:3407:1028/2 3 140 11 + AluSx SINE/Alu 154 291 21
1149 5.07 0.00 0.00 E00378:188:HVMVNCCXX:1:1220:3407:1028/2 3 140 (11) AluSx#SINE/Alu 154 291 (21) m_b4s357i29
E00378:188:HV 3 GCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGA 52
i i
AluSx#SINE/Al 154 GCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGA 203
E00378:188:HV 53 ACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 102
i i
AluSx#SINE/Al 204 ACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 253
E00378:188:HV 103 GCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 140
i i i
AluSx#SINE/Al 254 GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.22
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 137), avg. gap size = 0.0 (0 / 0)
+ 1071 12.1 0.0 1.3 E00378:188:HVMVNCCXX:1:1221:20517:46630/2 1 151 (0) C AluSx SINE/Alu (148) 164 16 127
ANNOTATION EVIDENCE:
1071 12.08 0.00 1.32 E00378:188:HVMVNCCXX:1:1221:20517:46630/2 1 151 0 C AluSx SINE/Alu 16 164 148
1071 12.08 0.00 1.32 E00378:188:HVMVNCCXX:1:1221:20517:46630/2 1 151 (0) C AluSx#SINE/Alu (148) 164 16 m_b5s356i25
E00378:188:HV 1 ATTACAGGCTCCCACCACAATGCCTGGCTAATTTTTTTGTATTTTTAGTA 50
v v i v i i --
C AluSx#SINE/Al 164 ATTACAGGCGCGCGCCACCACGCCCGGCTAA--TTTTTGTATTTTTAGTA 117
E00378:188:HV 51 GAGACGGGGCTTCAACACGTGGGCCAGGCTGGTCCCAAACTCCTGACCTC 100
i v i v i i
C AluSx#SINE/Al 116 GAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTC 67
E00378:188:HV 101 AAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGA 150
i i i i i i
C AluSx#SINE/Al 66 AGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA 17
E00378:188:HV 151 G 151
C AluSx#SINE/Al 16 G 16
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.64
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:1:1221:2240:72807/1 38 82 (69) C MIR SINE/MIR (0) 262 218 128
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:1:1221:2240:72807/1 38 82 69 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:1:1221:2240:72807/1 38 82 (69) C MIR#SINE/MIR (0) 262 218 m_b6s601i16
E00378:188:HV 38 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 82
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 15 5.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1221:2240:72807/2 1 19 (132) + (A)n Simple_repeat 1 19 (0) 129
ANNOTATION EVIDENCE:
15 5.56 0.00 0.00 E00378:188:HVMVNCCXX:1:1221:2240:72807/2 1 19 132 + (A)n Simple_repeat 1 19 0
15 5.56 0.00 0.00 E00378:188:HVMVNCCXX:1:1221:2240:72807/2 1 19 (132) (A)n#Simple_repeat 1 19 (0) m_b6s252i19
E00378:188:HV 1 AAAAAAAAAAAAAAAAGAA 19
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 1339 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1222:14326:32531/1 1 151 (0) C L1P1 LINE/L1 (372) 5783 5633 130
ANNOTATION EVIDENCE:
1339 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1222:14326:32531/1 1 151 0 C L1PA2_3end LINE/L1 380 530 372
1339 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:1222:14326:32531/1 1 151 (0) C L1PA2_3end#LINE/L1 (372) 530 380 m_b1s551i311
E00378:188:HV 1 TGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTT 50
v
C L1PA2_3end#LI 530 TGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTT 481
E00378:188:HV 51 CCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATG 100
i
C L1PA2_3end#LI 480 CCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATG 431
E00378:188:HV 101 TGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAAT 150
i
C L1PA2_3end#LI 430 TGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAAT 381
E00378:188:HV 151 G 151
C L1PA2_3end#LI 380 G 380
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1336 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:1222:14326:32531/2 1 151 (0) + L1P1 LINE/L1 5446 5596 (559) 131
ANNOTATION EVIDENCE:
1336 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1222:14326:32531/2 1 151 0 + L1PA3_3end LINE/L1 193 343 559
1336 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:1222:14326:32531/2 1 151 (0) L1PA3_3end#LINE/L1 193 343 (559) m_b1s551i260
E00378:188:HV 1 CATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAG 50
i
L1PA3_3end#LI 193 CATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAG 242
E00378:188:HV 51 GTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTGGG 100
iv
L1PA3_3end#LI 243 GTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGG 292
E00378:188:HV 101 ACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGG 150
i
L1PA3_3end#LI 293 ACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGG 342
E00378:188:HV 151 G 151
L1PA3_3end#LI 343 G 343
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1288 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1223:26027:9660/1 1 151 (0) + L1P3 LINE/L1 3537 3687 (2459) 132
ANNOTATION EVIDENCE:
1288 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1223:26027:9660/1 1 151 0 + L1P3_orf2 LINE/L1 1428 1578 1716
1288 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:1223:26027:9660/1 1 151 (0) L1P3_orf2#LINE/L1 1428 1578 (1716) m_b6s551i97
E00378:188:HV 1 CACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTACCATTCCTTC 50
i
L1P3_orf2#LIN 1428 CACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTACCATTCCTTC 1477
E00378:188:HV 51 TGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCCTAACTCATTT 100
i
L1P3_orf2#LIN 1478 TGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCCTAACTCATTT 1527
E00378:188:HV 101 TATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAAGAAA 150
v v v
L1P3_orf2#LIN 1528 TATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAAA 1577
E00378:188:HV 151 A 151
L1P3_orf2#LIN 1578 A 1578
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1085 7.4 2.0 0.0 E00378:188:HVMVNCCXX:1:1223:26027:9660/2 4 151 (0) C L1P3 LINE/L1 (2248) 3898 3748 133
ANNOTATION EVIDENCE:
1085 7.43 1.99 0.00 E00378:188:HVMVNCCXX:1:1223:26027:9660/2 4 151 0 C L1P3_orf2 LINE/L1 1639 1789 1505
1085 7.43 1.99 0.00 E00378:188:HVMVNCCXX:1:1223:26027:9660/2 4 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1639 m_b6s551i36
E00378:188:HV 4 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 53
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 54 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 103
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 104 TTGATAGTGGTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCA 150
v v --- i
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCA 1640
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 1639 G 1639
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.19
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 3.00 (3 / 1)
+ 18 4.7 0.0 0.0 E00378:188:HVMVNCCXX:1:1223:29843:10679/2 21 42 (109) + (T)n Simple_repeat 1 22 (0) 134
ANNOTATION EVIDENCE:
18 4.71 0.00 0.00 E00378:188:HVMVNCCXX:1:1223:29843:10679/2 21 42 109 + (T)n Simple_repeat 1 22 0
18 4.71 0.00 0.00 E00378:188:HVMVNCCXX:1:1223:29843:10679/2 21 42 (109) (T)n#Simple_repeat 1 22 (0) m_b2s252i11
E00378:188:HV 21 TTTTTTTTGTTTTTTTTTTTTT 42
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1097 12.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1224:32055:4104/1 1 150 (1) + AluSx SINE/Alu 26 175 (137) 135
ANNOTATION EVIDENCE:
1097 12.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1224:32055:4104/1 1 150 1 + AluSx SINE/Alu 26 175 137
1097 12.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1224:32055:4104/1 1 150 (1) AluSx#SINE/Alu 26 175 (137) m_b2s357i30
E00378:188:HV 1 TAATCTCAGCAATTTGGGAGGCAGAGCCAGGTGGATCACCTGAGGTCGGG 50
i v v v i i i
AluSx#SINE/Al 26 TAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGG 75
E00378:188:HV 51 AGTTCGAAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAAA 100
i ii i v
AluSx#SINE/Al 76 AGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAA 125
E00378:188:HV 101 TACAAAAATTAGCTGGGTGTGGTGATGGGCACCTGTAATCCCAGCTACTC 150
i i ii v i
AluSx#SINE/Al 126 TACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTC 175
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.27
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:1224:32055:4104/2 94 115 (36) + (T)n Simple_repeat 1 22 (0) 136
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1224:32055:4104/2 94 115 36 + (T)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:1224:32055:4104/2 94 115 (36) (T)n#Simple_repeat 1 22 (0) m_b2s252i10
E00378:188:HV 94 TTTTTTTTTTTTTTTTTTTTTT 115
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1005 5.3 7.4 0.0 E00378:188:HVMVNCCXX:1:1224:4716:27099/1 1 151 (0) C L1P3 LINE/L1 (2767) 3379 3217 137
ANNOTATION EVIDENCE:
1005 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1224:4716:27099/1 1 151 0 C L1P3_orf2 LINE/L1 1108 1270 2024
1005 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:1224:4716:27099/1 1 151 (0) C L1P3_orf2#LINE/L1 (2024) 1270 1108 m_b6s551i188
E00378:188:HV 1 CTAGTTTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGT 50
i i
C L1P3_orf2#LIN 1270 CTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGT 1221
E00378:188:HV 51 ATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTC 100
iv i v
C L1P3_orf2#LIN 1220 ATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTC 1171
E00378:188:HV 101 TATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----T 138
-------- v ----
C L1P3_orf2#LIN 1170 TATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTAT 1121
E00378:188:HV 139 CTGTTTTGTTAAT 151
i
C L1P3_orf2#LIN 1120 CTATTTTGTTAAT 1108
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1230 5.3 0.0 0.0 E00378:188:HVMVNCCXX:1:1224:4716:27099/2 1 151 (0) + L1P3 LINE/L1 2913 3063 (3083) 138
ANNOTATION EVIDENCE:
1230 5.30 0.00 0.00 E00378:188:HVMVNCCXX:1:1224:4716:27099/2 1 151 0 + L1P3_orf2 LINE/L1 804 954 2340
1230 5.30 0.00 0.00 E00378:188:HVMVNCCXX:1:1224:4716:27099/2 1 151 (0) L1P3_orf2#LINE/L1 804 954 (2340) m_b7s551i24
E00378:188:HV 1 AGAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACC 50
i? i i
L1P3_orf2#LIN 804 AGAAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACC 853
E00378:188:HV 51 AGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCA 100
L1P3_orf2#LIN 854 AGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCA 903
E00378:188:HV 101 CTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAAC 150
? v i i
L1P3_orf2#LIN 904 CTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAAC 953
E00378:188:HV 151 A 151
L1P3_orf2#LIN 954 A 954
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.25
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 531 16.8 17.3 0.0 E00378:188:HVMVNCCXX:1:2101:8176:64421/2 8 144 (7) C L1MC4 LINE/L1 (412) 7630 7443 139
ANNOTATION EVIDENCE:
426 20.44 19.41 0.00 E00378:188:HVMVNCCXX:1:2101:8176:64421/2 8 144 7 C L1MC4a_3end LINE/L1 2190 2359 270
426 20.44 19.41 0.00 E00378:188:HVMVNCCXX:1:2101:8176:64421/2 8 144 (7) C L1MC4a_3end#LINE/L1 (270) 2359 2190 m_b3s551i105
E00378:188:HV 8 GTCTGTTTAGTGTCCTTCAATCTGGAACAGTTC------TTTTTTTTATT 51
vi v i vi ------i ii i i
C L1MC4a_3end#L 2359 GTCTCCTTAGTCTCCTCCAATCTGTGACAGTTCCTCAGTCTTTCCTTGTC 2310
E00378:188:HV 52 TATCATGACCTTCATATATTTGAATAGTA-----CAG------------- 83
v v i iv v ----- -------------
C L1MC4a_3end#L 2309 TTTCATGACCTTGACACTTTTGAAGAGTACTGGTCAGTTATTTTGTAGAA 2260
E00378:188:HV 84 -GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAGAT-----T 127
- iiv i i i i -----
C L1MC4a_3end#L 2259 TGTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGT 2210
E00378:188:HV 128 TATAC---TTTGACGCGAAT 144
i --- i iv
C L1MC4a_3end#L 2209 TATGCATTTTTGGCAAGAAT 2190
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.53
Transitions / transversions = 2.11 (19/9)
Gap_init rate = 0.04 (6 / 136), avg. gap size = 5.50 (33 / 6)
531 16.39 17.01 0.00 E00378:188:HVMVNCCXX:1:2101:8176:64421/2 8 129 22 C L1MC4_3end LINE/L1 2231 2377 412
531 16.39 17.01 0.00 E00378:188:HVMVNCCXX:1:2101:8176:64421/2 8 129 (22) C L1MC4_3end#LINE/L1 (412) 2377 2231 m_b3s551i106
E00378:188:HV 8 GTCTGTTTAGTGTCCTTCAATCTGGAACAGTTCT------TTTTTTTATT 51
v v i i------ i i i
C L1MC4_3end#LI 2377 GTCTCTTTAGTCTCCTTTAATCTGGAACAGTTCCTCAGTCTTTCTTTGTC 2328
E00378:188:HV 52 TATCATGACCTTCATATATTTGAATAGTACAG------------------ 83
v ? v i v v ------------------
C L1MC4_3end#LI 2327 TTTCATGACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAA 2278
E00378:188:HV 84 -GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAGATTTA 129
- iiv i i i i
C L1MC4_3end#LI 2277 TGTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCA 2231
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.87
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 8.33 (25 / 3)
+ 813 15.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2102:13413:5317/1 17 146 (5) C AluSx SINE/Alu (54) 258 129 140
ANNOTATION EVIDENCE:
813 15.38 0.00 0.00 E00378:188:HVMVNCCXX:1:2102:13413:5317/1 17 146 5 C AluSx SINE/Alu 129 258 54
813 15.38 0.00 0.00 E00378:188:HVMVNCCXX:1:2102:13413:5317/1 17 146 (5) C AluSx#SINE/Alu (54) 258 129 m_b5s357i33
E00378:188:HV 17 CAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCCTAG 66
i v v v vv
C AluSx#SINE/Al 258 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCC 209
E00378:188:HV 67 TAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACA 116
ii i v i i iv
C AluSx#SINE/Al 208 CGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA 159
E00378:188:HV 117 GGCTCCCACCACAATGCCTGGCTAATTTTT 146
v v i v i i
C AluSx#SINE/Al 158 GGCGCGCGCCACCACGCCCGGCTAATTTTT 129
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.27
Transitions / transversions = 1.00 (10/10)
Gap_init rate = 0.00 (0 / 129), avg. gap size = 0.0 (0 / 0)
+ 528 13.0 0.0 7.1 E00378:188:HVMVNCCXX:1:2102:21917:22405/2 1 99 (52) + AluSx SINE/Alu 213 304 (8) 141
ANNOTATION EVIDENCE:
528 13.04 0.00 7.07 E00378:188:HVMVNCCXX:1:2102:21917:22405/2 1 99 52 + AluSx SINE/Alu 213 304 8
528 13.04 0.00 7.07 E00378:188:HVMVNCCXX:1:2102:21917:22405/2 1 99 (52) AluSx#SINE/Alu 213 304 (8) m_b5s357i6
E00378:188:HV 1 GCGGAGGTTGCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCAGC 50
v v v i ----
AluSx#SINE/Al 213 GCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG---- 258
E00378:188:HV 51 CTGGGTGATGGAGTGAGACTCCATCTCAAAAAAACACAAAAACAAAAAA 99
--- i ii i i v v v
AluSx#SINE/Al 259 ---GGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.74
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.00 (7 / 7)
+ 267 26.5 0.0 0.0 E00378:188:HVMVNCCXX:1:2102:23926:66074/1 77 144 (7) + L1M5 LINE/L1 5741 5808 (365) 142
ANNOTATION EVIDENCE:
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:2102:23926:66074/1 77 144 7 + L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:2102:23926:66074/1 77 144 (7) L1ME3A_3end#LINE/L1 488 555 (365) m_b1s551i518
E00378:188:HV 77 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 126
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
E00378:188:HV 127 ATAACAAAATAATATGCA 144
i iii v i
L1ME3A_3end#L 538 ACAATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1346 1.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2102:23926:66074/2 1 150 (1) + L1PA2 LINE/L1 5988 6137 (18) 143
ANNOTATION EVIDENCE:
1346 1.33 0.00 0.00 E00378:188:HVMVNCCXX:1:2102:23926:66074/2 1 150 1 + L1PA2_3end LINE/L1 735 884 18
1346 1.33 0.00 0.00 E00378:188:HVMVNCCXX:1:2102:23926:66074/2 1 150 (1) L1PA2_3end#LINE/L1 735 884 (18) m_b1s551i405
E00378:188:HV 1 GTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAA 50
v
L1PA2_3end#LI 735 GTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAA 784
E00378:188:HV 51 TGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATA 100
i
L1PA2_3end#LI 785 TGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATA 834
E00378:188:HV 101 CATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGT 150
L1PA2_3end#LI 835 CATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGT 884
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.74
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 15 18.1 0.0 0.0 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 46 90 (61) + (TGTG)n Simple_repeat 1 45 (0) 144
ANNOTATION EVIDENCE:
15 18.13 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 46 77 74 + (TGTG)n Simple_repeat 1 32 0
15 18.13 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 46 77 (74) (TGTG)n#Simple_repeat 1 32 (0) m_b4s252i73
E00378:188:HV 46 TGGGTGTGTGTGTGTATGTGTGTGCATGTATG 77
v i ii i
(TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
12 13.13 0.00 10.81 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 50 90 61 + (TGTGTA)n Simple_repeat 1 37 0
12 13.13 0.00 10.81 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 50 90 (61) (TGTGTA)n#Simple_repeat 1 37 (0) m_b4s252i74
E00378:188:HV 50 TGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 90
i i -- -- v v
(TGTGTA)n#Sim 1 TGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 37
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4)
+ 313 8.5 4.1 0.0 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 105 151 (0) C 7SLRNA srpRNA (11) 309 261 145
ANNOTATION EVIDENCE:
313 8.51 4.09 0.00 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 105 151 0 C 7SLRNA SINE/Alu 261 309 11
313 8.51 4.09 0.00 E00378:188:HVMVNCCXX:1:2105:14225:40266/2 105 151 (0) C 7SLRNA#SINE/Alu (11) 309 261 m_b4s502i1
E00378:188:HV 105 TTTTTTTTT--GAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCA 151
-- ii v i
C 7SLRNA#SINE/A 309 TTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGGAGTGCA 261
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.15
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1)
+ 1112 11.3 1.3 0.0 E00378:188:HVMVNCCXX:1:2105:19553:50551/2 1 151 (0) C AluSx SINE/Alu (114) 198 46 146
ANNOTATION EVIDENCE:
1112 11.26 1.30 0.00 E00378:188:HVMVNCCXX:1:2105:19553:50551/2 1 151 0 C AluSx SINE/Alu 46 198 114
1112 11.26 1.30 0.00 E00378:188:HVMVNCCXX:1:2105:19553:50551/2 1 151 (0) C AluSx#SINE/Alu (114) 198 46 m_b4s356i33
E00378:188:HV 1 CGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCC 50
i i vi
C AluSx#SINE/Al 198 CGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCC 149
E00378:188:HV 51 ACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAGATGGAGTTTCACCAT 100
v i i i i
C AluSx#SINE/Al 148 ACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT 99
E00378:188:HV 101 ATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCTTC 148
i v i i-- i i i
C AluSx#SINE/Al 98 GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTC 49
E00378:188:HV 149 AGC 151
i
C AluSx#SINE/Al 48 GGC 46
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.84
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1101 4.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2105:23663:22757/1 20 150 (1) C AluSx SINE/Alu (21) 291 161 147
ANNOTATION EVIDENCE:
1101 4.58 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:23663:22757/1 20 150 1 C AluSx SINE/Alu 161 291 21
1101 4.58 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:23663:22757/1 20 150 (1) C AluSx#SINE/Alu (21) 291 161 m_b4s357i26
E00378:188:HV 20 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 69
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 70 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCT 119
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
E00378:188:HV 120 CCTGCCTCAGCCTCCTGAGTAGCTGGGATTA 150
i
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.58
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 913 10.9 1.6 0.0 E00378:188:HVMVNCCXX:1:2105:23663:22757/2 33 151 (0) + AluSx SINE/Alu 1 121 (191) 148
ANNOTATION EVIDENCE:
913 10.92 1.65 0.00 E00378:188:HVMVNCCXX:1:2105:23663:22757/2 33 151 0 + AluSx SINE/Alu 1 121 191
913 10.92 1.65 0.00 E00378:188:HVMVNCCXX:1:2105:23663:22757/2 33 151 (0) AluSx#SINE/Alu 1 121 (191) m_b4s356i59
E00378:188:HV 33 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 82
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 83 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 130
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 131 GGTGAAACTCCATCTCTACTA 151
i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTA 121
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.09
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 2.00 (2 / 1)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:1:2105:26819:68764/1 22 113 (38) C MIRb SINE/MIR (107) 161 67 149
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:1:2105:26819:68764/1 22 113 38 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:1:2105:26819:68764/1 22 113 (38) C MIRb#SINE/MIR (107) 161 67 m_b6s601i66
E00378:188:HV 22 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 69
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 70 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 113
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1264 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2105:32065:55420/1 1 150 (1) C L1P1 LINE/L1 (757) 5389 5240 150
ANNOTATION EVIDENCE:
1264 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:32065:55420/1 1 150 1 C L1P1_orf2 LINE/L1 3131 3280 14
1264 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:32065:55420/1 1 150 (1) C L1P1_orf2#LINE/L1 (14) 3280 3131 m_b1s551i157
E00378:188:HV 1 TTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTG 50
C L1P1_orf2#LIN 3280 TTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTG 3231
E00378:188:HV 51 TTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTA 100
C L1P1_orf2#LIN 3230 TTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTA 3181
E00378:188:HV 101 AATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATG 150
C L1P1_orf2#LIN 3180 AATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATG 3131
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1279 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2105:32065:55420/2 1 151 (0) + L1P1 LINE/L1 5093 5243 (903) 151
ANNOTATION EVIDENCE:
1279 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:32065:55420/2 1 151 0 + L1P1_orf2 LINE/L1 2984 3134 160
1279 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2105:32065:55420/2 1 151 (0) L1P1_orf2#LINE/L1 2984 3134 (160) m_b1s551i95
E00378:188:HV 1 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGG 50
v i
L1P1_orf2#LIN 2984 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 3033
E00378:188:HV 51 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 100
L1P1_orf2#LIN 3034 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 3083
E00378:188:HV 101 AGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCAT 150
i
L1P1_orf2#LIN 3084 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCAT 3133
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3134 C 3134
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1185 6.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2106:22039:8341/2 1 151 (0) + L1PA3 LINE/L1 5949 6099 (56) 152
ANNOTATION EVIDENCE:
1185 6.62 0.00 0.00 E00378:188:HVMVNCCXX:1:2106:22039:8341/2 1 151 0 + L1PA3_3end LINE/L1 696 846 56
1185 6.62 0.00 0.00 E00378:188:HVMVNCCXX:1:2106:22039:8341/2 1 151 (0) L1PA3_3end#LINE/L1 696 846 (56) m_b1s551i399
E00378:188:HV 1 ACATGGACACAGGAAGGGGAATATCACACTCTGTGGACTGTTGTGGGGTG 50
i v
L1PA3_3end#LI 696 ACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGGTG 745
E00378:188:HV 51 GGGAGAGGGGGGAGGGATAGCATCAGGGGATAAACCTAATGCTAGATGAC 100
i ii i v
L1PA3_3end#LI 746 GGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGAC 795
E00378:188:HV 101 GAGTTAGTGGGTGCAGCACACCAGCATGGCTCATGTATACATATGTGACT 150
i v i
L1PA3_3end#LI 796 GAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACT 845
E00378:188:HV 151 A 151
L1PA3_3end#LI 846 A 846
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.32
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 501 14.1 0.0 0.0 E00378:188:HVMVNCCXX:1:2106:30198:53487/1 81 151 (0) + AluSx SINE/Alu 1 71 (241) 153
ANNOTATION EVIDENCE:
501 14.08 0.00 0.00 E00378:188:HVMVNCCXX:1:2106:30198:53487/1 81 151 0 + AluSx SINE/Alu 1 71 241
501 14.08 0.00 0.00 E00378:188:HVMVNCCXX:1:2106:30198:53487/1 81 151 (0) AluSx#SINE/Alu 1 71 (241) m_b5s357i69
E00378:188:HV 81 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 130
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 131 GGTGGGCAGATCACTTGAGGT 151
i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGT 71
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.44
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 658 15.2 0.0 5.6 E00378:188:HVMVNCCXX:1:2106:30198:53487/2 27 151 (0) C AluSx SINE/Alu (8) 304 187 154
ANNOTATION EVIDENCE:
658 15.25 0.00 5.60 E00378:188:HVMVNCCXX:1:2106:30198:53487/2 27 151 0 C AluSx SINE/Alu 187 304 8
658 15.25 0.00 5.60 E00378:188:HVMVNCCXX:1:2106:30198:53487/2 27 151 (0) C AluSx#SINE/Alu (8) 304 187 m_b5s357i20
E00378:188:HV 27 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 76
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 77 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 126
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 127 TAGTAGGTTCAAGCAATTGTCCTGC 151
vvii i v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGC 187
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.42
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.00 (7 / 7)
+ 585 10.4 0.0 1.0 E00378:188:HVMVNCCXX:1:2107:15706:57424/2 1 97 (54) + AluSx SINE/Alu 217 312 (0) 155
ANNOTATION EVIDENCE:
585 10.42 0.00 1.03 E00378:188:HVMVNCCXX:1:2107:15706:57424/2 1 97 54 + AluSx SINE/Alu 217 312 0
585 10.42 0.00 1.03 E00378:188:HVMVNCCXX:1:2107:15706:57424/2 1 97 (54) AluSx#SINE/Alu 217 312 (0) m_b6s357i7
E00378:188:HV 1 AGGCTGAAGTGAACCGAGATCACACCGTTGCACTCCAGCCTGGGAGACAT 50
i v i i i ii v -
AluSx#SINE/Al 217 AGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA- 265
E00378:188:HV 51 GAGCGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 97
i i
AluSx#SINE/Al 266 GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.10
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1)
+ 529 6.0 0.2 0.2 E00378:188:HVMVNCCXX:1:2107:20040:34904/1 1 75 (76) C L1PA3 LINE/L1 (77) 6078 6003 156
ANNOTATION EVIDENCE:
361 17.56 1.33 1.33 E00378:188:HVMVNCCXX:1:2107:20040:34904/1 1 75 76 C L1PA6_3end LINE/L1 750 824 77
361 17.56 1.33 1.33 E00378:188:HVMVNCCXX:1:2107:20040:34904/1 1 75 (76) C L1PA6_3end#LINE/L1 (77) 824 750 m_b1s551i426
E00378:188:HV 1 GCCATGCTGGTGTGCTGCACCCACTAACTCGTCATCTAGCATTAGGTAGA 50
i v ii i - vv
C L1PA6_3end#LI 824 GCCATGTTGGTTTGCTGCACCCATCAACTCGTCATTTA-CATTAGGTATT 776
E00378:188:HV 51 TCTCCCAATGCGA-CTCTTGGCCAGC 75
i v - i ivv
C L1PA6_3end#LI 775 TCTCCTAATGCTATCCCTCCCCCAGC 750
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.18
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.00 (2 / 2)
529 3.28 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:20040:34904/1 1 61 90 C L1PA3_3end LINE/L1 765 825 77
529 3.28 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:20040:34904/1 1 61 (90) C L1PA3_3end#LINE/L1 (77) 825 765 m_b1s551i427
E00378:188:HV 1 GCCATGCTGGTGTGCTGCACCCACTAACTCGTCATCTAGCATTAGGTAGA 50
i v
C L1PA3_3end#LI 825 GCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATA 776
E00378:188:HV 51 TCTCCCAATGC 61
C L1PA3_3end#LI 775 TCTCCCAATGC 765
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.83
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 1292 2.0 0.0 0.7 E00378:188:HVMVNCCXX:1:2107:20040:34904/2 1 151 (0) + L1PA3 LINE/L1 5796 5945 (210) 157
ANNOTATION EVIDENCE:
1292 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:2107:20040:34904/2 1 151 0 + L1PA3_3end LINE/L1 543 692 210
1292 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:2107:20040:34904/2 1 151 (0) L1PA3_3end#LINE/L1 543 692 (210) m_b1s551i370
E00378:188:HV 1 GGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGG 50
-
L1PA3_3end#LI 543 GGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGG 591
E00378:188:HV 51 ACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGA 100
i v
L1PA3_3end#LI 592 ACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACA 641
E00378:188:HV 101 AAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAACAATGA 150
i
L1PA3_3end#LI 642 AAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGA 691
E00378:188:HV 151 G 151
L1PA3_3end#LI 692 G 692
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1271 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2107:25976:3911/1 1 151 (0) C L1P1 LINE/L1 (1061) 5085 4935 158
ANNOTATION EVIDENCE:
1271 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:25976:3911/1 1 151 0 C L1P1_orf2 LINE/L1 2826 2976 318
1271 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:25976:3911/1 1 151 (0) C L1P1_orf2#LINE/L1 (318) 2976 2826 m_b1s551i30
E00378:188:HV 1 CTTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGG 50
?
C L1P1_orf2#LIN 2976 CTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGG 2927
E00378:188:HV 51 TTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTG 100
i i
C L1P1_orf2#LIN 2926 TTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTA 2877
E00378:188:HV 101 ATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATAT 150
v v
C L1P1_orf2#LIN 2876 ATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATAT 2827
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2826 G 2826
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1231 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2107:28564:21122/1 1 151 (0) + L1P1 LINE/L1 5099 5249 (897) 159
ANNOTATION EVIDENCE:
1231 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:28564:21122/1 1 151 0 + L1P1_orf2 LINE/L1 2990 3140 154
1231 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:28564:21122/1 1 151 (0) L1P1_orf2#LINE/L1 2990 3140 (154) m_b1s551i99
E00378:188:HV 1 AAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCTA 50
v i
L1P1_orf2#LIN 2990 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3039
E00378:188:HV 51 GTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 100
i
L1P1_orf2#LIN 3040 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3089
E00378:188:HV 101 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCCGACA 150
i i
L1P1_orf2#LIN 3090 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 3139
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3140 A 3140
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.41
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1307 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2107:28564:21122/2 1 151 (0) C L1P1 LINE/L1 (539) 5616 5466 160
ANNOTATION EVIDENCE:
1307 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:28564:21122/2 1 151 0 C L1PA3_3end LINE/L1 213 363 539
1307 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2107:28564:21122/2 1 151 (0) C L1PA3_3end#LINE/L1 (539) 363 213 m_b1s551i265
E00378:188:HV 1 TGGTATTTCCAGTTCTAGATCCCTGAGGAATCACCACACTGACTTCCACA 50
i i
C L1PA3_3end#LI 363 TGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACA 314
E00378:188:HV 51 ATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATT 100
vi
C L1PA3_3end#LI 313 ATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATT 264
E00378:188:HV 101 TCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGC 150
i
C L1PA3_3end#LI 263 TCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGC 214
E00378:188:HV 151 C 151
C L1PA3_3end#LI 213 C 213
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 832 3.1 0.0 0.0 E00378:188:HVMVNCCXX:1:2108:11698:12718/1 1 98 (53) + L1PA2 LINE/L1 6056 6153 (2) 161
ANNOTATION EVIDENCE:
832 3.06 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:11698:12718/1 1 98 53 + L1PA2_3end LINE/L1 803 900 2
832 3.06 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:11698:12718/1 1 98 (53) L1PA2_3end#LINE/L1 803 900 (2) m_b1s551i446
E00378:188:HV 1 TGGGTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAACCTGC 50
i
L1PA2_3end#LI 803 TGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGC 852
E00378:188:HV 51 ACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 98
i v
L1PA2_3end#LI 853 ACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.18
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0)
+ 500 8.3 0.0 2.7 E00378:188:HVMVNCCXX:1:2108:11698:12718/2 1 74 (77) + AluSx SINE/Alu 233 304 (8) 162
ANNOTATION EVIDENCE:
500 8.34 0.00 2.70 E00378:188:HVMVNCCXX:1:2108:11698:12718/2 1 74 77 + AluSx SINE/Alu 233 304 8
500 8.34 0.00 2.70 E00378:188:HVMVNCCXX:1:2108:11698:12718/2 1 74 (77) AluSx#SINE/Alu 233 304 (8) m_b2s357i0
E00378:188:HV 1 AGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAAGCGAGACTCTGTC 50
ii --i ii i
AluSx#SINE/Al 233 AGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGAGCGAGACTCCGTC 280
E00378:188:HV 51 TCAAAAAAAAAAAAAAAAAAAAAA 74
AluSx#SINE/Al 281 TCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.45
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2)
+ 1045 4.8 0.0 0.0 E00378:188:HVMVNCCXX:1:2108:13119:63208/1 1 126 (25) + AluSx SINE/Alu 166 291 (21) 163
ANNOTATION EVIDENCE:
1045 4.76 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:13119:63208/1 1 126 25 + AluSx SINE/Alu 166 291 21
1045 4.76 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:13119:63208/1 1 126 (25) AluSx#SINE/Alu 166 291 (21) m_b4s357i24
E00378:188:HV 1 CCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCG 50
i i
AluSx#SINE/Al 166 CCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCG 215
E00378:188:HV 51 AAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCAACA 100
i i i
AluSx#SINE/Al 216 GAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA 265
E00378:188:HV 101 GAGCGAGATTCCGTCTCAAAAAAAAA 126
i
AluSx#SINE/Al 266 GAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.69
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 125), avg. gap size = 0.0 (0 / 0)
+ 255 28.2 4.5 0.0 E00378:188:HVMVNCCXX:1:2108:13119:63208/2 2 86 (65) C MIRb SINE/MIR (58) 210 122 164
ANNOTATION EVIDENCE:
255 28.24 4.50 0.00 E00378:188:HVMVNCCXX:1:2108:13119:63208/2 2 86 65 C MIRb SINE/MIR 122 210 58
255 28.24 4.50 0.00 E00378:188:HVMVNCCXX:1:2108:13119:63208/2 2 86 (65) C MIRb#SINE/MIR (58) 210 122 m_b4s601i24
E00378:188:HV 2 TTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGCCAGGTAAGT 48
i vi v --- iiv i iv v i
C MIRb#SINE/MIR 210 TTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT 161
E00378:188:HV 49 GATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 86
iv - ii i i v iv vi i
C MIRb#SINE/MIR 160 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.65
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 84), avg. gap size = 2.00 (4 / 2)
+ 256 25.8 1.5 0.0 E00378:188:HVMVNCCXX:1:2108:15077:18748/1 2 67 (84) C MIRb SINE/MIR (135) 133 67 165
ANNOTATION EVIDENCE:
256 25.76 1.50 0.00 E00378:188:HVMVNCCXX:1:2108:15077:18748/1 2 67 84 C MIRb SINE/MIR 67 133 135
256 25.76 1.50 0.00 E00378:188:HVMVNCCXX:1:2108:15077:18748/1 2 67 (84) C MIRb#SINE/MIR (135) 133 67 m_b6s601i77
E00378:188:HV 2 AAACTGTGACTTAGTGAGGTAAAGTAACTTGCTTA-TGCCACAGAGCTAA 50
v i i v v ii -v i v i
C MIRb#SINE/MIR 133 AAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG 84
E00378:188:HV 51 CAAGTGGTTGACTCGAG 67
i iv vi i
C MIRb#SINE/MIR 83 TAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 32.26
Transitions / transversions = 1.43 (10/7)
Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1)
+ 285 12.1 0.0 1.7 E00378:188:HVMVNCCXX:1:2108:15077:18748/2 1 59 (92) + 7SLRNA srpRNA 263 320 (0) 166
ANNOTATION EVIDENCE:
285 12.06 0.00 1.69 E00378:188:HVMVNCCXX:1:2108:15077:18748/2 1 59 92 + 7SLRNA SINE/Alu 263 320 0
285 12.06 0.00 1.69 E00378:188:HVMVNCCXX:1:2108:15077:18748/2 1 59 (92) 7SLRNA#SINE/Alu 263 320 (0) m_b6s502i1
E00378:188:HV 1 CACTCCAGCCTGGGAGACATGAGCGAAACTCCATCTCAAAAAAAAAAAAA 50
vi - i i i vv
7SLRNA#SINE/A 263 CACTCCAGCCTGGGCAACAT-AGCGAGACCCCGTCTCTTAAAAAAAAAAA 311
E00378:188:HV 51 AAAAAAAAA 59
7SLRNA#SINE/A 312 AAAAAAAAA 320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.37
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)
+ 1131 4.0 0.7 0.0 E00378:188:HVMVNCCXX:1:2108:15199:16674/1 1 151 (0) + L1P3 LINE/L1 3014 3165 (2981) 167
ANNOTATION EVIDENCE:
1131 3.97 0.66 0.00 E00378:188:HVMVNCCXX:1:2108:15199:16674/1 1 151 0 + L1P3_orf2 LINE/L1 905 1056 2238
1131 3.97 0.66 0.00 E00378:188:HVMVNCCXX:1:2108:15199:16674/1 1 151 (0) L1P3_orf2#LINE/L1 905 1056 (2238) m_b6s551i263
E00378:188:HV 1 TAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACA 50
? v i i
L1P3_orf2#LIN 905 TAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACA 954
E00378:188:HV 51 TCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAG 100
L1P3_orf2#LIN 955 TCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAG 1004
E00378:188:HV 101 CAGAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAGA 149
v i-
L1P3_orf2#LIN 1005 CAGAAGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGA 1054
E00378:188:HV 150 CA 151
L1P3_orf2#LIN 1055 CA 1056
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.16
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 796 5.7 8.5 7.3 E00378:188:HVMVNCCXX:1:2108:15199:16674/2 1 151 (0) C L1P3 LINE/L1 (2872) 3274 3122 168
ANNOTATION EVIDENCE:
796 5.72 8.50 7.28 E00378:188:HVMVNCCXX:1:2108:15199:16674/2 1 151 0 C L1P3_orf2 LINE/L1 1013 1165 2129
796 5.72 8.50 7.28 E00378:188:HVMVNCCXX:1:2108:15199:16674/2 1 151 (0) C L1P3_orf2#LINE/L1 (2129) 1165 1013 m_b6s551i220
E00378:188:HV 1 GATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----TCTGTT 38
-------- v ---- i
C L1P3_orf2#LIN 1165 GATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCTATT 1116
E00378:188:HV 39 TTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAA 88
i v -
C L1P3_orf2#LIN 1115 TTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAA 1067
E00378:188:HV 89 AGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGAT 137
i i---------- -i v
C L1P3_orf2#LIN 1066 GGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCTCTGAT 1027
E00378:188:HV 138 CTTAGTTATTTCTT 151
C L1P3_orf2#LIN 1026 CTTAGTTATTTCTT 1013
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1293 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2108:23896:17360/1 1 151 (0) + L1P1 LINE/L1 5234 5384 (762) 169
ANNOTATION EVIDENCE:
1293 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:23896:17360/1 1 151 0 + L1P1_orf2 LINE/L1 3125 3275 19
1293 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:23896:17360/1 1 151 (0) L1P1_orf2#LINE/L1 3125 3275 (19) m_b1s551i153
E00378:188:HV 1 CCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAA 50
L1P1_orf2#LIN 3125 CCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAA 3174
E00378:188:HV 51 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGA 100
L1P1_orf2#LIN 3175 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGA 3224
E00378:188:HV 101 CATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACA 150
L1P1_orf2#LIN 3225 CATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACA 3274
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3275 T 3275
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1351 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2108:23896:17360/2 1 151 (0) C L1P2 LINE/L1 (504) 5651 5501 170
ANNOTATION EVIDENCE:
1351 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:23896:17360/2 1 151 0 C L1PA4_3end LINE/L1 248 398 504
1351 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2108:23896:17360/2 1 151 (0) C L1PA4_3end#LINE/L1 (504) 398 248 m_b1s551i276
E00378:188:HV 1 GGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTC 50
i
C L1PA4_3end#LI 398 GGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTC 349
E00378:188:HV 51 TAGATCCCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTAGTT 100
i
C L1PA4_3end#LI 348 TAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTT 299
E00378:188:HV 101 TACAGTCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATCCTCTC 150
vi
C L1PA4_3end#LI 298 TACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTC 249
E00378:188:HV 151 C 151
C L1PA4_3end#LI 248 C 248
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1335 1.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2109:6908:55051/1 1 151 (0) C L1P3 LINE/L1 (2540) 3606 3456 171
ANNOTATION EVIDENCE:
1335 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:2109:6908:55051/1 1 151 0 C L1P3_orf2 LINE/L1 1347 1497 1797
1335 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:2109:6908:55051/1 1 151 (0) C L1P3_orf2#LINE/L1 (1797) 1497 1347 m_b6s551i119
E00378:188:HV 1 TATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACC 50
C L1P3_orf2#LIN 1497 TATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACC 1448
E00378:188:HV 51 CCTGGTAGAATTCGGCTGTGAATCCCTCTGGTCCTGGGCTTTTTTTGGTT 100
i v
C L1P3_orf2#LIN 1447 TCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGGTT 1398
E00378:188:HV 101 GGTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATT 150
C L1P3_orf2#LIN 1397 GGTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATT 1348
E00378:188:HV 151 C 151
C L1P3_orf2#LIN 1347 C 1347
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1153 5.3 1.3 0.0 E00378:188:HVMVNCCXX:1:2109:6908:55051/2 1 151 (0) + L1P3 LINE/L1 3356 3508 (2638) 172
ANNOTATION EVIDENCE:
1153 5.30 1.30 0.00 E00378:188:HVMVNCCXX:1:2109:6908:55051/2 1 151 0 + L1P3_orf2 LINE/L1 1247 1399 1895
1153 5.30 1.30 0.00 E00378:188:HVMVNCCXX:1:2109:6908:55051/2 1 151 (0) L1P3_orf2#LINE/L1 1247 1399 (1895) m_b6s551i142
E00378:188:HV 1 AATACCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTC 50
i i vv
L1P3_orf2#LIN 1247 AACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTC 1296
E00378:188:HV 51 CTAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCT 98
i v -- v
L1P3_orf2#LIN 1297 CTGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCT 1346
E00378:188:HV 99 GAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAGTAGCCTAC 148
i
L1P3_orf2#LIN 1347 GAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTAC 1396
E00378:188:HV 149 CAA 151
L1P3_orf2#LIN 1397 CAA 1399
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1105 11.4 0.0 1.3 E00378:188:HVMVNCCXX:1:2111:15879:30369/2 1 151 (0) + AluSx SINE/Alu 13 161 (151) 173
ANNOTATION EVIDENCE:
1105 11.41 0.00 1.32 E00378:188:HVMVNCCXX:1:2111:15879:30369/2 1 151 0 + AluSx SINE/Alu 13 161 151
1105 11.41 0.00 1.32 E00378:188:HVMVNCCXX:1:2111:15879:30369/2 1 151 (0) AluSx#SINE/Alu 13 161 (151) m_b5s356i26
E00378:188:HV 1 TGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAAGGTGGGCAGATC 50
i i i i i
AluSx#SINE/Al 13 TGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATC 62
E00378:188:HV 51 ACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACGTGTTGAAACCCCA 100
i i i i v i
AluSx#SINE/Al 63 ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCG 112
E00378:188:HV 101 TCTCTACTAAAAATACAAAATAATTAGCCAGGCATTGTGGTGGGAGCCTG 150
-- i i v i v v
AluSx#SINE/Al 113 TCTCTACTAAAAATACAAAA--ATTAGCCGGGCGTGGTGGCGCGCGCCTG 160
E00378:188:HV 151 T 151
AluSx#SINE/Al 161 T 161
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.24
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1155 8.0 0.7 0.7 E00378:188:HVMVNCCXX:1:2111:16873:21368/1 1 151 (0) C AluY SINE/Alu (81) 230 80 174
ANNOTATION EVIDENCE:
1155 8.00 0.66 0.66 E00378:188:HVMVNCCXX:1:2111:16873:21368/1 1 151 0 C AluY SINE/Alu 80 230 81
1155 8.00 0.66 0.66 E00378:188:HVMVNCCXX:1:2111:16873:21368/1 1 151 (0) C AluY#SINE/Alu (81) 230 80 m_b2s356i65
E00378:188:HV 1 GGCTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCA 50
v i - i i i i
C AluY#SINE/Alu 230 GGCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCA 182
E00378:188:HV 51 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA- 99
iv -
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
E00378:188:HV 100 TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGGT 149
i i ii
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
E00378:188:HV 150 CT 151
C AluY#SINE/Alu 81 CT 80
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 15 10.0 2.9 2.9 E00378:188:HVMVNCCXX:1:2111:16873:21368/2 118 151 (0) + (TTTATT)n Simple_repeat 1 34 (0) 175
ANNOTATION EVIDENCE:
15 9.98 2.94 2.94 E00378:188:HVMVNCCXX:1:2111:16873:21368/2 118 151 0 + (TTTATT)n Simple_repeat 1 34 0
15 9.98 2.94 2.94 E00378:188:HVMVNCCXX:1:2111:16873:21368/2 118 151 (0) (TTTATT)n#Simple_repeat 1 34 (0) m_b2s252i9
E00378:188:HV 118 TTTATTTTT-TTTTTATTTTTACTTGAATTTATTA 151
- i vv -
(TTTATT)n#Sim 1 TTTATTTTTATTTTTATTTTTATTTTTATTT-TTA 34
Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2)
+ 290 27.4 3.9 10.8 E00378:188:HVMVNCCXX:1:2111:32400:19223/2 1 139 (12) C L1MC4 LINE/L1 (1450) 6592 6464 176
ANNOTATION EVIDENCE:
290 27.42 3.88 10.79 E00378:188:HVMVNCCXX:1:2111:32400:19223/2 1 139 12 C L1MC4_3end LINE/L1 1211 1339 1450
290 27.42 3.88 10.79 E00378:188:HVMVNCCXX:1:2111:32400:19223/2 1 139 (12) C L1MC4_3end#LINE/L1 (1450) 1339 1211 m_b3s551i157
E00378:188:HV 1 GATATCTTCAAATCCAAGCCAACATCACACAGTTTAT-----CTTTTTTT 45
i i v v i vi i ----- i iiii
C L1MC4_3end#LI 1339 GATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTAGCCTTCCCC 1290
E00378:188:HV 46 CTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAAAAACACCCCAA 95
v v i v iv iv iii v -------------i
C L1MC4_3end#LI 1289 CTTTCCATATTTGTAACTCCCTTCTCCGACAGTGA-------------GA 1253
E00378:188:HV 96 AACCTGACTATCCACTCAACCTGAATGCATTTACTTATTTGCTC 139
i -i - i v ?v ii
C L1MC4_3end#LI 1252 AACCTGGCT-CCCA-TTATCCNCAATATATTTACTTATTTGCTC 1211
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.11
Transitions / transversions = 2.00 (22/11)
Gap_init rate = 0.12 (16 / 138), avg. gap size = 1.25 (20 / 16)
+ 647 13.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2111:9364:73018/1 57 151 (0) + AluSx SINE/Alu 1 95 (217) 177
ANNOTATION EVIDENCE:
647 13.68 0.00 0.00 E00378:188:HVMVNCCXX:1:2111:9364:73018/1 57 151 0 + AluSx SINE/Alu 1 95 217
647 13.68 0.00 0.00 E00378:188:HVMVNCCXX:1:2111:9364:73018/1 57 151 (0) AluSx#SINE/Alu 1 95 (217) m_b2s357i47
E00378:188:HV 57 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 106
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 107 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCC 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCC 95
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.50
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0)
+ 452 22.8 0.8 2.3 E00378:188:HVMVNCCXX:1:2111:9364:73018/2 13 142 (9) C AluSx SINE/Alu (8) 304 177 178
ANNOTATION EVIDENCE:
452 22.84 0.78 2.31 E00378:188:HVMVNCCXX:1:2111:9364:73018/2 13 142 9 C AluSx SINE/Alu 177 304 8
452 22.84 0.78 2.31 E00378:188:HVMVNCCXX:1:2111:9364:73018/2 13 142 (9) C AluSx#SINE/Alu (8) 304 177 m_b2s357i12
E00378:188:HV 13 TTTTTTTTTTTTTTTTTTTTTTTAGACAGAGGTCCGCTTCGTCAAACCCG 62
v i vii ii i-- i
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCA 257
E00378:188:HV 63 GGCGGGAGTGCAGTGGTCTGTTCTCCGCTCACTGCAATCCCTTCCCCCTG 112
v ivi v v i i iv i i
C AluSx#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCG 207
E00378:188:HV 113 AGGTCCAGGTG-TTTACCCGCCTCCGCTTCC 142
- i i i - iv i v i
C AluSx#SINE/Al 206 -GGTTCAAGCGATTCTCCTGCCTCAGCCTCC 177
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 20.71
Transitions / transversions = 2.22 (20/9)
Gap_init rate = 0.03 (4 / 129), avg. gap size = 1.00 (4 / 4)
+ 1040 6.6 1.3 0.0 E00378:188:HVMVNCCXX:1:2112:14052:60888/1 1 151 (0) C L1P3 LINE/L1 (2709) 3437 3285 179
ANNOTATION EVIDENCE:
1040 6.62 1.30 0.00 E00378:188:HVMVNCCXX:1:2112:14052:60888/1 1 151 0 C L1P3_orf2 LINE/L1 1176 1328 1966
1040 6.62 1.30 0.00 E00378:188:HVMVNCCXX:1:2112:14052:60888/1 1 151 (0) C L1P3_orf2#LINE/L1 (1966) 1328 1176 m_b6s551i168
E00378:188:HV 1 TGCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTC 48
v -- v i vv
C L1P3_orf2#LIN 1328 TGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTC 1279
E00378:188:HV 49 TAGATTTTCTAGTTTATTTGCATAGAGGTATTTATAGTATTCTCTGATGG 98
i i
C L1P3_orf2#LIN 1278 TAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGG 1229
E00378:188:HV 99 TAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTT 148
iv i
C L1P3_orf2#LIN 1228 TAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTT 1179
E00378:188:HV 149 ATT 151
C L1P3_orf2#LIN 1178 ATT 1176
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.29
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1250 4.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2112:14052:60888/2 1 151 (0) + L1P3 LINE/L1 2930 3080 (3066) 180
ANNOTATION EVIDENCE:
1250 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:2112:14052:60888/2 1 151 0 + L1P3_orf2 LINE/L1 821 971 2323
1250 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:2112:14052:60888/2 1 151 (0) L1P3_orf2#LINE/L1 821 971 (2323) m_b7s551i19
E00378:188:HV 1 TTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGACACA 50
i i
L1P3_orf2#LIN 821 TTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGACACA 870
E00378:188:HV 51 GCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGAC 100
? v
L1P3_orf2#LIN 871 GCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAG 920
E00378:188:HV 101 AAAGTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAAC 150
i i
L1P3_orf2#LIN 921 AAAGCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAAC 970
E00378:188:HV 151 T 151
L1P3_orf2#LIN 971 T 971
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 797 5.7 8.5 7.3 E00378:188:HVMVNCCXX:1:2112:20506:21649/1 1 151 (0) C L1P3 LINE/L1 (2867) 3279 3127 181
ANNOTATION EVIDENCE:
797 5.72 8.50 7.28 E00378:188:HVMVNCCXX:1:2112:20506:21649/1 1 151 0 C L1P3_orf2 LINE/L1 1018 1170 2124
797 5.72 8.50 7.28 E00378:188:HVMVNCCXX:1:2112:20506:21649/1 1 151 (0) C L1P3_orf2#LINE/L1 (2124) 1170 1018 m_b6s551i217
E00378:188:HV 1 TATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----T 38
-------- v ----
C L1P3_orf2#LIN 1170 TATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTAT 1121
E00378:188:HV 39 CTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTT 88
i i v -
C L1P3_orf2#LIN 1120 CTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTT 1072
E00378:188:HV 89 TTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCT 137
i i---------- -i v
C L1P3_orf2#LIN 1071 TTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCT 1032
E00378:188:HV 138 CTGATCTTAGTTAT 151
C L1P3_orf2#LIN 1031 CTGATCTTAGTTAT 1018
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1190 5.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2112:20506:21649/2 3 151 (0) + L1P3 LINE/L1 2821 2969 (3177) 182
ANNOTATION EVIDENCE:
1190 5.37 0.00 0.00 E00378:188:HVMVNCCXX:1:2112:20506:21649/2 3 151 0 + L1P3_orf2 LINE/L1 712 860 2434
1190 5.37 0.00 0.00 E00378:188:HVMVNCCXX:1:2112:20506:21649/2 3 151 (0) L1P3_orf2#LINE/L1 712 860 (2434) m_b7s551i52
E00378:188:HV 3 AGGATTAAGAAACTCACTCAAAACCACACAACTACATGGAAACTGAACAA 52
i
L1P3_orf2#LIN 712 AGGATTAAGAAACTCACTCAAAACCGCACAACTACATGGAAACTGAACAA 761
E00378:188:HV 53 CCTGCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAA 102
i i v
L1P3_orf2#LIN 762 CCTGCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAA 811
E00378:188:HV 103 GTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCT 151
i? i i
L1P3_orf2#LIN 812 ANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCT 860
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.98
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 556 9.0 0.0 1.1 E00378:188:HVMVNCCXX:1:2112:25814:5599/1 3 92 (59) + AluSx SINE/Alu 224 312 (0) 183
ANNOTATION EVIDENCE:
556 8.99 0.00 1.11 E00378:188:HVMVNCCXX:1:2112:25814:5599/1 3 92 59 + AluSx SINE/Alu 224 312 0
556 8.99 0.00 1.11 E00378:188:HVMVNCCXX:1:2112:25814:5599/1 3 92 (59) AluSx#SINE/Alu 224 312 (0) m_b6s357i2
E00378:188:HV 3 AGTGAACCGAGATCACACCATTGCACTCCAGCCTGGGAGACATGAGCGAA 52
i i i i v - i
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGCGAG 272
E00378:188:HV 53 ACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 92
i i
AluSx#SINE/Al 273 ACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.28
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1)
+ 198 25.9 1.8 0.0 E00378:188:HVMVNCCXX:1:2112:25814:5599/2 2 55 (96) C MIRb SINE/MIR (147) 121 67 184
ANNOTATION EVIDENCE:
198 25.93 1.82 0.00 E00378:188:HVMVNCCXX:1:2112:25814:5599/2 2 55 96 C MIRb SINE/MIR 67 121 147
198 25.93 1.82 0.00 E00378:188:HVMVNCCXX:1:2112:25814:5599/2 2 55 (96) C MIRb#SINE/MIR (147) 121 67 m_b6s601i82
E00378:188:HV 2 AGTGAGGTAAAGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGAC 50
v v ii -v i v ii iv v
C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72
E00378:188:HV 51 TCGAG 55
i i
C MIRb#SINE/MIR 71 CCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 32.45
Transitions / transversions = 1.33 (8/6)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1)
+ 1138 4.6 1.3 0.0 E00378:188:HVMVNCCXX:1:2113:6776:46173/1 1 151 (0) + L1P3 LINE/L1 3315 3467 (2679) 185
ANNOTATION EVIDENCE:
1138 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:2113:6776:46173/1 1 151 0 + L1P3_orf2 LINE/L1 1206 1358 1936
1138 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:2113:6776:46173/1 1 151 (0) L1P3_orf2#LINE/L1 1206 1358 (1936) m_b6s551i155
E00378:188:HV 1 TGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAATACCTCT 50
i
L1P3_orf2#LIN 1206 TGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAACACCTCT 1255
E00378:188:HV 51 ATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAGACACA 100
i vv i
L1P3_orf2#LIN 1256 ACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGGACACA 1305
E00378:188:HV 101 TACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAATAGACC 148
v -- v
L1P3_orf2#LIN 1306 TACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAATAGACC 1355
E00378:188:HV 149 AAT 151
L1P3_orf2#LIN 1356 AAT 1358
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1032 8.2 2.0 0.0 E00378:188:HVMVNCCXX:1:2113:6776:46173/2 6 151 (0) C L1P3 LINE/L1 (2248) 3898 3750 186
ANNOTATION EVIDENCE:
1032 8.22 2.01 0.00 E00378:188:HVMVNCCXX:1:2113:6776:46173/2 6 151 0 C L1P3_orf2 LINE/L1 1641 1789 1505
1032 8.22 2.01 0.00 E00378:188:HVMVNCCXX:1:2113:6776:46173/2 6 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1641 m_b6s551i35
E00378:188:HV 6 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 55
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 56 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 105
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 106 TTGATAGTGGTGGATATGCGTTTTGATG---TGCTGGATTCAGTTTGCC 151
v v v --- i
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCC 1641
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.00
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 3.00 (3 / 1)
+ 19 4.5 0.0 0.0 E00378:188:HVMVNCCXX:1:2114:10592:46103/1 1 23 (128) + (A)n Simple_repeat 1 23 (0) 187
ANNOTATION EVIDENCE:
19 4.55 0.00 0.00 E00378:188:HVMVNCCXX:1:2114:10592:46103/1 1 23 128 + (A)n Simple_repeat 1 23 0
19 4.55 0.00 0.00 E00378:188:HVMVNCCXX:1:2114:10592:46103/1 1 23 (128) (A)n#Simple_repeat 1 23 (0) m_b6s252i18
E00378:188:HV 1 AAAAAAAAAAAAAAAAAAAAGAA 23
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 450 11.0 0.0 2.7 E00378:188:HVMVNCCXX:1:2115:16427:35010/1 76 150 (1) C AluSx SINE/Alu (8) 304 232 188
ANNOTATION EVIDENCE:
450 10.96 0.00 2.67 E00378:188:HVMVNCCXX:1:2115:16427:35010/1 76 150 1 C AluSx SINE/Alu 232 304 8
450 10.96 0.00 2.67 E00378:188:HVMVNCCXX:1:2115:16427:35010/1 76 150 (1) C AluSx#SINE/Alu (8) 304 232 m_b2s357i1
E00378:188:HV 76 TTTTTTTTTTTTTTTTTTTTTTTAGACAGAGTCTCGCTTCGTCAAACCCA 125
v i ii i--
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCA 257
E00378:188:HV 126 GGCTGGAGTGCAGTGGCATTATCTC 150
iiv
C AluSx#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCTC 232
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.30
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.00 (2 / 2)
+ 919 16.1 0.7 1.3 E00378:188:HVMVNCCXX:1:2115:16427:35010/2 1 151 (0) + AluY SINE/Alu 3 152 (159) 189
ANNOTATION EVIDENCE:
919 16.10 0.66 1.32 E00378:188:HVMVNCCXX:1:2115:16427:35010/2 1 151 0 + AluY SINE/Alu 3 152 159
919 16.10 0.66 1.32 E00378:188:HVMVNCCXX:1:2115:16427:35010/2 1 151 (0) AluY#SINE/Alu 3 152 (159) m_b2s356i36
E00378:188:HV 1 CTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGAGC 50
i i i ii i v v v
AluY#SINE/Alu 3 CCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG 52
E00378:188:HV 51 CAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACATGG 100
i i -- i v i v i i
AluY#SINE/Alu 53 CGGGCGGATCAC--GAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 101 TGAAACCTTGTCTCTATTTAAAATACAAAAA-TTAGCTGGGTGTGGTGGT 149
ii i v - i i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
E00378:188:HV 150 GG 151
AluY#SINE/Alu 151 GG 152
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 10.17
Transitions / transversions = 3.00 (18/6)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.00 (3 / 3)
+ 1341 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2115:20040:39335/1 1 151 (0) + L1P1 LINE/L1 5394 5544 (611) 190
ANNOTATION EVIDENCE:
1341 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:20040:39335/1 1 151 0 + L1PA2_3end LINE/L1 141 291 611
1341 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:20040:39335/1 1 151 (0) L1PA2_3end#LINE/L1 141 291 (611) m_b1s551i237
E00378:188:HV 1 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 50
L1PA2_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190
E00378:188:HV 51 ACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAAC 100
i
L1PA2_3end#LI 191 ACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAAC 240
E00378:188:HV 101 AGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTG 150
iv
L1PA2_3end#LI 241 AGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTG 290
E00378:188:HV 151 G 151
L1PA2_3end#LI 291 G 291
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1286 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2115:20040:39335/2 1 151 (0) C L1P1 LINE/L1 (353) 5802 5652 191
ANNOTATION EVIDENCE:
1286 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:20040:39335/2 1 151 0 C L1PA2_3end LINE/L1 399 549 353
1286 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:20040:39335/2 1 151 (0) C L1PA2_3end#LINE/L1 (353) 549 399 m_b1s551i320
E00378:188:HV 1 GTATATCATGGTGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTG 50
vi v
C L1PA2_3end#LI 549 GTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTG 500
E00378:188:HV 51 TTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACA 100
i
C L1PA2_3end#LI 499 TTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCA 450
E00378:188:HV 101 ATAAACATACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTT 150
i
C L1PA2_3end#LI 449 ATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTT 400
E00378:188:HV 151 T 151
C L1PA2_3end#LI 399 T 399
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.77
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1083 7.7 0.0 0.7 E00378:188:HVMVNCCXX:1:2115:30239:44310/1 1 144 (7) + AluY SINE/Alu 155 297 (14) 192
ANNOTATION EVIDENCE:
1083 7.69 0.00 0.69 E00378:188:HVMVNCCXX:1:2115:30239:44310/1 1 144 7 + AluY SINE/Alu 155 297 14
1083 7.69 0.00 0.69 E00378:188:HVMVNCCXX:1:2115:30239:44310/1 1 144 (7) AluY#SINE/Alu 155 297 (14) m_b2s357i94
E00378:188:HV 1 GCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAAC 50
i i i
AluY#SINE/Alu 155 GCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAAC 204
E00378:188:HV 51 CTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCATTCCAG 100
i - i v ii i
AluY#SINE/Alu 205 CCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAG 253
E00378:188:HV 101 CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAGAAATAAAA 144
i v
AluY#SINE/Alu 254 CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.71
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 1.00 (1 / 1)
+ 877 5.7 3.5 7.3 E00378:188:HVMVNCCXX:1:2115:5923:32953/1 1 151 (0) C L1P3 LINE/L1 (2898) 3248 3104 193
ANNOTATION EVIDENCE:
877 5.72 3.45 7.28 E00378:188:HVMVNCCXX:1:2115:5923:32953/1 1 151 0 C L1P3_orf2 LINE/L1 995 1139 2155
877 5.72 3.45 7.28 E00378:188:HVMVNCCXX:1:2115:5923:32953/1 1 151 (0) C L1P3_orf2#LINE/L1 (2155) 1139 995 m_b6s551i228
E00378:188:HV 1 AGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCT 46
v ---- i i
C L1P3_orf2#LIN 1139 AGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCT 1090
E00378:188:HV 47 CCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTC 96
v - i i----------
C L1P3_orf2#LIN 1089 CCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTC 1051
E00378:188:HV 97 TATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAG 145
-i v
C L1P3_orf2#LIN 1050 TATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAG 1001
E00378:188:HV 146 CTTTTG 151
C L1P3_orf2#LIN 1000 CTTTTG 995
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 1264 4.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2115:5923:32953/2 1 151 (0) + L1P3 LINE/L1 2874 3024 (3122) 194
ANNOTATION EVIDENCE:
1264 4.64 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:5923:32953/2 1 151 0 + L1P3_orf2 LINE/L1 765 915 2379
1264 4.64 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:5923:32953/2 1 151 (0) L1P3_orf2#LINE/L1 765 915 (2379) m_b7s551i35
E00378:188:HV 1 GCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAAGTA 50
i i v i?
L1P3_orf2#LIN 765 GCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAAANA 814
E00378:188:HV 51 AGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGG 100
i i
L1P3_orf2#LIN 815 AGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGG 864
E00378:188:HV 101 GACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCA 150
L1P3_orf2#LIN 865 GACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCA 914
E00378:188:HV 151 C 151
L1P3_orf2#LIN 915 C 915
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 877 5.7 3.5 7.3 E00378:188:HVMVNCCXX:1:2115:5974:38069/1 1 151 (0) C L1P3 LINE/L1 (2898) 3248 3104 195
ANNOTATION EVIDENCE:
877 5.72 3.45 7.28 E00378:188:HVMVNCCXX:1:2115:5974:38069/1 1 151 0 C L1P3_orf2 LINE/L1 995 1139 2155
877 5.72 3.45 7.28 E00378:188:HVMVNCCXX:1:2115:5974:38069/1 1 151 (0) C L1P3_orf2#LINE/L1 (2155) 1139 995 m_b6s551i229
E00378:188:HV 1 AGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCT 46
v ---- i i
C L1P3_orf2#LIN 1139 AGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCT 1090
E00378:188:HV 47 CCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTC 96
v - i i----------
C L1P3_orf2#LIN 1089 CCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTC 1051
E00378:188:HV 97 TATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAG 145
-i v
C L1P3_orf2#LIN 1050 TATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAG 1001
E00378:188:HV 146 CTTTTG 151
C L1P3_orf2#LIN 1000 CTTTTG 995
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 1264 4.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2115:5974:38069/2 1 151 (0) + L1P3 LINE/L1 2874 3024 (3122) 196
ANNOTATION EVIDENCE:
1264 4.64 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:5974:38069/2 1 151 0 + L1P3_orf2 LINE/L1 765 915 2379
1264 4.64 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:5974:38069/2 1 151 (0) L1P3_orf2#LINE/L1 765 915 (2379) m_b7s551i36
E00378:188:HV 1 GCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAAGTA 50
i i v i?
L1P3_orf2#LIN 765 GCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAAANA 814
E00378:188:HV 51 AGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGG 100
i i
L1P3_orf2#LIN 815 AGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGG 864
E00378:188:HV 101 GACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCA 150
L1P3_orf2#LIN 865 GACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCA 914
E00378:188:HV 151 C 151
L1P3_orf2#LIN 915 C 915
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 712 12.2 0.0 0.0 E00378:188:HVMVNCCXX:1:2115:9435:31758/2 1 98 (53) C AluSx SINE/Alu (214) 98 1 197
ANNOTATION EVIDENCE:
712 12.24 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:9435:31758/2 1 98 53 C AluSx SINE/Alu 1 98 214
712 12.24 0.00 0.00 E00378:188:HVMVNCCXX:1:2115:9435:31758/2 1 98 (53) C AluSx#SINE/Alu (214) 98 1 m_b5s357i57
E00378:188:HV 1 GTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAGTGATCTGCCCACCTT 50
i i i i i i
C AluSx#SINE/Al 98 GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTC 49
E00378:188:HV 51 GGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 98
i i vi i i
C AluSx#SINE/Al 48 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.11
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0)
+ 1227 3.4 1.3 0.0 E00378:188:HVMVNCCXX:1:2116:15676:19434/1 1 149 (2) + L1P3 LINE/L1 3561 3711 (2435) 198
ANNOTATION EVIDENCE:
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19434/1 1 149 2 + L1P3_orf2 LINE/L1 1452 1602 1692
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19434/1 1 149 (2) L1P3_orf2#LINE/L1 1452 1602 (1692) m_b6s551i88
E00378:188:HV 1 CAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAA 50
L1P3_orf2#LIN 1452 CAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAA 1501
E00378:188:HV 51 AAGAGGGACTCTTCCCTAACTCATTTTATGATGCCAGCATCATCCTGATT 100
i v v
L1P3_orf2#LIN 1502 AAGAGGGACTCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATA 1551
E00378:188:HV 101 CCAAAACCTGGCAGAGACACAA--GAAAAAGAAAATTTCAGGCCATTATC 148
--i v
L1P3_orf2#LIN 1552 CCAAAACCTGGCAGAGACACAACAAAAAAAGAAAATTTCAGGCCAATATC 1601
E00378:188:HV 149 C 149
L1P3_orf2#LIN 1602 C 1602
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.43
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 911 7.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:15676:19434/2 32 150 (1) C L1P3 LINE/L1 (2248) 3898 3780 199
ANNOTATION EVIDENCE:
911 7.56 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19434/2 32 150 1 C L1P3_orf2 LINE/L1 1671 1789 1505
911 7.56 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19434/2 32 150 (1) C L1P3_orf2#LINE/L1 (1505) 1789 1671 m_b6s551i26
E00378:188:HV 32 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 81
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 82 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 131
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 132 TTGATAGTGGTGGATAAGC 150
v
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGC 1671
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.52
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 1227 3.4 1.3 0.0 E00378:188:HVMVNCCXX:1:2116:15676:19504/1 1 149 (2) + L1P3 LINE/L1 3561 3711 (2435) 200
ANNOTATION EVIDENCE:
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19504/1 1 149 2 + L1P3_orf2 LINE/L1 1452 1602 1692
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19504/1 1 149 (2) L1P3_orf2#LINE/L1 1452 1602 (1692) m_b6s551i89
E00378:188:HV 1 CAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAA 50
L1P3_orf2#LIN 1452 CAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAA 1501
E00378:188:HV 51 AAGAGGGACTCTTCCCTAACTCATTTTATGATGCCAGCATCATCCTGATT 100
i v v
L1P3_orf2#LIN 1502 AAGAGGGACTCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATA 1551
E00378:188:HV 101 CCAAAACCTGGCAGAGACACAA--GAAAAAGAAAATTTCAGGCCATTATC 148
--i v
L1P3_orf2#LIN 1552 CCAAAACCTGGCAGAGACACAACAAAAAAAGAAAATTTCAGGCCAATATC 1601
E00378:188:HV 149 C 149
L1P3_orf2#LIN 1602 C 1602
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.43
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 911 7.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:15676:19504/2 32 150 (1) C L1P3 LINE/L1 (2248) 3898 3780 201
ANNOTATION EVIDENCE:
911 7.56 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19504/2 32 150 1 C L1P3_orf2 LINE/L1 1671 1789 1505
911 7.56 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:15676:19504/2 32 150 (1) C L1P3_orf2#LINE/L1 (1505) 1789 1671 m_b6s551i27
E00378:188:HV 32 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 81
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 82 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 131
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 132 TTGATAGTGGTGGATAAGC 150
v
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGC 1671
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.52
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 1227 3.4 1.3 0.0 E00378:188:HVMVNCCXX:1:2116:16041:19575/1 1 149 (2) + L1P3 LINE/L1 3561 3711 (2435) 202
ANNOTATION EVIDENCE:
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:1:2116:16041:19575/1 1 149 2 + L1P3_orf2 LINE/L1 1452 1602 1692
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:1:2116:16041:19575/1 1 149 (2) L1P3_orf2#LINE/L1 1452 1602 (1692) m_b6s551i90
E00378:188:HV 1 CAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAA 50
L1P3_orf2#LIN 1452 CAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAA 1501
E00378:188:HV 51 AAGAGGGACTCTTCCCTAACTCATTTTATGATGCCAGCATCATCCTGATT 100
i v v
L1P3_orf2#LIN 1502 AAGAGGGACTCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATA 1551
E00378:188:HV 101 CCAAAACCTGGCAGAGACACAA--GAAAAAGAAAATTTCAGGCCATTATC 148
--i v
L1P3_orf2#LIN 1552 CCAAAACCTGGCAGAGACACAACAAAAAAAGAAAATTTCAGGCCAATATC 1601
E00378:188:HV 149 C 149
L1P3_orf2#LIN 1602 C 1602
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.43
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 911 7.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:16041:19575/2 32 150 (1) C L1P3 LINE/L1 (2248) 3898 3780 203
ANNOTATION EVIDENCE:
911 7.56 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:16041:19575/2 32 150 1 C L1P3_orf2 LINE/L1 1671 1789 1505
911 7.56 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:16041:19575/2 32 150 (1) C L1P3_orf2#LINE/L1 (1505) 1789 1671 m_b6s551i28
E00378:188:HV 32 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 81
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 82 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 131
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 132 TTGATAGTGGTGGATAAGC 150
v
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGC 1671
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.52
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 959 13.1 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:17817:11084/1 22 151 (0) + AluSx SINE/Alu 1 130 (182) 204
ANNOTATION EVIDENCE:
959 13.08 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:17817:11084/1 22 151 0 + AluSx SINE/Alu 1 130 182
959 13.08 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:17817:11084/1 22 151 (0) AluSx#SINE/Alu 1 130 (182) m_b2s356i39
E00378:188:HV 22 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 71
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 72 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 121
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 122 GGTGAAACCTTGTCTCTATTTAAAATACAA 151
ii i v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAA 130
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.77
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 129), avg. gap size = 0.0 (0 / 0)
+ 22 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:17817:11084/2 83 106 (45) + (T)n Simple_repeat 1 24 (0) 205
ANNOTATION EVIDENCE:
22 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:17817:11084/2 83 106 45 + (T)n Simple_repeat 1 24 0
22 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:17817:11084/2 83 106 (45) (T)n#Simple_repeat 1 24 (0) m_b2s252i8
E00378:188:HV 83 TTTTTTTTTTTTTTTTTTTTTTTT 106
(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)
+ 504 16.9 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:1783:17905/1 2 84 (67) C L1MC4 LINE/L1 (198) 7844 7762 206
ANNOTATION EVIDENCE:
504 16.87 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:1783:17905/1 2 84 67 C L1MC4_3end LINE/L1 2509 2591 198
504 16.87 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:1783:17905/1 2 84 (67) C L1MC4_3end#LINE/L1 (198) 2591 2509 m_b3s551i56
E00378:188:HV 2 ATACTTCAGTGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCA 51
i i i iv ii iiv i
C L1MC4_3end#LI 2591 ATACTTCAGTGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCA 2542
E00378:188:HV 52 CAGTATAATCATCAAAATCAGGAAGTTAACATT 84
i i i
C L1MC4_3end#LI 2541 CAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.02
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 313 14.8 0.0 0.0 E00378:188:HVMVNCCXX:1:2116:1783:17905/1 89 142 (9) C L1MC4 LINE/L1 (393) 7649 7596 206
ANNOTATION EVIDENCE:
313 14.81 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:1783:17905/1 89 142 9 C L1MC4_3end LINE/L1 2343 2396 393
313 14.81 0.00 0.00 E00378:188:HVMVNCCXX:1:2116:1783:17905/1 89 142 (9) C L1MC4_3end#LINE/L1 (393) 2396 2343 m_b3s551i57
E00378:188:HV 89 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 138
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 139 TCTT 142
i
C L1MC4_3end#LI 2346 TCCT 2343
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.46
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 225 28.1 4.2 11.6 E00378:188:HVMVNCCXX:1:2116:1783:17905/2 21 149 (2) + L1MC4 LINE/L1 6462 6580 (1462) 207
ANNOTATION EVIDENCE:
225 28.08 4.21 11.63 E00378:188:HVMVNCCXX:1:2116:1783:17905/2 21 149 2 + L1MC4_3end LINE/L1 1209 1327 1462
225 28.08 4.21 11.63 E00378:188:HVMVNCCXX:1:2116:1783:17905/2 21 149 (2) L1MC4_3end#LINE/L1 1209 1327 (1462) m_b3s551i161
E00378:188:HV 21 TTGAGCAAATAAGTAAATGCATTCAGGTTGCGTGGATAGTCAGGTTTTGG 70
ii v? v i-i i- i i--
L1MC4_3end#LI 1209 TTGAGCAAATAAGTAAATATATTGNGGATA-ATGGG-AGCCAGGTTTC-- 1254
E00378:188:HV 71 GGTGTTTTTTTTAACTGCTAGTAAAGCAATTTATAAATTTGGACAGAAAA 120
----------- v iii vi vi v i v v iiii
L1MC4_3end#LI 1255 -----------TCACTGTCGGAGAAGGGAGTTACAAATATGGAAAGGGGG 1293
E00378:188:HV 121 AAAG-----ATAAACGGTGTGATGTTAGATTGGA 149
i ----- i vv i i
L1MC4_3end#LI 1294 AAGGCTAGAATGAACCCTGTGGTGTTGGATTGGA 1327
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.08
Transitions / transversions = 2.10 (21/10)
Gap_init rate = 0.12 (16 / 128), avg. gap size = 1.25 (20 / 16)
+ 1226 5.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2117:22039:63788/1 1 151 (0) C L1P3 LINE/L1 (3128) 3018 2868 208
ANNOTATION EVIDENCE:
1226 5.30 0.00 0.00 E00378:188:HVMVNCCXX:1:2117:22039:63788/1 1 151 0 C L1P3_orf2 LINE/L1 759 909 2385
1226 5.30 0.00 0.00 E00378:188:HVMVNCCXX:1:2117:22039:63788/1 1 151 (0) C L1P3_orf2#LINE/L1 (2385) 909 759 m_b7s551i39
E00378:188:HV 1 ATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGA 50
C L1P3_orf2#LIN 909 ATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGA 860
E00378:188:HV 51 GATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTCCTT 100
i i ?i
C L1P3_orf2#LIN 859 GATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTT 810
E00378:188:HV 101 ATTTCTGCCTTCATTTCATTATTTACCTAGTATTCATTCAGGAGCAGGTT 150
v i i v
C L1P3_orf2#LIN 809 ATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTT 760
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 759 G 759
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.56
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2117:2301:47843/1 52 96 (55) + MIR SINE/MIR 218 262 (0) 209
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:1:2117:2301:47843/1 52 96 55 + MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:1:2117:2301:47843/1 52 96 (55) MIR#SINE/MIR 218 262 (0) m_b6s601i13
E00378:188:HV 52 AATGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTATTTTT 96
i v iv viii i i v
MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 878 5.7 3.5 7.3 E00378:188:HVMVNCCXX:1:2117:29102:9888/1 1 151 (0) C L1P3 LINE/L1 (2895) 3251 3107 210
ANNOTATION EVIDENCE:
878 5.72 3.45 7.28 E00378:188:HVMVNCCXX:1:2117:29102:9888/1 1 151 0 C L1P3_orf2 LINE/L1 998 1142 2152
878 5.72 3.45 7.28 E00378:188:HVMVNCCXX:1:2117:29102:9888/1 1 151 (0) C L1P3_orf2#LINE/L1 (2152) 1142 998 m_b6s551i227
E00378:188:HV 1 ATTAGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCA 46
v ---- i i
C L1P3_orf2#LIN 1142 ATTAGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCA 1093
E00378:188:HV 47 GCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGT 96
v - i i----------
C L1P3_orf2#LIN 1092 GCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC----------GTGT 1054
E00378:188:HV 97 CTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGC 145
-i v
C L1P3_orf2#LIN 1053 CTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGC 1004
E00378:188:HV 146 TAGCTT 151
C L1P3_orf2#LIN 1003 TAGCTT 998
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 1138 4.0 0.7 0.0 E00378:188:HVMVNCCXX:1:2117:29102:9888/2 1 151 (0) + L1P3 LINE/L1 3013 3164 (2982) 211
ANNOTATION EVIDENCE:
1138 3.97 0.66 0.00 E00378:188:HVMVNCCXX:1:2117:29102:9888/2 1 151 0 + L1P3_orf2 LINE/L1 904 1055 2239
1138 3.97 0.66 0.00 E00378:188:HVMVNCCXX:1:2117:29102:9888/2 1 151 (0) L1P3_orf2#LINE/L1 904 1055 (2239) m_b6s551i264
E00378:188:HV 1 CTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAAC 50
? v i i
L1P3_orf2#LIN 904 CTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAAC 953
E00378:188:HV 51 ATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTA 100
L1P3_orf2#LIN 954 ATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTA 1003
E00378:188:HV 101 GCAGAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAG 149
v i-
L1P3_orf2#LIN 1004 GCAGAAGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAG 1053
E00378:188:HV 150 AC 151
L1P3_orf2#LIN 1054 AC 1055
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.16
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1282 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:17848:29736/1 1 151 (0) + L1P1 LINE/L1 4903 5053 (1093) 212
ANNOTATION EVIDENCE:
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:17848:29736/1 1 151 0 + L1P1_orf2 LINE/L1 2794 2944 350
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:17848:29736/1 1 151 (0) L1P1_orf2#LINE/L1 2794 2944 (350) m_b1s551i20
E00378:188:HV 1 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 50
L1P1_orf2#LIN 2794 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 2843
E00378:188:HV 51 ACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTA 100
v v i
L1P1_orf2#LIN 2844 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 2893
E00378:188:HV 101 AAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 150
i
L1P1_orf2#LIN 2894 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 2943
E00378:188:HV 151 G 151
L1P1_orf2#LIN 2944 G 2944
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1268 1.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:17848:29736/2 1 149 (2) C L1P1 LINE/L1 (797) 5349 5201 213
ANNOTATION EVIDENCE:
1268 1.34 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:17848:29736/2 1 149 2 C L1P1_orf2 LINE/L1 3092 3240 54
1268 1.34 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:17848:29736/2 1 149 (2) C L1P1_orf2#LINE/L1 (54) 3240 3092 m_b1s551i140
E00378:188:HV 1 GAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTT 50
C L1P1_orf2#LIN 3240 GAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTT 3191
E00378:188:HV 51 TTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCT 100
C L1P1_orf2#LIN 3190 TTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCT 3141
E00378:188:HV 101 TTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCGTTTTGTAGGTTGCC 149
i i
C L1P1_orf2#LIN 3140 TTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCC 3092
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1267 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:21531:31582/1 1 151 (0) C L1P1 LINE/L1 (995) 5151 5001 214
ANNOTATION EVIDENCE:
1267 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:21531:31582/1 1 151 0 C L1P1_orf2 LINE/L1 2892 3042 252
1267 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:21531:31582/1 1 151 (0) C L1P1_orf2#LINE/L1 (252) 3042 2892 m_b1s551i67
E00378:188:HV 1 AATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGTG 50
i v
C L1P1_orf2#LIN 3042 AATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTG 2993
E00378:188:HV 51 TTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCT 100
?
C L1P1_orf2#LIN 2992 TTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCT 2943
E00378:188:HV 101 AGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTT 150
i
C L1P1_orf2#LIN 2942 AGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTT 2893
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2892 A 2892
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:22556:27837/1 90 134 (17) C MIR SINE/MIR (0) 262 218 215
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:22556:27837/1 90 134 17 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:22556:27837/1 90 134 (17) C MIR#SINE/MIR (0) 262 218 m_b6s601i3
E00378:188:HV 90 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 134
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 1131 11.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:25530:34113/1 2 150 (1) + AluSx SINE/Alu 112 260 (52) 216
ANNOTATION EVIDENCE:
1131 11.41 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:25530:34113/1 2 150 1 + AluSx SINE/Alu 112 260 52
1131 11.41 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:25530:34113/1 2 150 (1) AluSx#SINE/Alu 112 260 (52) m_b2s357i26
E00378:188:HV 2 GTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGT 51
i v i i i v i
AluSx#SINE/Al 112 GTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGT 161
E00378:188:HV 52 AATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGA 101
i i i i i
AluSx#SINE/Al 162 AATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGA 211
E00378:188:HV 102 GGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGG 150
i i i ii
AluSx#SINE/Al 212 GGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.95
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1288 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:3417:48476/1 1 151 (0) + L1P1 LINE/L1 5026 5176 (970) 217
ANNOTATION EVIDENCE:
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:3417:48476/1 1 151 0 + L1P1_orf2 LINE/L1 2917 3067 227
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:3417:48476/1 1 151 (0) L1P1_orf2#LINE/L1 2917 3067 (227) m_b1s551i77
E00378:188:HV 1 ACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGG 50
?
L1P1_orf2#LIN 2917 ACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGG 2966
E00378:188:HV 51 CATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAG 100
L1P1_orf2#LIN 2967 CATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAG 3016
E00378:188:HV 101 ACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 150
v i
L1P1_orf2#LIN 3017 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 3066
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3067 A 3067
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1362 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:3417:48476/2 2 151 (0) C L1P1 LINE/L1 (451) 5704 5555 218
ANNOTATION EVIDENCE:
1362 2.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:3417:48476/2 2 151 0 C L1PA3_3end LINE/L1 302 451 451
1362 2.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:3417:48476/2 2 151 (0) C L1PA3_3end#LINE/L1 (451) 451 302 m_b1s551i289
E00378:188:HV 2 CAATAAACATACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCC 51
i
C L1PA3_3end#LI 451 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCC 402
E00378:188:HV 52 TTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAG 101
i
C L1PA3_3end#LI 401 TTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAG 352
E00378:188:HV 102 TTCTAGATCCCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTA 151
i
C L1PA3_3end#LI 351 TTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTA 302
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.42
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1139 11.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2119:4726:53451/2 6 151 (0) C AluSx SINE/Alu (52) 260 115 219
ANNOTATION EVIDENCE:
1139 11.64 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:4726:53451/2 6 151 0 C AluSx SINE/Alu 115 260 52
1139 11.64 0.00 0.00 E00378:188:HVMVNCCXX:1:2119:4726:53451/2 6 151 (0) C AluSx#SINE/Alu (52) 260 115 m_b2s356i9
E00378:188:HV 6 CCCAGGCTGGAGTGCAGTGGCATGATCTCAGCTCACTGCAATCTCTGCCT 55
ii i i i
C AluSx#SINE/Al 260 CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT 211
E00378:188:HV 56 CCTGAGTTCAAGTGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTA 105
i i i i i
C AluSx#SINE/Al 210 CCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
E00378:188:HV 106 CAGGTGCCCACCACCACACCCAGCTAATTTTTGTATTTTAAATAGA 151
i v i i i v i
C AluSx#SINE/Al 160 CAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGA 115
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.06
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0)
+ 1200 6.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2120:25560:44890/1 1 151 (0) + L1P3 LINE/L1 2897 3047 (3099) 220
ANNOTATION EVIDENCE:
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:1:2120:25560:44890/1 1 151 0 + L1P3_orf2 LINE/L1 788 938 2356
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:1:2120:25560:44890/1 1 151 (0) L1P3_orf2#LINE/L1 788 938 (2356) m_b7s551i27
E00378:188:HV 1 ATAATGAAATGAAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGAAC 50
i v i? i
L1P3_orf2#LIN 788 ATAACGAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGAAC 837
E00378:188:HV 51 AAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAG 100
i
L1P3_orf2#LIN 838 AAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAG 887
E00378:188:HV 101 AGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTA 150
? v i
L1P3_orf2#LIN 888 AGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTA 937
E00378:188:HV 151 A 151
L1P3_orf2#LIN 938 A 938
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.95
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 796 5.7 8.5 7.3 E00378:188:HVMVNCCXX:1:2120:25560:44890/2 1 151 (0) C L1P3 LINE/L1 (2872) 3274 3122 221
ANNOTATION EVIDENCE:
796 5.72 8.50 7.28 E00378:188:HVMVNCCXX:1:2120:25560:44890/2 1 151 0 C L1P3_orf2 LINE/L1 1013 1165 2129
796 5.72 8.50 7.28 E00378:188:HVMVNCCXX:1:2120:25560:44890/2 1 151 (0) C L1P3_orf2#LINE/L1 (2129) 1165 1013 m_b6s551i221
E00378:188:HV 1 GATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----TCTGTT 38
-------- v ---- i
C L1P3_orf2#LIN 1165 GATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCTATT 1116
E00378:188:HV 39 TTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAA 88
i v -
C L1P3_orf2#LIN 1115 TTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAA 1067
E00378:188:HV 89 AGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGAT 137
i i---------- -i v
C L1P3_orf2#LIN 1066 GGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCTCTGAT 1027
E00378:188:HV 138 CTTAGTTATTTCTT 151
C L1P3_orf2#LIN 1026 CTTAGTTATTTCTT 1013
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1258 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2120:31050:45716/1 1 151 (0) + L1P3 LINE/L1 2950 3100 (3046) 222
ANNOTATION EVIDENCE:
1258 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2120:31050:45716/1 1 151 0 + L1P3_orf2 LINE/L1 841 991 2303
1258 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2120:31050:45716/1 1 151 (0) L1P3_orf2#LINE/L1 841 991 (2303) m_b7s551i6
E00378:188:HV 1 GACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGG 50
i
L1P3_orf2#LIN 841 GACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGG 890
E00378:188:HV 51 GAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAA 100
? v i
L1P3_orf2#LIN 891 GAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAA 940
E00378:188:HV 101 TCAACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACA 150
i
L1P3_orf2#LIN 941 TCGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACA 990
E00378:188:HV 151 A 151
L1P3_orf2#LIN 991 A 991
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1131 4.6 1.3 0.0 E00378:188:HVMVNCCXX:1:2120:31050:45716/2 1 151 (0) C L1P3 LINE/L1 (2678) 3468 3316 223
ANNOTATION EVIDENCE:
1131 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:2120:31050:45716/2 1 151 0 C L1P3_orf2 LINE/L1 1207 1359 1935
1131 4.64 1.30 0.00 E00378:188:HVMVNCCXX:1:2120:31050:45716/2 1 151 (0) C L1P3_orf2#LINE/L1 (1935) 1359 1207 m_b6s551i154
E00378:188:HV 1 TATTGGTCTATTCAGGGATTCGACTTCTTCCTGCTTTAG--TTGGGAGGT 48
v -- v
C L1P3_orf2#LIN 1359 TATTGGTCTATTCAGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGG 1310
E00378:188:HV 49 TGTATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCTAGTTTATTT 98
i vv
C L1P3_orf2#LIN 1309 TGTATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTT 1260
E00378:188:HV 99 GCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGG 148
i i
C L1P3_orf2#LIN 1259 GCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGG 1210
E00378:188:HV 149 ATC 151
C L1P3_orf2#LIN 1209 ATC 1207
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 517 20.1 19.2 0.0 E00378:188:HVMVNCCXX:1:2122:13352:55069/1 1 139 (12) C L1MC4 LINE/L1 (424) 7618 7447 224
ANNOTATION EVIDENCE:
517 20.14 19.19 0.00 E00378:188:HVMVNCCXX:1:2122:13352:55069/1 1 139 12 C L1MC4_3end LINE/L1 2194 2365 424
517 20.14 19.19 0.00 E00378:188:HVMVNCCXX:1:2122:13352:55069/1 1 139 (12) C L1MC4_3end#LINE/L1 (424) 2365 2194 m_b3s551i111
E00378:188:HV 1 TCCTTCAATCTGGAACAGTTCT------TTTTTTTATTTATCATGACCTT 44
i i------ i i i v ?
C L1MC4_3end#LI 2365 TCCTTTAATCTGGAACAGTTCCTCAGTCTTTCTTTGTCTTTCATGACNTT 2316
E00378:188:HV 45 CATATATTTGAATAGTACAG-------------------GTCCCTTGCTC 75
v i v v ------------------- iiv i
C L1MC4_3end#LI 2315 GACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGTCCCTCAATT 2266
E00378:188:HV 76 TGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTATAC---TTTG 117
i i i ----- i ---
C L1MC4_3end#LI 2265 TGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTATGCATTTTTG 2216
E00378:188:HV 118 ACGAGAATGTTGCAAAAGTAAT 139
i ii iiii i i
C L1MC4_3end#LI 2215 GCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.81
Transitions / transversions = 4.40 (22/5)
Gap_init rate = 0.03 (4 / 138), avg. gap size = 8.25 (33 / 4)
+ 465 21.5 19.6 0.0 E00378:188:HVMVNCCXX:1:2122:1407:23126/2 1 135 (16) C L1MC4 LINE/L1 (428) 7614 7447 225
ANNOTATION EVIDENCE:
465 21.48 19.64 0.00 E00378:188:HVMVNCCXX:1:2122:1407:23126/2 1 135 16 C L1MC4_3end LINE/L1 2194 2361 428
465 21.48 19.64 0.00 E00378:188:HVMVNCCXX:1:2122:1407:23126/2 1 135 (16) C L1MC4_3end#LINE/L1 (428) 2361 2194 m_b3s551i112
E00378:188:HV 1 TCAATCTGGAACAGTTCT------TTTTTTTATTTATCATGACCTTCATA 44
i i------ i i i v ? v i
C L1MC4_3end#LI 2361 TTAATCTGGAACAGTTCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACA 2312
E00378:188:HV 45 TATTTGAATAGTACAG-------------------GTCCCTTGCTCTGAG 75
v v ------------------- iiv i i
C L1MC4_3end#LI 2311 TTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGG 2262
E00378:188:HV 76 TTTGTCTGATGTTTCCTTATGATTAAAT-----TTATAC---TTTGACGA 117
i i ----- i --- i ii
C L1MC4_3end#LI 2261 TTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTATGCATTTTTGGCAG 2212
E00378:188:HV 118 GGATGTTGCAAAAGTAAT 135
i iiii i i
C L1MC4_3end#LI 2211 GAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.89
Transitions / transversions = 4.60 (23/5)
Gap_init rate = 0.03 (4 / 134), avg. gap size = 8.25 (33 / 4)
+ 1152 8.7 0.7 0.7 E00378:188:HVMVNCCXX:1:2122:22759:22528/1 1 151 (0) C AluY SINE/Alu (55) 256 106 226
ANNOTATION EVIDENCE:
1152 8.67 0.66 0.66 E00378:188:HVMVNCCXX:1:2122:22759:22528/1 1 151 0 C AluY SINE/Alu 106 256 55
1152 8.67 0.66 0.66 E00378:188:HVMVNCCXX:1:2122:22759:22528/1 1 151 (0) C AluY#SINE/Alu (55) 256 106 m_b2s356i74
E00378:188:HV 1 AGGCTGGAATGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCC 50
i ii v i -
C AluY#SINE/Alu 256 AGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CC 208
E00378:188:HV 51 CAGGTTCATGCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACA 100
i i i i
C AluY#SINE/Alu 207 CGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACA 158
E00378:188:HV 101 GGCGCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGAGATGG 149
iv - i i
C AluY#SINE/Alu 157 GGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGG 108
E00378:188:HV 150 GG 151
C AluY#SINE/Alu 107 GG 106
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1041 13.3 0.0 0.7 E00378:188:HVMVNCCXX:1:2122:29041:15514/1 1 151 (0) C AluSx SINE/Alu (29) 283 134 227
ANNOTATION EVIDENCE:
1041 13.34 0.00 0.66 E00378:188:HVMVNCCXX:1:2122:29041:15514/1 1 151 0 C AluSx SINE/Alu 134 283 29
1041 13.34 0.00 0.66 E00378:188:HVMVNCCXX:1:2122:29041:15514/1 1 151 (0) C AluSx#SINE/Alu (29) 283 134 m_b6s356i7
E00378:188:HV 1 TGAGATGGAGTTTCGCTCATGTCTCCCAGGCTGGAGTGCAATGGTGTGAT 50
i i - v i i i
C AluSx#SINE/Al 283 TGAGACGGAGTCTCGCTC-TGTCGCCCAGGCTGGAGTGCAGTGGCGCGAT 235
E00378:188:HV 51 CTCGGTTCACTTCAGCCTCTACCTCCTCGGTTCAAGCAATTCTCCTGCCT 100
i v i ii iv i
C AluSx#SINE/Al 234 CTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCT 185
E00378:188:HV 101 CATCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCCAGCTA 150
v i vi i i
C AluSx#SINE/Al 184 CAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTA 135
E00378:188:HV 151 A 151
C AluSx#SINE/Al 134 A 134
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.66
Transitions / transversions = 3.00 (15/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 987 7.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2122:29041:15514/2 1 132 (19) + L1P3 LINE/L1 3767 3898 (2248) 228
ANNOTATION EVIDENCE:
987 7.58 0.00 0.00 E00378:188:HVMVNCCXX:1:2122:29041:15514/2 1 132 19 + L1P3_orf2 LINE/L1 1658 1789 1505
987 7.58 0.00 0.00 E00378:188:HVMVNCCXX:1:2122:29041:15514/2 1 132 (19) L1P3_orf2#LINE/L1 1658 1789 (1505) m_b6s551i32
E00378:188:HV 1 AGCACATCAAAACGCTTATCCACCACTATCAAGTCAGCTTCATCCCTGGG 50
v v i
L1P3_orf2#LIN 1658 AGCACATCAAAAAGCTTATCCACCACGATCAAGTCGGCTTCATCCCTGGG 1707
E00378:188:HV 51 ACGCAAGGCTGATTCAGCATACACAAATCAATAAACATAATCCATCACAT 100
i i i i i
L1P3_orf2#LIN 1708 ATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAATCCATCACAT 1757
E00378:188:HV 101 AAACAGAACGAATGACAAAAACTACATGATTA 132
v i
L1P3_orf2#LIN 1758 AAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.76
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 647 13.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2123:11962:61064/1 1 95 (56) C AluSx SINE/Alu (217) 95 1 229
ANNOTATION EVIDENCE:
647 13.68 0.00 0.00 E00378:188:HVMVNCCXX:1:2123:11962:61064/1 1 95 56 C AluSx SINE/Alu 1 95 217
647 13.68 0.00 0.00 E00378:188:HVMVNCCXX:1:2123:11962:61064/1 1 95 (56) C AluSx#SINE/Alu (217) 95 1 m_b2s357i46
E00378:188:HV 1 GGCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGC 50
i i i i v v
C AluSx#SINE/Al 95 GGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGC 46
E00378:188:HV 51 CTCCCAAATTGCTGAGATTACAGATGTGAGCCACTGTGCCCAGCC 95
v i ii i i i
C AluSx#SINE/Al 45 CTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.50
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0)
+ 1343 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2123:12987:45927/1 1 151 (0) C L1P1 LINE/L1 (440) 5715 5565 230
ANNOTATION EVIDENCE:
1343 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2123:12987:45927/1 1 151 0 C L1PA2_3end LINE/L1 312 462 440
1343 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2123:12987:45927/1 1 151 (0) C L1PA2_3end#LINE/L1 (440) 462 312 m_b1s551i293
E00378:188:HV 1 GAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCGGCATG 50
i i
C L1PA2_3end#LI 462 GAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATG 413
E00378:188:HV 51 ATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAAT 100
C L1PA2_3end#LI 412 ATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAAT 363
E00378:188:HV 101 GGTATTTCCGGTTCTAGATCCCTGAGGAATCACCACACTGACTTCCACAA 150
ii i
C L1PA2_3end#LI 362 GGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAA 313
E00378:188:HV 151 T 151
C L1PA2_3end#LI 312 T 312
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.17
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1311 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2123:12987:45927/2 1 151 (0) + L1P1 LINE/L1 5328 5478 (677) 231
ANNOTATION EVIDENCE:
1311 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2123:12987:45927/2 1 151 0 + L1PA2_3end LINE/L1 75 225 677
1311 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2123:12987:45927/2 1 151 (0) L1PA2_3end#LINE/L1 75 225 (677) m_b1s551i207
E00378:188:HV 1 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 50
L1PA2_3end#LI 75 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 124
E00378:188:HV 51 AACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATC 100
L1PA2_3end#LI 125 AACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATC 174
E00378:188:HV 101 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAA 150
i
L1PA2_3end#LI 175 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAA 224
E00378:188:HV 151 A 151
L1PA2_3end#LI 225 A 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 326 22.2 20.7 0.0 E00378:188:HVMVNCCXX:1:2124:22567:36117/2 1 108 (43) C L1MC4 LINE/L1 (470) 7572 7416 232
ANNOTATION EVIDENCE:
326 22.22 21.43 0.00 E00378:188:HVMVNCCXX:1:2124:22567:36117/2 1 99 52 C L1MC4_3end LINE/L1 2194 2319 470
326 22.22 21.43 0.00 E00378:188:HVMVNCCXX:1:2124:22567:36117/2 1 99 (52) C L1MC4_3end#LINE/L1 (470) 2319 2194 m_b3s551i117
E00378:188:HV 1 CCTTCATATATTTGAATAGTACAG-------------------GTCCCTT 31
? v i v v ------------------- i
C L1MC4_3end#LI 2319 CNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGTCCCTC 2270
E00378:188:HV 32 GCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTATAC--- 73
iv i i i i ----- i ---
C L1MC4_3end#LI 2269 AATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTATGCATT 2220
E00378:188:HV 74 TTTGACGAGAATGTTGCAAAAGTAAT 99
i ii iiii i i
C L1MC4_3end#LI 2219 TTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.66
Transitions / transversions = 4.25 (17/4)
Gap_init rate = 0.03 (3 / 98), avg. gap size = 9.00 (27 / 3)
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:1:2124:22567:36117/2 25 108 43 C L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:1:2124:22567:36117/2 25 108 (43) C L1MC4a_3end#LINE/L1 (371) 2258 2163 m_b3s551i118
E00378:188:HV 25 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 69
iiv i i i i i -----
C L1MC4a_3end#L 2258 GTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGTT 2209
E00378:188:HV 70 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT----TCCTCTTCT 108
i --- i i iiii i i ---- v i
C L1MC4a_3end#L 2208 ATGCATTTTTGGCAAGAATACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 4.00 (12 / 3)
+ 925 13.8 0.0 1.4 E00378:188:HVMVNCCXX:1:2124:6390:53487/2 1 147 (4) + AluSx SINE/Alu 114 258 (54) 233
ANNOTATION EVIDENCE:
925 13.80 0.00 1.36 E00378:188:HVMVNCCXX:1:2124:6390:53487/2 1 147 4 + AluSx SINE/Alu 114 258 54
925 13.80 0.00 1.36 E00378:188:HVMVNCCXX:1:2124:6390:53487/2 1 147 (4) AluSx#SINE/Alu 114 258 (54) m_b5s357i34
E00378:188:HV 1 CTCTACTAAAAATACAAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTGT 50
-- i i v i v v
AluSx#SINE/Al 114 CTCTACTAAAAATACAAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTGT 161
E00378:188:HV 51 AATCATAGCTGCTCAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACTA 100
vi i i v i iivv
AluSx#SINE/Al 162 AATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGA 211
E00378:188:HV 101 GGCGGAGGTTGCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTG 147
v v v i
AluSx#SINE/Al 212 GGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.02
Transitions / transversions = 1.00 (10/10)
Gap_init rate = 0.01 (2 / 146), avg. gap size = 1.00 (2 / 2)
+ 1335 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2201:14255:63982/1 1 151 (0) + L1P1 LINE/L1 5360 5510 (645) 234
ANNOTATION EVIDENCE:
1335 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2201:14255:63982/1 1 151 0 + L1PA2_3end LINE/L1 107 257 645
1335 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2201:14255:63982/1 1 151 (0) L1PA2_3end#LINE/L1 107 257 (645) m_b1s551i228
E00378:188:HV 1 ACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCC 50
L1PA2_3end#LI 107 ACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCC 156
E00378:188:HV 51 ATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGT 100
L1PA2_3end#LI 157 ATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGT 206
E00378:188:HV 101 TAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGAT 150
i
L1PA2_3end#LI 207 TAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGAT 256
E00378:188:HV 151 G 151
L1PA2_3end#LI 257 G 257
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1319 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2201:14255:63982/2 1 151 (0) C L1P1 LINE/L1 (583) 5572 5422 235
ANNOTATION EVIDENCE:
1319 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2201:14255:63982/2 1 151 0 C L1PA3_3end LINE/L1 169 319 583
1319 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2201:14255:63982/2 1 151 (0) C L1PA3_3end#LINE/L1 (583) 319 169 m_b1s551i249
E00378:188:HV 1 TCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATT 50
vi
C L1PA3_3end#LI 319 TCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTT 270
E00378:188:HV 51 CCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAAT 100
C L1PA3_3end#LI 269 CCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAAT 220
E00378:188:HV 101 GACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGGGGTTTTGATTT 150
i v
C L1PA3_3end#LI 219 GATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTT 170
E00378:188:HV 151 G 151
C L1PA3_3end#LI 169 G 169
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 363 21.4 20.8 0.0 E00378:188:HVMVNCCXX:1:2203:13535:71137/1 1 103 (48) C L1MC4 LINE/L1 (466) 7576 7447 236
ANNOTATION EVIDENCE:
363 21.36 20.77 0.00 E00378:188:HVMVNCCXX:1:2203:13535:71137/1 1 103 48 C L1MC4_3end LINE/L1 2194 2323 466
363 21.36 20.77 0.00 E00378:188:HVMVNCCXX:1:2203:13535:71137/1 1 103 (48) C L1MC4_3end#LINE/L1 (466) 2323 2194 m_b3s551i115
E00378:188:HV 1 ATGACCTTCATATATTTGAATAGTACAG-------------------GTC 31
? v i v v -------------------
C L1MC4_3end#LI 2323 ATGACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGTC 2274
E00378:188:HV 32 CCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTATA 76
iiv i i i i ----- i
C L1MC4_3end#LI 2273 CCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTATG 2224
E00378:188:HV 77 C---TTTGACGAGAATGTTGCAAAAGTAAT 103
--- i ii iiii i i
C L1MC4_3end#LI 2223 CATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.35
Transitions / transversions = 4.25 (17/4)
Gap_init rate = 0.03 (3 / 102), avg. gap size = 9.00 (27 / 3)
+ 1024 5.3 7.4 0.0 E00378:188:HVMVNCCXX:1:2205:23186:70943/1 1 151 (0) C L1P3 LINE/L1 (2802) 3344 3182 237
ANNOTATION EVIDENCE:
1024 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:2205:23186:70943/1 1 151 0 C L1P3_orf2 LINE/L1 1073 1235 2059
1024 5.30 7.36 0.00 E00378:188:HVMVNCCXX:1:2205:23186:70943/1 1 151 (0) C L1P3_orf2#LINE/L1 (2059) 1235 1073 m_b6s551i197
E00378:188:HV 1 CTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATC 50
iv i
C L1P3_orf2#LIN 1235 CTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATC 1186
E00378:188:HV 51 ATTTTTTATTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTC 92
v --------
C L1P3_orf2#LIN 1185 ATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTC 1136
E00378:188:HV 93 TTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTG 138
v ---- i i
C L1P3_orf2#LIN 1135 TGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTG 1086
E00378:188:HV 139 GATTAATTGATTT 151
v
C L1P3_orf2#LIN 1085 GATTCATTGATTT 1073
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.50
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1177 6.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2205:23186:70943/2 1 151 (0) + L1P3 LINE/L1 2808 2958 (3188) 238
ANNOTATION EVIDENCE:
1177 5.96 0.00 0.00 E00378:188:HVMVNCCXX:1:2205:23186:70943/2 1 151 0 + L1P3_orf2 LINE/L1 699 849 2445
1177 5.96 0.00 0.00 E00378:188:HVMVNCCXX:1:2205:23186:70943/2 1 151 (0) L1P3_orf2#LINE/L1 699 849 (2445) m_b7s551i58
E00378:188:HV 1 CAAATTAGAACTGAGGATTAAGAAACTCACTCAAAACCACACAACTACAT 50
v i
L1P3_orf2#LIN 699 CAAATTAGAACTCAGGATTAAGAAACTCACTCAAAACCGCACAACTACAT 748
E00378:188:HV 51 GGAAACTGAACAACCTGCTCCTGAATGACTACTAGGTAAATAATGAAATG 100
i i v
L1P3_orf2#LIN 749 GGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTAAATAACGAAATT 798
E00378:188:HV 101 AAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAAT 150
i? i i
L1P3_orf2#LIN 799 AAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAAC 848
E00378:188:HV 151 G 151
L1P3_orf2#LIN 849 G 849
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1228 2.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2205:23602:22932/1 1 149 (2) C L1P1 LINE/L1 (1022) 5124 4976 239
ANNOTATION EVIDENCE:
1228 2.68 0.00 0.00 E00378:188:HVMVNCCXX:1:2205:23602:22932/1 1 149 2 C L1P1_orf2 LINE/L1 2867 3015 279
1228 2.68 0.00 0.00 E00378:188:HVMVNCCXX:1:2205:23602:22932/1 1 149 (2) C L1P1_orf2#LINE/L1 (279) 3015 2867 m_b1s551i51
E00378:188:HV 1 TTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGC 50
C L1P1_orf2#LIN 3015 TTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGC 2966
E00378:188:HV 51 CTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTT 100
?
C L1P1_orf2#LIN 2965 CTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTT 2916
E00378:188:HV 101 TTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTAT 149
i i v
C L1P1_orf2#LIN 2915 TTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTAT 2867
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 330 27.1 3.5 0.0 E00378:188:HVMVNCCXX:1:2205:28402:21895/2 17 138 (13) C MIRb SINE/MIR (75) 187 60 240
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:1:2205:28402:21895/2 17 138 13 C MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:1:2205:28402:21895/2 17 138 (13) C MIR#SINE/MIR (75) 187 60 m_b6s601i51
E00378:188:HV 17 TTAATTCTT---ATACTTCTGTCACTTAGATTCTATTATTTCCTTCAATT 63
i i--- i vii i v vv i v vi ii v
C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTT 138
E00378:188:HV 64 TATAAATGA--AAACTGTGACTTAGTGAGGTAAAGTAACTTGCTT-ATGC 110
i i -- v i vi v v ii- v i
C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88
E00378:188:HV 111 CACAGAGCTAACAAGTGGTTGACTCGAG 138
v ii iv vi i
C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAGCCGGG 60
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:1:2205:28402:21895/2 47 138 13 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:1:2205:28402:21895/2 47 138 (13) C MIRb#SINE/MIR (107) 161 67 m_b6s601i52
E00378:188:HV 47 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 94
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 95 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 138
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1246 4.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2206:7030:45241/2 1 151 (0) C L1P1 LINE/L1 (1071) 5075 4925 241
ANNOTATION EVIDENCE:
1246 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:2206:7030:45241/2 1 151 0 C L1P1_orf2 LINE/L1 2816 2966 328
1246 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:2206:7030:45241/2 1 151 (0) C L1P1_orf2#LINE/L1 (328) 2966 2816 m_b1s551i28
E00378:188:HV 1 CCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGT 50
?
C L1P1_orf2#LIN 2966 CCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGT 2917
E00378:188:HV 51 TTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTAT 100
i i v
C L1P1_orf2#LIN 2916 TTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTAT 2867
E00378:188:HV 101 CATGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAG 150
v v
C L1P1_orf2#LIN 2866 AAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAG 2817
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2816 T 2816
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 988 12.9 0.0 1.3 E00378:188:HVMVNCCXX:1:2207:10084:44239/1 2 150 (1) + AluSx SINE/Alu 50 196 (116) 242
ANNOTATION EVIDENCE:
988 12.92 0.00 1.34 E00378:188:HVMVNCCXX:1:2207:10084:44239/1 2 150 1 + AluSx SINE/Alu 50 196 116
988 12.92 0.00 1.34 E00378:188:HVMVNCCXX:1:2207:10084:44239/1 2 150 (1) AluSx#SINE/Alu 50 196 (116) m_b5s357i41
E00378:188:HV 2 AGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACG 51
i i i i i i
AluSx#SINE/Al 50 AGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA 99
E00378:188:HV 52 TGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCATTG 101
v i -- i i v
AluSx#SINE/Al 100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCGTGG 147
E00378:188:HV 102 TGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGACAAT 150
i v v vi i i v
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAAT 196
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.51
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 1.00 (2 / 2)
+ 1214 8.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2207:9201:40319/1 1 151 (0) C AluSx SINE/Alu (33) 279 129 243
ANNOTATION EVIDENCE:
1214 7.95 0.00 0.00 E00378:188:HVMVNCCXX:1:2207:9201:40319/1 1 151 0 C AluSx SINE/Alu 129 279 33
1214 7.95 0.00 0.00 E00378:188:HVMVNCCXX:1:2207:9201:40319/1 1 151 (0) C AluSx#SINE/Alu (33) 279 129 m_b4s356i9
E00378:188:HV 1 ACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGG 50
i i i
C AluSx#SINE/Al 279 ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGG 230
E00378:188:HV 51 CTCACTGCAACCTTCGCCTCCCAGGGTCAAGCGATTCTCCTGCCTCAGCC 100
i i v
C AluSx#SINE/Al 229 CTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC 180
E00378:188:HV 101 TCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTTT 150
i i vi v i
C AluSx#SINE/Al 179 TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTT 130
E00378:188:HV 151 T 151
C AluSx#SINE/Al 129 T 129
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.15
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 759 14.5 1.7 0.0 E00378:188:HVMVNCCXX:1:2207:9201:40319/2 35 151 (0) + AluSx SINE/Alu 1 119 (193) 244
ANNOTATION EVIDENCE:
759 14.53 1.68 0.00 E00378:188:HVMVNCCXX:1:2207:9201:40319/2 35 151 0 + AluSx SINE/Alu 1 119 193
759 14.53 1.68 0.00 E00378:188:HVMVNCCXX:1:2207:9201:40319/2 35 151 (0) AluSx#SINE/Alu 1 119 (193) m_b4s357i44
E00378:188:HV 35 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTGTGGGAGGCTGA 84
i i i v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 85 AGCAGGCAGATCAC--AAGGTCAGGAGGTTGAGAACAGCCTGTCCAATAT 132
i i i --i v i v v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 133 TGTGAAACTCCATCTCTAC 151
v i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTAC 119
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.90
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.01 (1 / 116), avg. gap size = 2.00 (2 / 1)
+ 988 12.9 0.0 1.3 E00378:188:HVMVNCCXX:1:2207:9932:43870/1 2 150 (1) + AluSx SINE/Alu 50 196 (116) 245
ANNOTATION EVIDENCE:
988 12.92 0.00 1.34 E00378:188:HVMVNCCXX:1:2207:9932:43870/1 2 150 1 + AluSx SINE/Alu 50 196 116
988 12.92 0.00 1.34 E00378:188:HVMVNCCXX:1:2207:9932:43870/1 2 150 (1) AluSx#SINE/Alu 50 196 (116) m_b5s357i42
E00378:188:HV 2 AGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACG 51
i i i i i i
AluSx#SINE/Al 50 AGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA 99
E00378:188:HV 52 TGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCATTG 101
v i -- i i v
AluSx#SINE/Al 100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCGTGG 147
E00378:188:HV 102 TGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGACAAT 150
i v v vi i i v
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAAT 196
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.51
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 1.00 (2 / 2)
+ 267 27.1 0.0 0.0 E00378:188:HVMVNCCXX:1:2208:14448:50428/1 4 86 (65) C L1M5 LINE/L1 (298) 5826 5741 246
ANNOTATION EVIDENCE:
250 30.12 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:14448:50428/1 4 86 65 C L1ME4a_3end LINE/L1 491 573 298
250 30.12 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:14448:50428/1 4 86 (65) C L1ME4a_3end#LINE/L1 (298) 573 491 m_b1s551i515
E00378:188:HV 4 ATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATTACAGGT 53
? v vi v iii ii i i ii ii i iv
C L1ME4a_3end#L 573 ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACCATAATT 524
E00378:188:HV 54 TATATATCCATTTTACTATTGTTGGACATTTAG 86
v v ? iiv
C L1ME4a_3end#L 523 TATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.26
Transitions / transversions = 2.29 (16/7)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:14448:50428/1 19 86 65 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:14448:50428/1 19 86 (65) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i516
E00378:188:HV 19 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 68
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 69 CTATTGTTGGACATTTAG 86
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1131 11.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2208:14448:50428/2 1 149 (2) + AluSx SINE/Alu 89 237 (75) 247
ANNOTATION EVIDENCE:
1131 11.41 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:14448:50428/2 1 149 2 + AluSx SINE/Alu 89 237 75
1131 11.41 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:14448:50428/2 1 149 (2) AluSx#SINE/Alu 89 237 (75) m_b2s357i27
E00378:188:HV 1 CCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAAATACAAAAATTAGC 50
ii i v
AluSx#SINE/Al 89 CCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC 138
E00378:188:HV 51 TGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGC 100
i i i v i i i
AluSx#SINE/Al 139 CGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGC 188
E00378:188:HV 101 AGGAGAATCACTTGAACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATC 149
i i i i i i
AluSx#SINE/Al 189 AGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATC 237
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.61
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1300 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2208:22810:47720/1 1 151 (0) + L1P1 LINE/L1 4868 5018 (1128) 248
ANNOTATION EVIDENCE:
1300 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:22810:47720/1 1 151 0 + L1P1_orf2 LINE/L1 2759 2909 385
1300 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:22810:47720/1 1 151 (0) L1P1_orf2#LINE/L1 2759 2909 (385) m_b1s551i2
E00378:188:HV 1 CTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 50
L1P1_orf2#LIN 2759 CTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 2808
E00378:188:HV 51 TGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCT 100
L1P1_orf2#LIN 2809 TGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCT 2858
E00378:188:HV 101 TACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACATTA 150
v v i i
L1P1_orf2#LIN 2859 TACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTA 2908
E00378:188:HV 151 G 151
L1P1_orf2#LIN 2909 G 2909
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1284 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2208:22810:47720/2 1 151 (0) C L1P1 LINE/L1 (974) 5172 5022 249
ANNOTATION EVIDENCE:
1284 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:22810:47720/2 1 151 0 C L1P1_orf2 LINE/L1 2913 3063 231
1284 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:22810:47720/2 1 151 (0) C L1P1_orf2#LINE/L1 (231) 3063 2913 m_b1s551i75
E00378:188:HV 1 TGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTCTGTCTT 50
i v
C L1P1_orf2#LIN 3063 TGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTT 3014
E00378:188:HV 51 TTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCT 100
C L1P1_orf2#LIN 3013 TTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCT 2964
E00378:188:HV 101 ATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTT 150
?
C L1P1_orf2#LIN 2963 ATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTT 2914
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2913 A 2913
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1284 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2208:24606:61837/1 1 151 (0) + L1P LINE/L1 5259 5409 (746) 250
ANNOTATION EVIDENCE:
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:24606:61837/1 1 151 0 + L1PA2_3end LINE/L1 6 156 746
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:24606:61837/1 1 151 (0) L1PA2_3end#LINE/L1 6 156 (746) m_b1s551i165
E00378:188:HV 1 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 50
L1PA2_3end#LI 6 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 55
E00378:188:HV 51 ACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAA 100
L1PA2_3end#LI 56 ACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAA 105
E00378:188:HV 101 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGC 150
L1PA2_3end#LI 106 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGC 155
E00378:188:HV 151 C 151
L1PA2_3end#LI 156 C 156
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1336 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2208:24606:61837/2 1 151 (0) C L1P1 LINE/L1 (368) 5787 5637 251
ANNOTATION EVIDENCE:
1336 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:24606:61837/2 1 151 0 C L1PA2_3end LINE/L1 384 534 368
1336 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2208:24606:61837/2 1 151 (0) C L1PA2_3end#LINE/L1 (368) 534 384 m_b1s551i315
E00378:188:HV 1 TATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTT 50
v
C L1PA2_3end#LI 534 TATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTT 485
E00378:188:HV 51 GGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTG 100
i
C L1PA2_3end#LI 484 GGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTG 435
E00378:188:HV 101 CATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAG 150
i
C L1PA2_3end#LI 434 CATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAG 385
E00378:188:HV 151 T 151
C L1PA2_3end#LI 384 T 384
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 893 12.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2210:23794:42464/2 1 122 (29) C AluSx SINE/Alu (190) 122 1 252
ANNOTATION EVIDENCE:
893 12.30 0.00 0.00 E00378:188:HVMVNCCXX:1:2210:23794:42464/2 1 122 29 C AluSx SINE/Alu 1 122 190
893 12.30 0.00 0.00 E00378:188:HVMVNCCXX:1:2210:23794:42464/2 1 122 (29) C AluSx#SINE/Alu (190) 122 1 m_b5s357i50
E00378:188:HV 1 TTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCT 50
i v i i i
C AluSx#SINE/Al 122 TTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCT 73
E00378:188:HV 51 GACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAG 100
i i i i i
C AluSx#SINE/Al 72 GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAG 23
E00378:188:HV 101 GTGTGAGCCAGTGCACCCAGCC 122
i vi i i
C AluSx#SINE/Al 22 GCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.92
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 1059 13.2 0.0 0.0 E00378:188:HVMVNCCXX:1:2210:7720:5933/1 1 151 (0) + AluSx SINE/Alu 113 263 (49) 253
ANNOTATION EVIDENCE:
1059 13.25 0.00 0.00 E00378:188:HVMVNCCXX:1:2210:7720:5933/1 1 151 0 + AluSx SINE/Alu 113 263 49
1059 13.25 0.00 0.00 E00378:188:HVMVNCCXX:1:2210:7720:5933/1 1 151 (0) AluSx#SINE/Alu 113 263 (49) m_b6s356i12
E00378:188:HV 1 TCTCTACGAAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTA 50
v v i i iv
AluSx#SINE/Al 113 TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTA 162
E00378:188:HV 51 ATCCCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGAGGAG 100
i v i vi
AluSx#SINE/Al 163 ATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAG 212
E00378:188:HV 101 GTAGAGGCTGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTGGGAG 150
ii i v i i i i v
AluSx#SINE/Al 213 GCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCG 262
E00378:188:HV 151 A 151
AluSx#SINE/Al 263 A 263
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.26
Transitions / transversions = 1.86 (13/7)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:1:2210:7720:5933/2 7 98 (53) C MIRb SINE/MIR (107) 161 67 254
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:1:2210:7720:5933/2 7 98 53 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:1:2210:7720:5933/2 7 98 (53) C MIRb#SINE/MIR (107) 161 67 m_b6s601i71
E00378:188:HV 7 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 54
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 55 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 98
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 280 26.3 5.7 0.8 E00378:188:HVMVNCCXX:1:2211:4898:41022/1 18 151 (0) + L1ME4c LINE/L1 5696 5836 (247) 255
ANNOTATION EVIDENCE:
280 26.32 5.67 0.75 E00378:188:HVMVNCCXX:1:2211:4898:41022/1 18 151 0 + L1ME4c_3end LINE/L1 443 583 247
280 26.32 5.67 0.75 E00378:188:HVMVNCCXX:1:2211:4898:41022/1 18 151 (0) L1ME4c_3end#LINE/L1 443 583 (247) m_b2s551i19
E00378:188:HV 18 AAATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCT 65
i v iiiv i vi --i v i v i
L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492
E00378:188:HV 66 AAATTTCTGACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT-- 109
v ii iii- - i -- i? i--
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
E00378:188:HV 110 GACAGAAAAATGGTGAAGCCATTAAAAAGTATGACTATCAAG 151
ii v - vi v vv i i v
L1ME4c_3end#L 543 GATGGAATA-TTATGCAGCCATTAAAAATGATAATTATGAAG 583
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.32
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.50 (9 / 6)
+ 1043 9.4 0.7 0.7 E00378:188:HVMVNCCXX:1:2211:4898:41022/2 1 150 (1) + AluY SINE/Alu 112 261 (50) 256
ANNOTATION EVIDENCE:
1043 9.39 0.67 0.67 E00378:188:HVMVNCCXX:1:2211:4898:41022/2 1 150 1 + AluY SINE/Alu 112 261 50
1043 9.39 0.67 0.67 E00378:188:HVMVNCCXX:1:2211:4898:41022/2 1 150 (1) AluY#SINE/Alu 112 261 (50) m_b2s357i88
E00378:188:HV 1 CTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCTGTA 49
i - vi
AluY#SINE/Alu 112 CTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTA 161
E00378:188:HV 50 GTCCCAGCTACTCGGGGGGCTGAAGCAGGAGAACGGCATGAACCTGGGGA 99
i i i i i -
AluY#SINE/Alu 162 GTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGG-A 210
E00378:188:HV 100 GGTGGAGGTTGCAGGGAGCCGAGATCATGCCACTGCATTCCAGCCTGGGC 149
i v v ii i
AluY#SINE/Alu 211 GGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGC 260
E00378:188:HV 150 G 150
AluY#SINE/Alu 261 G 261
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.04
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 278 27.1 5.7 0.8 E00378:188:HVMVNCCXX:1:2211:4929:41005/1 18 151 (0) + L1ME4c LINE/L1 5696 5836 (247) 257
ANNOTATION EVIDENCE:
278 27.07 5.67 0.75 E00378:188:HVMVNCCXX:1:2211:4929:41005/1 18 151 0 + L1ME4c_3end LINE/L1 443 583 247
278 27.07 5.67 0.75 E00378:188:HVMVNCCXX:1:2211:4929:41005/1 18 151 (0) L1ME4c_3end#LINE/L1 443 583 (247) m_b2s551i20
E00378:188:HV 18 AAATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCT 65
i v iiiv i vi --i v i v i
L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492
E00378:188:HV 66 AAATTTCTGACAATAAAA-AATG-TCAAGTAAACTATGGTA--TTTAT-- 109
v ii iii- - i i -- i? i--
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
E00378:188:HV 110 GACAGAAAGATGGTGAAGCCATTAAAAAGTATGACTATCAAG 151
ii -v vi v vv i i v
L1ME4c_3end#L 543 GATGGAA-TATTATGCAGCCATTAAAAATGATAATTATGAAG 583
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.62
Transitions / transversions = 1.92 (23/12)
Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.50 (9 / 6)
+ 1065 8.7 0.7 0.7 E00378:188:HVMVNCCXX:1:2211:4929:41005/2 1 150 (1) + AluY SINE/Alu 112 261 (50) 258
ANNOTATION EVIDENCE:
1065 8.73 0.67 0.67 E00378:188:HVMVNCCXX:1:2211:4929:41005/2 1 150 1 + AluY SINE/Alu 112 261 50
1065 8.73 0.67 0.67 E00378:188:HVMVNCCXX:1:2211:4929:41005/2 1 150 (1) AluY#SINE/Alu 112 261 (50) m_b2s357i89
E00378:188:HV 1 CTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCTGTA 49
i - vi
AluY#SINE/Alu 112 CTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTA 161
E00378:188:HV 50 GTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAACCTGGGGA 99
i i i i -
AluY#SINE/Alu 162 GTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGG-A 210
E00378:188:HV 100 GGTGGAGGTTGCAGTGAGCCGAGAGCATGCCACTGCATTCCAGCCTGGGC 149
i v v ii i
AluY#SINE/Alu 211 GGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGC 260
E00378:188:HV 150 G 150
AluY#SINE/Alu 261 G 261
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.30
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 1370 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2211:6248:67340/1 1 151 (0) C L1P1 LINE/L1 (457) 5698 5548 259
ANNOTATION EVIDENCE:
1370 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2211:6248:67340/1 1 151 0 C L1PA3_3end LINE/L1 295 445 457
1370 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2211:6248:67340/1 1 151 (0) C L1PA3_3end#LINE/L1 (457) 445 295 m_b1s551i288
E00378:188:HV 1 ACATACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGG 50
i
C L1PA3_3end#LI 445 ACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGG 396
E00378:188:HV 51 TATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAG 100
i
C L1PA3_3end#LI 395 TATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAG 346
E00378:188:HV 101 ATCCCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTAGTTTAC 150
i
C L1PA3_3end#LI 345 ATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTAC 296
E00378:188:HV 151 A 151
C L1PA3_3end#LI 295 A 295
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2211:6248:67340/2 1 151 (0) + L1P LINE/L1 5269 5419 (736) 260
ANNOTATION EVIDENCE:
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2211:6248:67340/2 1 151 0 + L1PA2_3end LINE/L1 16 166 736
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2211:6248:67340/2 1 151 (0) L1PA2_3end#LINE/L1 16 166 (736) m_b1s551i174
E00378:188:HV 1 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 50
L1PA2_3end#LI 16 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 65
E00378:188:HV 51 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 100
L1PA2_3end#LI 66 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 115
E00378:188:HV 101 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAA 150
L1PA2_3end#LI 116 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAA 165
E00378:188:HV 151 A 151
L1PA2_3end#LI 166 A 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 929 14.3 0.0 1.3 E00378:188:HVMVNCCXX:1:2213:16346:72209/2 1 149 (2) C AluSx SINE/Alu (63) 249 103 261
ANNOTATION EVIDENCE:
929 14.28 0.00 1.34 E00378:188:HVMVNCCXX:1:2213:16346:72209/2 1 149 2 C AluSx SINE/Alu 103 249 63
929 14.28 0.00 1.34 E00378:188:HVMVNCCXX:1:2213:16346:72209/2 1 149 (2) C AluSx#SINE/Alu (63) 249 103 m_b5s357i36
E00378:188:HV 1 GTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCCTAGTAGGTTCAA 50
i v v v vvii
C AluSx#SINE/Al 249 GTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAA 200
E00378:188:HV 51 GCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACAGGCTCCCAC 100
i v i i iv v v i
C AluSx#SINE/Al 199 GCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGC 150
E00378:188:HV 101 CACAATGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGATGGGGTTTCA 149
v i i -- i
C AluSx#SINE/Al 149 CACCACGCCCGGCTAA--TTTTTGTATTTTTAGTAGAGACGGGGTTTCA 103
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.96
Transitions / transversions = 1.10 (11/10)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 1.00 (2 / 2)
+ 998 12.6 0.0 1.4 E00378:188:HVMVNCCXX:1:2213:18852:5212/2 7 151 (0) C AluSx SINE/Alu (106) 206 64 262
ANNOTATION EVIDENCE:
998 12.58 0.00 1.38 E00378:188:HVMVNCCXX:1:2213:18852:5212/2 7 151 0 C AluSx SINE/Alu 64 206 106
998 12.58 0.00 1.38 E00378:188:HVMVNCCXX:1:2213:18852:5212/2 7 151 (0) C AluSx#SINE/Alu (106) 206 64 m_b5s356i18
E00378:188:HV 7 GGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACAGG 56
i v i i iv
C AluSx#SINE/Al 206 GGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGG 157
E00378:188:HV 57 CTCCCACCACAATGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGATGGG 106
v v i v i i -- i
C AluSx#SINE/Al 156 CGCGCGCCACCACGCCCGGCTAA--TTTTTGTATTTTTAGTAGAGACGGG 109
E00378:188:HV 107 GTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAG 151
v i i i i
C AluSx#SINE/Al 108 GTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGG 64
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.68
Transitions / transversions = 2.00 (12/6)
Gap_init rate = 0.01 (2 / 144), avg. gap size = 1.00 (2 / 2)
+ 1299 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2213:26301:30703/1 2 151 (0) + L1P1 LINE/L1 5213 5362 (784) 263
ANNOTATION EVIDENCE:
1299 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:26301:30703/1 2 151 0 + L1P1_orf2 LINE/L1 3104 3253 41
1299 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:26301:30703/1 2 151 (0) L1P1_orf2#LINE/L1 3104 3253 (41) m_b1s551i145
E00378:188:HV 2 AATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCC 51
L1P1_orf2#LIN 3104 AATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCC 3153
E00378:188:HV 52 AGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCC 101
L1P1_orf2#LIN 3154 AGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCC 3203
E00378:188:HV 102 CATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACA 151
L1P1_orf2#LIN 3204 CATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACA 3253
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1124 6.8 0.0 0.0 E00378:188:HVMVNCCXX:1:2213:26301:30703/2 1 147 (4) C L1P1 LINE/L1 (399) 5756 5610 264
ANNOTATION EVIDENCE:
1124 6.80 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:26301:30703/2 1 147 4 C L1PA2_3end LINE/L1 357 503 399
1124 6.80 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:26301:30703/2 1 147 (4) C L1PA2_3end#LINE/L1 (399) 503 357 m_b1s551i303
E00378:188:HV 1 ATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGC 50
C L1PA2_3end#LI 503 ATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGC 454
E00378:188:HV 51 CACAATAAACATACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGT 100
i i
C L1PA2_3end#LI 453 CGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGT 404
E00378:188:HV 101 CCTTTTGGTATTTGCCCGGTTGTGGGATGGCTGGGTCGAATGGGATT 147
v v i i vi i v
C L1PA2_3end#LI 403 CCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATT 357
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.48
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 1311 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2213:30655:35362/1 1 151 (0) + L1P1 LINE/L1 5332 5482 (673) 265
ANNOTATION EVIDENCE:
1311 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:30655:35362/1 1 151 0 + L1PA2_3end LINE/L1 79 229 673
1311 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:30655:35362/1 1 151 (0) L1PA2_3end#LINE/L1 79 229 (673) m_b1s551i211
E00378:188:HV 1 GACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACA 50
L1PA2_3end#LI 79 GACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACA 128
E00378:188:HV 51 CATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAA 100
L1PA2_3end#LI 129 CATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAA 178
E00378:188:HV 101 CCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAG 150
i
L1PA2_3end#LI 179 CCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAG 228
E00378:188:HV 151 T 151
L1PA2_3end#LI 229 T 229
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1363 1.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2213:30655:35362/2 1 151 (0) C L1P1 LINE/L1 (382) 5773 5623 266
ANNOTATION EVIDENCE:
1363 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:30655:35362/2 1 151 0 C L1PA2_3end LINE/L1 370 520 382
1363 1.32 0.00 0.00 E00378:188:HVMVNCCXX:1:2213:30655:35362/2 1 151 (0) C L1PA2_3end#LINE/L1 (382) 520 370 m_b1s551i306
E00378:188:HV 1 TCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTT 50
C L1PA2_3end#LI 520 TCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTT 471
E00378:188:HV 51 GCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATA 100
i
C L1PA2_3end#LI 470 GCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATA 421
E00378:188:HV 101 GCGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTG 150
i
C L1PA2_3end#LI 420 GCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTG 371
E00378:188:HV 151 G 151
C L1PA2_3end#LI 370 G 370
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.73
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1228 5.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2214:24170:18080/2 1 151 (0) C L1P3 LINE/L1 (3164) 2982 2832 267
ANNOTATION EVIDENCE:
1228 5.30 0.00 0.00 E00378:188:HVMVNCCXX:1:2214:24170:18080/2 1 151 0 C L1P3_orf2 LINE/L1 723 873 2421
1228 5.30 0.00 0.00 E00378:188:HVMVNCCXX:1:2214:24170:18080/2 1 151 (0) C L1P3_orf2#LINE/L1 (2421) 873 723 m_b7s551i48
E00378:188:HV 1 AGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTT 50
i i
C L1P3_orf2#LIN 873 AGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTT 824
E00378:188:HV 51 CAAAGAACTTACTTATTTCTGCCTTCATTTCATTATTTACCTAGTAGTCA 100
?i v i i
C L1P3_orf2#LIN 823 CAAAGAACTTNTTTATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCA 774
E00378:188:HV 101 TTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGTGTGGTTTTGAGTGAG 150
i
C L1P3_orf2#LIN 773 TTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGTGCGGTTTTGAGTGAG 724
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 723 T 723
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1199 8.1 0.7 0.0 E00378:188:HVMVNCCXX:1:2214:4614:72912/2 3 151 (0) + AluY SINE/Alu 59 208 (103) 268
ANNOTATION EVIDENCE:
1199 8.05 0.67 0.00 E00378:188:HVMVNCCXX:1:2214:4614:72912/2 3 151 0 + AluY SINE/Alu 59 208 103
1199 8.05 0.67 0.00 E00378:188:HVMVNCCXX:1:2214:4614:72912/2 3 151 (0) AluY#SINE/Alu 59 208 (103) m_b2s356i62
E00378:188:HV 3 GATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGGTGAAACCC 52
i i ii
AluY#SINE/Alu 59 GATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCC 108
E00378:188:HV 53 CATCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCT 101
i i - vi
AluY#SINE/Alu 109 CGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCT 158
E00378:188:HV 102 GTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAACCTGG 151
i i i i
AluY#SINE/Alu 159 GTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGG 208
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.96
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 1257 3.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2216:10460:48828/1 1 151 (0) C L1P1 LINE/L1 (1036) 5110 4960 269
ANNOTATION EVIDENCE:
1257 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2216:10460:48828/1 1 151 0 C L1P1_orf2 LINE/L1 2851 3001 293
1257 3.31 0.00 0.00 E00378:188:HVMVNCCXX:1:2216:10460:48828/1 1 151 (0) C L1P1_orf2#LINE/L1 (293) 3001 2851 m_b1s551i40
E00378:188:HV 1 CTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATG 50
C L1P1_orf2#LIN 3001 CTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATG 2952
E00378:188:HV 51 GTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTT 100
? i
C L1P1_orf2#LIN 2951 GTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTT 2902
E00378:188:HV 101 TAAGTCTTTAATCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGG 150
i v v
C L1P1_orf2#LIN 2901 TAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGG 2852
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2851 G 2851
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 801 6.8 8.3 0.8 E00378:188:HVMVNCCXX:1:2216:6847:32021/1 3 136 (15) C L1P1 LINE/L1 (2839) 3307 3163 270
ANNOTATION EVIDENCE:
801 6.77 8.28 0.75 E00378:188:HVMVNCCXX:1:2216:6847:32021/1 3 136 15 C L1P1_orf2 LINE/L1 1054 1198 2096
801 6.77 8.28 0.75 E00378:188:HVMVNCCXX:1:2216:6847:32021/1 3 136 (15) C L1P1_orf2#LINE/L1 (2096) 1198 1054 m_b6s551i208
E00378:188:HV 3 TATCCTCTTTATCATTTTTTATTGAGTCTATTTGATTCTTCTC------- 45
i v -------
C L1P1_orf2#LIN 1198 TATCCCCTTTATCATTTTTTATTGCGTCTATTTGATTCTTCTCTCTTTTC 1149
E00378:188:HV 46 -TCTTTATTAGTCTTGCTAGCGGTCTG----TTTTGTTAATCTTTTCAAA 90
- i---- i i
C L1P1_orf2#LIN 1148 TTCTTTATTAGTCTTGCTAGCGGTCTATCAATTTTGTTGATCCTTTCAAA 1099
E00378:188:HV 91 AAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGT 136
i v - i v
C L1P1_orf2#LIN 1098 AAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTTGTGT 1054
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.14
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.03 (4 / 133), avg. gap size = 3.25 (13 / 4)
+ 1242 4.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2216:6847:32021/2 1 151 (0) + L1P3 LINE/L1 2936 3086 (3060) 271
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:2216:6847:32021/2 1 151 0 + L1P3_orf2 LINE/L1 827 977 2317
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:1:2216:6847:32021/2 1 151 (0) L1P3_orf2#LINE/L1 827 977 (2317) m_b7s551i14
E00378:188:HV 1 CCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAA 50
i i
L1P3_orf2#LIN 827 CCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAA 876
E00378:188:HV 51 GCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTG 100
? v i
L1P3_orf2#LIN 877 GCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCG 926
E00378:188:HV 101 GGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTAGAGA 150
i
L1P3_orf2#LIN 927 GGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTAGAGA 976
E00378:188:HV 151 A 151
L1P3_orf2#LIN 977 A 977
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1294 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2217:20517:44064/1 1 151 (0) + L1P1 LINE/L1 5111 5261 (885) 272
ANNOTATION EVIDENCE:
1294 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2217:20517:44064/1 1 151 0 + L1P1_orf2 LINE/L1 3002 3152 142
1294 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2217:20517:44064/1 1 151 (0) L1P1_orf2#LINE/L1 3002 3152 (142) m_b1s551i109
E00378:188:HV 1 CAATGGCAACAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAG 50
v i
L1P1_orf2#LIN 3002 CAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAG 3051
E00378:188:HV 51 AGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTAC 100
L1P1_orf2#LIN 3052 AGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTAC 3101
E00378:188:HV 101 AAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATAT 150
i
L1P1_orf2#LIN 3102 AGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATAT 3151
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3152 C 3152
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1301 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2217:20517:44064/2 1 151 (0) C L1P1 LINE/L1 (701) 5454 5304 273
ANNOTATION EVIDENCE:
1301 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2217:20517:44064/2 1 151 0 C L1PA2_3end LINE/L1 51 201 701
1301 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2217:20517:44064/2 1 151 (0) C L1PA2_3end#LINE/L1 (701) 201 51 m_b1s551i193
E00378:188:HV 1 TGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCA 50
C L1PA2_3end#LI 201 TGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCA 152
E00378:188:HV 51 GTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCT 100
C L1PA2_3end#LI 151 GTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCT 102
E00378:188:HV 101 TTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTT 150
C L1PA2_3end#LI 101 TTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTT 52
E00378:188:HV 151 T 151
C L1PA2_3end#LI 51 T 51
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1265 2.7 0.0 0.7 E00378:188:HVMVNCCXX:1:2217:8115:63929/1 1 151 (0) C L1PA3 LINE/L1 (238) 5917 5768 274
ANNOTATION EVIDENCE:
1265 2.67 0.00 0.66 E00378:188:HVMVNCCXX:1:2217:8115:63929/1 1 151 0 C L1PA3_3end LINE/L1 515 664 238
1265 2.67 0.00 0.66 E00378:188:HVMVNCCXX:1:2217:8115:63929/1 1 151 (0) C L1PA3_3end#LINE/L1 (238) 664 515 m_b1s551i356
E00378:188:HV 1 AGAACATGCGGTGTTTGGTTTTTTCTTCTTGCGACAGTTTACTGAGAATG 50
i v i
C L1PA3_3end#LI 664 AGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATG 615
E00378:188:HV 51 ATGATTTCCAATTTCATCCATGTCCCTAACAAAGGACATGAACTCATCAT 100
-
C L1PA3_3end#LI 614 ATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGACATGAACTCATCAT 566
E00378:188:HV 101 TTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGTTTCTTA 150
v
C L1PA3_3end#LI 565 TTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTA 516
E00378:188:HV 151 A 151
C L1PA3_3end#LI 515 A 515
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1340 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2217:8115:63929/2 1 151 (0) + L1P1 LINE/L1 5428 5578 (577) 275
ANNOTATION EVIDENCE:
1340 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2217:8115:63929/2 1 151 0 + L1PA3_3end LINE/L1 175 325 577
1340 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2217:8115:63929/2 1 151 (0) L1PA3_3end#LINE/L1 175 325 (577) m_b1s551i250
E00378:188:HV 1 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAA 50
i
L1PA3_3end#LI 175 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAA 224
E00378:188:HV 51 AAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCC 100
iv
L1PA3_3end#LI 225 AAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACAC 274
E00378:188:HV 101 TTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCA 150
L1PA3_3end#LI 275 TTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCA 324
E00378:188:HV 151 G 151
L1PA3_3end#LI 325 G 325
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 187 28.9 6.2 0.0 E00378:188:HVMVNCCXX:1:2218:20933:62048/1 76 151 (0) C MIRb SINE/MIR (49) 219 139 276
ANNOTATION EVIDENCE:
187 28.95 6.17 0.00 E00378:188:HVMVNCCXX:1:2218:20933:62048/1 76 151 0 C MIRb SINE/MIR 139 219 49
187 28.95 6.17 0.00 E00378:188:HVMVNCCXX:1:2218:20933:62048/1 76 151 (0) C MIRb#SINE/MIR (49) 219 139 m_b4s601i2
E00378:188:HV 76 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 121
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 122 CAGGTAAGTGATA-TATCTTCACTCTACTGA 151
v i iv - ii i i v
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGA 139
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.14 (15/7)
Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.67 (5 / 3)
+ 410 5.8 0.0 0.0 E00378:188:HVMVNCCXX:1:2218:20933:62048/2 1 52 (99) + AluSx SINE/Alu 240 291 (21) 277
ANNOTATION EVIDENCE:
410 5.77 0.00 0.00 E00378:188:HVMVNCCXX:1:2218:20933:62048/2 1 52 99 + AluSx SINE/Alu 240 291 21
410 5.77 0.00 0.00 E00378:188:HVMVNCCXX:1:2218:20933:62048/2 1 52 (99) AluSx#SINE/Alu 240 291 (21) m_b4s357i2
E00378:188:HV 1 GCCACTGCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAA 50
i i i
AluSx#SINE/Al 240 GCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 289
E00378:188:HV 51 AA 52
AluSx#SINE/Al 290 AA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.21
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:1:2218:20933:62048/2 80 111 (40) + (CA)n Simple_repeat 1 32 (0) 278
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:2218:20933:62048/2 80 111 40 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:1:2218:20933:62048/2 80 111 (40) (CA)n#Simple_repeat 1 32 (0) m_b4s252i72
E00378:188:HV 80 CATACATGCACACACATACACACACACACACA 111
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1073 5.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2219:14702:29103/2 20 150 (1) C AluSx SINE/Alu (21) 291 161 279
ANNOTATION EVIDENCE:
1073 5.34 0.00 0.00 E00378:188:HVMVNCCXX:1:2219:14702:29103/2 20 150 1 C AluSx SINE/Alu 161 291 21
1073 5.34 0.00 0.00 E00378:188:HVMVNCCXX:1:2219:14702:29103/2 20 150 (1) C AluSx#SINE/Alu (21) 291 161 m_b4s357i27
E00378:188:HV 20 TTTTTTTTTGAGACGGAATCTCGCTCTCTTGCCCGGGCTGGAGTGCAGTG 69
i v i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 70 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCT 119
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
E00378:188:HV 120 CCTGCCTCAGCCTCCTGAGTAGCTGGGATTA 150
i
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.37
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 1027 12.7 0.0 0.7 E00378:188:HVMVNCCXX:1:2219:14915:27187/2 1 151 (0) + AluSx SINE/Alu 121 270 (42) 280
ANNOTATION EVIDENCE:
1027 12.66 0.00 0.66 E00378:188:HVMVNCCXX:1:2219:14915:27187/2 1 151 0 + AluSx SINE/Alu 121 270 42
1027 12.66 0.00 0.66 E00378:188:HVMVNCCXX:1:2219:14915:27187/2 1 151 (0) AluSx#SINE/Alu 121 270 (42) m_b6s356i9
E00378:188:HV 1 AAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTAATCCCAGC 50
v i i iv
AluSx#SINE/Al 121 AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGC 170
E00378:188:HV 51 TACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGAGGAGGTAGAGGC 100
i v i vi ii i
AluSx#SINE/Al 171 TACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGT 220
E00378:188:HV 101 TGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTGGGAGACATGAGC 150
v i i i i v -
AluSx#SINE/Al 221 TGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGC 269
E00378:188:HV 151 G 151
AluSx#SINE/Al 270 G 270
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.58
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1298 2.0 0.0 0.7 E00378:188:HVMVNCCXX:1:2219:6593:31898/1 1 151 (0) + L1PA3 LINE/L1 5777 5926 (229) 281
ANNOTATION EVIDENCE:
1298 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:2219:6593:31898/1 1 151 0 + L1PA3_3end LINE/L1 524 673 229
1298 2.00 0.00 0.66 E00378:188:HVMVNCCXX:1:2219:6593:31898/1 1 151 (0) L1PA3_3end#LINE/L1 524 673 (229) m_b1s551i357
E00378:188:HV 1 TGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAG 50
L1PA3_3end#LI 524 TGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAG 573
E00378:188:HV 51 TTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAAATCATCATTCTCA 100
-
L1PA3_3end#LI 574 TTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCA 622
E00378:188:HV 101 GTAAACTGTCGCAAGAAGAAAAAACCAAACACCGCATGTTCTCACTCATA 150
i v i
L1PA3_3end#LI 623 GTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATA 672
E00378:188:HV 151 G 151
L1PA3_3end#LI 673 G 673
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1179 3.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2219:6593:31898/2 1 134 (17) C L1PA2 LINE/L1 (11) 6144 6011 282
ANNOTATION EVIDENCE:
1179 2.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2219:6593:31898/2 1 134 17 C L1PA2_3end LINE/L1 758 891 11
1179 2.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2219:6593:31898/2 1 134 (17) C L1PA2_3end#LINE/L1 (11) 891 758 m_b1s551i416
E00378:188:HV 1 TTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTT 50
i
C L1PA2_3end#LI 891 TTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTT 842
E00378:188:HV 51 ACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACTAACTCGTCA 100
i
C L1PA2_3end#LI 841 ACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCA 792
E00378:188:HV 101 TCTAGCATTAGGTATATCTCCCAAGGCTATCTCT 134
v i
C L1PA2_3end#LI 791 TCTAGCATTAGGTATATCTCCCAATGCTATCCCT 758
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.35
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 133), avg. gap size = 0.0 (0 / 0)
+ 1226 1.3 2.6 0.0 E00378:188:HVMVNCCXX:1:2220:6005:34113/1 1 150 (1) C L1P1 LINE/L1 (790) 5356 5203 283
ANNOTATION EVIDENCE:
1226 1.33 2.60 0.00 E00378:188:HVMVNCCXX:1:2220:6005:34113/1 1 150 1 C L1P1_orf2 LINE/L1 3094 3247 47
1226 1.33 2.60 0.00 E00378:188:HVMVNCCXX:1:2220:6005:34113/1 1 150 (1) C L1P1_orf2#LINE/L1 (47) 3247 3094 m_b1s551i143
E00378:188:HV 1 CTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTG 50
C L1P1_orf2#LIN 3247 CTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTG 3198
E00378:188:HV 51 TTTGTTTTTTTCTTGTAAA----TTTGAGTTCATTGTAGATTCTGGATAT 96
----
C L1P1_orf2#LIN 3197 TTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATAT 3148
E00378:188:HV 97 TAGCCCTTTGTCAGATGAGTAGGTTGAGAAAATTTTCTCCCATTTTGTAG 146
v i
C L1P1_orf2#LIN 3147 TAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAG 3098
E00378:188:HV 147 GTTG 150
C L1P1_orf2#LIN 3097 GTTG 3094
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 4.00 (4 / 1)
+ 785 16.7 0.7 0.0 E00378:188:HVMVNCCXX:1:2220:6005:34113/2 2 151 (0) + L1P1 LINE/L1 5110 5260 (886) 284
ANNOTATION EVIDENCE:
785 16.67 0.67 0.00 E00378:188:HVMVNCCXX:1:2220:6005:34113/2 2 151 0 + L1P1_orf2 LINE/L1 3001 3151 143
785 16.67 0.67 0.00 E00378:188:HVMVNCCXX:1:2220:6005:34113/2 2 151 (0) L1P1_orf2#LINE/L1 3001 3151 (143) m_b1s551i111
E00378:188:HV 2 GCAGTGTCGACAAAAGACAGAATTGACAAAGGGGAT-TAATTAAACTAAA 50
i v i v i v -
L1P1_orf2#LIN 3001 GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 3050
E00378:188:HV 51 TCGCTTCTGCACAGCAAAAGAAAATACAATCAGTGGTAACAGGCTACCAA 100
vv v v v vv v v
L1P1_orf2#LIN 3051 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 3100
E00378:188:HV 101 CAAAATGTGAAAAAATGTTTGCTGCCTACTCATATGACAAAGAGCTAATG 150
i v i v i vi v i i
L1P1_orf2#LIN 3101 CAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 3150
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3151 T 3151
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.08
Transitions / transversions = 0.56 (9/16)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 1230 8.0 0.7 0.0 E00378:188:HVMVNCCXX:1:2221:2737:42903/1 1 151 (0) C AluY SINE/Alu (147) 164 13 285
ANNOTATION EVIDENCE:
1230 7.95 0.66 0.00 E00378:188:HVMVNCCXX:1:2221:2737:42903/1 1 151 0 C AluY SINE/Alu 13 164 147
1230 7.95 0.66 0.00 E00378:188:HVMVNCCXX:1:2221:2737:42903/1 1 151 (0) C AluY#SINE/Alu (147) 164 13 m_b2s356i57
E00378:188:HV 1 GACTACAGGCGCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTA 49
iv - i
C AluY#SINE/Alu 164 GACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTA 115
E00378:188:HV 50 GAGATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGATCTCCTGACCTC 99
i ii i
C AluY#SINE/Alu 114 GAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTC 65
E00378:188:HV 100 ATGATCAGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTACAAGCGTGAGC 149
i v i i i
C AluY#SINE/Alu 64 GTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGC 15
E00378:188:HV 150 CA 151
C AluY#SINE/Alu 14 CA 13
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.52
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1180 5.3 1.3 0.0 E00378:188:HVMVNCCXX:1:2222:10419:57512/1 1 151 (0) C L1P3 LINE/L1 (2400) 3746 3594 286
ANNOTATION EVIDENCE:
1180 5.30 1.30 0.00 E00378:188:HVMVNCCXX:1:2222:10419:57512/1 1 151 0 C L1P3_orf2 LINE/L1 1485 1637 1657
1180 5.30 1.30 0.00 E00378:188:HVMVNCCXX:1:2222:10419:57512/1 1 151 (0) C L1P3_orf2#LINE/L1 (1657) 1637 1485 m_b6s551i75
E00378:188:HV 1 ATTTTATCGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAA 50
i i v v
C L1P3_orf2#LIN 1637 ATTTTATTGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAA 1588
E00378:188:HV 51 ATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGC 98
i-- v
C L1P3_orf2#LIN 1587 ATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGC 1538
E00378:188:HV 99 TGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGG 148
v i
C L1P3_orf2#LIN 1537 TGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGG 1488
E00378:188:HV 149 AAT 151
C L1P3_orf2#LIN 1487 AAT 1485
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1163 4.0 1.3 0.0 E00378:188:HVMVNCCXX:1:2222:10419:57512/2 1 151 (0) + L1P3 LINE/L1 3363 3515 (2631) 287
ANNOTATION EVIDENCE:
1163 3.97 1.30 0.00 E00378:188:HVMVNCCXX:1:2222:10419:57512/2 1 151 0 + L1P3_orf2 LINE/L1 1254 1406 1888
1163 3.97 1.30 0.00 E00378:188:HVMVNCCXX:1:2222:10419:57512/2 1 151 (0) L1P3_orf2#LINE/L1 1254 1406 (1888) m_b6s551i140
E00378:188:HV 1 CTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAGACA 50
i vv i
L1P3_orf2#LIN 1254 CTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGGACA 1303
E00378:188:HV 51 CATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAATAGA 98
v -- v
L1P3_orf2#LIN 1304 CATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAATAGA 1353
E00378:188:HV 99 CCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAA 148
L1P3_orf2#LIN 1354 CCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAA 1403
E00378:188:HV 149 AAA 151
L1P3_orf2#LIN 1404 AAA 1406
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.46
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1074 11.3 0.0 0.0 E00378:188:HVMVNCCXX:1:2223:2575:2575/2 2 151 (0) C AluSx SINE/Alu (36) 276 127 288
ANNOTATION EVIDENCE:
1074 11.33 0.00 0.00 E00378:188:HVMVNCCXX:1:2223:2575:2575/2 2 151 0 C AluSx SINE/Alu 127 276 36
1074 11.33 0.00 0.00 E00378:188:HVMVNCCXX:1:2223:2575:2575/2 2 151 (0) C AluSx#SINE/Alu (36) 276 127 m_b4s356i10
E00378:188:HV 2 GAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGGCTC 51
i i i
C AluSx#SINE/Al 276 GAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTC 227
E00378:188:HV 52 ACTGCAACCTTCGCCTCCCAGGTTCTAGCGAGTCTCCTGCCTCAGCCTCC 101
i i v v
C AluSx#SINE/Al 226 ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCC 177
E00378:188:HV 102 TGTGTAGTTGGGATTATAGGCGCCTGCCACCACACCTGGCTATTTGTTGT 151
i v i i vi i i v v
C AluSx#SINE/Al 176 CGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGT 127
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.17
Transitions / transversions = 1.83 (11/6)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1322 0.7 0.0 0.0 E00378:188:HVMVNCCXX:1:2223:27458:18959/1 1 151 (0) + L1P1 LINE/L1 5354 5504 (651) 289
ANNOTATION EVIDENCE:
1322 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2223:27458:18959/1 1 151 0 + L1PA2_3end LINE/L1 101 251 651
1322 0.66 0.00 0.00 E00378:188:HVMVNCCXX:1:2223:27458:18959/1 1 151 (0) L1PA2_3end#LINE/L1 101 251 (651) m_b1s551i223
E00378:188:HV 1 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 50
L1PA2_3end#LI 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 150
E00378:188:HV 51 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 100
L1PA2_3end#LI 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
E00378:188:HV 101 ACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 150
i
L1PA2_3end#LI 201 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 250
E00378:188:HV 151 G 151
L1PA2_3end#LI 251 G 251
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1354 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2223:27458:18959/2 1 151 (0) C L1P1 LINE/L1 (495) 5660 5510 290
ANNOTATION EVIDENCE:
1354 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2223:27458:18959/2 1 151 0 C L1PA3_3end LINE/L1 257 407 495
1354 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2223:27458:18959/2 1 151 (0) C L1PA3_3end#LINE/L1 (495) 407 257 m_b1s551i279
E00378:188:HV 1 TAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTAT 50
C L1PA3_3end#LI 407 TAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTAT 358
E00378:188:HV 51 TTCCAGTTCTAGATCCCTGAGGAATCACCACACTGACTTCCACAATGGTT 100
i i
C L1PA3_3end#LI 357 TTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTT 308
E00378:188:HV 101 GAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCA 150
vi
C L1PA3_3end#LI 307 GAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCA 258
E00378:188:HV 151 C 151
C L1PA3_3end#LI 257 C 257
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 667 15.1 0.0 5.6 E00378:188:HVMVNCCXX:1:2224:10094:3999/1 26 151 (0) C AluSx SINE/Alu (8) 304 186 291
ANNOTATION EVIDENCE:
667 15.13 0.00 5.56 E00378:188:HVMVNCCXX:1:2224:10094:3999/1 26 151 0 C AluSx SINE/Alu 186 304 8
667 15.13 0.00 5.56 E00378:188:HVMVNCCXX:1:2224:10094:3999/1 26 151 (0) C AluSx#SINE/Alu (8) 304 186 m_b5s357i21
E00378:188:HV 26 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 75
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 76 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 125
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 126 TAGTAGGTTCAAGCAATTGTCCTGCC 151
vvii i v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCC 186
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.32
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.00 (7 / 7)
+ 1334 0.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2224:12236:64456/1 1 151 (0) + L1P1 LINE/L1 5319 5469 (686) 292
ANNOTATION EVIDENCE:
1334 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2224:12236:64456/1 1 151 0 + L1PA2_3end LINE/L1 66 216 686
1334 0.00 0.00 0.00 E00378:188:HVMVNCCXX:1:2224:12236:64456/1 1 151 (0) L1PA2_3end#LINE/L1 66 216 (686) m_b1s551i202
E00378:188:HV 1 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 50
L1PA2_3end#LI 66 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 115
E00378:188:HV 51 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAA 100
L1PA2_3end#LI 116 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAA 165
E00378:188:HV 101 ATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGC 150
L1PA2_3end#LI 166 ATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGC 215
E00378:188:HV 151 A 151
L1PA2_3end#LI 216 A 216
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1352 2.6 0.0 0.0 E00378:188:HVMVNCCXX:1:2224:12236:64456/2 1 151 (0) C L1P2 LINE/L1 (500) 5655 5505 293
ANNOTATION EVIDENCE:
1352 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2224:12236:64456/2 1 151 0 C L1PA4_3end LINE/L1 252 402 500
1352 2.65 0.00 0.00 E00378:188:HVMVNCCXX:1:2224:12236:64456/2 1 151 (0) C L1PA4_3end#LINE/L1 (500) 402 252 m_b1s551i278
E00378:188:HV 1 CTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCA 50
i
C L1PA4_3end#LI 402 CTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTA 353
E00378:188:HV 51 GTTCTAGATCCCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACT 100
i
C L1PA4_3end#LI 352 GTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACT 303
E00378:188:HV 101 AGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATCC 150
vi
C L1PA4_3end#LI 302 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCC 253
E00378:188:HV 151 T 151
C L1PA4_3end#LI 252 T 252
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1303 2.0 0.0 0.0 E00378:188:HVMVNCCXX:1:2224:12418:22194/1 1 151 (0) C L1P3 LINE/L1 (2563) 3583 3433 294
ANNOTATION EVIDENCE:
1303 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2224:12418:22194/1 1 151 0 C L1P3_orf2 LINE/L1 1324 1474 1820
1303 1.99 0.00 0.00 E00378:188:HVMVNCCXX:1:2224:12418:22194/1 1 151 (0) C L1P3_orf2#LINE/L1 (1820) 1474 1324 m_b6s551i128
E00378:188:HV 1 GGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTGAAT 50
i
C L1P3_orf2#LIN 1474 GGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTGAAT 1425
E00378:188:HV 51 CCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTC 100
v
C L1P3_orf2#LIN 1424 CCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTC 1375
E00378:188:HV 101 AATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGCT 150
v
C L1P3_orf2#LIN 1374 AATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGGT 1325
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 1324 T 1324
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 947 4.3 0.7 7.3 E00378:188:HVMVNCCXX:1:2224:12418:22194/2 1 151 (0) + L1P3 LINE/L1 3082 3222 (2924) 295
ANNOTATION EVIDENCE:
947 4.28 0.71 7.28 E00378:188:HVMVNCCXX:1:2224:12418:22194/2 1 151 0 + L1P3_orf2 LINE/L1 973 1113 2181
947 4.28 0.71 7.28 E00378:188:HVMVNCCXX:1:2224:12418:22194/2 1 151 (0) L1P3_orf2#LINE/L1 973 1113 (2181) m_b6s551i242
E00378:188:HV 1 GAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAAC 50
L1P3_orf2#LIN 973 GAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAAC 1022
E00378:188:HV 51 TAAGATCAGAGCTGAG-TGAAGGAGATAGAGACACACACACACAAAAAAA 99
v i- ----------i
L1P3_orf2#LIN 1023 TAAGATCAGAGCAGAACTGAAGGAGATAGAGACAC----------GAAAA 1062
E00378:188:HV 100 ACCTTTCAAAAAAATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTA 149
i - v i
L1P3_orf2#LIN 1063 ACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTA 1111
E00378:188:HV 150 AC 151
L1P3_orf2#LIN 1112 AC 1113
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1307 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1101:13007:40829/1 1 150 (1) + L1P3 LINE/L1 3468 3617 (2529) 296
ANNOTATION EVIDENCE:
1307 2.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1101:13007:40829/1 1 150 1 + L1P3_orf2 LINE/L1 1359 1508 1786
1307 2.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1101:13007:40829/1 1 150 (1) L1P3_orf2#LINE/L1 1359 1508 (1786) m_b6s551i114
E00378:188:HV 1 AACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAA 50
L1P3_orf2#LIN 1359 AACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAA 1408
E00378:188:HV 51 GCCCAGGACCAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAG 100
v i
L1P3_orf2#LIN 1409 GCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAG 1458
E00378:188:HV 101 GAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAGTAGAAAAAGAGGG 150
i
L1P3_orf2#LIN 1459 GAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGG 1508
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1092 6.6 3.2 0.0 E00378:188:HVMVNCCXX:2:1101:13007:40829/2 1 151 (0) C L1P3 LINE/L1 (2333) 3813 3658 297
ANNOTATION EVIDENCE:
1092 6.62 3.20 0.00 E00378:188:HVMVNCCXX:2:1101:13007:40829/2 1 151 0 C L1P3_orf2 LINE/L1 1549 1704 1590
1092 6.62 3.20 0.00 E00378:188:HVMVNCCXX:2:1101:13007:40829/2 1 151 (0) C L1P3_orf2#LINE/L1 (1590) 1704 1549 m_b6s551i57
E00378:188:HV 1 AGGGATGAAGCTGACTTGATAGTGGTGGATAAGCGTTTTGATG---TGCT 47
i v v ---
C L1P3_orf2#LIN 1704 AGGGATGAAGCCGACTTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCT 1655
E00378:188:HV 48 GGATTCAGTTTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCATC 97
i i i
C L1P3_orf2#LIN 1654 GGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATC 1605
E00378:188:HV 98 ACGGATAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTT 145
v v i--
C L1P3_orf2#LIN 1604 AGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTT 1555
E00378:188:HV 146 TGGAAT 151
v
C L1P3_orf2#LIN 1554 TGGTAT 1549
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 1308 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1101:28544:40882/1 1 151 (0) C L1P1 LINE/L1 (698) 5457 5307 298
ANNOTATION EVIDENCE:
1308 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1101:28544:40882/1 1 151 0 C L1PA2_3end LINE/L1 54 204 698
1308 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1101:28544:40882/1 1 151 (0) C L1PA2_3end#LINE/L1 (698) 204 54 m_b1s551i194
E00378:188:HV 1 TGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGG 50
C L1PA2_3end#LI 204 TGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGG 155
E00378:188:HV 51 CCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCT 100
C L1PA2_3end#LI 154 CCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCT 105
E00378:188:HV 101 TCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTT 150
C L1PA2_3end#LI 104 TCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTT 55
E00378:188:HV 151 G 151
C L1PA2_3end#LI 54 G 54
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1233 3.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1101:28544:40882/2 1 151 (0) + L1P1 LINE/L1 4999 5149 (997) 299
ANNOTATION EVIDENCE:
1233 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1101:28544:40882/2 1 151 0 + L1P1_orf2 LINE/L1 2890 3040 254
1233 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1101:28544:40882/2 1 151 (0) L1P1_orf2#LINE/L1 2890 3040 (254) m_b1s551i65
E00378:188:HV 1 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 50
i
L1P1_orf2#LIN 2890 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2939
E00378:188:HV 51 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 100
?
L1P1_orf2#LIN 2940 CCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2989
E00378:188:HV 101 AAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAAGGGGATCTA 150
v i v
L1P1_orf2#LIN 2990 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3039
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3040 A 3040
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1098 6.0 3.2 0.0 E00378:188:HVMVNCCXX:2:1102:6482:56141/1 1 149 (2) C L1P3 LINE/L1 (2357) 3789 3636 300
ANNOTATION EVIDENCE:
1098 6.04 3.25 0.00 E00378:188:HVMVNCCXX:2:1102:6482:56141/1 1 149 2 C L1P3_orf2 LINE/L1 1527 1680 1614
1098 6.04 3.25 0.00 E00378:188:HVMVNCCXX:2:1102:6482:56141/1 1 149 (2) C L1P3_orf2#LINE/L1 (1614) 1680 1527 m_b6s551i66
E00378:188:HV 1 GTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTAT 47
v --- i
C L1P3_orf2#LIN 1680 GTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTAT 1631
E00378:188:HV 48 CGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCT 97
i i v v
C L1P3_orf2#LIN 1630 TGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCT 1581
E00378:188:HV 98 TTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATC 145
i-- v v
C L1P3_orf2#LIN 1580 TTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTC 1531
E00378:188:HV 146 ATAA 149
C L1P3_orf2#LIN 1530 ATAA 1527
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 2.50 (5 / 2)
+ 1136 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1102:6482:56141/2 1 151 (0) + L1P3 LINE/L1 3310 3462 (2684) 301
ANNOTATION EVIDENCE:
1136 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1102:6482:56141/2 1 151 0 + L1P3_orf2 LINE/L1 1201 1353 1941
1136 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1102:6482:56141/2 1 151 (0) L1P3_orf2#LINE/L1 1201 1353 (1941) m_b6s551i158
E00378:188:HV 1 ACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAATA 50
i
L1P3_orf2#LIN 1201 ACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAACA 1250
E00378:188:HV 51 CCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAG 100
i vv i
L1P3_orf2#LIN 1251 CCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGG 1300
E00378:188:HV 101 ACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAAT 148
v -- v
L1P3_orf2#LIN 1301 ACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAAT 1350
E00378:188:HV 149 AGA 151
L1P3_orf2#LIN 1351 AGA 1353
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1289 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1103:9313:62593/1 1 151 (0) C L1P1 LINE/L1 (953) 5193 5043 302
ANNOTATION EVIDENCE:
1289 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1103:9313:62593/1 1 151 0 C L1P1_orf2 LINE/L1 2934 3084 210
1289 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1103:9313:62593/1 1 151 (0) C L1P1_orf2#LINE/L1 (210) 3084 2934 m_b1s551i84
E00378:188:HV 1 TCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGAT 50
C L1P1_orf2#LIN 3084 TCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGAT 3035
E00378:188:HV 51 CCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGAC 100
i v
C L1P1_orf2#LIN 3034 CCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGAC 2985
E00378:188:HV 101 ATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTTTTC 150
?
C L1P1_orf2#LIN 2984 ATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTC 2935
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2934 T 2934
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1126 12.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1104:7243:54612/2 2 151 (0) C AluSx SINE/Alu (133) 179 30 303
ANNOTATION EVIDENCE:
1126 12.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7243:54612/2 2 151 0 C AluSx SINE/Alu 30 179 133
1126 12.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7243:54612/2 2 151 (0) C AluSx#SINE/Alu (133) 179 30 m_b2s356i32
E00378:188:HV 2 TCCTGAGTAGCTGGGATTACAGGTGCCCACCACCACACCCAGCTAATTTT 51
i i v i i i
C AluSx#SINE/Al 179 TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTT 130
E00378:188:HV 52 TGTATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCG 101
v i ii i
C AluSx#SINE/Al 129 TGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCG 80
E00378:188:HV 102 AACTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAG 151
i i i v v v i
C AluSx#SINE/Al 79 AACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGG 30
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.59
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 828 5.9 3.5 7.5 E00378:188:HVMVNCCXX:2:1104:7557:19434/1 5 151 (0) C L1P3 LINE/L1 (2890) 3256 3116 304
ANNOTATION EVIDENCE:
828 5.88 3.54 7.48 E00378:188:HVMVNCCXX:2:1104:7557:19434/1 5 151 0 C L1P3_orf2 LINE/L1 1007 1147 2147
828 5.88 3.54 7.48 E00378:188:HVMVNCCXX:2:1104:7557:19434/1 5 151 (0) C L1P3_orf2#LINE/L1 (2147) 1147 1007 m_b6s551i224
E00378:188:HV 5 TCTTTATTAGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAA 50
v ---- i
C L1P3_orf2#LIN 1147 TCTTTATTAGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAA 1098
E00378:188:HV 51 AATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTG 100
i v - i i---------
C L1P3_orf2#LIN 1097 AACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC--------- 1058
E00378:188:HV 101 TGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCT 149
- -i v
C L1P3_orf2#LIN 1057 -GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCT 1009
E00378:188:HV 150 TC 151
C L1P3_orf2#LIN 1008 TC 1007
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.43
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (13 / 146), avg. gap size = 1.23 (16 / 13)
+ 1200 6.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1104:7557:19434/2 1 151 (0) + L1P3 LINE/L1 2895 3045 (3101) 305
ANNOTATION EVIDENCE:
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7557:19434/2 1 151 0 + L1P3_orf2 LINE/L1 786 936 2358
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7557:19434/2 1 151 (0) L1P3_orf2#LINE/L1 786 936 (2358) m_b7s551i28
E00378:188:HV 1 AAATAATGAAATGAAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGA 50
i v i? i
L1P3_orf2#LIN 786 AAATAACGAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGA 835
E00378:188:HV 51 ACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 100
i
L1P3_orf2#LIN 836 ACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 885
E00378:188:HV 101 AGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATC 150
? v i
L1P3_orf2#LIN 886 AGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATC 935
E00378:188:HV 151 T 151
L1P3_orf2#LIN 936 T 936
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.95
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 838 8.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1104:7963:43624/1 1 112 (39) + L1P3 LINE/L1 3787 3898 (2248) 306
ANNOTATION EVIDENCE:
838 8.04 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7963:43624/1 1 112 39 + L1P3_orf2 LINE/L1 1678 1789 1505
838 8.04 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7963:43624/1 1 112 (39) L1P3_orf2#LINE/L1 1678 1789 (1505) m_b6s551i23
E00378:188:HV 1 CACCACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCAT 50
v i i i i
L1P3_orf2#LIN 1678 CACCACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACAT 1727
E00378:188:HV 51 ACACAAATCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAA 100
i i v
L1P3_orf2#LIN 1728 ACGCAAATCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAA 1777
E00378:188:HV 101 ACTACATGATTA 112
i
L1P3_orf2#LIN 1778 ACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.88
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
+ 28 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1104:7963:43624/2 61 87 (64) + (T)n Simple_repeat 1 27 (0) 307
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7963:43624/2 61 87 64 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1104:7963:43624/2 61 87 (64) (T)n#Simple_repeat 1 27 (0) c_b6s251i18
E00378:188:HV 61 TTTTTTTTTTTTTTTTTTTTTTTTTTT 87
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 1137 7.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1105:1194:28664/2 1 151 (0) C L1P1 LINE/L1 (1093) 5053 4903 308
ANNOTATION EVIDENCE:
1137 7.28 0.00 0.00 E00378:188:HVMVNCCXX:2:1105:1194:28664/2 1 151 0 C L1P1_orf2 LINE/L1 2794 2944 350
1137 7.28 0.00 0.00 E00378:188:HVMVNCCXX:2:1105:1194:28664/2 1 151 (0) C L1P1_orf2#LINE/L1 (350) 2944 2794 m_b1s551i23
E00378:188:HV 1 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTATAATGTTTAAGTCT 50
v i
C L1P1_orf2#LIN 2944 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCT 2895
E00378:188:HV 51 TTAATCCATCTTGAATTGATTTTTATATCAGGTGTAAGGAAGGGATCCAG 100
i i v
C L1P1_orf2#LIN 2894 TTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAG 2845
E00378:188:HV 101 TTTCAGCTTTCTACATATGGCTGCCCAGGTTTCGCGGCACCATTTCTTAA 150
iv v v i v
C L1P1_orf2#LIN 2844 TTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 2795
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2794 A 2794
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.01
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1282 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:1105:1996:21333/2 1 151 (0) C L1P1 LINE/L1 (1093) 5053 4903 309
ANNOTATION EVIDENCE:
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1105:1996:21333/2 1 151 0 C L1P1_orf2 LINE/L1 2794 2944 350
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1105:1996:21333/2 1 151 (0) C L1P1_orf2#LINE/L1 (350) 2944 2794 m_b1s551i24
E00378:188:HV 1 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCT 50
i
C L1P1_orf2#LIN 2944 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCT 2895
E00378:188:HV 51 TTAATCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAG 100
i v v
C L1P1_orf2#LIN 2894 TTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAG 2845
E00378:188:HV 101 TTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 150
C L1P1_orf2#LIN 2844 TTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 2795
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2794 A 2794
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 856 5.7 3.5 7.3 E00378:188:HVMVNCCXX:2:1105:23236:53803/1 1 151 (0) C L1P3 LINE/L1 (2906) 3240 3096 310
ANNOTATION EVIDENCE:
856 5.72 3.45 7.28 E00378:188:HVMVNCCXX:2:1105:23236:53803/1 1 151 0 C L1P3_orf2 LINE/L1 987 1131 2163
856 5.72 3.45 7.28 E00378:188:HVMVNCCXX:2:1105:23236:53803/1 1 151 (0) C L1P3_orf2#LINE/L1 (2163) 1131 987 m_b6s551i231
E00378:188:HV 1 TAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATT 46
---- i i
C L1P3_orf2#LIN 1131 TAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATT 1082
E00378:188:HV 47 AATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCT 96
v - i i----------
C L1P3_orf2#LIN 1081 CATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCT 1043
E00378:188:HV 97 TCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTTAA 145
-i v v
C L1P3_orf2#LIN 1042 TCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAA 993
E00378:188:HV 146 TTTGTT 151
C L1P3_orf2#LIN 992 TTTGTT 987
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 905 5.0 3.4 6.0 E00378:188:HVMVNCCXX:2:1105:23368:53961/1 1 150 (1) C L1P3 LINE/L1 (2906) 3240 3095 311
ANNOTATION EVIDENCE:
905 4.97 3.42 6.00 E00378:188:HVMVNCCXX:2:1105:23368:53961/1 1 150 1 C L1P3_orf2 LINE/L1 986 1131 2163
905 4.97 3.42 6.00 E00378:188:HVMVNCCXX:2:1105:23368:53961/1 1 150 (1) C L1P3_orf2#LINE/L1 (2163) 1131 986 m_b6s551i232
E00378:188:HV 1 TAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATT 46
---- i i
C L1P3_orf2#LIN 1131 TAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATT 1082
E00378:188:HV 47 AATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTCTCTATCTCCTTC 96
v - i i--------
C L1P3_orf2#LIN 1081 CATTGA-TTTTTTGAAGGGTTTTTC--------GTGTCTCTATCTCCTTC 1041
E00378:188:HV 97 A-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATT 145
-i v
C L1P3_orf2#LIN 1040 AGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATT 991
E00378:188:HV 146 TGTTT 150
C L1P3_orf2#LIN 990 TGTTT 986
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.47
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.07 (11 / 149), avg. gap size = 1.27 (14 / 11)
+ 1177 4.0 1.3 0.0 E00378:188:HVMVNCCXX:2:1106:18345:28734/1 1 151 (0) C L1P3 LINE/L1 (2603) 3543 3391 312
ANNOTATION EVIDENCE:
1177 3.97 1.30 0.00 E00378:188:HVMVNCCXX:2:1106:18345:28734/1 1 151 0 C L1P3_orf2 LINE/L1 1282 1434 1860
1177 3.97 1.30 0.00 E00378:188:HVMVNCCXX:2:1106:18345:28734/1 1 151 (0) C L1P3_orf2#LINE/L1 (1860) 1434 1282 m_b6s551i136
E00378:188:HV 1 GGCTGTGAATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAA 50
v
C L1P3_orf2#LIN 1434 GGCTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAA 1385
E00378:188:HV 51 TTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCGACT 100
C L1P3_orf2#LIN 1384 TTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCGACT 1335
E00378:188:HV 101 TCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAATTTATCACT 148
v -- v i vv
C L1P3_orf2#LIN 1334 TCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCAT 1285
E00378:188:HV 149 TTC 151
C L1P3_orf2#LIN 1284 TTC 1282
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.09
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 960 7.3 7.4 0.0 E00378:188:HVMVNCCXX:2:1106:18345:28734/2 1 151 (0) + L1P3 LINE/L1 3180 3342 (2804) 313
ANNOTATION EVIDENCE:
960 7.28 7.36 0.00 E00378:188:HVMVNCCXX:2:1106:18345:28734/2 1 151 0 + L1P3_orf2 LINE/L1 1071 1233 2061
960 7.28 7.36 0.00 E00378:188:HVMVNCCXX:2:1106:18345:28734/2 1 151 (0) L1P3_orf2#LINE/L1 1071 1233 (2061) m_b6s551i200
E00378:188:HV 1 AAAAATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAACAG 50
v i i
L1P3_orf2#LIN 1071 AAAAATCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAATAG 1120
E00378:188:HV 51 A----CCGCTAGCAAGACTAATAAAGA--------GAGAAGAATCAAATA 88
---- v --------
L1P3_orf2#LIN 1121 ATAGACCGCTAGCCAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATA 1170
E00378:188:HV 89 GACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCCACCGAACT 138
v i vi v v
L1P3_orf2#LIN 1171 GACACAATAAAAAATGATAAAGGGGATATCACCACTGATCCCACAGAAAT 1220
E00378:188:HV 139 ACAAACTCCCATC 151
v
L1P3_orf2#LIN 1221 ACAAACTACCATC 1233
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.66
Transitions / transversions = 0.57 (4/7)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 714 14.5 0.0 5.3 E00378:188:HVMVNCCXX:2:1106:22972:66672/1 1 131 (20) + AluSx SINE/Alu 181 304 (8) 314
ANNOTATION EVIDENCE:
714 14.52 0.00 5.34 E00378:188:HVMVNCCXX:2:1106:22972:66672/1 1 131 20 + AluSx SINE/Alu 181 304 8
714 14.52 0.00 5.34 E00378:188:HVMVNCCXX:2:1106:22972:66672/1 1 131 (20) AluSx#SINE/Alu 181 304 (8) m_b5s357i25
E00378:188:HV 1 GCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGC 50
v i iivv
AluSx#SINE/Al 181 GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGC 230
E00378:188:HV 51 AGATATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGA 100
v v v i ------- i ii i
AluSx#SINE/Al 231 CGAGATCGCGCCACTGCACTCCAGCCTG-------GGCGACAGAGCGAGA 273
E00378:188:HV 101 CTCCATCTCAAAAAAACACAAAAACAAAAAA 131
i v v v
AluSx#SINE/Al 274 CTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.83
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.00 (7 / 7)
+ 1250 3.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1106:24342:49179/1 1 151 (0) + L1P1 LINE/L1 4965 5115 (1031) 315
ANNOTATION EVIDENCE:
1250 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1106:24342:49179/1 1 151 0 + L1P1_orf2 LINE/L1 2856 3006 288
1250 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1106:24342:49179/1 1 151 (0) L1P1_orf2#LINE/L1 2856 3006 (288) m_b1s551i46
E00378:188:HV 1 CCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACA 50
v v i i
L1P1_orf2#LIN 2856 CCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACG 2905
E00378:188:HV 51 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATT 100
?
L1P1_orf2#LIN 2906 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATT 2955
E00378:188:HV 101 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 150
L1P1_orf2#LIN 2956 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 3005
E00378:188:HV 151 G 151
L1P1_orf2#LIN 3006 G 3006
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1316 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1106:24342:49179/2 1 151 (0) C L1P1 LINE/L1 (776) 5370 5220 316
ANNOTATION EVIDENCE:
1316 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1106:24342:49179/2 1 151 0 C L1P1_orf2 LINE/L1 3111 3261 33
1316 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1106:24342:49179/2 1 151 (0) C L1P1_orf2#LINE/L1 (33) 3261 3111 m_b1s551i148
E00378:188:HV 1 TGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACT 50
C L1P1_orf2#LIN 3261 TGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACT 3212
E00378:188:HV 51 TTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTG 100
C L1P1_orf2#LIN 3211 TTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTG 3162
E00378:188:HV 101 TAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTT 150
C L1P1_orf2#LIN 3161 TAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTT 3112
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 3111 C 3111
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1156 6.8 0.0 0.7 E00378:188:HVMVNCCXX:2:1106:6877:51236/2 5 151 (0) + AluY SINE/Alu 139 284 (27) 317
ANNOTATION EVIDENCE:
1156 6.85 0.00 0.68 E00378:188:HVMVNCCXX:2:1106:6877:51236/2 5 151 0 + AluY SINE/Alu 139 284 27
1156 6.85 0.00 0.68 E00378:188:HVMVNCCXX:2:1106:6877:51236/2 5 151 (0) AluY#SINE/Alu 139 284 (27) m_b2s356i84
E00378:188:HV 5 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCA 54
i
AluY#SINE/Alu 139 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCA 188
E00378:188:HV 55 GGAGAACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCA 104
i i i - i v i
AluY#SINE/Alu 189 GGAGAATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCG 237
E00378:188:HV 105 TGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCGGTCTCAAA 151
i i v
AluY#SINE/Alu 238 CGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAA 284
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.88
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.01 (1 / 146), avg. gap size = 1.00 (1 / 1)
+ 1311 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:1107:5020:67990/1 1 151 (0) + L1P1 LINE/L1 5328 5478 (677) 318
ANNOTATION EVIDENCE:
1311 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:1107:5020:67990/1 1 151 0 + L1PA2_3end LINE/L1 75 225 677
1311 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:1107:5020:67990/1 1 151 (0) L1PA2_3end#LINE/L1 75 225 (677) m_b1s551i208
E00378:188:HV 1 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 50
L1PA2_3end#LI 75 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 124
E00378:188:HV 51 AACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATC 100
L1PA2_3end#LI 125 AACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATC 174
E00378:188:HV 101 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAA 150
i
L1PA2_3end#LI 175 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAA 224
E00378:188:HV 151 A 151
L1PA2_3end#LI 225 A 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1331 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1107:5020:67990/2 1 151 (0) C L1P1 LINE/L1 (364) 5791 5641 319
ANNOTATION EVIDENCE:
1331 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1107:5020:67990/2 1 151 0 C L1PA2_3end LINE/L1 388 538 364
1331 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1107:5020:67990/2 1 151 (0) C L1PA2_3end#LINE/L1 (364) 538 388 m_b1s551i316
E00378:188:HV 1 TGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTG 50
v
C L1PA2_3end#LI 538 TGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTG 489
E00378:188:HV 51 GGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACG 100
i
C L1PA2_3end#LI 488 GGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACG 439
E00378:188:HV 101 TGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATAC 150
i
C L1PA2_3end#LI 438 TGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATAC 389
E00378:188:HV 151 C 151
C L1PA2_3end#LI 388 C 388
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1276 2.0 0.0 0.7 E00378:188:HVMVNCCXX:2:1108:13636:16604/1 1 151 (0) + L1PA3 LINE/L1 5748 5897 (258) 320
ANNOTATION EVIDENCE:
1276 2.00 0.00 0.66 E00378:188:HVMVNCCXX:2:1108:13636:16604/1 1 151 0 + L1PA3_3end LINE/L1 495 644 258
1276 2.00 0.00 0.66 E00378:188:HVMVNCCXX:2:1108:13636:16604/1 1 151 (0) L1PA3_3end#LINE/L1 495 644 (258) m_b1s551i354
E00378:188:HV 1 TCCAACAATGATAGACTGGATTAAGAAACTGTGGCACATATACACCATGG 50
v
L1PA3_3end#LI 495 TCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG 544
E00378:188:HV 51 AATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGAC 100
-
L1PA3_3end#LI 545 AATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGAC 593
E00378:188:HV 101 ATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGAAA 150
i v
L1PA3_3end#LI 594 ATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAA 643
E00378:188:HV 151 A 151
L1PA3_3end#LI 644 A 644
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 354 20.9 3.7 1.5 E00378:188:HVMVNCCXX:2:1108:13636:16604/2 1 131 (20) C L1PA3 LINE/L1 (134) 6021 5888 321
ANNOTATION EVIDENCE:
354 20.93 3.73 1.53 E00378:188:HVMVNCCXX:2:1108:13636:16604/2 1 131 20 C L1PA3_3end LINE/L1 635 768 134
354 20.93 3.73 1.53 E00378:188:HVMVNCCXX:2:1108:13636:16604/2 1 131 (20) C L1PA3_3end#LINE/L1 (134) 768 635 m_b1s551i406
E00378:188:HV 1 ATGCTATCCCTCCCCCCGCCCCCCCCTCCCCAACAGTCCGCCAG-GTGAG 49
v v i v - - v
C L1PA3_3end#LI 768 ATGCTATCCCTCCCCCCTCCCCCCACCCCACAACAGTCC-CCAGAGTGTG 720
E00378:188:HV 50 AGATTGCCCTCCCTGT-TCCCCTCGTTCCCCCTTGTTCCATTCCCAACTA 98
vi v i - vivi i v- v v
C L1PA3_3end#LI 719 ATGTTCCCCTTCCTGTGTCCATGTGTTCTCA-TTGTTCAATTCCCACCTA 671
E00378:188:HV 99 TGCGTCGGAAGACTCGGGGAT---TTTTCTGTTTTT 131
v vi v iv v v --- i i
C L1PA3_3end#LI 670 TGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTT 635
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.55
Transitions / transversions = 0.59 (10/17)
Gap_init rate = 0.04 (5 / 130), avg. gap size = 1.40 (7 / 5)
+ 513 13.8 0.0 6.9 E00378:188:HVMVNCCXX:2:1108:16163:13808/1 46 146 (5) C AluSx SINE/Alu (8) 304 211 322
ANNOTATION EVIDENCE:
513 13.83 0.00 6.93 E00378:188:HVMVNCCXX:2:1108:16163:13808/1 46 146 5 C AluSx SINE/Alu 211 304 8
513 13.83 0.00 6.93 E00378:188:HVMVNCCXX:2:1108:16163:13808/1 46 146 (5) C AluSx#SINE/Alu (8) 304 211 m_b5s357i8
E00378:188:HV 46 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 95
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 96 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCACCCTCCGCC 145
--- i v v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 146 T 146
C AluSx#SINE/Al 211 T 211
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.74
Transitions / transversions = 0.86 (6/7)
Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7)
+ 958 13.5 0.0 1.3 E00378:188:HVMVNCCXX:2:1108:16163:13808/2 1 150 (1) + AluSx SINE/Alu 86 233 (79) 323
ANNOTATION EVIDENCE:
958 13.51 0.00 1.33 E00378:188:HVMVNCCXX:2:1108:16163:13808/2 1 150 1 + AluSx SINE/Alu 86 233 79
958 13.51 0.00 1.33 E00378:188:HVMVNCCXX:2:1108:16163:13808/2 1 150 (1) AluSx#SINE/Alu 86 233 (79) m_b5s357i38
E00378:188:HV 1 CAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAA 50
i v i --
AluSx#SINE/Al 86 CAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA-- 133
E00378:188:HV 51 TTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCT 100
i i v i v v vi i i
AluSx#SINE/Al 134 TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCT 183
E00378:188:HV 101 GAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGA 150
v i iivv v
AluSx#SINE/Al 184 GAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGA 233
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.80
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 1051 4.7 5.1 0.0 E00378:188:HVMVNCCXX:2:1108:26829:63366/1 1 150 (1) + L1P3 LINE/L1 3237 3394 (2752) 324
ANNOTATION EVIDENCE:
1051 4.67 5.06 0.00 E00378:188:HVMVNCCXX:2:1108:26829:63366/1 1 150 1 + L1P3_orf2 LINE/L1 1128 1285 2009
1051 4.67 5.06 0.00 E00378:188:HVMVNCCXX:2:1108:26829:63366/1 1 150 (1) L1P3_orf2#LINE/L1 1128 1285 (2009) m_b6s551i183
E00378:188:HV 1 GCTAGCAAGACTAATAAAGA--------GAGAAGAATCAAATAGACTCAA 42
v -------- v
L1P3_orf2#LIN 1128 GCTAGCCAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGACACAA 1177
E00378:188:HV 43 TAAAAAATGATAAAGAGGATAATACCACTGATCCCACAGAAATACAAACT 92
i vi
L1P3_orf2#LIN 1178 TAAAAAATGATAAAGGGGATATCACCACTGATCCCACAGAAATACAAACT 1227
E00378:188:HV 93 ACCATCAGAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAATCT 142
i i
L1P3_orf2#LIN 1228 ACCATCAGAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATCT 1277
E00378:188:HV 143 AGAAGAAA 150
L1P3_orf2#LIN 1278 AGAAGAAA 1285
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.19
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 8.00 (8 / 1)
+ 926 11.3 1.3 0.0 E00378:188:HVMVNCCXX:2:1108:26829:63366/2 1 151 (0) C L1P3 LINE/L1 (2446) 3700 3548 325
ANNOTATION EVIDENCE:
926 11.26 1.30 0.00 E00378:188:HVMVNCCXX:2:1108:26829:63366/2 1 151 0 C L1P3_orf2 LINE/L1 1439 1591 1703
926 11.26 1.30 0.00 E00378:188:HVMVNCCXX:2:1108:26829:63366/2 1 151 (0) C L1P3_orf2#LINE/L1 (1703) 1591 1439 m_b6s551i94
E00378:188:HV 1 TGAAATTTTCTTATTC--TTGTGTCTCTGCCTGGTTTTGGAATCAGGGTG 48
v i-- v v i
C L1P3_orf2#LIN 1591 TGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATG 1542
E00378:188:HV 49 ATGCTGGCATCATAAGATGAGTTCGTGTTGAGTCCCTGTTTTTGTCTTGT 98
v i v v vv v v v
C L1P3_orf2#LIN 1541 ATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGT 1492
E00378:188:HV 99 TTGGAATAGTTTCAGAAGGAATGTTACCAGCTCCTCTTTGTACCCCTGGT 148
v i
C L1P3_orf2#LIN 1491 TTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGT 1442
E00378:188:HV 149 TGA 151
v
C L1P3_orf2#LIN 1441 AGA 1439
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.21
Transitions / transversions = 0.31 (4/13)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 19 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1109:26149:48687/1 1 21 (10) + (A)n Simple_repeat 1 21 (0) 326
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1109:26149:48687/1 1 21 10 + (A)n Simple_repeat 1 21 0
19 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1109:26149:48687/1 1 21 (10) (A)n#Simple_repeat 1 21 (0) m_b2s252i7
E00378:188:HV 1 AAAAAAAAAAAAAAAAAAAAA 21
(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)
+ 747 9.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1109:9242:37190/1 53 148 (3) + AluY SINE/Alu 1 96 (215) 327
ANNOTATION EVIDENCE:
747 9.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1109:9242:37190/1 53 148 3 + AluY SINE/Alu 1 96 215
747 9.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1109:9242:37190/1 53 148 (3) AluY#SINE/Alu 1 96 (215) m_b2s357i71
E00378:188:HV 53 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 102
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 103 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAAC 148
v i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAAC 96
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.86
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 1189 7.3 0.0 0.7 E00378:188:HVMVNCCXX:2:1109:9242:37190/2 1 151 (0) C AluY SINE/Alu (34) 277 128 328
ANNOTATION EVIDENCE:
1189 7.33 0.00 0.66 E00378:188:HVMVNCCXX:2:1109:9242:37190/2 1 151 0 C AluY SINE/Alu 128 277 34
1189 7.33 0.00 0.66 E00378:188:HVMVNCCXX:2:1109:9242:37190/2 1 151 (0) C AluY#SINE/Alu (34) 277 128 m_b2s356i80
E00378:188:HV 1 CGGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATCTCGGC 50
i ii
C AluY#SINE/Alu 277 CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGC 228
E00378:188:HV 51 TCACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCC 100
v i - i i i i
C AluY#SINE/Alu 227 TCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAGCC 179
E00378:188:HV 101 TCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAATTTT 150
iv
C AluY#SINE/Alu 178 TCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTT 129
E00378:188:HV 151 T 151
C AluY#SINE/Alu 128 T 128
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.84
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 240 29.7 7.1 0.0 E00378:188:HVMVNCCXX:2:1110:17381:62575/1 32 122 (29) C L1MC4 LINE/L1 (1441) 6601 6504 329
ANNOTATION EVIDENCE:
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:2:1110:17381:62575/1 32 122 29 C L1MC4_3end LINE/L1 1251 1348 1441
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:2:1110:17381:62575/1 32 122 (29) C L1MC4_3end#LINE/L1 (1441) 1348 1251 m_b3s551i149
E00378:188:HV 32 GTTGATA--GATATCTTCAAATCCAAGCCAACATCACACAGTTTAT---- 75
v -- i i v v i vi i ----
C L1MC4_3end#LI 1348 GTTCATACCGATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTA 1299
E00378:188:HV 76 -CTTTTTTTCTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAA 122
- i iiii v v i v iv iv iii v i
C L1MC4_3end#LI 1298 GCCTTCCCCCTTTCCATATTTGTAACTCCCTTCTCCGACAGTGAGAAA 1251
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.16
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 651 13.2 0.0 0.0 E00378:188:HVMVNCCXX:2:1110:24241:71541/2 61 151 (0) + AluSx SINE/Alu 1 91 (221) 330
ANNOTATION EVIDENCE:
651 13.19 0.00 0.00 E00378:188:HVMVNCCXX:2:1110:24241:71541/2 61 151 0 + AluSx SINE/Alu 1 91 221
651 13.19 0.00 0.00 E00378:188:HVMVNCCXX:2:1110:24241:71541/2 61 151 (0) AluSx#SINE/Alu 1 91 (221) m_b5s357i60
E00378:188:HV 61 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 110
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 111 GGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCT 151
i i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCT 91
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.52
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0)
+ 1170 11.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1110:26118:53381/2 3 151 (0) C AluSx SINE/Alu (52) 260 112 331
ANNOTATION EVIDENCE:
1170 11.41 0.00 0.00 E00378:188:HVMVNCCXX:2:1110:26118:53381/2 3 151 0 C AluSx SINE/Alu 112 260 52
1170 11.41 0.00 0.00 E00378:188:HVMVNCCXX:2:1110:26118:53381/2 3 151 (0) C AluSx#SINE/Alu (52) 260 112 m_b2s356i10
E00378:188:HV 3 CCCAGGCTGGAGTGCAGTGGCATGATCTCAGCTCACTGCAATCTCTGCCT 52
ii i i i
C AluSx#SINE/Al 260 CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT 211
E00378:188:HV 53 CCTGAGTTCAAGTGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTA 102
i i i i i
C AluSx#SINE/Al 210 CCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
E00378:188:HV 103 CAGGTGCCCACCACCACACCCAGCTAATTTTTGTATTTTAAATAGAGAC 151
i v i i i v i
C AluSx#SINE/Al 160 CAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGAC 112
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.95
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1239 7.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1110:4422:3630/2 1 151 (0) C AluSx SINE/Alu (25) 287 137 332
ANNOTATION EVIDENCE:
1239 7.28 0.00 0.00 E00378:188:HVMVNCCXX:2:1110:4422:3630/2 1 151 0 C AluSx SINE/Alu 137 287 25
1239 7.28 0.00 0.00 E00378:188:HVMVNCCXX:2:1110:4422:3630/2 1 151 (0) C AluSx#SINE/Alu (25) 287 137 m_b4s356i5
E00378:188:HV 1 TTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGC 50
i i i
C AluSx#SINE/Al 287 TTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGC 238
E00378:188:HV 51 GATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCTCCTG 100
i i
C AluSx#SINE/Al 237 GATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTG 188
E00378:188:HV 101 CCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGG 150
i i vi v i
C AluSx#SINE/Al 187 CCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGG 138
E00378:188:HV 151 C 151
C AluSx#SINE/Al 137 C 137
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 303 28.5 14.2 0.0 E00378:188:HVMVNCCXX:2:1111:19624:71418/1 1 151 (0) + MIR SINE/MIR 81 256 (6) 333
ANNOTATION EVIDENCE:
303 28.48 14.21 0.00 E00378:188:HVMVNCCXX:2:1111:19624:71418/1 1 151 0 + MIR SINE/MIR 81 256 6
303 28.48 14.21 0.00 E00378:188:HVMVNCCXX:2:1111:19624:71418/1 1 151 (0) MIR#SINE/MIR 81 256 (6) m_b6s601i36
E00378:188:HV 1 CTCTGTGGCAT-AAGCAAGTTACTTTACCTCACTAAGTCACAGTTT--TC 47
v i v -ii v v iv i v --
MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130
E00378:188:HV 48 ATTTATAAATTGAAGGAAATAATAGAATCTAAGTGACAGAAGTAT---AA 94
i i v ii iv v i vv v i iiv i ---i
MIR#SINE/MIR 131 ATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGA 180
E00378:188:HV 95 GAATTAAG------AATAAACATAAA-------------TGCCAGGCACA 125
i i------ v ii ------------- v
MIR#SINE/MIR 181 GGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACA 230
E00378:188:HV 126 CCGTATATACTCAACAAGTGTTAGCT 151
iv viii i i
MIR#SINE/MIR 231 TAGTAAGCGCTCAATAAATGTTAGCT 256
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.70
Transitions / transversions = 1.53 (26/17)
Gap_init rate = 0.03 (5 / 150), avg. gap size = 5.00 (25 / 5)
+ 1277 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:23987:41813/1 1 151 (0) C L1P1 LINE/L1 (894) 5252 5102 334
ANNOTATION EVIDENCE:
1277 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:23987:41813/1 1 151 0 C L1P1_orf2 LINE/L1 2993 3143 151
1277 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:23987:41813/1 1 151 (0) C L1P1_orf2#LINE/L1 (151) 3143 2993 m_b1s551i102
E00378:188:HV 1 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTG 50
i
C L1P1_orf2#LIN 3143 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTG 3094
E00378:188:HV 51 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 100
C L1P1_orf2#LIN 3093 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 3044
E00378:188:HV 101 TAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGT 150
i v
C L1P1_orf2#LIN 3043 TAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGT 2994
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2993 G 2993
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1206 4.6 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:23987:41813/2 1 151 (0) + L1P1 LINE/L1 4962 5112 (1034) 335
ANNOTATION EVIDENCE:
1206 4.64 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:23987:41813/2 1 151 0 + L1P1_orf2 LINE/L1 2853 3003 291
1206 4.64 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:23987:41813/2 1 151 (0) L1P1_orf2#LINE/L1 2853 3003 (291) m_b1s551i43
E00378:188:HV 1 CTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAA 50
v v i
L1P1_orf2#LIN 2853 CTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAA 2902
E00378:188:HV 51 ACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACC 100
i ?
L1P1_orf2#LIN 2903 ACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACC 2952
E00378:188:HV 101 ATTCAGGACATAGTCATGGGCAAGGACTTCATATCTAAAACACCAAAAGC 150
v i
L1P1_orf2#LIN 2953 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 3002
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3003 A 3003
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.48
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1277 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:24089:41532/1 1 151 (0) C L1P1 LINE/L1 (894) 5252 5102 336
ANNOTATION EVIDENCE:
1277 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24089:41532/1 1 151 0 C L1P1_orf2 LINE/L1 2993 3143 151
1277 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24089:41532/1 1 151 (0) C L1P1_orf2#LINE/L1 (151) 3143 2993 m_b1s551i103
E00378:188:HV 1 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTG 50
i
C L1P1_orf2#LIN 3143 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTG 3094
E00378:188:HV 51 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 100
C L1P1_orf2#LIN 3093 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 3044
E00378:188:HV 101 TAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGT 150
i v
C L1P1_orf2#LIN 3043 TAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGT 2994
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2993 G 2993
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1253 3.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:24089:41532/2 1 151 (0) + L1P1 LINE/L1 4962 5112 (1034) 337
ANNOTATION EVIDENCE:
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24089:41532/2 1 151 0 + L1P1_orf2 LINE/L1 2853 3003 291
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24089:41532/2 1 151 (0) L1P1_orf2#LINE/L1 2853 3003 (291) m_b1s551i44
E00378:188:HV 1 CTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAA 50
v v i
L1P1_orf2#LIN 2853 CTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAA 2902
E00378:188:HV 51 ACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACC 100
i ?
L1P1_orf2#LIN 2903 ACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACC 2952
E00378:188:HV 101 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 150
L1P1_orf2#LIN 2953 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 3002
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3003 A 3003
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1277 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:24474:41778/1 1 151 (0) C L1P1 LINE/L1 (894) 5252 5102 338
ANNOTATION EVIDENCE:
1277 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24474:41778/1 1 151 0 C L1P1_orf2 LINE/L1 2993 3143 151
1277 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24474:41778/1 1 151 (0) C L1P1_orf2#LINE/L1 (151) 3143 2993 m_b1s551i104
E00378:188:HV 1 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTG 50
i
C L1P1_orf2#LIN 3143 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTG 3094
E00378:188:HV 51 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 100
C L1P1_orf2#LIN 3093 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 3044
E00378:188:HV 101 TAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGT 150
i v
C L1P1_orf2#LIN 3043 TAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGT 2994
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2993 G 2993
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1227 4.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:24474:41778/2 1 151 (0) + L1P1 LINE/L1 4962 5112 (1034) 339
ANNOTATION EVIDENCE:
1227 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24474:41778/2 1 151 0 + L1P1_orf2 LINE/L1 2853 3003 291
1227 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:24474:41778/2 1 151 (0) L1P1_orf2#LINE/L1 2853 3003 (291) m_b1s551i45
E00378:188:HV 1 CTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAA 50
v v i
L1P1_orf2#LIN 2853 CTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAA 2902
E00378:188:HV 51 ACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACC 100
i ?
L1P1_orf2#LIN 2903 ACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACC 2952
E00378:188:HV 101 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAATC 150
v
L1P1_orf2#LIN 2953 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 3002
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3003 A 3003
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1255 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:32684:45417/1 1 149 (2) C L1P1 LINE/L1 (659) 5496 5348 340
ANNOTATION EVIDENCE:
1255 2.01 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:32684:45417/1 1 149 2 C L1PA2_3end LINE/L1 95 243 659
1255 2.01 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:32684:45417/1 1 149 (2) C L1PA2_3end#LINE/L1 (659) 243 95 m_b1s551i220
E00378:188:HV 1 CCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACCGGTGTGAGAT 50
i i
C L1PA2_3end#LI 243 CCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGAT 194
E00378:188:HV 51 GGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGAT 100
C L1PA2_3end#LI 193 GGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGAT 144
E00378:188:HV 101 GACCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGA 149
v
C L1PA2_3end#LI 143 GAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGA 95
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.04
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1283 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1111:32684:45417/2 1 151 (0) + L1P1 LINE/L1 5078 5228 (918) 341
ANNOTATION EVIDENCE:
1283 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:32684:45417/2 1 151 0 + L1P1_orf2 LINE/L1 2969 3119 175
1283 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1111:32684:45417/2 1 151 (0) L1P1_orf2#LINE/L1 2969 3119 (175) m_b1s551i93
E00378:188:HV 1 TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGAC 50
v
L1P1_orf2#LIN 2969 TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCC 3018
E00378:188:HV 51 AGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 100
i
L1P1_orf2#LIN 3019 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 3068
E00378:188:HV 101 AGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTT 150
i
L1P1_orf2#LIN 3069 AGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTT 3118
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3119 T 3119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1205 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1111:9790:26185/1 1 151 (0) C L1P3 LINE/L1 (2408) 3738 3586 342
ANNOTATION EVIDENCE:
1205 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1111:9790:26185/1 1 151 0 C L1P3_orf2 LINE/L1 1477 1629 1665
1205 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1111:9790:26185/1 1 151 (0) C L1P3_orf2#LINE/L1 (1665) 1629 1477 m_b6s551i78
E00378:188:HV 1 GAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCTT 50
i v v
C L1P3_orf2#LIN 1629 GAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCTT 1580
E00378:188:HV 51 TTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATCA 98
i-- v v
C L1P3_orf2#LIN 1579 TTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCA 1530
E00378:188:HV 99 TAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTT 148
i
C L1P3_orf2#LIN 1529 TAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTT 1480
E00378:188:HV 149 CAG 151
C L1P3_orf2#LIN 1479 CAG 1477
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1140 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1111:9790:26185/2 1 151 (0) + L1P3 LINE/L1 3312 3464 (2682) 343
ANNOTATION EVIDENCE:
1140 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1111:9790:26185/2 1 151 0 + L1P3_orf2 LINE/L1 1203 1355 1939
1140 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1111:9790:26185/2 1 151 (0) L1P3_orf2#LINE/L1 1203 1355 (1939) m_b6s551i156
E00378:188:HV 1 CACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAATACC 50
i
L1P3_orf2#LIN 1203 CACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTATAAACACC 1252
E00378:188:HV 51 TCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAGAC 100
i vv i
L1P3_orf2#LIN 1253 TCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGGAC 1302
E00378:188:HV 101 ACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAATAG 148
v -- v
L1P3_orf2#LIN 1303 ACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAATAG 1352
E00378:188:HV 149 ACC 151
L1P3_orf2#LIN 1353 ACC 1355
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1165 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1112:20364:42499/1 1 151 (0) + L1P3 LINE/L1 3352 3504 (2642) 344
ANNOTATION EVIDENCE:
1165 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1112:20364:42499/1 1 151 0 + L1P3_orf2 LINE/L1 1243 1395 1899
1165 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1112:20364:42499/1 1 151 (0) L1P3_orf2#LINE/L1 1243 1395 (1899) m_b6s551i144
E00378:188:HV 1 TATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAA 50
i i vv
L1P3_orf2#LIN 1243 TATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAA 1292
E00378:188:HV 51 ATTCCTAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAAT 98
i v -- v
L1P3_orf2#LIN 1293 ATTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAAT 1342
E00378:188:HV 99 CCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGC 148
L1P3_orf2#LIN 1343 CCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGC 1392
E00378:188:HV 149 CTA 151
L1P3_orf2#LIN 1393 CTA 1395
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1300 3.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1112:20364:42499/2 1 151 (0) C L1P3 LINE/L1 (2479) 3667 3517 345
ANNOTATION EVIDENCE:
1300 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1112:20364:42499/2 1 151 0 C L1P3_orf2 LINE/L1 1408 1558 1736
1300 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1112:20364:42499/2 1 151 (0) C L1P3_orf2#LINE/L1 (1736) 1558 1408 m_b6s551i102
E00378:188:HV 1 GTTTTGGAATCAGGATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGT 50
v v i
C L1P3_orf2#LIN 1558 GTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGT 1509
E00378:188:HV 51 CCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTC 100
C L1P3_orf2#LIN 1508 CCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTC 1459
E00378:188:HV 101 CTCTTTGTACCCCTGGTAGAATTCGGCTGTGAATCCCTCTGGTCCTGGGC 150
i v
C L1P3_orf2#LIN 1458 CTCTTTGTACCTCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTGGGC 1409
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 1408 T 1408
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1293 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1113:31791:64544/1 1 151 (0) + L1P1 LINE/L1 5229 5379 (767) 346
ANNOTATION EVIDENCE:
1293 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1113:31791:64544/1 1 151 0 + L1P1_orf2 LINE/L1 3120 3270 24
1293 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1113:31791:64544/1 1 151 (0) L1P1_orf2#LINE/L1 3120 3270 (24) m_b1s551i149
E00378:188:HV 1 CGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAAC 50
L1P1_orf2#LIN 3120 CGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAAC 3169
E00378:188:HV 51 TCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCG 100
L1P1_orf2#LIN 3170 TCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCG 3219
E00378:188:HV 101 AAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA 150
L1P1_orf2#LIN 3220 AAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA 3269
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3270 A 3270
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1263 4.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1113:31791:64544/2 1 151 (0) C L1P1 LINE/L1 (590) 5565 5415 347
ANNOTATION EVIDENCE:
1263 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:1113:31791:64544/2 1 151 0 C L1PA3_3end LINE/L1 162 312 590
1263 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:1113:31791:64544/2 1 151 (0) C L1PA3_3end#LINE/L1 (590) 312 162 m_b1s551i246
E00378:188:HV 1 TGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATTT 50
vi
C L1PA3_3end#LI 312 TGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTT 263
E00378:188:HV 51 CTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCC 100
i
C L1PA3_3end#LI 262 CTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCC 213
E00378:188:HV 101 ATTCTAACTGGTGTGAGATGGTATCTCATGCTGGTTTTGATTTGCGTTTC 150
vv i
C L1PA3_3end#LI 212 ATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTC 163
E00378:188:HV 151 T 151
C L1PA3_3end#LI 162 T 162
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.09
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1051 13.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1113:4767:68922/1 1 146 (5) C AluSx SINE/Alu (166) 146 1 348
ANNOTATION EVIDENCE:
1051 13.01 0.00 0.00 E00378:188:HVMVNCCXX:2:1113:4767:68922/1 1 146 5 C AluSx SINE/Alu 1 146 166
1051 13.01 0.00 0.00 E00378:188:HVMVNCCXX:2:1113:4767:68922/1 1 146 (5) C AluSx#SINE/Alu (166) 146 1 m_b2s357i31
E00378:188:HV 1 CACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCATGT 50
i i v i ii
C AluSx#SINE/Al 146 CACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGT 97
E00378:188:HV 51 TGGCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTG 100
i i i i v v
C AluSx#SINE/Al 96 TGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG 47
E00378:188:HV 101 CCTCCCAAATTGCTGAGATTACAGATGTGAGCCACTGTGCCCAGCC 146
v i ii i i i
C AluSx#SINE/Al 46 CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.91
Transitions / transversions = 3.75 (15/4)
Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0)
+ 958 13.5 0.0 1.3 E00378:188:HVMVNCCXX:2:1114:13261:56458/2 1 150 (1) + AluSx SINE/Alu 86 233 (79) 349
ANNOTATION EVIDENCE:
958 13.51 0.00 1.33 E00378:188:HVMVNCCXX:2:1114:13261:56458/2 1 150 1 + AluSx SINE/Alu 86 233 79
958 13.51 0.00 1.33 E00378:188:HVMVNCCXX:2:1114:13261:56458/2 1 150 (1) AluSx#SINE/Alu 86 233 (79) m_b5s357i39
E00378:188:HV 1 CAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAA 50
i v i --
AluSx#SINE/Al 86 CAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA-- 133
E00378:188:HV 51 TTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCT 100
i i v i v v vi i i
AluSx#SINE/Al 134 TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCT 183
E00378:188:HV 101 GAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGA 150
v i iivv v
AluSx#SINE/Al 184 GAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGA 233
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.80
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 1065 6.7 0.0 0.0 E00378:188:HVMVNCCXX:2:1114:18781:29384/1 3 151 (0) C L1P3 LINE/L1 (2719) 3427 3279 350
ANNOTATION EVIDENCE:
1065 6.71 0.00 0.00 E00378:188:HVMVNCCXX:2:1114:18781:29384/1 3 151 0 C L1P3_orf2 LINE/L1 1170 1318 1976
1065 6.71 0.00 0.00 E00378:188:HVMVNCCXX:2:1114:18781:29384/1 3 151 (0) C L1P3_orf2#LINE/L1 (1976) 1318 1170 m_b6s551i171
E00378:188:HV 3 TTGGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCT 52
v i vv
C L1P3_orf2#LIN 1318 TTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCT 1269
E00378:188:HV 53 AGTTTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTAT 102
i i
C L1P3_orf2#LIN 1268 AGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTAT 1219
E00378:188:HV 103 TTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCT 151
iv i v
C L1P3_orf2#LIN 1218 TTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCT 1170
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.37
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1242 4.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1114:18781:29384/2 1 151 (0) + L1P3 LINE/L1 2934 3084 (3062) 351
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:1114:18781:29384/2 1 151 0 + L1P3_orf2 LINE/L1 825 975 2319
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:1114:18781:29384/2 1 151 (0) L1P3_orf2#LINE/L1 825 975 (2319) m_b7s551i18
E00378:188:HV 1 AACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTA 50
i i
L1P3_orf2#LIN 825 AACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTA 874
E00378:188:HV 51 AAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAG 100
? v
L1P3_orf2#LIN 875 AAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAG 924
E00378:188:HV 101 TGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTAGA 150
i i
L1P3_orf2#LIN 925 CGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTAGA 974
E00378:188:HV 151 G 151
L1P3_orf2#LIN 975 G 975
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 562 6.9 0.0 0.0 E00378:188:HVMVNCCXX:2:1114:26189:5475/2 80 151 (0) C AluSx SINE/Alu (14) 298 227 352
ANNOTATION EVIDENCE:
562 6.94 0.00 0.00 E00378:188:HVMVNCCXX:2:1114:26189:5475/2 80 151 0 C AluSx SINE/Alu 227 298 14
562 6.94 0.00 0.00 E00378:188:HVMVNCCXX:2:1114:26189:5475/2 80 151 (0) C AluSx#SINE/Alu (14) 298 227 m_b2s357i110
E00378:188:HV 80 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 129
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 130 TGCAGTGGCATGATCTCGGCTC 151
ii
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTC 227
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.60
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:2:1115:17482:71858/1 30 121 (30) C MIRb SINE/MIR (107) 161 67 353
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:2:1115:17482:71858/1 30 121 30 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:2:1115:17482:71858/1 30 121 (30) C MIRb#SINE/MIR (107) 161 67 m_b6s601i61
E00378:188:HV 30 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 77
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 78 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 121
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:2:1115:17523:71858/1 30 121 (30) C MIRb SINE/MIR (107) 161 67 354
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:2:1115:17523:71858/1 30 121 30 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:2:1115:17523:71858/1 30 121 (30) C MIRb#SINE/MIR (107) 161 67 m_b6s601i62
E00378:188:HV 30 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 77
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 78 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 121
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1296 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:1115:26220:53381/1 1 151 (0) + L1P1 LINE/L1 4883 5033 (1113) 355
ANNOTATION EVIDENCE:
1296 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:26220:53381/1 1 151 0 + L1P1_orf2 LINE/L1 2774 2924 370
1296 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:26220:53381/1 1 151 (0) L1P1_orf2#LINE/L1 2774 2924 (370) m_b1s551i10
E00378:188:HV 1 AATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTA 50
L1P1_orf2#LIN 2774 AATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTA 2823
E00378:188:HV 51 GCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTGATAGAAA 100
v v
L1P1_orf2#LIN 2824 GCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAA 2873
E00378:188:HV 101 AATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAA 150
i i
L1P1_orf2#LIN 2874 AATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAA 2923
E00378:188:HV 151 A 151
L1P1_orf2#LIN 2924 A 2924
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1279 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1115:26220:53381/2 1 151 (0) C L1P LINE/L1 (740) 5415 5265 356
ANNOTATION EVIDENCE:
1279 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:26220:53381/2 1 151 0 C L1PA2_3end LINE/L1 12 162 740
1279 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:26220:53381/2 1 151 (0) C L1PA2_3end#LINE/L1 (740) 162 12 m_b1s551i170
E00378:188:HV 1 TCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCAT 50
C L1PA2_3end#LI 162 TCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCAT 113
E00378:188:HV 51 AAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTG 100
C L1PA2_3end#LI 112 AAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTG 63
E00378:188:HV 101 ATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGAT 150
C L1PA2_3end#LI 62 ATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGAT 13
E00378:188:HV 151 T 151
C L1PA2_3end#LI 12 T 12
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1010 10.4 1.5 0.0 E00378:188:HVMVNCCXX:2:1115:27377:21350/1 18 151 (0) + AluSx SINE/Alu 1 136 (176) 357
ANNOTATION EVIDENCE:
1010 10.45 1.47 0.00 E00378:188:HVMVNCCXX:2:1115:27377:21350/1 18 151 0 + AluSx SINE/Alu 1 136 176
1010 10.45 1.47 0.00 E00378:188:HVMVNCCXX:2:1115:27377:21350/1 18 151 (0) AluSx#SINE/Alu 1 136 (176) m_b2s356i47
E00378:188:HV 18 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 67
i ii i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 68 GGCGGGCTGATCA--TGAGGTCAGGAGATCAAGACCATCCTGGCTAACGT 115
v -- v i v i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 116 GGTGAAACCCCATCTCTACTAAAAACACAAAAATTA 151
i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTA 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.75
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 2.00 (2 / 1)
+ 647 6.2 0.0 0.0 E00378:188:HVMVNCCXX:2:1115:27377:21350/2 72 151 (0) C AluSx SINE/Alu (14) 298 219 358
ANNOTATION EVIDENCE:
647 6.25 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:27377:21350/2 72 151 0 C AluSx SINE/Alu 219 298 14
647 6.25 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:27377:21350/2 72 151 (0) C AluSx#SINE/Alu (14) 298 219 m_b2s357i108
E00378:188:HV 72 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 121
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 122 TGCAGTGGCATGATCTCGGCTCACTGCAAC 151
ii
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAAC 219
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.13
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 1249 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1115:3062:49549/1 2 151 (0) C L1P1 LINE/L1 (631) 5524 5375 359
ANNOTATION EVIDENCE:
1249 2.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:3062:49549/1 2 151 0 C L1PA2_3end LINE/L1 122 271 631
1249 2.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:3062:49549/1 2 151 (0) C L1PA2_3end#LINE/L1 (631) 271 122 m_b1s551i231
E00378:188:HV 2 TTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTA 51
C L1PA2_3end#LI 271 TTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTA 222
E00378:188:HV 52 ATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGAT 101
i
C L1PA2_3end#LI 221 ATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGAT 172
E00378:188:HV 102 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATTTTTTTTT 151
v v
C L1PA2_3end#LI 171 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTT 122
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1301 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:1115:3062:49549/2 1 151 (0) + L1P1 LINE/L1 5160 5310 (836) 360
ANNOTATION EVIDENCE:
1301 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:3062:49549/2 1 151 0 + L1P1_orf2 LINE/L1 3051 3201 93
1301 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:1115:3062:49549/2 1 151 (0) L1P1_orf2#LINE/L1 3051 3201 (93) m_b1s551i127
E00378:188:HV 1 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 50
L1P1_orf2#LIN 3051 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 3100
E00378:188:HV 51 CAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 100
i
L1P1_orf2#LIN 3101 CAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 3150
E00378:188:HV 101 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 150
L1P1_orf2#LIN 3151 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 3200
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3201 C 3201
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 712 12.2 0.0 0.0 E00378:188:HVMVNCCXX:2:1116:15402:56053/2 53 150 (1) + AluSx SINE/Alu 1 98 (214) 361
ANNOTATION EVIDENCE:
712 12.24 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:15402:56053/2 53 150 1 + AluSx SINE/Alu 1 98 214
712 12.24 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:15402:56053/2 53 150 (1) AluSx#SINE/Alu 1 98 (214) m_b5s357i56
E00378:188:HV 53 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 102
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 103 GGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAAC 150
i i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAAC 98
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.11
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:2:1116:17350:1309/1 35 127 (24) + MIRb SINE/MIR 122 219 (49) 362
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:2:1116:17350:1309/1 35 127 24 + MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:2:1116:17350:1309/1 35 127 (24) MIRb#SINE/MIR 122 219 (49) m_b4s601i16
E00378:188:HV 35 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 83
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
E00378:188:HV 84 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAAA-GTCTAGC 127
vi i vii --- v iv i i- ii
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1274 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1116:19136:23390/1 1 151 (0) C L1P LINE/L1 (726) 5429 5279 363
ANNOTATION EVIDENCE:
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19136:23390/1 1 151 0 C L1PA2_3end LINE/L1 26 176 726
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19136:23390/1 1 151 (0) C L1PA2_3end#LINE/L1 (726) 176 26 m_b1s551i180
E00378:188:HV 1 TTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTG 50
C L1PA2_3end#LI 176 TTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTG 127
E00378:188:HV 51 TTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 100
C L1PA2_3end#LI 126 TTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 77
E00378:188:HV 101 TCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTG 150
C L1PA2_3end#LI 76 TCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTG 27
E00378:188:HV 151 A 151
C L1PA2_3end#LI 26 A 26
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1286 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1116:19136:23390/2 1 151 (0) + L1P1 LINE/L1 5015 5165 (981) 364
ANNOTATION EVIDENCE:
1286 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19136:23390/2 1 151 0 + L1P1_orf2 LINE/L1 2906 3056 238
1286 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19136:23390/2 1 151 (0) L1P1_orf2#LINE/L1 2906 3056 (238) m_b1s551i70
E00378:188:HV 1 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATT 50
?
L1P1_orf2#LIN 2906 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATT 2955
E00378:188:HV 51 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 100
L1P1_orf2#LIN 2956 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 3005
E00378:188:HV 101 GGCAACAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCT 150
v i
L1P1_orf2#LIN 3006 GGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCT 3055
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3056 T 3056
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1116:19207:23372/1 1 151 (0) C L1P LINE/L1 (726) 5429 5279 365
ANNOTATION EVIDENCE:
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19207:23372/1 1 151 0 C L1PA2_3end LINE/L1 26 176 726
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19207:23372/1 1 151 (0) C L1PA2_3end#LINE/L1 (726) 176 26 m_b1s551i181
E00378:188:HV 1 TTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTG 50
C L1PA2_3end#LI 176 TTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTG 127
E00378:188:HV 51 TTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 100
C L1PA2_3end#LI 126 TTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 77
E00378:188:HV 101 TCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTG 150
C L1PA2_3end#LI 76 TCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTG 27
E00378:188:HV 151 A 151
C L1PA2_3end#LI 26 A 26
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1286 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1116:19207:23372/2 1 151 (0) + L1P1 LINE/L1 5015 5165 (981) 366
ANNOTATION EVIDENCE:
1286 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19207:23372/2 1 151 0 + L1P1_orf2 LINE/L1 2906 3056 238
1286 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:19207:23372/2 1 151 (0) L1P1_orf2#LINE/L1 2906 3056 (238) m_b1s551i71
E00378:188:HV 1 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATT 50
?
L1P1_orf2#LIN 2906 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATT 2955
E00378:188:HV 51 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 100
L1P1_orf2#LIN 2956 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 3005
E00378:188:HV 101 GGCAACAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCT 150
v i
L1P1_orf2#LIN 3006 GGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCT 3055
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3056 T 3056
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1116:3863:62927/2 92 136 (15) C MIR SINE/MIR (0) 262 218 367
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:3863:62927/2 92 136 15 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:2:1116:3863:62927/2 92 136 (15) C MIR#SINE/MIR (0) 262 218 m_b6s601i2
E00378:188:HV 92 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 136
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 285 26.1 5.6 0.7 E00378:188:HVMVNCCXX:2:1117:2148:71348/2 11 145 (6) C L1ME4c LINE/L1 (246) 5837 5696 368
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:2:1117:2148:71348/2 11 145 6 C L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:2:1117:2148:71348/2 11 145 (6) C L1ME4c_3end#LINE/L1 (246) 584 443 m_b2s551i14
E00378:188:HV 11 TCTTGATAGTCATACTTTTTAATGGCTTCACCATTTTTCTGTC--ATAAA 58
v i i vv v iv - v ii --i ?i
C L1ME4c_3end#L 584 TCTTCATAATTATCATTTTTAATGGCTGCATAA-TATTCCATCGAGTNGA 536
E00378:188:HV 59 --TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCT 104
-- i - -iii ii v i v
C L1ME4c_3end#L 535 TGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGT 486
E00378:188:HV 105 TTTCTATTTTC--CTACAATAAACATTATTGCAATGATCATTT 145
i v i-- iv i viii v i
C L1ME4c_3end#L 485 TTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 1263 2.7 0.0 0.7 E00378:188:HVMVNCCXX:2:1120:19197:54471/2 1 150 (1) + L1PA3 LINE/L1 5791 5939 (216) 369
ANNOTATION EVIDENCE:
1263 2.69 0.00 0.67 E00378:188:HVMVNCCXX:2:1120:19197:54471/2 1 150 1 + L1PA3_3end LINE/L1 538 686 216
1263 2.69 0.00 0.67 E00378:188:HVMVNCCXX:2:1120:19197:54471/2 1 150 (1) L1PA3_3end#LINE/L1 538 686 (216) m_b1s551i365
E00378:188:HV 1 ACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT 50
L1PA3_3end#LI 538 ACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT 587
E00378:188:HV 51 TAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAA 100
- i
L1PA3_3end#LI 588 -AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAA 636
E00378:188:HV 101 GAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATGGAAC 150
v i v
L1PA3_3end#LI 637 GAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAAC 686
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.74
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 1302 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:1121:26332:30509/1 1 151 (0) + L1P1 LINE/L1 4877 5027 (1119) 370
ANNOTATION EVIDENCE:
1302 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1121:26332:30509/1 1 151 0 + L1P1_orf2 LINE/L1 2768 2918 376
1302 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1121:26332:30509/1 1 151 (0) L1P1_orf2#LINE/L1 2768 2918 (376) m_b1s551i7
E00378:188:HV 1 ACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAAC 50
L1P1_orf2#LIN 2768 ACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAAC 2817
E00378:188:HV 51 TGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTGA 100
v
L1P1_orf2#LIN 2818 TGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTA 2867
E00378:188:HV 101 TAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAA 150
v i i
L1P1_orf2#LIN 2868 TACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAA 2917
E00378:188:HV 151 C 151
L1P1_orf2#LIN 2918 C 2918
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1292 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:1121:26332:30509/2 1 151 (0) C L1P1 LINE/L1 (791) 5355 5205 371
ANNOTATION EVIDENCE:
1292 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:1121:26332:30509/2 1 151 0 C L1P1_orf2 LINE/L1 3096 3246 48
1292 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:1121:26332:30509/2 1 151 (0) C L1P1_orf2#LINE/L1 (48) 3246 3096 m_b1s551i144
E00378:188:HV 1 TTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGT 50
C L1P1_orf2#LIN 3246 TTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGT 3197
E00378:188:HV 51 TTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATT 100
C L1P1_orf2#LIN 3196 TTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATT 3147
E00378:188:HV 101 AGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGG 150
i
C L1P1_orf2#LIN 3146 AGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGG 3097
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 3096 T 3096
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1288 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1122:21876:71664/1 1 151 (0) C L1P1 LINE/L1 (879) 5267 5117 372
ANNOTATION EVIDENCE:
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:21876:71664/1 1 151 0 C L1P1_orf2 LINE/L1 3008 3158 136
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:21876:71664/1 1 151 (0) C L1P1_orf2#LINE/L1 (136) 3158 3008 m_b1s551i110
E00378:188:HV 1 ATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTC 50
C L1P1_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTC 3109
E00378:188:HV 51 CCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGC 100
i
C L1P1_orf2#LIN 3108 CCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGC 3059
E00378:188:HV 101 AGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTCTGTCTTTTGTT 150
i v
C L1P1_orf2#LIN 3058 AGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTT 3009
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 3008 G 3008
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 3.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1122:21876:71664/2 1 151 (0) + L1P1 LINE/L1 4930 5080 (1066) 373
ANNOTATION EVIDENCE:
1274 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:21876:71664/2 1 151 0 + L1P1_orf2 LINE/L1 2821 2971 323
1274 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:21876:71664/2 1 151 (0) L1P1_orf2#LINE/L1 2821 2971 (323) m_b1s551i29
E00378:188:HV 1 CTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTGATAG 50
v v
L1P1_orf2#LIN 2821 CTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATAC 2870
E00378:188:HV 51 AAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCA 100
i i
L1P1_orf2#LIN 2871 AAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCA 2920
E00378:188:HV 101 TAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATG 150
?
L1P1_orf2#LIN 2921 TAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATG 2970
E00378:188:HV 151 G 151
L1P1_orf2#LIN 2971 G 2971
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 408 15.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1122:22861:43097/1 92 151 (0) + AluSx SINE/Alu 1 60 (252) 374
ANNOTATION EVIDENCE:
408 15.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:22861:43097/1 92 151 0 + AluSx SINE/Alu 1 60 252
408 15.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:22861:43097/1 92 151 (0) AluSx#SINE/Alu 1 60 (252) m_b5s357i71
E00378:188:HV 92 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 141
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 142 GGTGGGCAGA 151
i i
AluSx#SINE/Al 51 GGCGGGCGGA 60
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.66
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 615 15.4 0.0 6.0 E00378:188:HVMVNCCXX:2:1122:22861:43097/2 35 151 (0) C AluSx SINE/Alu (8) 304 195 375
ANNOTATION EVIDENCE:
615 15.45 0.00 5.98 E00378:188:HVMVNCCXX:2:1122:22861:43097/2 35 151 0 C AluSx SINE/Alu 195 304 8
615 15.45 0.00 5.98 E00378:188:HVMVNCCXX:2:1122:22861:43097/2 35 151 (0) C AluSx#SINE/Alu (8) 304 195 m_b5s357i11
E00378:188:HV 35 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 84
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 85 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 134
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 135 TAGTAGGTTCAAGCAAT 151
vvii i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGAT 195
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.26
Transitions / transversions = 1.12 (9/8)
Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7)
+ 1157 11.9 0.0 0.0 E00378:188:HVMVNCCXX:2:1122:26372:65388/1 1 151 (0) + AluSx SINE/Alu 67 217 (95) 376
ANNOTATION EVIDENCE:
1157 11.92 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:26372:65388/1 1 151 0 + AluSx SINE/Alu 67 217 95
1157 11.92 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:26372:65388/1 1 151 (0) AluSx#SINE/Alu 67 217 (95) m_b2s356i26
E00378:188:HV 1 GAGGTCGGGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCTTGTCTC 50
i i ii
AluSx#SINE/Al 67 GAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTC 116
E00378:188:HV 51 TATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCC 100
i v i i i v i
AluSx#SINE/Al 117 TACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCC 166
E00378:188:HV 101 CAGCTACTCAGGAAGCTGAGGCAGGAGGATCACTTGAACTCAGGAGGCAG 150
i i i i i i i
AluSx#SINE/Al 167 CAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGG 216
E00378:188:HV 151 A 151
AluSx#SINE/Al 217 A 217
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.94
Transitions / transversions = 8.00 (16/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:2:1122:26372:65388/2 11 99 (52) C L1M5 LINE/L1 (293) 5831 5741 377
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:1122:26372:65388/2 11 99 52 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:1122:26372:65388/2 11 99 (52) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i506
E00378:188:HV 11 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 60
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 61 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 99
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:26372:65388/2 32 99 52 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:26372:65388/2 32 99 (52) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i507
E00378:188:HV 32 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 81
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 82 CTATTGTTGGACATTTAG 99
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 184 30.4 16.1 0.0 E00378:188:HVMVNCCXX:2:1122:30452:45699/1 36 150 (1) C MIR SINE/MIR (0) 262 126 378
ANNOTATION EVIDENCE:
184 30.43 16.06 0.00 E00378:188:HVMVNCCXX:2:1122:30452:45699/1 36 150 1 C MIR SINE/MIR 126 262 0
184 30.43 16.06 0.00 E00378:188:HVMVNCCXX:2:1122:30452:45699/1 36 150 (1) C MIR#SINE/MIR (0) 262 126 m_b6s601i19
E00378:188:HV 36 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 78
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
E00378:188:HV 79 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 113
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
E00378:188:HV 114 TTAGATTCTATTATTTCCTTCAATTTATAAATGAAAA 150
v i v vi ii v i i ii
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGA 126
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 39.22
Transitions / transversions = 1.92 (23/12)
Gap_init rate = 0.04 (4 / 114), avg. gap size = 5.50 (22 / 4)
+ 298 26.5 3.5 0.0 E00378:188:HVMVNCCXX:2:1122:30452:45699/2 67 149 (2) + MIRb SINE/MIR 67 152 (116) 379
ANNOTATION EVIDENCE:
298 26.51 3.48 0.00 E00378:188:HVMVNCCXX:2:1122:30452:45699/2 67 149 2 + MIRb SINE/MIR 67 152 116
298 26.51 3.48 0.00 E00378:188:HVMVNCCXX:2:1122:30452:45699/2 67 149 (2) MIRb#SINE/MIR 67 152 (116) m_b6s601i74
E00378:188:HV 67 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 115
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 116 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAG 149
v i i v -- i i v ii
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 152
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.79
Transitions / transversions = 1.75 (14/8)
Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.50 (3 / 2)
+ 1197 6.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1122:6593:45294/1 2 151 (0) C L1P3 LINE/L1 (3113) 3033 2884 380
ANNOTATION EVIDENCE:
1197 6.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:6593:45294/1 2 151 0 C L1P3_orf2 LINE/L1 775 924 2370
1197 6.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1122:6593:45294/1 2 151 (0) C L1P3_orf2#LINE/L1 (2370) 924 775 m_b7s551i31
E00378:188:HV 2 CTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTT 51
v ?
C L1P3_orf2#LIN 924 CTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTT 875
E00378:188:HV 52 TAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGTT 101
i i
C L1P3_orf2#LIN 874 TAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTT 825
E00378:188:HV 102 TCAAAGAACTTACTTATTTCTGCCTTCATTTCATTATTTACCTAGTAGTC 151
?i v i i
C L1P3_orf2#LIN 824 TCAAAGAACTTNTTTATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTC 775
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.61
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 247 33.6 6.7 2.8 E00378:188:HVMVNCCXX:2:1123:20019:64369/1 1 144 (7) C MIRb SINE/MIR (84) 184 35 381
ANNOTATION EVIDENCE:
247 33.57 6.66 2.78 E00378:188:HVMVNCCXX:2:1123:20019:64369/1 1 144 7 C MIRb SINE/MIR 35 184 84
247 33.57 6.66 2.78 E00378:188:HVMVNCCXX:2:1123:20019:64369/1 1 144 (7) C MIRb#SINE/MIR (84) 184 35 m_b4s601i31
E00378:188:HV 1 TCACAGTTATCTGGCCAGGTAAGTGATA-TATCTTCACTCTACTGATGAG 49
iiv i iv v i iv - ii i i v
C MIRb#SINE/MIR 184 TCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAG 135
E00378:188:HV 50 GGTACGAAGGCCCTAGATGACATAAGGCAAGTTTTTTACCAGA----AAA 95
iv vi i - - vi v i i v viii -- i---- v
C MIRb#SINE/MIR 134 GAAACTGAGGCTC-AGA-GAGGTTAAGTAACTTGCCCA--AGGTCACACA 89
E00378:188:HV 96 GTTA--AGGCTGTGGTACTGGGATTTGAATTT---TCTGTTTGACTTCAA 140
i -- i iv ii vi i i iii--- i i
C MIRb#SINE/MIR 88 GCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAA 39
E00378:188:HV 141 AGCC 144
C MIRb#SINE/MIR 38 AGCC 35
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 45.03
Transitions / transversions = 2.36 (33/14)
Gap_init rate = 0.06 (8 / 143), avg. gap size = 1.75 (14 / 8)
+ 797 5.2 0.0 0.0 E00378:188:HVMVNCCXX:2:1123:20019:64369/2 1 96 (55) + AluSx SINE/Alu 196 291 (21) 382
ANNOTATION EVIDENCE:
797 5.21 0.00 0.00 E00378:188:HVMVNCCXX:2:1123:20019:64369/2 1 96 55 + AluSx SINE/Alu 196 291 21
797 5.21 0.00 0.00 E00378:188:HVMVNCCXX:2:1123:20019:64369/2 1 96 (55) AluSx#SINE/Alu 196 291 (21) m_b4s357i21
E00378:188:HV 1 TCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACT 50
i i
AluSx#SINE/Al 196 TCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT 245
E00378:188:HV 51 GCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 96
i i i
AluSx#SINE/Al 246 GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.45
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 13 16.8 0.0 0.0 E00378:188:HVMVNCCXX:2:1123:20019:64369/2 124 151 (0) + (CACA)n Simple_repeat 1 28 (0) 383
ANNOTATION EVIDENCE:
13 16.82 0.00 0.00 E00378:188:HVMVNCCXX:2:1123:20019:64369/2 124 151 0 + (CACA)n Simple_repeat 1 28 0
13 16.82 0.00 0.00 E00378:188:HVMVNCCXX:2:1123:20019:64369/2 124 151 (0) (CACA)n#Simple_repeat 1 28 (0) m_b4s252i71
E00378:188:HV 124 CATACATGCACACACATACACACACACA 151
i ii i
(CACA)n#Simpl 1 CACACACACACACACACACACACACACA 28
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 1203 8.0 0.7 0.0 E00378:188:HVMVNCCXX:2:1123:21917:63296/2 1 151 (0) C AluY SINE/Alu (113) 198 47 384
ANNOTATION EVIDENCE:
1203 7.95 0.66 0.00 E00378:188:HVMVNCCXX:2:1123:21917:63296/2 1 151 0 C AluY SINE/Alu 47 198 113
1203 7.95 0.66 0.00 E00378:188:HVMVNCCXX:2:1123:21917:63296/2 1 151 (0) C AluY#SINE/Alu (113) 198 47 c_b2s352i4
E00378:188:HV 1 GCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGC 50
i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGC 149
E00378:188:HV 51 CACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACC 99
iv - i i
C AluY#SINE/Alu 148 CACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 99
E00378:188:HV 100 ACGTTAGCCAGGATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCCTT 149
ii i i v i
C AluY#SINE/Alu 98 GTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTC 49
E00378:188:HV 150 GG 151
C AluY#SINE/Alu 48 GG 47
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.52
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 285 26.1 5.6 0.7 E00378:188:HVMVNCCXX:2:1123:23531:1784/1 3 137 (14) C L1ME4c LINE/L1 (246) 5837 5696 385
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:2:1123:23531:1784/1 3 137 14 C L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 E00378:188:HVMVNCCXX:2:1123:23531:1784/1 3 137 (14) C L1ME4c_3end#LINE/L1 (246) 584 443 m_b2s551i16
E00378:188:HV 3 TCTTGATAGTCATACTTTTTAATGGCTTCACCATTTTTCTGTC--ATAAA 50
v i i vv v iv - v ii --i ?i
C L1ME4c_3end#L 584 TCTTCATAATTATCATTTTTAATGGCTGCATAA-TATTCCATCGAGTNGA 536
E00378:188:HV 51 --TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCT 96
-- i - -iii ii v i v
C L1ME4c_3end#L 535 TGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGT 486
E00378:188:HV 97 TTTCTATTTTC--CTACAATAAACATTATTGCAATGATCATTT 137
i v i-- iv i viii v i
C L1ME4c_3end#L 485 TTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 1008 14.0 0.0 0.7 E00378:188:HVMVNCCXX:2:1123:31497:32144/1 1 151 (0) + AluSx SINE/Alu 136 285 (27) 386
ANNOTATION EVIDENCE:
1008 14.00 0.00 0.66 E00378:188:HVMVNCCXX:2:1123:31497:32144/1 1 151 0 + AluSx SINE/Alu 136 285 27
1008 14.00 0.00 0.66 E00378:188:HVMVNCCXX:2:1123:31497:32144/1 1 151 (0) AluSx#SINE/Alu 136 285 (27) m_b6s356i6
E00378:188:HV 1 AGCTGGGCATGGTGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGGATGA 50
i i iv i v
AluSx#SINE/Al 136 AGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA 185
E00378:188:HV 51 GGCAGGAGAACTGCTTGAACCGAGGAGGTAGAGGCTGAAGTGAACCGAGA 100
ii vi ii i v i
AluSx#SINE/Al 186 GGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGA 235
E00378:188:HV 101 TCACACCATTGCACTCCAGCCTGGGAGACATGAGCGAAACTCCATCTCAA 150
i i i v - i i
AluSx#SINE/Al 236 TCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAA 284
E00378:188:HV 151 A 151
AluSx#SINE/Al 285 A 285
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.42
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 205 26.8 1.8 0.0 E00378:188:HVMVNCCXX:2:1123:31497:32144/2 1 56 (95) C MIRb SINE/MIR (145) 123 67 387
ANNOTATION EVIDENCE:
205 26.79 1.76 0.00 E00378:188:HVMVNCCXX:2:1123:31497:32144/2 1 56 95 C MIRb SINE/MIR 67 123 145
205 26.79 1.76 0.00 E00378:188:HVMVNCCXX:2:1123:31497:32144/2 1 56 (95) C MIRb#SINE/MIR (145) 123 67 m_b6s601i80
E00378:188:HV 1 TTAGTGAGGTAAAGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTG 49
i v v ii -v i v ii iv
C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74
E00378:188:HV 50 ACTCGAG 56
vi i
C MIRb#SINE/MIR 73 AGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.01
Transitions / transversions = 1.50 (9/6)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1)
+ 485 5.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1124:20740:28136/1 1 60 (91) + AluSx SINE/Alu 232 291 (21) 388
ANNOTATION EVIDENCE:
485 5.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1124:20740:28136/1 1 60 91 + AluSx SINE/Alu 232 291 21
485 5.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1124:20740:28136/1 1 60 (91) AluSx#SINE/Alu 232 291 (21) m_b4s357i5
E00378:188:HV 1 GAGATCGCGCCACTGCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCT 50
i i i
AluSx#SINE/Al 232 GAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT 281
E00378:188:HV 51 CAAAAAAAAA 60
AluSx#SINE/Al 282 CAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1124:20740:28136/1 88 119 (32) + (CA)n Simple_repeat 1 32 (0) 389
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1124:20740:28136/1 88 119 32 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1124:20740:28136/1 88 119 (32) (CA)n#Simple_repeat 1 32 (0) m_b4s252i70
E00378:188:HV 88 CATACATGCACACACATACACACACACACACA 119
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 19 4.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1124:20740:28136/2 122 145 (6) + (TG)n Simple_repeat 1 24 (0) 390
ANNOTATION EVIDENCE:
19 4.35 0.00 0.00 E00378:188:HVMVNCCXX:2:1124:20740:28136/2 122 145 6 + (TG)n Simple_repeat 1 24 0
19 4.35 0.00 0.00 E00378:188:HVMVNCCXX:2:1124:20740:28136/2 122 145 (6) (TG)n#Simple_repeat 1 24 (0) m_b4s252i69
E00378:188:HV 122 TGTGTGTGTGTGTGTATGTGTGTG 145
i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 1345 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1201:15747:68676/1 1 151 (0) C L1P1 LINE/L1 (572) 5583 5433 391
ANNOTATION EVIDENCE:
1345 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:15747:68676/1 1 151 0 C L1PA3_3end LINE/L1 180 330 572
1345 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:15747:68676/1 1 151 (0) C L1PA3_3end#LINE/L1 (572) 330 180 m_b1s551i255
E00378:188:HV 1 CCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGT 50
C L1PA3_3end#LI 330 CCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGT 281
E00378:188:HV 51 GTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCT 100
vi
C L1PA3_3end#LI 280 GTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCT 231
E00378:188:HV 101 GACTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGT 150
i
C L1PA3_3end#LI 230 GACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGT 181
E00378:188:HV 151 G 151
C L1PA3_3end#LI 180 G 180
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1237 1.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1201:15747:68676/2 1 151 (0) + L1P LINE/L1 5259 5409 (746) 392
ANNOTATION EVIDENCE:
1237 1.32 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:15747:68676/2 1 151 0 + L1PA2_3end LINE/L1 6 156 746
1237 1.32 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:15747:68676/2 1 151 (0) L1PA2_3end#LINE/L1 6 156 (746) m_b1s551i166
E00378:188:HV 1 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 50
L1PA2_3end#LI 6 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 55
E00378:188:HV 51 ACCCCATCAAAAAGTGGGCGAATGACATGAACAGACACTTCTCAAAAGAA 100
v
L1PA2_3end#LI 56 ACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAA 105
E00378:188:HV 101 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACCGGC 150
i
L1PA2_3end#LI 106 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGC 155
E00378:188:HV 151 C 151
L1PA2_3end#LI 156 C 156
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1345 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1201:16325:68658/1 1 151 (0) C L1P1 LINE/L1 (572) 5583 5433 393
ANNOTATION EVIDENCE:
1345 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:16325:68658/1 1 151 0 C L1PA3_3end LINE/L1 180 330 572
1345 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:16325:68658/1 1 151 (0) C L1PA3_3end#LINE/L1 (572) 330 180 m_b1s551i256
E00378:188:HV 1 CCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGT 50
C L1PA3_3end#LI 330 CCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGT 281
E00378:188:HV 51 GTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCT 100
vi
C L1PA3_3end#LI 280 GTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCT 231
E00378:188:HV 101 GACTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGT 150
i
C L1PA3_3end#LI 230 GACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGT 181
E00378:188:HV 151 G 151
C L1PA3_3end#LI 180 G 180
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1284 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1201:16325:68658/2 1 151 (0) + L1P LINE/L1 5259 5409 (746) 394
ANNOTATION EVIDENCE:
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:16325:68658/2 1 151 0 + L1PA2_3end LINE/L1 6 156 746
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1201:16325:68658/2 1 151 (0) L1PA2_3end#LINE/L1 6 156 (746) m_b1s551i167
E00378:188:HV 1 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 50
L1PA2_3end#LI 6 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 55
E00378:188:HV 51 ACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAA 100
L1PA2_3end#LI 56 ACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAA 105
E00378:188:HV 101 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGC 150
L1PA2_3end#LI 106 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGC 155
E00378:188:HV 151 C 151
L1PA2_3end#LI 156 C 156
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1156 8.1 0.7 0.7 E00378:188:HVMVNCCXX:2:1201:23581:44872/1 2 151 (0) C AluY SINE/Alu (94) 217 68 395
ANNOTATION EVIDENCE:
1156 8.05 0.67 0.67 E00378:188:HVMVNCCXX:2:1201:23581:44872/1 2 151 0 C AluY SINE/Alu 68 217 94
1156 8.05 0.67 0.67 E00378:188:HVMVNCCXX:2:1201:23581:44872/1 2 151 (0) C AluY#SINE/Alu (94) 217 68 m_b2s356i63
E00378:188:HV 2 CTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCCTCCCGAGTAG 51
i - i i i i
C AluY#SINE/Alu 217 CTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAG 169
E00378:188:HV 52 CTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTTT 100
iv - i
C AluY#SINE/Alu 168 CTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTT 119
E00378:188:HV 101 AGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGATCTCCTGA 150
i ii i
C AluY#SINE/Alu 118 AGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGA 69
E00378:188:HV 151 C 151
C AluY#SINE/Alu 68 C 68
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.96
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 1182 9.3 0.7 0.0 E00378:188:HVMVNCCXX:2:1201:23581:44872/2 2 151 (0) + AluY SINE/Alu 6 156 (155) 396
ANNOTATION EVIDENCE:
1182 9.33 0.67 0.00 E00378:188:HVMVNCCXX:2:1201:23581:44872/2 2 151 0 + AluY SINE/Alu 6 156 155
1182 9.33 0.67 0.00 E00378:188:HVMVNCCXX:2:1201:23581:44872/2 2 151 (0) AluY#SINE/Alu 6 156 (155) m_b2s356i51
E00378:188:HV 2 GGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAAGGCGG 51
ii i i i
AluY#SINE/Alu 6 GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGG 55
E00378:188:HV 52 GCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGGTGAAA 101
v i i ii
AluY#SINE/Alu 56 GCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAA 105
E00378:188:HV 102 CCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCG 150
i i - vi
AluY#SINE/Alu 106 CCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCG 155
E00378:188:HV 151 C 151
AluY#SINE/Alu 156 C 156
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.70
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 242 20.3 0.0 9.9 E00378:188:HVMVNCCXX:2:1201:27103:43870/1 76 146 (5) C 7SLRNA srpRNA (0) 320 257 397
ANNOTATION EVIDENCE:
242 20.31 0.00 9.86 E00378:188:HVMVNCCXX:2:1201:27103:43870/1 76 146 5 C 7SLRNA SINE/Alu 257 320 0
242 20.31 0.00 9.86 E00378:188:HVMVNCCXX:2:1201:27103:43870/1 76 146 (5) C 7SLRNA#SINE/Alu (0) 320 257 m_b5s502i2
E00378:188:HV 76 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 125
v v v vv i i i vii ii ----
C 7SLRNA#SINE/A 320 TTTTTTTTTTTTTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCC---- 275
E00378:188:HV 126 CTGCAGGCTGGAGTGCAGTGG 146
---
C 7SLRNA#SINE/A 274 ---CAGGCTGGAGTGCAGTGG 257
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.99
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.00 (7 / 7)
+ 1057 10.8 0.0 1.4 E00378:188:HVMVNCCXX:2:1201:27103:43870/2 11 151 (0) + AluSx SINE/Alu 1 139 (173) 398
ANNOTATION EVIDENCE:
1057 10.79 0.00 1.42 E00378:188:HVMVNCCXX:2:1201:27103:43870/2 11 151 0 + AluSx SINE/Alu 1 139 173
1057 10.79 0.00 1.42 E00378:188:HVMVNCCXX:2:1201:27103:43870/2 11 151 (0) AluSx#SINE/Alu 1 139 (173) m_b5s356i29
E00378:188:HV 11 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 60
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 61 GGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACGT 110
i i i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 111 GTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCC 151
v i --
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCC 139
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.00 (2 / 2)
+ 1177 6.2 0.0 0.0 E00378:188:HVMVNCCXX:2:1202:10155:59270/1 1 146 (5) + AluSx SINE/Alu 146 291 (21) 399
ANNOTATION EVIDENCE:
1177 6.16 0.00 0.00 E00378:188:HVMVNCCXX:2:1202:10155:59270/1 1 146 5 + AluSx SINE/Alu 146 291 21
1177 6.16 0.00 0.00 E00378:188:HVMVNCCXX:2:1202:10155:59270/1 1 146 (5) AluSx#SINE/Alu 146 291 (21) m_b4s357i32
E00378:188:HV 1 GGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAA 50
iv i i
AluSx#SINE/Al 146 GGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAA 195
E00378:188:HV 51 TCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACT 100
i i
AluSx#SINE/Al 196 TCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT 245
E00378:188:HV 101 GCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 146
i i i
AluSx#SINE/Al 246 GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.82
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:2:1202:10155:59270/2 40 132 (19) C MIRb SINE/MIR (49) 219 122 400
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:2:1202:10155:59270/2 40 132 19 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:2:1202:10155:59270/2 40 132 (19) C MIRb#SINE/MIR (49) 219 122 m_b4s601i12
E00378:188:HV 40 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 85
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 86 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 132
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1123 7.7 0.0 0.7 E00378:188:HVMVNCCXX:2:1202:14143:26308/2 9 151 (0) C AluY SINE/Alu (14) 297 156 401
ANNOTATION EVIDENCE:
1123 7.74 0.00 0.70 E00378:188:HVMVNCCXX:2:1202:14143:26308/2 9 151 0 C AluY SINE/Alu 156 297 14
1123 7.74 0.00 0.70 E00378:188:HVMVNCCXX:2:1202:14143:26308/2 9 151 (0) C AluY#SINE/Alu (14) 297 156 m_b2s356i93
E00378:188:HV 9 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 58
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
E00378:188:HV 59 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 108
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
E00378:188:HV 109 GCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGG 151
i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 156
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.75
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 142), avg. gap size = 1.00 (1 / 1)
+ 1121 11.3 1.3 0.0 E00378:188:HVMVNCCXX:2:1202:19867:27855/1 1 151 (0) + AluSx SINE/Alu 37 189 (123) 402
ANNOTATION EVIDENCE:
1121 11.26 1.30 0.00 E00378:188:HVMVNCCXX:2:1202:19867:27855/1 1 151 0 + AluSx SINE/Alu 37 189 123
1121 11.26 1.30 0.00 E00378:188:HVMVNCCXX:2:1202:19867:27855/1 1 151 (0) AluSx#SINE/Alu 37 189 (123) m_b4s356i35
E00378:188:HV 1 CTTTGGGAGGCTGAAGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAAC 48
i i i i --i i v
AluSx#SINE/Al 37 CTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACC 86
E00378:188:HV 49 AGCCTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAAAATTA 98
i i i i
AluSx#SINE/Al 87 AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTA 136
E00378:188:HV 99 GCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAG 148
i v iv i i
AluSx#SINE/Al 137 GCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAG 186
E00378:188:HV 149 GCA 151
AluSx#SINE/Al 187 GCA 189
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.84
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 7 38 (113) + (TG)n Simple_repeat 1 32 (0) 403
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 7 38 113 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 7 38 (113) (TG)n#Simple_repeat 1 32 (0) m_b4s252i68
E00378:188:HV 7 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 38
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 39 51 (100) + (TGTATG)n Simple_repeat 1 41 (0) 404
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 7 51 100 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 7 51 (100) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i67
E00378:188:HV 7 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 51
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 696 5.8 0.0 0.0 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 66 151 (0) C AluSx SINE/Alu (21) 291 206 405
ANNOTATION EVIDENCE:
696 5.81 0.00 0.00 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 66 151 0 C AluSx SINE/Alu 206 291 21
696 5.81 0.00 0.00 E00378:188:HVMVNCCXX:2:1202:19867:27855/2 66 151 (0) C AluSx#SINE/Alu (21) 291 206 m_b4s357i18
E00378:188:HV 66 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 115
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 116 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAG 151
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGG 206
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.87
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)
+ 580 18.1 15.3 0.0 E00378:188:HVMVNCCXX:2:1203:14022:69344/1 7 144 (7) C L1MC4 LINE/L1 (393) 7649 7487 406
ANNOTATION EVIDENCE:
580 18.12 15.34 0.00 E00378:188:HVMVNCCXX:2:1203:14022:69344/1 7 144 7 C L1MC4_3end LINE/L1 2234 2396 393
580 18.12 15.34 0.00 E00378:188:HVMVNCCXX:2:1203:14022:69344/1 7 144 (7) C L1MC4_3end#LINE/L1 (393) 2396 2234 m_b3s551i99
E00378:188:HV 7 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 56
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 57 ------GCTTTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 100
------ ii i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
E00378:188:HV 101 G-------------------GTCCCTTGCTCTGAGTTTGTCTGATGTTTC 131
------------------- iiv i i
C L1MC4_3end#LI 2296 GGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTTC 2247
E00378:188:HV 132 CTTATGATTAAAT 144
i i
C L1MC4_3end#LI 2246 CTCATGATTAGAT 2234
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.29
Transitions / transversions = 1.40 (14/10)
Gap_init rate = 0.01 (2 / 137), avg. gap size = 12.50 (25 / 2)
+ 747 9.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1203:21927:64298/1 2 97 (54) C AluY SINE/Alu (215) 96 1 407
ANNOTATION EVIDENCE:
747 9.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1203:21927:64298/1 2 97 54 C AluY SINE/Alu 1 96 215
747 9.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1203:21927:64298/1 2 97 (54) C AluY#SINE/Alu (215) 96 1 m_b2s357i70
E00378:188:HV 2 GTTAGCCAGGATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCCTTGG 51
i i v i
C AluY#SINE/Alu 96 GTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGG 47
E00378:188:HV 52 CCTCCCAAAGTGCTGAGATTACAAGCGTGAGCCACCATGCCTGGCC 97
i i ii i
C AluY#SINE/Alu 46 CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.86
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 1218 6.7 0.0 0.7 E00378:188:HVMVNCCXX:2:1204:18020:23706/1 1 151 (0) + AluY SINE/Alu 143 292 (19) 408
ANNOTATION EVIDENCE:
1218 6.66 0.00 0.66 E00378:188:HVMVNCCXX:2:1204:18020:23706/1 1 151 0 + AluY SINE/Alu 143 292 19
1218 6.66 0.00 0.66 E00378:188:HVMVNCCXX:2:1204:18020:23706/1 1 151 (0) AluY#SINE/Alu 143 292 (19) m_b2s356i88
E00378:188:HV 1 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAG 50
i
AluY#SINE/Alu 143 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAG 192
E00378:188:HV 51 AACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCC 100
i i i - i v ii
AluY#SINE/Alu 193 AATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCC 241
E00378:188:HV 101 ACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAGAA 150
i i
AluY#SINE/Alu 242 ACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA 291
E00378:188:HV 151 A 151
AluY#SINE/Alu 292 A 292
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.79
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 411 3.8 0.0 0.0 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 1 53 (98) + L1PA2 LINE/L1 6101 6153 (2) 409
ANNOTATION EVIDENCE:
411 3.77 0.00 0.00 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 1 53 98 + L1PA2_3end LINE/L1 848 900 2
411 3.77 0.00 0.00 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 1 53 (98) L1PA2_3end#LINE/L1 848 900 (2) m_b1s551i469
E00378:188:HV 1 CCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAA 50
i
L1PA2_3end#LI 848 CCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAA 897
E00378:188:HV 51 TAA 53
v
L1PA2_3end#LI 898 AAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.88
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 47 135 (16) C L1M5 LINE/L1 (293) 5831 5741 410 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 47 135 16 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 47 135 (16) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i470
E00378:188:HV 47 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 96
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 97 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 135
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 68 135 16 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:1205:15108:5054/1 68 135 (16) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i471
E00378:188:HV 68 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 117
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 118 CTATTGTTGGACATTTAG 135
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1131 11.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1205:15108:5054/2 1 149 (2) + AluSx SINE/Alu 112 260 (52) 411
ANNOTATION EVIDENCE:
1131 11.41 0.00 0.00 E00378:188:HVMVNCCXX:2:1205:15108:5054/2 1 149 2 + AluSx SINE/Alu 112 260 52
1131 11.41 0.00 0.00 E00378:188:HVMVNCCXX:2:1205:15108:5054/2 1 149 (2) AluSx#SINE/Alu 112 260 (52) m_b2s357i25
E00378:188:HV 1 GTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGT 50
i v i i i v i
AluSx#SINE/Al 112 GTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGT 161
E00378:188:HV 51 AATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGA 100
i i i i i
AluSx#SINE/Al 162 AATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGA 211
E00378:188:HV 101 GGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGG 149
i i i ii
AluSx#SINE/Al 212 GGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.95
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1209:14397:45523/1 81 112 (39) + (TG)n Simple_repeat 1 32 (0) 412
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1209:14397:45523/1 81 112 39 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1209:14397:45523/1 81 112 (39) (TG)n#Simple_repeat 1 32 (0) m_b4s252i66
E00378:188:HV 81 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 112
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:2:1209:14397:45523/1 113 125 (26) + (TGTATG)n Simple_repeat 1 41 (0) 413
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:2:1209:14397:45523/1 81 125 26 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:2:1209:14397:45523/1 81 125 (26) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i65
E00378:188:HV 81 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 125
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 1134 10.7 1.3 0.0 E00378:188:HVMVNCCXX:2:1209:14397:45523/2 2 151 (0) + AluSx SINE/Alu 22 173 (139) 414
ANNOTATION EVIDENCE:
1134 10.67 1.31 0.00 E00378:188:HVMVNCCXX:2:1209:14397:45523/2 2 151 0 + AluSx SINE/Alu 22 173 139
1134 10.67 1.31 0.00 E00378:188:HVMVNCCXX:2:1209:14397:45523/2 2 151 (0) AluSx#SINE/Alu 22 173 (139) m_b4s356i38
E00378:188:HV 2 CCTGTAATCCCAGCACTTTGGGAGGCTGAAGCAGGCAGATCAC--AAGGT 49
i i i i --i
AluSx#SINE/Al 22 CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGT 71
E00378:188:HV 50 CAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCTACTA 99
i v i i i
AluSx#SINE/Al 72 CAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTA 121
E00378:188:HV 100 AAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCT 149
i i v iv i
AluSx#SINE/Al 122 AAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCT 171
E00378:188:HV 150 AC 151
AluSx#SINE/Al 172 AC 173
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.81
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 904 15.4 0.0 1.3 E00378:188:HVMVNCCXX:2:1209:16407:1924/1 1 151 (0) C AluSx SINE/Alu (64) 248 100 415
ANNOTATION EVIDENCE:
904 15.43 0.00 1.32 E00378:188:HVMVNCCXX:2:1209:16407:1924/1 1 151 0 C AluSx SINE/Alu 100 248 64
904 15.43 0.00 1.32 E00378:188:HVMVNCCXX:2:1209:16407:1924/1 1 151 (0) C AluSx#SINE/Alu (64) 248 100 m_b5s356i7
E00378:188:HV 1 TGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCCTAGTAGGTTCAAG 50
i v v v vvii
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAG 199
E00378:188:HV 51 CAATTGTCCTGCCTCAGCCTCCGGAGCAGCTATGATTACAGGCTCCCACC 100
i v v i iv v v i
C AluSx#SINE/Al 198 CGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCC 149
E00378:188:HV 101 ACAATGCCTGGCTAAGTTTTTTGTATTTTGAGTAGAGATGGGGTTTCAAC 150
v i i -- v i v
C AluSx#SINE/Al 148 ACCACGCCCGGCTAA--TTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 101
E00378:188:HV 151 A 151
C AluSx#SINE/Al 100 A 100
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 12.08
Transitions / transversions = 0.77 (10/13)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1161 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1210:16711:15109/1 1 151 (0) + L1P3 LINE/L1 3344 3496 (2650) 416
ANNOTATION EVIDENCE:
1161 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1210:16711:15109/1 1 151 0 + L1P3_orf2 LINE/L1 1235 1387 1907
1161 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1210:16711:15109/1 1 151 (0) L1P3_orf2#LINE/L1 1235 1387 (1907) m_b6s551i148
E00378:188:HV 1 GAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAAGAA 50
i i
L1P3_orf2#LIN 1235 GAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAA 1284
E00378:188:HV 51 AGTGATAAATTCCTAGACACATACAACCTCCCAA--CTAAAGCAGGAAGA 98
vv i v -- v
L1P3_orf2#LIN 1285 ATGGATAAATTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGA 1334
E00378:188:HV 99 AGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAA 148
L1P3_orf2#LIN 1335 AGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAA 1384
E00378:188:HV 149 TTA 151
L1P3_orf2#LIN 1385 TTA 1387
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1212 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1210:16711:15109/2 1 151 (0) C L1P3 LINE/L1 (2416) 3730 3578 417
ANNOTATION EVIDENCE:
1212 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1210:16711:15109/2 1 151 0 C L1P3_orf2 LINE/L1 1469 1621 1673
1212 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:1210:16711:15109/2 1 151 (0) C L1P3_orf2#LINE/L1 (1673) 1621 1469 m_b6s551i81
E00378:188:HV 1 TCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCTTTTTC--TT 48
i v v i--
C L1P3_orf2#LIN 1621 TCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCTTTTTTTGTT 1572
E00378:188:HV 49 GTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATCATAAAATGA 98
v v
C L1P3_orf2#LIN 1571 GTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGA 1522
E00378:188:HV 99 GTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGA 148
i
C L1P3_orf2#LIN 1521 GTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGA 1472
E00378:188:HV 149 ATG 151
C L1P3_orf2#LIN 1471 ATG 1469
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:2:1210:27082:31459/1 26 118 (33) + MIRb SINE/MIR 122 219 (49) 418
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:2:1210:27082:31459/1 26 118 33 + MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:2:1210:27082:31459/1 26 118 (33) MIRb#SINE/MIR 122 219 (49) m_b4s601i14
E00378:188:HV 26 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 74
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
E00378:188:HV 75 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAAA-GTCTAGC 118
vi i vii --- v iv i i- ii
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1329 0.7 0.0 0.7 E00378:188:HVMVNCCXX:2:1211:20029:71805/1 1 151 (0) C L1PA3 LINE/L1 (276) 5879 5730 419
ANNOTATION EVIDENCE:
1329 0.66 0.00 0.66 E00378:188:HVMVNCCXX:2:1211:20029:71805/1 1 151 0 C L1PA3_3end LINE/L1 477 626 276
1329 0.66 0.00 0.66 E00378:188:HVMVNCCXX:2:1211:20029:71805/1 1 151 (0) C L1PA3_3end#LINE/L1 (276) 626 477 m_b1s551i350
E00378:188:HV 1 TTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCTAACAAAGGACA 50
-
C L1PA3_3end#LI 626 TTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGACA 578
E00378:188:HV 51 TGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC 100
C L1PA3_3end#LI 577 TGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC 528
E00378:188:HV 101 CACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCA 150
v
C L1PA3_3end#LI 527 CACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCA 478
E00378:188:HV 151 A 151
C L1PA3_3end#LI 477 A 477
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1330 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:1211:20029:71805/2 1 151 (0) + L1P1 LINE/L1 5438 5588 (567) 420
ANNOTATION EVIDENCE:
1330 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1211:20029:71805/2 1 151 0 + L1PA3_3end LINE/L1 185 335 567
1330 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1211:20029:71805/2 1 151 (0) L1PA3_3end#LINE/L1 185 335 (567) m_b1s551i258
E00378:188:HV 1 TGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGA 50
i
L1PA3_3end#LI 185 TGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGA 234
E00378:188:HV 51 AACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTG 100
iv
L1PA3_3end#LI 235 AACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTG 284
E00378:188:HV 101 TTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGAT 150
i
L1PA3_3end#LI 285 TTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGAT 334
E00378:188:HV 151 T 151
L1PA3_3end#LI 335 T 335
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 500 22.4 7.2 0.8 E00378:188:HVMVNCCXX:2:1212:12246:53926/2 2 118 (33) + L1MC4 LINE/L1 7786 7910 (132) 421
ANNOTATION EVIDENCE:
500 22.41 7.20 0.85 E00378:188:HVMVNCCXX:2:1212:12246:53926/2 2 118 33 + L1MC4_3end LINE/L1 2533 2657 132
500 22.41 7.20 0.85 E00378:188:HVMVNCCXX:2:1212:12246:53926/2 2 118 (33) L1MC4_3end#LINE/L1 2533 2657 (132) m_b3s551i16
E00378:188:HV 2 ATTATACTGTGGCTAAACAGAAGTGTATCCTTGTTTTTAGGAAATATACA 51
i i vii ii vi i i i
L1MC4_3end#LI 2533 ATTGTACTGTGGTTATGTAAGAGAATGTCCTTGTTCTTAGGAAATACACA 2582
E00378:188:HV 52 CTGAAGTAT---------AAGGAACATCACGTGTGCGATTTCATCTCAAA 92
--------- ii ? i v i i vv
L1MC4_3end#LI 2583 CTGAAGTATTTAGGGGTAAAGGGGCATNATGTCTGCAACTTACTCTCAAA 2632
E00378:188:HV 93 ATGGTTCAGAGAAAATGATGTGTGTA 118
- i vi i i
L1MC4_3end#LI 2633 -TGGTTCAGAAAAAAAAATATGTATA 2657
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.87
Transitions / transversions = 3.17 (19/6)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 5.00 (10 / 2)
+ 1250 8.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1212:17807:62364/1 1 151 (0) + AluSx SINE/Alu 90 240 (72) 422
ANNOTATION EVIDENCE:
1250 7.95 0.00 0.00 E00378:188:HVMVNCCXX:2:1212:17807:62364/1 1 151 0 + AluSx SINE/Alu 90 240 72
1250 7.95 0.00 0.00 E00378:188:HVMVNCCXX:2:1212:17807:62364/1 1 151 (0) AluSx#SINE/Alu 90 240 (72) m_b4s356i21
E00378:188:HV 1 CTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCC 50
i i i i
AluSx#SINE/Al 90 CTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCC 139
E00378:188:HV 51 AGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCA 100
i v iv i i
AluSx#SINE/Al 140 GGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCA 189
E00378:188:HV 101 GGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGC 150
i i
AluSx#SINE/Al 190 GGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGC 239
E00378:188:HV 151 G 151
AluSx#SINE/Al 240 G 240
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 548 19.7 18.9 0.0 E00378:188:HVMVNCCXX:2:1214:14072:35397/1 10 151 (0) + L1MC4 LINE/L1 7447 7621 (421) 423
ANNOTATION EVIDENCE:
548 19.72 18.86 0.00 E00378:188:HVMVNCCXX:2:1214:14072:35397/1 10 151 0 + L1MC4_3end LINE/L1 2194 2368 421
548 19.72 18.86 0.00 E00378:188:HVMVNCCXX:2:1214:14072:35397/1 10 151 (0) L1MC4_3end#LINE/L1 2194 2368 (421) m_b3s551i108
E00378:188:HV 10 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 51
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
E00378:188:HV 52 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC----------------- 84
i i i vii -----------------
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGACATTCTACAAAATAACTG 2293
E00378:188:HV 85 --CTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA------ 126
-- v v i v ? v i i i ------
L1MC4_3end#LI 2294 GCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTGA 2343
E00378:188:HV 127 AGAACTGTTCCAGATTGAAGGAGAC 151
i i
L1MC4_3end#LI 2344 GGAACTGTTCCAGATTAAAGGAGAC 2368
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.19
Transitions / transversions = 4.40 (22/5)
Gap_init rate = 0.03 (4 / 141), avg. gap size = 8.25 (33 / 4)
+ 551 17.8 8.2 0.0 E00378:188:HVMVNCCXX:2:1214:14072:35397/2 1 101 (50) C L1MC4 LINE/L1 (171) 7871 7762 424
ANNOTATION EVIDENCE:
551 17.82 8.18 0.00 E00378:188:HVMVNCCXX:2:1214:14072:35397/2 1 101 50 C L1MC4_3end LINE/L1 2509 2618 171
551 17.82 8.18 0.00 E00378:188:HVMVNCCXX:2:1214:14072:35397/2 1 101 (50) C L1MC4_3end#LINE/L1 (171) 2618 2509 m_b3s551i36
E00378:188:HV 1 GCACACGTGATGCTCCTT---------ATACTTCAGTGTATATTTCCTAA 41
v i ? i --------- i
C L1MC4_3end#LI 2618 GCAGACATNATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAA 2569
E00378:188:HV 42 AAACAAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAAATCAGGA 91
i i iv ii iiv i i i
C L1MC4_3end#LI 2568 GAACAAGGACATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGA 2519
E00378:188:HV 92 AGTTAACATT 101
i
C L1MC4_3end#LI 2518 AATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.10
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 9.00 (9 / 1)
+ 258 15.2 0.0 0.0 E00378:188:HVMVNCCXX:2:1214:14072:35397/2 106 151 (0) C L1MC4 LINE/L1 (393) 7649 7604 424
ANNOTATION EVIDENCE:
258 15.22 0.00 0.00 E00378:188:HVMVNCCXX:2:1214:14072:35397/2 106 151 0 C L1MC4_3end LINE/L1 2351 2396 393
258 15.22 0.00 0.00 E00378:188:HVMVNCCXX:2:1214:14072:35397/2 106 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2351 m_b3s551i37
E00378:188:HV 106 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAA 151
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAA 2351
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.64
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 922 4.3 0.7 7.3 E00378:188:HVMVNCCXX:2:1215:19948:69660/1 1 151 (0) + L1P3 LINE/L1 3066 3206 (2940) 425
ANNOTATION EVIDENCE:
922 4.28 0.71 7.28 E00378:188:HVMVNCCXX:2:1215:19948:69660/1 1 151 0 + L1P3_orf2 LINE/L1 957 1097 2197
922 4.28 0.71 7.28 E00378:188:HVMVNCCXX:2:1215:19948:69660/1 1 151 (0) L1P3_orf2#LINE/L1 957 1097 (2197) m_b6s551i250
E00378:188:HV 1 ACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCA 50
L1P3_orf2#LIN 957 ACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCA 1006
E00378:188:HV 51 GAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAGACA 99
v i-
L1P3_orf2#LIN 1007 GAAGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGACA 1056
E00378:188:HV 100 CACACACACAAAAAAAACCTTTCAAAAAAATCAATTAATCCAGGAGCTGA 149
----------i i - v i
L1P3_orf2#LIN 1057 C----------GAAAAACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGG 1095
E00378:188:HV 150 TT 151
L1P3_orf2#LIN 1096 TT 1097
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1072 6.6 1.3 0.0 E00378:188:HVMVNCCXX:2:1215:19948:69660/2 1 151 (0) C L1P3 LINE/L1 (2699) 3447 3295 426
ANNOTATION EVIDENCE:
1072 6.62 1.30 0.00 E00378:188:HVMVNCCXX:2:1215:19948:69660/2 1 151 0 C L1P3_orf2 LINE/L1 1186 1338 1956
1072 6.62 1.30 0.00 E00378:188:HVMVNCCXX:2:1215:19948:69660/2 1 151 (0) C L1P3_orf2#LINE/L1 (1956) 1338 1186 m_b6s551i166
E00378:188:HV 1 GACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAATTTAT 48
v -- v i
C L1P3_orf2#LIN 1338 GACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTAT 1289
E00378:188:HV 49 CACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTATTTATAGTAT 98
vv i i
C L1P3_orf2#LIN 1288 CCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAGTAT 1239
E00378:188:HV 99 TCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCGCTTT 148
iv v
C L1P3_orf2#LIN 1238 TCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTT 1189
E00378:188:HV 149 ATC 151
C L1P3_orf2#LIN 1188 ATC 1186
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.28
Transitions / transversions = 0.67 (4/6)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1033 13.3 0.0 0.7 E00378:188:HVMVNCCXX:2:1215:22993:19663/1 1 151 (0) C AluSx SINE/Alu (27) 285 136 427
ANNOTATION EVIDENCE:
1033 13.34 0.00 0.66 E00378:188:HVMVNCCXX:2:1215:22993:19663/1 1 151 0 C AluSx SINE/Alu 136 285 27
1033 13.34 0.00 0.66 E00378:188:HVMVNCCXX:2:1215:22993:19663/1 1 151 (0) C AluSx#SINE/Alu (27) 285 136 m_b6s356i4
E00378:188:HV 1 TTTGAGATGGAGTTTCGCTCATGTCTCCCAGGCTGGAGTGCAATGGTGTG 50
i i - v i i i
C AluSx#SINE/Al 285 TTTGAGACGGAGTCTCGCTC-TGTCGCCCAGGCTGGAGTGCAGTGGCGCG 237
E00378:188:HV 51 ATCTCGGTTCACTTCAGCCTCTACCTCCTCGGTTCAAGCAATTCTCCTGC 100
i v i ii iv i
C AluSx#SINE/Al 236 ATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGC 187
E00378:188:HV 101 CTCATCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCCAGC 150
v i vi i i
C AluSx#SINE/Al 186 CTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGC 137
E00378:188:HV 151 T 151
C AluSx#SINE/Al 136 T 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.66
Transitions / transversions = 3.00 (15/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 388 5.5 0.0 0.0 E00378:188:HVMVNCCXX:2:1215:22993:19663/2 1 55 (96) + L1P3 LINE/L1 3844 3898 (2248) 428
ANNOTATION EVIDENCE:
388 5.45 0.00 0.00 E00378:188:HVMVNCCXX:2:1215:22993:19663/2 1 55 96 + L1P3_orf2 LINE/L1 1735 1789 1505
388 5.45 0.00 0.00 E00378:188:HVMVNCCXX:2:1215:22993:19663/2 1 55 (96) L1P3_orf2#LINE/L1 1735 1789 (1505) m_b6s551i9
E00378:188:HV 1 TCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAAACTACAT 50
i v i
L1P3_orf2#LIN 1735 TCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAACCACAT 1784
E00378:188:HV 51 GATTA 55
L1P3_orf2#LIN 1785 GATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.92
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 812 6.4 0.0 0.0 E00378:188:HVMVNCCXX:2:1215:22993:19663/2 58 151 (0) + AluSx SINE/Alu 14 107 (205) 429
ANNOTATION EVIDENCE:
812 6.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1215:22993:19663/2 58 151 0 + AluSx SINE/Alu 14 107 205
812 6.38 0.00 0.00 E00378:188:HVMVNCCXX:2:1215:22993:19663/2 58 151 (0) AluSx#SINE/Alu 14 107 (205) m_b6s356i25
E00378:188:HV 58 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 107
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 108 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAA 151
i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAA 107
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.60
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0)
+ 644 20.1 6.3 0.7 E00378:188:HVMVNCCXX:2:1216:15716:46156/1 17 151 (0) C L1MC4 LINE/L1 (131) 7911 7769 430
ANNOTATION EVIDENCE:
644 20.15 6.30 0.74 E00378:188:HVMVNCCXX:2:1216:15716:46156/1 17 151 0 C L1MC4_3end LINE/L1 2516 2658 131
644 20.15 6.30 0.74 E00378:188:HVMVNCCXX:2:1216:15716:46156/1 17 151 (0) C L1MC4_3end#LINE/L1 (131) 2658 2516 m_b3s551i21
E00378:188:HV 17 ATACACACATCATTTTCTCTGAACCATTTTGAGATGAAATCGCACACGTG 66
i i iv i - vv i i v i ?
C L1MC4_3end#LI 2658 ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAGTTGCAGACATN 2610
E00378:188:HV 67 ATGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAACAAGGA 107
i --------- i i
C L1MC4_3end#LI 2609 ATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAACAAGGA 2560
E00378:188:HV 108 TACACTTCTGTTTAGCCACAGTATAATCATCAAAATCAGGAAGT 151
i iv ii iiv i i i i
C L1MC4_3end#LI 2559 CATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGAAAT 2516
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.59
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 5.00 (10 / 2)
+ 273 27.6 3.9 10.9 E00378:188:HVMVNCCXX:2:1216:8359:33164/2 1 138 (13) C L1MC4 LINE/L1 (1453) 6589 6462 431
ANNOTATION EVIDENCE:
273 27.65 3.90 10.87 E00378:188:HVMVNCCXX:2:1216:8359:33164/2 1 138 13 C L1MC4_3end LINE/L1 1209 1336 1453
273 27.65 3.90 10.87 E00378:188:HVMVNCCXX:2:1216:8359:33164/2 1 138 (13) C L1MC4_3end#LINE/L1 (1453) 1336 1209 m_b3s551i158
E00378:188:HV 1 ATCTTCAAATCCAAGCCAACATCACACAGTTTAT-----CTTTTTTTCTG 45
i i v v i vi i ----- i iiii v
C L1MC4_3end#LI 1336 ACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTAGCCTTCCCCCTT 1287
E00378:188:HV 46 TCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAAAAACACCCCAAAAC 95
v i v iv iv iii v -------------i
C L1MC4_3end#LI 1286 TCCATATTTGTAACTCCCTTCTCCGACAGTGA-------------GAAAC 1250
E00378:188:HV 96 CTGACTATCCACTCAACCTGAATGCATTTACTTATTTGCTCAA 138
i -i - i v ?v ii
C L1MC4_3end#LI 1249 CTGGCT-CCCA-TTATCCNCAATATATTTACTTATTTGCTCAA 1209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.47
Transitions / transversions = 2.00 (22/11)
Gap_init rate = 0.12 (16 / 137), avg. gap size = 1.25 (20 / 16)
+ 1189 6.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1217:32075:21825/2 1 151 (0) C L1P3 LINE/L1 (3178) 2968 2818 432
ANNOTATION EVIDENCE:
1189 5.96 0.00 0.00 E00378:188:HVMVNCCXX:2:1217:32075:21825/2 1 151 0 C L1P3_orf2 LINE/L1 709 859 2435
1189 5.96 0.00 0.00 E00378:188:HVMVNCCXX:2:1217:32075:21825/2 1 151 (0) C L1P3_orf2#LINE/L1 (2435) 859 709 m_b7s551i53
E00378:188:HV 1 GATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTT 50
i i ?i
C L1P3_orf2#LIN 859 GATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTT 810
E00378:188:HV 51 ATTTCTGCCTTCATTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTT 100
v i i
C L1P3_orf2#LIN 809 ATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTT 760
E00378:188:HV 101 GTTCAGTTTCCATGTAGTTGTGTGGTTTTGAGTGAGTTTCTTAATCCTCA 150
i v
C L1P3_orf2#LIN 759 GTTCAGTTTCCATGTAGTTGTGCGGTTTTGAGTGAGTTTCTTAATCCTGA 710
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 709 G 709
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1286 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1218:27986:48599/1 1 151 (0) C L1P1 LINE/L1 (891) 5255 5105 433
ANNOTATION EVIDENCE:
1286 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1218:27986:48599/1 1 151 0 C L1P1_orf2 LINE/L1 2996 3146 148
1286 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1218:27986:48599/1 1 151 (0) C L1P1_orf2#LINE/L1 (148) 3146 2996 m_b1s551i105
E00378:188:HV 1 AGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGG 50
i
C L1P1_orf2#LIN 3146 AGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGG 3097
E00378:188:HV 51 TTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTA 100
C L1P1_orf2#LIN 3096 TTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTA 3047
E00378:188:HV 101 GTTTAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTT 150
i v
C L1P1_orf2#LIN 3046 GTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTT 2997
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2996 G 2996
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 918 2.8 0.0 0.0 E00378:188:HVMVNCCXX:2:1220:11749:64175/1 1 107 (44) + L1PA2 LINE/L1 6047 6153 (2) 434
ANNOTATION EVIDENCE:
918 2.80 0.00 0.00 E00378:188:HVMVNCCXX:2:1220:11749:64175/1 1 107 44 + L1PA2_3end LINE/L1 794 900 2
918 2.80 0.00 0.00 E00378:188:HVMVNCCXX:2:1220:11749:64175/1 1 107 (44) L1PA2_3end#LINE/L1 794 900 (2) m_b1s551i440
E00378:188:HV 1 ACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATACATATGTAA 50
i
L1PA2_3end#LI 794 ACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAA 843
E00378:188:HV 51 CTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAA 100
i
L1PA2_3end#LI 844 CTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAA 893
E00378:188:HV 101 AAAATAA 107
v
L1PA2_3end#LI 894 AAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.99
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0)
+ 1109 12.1 0.0 1.3 E00378:188:HVMVNCCXX:2:1220:11749:64175/2 1 151 (0) + AluSx SINE/Alu 141 289 (23) 435
ANNOTATION EVIDENCE:
1109 12.08 0.00 1.32 E00378:188:HVMVNCCXX:2:1220:11749:64175/2 1 151 0 + AluSx SINE/Alu 141 289 23
1109 12.08 0.00 1.32 E00378:188:HVMVNCCXX:2:1220:11749:64175/2 1 151 (0) AluSx#SINE/Alu 141 289 (23) m_b2s356i2
E00378:188:HV 1 GGTGTGGTGGTGGGCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAG 50
i i v i i i
AluSx#SINE/Al 141 GGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAG 190
E00378:188:HV 51 GAGAATCACTTGAACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATG 100
i i i i i i ii
AluSx#SINE/Al 191 GAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG 240
E00378:188:HV 101 CCACTGCACTCCAGCCTGGGTTTGACGAAGCGAGACTCTGTCTCAAAAAA 150
--i ii i
AluSx#SINE/Al 241 CCACTGCACTCCAGCCTGGG--CGACAGAGCGAGACTCCGTCTCAAAAAA 288
E00378:188:HV 151 A 151
AluSx#SINE/Al 289 A 289
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.05
Transitions / transversions = 17.00 (17/1)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 949 12.9 0.0 0.0 E00378:188:HVMVNCCXX:2:1220:24738:56370/2 1 132 (19) C AluSx SINE/Alu (180) 132 1 436
ANNOTATION EVIDENCE:
949 12.88 0.00 0.00 E00378:188:HVMVNCCXX:2:1220:24738:56370/2 1 132 19 C AluSx SINE/Alu 1 132 180
949 12.88 0.00 0.00 E00378:188:HVMVNCCXX:2:1220:24738:56370/2 1 132 (19) C AluSx#SINE/Alu (180) 132 1 m_b2s357i34
E00378:188:HV 1 TTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTT 50
v i ii i
C AluSx#SINE/Al 132 TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTC 83
E00378:188:HV 51 TCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCT 100
i i i v v v
C AluSx#SINE/Al 82 TCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
E00378:188:HV 101 GAGATTACAGATGTGAGCCACTGTGCCCAGCC 132
i ii i i i
C AluSx#SINE/Al 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.63
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 31 10.3 0.0 0.0 E00378:188:HVMVNCCXX:2:1221:27336:41708/1 87 138 (13) + (T)n Simple_repeat 1 52 (0) 437
ANNOTATION EVIDENCE:
31 10.35 0.00 0.00 E00378:188:HVMVNCCXX:2:1221:27336:41708/1 87 138 13 + (T)n Simple_repeat 1 52 0
31 10.35 0.00 0.00 E00378:188:HVMVNCCXX:2:1221:27336:41708/1 87 138 (13) (T)n#Simple_repeat 1 52 (0) c_b6s251i17
E00378:188:HV 87 TTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTCATTTTTTTCTTTTCTT 136
v iv i i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
E00378:188:HV 137 TT 138
(T)n#Simple_r 51 TT 52
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 1011 11.3 0.0 0.7 E00378:188:HVMVNCCXX:2:1221:27336:41708/2 1 151 (0) + AluSx SINE/Alu 159 308 (4) 438
ANNOTATION EVIDENCE:
1011 11.33 0.00 0.66 E00378:188:HVMVNCCXX:2:1221:27336:41708/2 1 151 0 + AluSx SINE/Alu 159 308 4
1011 11.33 0.00 0.66 E00378:188:HVMVNCCXX:2:1221:27336:41708/2 1 151 (0) AluSx#SINE/Alu 159 308 (4) m_b6s356i0
E00378:188:HV 1 TGTAATCCCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGA 50
i v i vi
AluSx#SINE/Al 159 TGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCG 208
E00378:188:HV 51 GGAGGTAGAGGCTGAAGTGAACCGAGATCACACCATTGCACTCCAGCCAG 100
ii i v i i i i v
AluSx#SINE/Al 209 GGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258
E00378:188:HV 101 GGAGACATGAGCGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAA 150
v - i i
AluSx#SINE/Al 259 GGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAA 307
E00378:188:HV 151 A 151
AluSx#SINE/Al 308 A 308
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.44
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 32 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1221:27346:41972/1 87 116 (35) + (T)n Simple_repeat 1 30 (0) 439
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1221:27346:41972/1 87 116 35 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:1221:27346:41972/1 87 116 (35) (T)n#Simple_repeat 1 30 (0) c_b6s251i16
E00378:188:HV 87 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 116
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1050 10.7 0.0 0.7 E00378:188:HVMVNCCXX:2:1221:27346:41972/2 1 151 (0) + AluSx SINE/Alu 159 308 (4) 440
ANNOTATION EVIDENCE:
1050 10.67 0.00 0.66 E00378:188:HVMVNCCXX:2:1221:27346:41972/2 1 151 0 + AluSx SINE/Alu 159 308 4
1050 10.67 0.00 0.66 E00378:188:HVMVNCCXX:2:1221:27346:41972/2 1 151 (0) AluSx#SINE/Alu 159 308 (4) m_b6s356i1
E00378:188:HV 1 TGTAATCCCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGA 50
i v i vi
AluSx#SINE/Al 159 TGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCG 208
E00378:188:HV 51 GGAGGTAGAGGCTGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTG 100
ii i v i i i i
AluSx#SINE/Al 209 GGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258
E00378:188:HV 101 GGAGACATGAGCGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAA 150
v - i i
AluSx#SINE/Al 259 GGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAA 307
E00378:188:HV 151 A 151
AluSx#SINE/Al 308 A 308
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.71
Transitions / transversions = 3.00 (12/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1327 0.7 0.0 0.7 E00378:188:HVMVNCCXX:2:1223:16051:35414/1 1 151 (0) + L1PA3 LINE/L1 5723 5872 (283) 441
ANNOTATION EVIDENCE:
1327 0.66 0.00 0.66 E00378:188:HVMVNCCXX:2:1223:16051:35414/1 1 151 0 + L1PA3_3end LINE/L1 470 619 283
1327 0.66 0.00 0.66 E00378:188:HVMVNCCXX:2:1223:16051:35414/1 1 151 (0) L1PA3_3end#LINE/L1 470 619 (283) m_b1s551i346
E00378:188:HV 1 CAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAG 50
L1PA3_3end#LI 470 CAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAG 519
E00378:188:HV 51 AAACTGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGA 100
v
L1PA3_3end#LI 520 AAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGA 569
E00378:188:HV 101 TGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAAATCATCATT 150
-
L1PA3_3end#LI 570 TGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAATCATCATT 618
E00378:188:HV 151 C 151
L1PA3_3end#LI 619 C 619
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 983 4.0 0.0 0.1 E00378:188:HVMVNCCXX:2:1223:16051:35414/2 1 134 (17) C L1PA3 LINE/L1 (43) 6112 5980 442
ANNOTATION EVIDENCE:
881 11.27 0.00 0.75 E00378:188:HVMVNCCXX:2:1223:16051:35414/2 1 134 17 C L1PA4_3end LINE/L1 727 859 43
881 11.27 0.00 0.75 E00378:188:HVMVNCCXX:2:1223:16051:35414/2 1 134 (17) C L1PA4_3end#LINE/L1 (43) 859 727 m_b1s551i408
E00378:188:HV 1 ACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCT 50
i v i
C L1PA4_3end#LI 859 ACAACGTGCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCT 810
E00378:188:HV 51 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 100
i i i
C L1PA4_3end#LI 809 GCACCCATTAACTCGTCATTTAGCATTAGGTATATCTCCTAATGCTATCC 760
E00378:188:HV 101 CACCCCCCCCCCCGCTGGCCCGCACCGTGCCCCG 134
v i - iiv i v iv
C L1PA4_3end#LI 759 CTCCCCCCTCCCC-CCACCCCACAACAGGCCCCG 727
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.54
Transitions / transversions = 2.00 (10/5)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1)
983 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1223:16051:35414/2 1 113 38 C L1PA3_3end LINE/L1 747 859 43
983 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:1223:16051:35414/2 1 113 (38) C L1PA3_3end#LINE/L1 (43) 859 747 m_b1s551i409
E00378:188:HV 1 ACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCT 50
i
C L1PA3_3end#LI 859 ACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCT 810
E00378:188:HV 51 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 100
C L1PA3_3end#LI 809 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 760
E00378:188:HV 101 CACCCCCCCCCCC 113
v i
C L1PA3_3end#LI 759 CTCCCCCCTCCCC 747
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.88
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.0 (0 / 0)
+ 1270 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1224:26017:48986/1 1 151 (0) + L1P1 LINE/L1 5075 5225 (921) 443
ANNOTATION EVIDENCE:
1270 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1224:26017:48986/1 1 151 0 + L1P1_orf2 LINE/L1 2966 3116 178
1270 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1224:26017:48986/1 1 151 (0) L1P1_orf2#LINE/L1 2966 3116 (178) m_b1s551i92
E00378:188:HV 1 GCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAA 50
L1P1_orf2#LIN 2966 GCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAA 3015
E00378:188:HV 51 GACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 100
v i
L1P1_orf2#LIN 3016 GCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 3065
E00378:188:HV 101 AAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAA 150
i
L1P1_orf2#LIN 3066 AAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAA 3115
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3116 T 3116
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1334 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:1224:26017:48986/2 1 151 (0) C L1P1 LINE/L1 (600) 5555 5405 444
ANNOTATION EVIDENCE:
1334 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1224:26017:48986/2 1 151 0 C L1PA3_3end LINE/L1 152 302 600
1334 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:1224:26017:48986/2 1 151 (0) C L1PA3_3end#LINE/L1 (600) 302 152 m_b1s551i242
E00378:188:HV 1 AGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATCC 50
vi
C L1PA3_3end#LI 302 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCC 253
E00378:188:HV 51 TCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACTG 100
i
C L1PA3_3end#LI 252 TCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTG 203
E00378:188:HV 101 GTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCC 150
C L1PA3_3end#LI 202 GTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCC 153
E00378:188:HV 151 A 151
C L1PA3_3end#LI 152 A 152
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1084 8.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2101:22709:3559/1 1 151 (0) C L1PA2 LINE/L1 (92) 6063 5913 445
ANNOTATION EVIDENCE:
1084 8.61 0.00 0.00 E00378:188:HVMVNCCXX:2:2101:22709:3559/1 1 151 0 C L1PA2_3end LINE/L1 660 810 92
1084 8.61 0.00 0.00 E00378:188:HVMVNCCXX:2:2101:22709:3559/1 1 151 (0) C L1PA2_3end#LINE/L1 (92) 810 660 m_b1s551i391
E00378:188:HV 1 TGCACCCACTAACTCGTCGTCTAGCATTAGTTATATCTCCCAATGCTATC 50
i v
C L1PA2_3end#LI 810 TGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATC 761
E00378:188:HV 51 TCTCCACCCTCTACCCACCCCACAATAGTCCCCAGAGTGTGATATTCCCC 100
i v iv v i
C L1PA2_3end#LI 760 CCTCCCCCCTCCCCCCACCCCACCACAGTCCCCAGAGTGTGATATTCCCC 711
E00378:188:HV 101 TTCCTGTTTCCATGTGATCTCATTTTTCAATTCCCACATATGGTTGAGAA 150
v v v iv
C L1PA2_3end#LI 710 TTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAA 661
E00378:188:HV 151 T 151
C L1PA2_3end#LI 660 T 660
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.15
Transitions / transversions = 0.62 (5/8)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1176 6.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2101:22709:3559/2 1 151 (0) + L1P1 LINE/L1 5674 5824 (331) 446
ANNOTATION EVIDENCE:
1176 6.62 0.00 0.00 E00378:188:HVMVNCCXX:2:2101:22709:3559/2 1 151 0 + L1PA2_3end LINE/L1 421 571 331
1176 6.62 0.00 0.00 E00378:188:HVMVNCCXX:2:2101:22709:3559/2 1 151 (0) L1PA2_3end#LINE/L1 421 571 (331) m_b1s551i326
E00378:188:HV 1 TATAAAGACACATGCACACGTATGTTTATTGTGGCATTATTCACAATAGC 50
i
L1PA2_3end#LI 421 TATAAAGACACATGCACACGTATGTTTATTGCGGCATTATTCACAATAGC 470
E00378:188:HV 51 AAAGACTTGGAACCAACCCAAATGTCCAAAAATGGTAGACTGGATTAAGC 100
v i v
L1PA2_3end#LI 471 AAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGA 520
E00378:188:HV 101 AACTGCGACACATATACACCATGGAATACTATCCCGCCATAAAAAATGAC 150
v i i v v i
L1PA2_3end#LI 521 AAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGAT 570
E00378:188:HV 151 G 151
L1PA2_3end#LI 571 G 571
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.29
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1287 1.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2102:14722:52836/1 1 151 (0) C L1P1 LINE/L1 (678) 5477 5327 447
ANNOTATION EVIDENCE:
1287 1.32 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:14722:52836/1 1 151 0 C L1PA2_3end LINE/L1 74 224 678
1287 1.32 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:14722:52836/1 1 151 (0) C L1PA2_3end#LINE/L1 (678) 224 74 m_b1s551i206
E00378:188:HV 1 TTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTT 50
i
C L1PA2_3end#LI 224 TTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTT 175
E00378:188:HV 51 GATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTT 100
C L1PA2_3end#LI 174 GATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTT 125
E00378:188:HV 101 TTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTTTTCATGTCCTTC 150
v
C L1PA2_3end#LI 124 TTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTC 75
E00378:188:HV 151 G 151
C L1PA2_3end#LI 74 G 74
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2102:14722:52836/2 1 151 (0) + L1P LINE/L1 5269 5419 (736) 448
ANNOTATION EVIDENCE:
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:14722:52836/2 1 151 0 + L1PA2_3end LINE/L1 16 166 736
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:14722:52836/2 1 151 (0) L1PA2_3end#LINE/L1 16 166 (736) m_b1s551i175
E00378:188:HV 1 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 50
L1PA2_3end#LI 16 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 65
E00378:188:HV 51 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 100
L1PA2_3end#LI 66 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 115
E00378:188:HV 101 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAA 150
L1PA2_3end#LI 116 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAA 165
E00378:188:HV 151 A 151
L1PA2_3end#LI 166 A 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 323 16.9 7.8 0.0 E00378:188:HVMVNCCXX:2:2102:31000:5968/1 1 71 (80) + L1MC4 LINE/L1 7573 7649 (393) 449
ANNOTATION EVIDENCE:
323 16.90 7.79 0.00 E00378:188:HVMVNCCXX:2:2102:31000:5968/1 1 71 80 + L1MC4_3end LINE/L1 2320 2396 393
323 16.90 7.79 0.00 E00378:188:HVMVNCCXX:2:2102:31000:5968/1 1 71 (80) L1MC4_3end#LINE/L1 2320 2396 (393) m_b3s551i62
E00378:188:HV 1 TCATGATAAATAAAAAAA------AGAACTGTTCCAGATTGAAGGAGACT 44
v i i i ------i i
L1MC4_3end#LI 2320 TCATGAAAGACAAAGAAAGACTGAGGAACTGTTCCAGATTAAAGGAGACT 2369
E00378:188:HV 45 AAACAGACTACACACCTAAATGCAATG 71
v vvv v i
L1MC4_3end#LI 2370 AAAGAGACATGACAACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.58
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.01 (1 / 70), avg. gap size = 6.00 (6 / 1)
+ 443 18.4 0.0 0.0 E00378:188:HVMVNCCXX:2:2102:31000:5968/1 76 151 (0) + L1MC4 LINE/L1 7762 7837 (205) 449
ANNOTATION EVIDENCE:
443 18.42 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:31000:5968/1 76 151 0 + L1MC4_3end LINE/L1 2509 2584 205
443 18.42 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:31000:5968/1 76 151 (0) L1MC4_3end#LINE/L1 2509 2584 (205) m_b3s551i63
E00378:188:HV 76 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 125
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
E00378:188:HV 126 ATCCTTGTTTTTAGGAAATATACACT 151
i i i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACT 2584
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.29
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0)
+ 16 19.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2102:31000:5968/2 111 140 (11) + (CA)n Simple_repeat 1 30 (0) 450
ANNOTATION EVIDENCE:
16 19.56 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:31000:5968/2 111 140 11 + (CA)n Simple_repeat 1 30 0
16 19.56 0.00 0.00 E00378:188:HVMVNCCXX:2:2102:31000:5968/2 111 140 (11) (CA)n#Simple_repeat 1 30 (0) m_b3s252i5
E00378:188:HV 111 CACACACACACTCATACGCATATACACACA 140
v i i i i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACA 30
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 524 7.2 0.0 1.2 E00378:188:HVMVNCCXX:2:2103:11728:67445/1 1 84 (67) + AluSx SINE/Alu 230 312 (0) 451
ANNOTATION EVIDENCE:
524 7.23 0.00 1.19 E00378:188:HVMVNCCXX:2:2103:11728:67445/1 1 84 67 + AluSx SINE/Alu 230 312 0
524 7.23 0.00 1.19 E00378:188:HVMVNCCXX:2:2103:11728:67445/1 1 84 (67) AluSx#SINE/Alu 230 312 (0) m_b6s357i1
E00378:188:HV 1 CCGAGATCACACCATTGCACTCCAGCCTGGGAGACATGAGCGAAACTCCA 50
i i i v - i i
AluSx#SINE/Al 230 CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGCGAGACTCCG 278
E00378:188:HV 51 TCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 84
AluSx#SINE/Al 279 TCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.10
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1)
+ 308 27.1 14.3 0.0 E00378:188:HVMVNCCXX:2:2103:11728:67445/2 7 150 (1) C MIR SINE/MIR (0) 262 95 452
ANNOTATION EVIDENCE:
308 27.08 14.29 0.00 E00378:188:HVMVNCCXX:2:2103:11728:67445/2 7 150 1 C MIR SINE/MIR 95 262 0
308 27.08 14.29 0.00 E00378:188:HVMVNCCXX:2:2103:11728:67445/2 7 150 (1) C MIR#SINE/MIR (0) 262 95 m_b6s601i31
E00378:188:HV 7 AAAAATAGCTAACACTTGTTGAGGATATACGGTGTGCCTGGCA------- 49
v i i viiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
E00378:188:HV 50 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 84
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
E00378:188:HV 85 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 132
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
E00378:188:HV 133 TGAGGTAAAGTAACTTGC 150
v v
C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGC 95
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.21
Transitions / transversions = 1.29 (22/17)
Gap_init rate = 0.03 (5 / 143), avg. gap size = 4.80 (24 / 5)
+ 515 8.4 0.0 1.2 E00378:188:HVMVNCCXX:2:2103:12621:66039/1 1 84 (67) + AluSx SINE/Alu 230 312 (0) 453
ANNOTATION EVIDENCE:
515 8.43 0.00 1.19 E00378:188:HVMVNCCXX:2:2103:12621:66039/1 1 84 67 + AluSx SINE/Alu 230 312 0
515 8.43 0.00 1.19 E00378:188:HVMVNCCXX:2:2103:12621:66039/1 1 84 (67) AluSx#SINE/Alu 230 312 (0) m_b6s357i0
E00378:188:HV 1 CCGAGATCACACCATTGCACTCCAGCCTGGGAGACATGAGCGAAACTCCA 50
i i i v - i i
AluSx#SINE/Al 230 CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGCGAGACTCCG 278
E00378:188:HV 51 TCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 84
i
AluSx#SINE/Al 279 TCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.41
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1)
+ 314 27.1 14.3 0.0 E00378:188:HVMVNCCXX:2:2103:12621:66039/2 7 150 (1) C MIR SINE/MIR (0) 262 95 454
ANNOTATION EVIDENCE:
314 27.08 14.29 0.00 E00378:188:HVMVNCCXX:2:2103:12621:66039/2 7 150 1 C MIR SINE/MIR 95 262 0
314 27.08 14.29 0.00 E00378:188:HVMVNCCXX:2:2103:12621:66039/2 7 150 (1) C MIR#SINE/MIR (0) 262 95 m_b6s601i32
E00378:188:HV 7 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 49
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
E00378:188:HV 50 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 84
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
E00378:188:HV 85 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 132
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
E00378:188:HV 133 TGAGGTAAAGTAACTTGC 150
v v
C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGC 95
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.23
Transitions / transversions = 1.44 (23/16)
Gap_init rate = 0.03 (5 / 143), avg. gap size = 4.80 (24 / 5)
+ 547 18.7 18.0 0.0 E00378:188:HVMVNCCXX:2:2103:20334:2856/2 2 151 (0) + L1MC4 LINE/L1 7461 7643 (399) 455
ANNOTATION EVIDENCE:
547 18.67 18.03 0.00 E00378:188:HVMVNCCXX:2:2103:20334:2856/2 2 151 0 + L1MC4_3end LINE/L1 2208 2390 399
547 18.67 18.03 0.00 E00378:188:HVMVNCCXX:2:2103:20334:2856/2 2 151 (0) L1MC4_3end#LINE/L1 2208 2390 (399) m_b3s551i102
E00378:188:HV 2 ATTCTCGTCAAA---GTATAA-----ATTTAATCATAAGGAAACATCAGA 43
ii i --- i ----- i i
L1MC4_3end#LI 2208 ATTCCTGCCAAAAATGCATAACCTGAATCTAATCATGAGGAAACATCAGA 2257
E00378:188:HV 44 CAAACTCAGAGCAAGGGAC-------------------CTGTACTATTCA 74
i i vii ------------------- v
L1MC4_3end#LI 2258 CAAACCCAAATTGAGGGACATTCTACAAAATAACTGGCCTGTACTCTTCA 2307
E00378:188:HV 75 AATATATGAAGGTCATGATAAATAAAAAAA------AGAACTGTTCCATA 118
v i v ? v i i i ------i v
L1MC4_3end#LI 2308 AAAATGTCAANGTCATGAAAGACAAAGAAAGACTGAGGAACTGTTCCAGA 2357
E00378:188:HV 119 TTGAAGGAGACTAAACAGACGACACACCTAAAT 151
i v ivv v
L1MC4_3end#LI 2358 TTAAAGGAGACTAAAGAGACATGACAACTAAAT 2390
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.10
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (4 / 149), avg. gap size = 8.25 (33 / 4)
+ 1314 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:2103:31832:17289/1 1 151 (0) C L1P1 LINE/L1 (657) 5498 5348 456
ANNOTATION EVIDENCE:
1314 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2103:31832:17289/1 1 151 0 C L1PA2_3end LINE/L1 95 245 657
1314 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2103:31832:17289/1 1 151 (0) C L1PA2_3end#LINE/L1 (657) 245 95 m_b1s551i221
E00378:188:HV 1 CACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAG 50
i
C L1PA2_3end#LI 245 CACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAG 196
E00378:188:HV 51 ATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATG 100
C L1PA2_3end#LI 195 ATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATG 146
E00378:188:HV 101 ATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAG 150
C L1PA2_3end#LI 145 ATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAG 96
E00378:188:HV 151 A 151
C L1PA2_3end#LI 95 A 95
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1256 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2103:31832:17289/2 1 151 (0) + L1P1 LINE/L1 5029 5179 (967) 457
ANNOTATION EVIDENCE:
1256 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2103:31832:17289/2 1 151 0 + L1P1_orf2 LINE/L1 2920 3070 224
1256 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2103:31832:17289/2 1 151 (0) L1P1_orf2#LINE/L1 2920 3070 (224) m_b1s551i79
E00378:188:HV 1 ATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCAT 50
?
L1P1_orf2#LIN 2920 ATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCAT 2969
E00378:188:HV 51 GGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACA 100
v
L1P1_orf2#LIN 2970 GGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCA 3019
E00378:188:HV 101 GAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCGGCACAGCAAAA 150
i v
L1P1_orf2#LIN 3020 AAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAA 3069
E00378:188:HV 151 G 151
L1P1_orf2#LIN 3070 G 3070
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1333 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2104:20425:34869/1 1 151 (0) + L1P3 LINE/L1 3477 3627 (2519) 458
ANNOTATION EVIDENCE:
1333 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2104:20425:34869/1 1 151 0 + L1P3_orf2 LINE/L1 1368 1518 1776
1333 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2104:20425:34869/1 1 151 (0) L1P3_orf2#LINE/L1 1368 1518 (1776) m_b6s551i111
E00378:188:HV 1 TGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGAC 50
L1P3_orf2#LIN 1368 TGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGAC 1417
E00378:188:HV 51 CAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTA 100
v i
L1P3_orf2#LIN 1418 CAGACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTA 1467
E00378:188:HV 101 CCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCC 150
i
L1P3_orf2#LIN 1468 CCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCC 1517
E00378:188:HV 151 T 151
L1P3_orf2#LIN 1518 T 1518
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1140 8.0 1.9 0.0 E00378:188:HVMVNCCXX:2:2104:20425:34869/2 1 151 (0) C L1P3 LINE/L1 (2306) 3840 3687 459
ANNOTATION EVIDENCE:
1140 7.95 1.95 0.00 E00378:188:HVMVNCCXX:2:2104:20425:34869/2 1 151 0 C L1P3_orf2 LINE/L1 1578 1731 1563
1140 7.95 1.95 0.00 E00378:188:HVMVNCCXX:2:2104:20425:34869/2 1 151 (0) C L1P3_orf2#LINE/L1 (1563) 1731 1578 m_b6s551i54
E00378:188:HV 1 GTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGT 50
i i i i i v
C L1P3_orf2#LIN 1731 GCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGT 1682
E00378:188:HV 51 GGTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTA 97
v --- i
C L1P3_orf2#LIN 1681 GGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTA 1632
E00378:188:HV 98 TCGAGGATTTTCACATCGATGTTCATCACGGATACTGGCCTGAAATTTTC 147
i i v i
C L1P3_orf2#LIN 1631 TTGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTC 1582
E00378:188:HV 148 TTTT 151
C L1P3_orf2#LIN 1581 TTTT 1578
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.81
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1333 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2104:20720:33586/1 1 151 (0) + L1P3 LINE/L1 3477 3627 (2519) 460
ANNOTATION EVIDENCE:
1333 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2104:20720:33586/1 1 151 0 + L1P3_orf2 LINE/L1 1368 1518 1776
1333 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2104:20720:33586/1 1 151 (0) L1P3_orf2#LINE/L1 1368 1518 (1776) m_b6s551i112
E00378:188:HV 1 TGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGAC 50
L1P3_orf2#LIN 1368 TGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGAC 1417
E00378:188:HV 51 CAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTA 100
v i
L1P3_orf2#LIN 1418 CAGACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTA 1467
E00378:188:HV 101 CCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCC 150
i
L1P3_orf2#LIN 1468 CCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCC 1517
E00378:188:HV 151 T 151
L1P3_orf2#LIN 1518 T 1518
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1131 8.0 1.9 0.0 E00378:188:HVMVNCCXX:2:2104:20720:33586/2 1 151 (0) C L1P3 LINE/L1 (2306) 3840 3687 461
ANNOTATION EVIDENCE:
1131 7.95 1.95 0.00 E00378:188:HVMVNCCXX:2:2104:20720:33586/2 1 151 0 C L1P3_orf2 LINE/L1 1578 1731 1563
1131 7.95 1.95 0.00 E00378:188:HVMVNCCXX:2:2104:20720:33586/2 1 151 (0) C L1P3_orf2#LINE/L1 (1563) 1731 1578 m_b6s551i55
E00378:188:HV 1 GTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGT 50
i i i i i v
C L1P3_orf2#LIN 1731 GCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGT 1682
E00378:188:HV 51 GGTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTA 97
v --- i
C L1P3_orf2#LIN 1681 GGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTA 1632
E00378:188:HV 98 TCGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTC 147
i i v v
C L1P3_orf2#LIN 1631 TTGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTC 1582
E00378:188:HV 148 TTTT 151
C L1P3_orf2#LIN 1581 TTTT 1578
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.79
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 663 6.1 0.0 0.0 E00378:188:HVMVNCCXX:2:2105:28128:18256/2 70 151 (0) C AluSx SINE/Alu (14) 298 217 462
ANNOTATION EVIDENCE:
663 6.10 0.00 0.00 E00378:188:HVMVNCCXX:2:2105:28128:18256/2 70 151 0 C AluSx SINE/Alu 217 298 14
663 6.10 0.00 0.00 E00378:188:HVMVNCCXX:2:2105:28128:18256/2 70 151 (0) C AluSx#SINE/Alu (14) 298 217 m_b2s357i106
E00378:188:HV 70 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 119
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 120 TGCAGTGGCATGATCTCGGCTCACTGCAACCT 151
ii
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCT 217
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.02
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0)
+ 1184 6.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2106:19421:48775/1 1 151 (0) C L1P3 LINE/L1 (3106) 3040 2890 463
ANNOTATION EVIDENCE:
1184 6.62 0.00 0.00 E00378:188:HVMVNCCXX:2:2106:19421:48775/1 1 151 0 C L1P3_orf2 LINE/L1 781 931 2363
1184 6.62 0.00 0.00 E00378:188:HVMVNCCXX:2:2106:19421:48775/1 1 151 (0) C L1P3_orf2#LINE/L1 (2363) 931 781 m_b7s551i30
E00378:188:HV 1 TTTCCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAAC 50
i v ?
C L1P3_orf2#LIN 931 TTTCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAAC 882
E00378:188:HV 51 ACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTT 100
i i
C L1P3_orf2#LIN 881 ACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTC 832
E00378:188:HV 101 ATTGGTTTCAAAGAACTTACTTATTTCTGCCTTCATTTCATTATTTACCT 150
?i v i i
C L1P3_orf2#LIN 831 ATTGGTTTCAAAGAACTTNTTTATTTCTGCCTTAATTTCGTTATTTACCC 782
E00378:188:HV 151 A 151
C L1P3_orf2#LIN 781 A 781
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.65
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1250 8.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2109:30025:69361/1 1 151 (0) + AluSx SINE/Alu 91 241 (71) 464
ANNOTATION EVIDENCE:
1250 7.95 0.00 0.00 E00378:188:HVMVNCCXX:2:2109:30025:69361/1 1 151 0 + AluSx SINE/Alu 91 241 71
1250 7.95 0.00 0.00 E00378:188:HVMVNCCXX:2:2109:30025:69361/1 1 151 (0) AluSx#SINE/Alu 91 241 (71) m_b4s356i20
E00378:188:HV 1 TGGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCA 50
i i i i i
AluSx#SINE/Al 91 TGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCG 140
E00378:188:HV 51 GGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAG 100
v iv i i
AluSx#SINE/Al 141 GGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAG 190
E00378:188:HV 101 GAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCG 150
i i
AluSx#SINE/Al 191 GAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG 240
E00378:188:HV 151 C 151
AluSx#SINE/Al 241 C 241
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 512 7.7 0.0 0.0 E00378:188:HVMVNCCXX:2:2111:19136:16744/1 1 65 (86) C AluSx SINE/Alu (234) 78 14 465
ANNOTATION EVIDENCE:
512 7.69 0.00 0.00 E00378:188:HVMVNCCXX:2:2111:19136:16744/1 1 65 86 C AluSx SINE/Alu 14 78 234
512 7.69 0.00 0.00 E00378:188:HVMVNCCXX:2:2111:19136:16744/1 1 65 (86) C AluSx#SINE/Alu (234) 78 14 m_b6s357i22
E00378:188:HV 1 ACTCCTGACCTCAGGTGATCCACCCACCTTGTCCTCCCAAAGTGCTGAGA 50
i i i v i
C AluSx#SINE/Al 78 ACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGA 29
E00378:188:HV 51 TTACAGGCGTGAGCC 65
C AluSx#SINE/Al 28 TTACAGGCGTGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 607 8.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2111:19136:16744/1 68 151 (0) C L1P3 LINE/L1 (2248) 3898 3815 466
ANNOTATION EVIDENCE:
607 8.33 0.00 0.00 E00378:188:HVMVNCCXX:2:2111:19136:16744/1 68 151 0 C L1P3_orf2 LINE/L1 1706 1789 1505
607 8.33 0.00 0.00 E00378:188:HVMVNCCXX:2:2111:19136:16744/1 68 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1706 m_b6s551i15
E00378:188:HV 68 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 117
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 118 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCC 151
i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCC 1706
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.54
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0)
+ 1124 6.6 3.2 0.0 E00378:188:HVMVNCCXX:2:2111:19136:16744/2 1 151 (0) + L1P3 LINE/L1 3620 3775 (2371) 467
ANNOTATION EVIDENCE:
1124 6.62 3.20 0.00 E00378:188:HVMVNCCXX:2:2111:19136:16744/2 1 151 0 + L1P3_orf2 LINE/L1 1511 1666 1628
1124 6.62 3.20 0.00 E00378:188:HVMVNCCXX:2:2111:19136:16744/2 1 151 (0) L1P3_orf2#LINE/L1 1511 1666 (1628) m_b6s551i71
E00378:188:HV 1 TCTTCCCTAACTCATTTTATGATGCCAGCATCATCCTGATTCCAAAACCT 50
i v v
L1P3_orf2#LIN 1511 TCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAACCT 1560
E00378:188:HV 51 GGCAGAGACACAA--GAAAAAGAAAATTTCAGGCCATTATCCGTGATGAA 98
--i v v
L1P3_orf2#LIN 1561 GGCAGAGACACAACAAAAAAAGAAAATTTCAGGCCAATATCCCTGATGAA 1610
E00378:188:HV 99 CATCGATGTGAAAATCCTCGATAGAATACTGGCAAACTGAATCCAGCA-- 146
i i i i --
L1P3_orf2#LIN 1611 CATCGATGCGAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGC 1660
E00378:188:HV 147 -CATCA 151
-
L1P3_orf2#LIN 1661 ACATCA 1666
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.65
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.67 (5 / 3)
+ 1223 7.3 0.7 0.0 E00378:188:HVMVNCCXX:2:2111:21785:25060/1 1 151 (0) + AluY SINE/Alu 40 191 (120) 468
ANNOTATION EVIDENCE:
1223 7.28 0.66 0.00 E00378:188:HVMVNCCXX:2:2111:21785:25060/1 1 151 0 + AluY SINE/Alu 40 191 120
1223 7.28 0.66 0.00 E00378:188:HVMVNCCXX:2:2111:21785:25060/1 1 151 (0) AluY#SINE/Alu 40 191 (120) c_b2s352i2
E00378:188:HV 1 TGGGAGGCCAAGGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCT 50
i v i i
AluY#SINE/Alu 40 TGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCT 89
E00378:188:HV 51 GGCTAACGTGGTGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATG 99
ii i i - vi
AluY#SINE/Alu 90 GGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG 139
E00378:188:HV 100 GGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAG 149
i
AluY#SINE/Alu 140 GGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAG 189
E00378:188:HV 150 GA 151
AluY#SINE/Alu 190 GA 191
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.81
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 622 10.2 0.0 0.0 E00378:188:HVMVNCCXX:2:2111:21785:25060/2 64 151 (0) C AluSx SINE/Alu (14) 298 211 469
ANNOTATION EVIDENCE:
622 10.23 0.00 0.00 E00378:188:HVMVNCCXX:2:2111:21785:25060/2 64 151 0 C AluSx SINE/Alu 211 298 14
622 10.23 0.00 0.00 E00378:188:HVMVNCCXX:2:2111:21785:25060/2 64 151 (0) C AluSx#SINE/Alu (14) 298 211 m_b2s357i103
E00378:188:HV 64 TTTTATTTCTTTTTTTGAGACGGAGGCTCGCTCTGTCGCCCATGCTGGAA 113
v i v v i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 114 TGCAGTGGCATGATCTCGGCTCACTGCCACCTCCACCT 151
ii v i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT 211
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.52
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0)
+ 30 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2112:28006:47966/1 94 121 (30) + (T)n Simple_repeat 1 28 (0) 470
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:28006:47966/1 94 121 30 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:28006:47966/1 94 121 (30) (T)n#Simple_repeat 1 28 (0) c_b6s251i15
E00378:188:HV 94 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 121
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 298 4.9 0.0 0.0 E00378:188:HVMVNCCXX:2:2112:28006:47966/2 1 41 (110) + L1P3 LINE/L1 3858 3898 (2248) 471
ANNOTATION EVIDENCE:
298 4.88 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:28006:47966/2 1 41 110 + L1P3_orf2 LINE/L1 1749 1789 1505
298 4.88 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:28006:47966/2 1 41 (110) L1P3_orf2#LINE/L1 1749 1789 (1505) m_b6s551i2
E00378:188:HV 1 CCATCACATAAACAGAACGAATGACAAAAACTACATGATTA 41
v i
L1P3_orf2#LIN 1749 CCATCACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.05
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 864 7.5 0.0 0.0 E00378:188:HVMVNCCXX:2:2112:28006:47966/2 44 149 (2) + AluSx SINE/Alu 14 119 (193) 472
ANNOTATION EVIDENCE:
864 7.55 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:28006:47966/2 44 149 2 + AluSx SINE/Alu 14 119 193
864 7.55 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:28006:47966/2 44 149 (2) AluSx#SINE/Alu 14 119 (193) m_b6s357i14
E00378:188:HV 44 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 93
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 94 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCAT 143
i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
E00378:188:HV 144 CTCTAC 149
AluSx#SINE/Al 114 CTCTAC 119
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0)
+ 1300 4.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2112:3305:25745/1 1 151 (0) C L1P2 LINE/L1 (507) 5648 5498 473
ANNOTATION EVIDENCE:
1300 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:3305:25745/1 1 151 0 C L1PA4_3end LINE/L1 245 395 507
1300 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:3305:25745/1 1 151 (0) C L1PA4_3end#LINE/L1 (507) 395 245 m_b1s551i275
E00378:188:HV 1 TATATACCCAGTAATGGGATAGCTGGGTCAAATGGTATTTCCAGTTCTAG 50
i i
C L1PA4_3end#LI 395 TATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAG 346
E00378:188:HV 51 ATCCCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTAGGTTAC 100
i v
C L1PA4_3end#LI 345 ATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTAC 296
E00378:188:HV 101 AGTCCCACCAACAGGGTAAAAGGGTTCCTATTTCTCCACATCCTCTCCAG 150
v v
C L1PA4_3end#LI 295 AGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAG 246
E00378:188:HV 151 C 151
C L1PA4_3end#LI 245 C 245
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.46
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1002 6.1 0.0 0.0 E00378:188:HVMVNCCXX:2:2112:3305:25745/2 20 151 (0) + L1P1 LINE/L1 5182 5313 (833) 474
ANNOTATION EVIDENCE:
1002 6.06 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:3305:25745/2 20 151 0 + L1P1_orf2 LINE/L1 3073 3204 90
1002 6.06 0.00 0.00 E00378:188:HVMVNCCXX:2:2112:3305:25745/2 20 151 (0) L1P1_orf2#LINE/L1 3073 3204 (90) m_b1s551i135
E00378:188:HV 20 ACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAGTTTTCGC 69
i i
L1P1_orf2#LIN 3073 ACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGC 3122
E00378:188:HV 70 AACCTACTCATCTGACAAAGGGATAATATGCAGAATCTACAATGAATTCA 119
v v i
L1P1_orf2#LIN 3123 AACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCA 3172
E00378:188:HV 120 AACAAATGTAGAAGAAAAAAACAAGCAACCCC 151
v v i
L1P1_orf2#LIN 3173 AACAAATTTACAAGAAAAAAACAAACAACCCC 3204
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.33
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 255 24.2 6.2 4.0 E00378:188:HVMVNCCXX:2:2112:8887:63718/1 1 125 (26) + L1ME4c LINE/L1 5659 5786 (297) 475
ANNOTATION EVIDENCE:
255 24.17 6.25 4.00 E00378:188:HVMVNCCXX:2:2112:8887:63718/1 1 125 26 + L1ME4c_3end LINE/L1 406 533 297
255 24.17 6.25 4.00 E00378:188:HVMVNCCXX:2:2112:8887:63718/1 1 125 (26) L1ME4c_3end#LINE/L1 406 533 (297) m_b2s551i26
E00378:188:HV 1 GAAATAATTTAAAATATGAGAAAAAAAAACCCTTAGACA----AATGATC 46
i ----- ii v iv vi ----i v
L1ME4c_3end#L 406 GAAATAATTCAAAA-----GAAGGAAAAAGCTATATGCACGAAGATGTTC 450
E00378:188:HV 47 ATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCTAAATTTCT 94
iiiv i vi --i v i v i v i
L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500
E00378:188:HV 95 GACAATAAAA-AATG-TCAAGTAAATTATGGTA 125
i iii- - i
L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTA 533
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.91
Transitions / transversions = 2.22 (20/9)
Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.44 (13 / 9)
+ 1288 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2113:19745:69133/1 1 151 (0) + L1P1 LINE/L1 5109 5259 (887) 476
ANNOTATION EVIDENCE:
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2113:19745:69133/1 1 151 0 + L1P1_orf2 LINE/L1 3000 3150 144
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2113:19745:69133/1 1 151 (0) L1P1_orf2#LINE/L1 3000 3150 (144) m_b1s551i108
E00378:188:HV 1 AGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAA 50
v i
L1P1_orf2#LIN 3000 AGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAA 3049
E00378:188:HV 51 AGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCT 100
L1P1_orf2#LIN 3050 AGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCT 3099
E00378:188:HV 101 ACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAAT 150
i
L1P1_orf2#LIN 3100 ACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAAT 3149
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3150 A 3150
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2113:19745:69133/2 1 151 (0) C L1P LINE/L1 (735) 5420 5270 477
ANNOTATION EVIDENCE:
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2113:19745:69133/2 1 151 0 C L1PA2_3end LINE/L1 17 167 735
1274 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2113:19745:69133/2 1 151 (0) C L1PA2_3end#LINE/L1 (735) 167 17 m_b1s551i176
E00378:188:HV 1 ATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGC 50
C L1PA2_3end#LI 167 ATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGC 118
E00378:188:HV 51 TGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACT 100
C L1PA2_3end#LI 117 TGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACT 68
E00378:188:HV 101 TTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTG 150
C L1PA2_3end#LI 67 TTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTG 18
E00378:188:HV 151 T 151
C L1PA2_3end#LI 17 T 17
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 888 5.0 3.5 7.3 E00378:188:HVMVNCCXX:2:2114:29691:40583/1 1 151 (0) C L1P3 LINE/L1 (2906) 3240 3096 478
ANNOTATION EVIDENCE:
888 5.00 3.45 7.28 E00378:188:HVMVNCCXX:2:2114:29691:40583/1 1 151 0 C L1P3_orf2 LINE/L1 987 1131 2163
888 5.00 3.45 7.28 E00378:188:HVMVNCCXX:2:2114:29691:40583/1 1 151 (0) C L1P3_orf2#LINE/L1 (2163) 1131 987 m_b6s551i233
E00378:188:HV 1 TAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATT 46
---- i i
C L1P3_orf2#LIN 1131 TAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATT 1082
E00378:188:HV 47 AATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCT 96
v - i i----------
C L1P3_orf2#LIN 1081 CATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCT 1043
E00378:188:HV 97 TCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAA 145
-i v
C L1P3_orf2#LIN 1042 TCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAA 993
E00378:188:HV 146 TTTGTT 151
C L1P3_orf2#LIN 992 TTTGTT 987
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 1264 4.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2114:29691:40583/2 1 151 (0) + L1P3 LINE/L1 2926 3076 (3070) 479
ANNOTATION EVIDENCE:
1264 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:2114:29691:40583/2 1 151 0 + L1P3_orf2 LINE/L1 817 967 2327
1264 3.97 0.00 0.00 E00378:188:HVMVNCCXX:2:2114:29691:40583/2 1 151 (0) L1P3_orf2#LINE/L1 817 967 (2327) m_b7s551i20
E00378:188:HV 1 TTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGA 50
i i
L1P3_orf2#LIN 817 TTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGA 866
E00378:188:HV 51 CACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACA 100
L1P3_orf2#LIN 867 CACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACA 916
E00378:188:HV 101 GGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAA 150
? v i i
L1P3_orf2#LIN 917 NGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAA 966
E00378:188:HV 151 G 151
L1P3_orf2#LIN 967 G 967
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 487 15.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2114:6563:9835/1 1 72 (79) C AluSx SINE/Alu (240) 72 1 480
ANNOTATION EVIDENCE:
487 15.28 0.00 0.00 E00378:188:HVMVNCCXX:2:2114:6563:9835/1 1 72 79 C AluSx SINE/Alu 1 72 240
487 15.28 0.00 0.00 E00378:188:HVMVNCCXX:2:2114:6563:9835/1 1 72 (79) C AluSx#SINE/Alu (240) 72 1 m_b5s357i67
E00378:188:HV 1 GACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAG 50
i i i i i
C AluSx#SINE/Al 72 GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAG 23
E00378:188:HV 51 GTGTGATCCAGTGCACCCAGCC 72
i v vi i i
C AluSx#SINE/Al 22 GCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.85
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 1045 6.0 1.3 0.0 E00378:188:HVMVNCCXX:2:2115:16955:53117/1 2 150 (1) + L1P3 LINE/L1 3284 3434 (2712) 481
ANNOTATION EVIDENCE:
1045 6.04 1.32 0.00 E00378:188:HVMVNCCXX:2:2115:16955:53117/1 2 150 1 + L1P3_orf2 LINE/L1 1175 1325 1969
1045 6.04 1.32 0.00 E00378:188:HVMVNCCXX:2:2115:16955:53117/1 2 150 (1) L1P3_orf2#LINE/L1 1175 1325 (1969) m_b6s551i169
E00378:188:HV 2 CAATAAAAAATGATAAAGAGGATAATACCACTGATCCCACAGAAATACAA 51
i vi
L1P3_orf2#LIN 1175 CAATAAAAAATGATAAAGGGGATATCACCACTGATCCCACAGAAATACAA 1224
E00378:188:HV 52 ACTACCATCAGAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAA 101
i i
L1P3_orf2#LIN 1225 ACTACCATCAGAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAA 1274
E00378:188:HV 102 TCTAGAAGAAAGTGATAAATTCCTAGACACATACAACCTCCCAA--CTAA 149
vv i v --
L1P3_orf2#LIN 1275 TCTAGAAGAAATGGATAAATTCCTGGACACATACACCCTCCCAAGACTAA 1324
E00378:188:HV 150 A 150
L1P3_orf2#LIN 1325 A 1325
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.65
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 1227 3.4 1.3 0.0 E00378:188:HVMVNCCXX:2:2115:16955:53117/2 3 151 (0) C L1P3 LINE/L1 (2435) 3711 3561 482
ANNOTATION EVIDENCE:
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:2:2115:16955:53117/2 3 151 0 C L1P3_orf2 LINE/L1 1452 1602 1692
1227 3.36 1.32 0.00 E00378:188:HVMVNCCXX:2:2115:16955:53117/2 3 151 (0) C L1P3_orf2#LINE/L1 (1692) 1602 1452 m_b6s551i87
E00378:188:HV 3 GGATAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTG 50
v i--
C L1P3_orf2#LIN 1602 GGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTG 1553
E00378:188:HV 51 GAATCAGGATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCT 100
v v i
C L1P3_orf2#LIN 1552 GTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCT 1503
E00378:188:HV 101 TTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTT 150
C L1P3_orf2#LIN 1502 TTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTT 1453
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 1452 G 1452
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.43
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 728 10.9 1.9 0.0 E00378:188:HVMVNCCXX:2:2115:30675:44327/1 1 101 (50) C AluSx SINE/Alu (209) 103 1 483
ANNOTATION EVIDENCE:
728 10.89 1.94 0.00 E00378:188:HVMVNCCXX:2:2115:30675:44327/1 1 101 50 C AluSx SINE/Alu 1 103 209
728 10.89 1.94 0.00 E00378:188:HVMVNCCXX:2:2115:30675:44327/1 1 101 (50) C AluSx#SINE/Alu (209) 103 1 m_b4s357i49
E00378:188:HV 1 ACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCT 48
i v i i-- i i
C AluSx#SINE/Al 103 ACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCC 54
E00378:188:HV 49 GCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCG 98
i i i i i
C AluSx#SINE/Al 53 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
E00378:188:HV 99 GCC 101
C AluSx#SINE/Al 3 GCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.84
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 2.00 (2 / 1)
+ 728 10.9 1.9 0.0 E00378:188:HVMVNCCXX:2:2115:31152:44134/1 1 101 (50) C AluSx SINE/Alu (209) 103 1 484
ANNOTATION EVIDENCE:
728 10.89 1.94 0.00 E00378:188:HVMVNCCXX:2:2115:31152:44134/1 1 101 50 C AluSx SINE/Alu 1 103 209
728 10.89 1.94 0.00 E00378:188:HVMVNCCXX:2:2115:31152:44134/1 1 101 (50) C AluSx#SINE/Alu (209) 103 1 m_b4s357i50
E00378:188:HV 1 ACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCT 48
i v i i-- i i
C AluSx#SINE/Al 103 ACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCC 54
E00378:188:HV 49 GCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCG 98
i i i i i
C AluSx#SINE/Al 53 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
E00378:188:HV 99 GCC 101
C AluSx#SINE/Al 3 GCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.84
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 2.00 (2 / 1)
+ 258 15.2 0.0 0.0 E00378:188:HVMVNCCXX:2:2115:5213:54155/1 1 46 (105) + L1MC4 LINE/L1 7604 7649 (393) 485
ANNOTATION EVIDENCE:
258 15.22 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:5213:54155/1 1 46 105 + L1MC4_3end LINE/L1 2351 2396 393
258 15.22 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:5213:54155/1 1 46 (105) L1MC4_3end#LINE/L1 2351 2396 (393) m_b3s551i40
E00378:188:HV 1 TTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGCAATG 46
i v vvv v i
L1MC4_3end#LI 2351 TTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.64
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 551 17.8 8.2 0.0 E00378:188:HVMVNCCXX:2:2115:5213:54155/1 51 151 (0) + L1MC4 LINE/L1 7762 7871 (171) 485
ANNOTATION EVIDENCE:
551 17.82 8.18 0.00 E00378:188:HVMVNCCXX:2:2115:5213:54155/1 51 151 0 + L1MC4_3end LINE/L1 2509 2618 171
551 17.82 8.18 0.00 E00378:188:HVMVNCCXX:2:2115:5213:54155/1 51 151 (0) L1MC4_3end#LINE/L1 2509 2618 (171) m_b3s551i41
E00378:188:HV 51 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 100
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
E00378:188:HV 101 ATCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCA 141
i i i --------- i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCA 2608
E00378:188:HV 142 TCACGTGTGC 151
? i v
L1MC4_3end#LI 2609 TNATGTCTGC 2618
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.10
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 9.00 (9 / 1)
+ 363 18.3 7.6 16.1 E00378:188:HVMVNCCXX:2:2115:5213:54155/2 22 151 (0) C L1MC4 LINE/L1 (90) 7952 7835 486
ANNOTATION EVIDENCE:
363 18.34 7.62 16.15 E00378:188:HVMVNCCXX:2:2115:5213:54155/2 22 151 0 C L1MC4_3end LINE/L1 2582 2699 90
363 18.34 7.62 16.15 E00378:188:HVMVNCCXX:2:2115:5213:54155/2 22 151 (0) C L1MC4_3end#LINE/L1 (90) 2699 2582 m_b3s551i8
E00378:188:HV 22 GTTAACGTTTTACCATATTTGCTTAATCATTCCCTCTCTCCACACACACA 71
i i i v i ? ? -----------
C L1MC4_3end#LI 2699 GTTAACATTTTGCCACATTTGCTTTATCATTCTCTNTNT----------- 2661
E00378:188:HV 72 CTCATACGCAGATACACACATCATTTTCTCTGAACCATTTTGAGATGAAA 121
------- -- i i iv i - vv i
C L1MC4_3end#LI 2660 -------GC--ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAG 2621
E00378:188:HV 122 TCGCACACGTGATGCTCCTT---------ATACTTCAGT 151
i v i ? i ---------
C L1MC4_3end#LI 2620 TTGCAGACATNATGCCCCTTTACCCCTAAATACTTCAGT 2582
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.46
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.17 (22 / 129), avg. gap size = 1.36 (30 / 22)
+ 1301 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2115:9546:10187/1 1 151 (0) + L1P1 LINE/L1 5048 5198 (948) 487
ANNOTATION EVIDENCE:
1301 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:9546:10187/1 1 151 0 + L1P1_orf2 LINE/L1 2939 3089 205
1301 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:9546:10187/1 1 151 (0) L1P1_orf2#LINE/L1 2939 3089 (205) m_b1s551i86
E00378:188:HV 1 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 50
?
L1P1_orf2#LIN 2939 ACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 2988
E00378:188:HV 51 AAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCT 100
v i
L1P1_orf2#LIN 2989 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3038
E00378:188:HV 101 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 150
L1P1_orf2#LIN 3039 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3088
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3089 A 3089
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1256 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:2115:9546:10187/2 1 151 (0) C L1P1 LINE/L1 (747) 5399 5249 488
ANNOTATION EVIDENCE:
1256 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:9546:10187/2 1 151 0 C L1P1_orf2 LINE/L1 3140 3290 4
1256 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:9546:10187/2 1 151 (0) C L1P1_orf2#LINE/L1 (4) 3290 3140 m_b1s551i162
E00378:188:HV 1 GATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGA 50
C L1P1_orf2#LIN 3290 GATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGA 3241
E00378:188:HV 51 GAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTT 100
C L1P1_orf2#LIN 3240 GAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTT 3191
E00378:188:HV 101 TTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCTT 150
i
C L1P1_orf2#LIN 3190 TTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCT 3141
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 3140 T 3140
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 373 19.4 0.0 0.0 E00378:188:HVMVNCCXX:2:2115:9617:48388/1 1 67 (84) C L1MC4 LINE/L1 (214) 7828 7762 489
ANNOTATION EVIDENCE:
373 19.40 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:9617:48388/1 1 67 84 C L1MC4_3end LINE/L1 2509 2575 214
373 19.40 0.00 0.00 E00378:188:HVMVNCCXX:2:2115:9617:48388/1 1 67 (84) C L1MC4_3end#LINE/L1 (214) 2575 2509 m_b3s551i64
E00378:188:HV 1 TTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAA 50
i i iv ii iiv i i i
C L1MC4_3end#LI 2575 TTCCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTATCAAA 2526
E00378:188:HV 51 ATCAGGAAGTTAACATT 67
i
C L1MC4_3end#LI 2525 ATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.71
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 353 18.8 7.0 0.0 E00378:188:HVMVNCCXX:2:2115:9617:48388/1 72 151 (0) C L1MC4 LINE/L1 (393) 7649 7564 489
ANNOTATION EVIDENCE:
353 18.75 6.98 0.00 E00378:188:HVMVNCCXX:2:2115:9617:48388/1 72 151 0 C L1MC4_3end LINE/L1 2311 2396 393
353 18.75 6.98 0.00 E00378:188:HVMVNCCXX:2:2115:9617:48388/1 72 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2311 m_b3s551i65
E00378:188:HV 72 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 121
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 122 TCT------TTTTTTTATTTATCATGACCTTCATAT 151
i------ i i i v ? v i
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACAT 2311
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 6.00 (6 / 1)
+ 1090 10.6 0.7 0.0 E00378:188:HVMVNCCXX:2:2116:15514:30193/1 10 151 (0) + AluY SINE/Alu 1 143 (168) 490
ANNOTATION EVIDENCE:
1090 10.56 0.70 0.00 E00378:188:HVMVNCCXX:2:2116:15514:30193/1 10 151 0 + AluY SINE/Alu 1 143 168
1090 10.56 0.70 0.00 E00378:188:HVMVNCCXX:2:2116:15514:30193/1 10 151 (0) AluY#SINE/Alu 1 143 (168) m_b2s356i49
E00378:188:HV 10 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 59
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 60 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 109
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 110 TGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCG 151
i i - vi
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCG 143
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.05
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.01 (1 / 141), avg. gap size = 1.00 (1 / 1)
+ 1251 4.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2116:22150:56879/1 1 151 (0) C L1P3 LINE/L1 (3142) 3004 2854 491
ANNOTATION EVIDENCE:
1251 4.64 0.00 0.00 E00378:188:HVMVNCCXX:2:2116:22150:56879/1 1 151 0 C L1P3_orf2 LINE/L1 745 895 2399
1251 4.64 0.00 0.00 E00378:188:HVMVNCCXX:2:2116:22150:56879/1 1 151 (0) C L1P3_orf2#LINE/L1 (2399) 895 745 m_b7s551i43
E00378:188:HV 1 ATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACATT 50
i
C L1P3_orf2#LIN 895 ATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTT 846
E00378:188:HV 51 GTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTTATTTCTGCCTTCAT 100
i ?i v
C L1P3_orf2#LIN 845 GTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTTATTTCTGCCTTAAT 796
E00378:188:HV 101 TTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATG 150
i i
C L1P3_orf2#LIN 795 TTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATG 746
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 745 T 745
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1070 12.3 0.0 1.4 E00378:188:HVMVNCCXX:2:2116:28310:56616/1 4 151 (0) C AluSx SINE/Alu (160) 152 7 492
ANNOTATION EVIDENCE:
1070 12.33 0.00 1.35 E00378:188:HVMVNCCXX:2:2116:28310:56616/1 4 151 0 C AluSx SINE/Alu 7 152 160
1070 12.33 0.00 1.35 E00378:188:HVMVNCCXX:2:2116:28310:56616/1 4 151 (0) C AluSx#SINE/Alu (160) 152 7 m_b5s356i27
E00378:188:HV 4 CACCACAATGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGATGGGGTTT 53
i v i i -- i
C AluSx#SINE/Al 152 CGCCACCACGCCCGGCTAA--TTTTTGTATTTTTAGTAGAGACGGGGTTT 105
E00378:188:HV 54 CAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAGTGATCTGCC 103
v i i i i i
C AluSx#SINE/Al 104 CACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCC 55
E00378:188:HV 104 CACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGCAC 151
i i i i vi i
C AluSx#SINE/Al 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGC 7
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.79
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 473 21.8 7.6 0.9 E00378:188:HVMVNCCXX:2:2116:31588:18133/1 1 111 (40) + L1MC4 LINE/L1 7793 7911 (131) 493
ANNOTATION EVIDENCE:
473 21.82 7.56 0.90 E00378:188:HVMVNCCXX:2:2116:31588:18133/1 1 111 40 + L1MC4_3end LINE/L1 2540 2658 131
473 21.82 7.56 0.90 E00378:188:HVMVNCCXX:2:2116:31588:18133/1 1 111 (40) L1MC4_3end#LINE/L1 2540 2658 (131) m_b3s551i15
E00378:188:HV 1 TGTGGCTAAACAGAAGTGTATCCTTGTTTTTAGGAAATATACACTGAAGT 50
i vii ii vi i i i
L1MC4_3end#LI 2540 TGTGGTTATGTAAGAGAATGTCCTTGTTCTTAGGAAATACACACTGAAGT 2589
E00378:188:HV 51 AT---------AAGGAGCATCACGTGTGCGATTTCATCTCAAAATGGTTC 91
--------- i ? i v i i vv -
L1MC4_3end#LI 2590 ATTTAGGGGTAAAGGGGCATNATGTCTGCAACTTACTCTCAAA-TGGTTC 2638
E00378:188:HV 92 AGAGAAAATGATGTGTGTAT 111
i vi i i
L1MC4_3end#LI 2639 AGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.78
Transitions / transversions = 2.83 (17/6)
Gap_init rate = 0.02 (2 / 110), avg. gap size = 5.00 (10 / 2)
+ 1042 12.7 0.0 0.7 E00378:188:HVMVNCCXX:2:2117:23551:11875/2 1 151 (0) + AluSx SINE/Alu 143 292 (20) 494
ANNOTATION EVIDENCE:
1042 12.66 0.00 0.66 E00378:188:HVMVNCCXX:2:2117:23551:11875/2 1 151 0 + AluSx SINE/Alu 143 292 20
1042 12.66 0.00 0.66 E00378:188:HVMVNCCXX:2:2117:23551:11875/2 1 151 (0) AluSx#SINE/Alu 143 292 (20) m_b6s356i2
E00378:188:HV 1 CATGGTGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGGATGAGGCAGGA 50
i iv i v
AluSx#SINE/Al 143 CGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
E00378:188:HV 51 GAATTGCTTGAACCGAGGAGGTAGAGGCTGAAGTGAACCGAGATCACACC 100
i vi ii i v i i i
AluSx#SINE/Al 193 GAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCC 242
E00378:188:HV 101 ATTGCACTCCAGCCTGGGAGACATGAGCGAAACTCCATCTCAAAAAAAAA 150
i v - i i
AluSx#SINE/Al 243 ACTGCACTCCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAA 291
E00378:188:HV 151 A 151
AluSx#SINE/Al 292 A 292
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.59
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:2:2118:2047:53627/1 26 70 (81) + MIR SINE/MIR 218 262 (0) 495
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:2:2118:2047:53627/1 26 70 81 + MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:2:2118:2047:53627/1 26 70 (81) MIR#SINE/MIR 218 262 (0) m_b6s601i7
E00378:188:HV 26 AATGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTATTTTT 70
i v iv viii i i v
MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 411 6.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2118:28412:69801/1 1 61 (90) + L1P3 LINE/L1 3838 3898 (2248) 496
ANNOTATION EVIDENCE:
411 6.56 0.00 0.00 E00378:188:HVMVNCCXX:2:2118:28412:69801/1 1 61 90 + L1P3_orf2 LINE/L1 1729 1789 1505
411 6.56 0.00 0.00 E00378:188:HVMVNCCXX:2:2118:28412:69801/1 1 61 (90) L1P3_orf2#LINE/L1 1729 1789 (1505) m_b6s551i11
E00378:188:HV 1 CACAAATCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAAA 50
i i v
L1P3_orf2#LIN 1729 CGCAAATCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAA 1778
E00378:188:HV 51 CTACATGATTA 61
i
L1P3_orf2#LIN 1779 CCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.70
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 716 6.8 0.0 0.0 E00378:188:HVMVNCCXX:2:2118:28412:69801/1 64 151 (0) + AluSx SINE/Alu 14 101 (211) 497
ANNOTATION EVIDENCE:
716 6.82 0.00 0.00 E00378:188:HVMVNCCXX:2:2118:28412:69801/1 64 151 0 + AluSx SINE/Alu 14 101 211
716 6.82 0.00 0.00 E00378:188:HVMVNCCXX:2:2118:28412:69801/1 64 151 (0) AluSx#SINE/Alu 14 101 (211) m_b6s357i18
E00378:188:HV 64 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 113
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 114 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATG 151
i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATG 101
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0)
+ 1266 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2119:17848:68975/1 1 151 (0) + L1P3 LINE/L1 2960 3110 (3036) 498
ANNOTATION EVIDENCE:
1266 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2119:17848:68975/1 1 151 0 + L1P3_orf2 LINE/L1 851 1001 2293
1266 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2119:17848:68975/1 1 151 (0) L1P3_orf2#LINE/L1 851 1001 (2293) m_b7s551i1
E00378:188:HV 1 ACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATA 50
L1P3_orf2#LIN 851 ACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATA 900
E00378:188:HV 51 GCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCT 100
? v i i
L1P3_orf2#LIN 901 GCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCT 950
E00378:188:HV 101 AACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAG 150
L1P3_orf2#LIN 951 AACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAG 1000
E00378:188:HV 151 C 151
L1P3_orf2#LIN 1001 C 1001
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1045 6.0 1.3 0.0 E00378:188:HVMVNCCXX:2:2119:17848:68975/2 1 149 (2) C L1P3 LINE/L1 (2712) 3434 3284 499
ANNOTATION EVIDENCE:
1045 6.04 1.32 0.00 E00378:188:HVMVNCCXX:2:2119:17848:68975/2 1 149 2 C L1P3_orf2 LINE/L1 1175 1325 1969
1045 6.04 1.32 0.00 E00378:188:HVMVNCCXX:2:2119:17848:68975/2 1 149 (2) C L1P3_orf2#LINE/L1 (1969) 1325 1175 m_b6s551i170
E00378:188:HV 1 TTTAG--TTGGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCTAG 48
-- v i vv
C L1P3_orf2#LIN 1325 TTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTAG 1276
E00378:188:HV 49 ATTTTCTAGTTTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAG 98
i i
C L1P3_orf2#LIN 1275 ATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAG 1226
E00378:188:HV 99 TTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATT 148
iv i
C L1P3_orf2#LIN 1225 TTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATT 1176
E00378:188:HV 149 G 149
C L1P3_orf2#LIN 1175 G 1175
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.65
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 1346 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2119:23358:67445/1 1 151 (0) + L1P2 LINE/L1 5497 5647 (508) 500
ANNOTATION EVIDENCE:
1346 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2119:23358:67445/1 1 151 0 + L1PA4_3end LINE/L1 244 394 508
1346 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2119:23358:67445/1 1 151 (0) L1PA4_3end#LINE/L1 244 394 (508) m_b1s551i274
E00378:188:HV 1 TGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTGGGA 50
iv
L1PA4_3end#LI 244 TGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGA 293
E00378:188:HV 51 CTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGGG 100
i
L1PA4_3end#LI 294 CTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGG 343
E00378:188:HV 101 ATCTAGAACTGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATA 150
i
L1PA4_3end#LI 344 ATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATA 393
E00378:188:HV 151 T 151
L1PA4_3end#LI 394 T 394
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1315 1.3 0.0 0.7 E00378:188:HVMVNCCXX:2:2119:23358:67445/2 1 151 (0) C L1PA3 LINE/L1 (265) 5890 5741 501
ANNOTATION EVIDENCE:
1315 1.33 0.00 0.66 E00378:188:HVMVNCCXX:2:2119:23358:67445/2 1 151 0 C L1PA3_3end LINE/L1 488 637 265
1315 1.33 0.00 0.66 E00378:188:HVMVNCCXX:2:2119:23358:67445/2 1 151 (0) C L1PA3_3end#LINE/L1 (265) 637 488 m_b1s551i352
E00378:188:HV 1 CTTGCGACAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCT 50
i
C L1PA3_3end#LI 637 CTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCT 588
E00378:188:HV 51 AACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGG 100
-
C L1PA3_3end#LI 587 -ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGG 539
E00378:188:HV 101 TGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTG 150
v
C L1PA3_3end#LI 538 TGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTG 489
E00378:188:HV 151 G 151
C L1PA3_3end#LI 488 G 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1239 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2119:29417:7128/1 1 151 (0) C L1P3 LINE/L1 (3018) 3128 2978 502
ANNOTATION EVIDENCE:
1239 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2119:29417:7128/1 1 151 0 C L1P3_orf2 LINE/L1 869 1019 2275
1239 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2119:29417:7128/1 1 151 (0) C L1P3_orf2#LINE/L1 (2275) 1019 869 m_b6s551i274
E00378:188:HV 1 ATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAG 50
C L1P3_orf2#LIN 1019 ATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAG 970
E00378:188:HV 51 TTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTTTCCCACTTTG 100
i i v
C L1P3_orf2#LIN 969 TTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTTCCCGCTTTC 920
E00378:188:HV 101 TCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCT 150
?
C L1P3_orf2#LIN 919 TCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCT 870
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 869 G 869
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1283 2.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2120:12682:70188/1 1 151 (0) + L1PA2 LINE/L1 5961 6111 (44) 503
ANNOTATION EVIDENCE:
1283 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2120:12682:70188/1 1 151 0 + L1PA2_3end LINE/L1 708 858 44
1283 2.65 0.00 0.00 E00378:188:HVMVNCCXX:2:2120:12682:70188/1 1 151 (0) L1PA2_3end#LINE/L1 708 858 (44) m_b1s551i402
E00378:188:HV 1 GAAGGGGAATATCACACTCTGTGGACTGTTGTGGGGTGGGGGGAGGGGGG 50
v v
L1PA2_3end#LI 708 GAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGG 757
E00378:188:HV 51 AGGGATAGCATGGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGT 100
v
L1PA2_3end#LI 758 AGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGT 807
E00378:188:HV 101 GCAGCACACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAAT 150
i
L1PA2_3end#LI 808 GCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAAT 857
E00378:188:HV 151 G 151
L1PA2_3end#LI 858 G 858
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1049 3.2 0.0 0.0 E00378:188:HVMVNCCXX:2:2120:12682:70188/2 28 150 (1) C L1PA2 LINE/L1 (2) 6153 6031 504
ANNOTATION EVIDENCE:
1049 3.25 0.00 0.00 E00378:188:HVMVNCCXX:2:2120:12682:70188/2 28 150 1 C L1PA2_3end LINE/L1 778 900 2
1049 3.25 0.00 0.00 E00378:188:HVMVNCCXX:2:2120:12682:70188/2 28 150 (1) C L1PA2_3end#LINE/L1 (2) 900 778 m_b1s551i434
E00378:188:HV 28 TTATTTTTTTTATTACACTTTAAGTTGTAGGGTACATGTGCACATTGTGC 77
v i v
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 78 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 127
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
E00378:188:HV 128 AACTCGTCATCTAGCATTAGGTA 150
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTA 778
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.56
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0)
+ 478 13.9 0.0 0.0 E00378:188:HVMVNCCXX:2:2121:2128:43220/1 80 151 (0) + AluY SINE/Alu 1 72 (239) 505
ANNOTATION EVIDENCE:
478 13.89 0.00 0.00 E00378:188:HVMVNCCXX:2:2121:2128:43220/1 80 151 0 + AluY SINE/Alu 1 72 239
478 13.89 0.00 0.00 E00378:188:HVMVNCCXX:2:2121:2128:43220/1 80 151 (0) AluY#SINE/Alu 1 72 (239) m_b2s357i60
E00378:188:HV 80 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 129
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 130 GGCGGGCTGATAATGAGGACAG 151
v v i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAG 72
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.06
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 767 5.4 0.0 0.0 E00378:188:HVMVNCCXX:2:2122:21714:40970/2 1 93 (58) + AluSx SINE/Alu 199 291 (21) 506
ANNOTATION EVIDENCE:
767 5.38 0.00 0.00 E00378:188:HVMVNCCXX:2:2122:21714:40970/2 1 93 58 + AluSx SINE/Alu 199 291 21
767 5.38 0.00 0.00 E00378:188:HVMVNCCXX:2:2122:21714:40970/2 1 93 (58) AluSx#SINE/Alu 199 291 (21) m_b4s357i20
E00378:188:HV 1 CTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 50
i i
AluSx#SINE/Al 199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248
E00378:188:HV 51 CTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 93
i i i
AluSx#SINE/Al 249 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.56
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0)
+ 19 14.9 0.0 0.0 E00378:188:HVMVNCCXX:2:2122:21714:40970/2 121 151 (0) + (CA)n Simple_repeat 1 31 (0) 507
ANNOTATION EVIDENCE:
19 14.92 0.00 0.00 E00378:188:HVMVNCCXX:2:2122:21714:40970/2 121 151 0 + (CA)n Simple_repeat 1 31 0
19 14.92 0.00 0.00 E00378:188:HVMVNCCXX:2:2122:21714:40970/2 121 151 (0) (CA)n#Simple_repeat 1 31 (0) m_b4s252i64
E00378:188:HV 121 CATACATGCACACACATACACACACACACAC 151
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACAC 31
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 917 4.4 2.1 1.4 E00378:188:HVMVNCCXX:2:2122:5112:32953/1 1 139 (12) + L1P3 LINE/L1 3027 3166 (2980) 508
ANNOTATION EVIDENCE:
917 4.38 2.14 1.44 E00378:188:HVMVNCCXX:2:2122:5112:32953/1 1 139 12 + L1P3_orf2 LINE/L1 918 1057 2237
917 4.38 2.14 1.44 E00378:188:HVMVNCCXX:2:2122:5112:32953/1 1 139 (12) L1P3_orf2#LINE/L1 918 1057 (2237) m_b6s551i258
E00378:188:HV 1 GACAAAGTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAG 50
v i i
L1P3_orf2#LIN 918 GAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAG 967
E00378:188:HV 51 AACGAGAGAAGCAAGAGCAAACAAATGCAAAAGCTAGCAGAAGACAAGAA 100
v v
L1P3_orf2#LIN 968 AACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAA 1017
E00378:188:HV 101 ATAACTAAGATCAGAGCTGAGA---GAAGGAGGTAGAGACAC 139
-- --- i
L1P3_orf2#LIN 1018 ATAACTAAGATCAGAGC--AGAACTGAAGGAGATAGAGACAC 1057
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.13
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.67 (5 / 3)
+ 589 19.3 1.5 0.0 E00378:188:HVMVNCCXX:2:2122:5112:32953/2 1 135 (16) C L1P3 LINE/L1 (2648) 3498 3362 509
ANNOTATION EVIDENCE:
589 19.26 1.46 0.00 E00378:188:HVMVNCCXX:2:2122:5112:32953/2 1 135 16 C L1P3_orf2 LINE/L1 1253 1389 1905
589 19.26 1.46 0.00 E00378:188:HVMVNCCXX:2:2122:5112:32953/2 1 135 (16) C L1P3_orf2#LINE/L1 (1905) 1389 1253 m_b6s551i146
E00378:188:HV 1 ATTAATTCCTGCCTCAATTTCCGAACTTGGGATTGGTCTATTCAGGGATT 50
v v vv
C L1P3_orf2#LIN 1389 ATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATT 1340
E00378:188:HV 51 CGACTTCTTCCTGCTTTA--TGTGGGGGGTGGTCTGTGTCTAGGCGTGTG 98
v --iv i vv v i vi v i
C L1P3_orf2#LIN 1339 CGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTA 1290
E00378:188:HV 99 GCCCGTTCTTCTCGTTTGTCTAGTTTCTTCGCACAGA 135
v vv v v v v i ii
C L1P3_orf2#LIN 1289 TCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGA 1253
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.38
Transitions / transversions = 0.44 (8/18)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 2.00 (2 / 1)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:2:2123:7253:48828/1 16 107 (44) C MIRb SINE/MIR (107) 161 67 510
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:2:2123:7253:48828/1 16 107 44 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:2:2123:7253:48828/1 16 107 (44) C MIRb#SINE/MIR (107) 161 67 m_b6s601i69
E00378:188:HV 16 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 63
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 64 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 107
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 24 3.6 0.0 0.0 E00378:188:HVMVNCCXX:2:2123:7253:48828/2 1 29 (122) + (A)n Simple_repeat 1 29 (0) 511
ANNOTATION EVIDENCE:
24 3.57 0.00 0.00 E00378:188:HVMVNCCXX:2:2123:7253:48828/2 1 29 122 + (A)n Simple_repeat 1 29 0
24 3.57 0.00 0.00 E00378:188:HVMVNCCXX:2:2123:7253:48828/2 1 29 (122) (A)n#Simple_repeat 1 29 (0) m_b6s252i17
E00378:188:HV 1 AAAAAAAAAAAAAAAAAAAAAAAAAAGAA 29
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 1235 2.7 0.0 0.0 E00378:188:HVMVNCCXX:2:2202:8359:11435/2 3 151 (0) C L1P1 LINE/L1 (1021) 5125 4977 512
ANNOTATION EVIDENCE:
1235 2.68 0.00 0.00 E00378:188:HVMVNCCXX:2:2202:8359:11435/2 3 151 0 C L1P1_orf2 LINE/L1 2868 3016 278
1235 2.68 0.00 0.00 E00378:188:HVMVNCCXX:2:2202:8359:11435/2 3 151 (0) C L1P1_orf2#LINE/L1 (278) 3016 2868 m_b1s551i53
E00378:188:HV 3 CTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATG 52
C L1P1_orf2#LIN 3016 CTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATG 2967
E00378:188:HV 53 CCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGT 102
?
C L1P1_orf2#LIN 2966 CCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGT 2917
E00378:188:HV 103 TTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTA 151
i i v
C L1P1_orf2#LIN 2916 TTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTA 2868
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 904 4.3 0.7 7.3 E00378:188:HVMVNCCXX:2:2204:7710:9115/2 1 150 (1) + L1P3 LINE/L1 3057 3196 (2950) 513
ANNOTATION EVIDENCE:
904 4.32 0.72 7.33 E00378:188:HVMVNCCXX:2:2204:7710:9115/2 1 150 1 + L1P3_orf2 LINE/L1 948 1087 2207
904 4.32 0.72 7.33 E00378:188:HVMVNCCXX:2:2204:7710:9115/2 1 150 (1) L1P3_orf2#LINE/L1 948 1087 (2207) m_b6s551i253
E00378:188:HV 1 CCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAA 50
L1P3_orf2#LIN 948 CCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAA 997
E00378:188:HV 51 AAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAG 99
v i-
L1P3_orf2#LIN 998 AAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAG 1047
E00378:188:HV 100 ATAGAGACACACACACACAAAAAAAACCTTTCAAAAAAATCAATTAATCT 149
----------i i - v i
L1P3_orf2#LIN 1048 ATAGAGACAC----------GAAAAACCCTTCAAAAAA-TCAATGAATCC 1086
E00378:188:HV 150 A 150
L1P3_orf2#LIN 1087 A 1087
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.77
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.00 (12 / 12)
+ 917 5.0 0.7 7.3 E00378:188:HVMVNCCXX:2:2207:13139:35186/1 1 151 (0) + L1P3 LINE/L1 3088 3228 (2918) 514
ANNOTATION EVIDENCE:
917 5.00 0.71 7.28 E00378:188:HVMVNCCXX:2:2207:13139:35186/1 1 151 0 + L1P3_orf2 LINE/L1 979 1119 2175
917 5.00 0.71 7.28 E00378:188:HVMVNCCXX:2:2207:13139:35186/1 1 151 (0) L1P3_orf2#LINE/L1 979 1119 (2175) m_b6s551i240
E00378:188:HV 1 CAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGAT 50
L1P3_orf2#LIN 979 CAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGAT 1028
E00378:188:HV 51 CAGAGCTGAG-TGAAGGAGATAGAGACACACACACACAAAAAAAACCTTT 99
v i- ----------i i
L1P3_orf2#LIN 1029 CAGAGCAGAACTGAAGGAGATAGAGACAC----------GAAAAACCCTT 1068
E00378:188:HV 100 CAAAAAAATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAA 149
- v i
L1P3_orf2#LIN 1069 CAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAA 1117
E00378:188:HV 150 CA 151
i
L1P3_orf2#LIN 1118 TA 1119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1164 4.6 1.3 0.0 E00378:188:HVMVNCCXX:2:2207:13139:35186/2 1 151 (0) C L1P3 LINE/L1 (2641) 3505 3353 515
ANNOTATION EVIDENCE:
1164 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:2207:13139:35186/2 1 151 0 C L1P3_orf2 LINE/L1 1244 1396 1898
1164 4.64 1.30 0.00 E00378:188:HVMVNCCXX:2:2207:13139:35186/2 1 151 (0) C L1P3_orf2#LINE/L1 (1898) 1396 1244 m_b6s551i143
E00378:188:HV 1 GTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTC 50
C L1P3_orf2#LIN 1396 GTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTC 1347
E00378:188:HV 51 AGGGATTCGACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTAG 98
v -- v i
C L1P3_orf2#LIN 1346 AGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAG 1297
E00378:188:HV 99 GAATTTATCACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTATT 148
vv i i
C L1P3_orf2#LIN 1296 GAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTT 1247
E00378:188:HV 149 TAT 151
C L1P3_orf2#LIN 1246 TAT 1244
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1288 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2208:25997:43712/1 1 151 (0) + L1P1 LINE/L1 5026 5176 (970) 516
ANNOTATION EVIDENCE:
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2208:25997:43712/1 1 151 0 + L1P1_orf2 LINE/L1 2917 3067 227
1288 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2208:25997:43712/1 1 151 (0) L1P1_orf2#LINE/L1 2917 3067 (227) m_b1s551i78
E00378:188:HV 1 ACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGG 50
?
L1P1_orf2#LIN 2917 ACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGG 2966
E00378:188:HV 51 CATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAG 100
L1P1_orf2#LIN 2967 CATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAG 3016
E00378:188:HV 101 ACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 150
v i
L1P1_orf2#LIN 3017 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 3066
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3067 A 3067
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1300 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:2208:25997:43712/2 1 151 (0) C L1P1 LINE/L1 (691) 5464 5314 517
ANNOTATION EVIDENCE:
1300 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2208:25997:43712/2 1 151 0 C L1PA2_3end LINE/L1 61 211 691
1300 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2208:25997:43712/2 1 151 (0) C L1PA2_3end#LINE/L1 (691) 211 61 m_b1s551i200
E00378:188:HV 1 TTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCT 50
C L1PA2_3end#LI 211 TTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCT 162
E00378:188:HV 51 CTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATA 100
C L1PA2_3end#LI 161 CTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATA 112
E00378:188:HV 101 AATGTCTTCTTTTGAGAAGTGTCTGGTCATGTCCTTCGCCCACTTTTTGA 150
v
C L1PA2_3end#LI 111 AATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGA 62
E00378:188:HV 151 T 151
C L1PA2_3end#LI 61 T 61
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1374 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2209:11535:32443/1 1 151 (0) C L1P1 LINE/L1 (472) 5683 5533 518
ANNOTATION EVIDENCE:
1374 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:11535:32443/1 1 151 0 C L1PA3_3end LINE/L1 280 430 472
1374 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:11535:32443/1 1 151 (0) C L1PA3_3end#LINE/L1 (472) 430 280 m_b1s551i284
E00378:188:HV 1 TGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAAT 50
i
C L1PA3_3end#LI 430 TGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAAT 381
E00378:188:HV 51 GGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCA 100
i i
C L1PA3_3end#LI 380 GGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCG 331
E00378:188:HV 101 CCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGT 150
C L1PA3_3end#LI 330 CCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGT 281
E00378:188:HV 151 G 151
C L1PA3_3end#LI 280 G 280
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1308 0.7 0.0 0.0 E00378:188:HVMVNCCXX:2:2209:11535:32443/2 1 151 (0) + L1P1 LINE/L1 5340 5490 (665) 519
ANNOTATION EVIDENCE:
1308 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:11535:32443/2 1 151 0 + L1PA2_3end LINE/L1 87 237 665
1308 0.66 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:11535:32443/2 1 151 (0) L1PA2_3end#LINE/L1 87 237 (665) m_b1s551i215
E00378:188:HV 1 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA 50
L1PA2_3end#LI 87 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA 136
E00378:188:HV 51 AATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATG 100
L1PA2_3end#LI 137 AATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATG 186
E00378:188:HV 101 AGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAA 150
i
L1PA2_3end#LI 187 AGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAA 236
E00378:188:HV 151 C 151
L1PA2_3end#LI 237 C 237
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 541 2.9 0.0 0.0 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 1 69 (82) + L1PA2 LINE/L1 6085 6153 (2) 520
ANNOTATION EVIDENCE:
541 2.90 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 1 69 82 + L1PA2_3end LINE/L1 832 900 2
541 2.90 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 1 69 (82) L1PA2_3end#LINE/L1 832 900 (2) m_b1s551i460
E00378:188:HV 1 ATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAA 50
L1PA2_3end#LI 832 ATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAA 881
E00378:188:HV 51 AGTGTAATAAAAAAAATAA 69
i v
L1PA2_3end#LI 882 AGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.96
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 63 151 (0) C L1M5 LINE/L1 (293) 5831 5741 521 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 63 151 0 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 63 151 (0) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i461
E00378:188:HV 63 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 112
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 113 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 151
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 84 151 0 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:2209:17766:60642/1 84 151 (0) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i462
E00378:188:HV 84 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 133
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 134 CTATTGTTGGACATTTAG 151
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1042 9.9 0.0 1.4 E00378:188:HVMVNCCXX:2:2209:17766:60642/2 1 143 (8) + AluSx SINE/Alu 164 304 (8) 522
ANNOTATION EVIDENCE:
1042 9.93 0.00 1.40 E00378:188:HVMVNCCXX:2:2209:17766:60642/2 1 143 8 + AluSx SINE/Alu 164 304 8
1042 9.93 0.00 1.40 E00378:188:HVMVNCCXX:2:2209:17766:60642/2 1 143 (8) AluSx#SINE/Alu 164 304 (8) m_b2s357i14
E00378:188:HV 1 TCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGG 50
i i i i i
AluSx#SINE/Al 164 TCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGG 213
E00378:188:HV 51 CAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTTG 100
i i i ii i--
AluSx#SINE/Al 214 CGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGC-- 261
E00378:188:HV 101 GACGAAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA 143
ii i
AluSx#SINE/Al 262 GACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.37
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.01 (2 / 142), avg. gap size = 1.00 (2 / 2)
+ 463 18.4 5.8 0.0 E00378:188:HVMVNCCXX:2:2210:16498:28910/2 1 98 (53) + L1MC4 LINE/L1 7546 7649 (393) 523
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:2:2210:16498:28910/2 1 98 53 + L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:2:2210:16498:28910/2 1 98 (53) L1MC4_3end#LINE/L1 2293 2396 (393) m_b3s551i76
E00378:188:HV 1 GACCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA----- 45
i v v i v ? v i i i -----
L1MC4_3end#LI 2293 GGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTG 2342
E00378:188:HV 46 -AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 94
-i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
E00378:188:HV 95 AATG 98
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 3.00 (6 / 2)
+ 278 10.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2210:16498:28910/2 103 141 (10) + L1MC4 LINE/L1 7762 7800 (242) 523
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 E00378:188:HVMVNCCXX:2:2210:16498:28910/2 103 141 10 + L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 E00378:188:HVMVNCCXX:2:2210:16498:28910/2 103 141 (10) L1MC4_3end#LINE/L1 2509 2547 (242) m_b3s551i77
E00378:188:HV 103 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTA 141
i i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTA 2547
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 615 15.4 0.0 6.0 E00378:188:HVMVNCCXX:2:2212:17005:31195/1 35 151 (0) C AluSx SINE/Alu (8) 304 195 524
ANNOTATION EVIDENCE:
615 15.45 0.00 5.98 E00378:188:HVMVNCCXX:2:2212:17005:31195/1 35 151 0 C AluSx SINE/Alu 195 304 8
615 15.45 0.00 5.98 E00378:188:HVMVNCCXX:2:2212:17005:31195/1 35 151 (0) C AluSx#SINE/Alu (8) 304 195 m_b5s357i12
E00378:188:HV 35 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 84
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 85 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 134
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 135 TAGTAGGTTCAAGCAAT 151
vvii i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGAT 195
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.26
Transitions / transversions = 1.12 (9/8)
Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7)
+ 1017 13.4 0.0 1.3 E00378:188:HVMVNCCXX:2:2212:17005:31195/2 1 151 (0) + AluSx SINE/Alu 48 196 (116) 525
ANNOTATION EVIDENCE:
1017 13.43 0.00 1.32 E00378:188:HVMVNCCXX:2:2212:17005:31195/2 1 151 0 + AluSx SINE/Alu 48 196 116
1017 13.43 0.00 1.32 E00378:188:HVMVNCCXX:2:2212:17005:31195/2 1 151 (0) AluSx#SINE/Alu 48 196 (116) m_b5s356i19
E00378:188:HV 1 CAAGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAA 50
i i i i i i
AluSx#SINE/Al 48 CGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAA 97
E00378:188:HV 51 CGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCAT 100
i v i -- i i
AluSx#SINE/Al 98 CATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCGT 145
E00378:188:HV 101 TGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGACAA 150
v i v v vi i i v
AluSx#SINE/Al 146 GGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAA 195
E00378:188:HV 151 T 151
AluSx#SINE/Al 196 T 196
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.46
Transitions / transversions = 2.33 (14/6)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 233 13.2 0.0 1.9 E00378:188:HVMVNCCXX:2:2213:6512:35660/1 1 54 (97) + 7SLRNA srpRNA 268 320 (0) 526
ANNOTATION EVIDENCE:
233 13.20 0.00 1.85 E00378:188:HVMVNCCXX:2:2213:6512:35660/1 1 54 97 + 7SLRNA SINE/Alu 268 320 0
233 13.20 0.00 1.85 E00378:188:HVMVNCCXX:2:2213:6512:35660/1 1 54 (97) 7SLRNA#SINE/Alu 268 320 (0) m_b6s502i0
E00378:188:HV 1 CAGCCTGGGAGACATGAGCGAAACTCCATCTCAAAAAAAAAAAAAAAAAA 50
vi - i i i vv
7SLRNA#SINE/A 268 CAGCCTGGGCAACAT-AGCGAGACCCCGTCTCTTAAAAAAAAAAAAAAAA 316
E00378:188:HV 51 AAAA 54
7SLRNA#SINE/A 317 AAAA 320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.54
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1)
+ 254 31.5 5.3 0.0 E00378:188:HVMVNCCXX:2:2213:6512:35660/2 32 139 (12) C MIR SINE/MIR (75) 187 74 527
ANNOTATION EVIDENCE:
254 31.48 5.27 0.00 E00378:188:HVMVNCCXX:2:2213:6512:35660/2 32 139 12 C MIR SINE/MIR 74 187 75
254 31.48 5.27 0.00 E00378:188:HVMVNCCXX:2:2213:6512:35660/2 32 139 (12) C MIR#SINE/MIR (75) 187 74 m_b6s601i44
E00378:188:HV 32 TTAATTCTT---ATACTTCTGTCACTTAGGTTCTATTATTTCCTTCAATT 78
i i--- i vii i v vv v vi ii v
C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTT 138
E00378:188:HV 79 TATAAGTGA--AAACGGTGACTTAGGGAGGTAAAGTAACTTG-CTGATGC 125
i ii -- v v i vi i v - ii v i
C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88
E00378:188:HV 126 CGCAGAGCTAACAA 139
i v ii
C MIR#SINE/MIR 87 CACACAGCTAGTAA 74
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 42.48
Transitions / transversions = 1.62 (21/13)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 2.00 (6 / 3)
+ 548 19.7 18.9 0.0 E00378:188:HVMVNCCXX:2:2214:14377:34834/1 10 151 (0) + L1MC4 LINE/L1 7447 7621 (421) 528
ANNOTATION EVIDENCE:
548 19.72 18.86 0.00 E00378:188:HVMVNCCXX:2:2214:14377:34834/1 10 151 0 + L1MC4_3end LINE/L1 2194 2368 421
548 19.72 18.86 0.00 E00378:188:HVMVNCCXX:2:2214:14377:34834/1 10 151 (0) L1MC4_3end#LINE/L1 2194 2368 (421) m_b3s551i109
E00378:188:HV 10 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 51
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
E00378:188:HV 52 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC----------------- 84
i i i vii -----------------
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGACATTCTACAAAATAACTG 2293
E00378:188:HV 85 --CTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA------ 126
-- v v i v ? v i i i ------
L1MC4_3end#LI 2294 GCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTGA 2343
E00378:188:HV 127 AGAACTGTTCCAGATTGAAGGAGAC 151
i i
L1MC4_3end#LI 2344 GGAACTGTTCCAGATTAAAGGAGAC 2368
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.19
Transitions / transversions = 4.40 (22/5)
Gap_init rate = 0.03 (4 / 141), avg. gap size = 8.25 (33 / 4)
+ 551 17.8 8.2 0.0 E00378:188:HVMVNCCXX:2:2214:14377:34834/2 1 101 (50) C L1MC4 LINE/L1 (171) 7871 7762 529
ANNOTATION EVIDENCE:
551 17.82 8.18 0.00 E00378:188:HVMVNCCXX:2:2214:14377:34834/2 1 101 50 C L1MC4_3end LINE/L1 2509 2618 171
551 17.82 8.18 0.00 E00378:188:HVMVNCCXX:2:2214:14377:34834/2 1 101 (50) C L1MC4_3end#LINE/L1 (171) 2618 2509 m_b3s551i38
E00378:188:HV 1 GCACACGTGATGCTCCTT---------ATACTTCAGTGTATATTTCCTAA 41
v i ? i --------- i
C L1MC4_3end#LI 2618 GCAGACATNATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAA 2569
E00378:188:HV 42 AAACAAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAAATCAGGA 91
i i iv ii iiv i i i
C L1MC4_3end#LI 2568 GAACAAGGACATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGA 2519
E00378:188:HV 92 AGTTAACATT 101
i
C L1MC4_3end#LI 2518 AATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.10
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 9.00 (9 / 1)
+ 258 15.2 0.0 0.0 E00378:188:HVMVNCCXX:2:2214:14377:34834/2 106 151 (0) C L1MC4 LINE/L1 (393) 7649 7604 529
ANNOTATION EVIDENCE:
258 15.22 0.00 0.00 E00378:188:HVMVNCCXX:2:2214:14377:34834/2 106 151 0 C L1MC4_3end LINE/L1 2351 2396 393
258 15.22 0.00 0.00 E00378:188:HVMVNCCXX:2:2214:14377:34834/2 106 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2351 m_b3s551i39
E00378:188:HV 106 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAA 151
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAA 2351
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.64
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 1250 3.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2215:11546:8693/2 1 151 (0) C L1P1 LINE/L1 (1031) 5115 4965 530
ANNOTATION EVIDENCE:
1250 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:2215:11546:8693/2 1 151 0 C L1P1_orf2 LINE/L1 2856 3006 288
1250 3.31 0.00 0.00 E00378:188:HVMVNCCXX:2:2215:11546:8693/2 1 151 (0) C L1P1_orf2#LINE/L1 (288) 3006 2856 m_b1s551i48
E00378:188:HV 1 CATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCT 50
C L1P1_orf2#LIN 3006 CATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCT 2957
E00378:188:HV 51 GAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTA 100
?
C L1P1_orf2#LIN 2956 GAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTA 2907
E00378:188:HV 101 ATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTATCAGGTGTAAG 150
i i v v
C L1P1_orf2#LIN 2906 ACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAG 2857
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2856 G 2856
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 503 11.8 0.0 0.0 E00378:188:HVMVNCCXX:2:2215:19522:38086/1 1 68 (83) C AluY SINE/Alu (243) 68 1 531
ANNOTATION EVIDENCE:
503 11.76 0.00 0.00 E00378:188:HVMVNCCXX:2:2215:19522:38086/1 1 68 83 C AluY SINE/Alu 1 68 243
503 11.76 0.00 0.00 E00378:188:HVMVNCCXX:2:2215:19522:38086/1 1 68 (83) C AluY#SINE/Alu (243) 68 1 m_b4s357i62
E00378:188:HV 1 CCTTGTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGT 50
i i i i i i
C AluY#SINE/Alu 68 CCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 19
E00378:188:HV 51 GAGCCACTGCACCCGGCC 68
i i
C AluY#SINE/Alu 18 GAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.56
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1085 11.3 1.3 0.0 E00378:188:HVMVNCCXX:2:2215:2483:46648/2 1 150 (1) C AluSx SINE/Alu (149) 163 12 532
ANNOTATION EVIDENCE:
1085 11.33 1.31 0.00 E00378:188:HVMVNCCXX:2:2215:2483:46648/2 1 150 1 C AluSx SINE/Alu 12 163 149
1085 11.33 1.31 0.00 E00378:188:HVMVNCCXX:2:2215:2483:46648/2 1 150 (1) C AluSx#SINE/Alu (149) 163 12 m_b4s357i36
E00378:188:HV 1 TTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAG 50
i vi v i i
C AluSx#SINE/Al 163 TTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAG 114
E00378:188:HV 51 ATGGAGTTTCACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--G 98
i i i v i i--
C AluSx#SINE/Al 113 ACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGG 64
E00378:188:HV 99 TGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCC 148
i i i i i
C AluSx#SINE/Al 63 TGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
E00378:188:HV 149 AC 150
C AluSx#SINE/Al 13 AC 12
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.88
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 914 12.1 0.0 0.0 E00378:188:HVMVNCCXX:2:2216:7831:11470/1 1 124 (27) C AluSx SINE/Alu (188) 124 1 533
ANNOTATION EVIDENCE:
914 12.10 0.00 0.00 E00378:188:HVMVNCCXX:2:2216:7831:11470/1 1 124 27 C AluSx SINE/Alu 1 124 188
914 12.10 0.00 0.00 E00378:188:HVMVNCCXX:2:2216:7831:11470/1 1 124 (27) C AluSx#SINE/Alu (188) 124 1 m_b5s357i49
E00378:188:HV 1 TTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCCCAAACTC 50
i v i i i
C AluSx#SINE/Al 124 TTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTC 75
E00378:188:HV 51 CTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTAC 100
i i i i i
C AluSx#SINE/Al 74 CTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTAC 25
E00378:188:HV 101 AGGTGTGAGCCAGTGCACCCAGCC 124
i vi i i
C AluSx#SINE/Al 24 AGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.82
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0)
+ 1241 5.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2217:4594:24567/1 1 151 (0) C L1P3 LINE/L1 (3151) 2995 2845 534
ANNOTATION EVIDENCE:
1241 5.30 0.00 0.00 E00378:188:HVMVNCCXX:2:2217:4594:24567/1 1 151 0 C L1P3_orf2 LINE/L1 736 886 2408
1241 5.30 0.00 0.00 E00378:188:HVMVNCCXX:2:2217:4594:24567/1 1 151 (0) C L1P3_orf2#LINE/L1 (2408) 886 736 m_b7s551i45
E00378:188:HV 1 TAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTG 50
i
C L1P3_orf2#LIN 886 TAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTG 837
E00378:188:HV 51 TTCTTATTGGTTTCAAAGAACTTACTTATTTCTGCCTTCATTTCATTATT 100
i ?i v i
C L1P3_orf2#LIN 836 TTCTCATTGGTTTCAAAGAACTTNTTTATTTCTGCCTTAATTTCGTTATT 787
E00378:188:HV 101 TACCTAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGTGT 150
i i
C L1P3_orf2#LIN 786 TACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGTGC 737
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 736 G 736
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1295 2.0 0.0 0.7 E00378:188:HVMVNCCXX:2:2218:22567:52924/1 1 151 (0) + L1PA3 LINE/L1 5784 5933 (222) 535
ANNOTATION EVIDENCE:
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:2:2218:22567:52924/1 1 151 0 + L1PA3_3end LINE/L1 531 680 222
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:2:2218:22567:52924/1 1 151 (0) L1PA3_3end#LINE/L1 531 680 (222) m_b1s551i360
E00378:188:HV 1 CATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGT 50
L1PA3_3end#LI 531 CATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGT 580
E00378:188:HV 51 CCTTTGTTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACT 100
-
L1PA3_3end#LI 581 CCTTTGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACT 629
E00378:188:HV 101 GTCGCAAGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGA 150
i v i
L1PA3_3end#LI 630 ATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGA 679
E00378:188:HV 151 A 151
L1PA3_3end#LI 680 A 680
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 525 8.0 0.0 0.1 E00378:188:HVMVNCCXX:2:2218:22567:52924/2 1 88 (63) C L1PA3 LINE/L1 (88) 6067 5981 536
ANNOTATION EVIDENCE:
496 9.19 0.00 1.14 E00378:188:HVMVNCCXX:2:2218:22567:52924/2 1 88 63 C L1PA2_3end LINE/L1 728 814 88
496 9.19 0.00 1.14 E00378:188:HVMVNCCXX:2:2218:22567:52924/2 1 88 (63) C L1PA2_3end#LINE/L1 (88) 814 728 m_b1s551i411
E00378:188:HV 1 GTGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGC 50
i
C L1PA2_3end#LI 814 GCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGC 765
E00378:188:HV 51 TATCCCTCCCCCCCCTCCGCCCCCCGCCCCGACTCCCC 88
i i v v i v - v
C L1PA2_3end#LI 764 TATCCCTCCCCCCTCCCCCCACCCCACCAC-AGTCCCC 728
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.65
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1)
525 7.79 0.00 0.00 E00378:188:HVMVNCCXX:2:2218:22567:52924/2 1 77 74 C L1PA3_3end LINE/L1 738 814 88
525 7.79 0.00 0.00 E00378:188:HVMVNCCXX:2:2218:22567:52924/2 1 77 (74) C L1PA3_3end#LINE/L1 (88) 814 738 m_b1s551i410
E00378:188:HV 1 GTGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGC 50
i
C L1PA3_3end#LI 814 GCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGC 765
E00378:188:HV 51 TATCCCTCCCCCCCCTCCGCCCCCCGC 77
i i v v i
C L1PA3_3end#LI 764 TATCCCTCCCCCCTCCCCCCACCCCAC 738
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.96
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 1009 13.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2219:14499:11136/1 1 150 (1) + AluSx SINE/Alu 116 265 (47) 537
ANNOTATION EVIDENCE:
1009 13.33 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:14499:11136/1 1 150 1 + AluSx SINE/Alu 116 265 47
1009 13.33 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:14499:11136/1 1 150 (1) AluSx#SINE/Alu 116 265 (47) m_b6s357i8
E00378:188:HV 1 CTACGAAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTAATC 50
v v i i iv
AluSx#SINE/Al 116 CTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATC 165
E00378:188:HV 51 CCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGAGGAGGTA 100
i v i vi ii
AluSx#SINE/Al 166 CCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCG 215
E00378:188:HV 101 GAGGCTGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTGGGAGACA 150
i v i i i i v
AluSx#SINE/Al 216 GAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA 265
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.31
Transitions / transversions = 1.86 (13/7)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 31 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2219:14499:11136/2 82 110 (41) + (T)n Simple_repeat 1 29 (0) 538
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:14499:11136/2 82 110 41 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:14499:11136/2 82 110 (41) (T)n#Simple_repeat 1 29 (0) c_b6s251i14
E00378:188:HV 82 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 110
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 1009 13.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2219:15128:16340/1 1 150 (1) + AluSx SINE/Alu 116 265 (47) 539
ANNOTATION EVIDENCE:
1009 13.33 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:15128:16340/1 1 150 1 + AluSx SINE/Alu 116 265 47
1009 13.33 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:15128:16340/1 1 150 (1) AluSx#SINE/Alu 116 265 (47) m_b6s357i9
E00378:188:HV 1 CTACGAAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCTGTAATC 50
v v i i iv
AluSx#SINE/Al 116 CTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATC 165
E00378:188:HV 51 CCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACCGAGGAGGTA 100
i v i vi ii
AluSx#SINE/Al 166 CCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCG 215
E00378:188:HV 101 GAGGCTGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTGGGAGACA 150
i v i i i i v
AluSx#SINE/Al 216 GAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA 265
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.31
Transitions / transversions = 1.86 (13/7)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 32 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2219:15128:16340/2 82 111 (40) + (T)n Simple_repeat 1 30 (0) 540
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:15128:16340/2 82 111 40 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2219:15128:16340/2 82 111 (40) (T)n#Simple_repeat 1 30 (0) c_b6s251i13
E00378:188:HV 82 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 111
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 975 10.9 1.5 0.0 E00378:188:HVMVNCCXX:2:2220:17391:31511/1 24 151 (0) + AluSx SINE/Alu 1 130 (182) 541
ANNOTATION EVIDENCE:
975 10.94 1.54 0.00 E00378:188:HVMVNCCXX:2:2220:17391:31511/1 24 151 0 + AluSx SINE/Alu 1 130 182
975 10.94 1.54 0.00 E00378:188:HVMVNCCXX:2:2220:17391:31511/1 24 151 (0) AluSx#SINE/Alu 1 130 (182) m_b4s356i53
E00378:188:HV 24 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 73
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 74 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 121
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 122 GGTGAAACTCCATCTCTACTAAAAACACAA 151
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAA 130
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.58
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 127), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:2:2220:17391:31511/2 54 85 (66) + (TG)n Simple_repeat 1 32 (0) 542
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:17391:31511/2 54 85 66 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:17391:31511/2 54 85 (66) (TG)n#Simple_repeat 1 32 (0) m_b4s252i63
E00378:188:HV 54 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 85
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:2:2220:17391:31511/2 86 98 (53) + (TGTATG)n Simple_repeat 1 41 (0) 543
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:2:2220:17391:31511/2 54 98 53 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:2:2220:17391:31511/2 54 98 (53) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i62
E00378:188:HV 54 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 98
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 1299 2.0 0.0 0.7 E00378:188:HVMVNCCXX:2:2220:2290:37946/1 1 151 (0) + L1PA3 LINE/L1 5790 5939 (216) 544
ANNOTATION EVIDENCE:
1299 2.00 0.00 0.66 E00378:188:HVMVNCCXX:2:2220:2290:37946/1 1 151 0 + L1PA3_3end LINE/L1 537 686 216
1299 2.00 0.00 0.66 E00378:188:HVMVNCCXX:2:2220:2290:37946/1 1 151 (0) L1PA3_3end#LINE/L1 537 686 (216) m_b1s551i364
E00378:188:HV 1 CACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTG 50
L1PA3_3end#LI 537 CACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTG 586
E00378:188:HV 51 TTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCA 100
- i
L1PA3_3end#LI 587 T-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCA 635
E00378:188:HV 101 AGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAA 150
v i
L1PA3_3end#LI 636 AGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAA 685
E00378:188:HV 151 C 151
L1PA3_3end#LI 686 C 686
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1172 6.8 0.0 0.0 E00378:188:HVMVNCCXX:2:2220:2290:37946/2 1 148 (3) C L1PA2 LINE/L1 (10) 6145 5998 545
ANNOTATION EVIDENCE:
1172 6.76 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:2290:37946/2 1 148 3 C L1PA2_3end LINE/L1 745 892 10
1172 6.76 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:2290:37946/2 1 148 (3) C L1PA2_3end#LINE/L1 (10) 892 745 m_b1s551i430
E00378:188:HV 1 TTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGT 50
i
C L1PA2_3end#LI 892 TTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGT 843
E00378:188:HV 51 TACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACTAACTCGTC 100
i
C L1PA2_3end#LI 842 TACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTC 793
E00378:188:HV 101 ATCTAGCATTAGGTATATCTCCGGATGCTATAGCACCGCCCTCCACTC 148
vi vv v v v i
C L1PA2_3end#LI 792 ATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCC 745
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.42
Transitions / transversions = 0.67 (4/6)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 1362 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2220:3397:42956/1 2 151 (0) C L1P1 LINE/L1 (451) 5704 5555 546
ANNOTATION EVIDENCE:
1362 2.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:3397:42956/1 2 151 0 C L1PA3_3end LINE/L1 302 451 451
1362 2.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:3397:42956/1 2 151 (0) C L1PA3_3end#LINE/L1 (451) 451 302 m_b1s551i290
E00378:188:HV 2 CAATAAACATACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCC 51
i
C L1PA3_3end#LI 451 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCC 402
E00378:188:HV 52 TTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAG 101
i
C L1PA3_3end#LI 401 TTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAG 352
E00378:188:HV 102 TTCTAGATCCCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTA 151
i
C L1PA3_3end#LI 351 TTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTA 302
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.42
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1317 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2220:3397:42956/2 1 151 (0) + L1P1 LINE/L1 5386 5536 (619) 547
ANNOTATION EVIDENCE:
1317 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:3397:42956/2 1 151 0 + L1PA2_3end LINE/L1 133 283 619
1317 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2220:3397:42956/2 1 151 (0) L1PA2_3end#LINE/L1 133 283 (619) m_b1s551i235
E00378:188:HV 1 AAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCAC 50
L1PA2_3end#LI 133 AAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCAC 182
E00378:188:HV 51 AATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAG 100
i
L1PA2_3end#LI 183 AATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAG 232
E00378:188:HV 101 GAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACAC 150
iv
L1PA2_3end#LI 233 GAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACAC 282
E00378:188:HV 151 T 151
L1PA2_3end#LI 283 T 283
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1152 11.3 0.0 0.0 E00378:188:HVMVNCCXX:2:2221:18923:44503/1 1 151 (0) C AluSx SINE/Alu (117) 195 45 548
ANNOTATION EVIDENCE:
1152 11.26 0.00 0.00 E00378:188:HVMVNCCXX:2:2221:18923:44503/1 1 151 0 C AluSx SINE/Alu 45 195 117
1152 11.26 0.00 0.00 E00378:188:HVMVNCCXX:2:2221:18923:44503/1 1 151 (0) C AluSx#SINE/Alu (117) 195 45 m_b2s356i29
E00378:188:HV 1 TTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACC 50
i i i v i
C AluSx#SINE/Al 195 TTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC 146
E00378:188:HV 51 ACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTT 100
i i v i ii
C AluSx#SINE/Al 145 ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTT 96
E00378:188:HV 101 GGCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGC 150
i i i i v v
C AluSx#SINE/Al 95 GGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGC 46
E00378:188:HV 151 C 151
C AluSx#SINE/Al 45 C 45
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.81
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1293 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2221:21237:5475/1 1 151 (0) + L1PA2 LINE/L1 5935 6085 (70) 549
ANNOTATION EVIDENCE:
1293 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2221:21237:5475/1 1 151 0 + L1PA2_3end LINE/L1 682 832 70
1293 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2221:21237:5475/1 1 151 (0) L1PA2_3end#LINE/L1 682 832 (70) m_b1s551i392
E00378:188:HV 1 TGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGTGG 50
v
L1PA2_3end#LI 682 TGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGG 731
E00378:188:HV 51 ACTGTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACC 100
v
L1PA2_3end#LI 732 ACTGTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACC 781
E00378:188:HV 101 TAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGT 150
i
L1PA2_3end#LI 782 TAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGT 831
E00378:188:HV 151 A 151
L1PA2_3end#LI 832 A 832
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:2:2221:21237:5475/2 44 132 (19) + L1M5 LINE/L1 5741 5831 (293) 550
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:2221:21237:5475/2 44 132 19 + L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:2:2221:21237:5475/2 44 132 (19) L1ME4a_3end#LINE/L1 491 578 (293) m_b1s551i496
E00378:188:HV 44 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 93
vii ? v v vi i ii ii i i
L1ME4a_3end#L 491 CTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCAT 540
E00378:188:HV 94 ATAACAAAATAATATGCAAACTTTAAAAATTATTATTTT 132
ii iii v iv v ? -i
L1ME4a_3end#L 541 ACGATGGAATATTATGCAGCCATTAAAAATNAT-GTTTT 578
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:2221:21237:5475/2 44 111 40 + L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:2:2221:21237:5475/2 44 111 (40) L1ME3A_3end#LINE/L1 488 555 (365) m_b1s551i497
E00378:188:HV 44 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 93
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
E00378:188:HV 94 ATAACAAAATAATATGCA 111
i iii v i
L1ME3A_3end#L 538 ACAATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 702 11.2 2.0 0.0 E00378:188:HVMVNCCXX:2:2222:18446:8271/2 1 98 (53) C AluSx SINE/Alu (212) 100 1 551
ANNOTATION EVIDENCE:
702 11.22 2.00 0.00 E00378:188:HVMVNCCXX:2:2222:18446:8271/2 1 98 53 C AluSx SINE/Alu 1 100 212
702 11.22 2.00 0.00 E00378:188:HVMVNCCXX:2:2222:18446:8271/2 1 98 (53) C AluSx#SINE/Alu (212) 100 1 m_b4s357i51
E00378:188:HV 1 ATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCT 48
i v i i-- i i i
C AluSx#SINE/Al 100 ATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCC 51
E00378:188:HV 49 TCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCC 98
i i i i
C AluSx#SINE/Al 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 2.00 (2 / 1)
+ 1303 0.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2222:28503:4596/1 2 151 (0) + L1P1 LINE/L1 5221 5370 (776) 552
ANNOTATION EVIDENCE:
1303 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2222:28503:4596/1 2 151 0 + L1P1_orf2 LINE/L1 3112 3261 33
1303 0.00 0.00 0.00 E00378:188:HVMVNCCXX:2:2222:28503:4596/1 2 151 (0) L1P1_orf2#LINE/L1 3112 3261 (33) m_b1s551i147
E00378:188:HV 2 AAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTA 51
L1P1_orf2#LIN 3112 AAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTA 3161
E00378:188:HV 52 CAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAA 101
L1P1_orf2#LIN 3162 CAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAA 3211
E00378:188:HV 102 AGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCA 151
L1P1_orf2#LIN 3212 AGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCA 3261
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1348 2.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2222:28503:4596/2 1 151 (0) C L1P1 LINE/L1 (574) 5581 5431 553
ANNOTATION EVIDENCE:
1348 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2222:28503:4596/2 1 151 0 C L1PA3_3end LINE/L1 178 328 574
1348 1.99 0.00 0.00 E00378:188:HVMVNCCXX:2:2222:28503:4596/2 1 151 (0) C L1PA3_3end#LINE/L1 (574) 328 178 m_b1s551i252
E00378:188:HV 1 ACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGT 50
C L1PA3_3end#LI 328 ACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGT 279
E00378:188:HV 51 AAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGA 100
vi
C L1PA3_3end#LI 278 AAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGA 229
E00378:188:HV 101 CTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGG 150
i
C L1PA3_3end#LI 228 CTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGG 179
E00378:188:HV 151 T 151
C L1PA3_3end#LI 178 T 178
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 238 26.2 5.1 1.5 E00378:188:HVMVNCCXX:2:2223:19045:18379/2 20 151 (0) C L1ME4c LINE/L1 (216) 5867 5731 554
ANNOTATION EVIDENCE:
238 26.16 5.11 1.52 E00378:188:HVMVNCCXX:2:2223:19045:18379/2 20 151 0 C L1ME4c_3end LINE/L1 478 614 216
238 26.16 5.11 1.52 E00378:188:HVMVNCCXX:2:2223:19045:18379/2 20 151 (0) C L1ME4c_3end#LINE/L1 (216) 614 478 m_b2s551i1
E00378:188:HV 20 ATTATAAGTATTTTTCCAGGTAGTTGC-TTTTCTTGATAGTCATACTTTT 68
i ii - v v i i - vv v i i vv
C L1ME4c_3end#L 614 ATCATAAACA-TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTT 566
E00378:188:HV 69 TAATGGCTTCACCATTTTTCTGTC--ATAAA--TACCATAATTTACTTGA 114
v iv - v ii --i ?i -- i
C L1ME4c_3end#L 565 TAATGGCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAA 517
E00378:188:HV 115 -CATT-TTTTATTGTCAGAAATTTAGATTCTTTTCTATT 151
- -iii ii v i v i v
C L1ME4c_3end#L 516 CCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATT 478
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.08
Transitions / transversions = 1.54 (20/13)
Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.29 (9 / 7)
+ 1205 8.0 0.0 0.0 E00378:188:HVMVNCCXX:2:2224:4178:65160/2 1 151 (0) C AluSx SINE/Alu (42) 270 120 555
ANNOTATION EVIDENCE:
1205 7.95 0.00 0.00 E00378:188:HVMVNCCXX:2:2224:4178:65160/2 1 151 0 C AluSx SINE/Alu 120 270 42
1205 7.95 0.00 0.00 E00378:188:HVMVNCCXX:2:2224:4178:65160/2 1 151 (0) C AluSx#SINE/Alu (42) 270 120 m_b4s356i11
E00378:188:HV 1 CGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA 50
i i
C AluSx#SINE/Al 270 CGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA 221
E00378:188:HV 51 ACCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTA 100
i i i
C AluSx#SINE/Al 220 ACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTA 171
E00378:188:HV 101 GCTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGGGTTTTT 150
i vi v i vi
C AluSx#SINE/Al 170 GCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTT 121
E00378:188:HV 151 A 151
C AluSx#SINE/Al 120 A 120
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.15
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:3:1102:16823:36258/1 9 97 (54) C L1M5 LINE/L1 (293) 5831 5741 556
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:1102:16823:36258/1 9 97 54 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:1102:16823:36258/1 9 97 (54) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i508
E00378:188:HV 9 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 58
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 59 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 97
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:1102:16823:36258/1 30 97 54 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:1102:16823:36258/1 30 97 (54) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i509
E00378:188:HV 30 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 79
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 80 CTATTGTTGGACATTTAG 97
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1066 10.8 0.0 0.0 E00378:188:HVMVNCCXX:3:1102:16823:36258/2 4 142 (9) + AluSx SINE/Alu 122 260 (52) 557
ANNOTATION EVIDENCE:
1066 10.79 0.00 0.00 E00378:188:HVMVNCCXX:3:1102:16823:36258/2 4 142 9 + AluSx SINE/Alu 122 260 52
1066 10.79 0.00 0.00 E00378:188:HVMVNCCXX:3:1102:16823:36258/2 4 142 (9) AluSx#SINE/Alu 122 260 (52) m_b2s357i19
E00378:188:HV 4 AAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCT 53
i i i v i
AluSx#SINE/Al 122 AAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCT 171
E00378:188:HV 54 ACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGATT 103
i i i i i i i
AluSx#SINE/Al 172 ACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT 221
E00378:188:HV 104 GCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGG 142
i ii
AluSx#SINE/Al 222 GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.79
Transitions / transversions = 14.00 (14/1)
Gap_init rate = 0.00 (0 / 138), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:3:1103:12297:45259/2 43 134 (17) + MIRb SINE/MIR 67 161 (107) 558
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:1103:12297:45259/2 43 134 17 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:1103:12297:45259/2 43 134 (17) MIRb#SINE/MIR 67 161 (107) m_b6s601i68
E00378:188:HV 43 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 91
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 92 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 134
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 803 14.6 0.0 4.9 E00378:188:HVMVNCCXX:3:1103:26281:12701/1 6 149 (2) C AluSx SINE/Alu (8) 304 168 559
ANNOTATION EVIDENCE:
803 14.60 0.00 4.86 E00378:188:HVMVNCCXX:3:1103:26281:12701/1 6 149 2 C AluSx SINE/Alu 168 304 8
803 14.60 0.00 4.86 E00378:188:HVMVNCCXX:3:1103:26281:12701/1 6 149 (2) C AluSx#SINE/Alu (8) 304 168 m_b5s357i30
E00378:188:HV 6 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 55
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 56 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 105
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 106 TAGTAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCT 149
vvii i v i i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCT 168
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.65
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.00 (7 / 7)
+ 780 6.4 8.5 7.3 E00378:188:HVMVNCCXX:3:1104:27052:56616/1 1 151 (0) C L1P3 LINE/L1 (2858) 3288 3136 560
ANNOTATION EVIDENCE:
780 6.43 8.50 7.28 E00378:188:HVMVNCCXX:3:1104:27052:56616/1 1 151 0 C L1P3_orf2 LINE/L1 1027 1179 2115
780 6.43 8.50 7.28 E00378:188:HVMVNCCXX:3:1104:27052:56616/1 1 151 (0) C L1P3_orf2#LINE/L1 (2115) 1179 1027 m_b6s551i210
E00378:188:HV 1 TATTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTA 42
v -------- v
C L1P3_orf2#LIN 1179 TATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTA 1130
E00378:188:HV 43 GCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAA 88
---- i i v
C L1P3_orf2#LIN 1129 GCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCA 1080
E00378:188:HV 89 TTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTC 138
- i i----------
C L1P3_orf2#LIN 1079 TTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTC 1041
E00378:188:HV 139 A-CTCAGCTCTGAT 151
-i v
C L1P3_orf2#LIN 1040 AGTTCTGCTCTGAT 1027
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1242 4.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1104:27052:56616/2 1 151 (0) + L1P3 LINE/L1 2935 3085 (3061) 561
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:3:1104:27052:56616/2 1 151 0 + L1P3_orf2 LINE/L1 826 976 2318
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:3:1104:27052:56616/2 1 151 (0) L1P3_orf2#LINE/L1 826 976 (2318) m_b7s551i16
E00378:188:HV 1 ACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTAA 50
i i
L1P3_orf2#LIN 826 ACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAA 875
E00378:188:HV 51 AGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGT 100
? v i
L1P3_orf2#LIN 876 AGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGC 925
E00378:188:HV 101 GGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTAGAG 150
i
L1P3_orf2#LIN 926 GGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTAGAG 975
E00378:188:HV 151 A 151
L1P3_orf2#LIN 976 A 976
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 970 10.7 1.5 0.0 E00378:188:HVMVNCCXX:3:1104:28676:42657/1 1 131 (20) C AluSx SINE/Alu (179) 133 1 562
ANNOTATION EVIDENCE:
970 10.69 1.51 0.00 E00378:188:HVMVNCCXX:3:1104:28676:42657/1 1 131 20 C AluSx SINE/Alu 1 133 179
970 10.69 1.51 0.00 E00378:188:HVMVNCCXX:3:1104:28676:42657/1 1 131 (20) C AluSx#SINE/Alu (179) 133 1 m_b4s357i40
E00378:188:HV 1 TTTTTGTGTTTTTAGTAGAGATGGAGTTTCACCATATTGGCCAGGCTGTT 50
i i i i v
C AluSx#SINE/Al 133 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGT 84
E00378:188:HV 51 CTCAAACTCCTGACCTT--GTGATCTGCCTGCTTCAGCCTCCCAAAGTGC 98
i i-- i i i i
C AluSx#SINE/Al 83 CTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC 34
E00378:188:HV 99 TGGGATTACAGGTGTGAGCCACTGCACCCGGCC 131
i i i
C AluSx#SINE/Al 33 TGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.44
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 130), avg. gap size = 2.00 (2 / 1)
+ 1163 4.6 1.3 0.0 E00378:188:HVMVNCCXX:3:1104:8755:57337/1 1 151 (0) + L1P3 LINE/L1 3336 3488 (2658) 563
ANNOTATION EVIDENCE:
1163 4.64 1.30 0.00 E00378:188:HVMVNCCXX:3:1104:8755:57337/1 1 151 0 + L1P3_orf2 LINE/L1 1227 1379 1915
1163 4.64 1.30 0.00 E00378:188:HVMVNCCXX:3:1104:8755:57337/1 1 151 (0) L1P3_orf2#LINE/L1 1227 1379 (1915) m_b6s551i150
E00378:188:HV 1 TACCATCAGAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAATC 50
i i
L1P3_orf2#LIN 1227 TACCATCAGAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATC 1276
E00378:188:HV 51 TAGAAGAAAGTGATAAATTCCTAGACACATACAACCTCCCAA--CTAAAG 98
vv i v -- v
L1P3_orf2#LIN 1277 TAGAAGAAATGGATAAATTCCTGGACACATACACCCTCCCAAGACTAAAC 1326
E00378:188:HV 99 CAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGA 148
L1P3_orf2#LIN 1327 CAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGA 1376
E00378:188:HV 149 GGC 151
L1P3_orf2#LIN 1377 GGC 1379
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1335 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1104:8755:57337/2 1 151 (0) C L1P3 LINE/L1 (2510) 3636 3486 564
ANNOTATION EVIDENCE:
1335 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1104:8755:57337/2 1 151 0 C L1P3_orf2 LINE/L1 1377 1527 1767
1335 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1104:8755:57337/2 1 151 (0) C L1P3_orf2#LINE/L1 (1767) 1527 1377 m_b6s551i107
E00378:188:HV 1 AAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 50
i
C L1P3_orf2#LIN 1527 AAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 1478
E00378:188:HV 51 GAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTG 100
i
C L1P3_orf2#LIN 1477 GAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTG 1428
E00378:188:HV 101 AATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGC 150
v
C L1P3_orf2#LIN 1427 AATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGC 1378
E00378:188:HV 151 C 151
C L1P3_orf2#LIN 1377 C 1377
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 838 8.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1105:10632:27222/1 1 112 (39) + L1P3 LINE/L1 3787 3898 (2248) 565
ANNOTATION EVIDENCE:
838 8.04 0.00 0.00 E00378:188:HVMVNCCXX:3:1105:10632:27222/1 1 112 39 + L1P3_orf2 LINE/L1 1678 1789 1505
838 8.04 0.00 0.00 E00378:188:HVMVNCCXX:3:1105:10632:27222/1 1 112 (39) L1P3_orf2#LINE/L1 1678 1789 (1505) m_b6s551i24
E00378:188:HV 1 CACCACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCAT 50
v i i i i
L1P3_orf2#LIN 1678 CACCACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACAT 1727
E00378:188:HV 51 ACACAAATCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAA 100
i i v
L1P3_orf2#LIN 1728 ACGCAAATCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAA 1777
E00378:188:HV 101 ACTACATGATTA 112
i
L1P3_orf2#LIN 1778 ACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.88
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
+ 32 5.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1105:10632:27222/2 94 132 (19) + (T)n Simple_repeat 1 39 (0) 566
ANNOTATION EVIDENCE:
32 5.34 0.00 0.00 E00378:188:HVMVNCCXX:3:1105:10632:27222/2 94 132 19 + (T)n Simple_repeat 1 39 0
32 5.34 0.00 0.00 E00378:188:HVMVNCCXX:3:1105:10632:27222/2 94 132 (19) (T)n#Simple_repeat 1 39 (0) c_b6s251i12
E00378:188:HV 94 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTGTTTT 132
v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 535 19.9 19.0 0.0 E00378:188:HVMVNCCXX:3:1106:26068:55684/1 11 151 (0) + L1MC4 LINE/L1 7447 7620 (422) 567
ANNOTATION EVIDENCE:
535 19.86 18.96 0.00 E00378:188:HVMVNCCXX:3:1106:26068:55684/1 11 151 0 + L1MC4_3end LINE/L1 2194 2367 422
535 19.86 18.96 0.00 E00378:188:HVMVNCCXX:3:1106:26068:55684/1 11 151 (0) L1MC4_3end#LINE/L1 2194 2367 (422) m_b3s551i110
E00378:188:HV 11 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 52
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
E00378:188:HV 53 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC----------------- 85
i i i vii -----------------
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGACATTCTACAAAATAACTG 2293
E00378:188:HV 86 --CTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA------ 127
-- v v i v ? v i i i ------
L1MC4_3end#LI 2294 GCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTGA 2343
E00378:188:HV 128 AGAACTGTTCCAGATTGAAGGAGA 151
i i
L1MC4_3end#LI 2344 GGAACTGTTCCAGATTAAAGGAGA 2367
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.39
Transitions / transversions = 4.40 (22/5)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 8.25 (33 / 4)
+ 278 10.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1106:26068:55684/2 7 45 (106) C L1MC4 LINE/L1 (242) 7800 7762 568
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 E00378:188:HVMVNCCXX:3:1106:26068:55684/2 7 45 106 C L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 E00378:188:HVMVNCCXX:3:1106:26068:55684/2 7 45 (106) C L1MC4_3end#LINE/L1 (242) 2547 2509 m_b3s551i80
E00378:188:HV 7 TAGCCACAGTATAATCATCAAAATCAGGAAGTTAACATT 45
i i i i
C L1MC4_3end#LI 2547 TAACCACAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 463 18.4 5.8 0.0 E00378:188:HVMVNCCXX:3:1106:26068:55684/2 50 147 (4) C L1MC4 LINE/L1 (393) 7649 7546 568
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:3:1106:26068:55684/2 50 147 4 C L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:3:1106:26068:55684/2 50 147 (4) C L1MC4_3end#LINE/L1 (393) 2396 2293 m_b3s551i81
E00378:188:HV 50 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 99
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 100 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 143
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
E00378:188:HV 144 GGTC 147
i
C L1MC4_3end#LI 2296 GGCC 2293
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 6.00 (6 / 1)
+ 959 13.7 0.0 1.4 E00378:188:HVMVNCCXX:3:1108:29356:12859/1 4 151 (0) C AluSx SINE/Alu (54) 258 113 569
ANNOTATION EVIDENCE:
959 13.69 0.00 1.35 E00378:188:HVMVNCCXX:3:1108:29356:12859/1 4 151 0 C AluSx SINE/Alu 113 258 54
959 13.69 0.00 1.35 E00378:188:HVMVNCCXX:3:1108:29356:12859/1 4 151 (0) C AluSx#SINE/Alu (54) 258 113 m_b5s356i5
E00378:188:HV 4 CAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCCTAG 53
i v v v vv
C AluSx#SINE/Al 258 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCC 209
E00378:188:HV 54 TAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACA 103
ii i v i i iv
C AluSx#SINE/Al 208 CGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA 159
E00378:188:HV 104 GGCTCCCACCACAATGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGA 151
v v i v i i --
C AluSx#SINE/Al 158 GGCGCGCGCCACCACGCCCGGCTAA--TTTTTGTATTTTTAGTAGAGA 113
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.95
Transitions / transversions = 1.00 (10/10)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 552 10.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1109:18690:63437/1 77 151 (0) + AluY SINE/Alu 1 75 (236) 570
ANNOTATION EVIDENCE:
552 10.67 0.00 0.00 E00378:188:HVMVNCCXX:3:1109:18690:63437/1 77 151 0 + AluY SINE/Alu 1 75 236
552 10.67 0.00 0.00 E00378:188:HVMVNCCXX:3:1109:18690:63437/1 77 151 (0) AluY#SINE/Alu 1 75 (236) m_b2s357i63
E00378:188:HV 77 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 126
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 127 GGCGGGCTGATCATGAGGTCAGGAG 151
v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAG 75
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.84
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 753 9.5 0.0 0.9 E00378:188:HVMVNCCXX:3:1109:18690:63437/2 46 151 (0) C AluY SINE/Alu (14) 297 193 571
ANNOTATION EVIDENCE:
753 9.52 0.00 0.94 E00378:188:HVMVNCCXX:3:1109:18690:63437/2 46 151 0 C AluY SINE/Alu 193 297 14
753 9.52 0.00 0.94 E00378:188:HVMVNCCXX:3:1109:18690:63437/2 46 151 (0) C AluY#SINE/Alu (14) 297 193 m_b2s357i99
E00378:188:HV 46 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 95
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
E00378:188:HV 96 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 145
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
E00378:188:HV 146 GCCGTT 151
i
C AluY#SINE/Alu 198 GCCATT 193
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.45
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1)
+ 1284 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1110:12976:36346/1 1 151 (0) + L1P LINE/L1 5262 5412 (743) 572
ANNOTATION EVIDENCE:
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1110:12976:36346/1 1 151 0 + L1PA2_3end LINE/L1 9 159 743
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1110:12976:36346/1 1 151 (0) L1PA2_3end#LINE/L1 9 159 (743) m_b1s551i168
E00378:188:HV 1 CAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACC 50
L1PA2_3end#LI 9 CAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACC 58
E00378:188:HV 51 CCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGAC 100
L1PA2_3end#LI 59 CCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGAC 108
E00378:188:HV 101 ATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 150
L1PA2_3end#LI 109 ATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 158
E00378:188:HV 151 C 151
L1PA2_3end#LI 159 C 159
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1348 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1110:12976:36346/2 1 151 (0) C L1P2 LINE/L1 (519) 5636 5486 573
ANNOTATION EVIDENCE:
1348 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1110:12976:36346/2 1 151 0 C L1PA4_3end LINE/L1 233 383 519
1348 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1110:12976:36346/2 1 151 (0) C L1PA4_3end#LINE/L1 (519) 383 233 m_b1s551i270
E00378:188:HV 1 AATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAA 50
i
C L1PA4_3end#LI 383 AATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAA 334
E00378:188:HV 51 TCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAAC 100
i
C L1PA4_3end#LI 333 TCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAAC 284
E00378:188:HV 101 AGTGTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTT 150
vi
C L1PA4_3end#LI 283 AGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTT 234
E00378:188:HV 151 C 151
C L1PA4_3end#LI 233 C 233
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1333 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1111:24129:64984/1 1 151 (0) + L1PA2 LINE/L1 5976 6126 (29) 574
ANNOTATION EVIDENCE:
1333 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1111:24129:64984/1 1 151 0 + L1PA2_3end LINE/L1 723 873 29
1333 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1111:24129:64984/1 1 151 (0) L1PA2_3end#LINE/L1 723 873 (29) m_b1s551i404
E00378:188:HV 1 ACTCTGTGGACTGTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGG 50
v v
L1PA2_3end#LI 723 ACTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGG 772
E00378:188:HV 51 AGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCAT 100
i
L1PA2_3end#LI 773 AGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCAT 822
E00378:188:HV 101 GGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCT 150
L1PA2_3end#LI 823 GGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCT 872
E00378:188:HV 151 A 151
L1PA2_3end#LI 873 A 873
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1111:24129:64984/2 11 32 (119) + (A)n Simple_repeat 1 22 (0) 575
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1111:24129:64984/2 11 32 119 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1111:24129:64984/2 11 32 (119) (A)n#Simple_repeat 1 22 (0) m_b1s252i14
E00378:188:HV 11 AAAAAAAAAAAAAAAAAAAAAA 32
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 243 24.1 0.0 0.0 E00378:188:HVMVNCCXX:3:1111:24129:64984/2 94 147 (4) + L1M5 LINE/L1 5741 5794 (379) 576
ANNOTATION EVIDENCE:
243 24.07 0.00 0.00 E00378:188:HVMVNCCXX:3:1111:24129:64984/2 94 147 4 + L1ME3A_3end LINE/L1 488 541 379
243 24.07 0.00 0.00 E00378:188:HVMVNCCXX:3:1111:24129:64984/2 94 147 (4) L1ME3A_3end#LINE/L1 488 541 (379) m_b1s551i526
E00378:188:HV 94 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 143
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
E00378:188:HV 144 ATAA 147
i
L1ME3A_3end#L 538 ACAA 541
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.69
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 1312 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1112:20101:25411/1 1 151 (0) C L1P1 LINE/L1 (697) 5458 5308 577
ANNOTATION EVIDENCE:
1312 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1112:20101:25411/1 1 151 0 C L1PA2_3end LINE/L1 55 205 697
1312 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1112:20101:25411/1 1 151 (0) C L1PA2_3end#LINE/L1 (697) 205 55 m_b1s551i196
E00378:188:HV 1 CTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATG 50
C L1PA2_3end#LI 205 CTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATG 156
E00378:188:HV 51 GCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTC 100
C L1PA2_3end#LI 155 GCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTC 106
E00378:188:HV 101 TTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGT 150
C L1PA2_3end#LI 105 TTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGT 56
E00378:188:HV 151 T 151
C L1PA2_3end#LI 55 T 55
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1259 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1112:20101:25411/2 1 151 (0) + L1P1 LINE/L1 4989 5139 (1007) 578
ANNOTATION EVIDENCE:
1259 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1112:20101:25411/2 1 151 0 + L1P1_orf2 LINE/L1 2880 3030 264
1259 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1112:20101:25411/2 1 151 (0) L1P1_orf2#LINE/L1 2880 3030 (264) m_b1s551i59
E00378:188:HV 1 TTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCC 50
i
L1P1_orf2#LIN 2880 TTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCC 2929
E00378:188:HV 51 TAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGAC 100
?
L1P1_orf2#LIN 2930 TAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGAC 2979
E00378:188:HV 101 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAA 150
v i
L1P1_orf2#LIN 2980 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA 3029
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3030 A 3030
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:3:1112:31223:38737/2 36 127 (24) + MIRb SINE/MIR 67 161 (107) 579
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:1112:31223:38737/2 36 127 24 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:1112:31223:38737/2 36 127 (24) MIRb#SINE/MIR 67 161 (107) m_b6s601i64
E00378:188:HV 36 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 84
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 85 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 127
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 268 28.1 14.7 0.0 E00378:188:HVMVNCCXX:3:1112:3559:65248/2 1 139 (12) + MIR SINE/MIR 100 262 (0) 580
ANNOTATION EVIDENCE:
268 28.06 14.73 0.00 E00378:188:HVMVNCCXX:3:1112:3559:65248/2 1 139 12 + MIR SINE/MIR 100 262 0
268 28.06 14.73 0.00 E00378:188:HVMVNCCXX:3:1112:3559:65248/2 1 139 (12) MIR#SINE/MIR 100 262 (0) m_b6s601i29
E00378:188:HV 1 TTACTTTACCTCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAA 48
v v iv i v -- i i v ii iv
MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 149
E00378:188:HV 49 TAATAGAATCTAAGTGACAG---CAGTATAAGAATTAAG------AATAA 89
v i vv v i ---iiv i i i i------ v
MIR#SINE/MIR 150 TAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATAC 199
E00378:188:HV 90 ACATAAA-------------TGCCAGGCACACCGTATATACTCAACAAGT 126
ii ------------- v iv viii i i
MIR#SINE/MIR 200 ATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 249
E00378:188:HV 127 GTTAGCTATTTTT 139
v
MIR#SINE/MIR 250 GTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.79
Transitions / transversions = 1.44 (23/16)
Gap_init rate = 0.03 (4 / 138), avg. gap size = 6.00 (24 / 4)
+ 280 26.3 5.7 0.8 E00378:188:HVMVNCCXX:3:1113:1702:47966/1 1 134 (17) C L1ME4c LINE/L1 (247) 5836 5696 581
ANNOTATION EVIDENCE:
280 26.32 5.67 0.75 E00378:188:HVMVNCCXX:3:1113:1702:47966/1 1 134 17 C L1ME4c_3end LINE/L1 443 583 247
280 26.32 5.67 0.75 E00378:188:HVMVNCCXX:3:1113:1702:47966/1 1 134 (17) C L1ME4c_3end#LINE/L1 (247) 583 443 m_b2s551i18
E00378:188:HV 1 CTTGATAGTCATACTTTTTAATGGCTTCACCATTTTTCTGTC--ATAAA- 47
v i i vv v iv - v ii --i ?i -
C L1ME4c_3end#L 583 CTTCATAATTATCATTTTTAATGGCTGCATAA-TATTCCATCGAGTNGAT 535
E00378:188:HV 48 -TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTT 94
- i - -iii ii v i v
C L1ME4c_3end#L 534 GTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTT 485
E00378:188:HV 95 TTCTATTTTC--CTACAATAAACATTATTGCAATGATCATTT 134
i v i-- iv i viii v i
C L1ME4c_3end#L 484 TCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.32
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.29 (9 / 7)
+ 242 26.7 1.6 1.6 E00378:188:HVMVNCCXX:3:1114:15037:39669/1 91 102 (49) C SVA_A Retroposon/SVA (1177) 210 150 582
ANNOTATION EVIDENCE:
242 26.67 1.64 1.64 E00378:188:HVMVNCCXX:3:1114:15037:39669/1 91 151 0 C SVA_A Retroposon/SVA 150 210 1177
242 26.67 1.64 1.64 E00378:188:HVMVNCCXX:3:1114:15037:39669/1 91 151 (0) C SVA_A#Retroposon/SVA (1177) 210 150 m_b4s502i6
E00378:188:HV 91 ATATAAACATAGGCCGGGTGCAGTGGCTCACACCTGTAATCCCA-GCACT 139
i v ivi i i ii i v i i i - -
C SVA_A#Retropo 210 ATACAAAAACCAGTCGGGCGTGGCGGCGCGCGCCTGCAATCCCAGGCAC- 162
E00378:188:HV 140 TTGGGAGGCTGA 151
i i
C SVA_A#Retropo 161 TCGGGAGGCCGA 150
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.71
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2)
+ 278 20.4 0.0 0.0 E00378:188:HVMVNCCXX:3:1114:15037:39669/1 103 151 (0) + 7SLRNA srpRNA 1 49 (271) 583
ANNOTATION EVIDENCE:
278 20.41 0.00 0.00 E00378:188:HVMVNCCXX:3:1114:15037:39669/1 103 151 0 + 7SLRNA SINE/Alu 1 49 271
278 20.41 0.00 0.00 E00378:188:HVMVNCCXX:3:1114:15037:39669/1 103 151 (0) 7SLRNA#SINE/Alu 1 49 (271) m_b4s502i7
E00378:188:HV 103 GCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 151
i i v i i i vvi i
7SLRNA#SINE/A 1 GCCGGGCGCGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGA 49
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.18
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 1181 9.9 0.0 0.0 E00378:188:HVMVNCCXX:3:1114:15037:39669/2 1 151 (0) C AluSx SINE/Alu (94) 218 68 584
ANNOTATION EVIDENCE:
1181 9.93 0.00 0.00 E00378:188:HVMVNCCXX:3:1114:15037:39669/2 1 151 0 C AluSx SINE/Alu 68 218 94
1181 9.93 0.00 0.00 E00378:188:HVMVNCCXX:3:1114:15037:39669/2 1 151 (0) C AluSx#SINE/Alu (94) 218 68 m_b4s356i28
E00378:188:HV 1 CTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGC 50
i i i
C AluSx#SINE/Al 218 CTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGC 169
E00378:188:HV 51 TGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTGTTTTTAG 100
i vi v i i
C AluSx#SINE/Al 168 TGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAG 119
E00378:188:HV 101 TAGAGATGGAGTTTCACCATATTGGCCAGGCTGTTCTCAGACTCCTGACC 150
i i i v ii
C AluSx#SINE/Al 118 TAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACC 69
E00378:188:HV 151 T 151
C AluSx#SINE/Al 68 T 68
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.69
Transitions / transversions = 4.00 (12/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1131 8.0 1.9 0.0 E00378:188:HVMVNCCXX:3:1114:21420:66654/1 1 151 (0) C L1P3 LINE/L1 (2303) 3843 3690 585
ANNOTATION EVIDENCE:
1131 7.95 1.95 0.00 E00378:188:HVMVNCCXX:3:1114:21420:66654/1 1 151 0 C L1P3_orf2 LINE/L1 1581 1734 1560
1131 7.95 1.95 0.00 E00378:188:HVMVNCCXX:3:1114:21420:66654/1 1 151 (0) C L1P3_orf2#LINE/L1 (1560) 1734 1581 m_b6s551i52
E00378:188:HV 1 TTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGAT 50
i i i i i
C L1P3_orf2#LIN 1734 TTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGAT 1685
E00378:188:HV 51 AGTGGTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATT 97
v v --- i
C L1P3_orf2#LIN 1684 CGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATT 1635
E00378:188:HV 98 TTATCGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATT 147
i i v v
C L1P3_orf2#LIN 1634 TTATTGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATT 1585
E00378:188:HV 148 TTCT 151
C L1P3_orf2#LIN 1584 TTCT 1581
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.79
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 967 7.3 7.4 0.0 E00378:188:HVMVNCCXX:3:1114:21420:66654/2 1 151 (0) + L1P3 LINE/L1 3199 3361 (2785) 586
ANNOTATION EVIDENCE:
967 7.28 7.36 0.00 E00378:188:HVMVNCCXX:3:1114:21420:66654/2 1 151 0 + L1P3_orf2 LINE/L1 1090 1252 2042
967 7.28 7.36 0.00 E00378:188:HVMVNCCXX:3:1114:21420:66654/2 1 151 (0) L1P3_orf2#LINE/L1 1090 1252 (2042) m_b6s551i194
E00378:188:HV 1 AGCTGATTGTTTGAAAAGATTGACAAAACAGA----CCGCTAGCAAGACT 46
i v i i ---- v
L1P3_orf2#LIN 1090 AGCTGGTTTTTTGAAAAGATTAACAAAATAGATAGACCGCTAGCCAGACT 1139
E00378:188:HV 47 AATAAAGA--------GAGAAGAATCAAATAGACTCAATAAAAAATGATA 88
-------- v
L1P3_orf2#LIN 1140 AATAAAGAAGAAAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATA 1189
E00378:188:HV 89 AAGAGGATAATACCACTGATCCCACAGAAATACAAACTACCATCAGAGAA 138
i vi
L1P3_orf2#LIN 1190 AAGGGGATATCACCACTGATCCCACAGAAATACAAACTACCATCAGAGAA 1239
E00378:188:HV 139 TACTAGAAATACC 151
v i
L1P3_orf2#LIN 1240 TACTATAAACACC 1252
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.69
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1355 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1115:17787:54313/1 1 151 (0) C L1P1 LINE/L1 (433) 5722 5572 587
ANNOTATION EVIDENCE:
1355 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:17787:54313/1 1 151 0 C L1PA2_3end LINE/L1 319 469 433
1355 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:17787:54313/1 1 151 (0) C L1PA2_3end#LINE/L1 (433) 469 319 m_b1s551i295
E00378:188:HV 1 CTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATAG 50
i
C L1PA2_3end#LI 469 CTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAG 420
E00378:188:HV 51 CGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGG 100
i
C L1PA2_3end#LI 419 CAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGG 370
E00378:188:HV 101 GTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCACCACACTGACT 150
i i
C L1PA2_3end#LI 369 GTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACT 320
E00378:188:HV 151 T 151
C L1PA2_3end#LI 319 T 319
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1279 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1115:17787:54313/2 1 151 (0) + L1P LINE/L1 5268 5418 (737) 588
ANNOTATION EVIDENCE:
1279 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:17787:54313/2 1 151 0 + L1PA2_3end LINE/L1 15 165 737
1279 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:17787:54313/2 1 151 (0) L1PA2_3end#LINE/L1 15 165 (737) m_b1s551i173
E00378:188:HV 1 CTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCA 50
L1PA2_3end#LI 15 CTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCA 64
E00378:188:HV 51 AAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTAT 100
L1PA2_3end#LI 65 AAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTAT 114
E00378:188:HV 101 GCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGA 150
L1PA2_3end#LI 115 GCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGA 164
E00378:188:HV 151 A 151
L1PA2_3end#LI 165 A 165
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1169 11.9 0.0 0.0 E00378:188:HVMVNCCXX:3:1115:27255:29824/1 1 151 (0) C AluSx SINE/Alu (80) 232 82 589
ANNOTATION EVIDENCE:
1169 11.92 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:27255:29824/1 1 151 0 C AluSx SINE/Alu 82 232 80
1169 11.92 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:27255:29824/1 1 151 (0) C AluSx#SINE/Alu (80) 232 82 m_b2s356i23
E00378:188:HV 1 CAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAGTGATTCTCCTGCCTCA 50
i i i i i i
C AluSx#SINE/Al 232 CGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCA 183
E00378:188:HV 51 GCTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCACACCCAGCTAAT 100
i i i v i i i
C AluSx#SINE/Al 182 GCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT 133
E00378:188:HV 101 TTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTT 150
v i ii i
C AluSx#SINE/Al 132 TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTC 83
E00378:188:HV 151 T 151
C AluSx#SINE/Al 82 T 82
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.27
Transitions / transversions = 8.00 (16/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1169 11.9 0.0 0.0 E00378:188:HVMVNCCXX:3:1115:28077:30545/1 1 151 (0) C AluSx SINE/Alu (80) 232 82 590
ANNOTATION EVIDENCE:
1169 11.92 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:28077:30545/1 1 151 0 C AluSx SINE/Alu 82 232 80
1169 11.92 0.00 0.00 E00378:188:HVMVNCCXX:3:1115:28077:30545/1 1 151 (0) C AluSx#SINE/Alu (80) 232 82 m_b2s356i24
E00378:188:HV 1 CAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAGTGATTCTCCTGCCTCA 50
i i i i i i
C AluSx#SINE/Al 232 CGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCA 183
E00378:188:HV 51 GCTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCACACCCAGCTAAT 100
i i i v i i i
C AluSx#SINE/Al 182 GCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT 133
E00378:188:HV 101 TTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTT 150
v i ii i
C AluSx#SINE/Al 132 TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTC 83
E00378:188:HV 151 T 151
C AluSx#SINE/Al 82 T 82
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.27
Transitions / transversions = 8.00 (16/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 596 17.3 15.2 0.0 E00378:188:HVMVNCCXX:3:1116:25631:52854/1 1 139 (12) + L1MC4 LINE/L1 7486 7649 (393) 591
ANNOTATION EVIDENCE:
596 17.27 15.25 0.00 E00378:188:HVMVNCCXX:3:1116:25631:52854/1 1 139 12 + L1MC4_3end LINE/L1 2233 2396 393
596 17.27 15.25 0.00 E00378:188:HVMVNCCXX:3:1116:25631:52854/1 1 139 (12) L1MC4_3end#LINE/L1 2233 2396 (393) m_b3s551i96
E00378:188:HV 1 AATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGGAC------ 44
i i i i vii ------
L1MC4_3end#LI 2233 AATCTAATCATGAGGAAACATCAGACAAACCCAAATTGAGGGACATTCTA 2282
E00378:188:HV 45 -------------CTGTACTATTCAAATATATGAAGGTCATGATAAATAA 81
------------- v v i v ? v i i
L1MC4_3end#LI 2283 CAAAATAACTGGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAA 2332
E00378:188:HV 82 AAAAA------AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACAC 125
i ------i i v vvv
L1MC4_3end#LI 2333 AGAAAGACTGAGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGAC 2382
E00378:188:HV 126 ACCTAAATGCAATG 139
v i
L1MC4_3end#LI 2383 AACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.15
Transitions / transversions = 1.30 (13/10)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 8.33 (25 / 3)
+ 343 20.2 0.0 17.5 E00378:188:HVMVNCCXX:3:1116:25631:52854/2 29 148 (3) C L1MC4 LINE/L1 (90) 7952 7854 592
ANNOTATION EVIDENCE:
343 20.21 0.00 17.50 E00378:188:HVMVNCCXX:3:1116:25631:52854/2 29 148 3 C L1MC4_3end LINE/L1 2601 2699 90
343 20.21 0.00 17.50 E00378:188:HVMVNCCXX:3:1116:25631:52854/2 29 148 (3) C L1MC4_3end#LINE/L1 (90) 2699 2601 m_b3s551i7
E00378:188:HV 29 GTTAACGTTTTACCATATTTGCTTAATCATTCCCTCTCTCCACACACACA 78
i i i v i ? ? -----------
C L1MC4_3end#LI 2699 GTTAACATTTTGCCACATTTGCTTTATCATTCTCTNTNT----------- 2661
E00378:188:HV 79 CTCATACGCAGATACACACATCATTTTCTCTGAACCATTTTGAGATGAAA 128
------- -- i i iv i - vv i
C L1MC4_3end#LI 2660 -------GC--ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAG 2621
E00378:188:HV 129 TCGCACACGTGATGCTCCTT 148
i v i ? i
C L1MC4_3end#LI 2620 TTGCAGACATNATGCCCCTT 2601
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.73
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.18 (21 / 119), avg. gap size = 1.00 (21 / 21)
+ 1178 6.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1117:2250:46419/2 1 151 (0) C L1P3 LINE/L1 (3187) 2959 2809 593
ANNOTATION EVIDENCE:
1178 5.96 0.00 0.00 E00378:188:HVMVNCCXX:3:1117:2250:46419/2 1 151 0 C L1P3_orf2 LINE/L1 700 850 2444
1178 5.96 0.00 0.00 E00378:188:HVMVNCCXX:3:1117:2250:46419/2 1 151 (0) C L1P3_orf2#LINE/L1 (2444) 850 700 m_b7s551i55
E00378:188:HV 1 ACATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTTATTTCTGCC 50
i i ?i
C L1P3_orf2#LIN 850 ACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTTATTTCTGCC 801
E00378:188:HV 51 TTCATTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTTGTTCAGTTT 100
v i i
C L1P3_orf2#LIN 800 TTAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTT 751
E00378:188:HV 101 CCATGTAGTTGTGTGGTTTTGAGTGAGTTTCTTAATCCTCAGTTCTAATT 150
i v
C L1P3_orf2#LIN 750 CCATGTAGTTGTGCGGTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAATT 701
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 700 T 700
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1355 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1118:13524:8359/1 1 151 (0) + L1P1 LINE/L1 5589 5739 (416) 594
ANNOTATION EVIDENCE:
1355 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:13524:8359/1 1 151 0 + L1PA2_3end LINE/L1 336 486 416
1355 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:13524:8359/1 1 151 (0) L1PA2_3end#LINE/L1 336 486 (416) m_b1s551i300
E00378:188:HV 1 CCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAGCCATCCCATTAC 50
i
L1PA2_3end#LI 336 CCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTAC 385
E00378:188:HV 51 TGGGTATATACCCAAAGGACTATAAATCATGCCGCTATAAAGACACATGC 100
i
L1PA2_3end#LI 386 TGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGC 435
E00378:188:HV 101 ACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAACCA 150
i
L1PA2_3end#LI 436 ACACGTATGTTTATTGCGGCATTATTCACAATAGCAAAGACTTGGAACCA 485
E00378:188:HV 151 A 151
L1PA2_3end#LI 486 A 486
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 263 25.7 3.9 0.0 E00378:188:HVMVNCCXX:3:1118:14377:48652/1 78 151 (0) + MIRb SINE/MIR 67 143 (125) 595
ANNOTATION EVIDENCE:
263 25.68 3.89 0.00 E00378:188:HVMVNCCXX:3:1118:14377:48652/1 78 151 0 + MIRb SINE/MIR 67 143 125
263 25.68 3.89 0.00 E00378:188:HVMVNCCXX:3:1118:14377:48652/1 78 151 (0) MIRb#SINE/MIR 67 143 (125) m_b6s601i75
E00378:188:HV 78 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 126
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 127 TCACTAAGTCACAGTTT--TCATTTAT 151
v i i v -- i i
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGT 143
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 32.39
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.50 (3 / 2)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:3:1118:14377:48652/2 97 141 (10) C MIR SINE/MIR (0) 262 218 596
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:14377:48652/2 97 141 10 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:14377:48652/2 97 141 (10) C MIR#SINE/MIR (0) 262 218 m_b6s601i1
E00378:188:HV 97 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 141
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 282 19.4 2.9 0.0 E00378:188:HVMVNCCXX:3:1118:22100:24479/2 1 67 (84) + L1MC4 LINE/L1 7581 7649 (393) 597
ANNOTATION EVIDENCE:
282 19.40 2.90 0.00 E00378:188:HVMVNCCXX:3:1118:22100:24479/2 1 67 84 + L1MC4_3end LINE/L1 2328 2396 393
282 19.40 2.90 0.00 E00378:188:HVMVNCCXX:3:1118:22100:24479/2 1 67 (84) L1MC4_3end#LINE/L1 2328 2396 (393) m_b3s551i60
E00378:188:HV 1 GATAAATAAAAA--AAAGAACTGTTCCAGATTGAAGAAGACTAAACAGAC 48
i v i --i i i i v
L1MC4_3end#LI 2328 GACAAAGAAAGACTGAGGAACTGTTCCAGATTAAAGGAGACTAAAGAGAC 2377
E00378:188:HV 49 TACACACCTAAATGCAATG 67
vvv v i
L1MC4_3end#LI 2378 ATGACAACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.78
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.02 (1 / 66), avg. gap size = 2.00 (2 / 1)
+ 483 17.5 0.0 0.0 E00378:188:HVMVNCCXX:3:1118:22100:24479/2 72 151 (0) + L1MC4 LINE/L1 7762 7841 (201) 597
ANNOTATION EVIDENCE:
483 17.50 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:22100:24479/2 72 151 0 + L1MC4_3end LINE/L1 2509 2588 201
483 17.50 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:22100:24479/2 72 151 (0) L1MC4_3end#LINE/L1 2509 2588 (201) m_b3s551i61
E00378:188:HV 72 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 121
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
E00378:188:HV 122 ATCCTTGTTTTTAGGAAATATACACTGAAG 151
i i i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACTGAAG 2588
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.93
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 669 15.5 0.0 0.0 E00378:188:HVMVNCCXX:3:1118:31213:24901/2 46 148 (3) + AluY SINE/Alu 1 103 (208) 598
ANNOTATION EVIDENCE:
669 15.53 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:31213:24901/2 46 148 3 + AluY SINE/Alu 1 103 208
669 15.53 0.00 0.00 E00378:188:HVMVNCCXX:3:1118:31213:24901/2 46 148 (3) AluY#SINE/Alu 1 103 (208) m_b2s357i73
E00378:188:HV 46 GGCCAGGCATGGTCGCCCACGCTTGTCATCTCAGCACTTTGGGAGGCCAA 95
i ii v i i v i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 96 GACGGGCTGATCATGAGGTCAGCAGATCAAGACCATCCTGGCTAACGTGG 145
i v i v i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 146 TGA 148
AluY#SINE/Alu 101 TGA 103
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.12
Transitions / transversions = 3.00 (12/4)
Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0)
+ 1253 7.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1119:24424:49672/1 1 151 (0) C AluSx SINE/Alu (49) 263 113 599
ANNOTATION EVIDENCE:
1253 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:1119:24424:49672/1 1 151 0 C AluSx SINE/Alu 113 263 49
1253 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:1119:24424:49672/1 1 151 (0) C AluSx#SINE/Alu (49) 263 113 m_b4s356i15
E00378:188:HV 1 TTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTTCG 50
i i i
C AluSx#SINE/Al 263 TCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCG 214
E00378:188:HV 51 CCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGA 100
i i
C AluSx#SINE/Al 213 CCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGA 164
E00378:188:HV 101 TTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAG 150
i vi v i i
C AluSx#SINE/Al 163 TTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAG 114
E00378:188:HV 151 A 151
C AluSx#SINE/Al 113 A 113
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1113 6.0 3.2 0.0 E00378:188:HVMVNCCXX:3:1119:3975:54401/2 1 151 (0) + L1P3 LINE/L1 3636 3791 (2355) 600
ANNOTATION EVIDENCE:
1113 5.96 3.20 0.00 E00378:188:HVMVNCCXX:3:1119:3975:54401/2 1 151 0 + L1P3_orf2 LINE/L1 1527 1682 1612
1113 5.96 3.20 0.00 E00378:188:HVMVNCCXX:3:1119:3975:54401/2 1 151 (0) L1P3_orf2#LINE/L1 1527 1682 (1612) m_b6s551i64
E00378:188:HV 1 TTATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAA--G 48
v v --i
L1P3_orf2#LIN 1527 TTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAA 1576
E00378:188:HV 49 AAAAAGAAAATTTCAGGCCATTATCCGTGATGAACATCGATGTGAAAATC 98
v v i
L1P3_orf2#LIN 1577 AAAAAGAAAATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATC 1626
E00378:188:HV 99 CTCGATAAAATACTGGCAAACTGAATCCAGCA---CATCAAAACGCTTAT 145
i i --- v
L1P3_orf2#LIN 1627 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTAT 1676
E00378:188:HV 146 CCACCA 151
L1P3_orf2#LIN 1677 CCACCA 1682
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 260 26.2 5.8 1.4 E00378:188:HVMVNCCXX:3:1119:8978:70381/2 5 151 (0) C L1ME4c LINE/L1 (216) 5867 5714 601
ANNOTATION EVIDENCE:
260 26.21 5.84 1.36 E00378:188:HVMVNCCXX:3:1119:8978:70381/2 5 151 0 C L1ME4c_3end LINE/L1 461 614 216
260 26.21 5.84 1.36 E00378:188:HVMVNCCXX:3:1119:8978:70381/2 5 151 (0) C L1ME4c_3end#LINE/L1 (216) 614 461 m_b2s551i7
E00378:188:HV 5 ATTATAAGTATTTTTCCAGGTAGTTGC-TTTTCTTGATAGTCATACTTTT 53
i ii - v v i i - vv v i i vv
C L1ME4c_3end#L 614 ATCATAAACA-TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTT 566
E00378:188:HV 54 TAATGGCTTCACCATTTTTCTGTC--ATAAA--TACCATAATTTACTTGA 99
v iv - v ii --i ?i -- i
C L1ME4c_3end#L 565 TAATGGCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAA 517
E00378:188:HV 100 -CATT-TTTTATTGTCAGAAATTTAGATTCTTTTCTATTTTC--CTACAA 145
- -iii ii v i v i v i-- iv
C L1ME4c_3end#L 516 CCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTA 467
E00378:188:HV 146 TAAACA 151
i
C L1ME4c_3end#L 466 TAAATA 461
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.36
Transitions / transversions = 1.64 (23/14)
Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.38 (11 / 8)
+ 1131 8.0 1.9 0.0 E00378:188:HVMVNCCXX:3:1120:20679:38368/1 1 151 (0) + L1P3 LINE/L1 3690 3843 (2303) 602
ANNOTATION EVIDENCE:
1131 7.95 1.95 0.00 E00378:188:HVMVNCCXX:3:1120:20679:38368/1 1 151 0 + L1P3_orf2 LINE/L1 1581 1734 1560
1131 7.95 1.95 0.00 E00378:188:HVMVNCCXX:3:1120:20679:38368/1 1 151 (0) L1P3_orf2#LINE/L1 1581 1734 (1560) m_b6s551i53
E00378:188:HV 1 AGAAAATTTCAGGCCATTATCCGTGATGAACATCGATGTGAAAATCCTCG 50
v v i i
L1P3_orf2#LIN 1581 AGAAAATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATCCTCA 1630
E00378:188:HV 51 ATAAAATACTGGCAAACTGAATCCAGCA---CATCAAAACGCTTATCCAC 97
i --- v
L1P3_orf2#LIN 1631 ATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCAC 1680
E00378:188:HV 98 CACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCATACA 147
v i i i i i
L1P3_orf2#LIN 1681 CACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACATACG 1730
E00378:188:HV 148 CAAA 151
L1P3_orf2#LIN 1731 CAAA 1734
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.79
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1132 7.3 1.9 0.0 E00378:188:HVMVNCCXX:3:1120:20679:38368/2 1 151 (0) C L1P3 LINE/L1 (2271) 3875 3722 603
ANNOTATION EVIDENCE:
1132 7.28 1.95 0.00 E00378:188:HVMVNCCXX:3:1120:20679:38368/2 1 151 0 C L1P3_orf2 LINE/L1 1613 1766 1528
1132 7.28 1.95 0.00 E00378:188:HVMVNCCXX:3:1120:20679:38368/2 1 151 (0) C L1P3_orf2#LINE/L1 (1528) 1766 1613 m_b6s551i45
E00378:188:HV 1 GTTCTGTTTATGTGATGGATTATGTTTATTGATTTGTGTATGCTGAATCA 50
i i i i
C L1P3_orf2#LIN 1766 GTTCTGTTTATGTGATGGATTACGTTTATTGATTTGCGTATGTTGAACCA 1717
E00378:188:HV 51 GCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGGTGGATAAGCGTTT 100
i i v v
C L1P3_orf2#LIN 1716 GCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGGTGGATAAGCTTTT 1667
E00378:188:HV 101 TGATG---TGCTGGATTCAGTTTGCCAGTATTTTATCGAGGATTTTCACA 147
--- i i i
C L1P3_orf2#LIN 1666 TGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCA 1617
E00378:188:HV 148 TCGA 151
C L1P3_orf2#LIN 1616 TCGA 1613
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1015 5.3 7.4 0.0 E00378:188:HVMVNCCXX:3:1121:12855:66970/1 1 151 (0) + L1P3 LINE/L1 3181 3343 (2803) 604
ANNOTATION EVIDENCE:
1015 5.30 7.36 0.00 E00378:188:HVMVNCCXX:3:1121:12855:66970/1 1 151 0 + L1P3_orf2 LINE/L1 1072 1234 2060
1015 5.30 7.36 0.00 E00378:188:HVMVNCCXX:3:1121:12855:66970/1 1 151 (0) L1P3_orf2#LINE/L1 1072 1234 (2060) m_b6s551i199
E00378:188:HV 1 AAAATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAACAGA 50
v i i
L1P3_orf2#LIN 1072 AAAATCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAATAGA 1121
E00378:188:HV 51 ----CCGCTAGCAAGACTAATAAAGA--------GAGAAGAATCAAATAG 88
---- v --------
L1P3_orf2#LIN 1122 TAGACCGCTAGCCAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAG 1171
E00378:188:HV 89 ACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCCACAGAAATA 138
v i vi
L1P3_orf2#LIN 1172 ACACAATAAAAAATGATAAAGGGGATATCACCACTGATCCCACAGAAATA 1221
E00378:188:HV 139 CAAACTACCATCA 151
L1P3_orf2#LIN 1222 CAAACTACCATCA 1234
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.50
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1132 7.3 1.9 0.0 E00378:188:HVMVNCCXX:3:1121:12855:66970/2 1 151 (0) C L1P3 LINE/L1 (2271) 3875 3722 605
ANNOTATION EVIDENCE:
1132 7.28 1.95 0.00 E00378:188:HVMVNCCXX:3:1121:12855:66970/2 1 151 0 C L1P3_orf2 LINE/L1 1613 1766 1528
1132 7.28 1.95 0.00 E00378:188:HVMVNCCXX:3:1121:12855:66970/2 1 151 (0) C L1P3_orf2#LINE/L1 (1528) 1766 1613 m_b6s551i46
E00378:188:HV 1 GTTCTGTTTATGTGATGGATTATGTTTATTGATTTGTGTATGCTGAATCA 50
i i i i
C L1P3_orf2#LIN 1766 GTTCTGTTTATGTGATGGATTACGTTTATTGATTTGCGTATGTTGAACCA 1717
E00378:188:HV 51 GCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGGTGGATAAGCGTTT 100
i i v v
C L1P3_orf2#LIN 1716 GCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGGTGGATAAGCTTTT 1667
E00378:188:HV 101 TGATG---TGCTGGATTCAGTTTGCCAGTATTTTATCGAGGATTTTCACA 147
--- i i i
C L1P3_orf2#LIN 1666 TGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCA 1617
E00378:188:HV 148 TCGA 151
C L1P3_orf2#LIN 1616 TCGA 1613
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1334 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1124:30553:45523/1 1 151 (0) + L1P1 LINE/L1 5404 5554 (601) 606
ANNOTATION EVIDENCE:
1334 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1124:30553:45523/1 1 151 0 + L1PA3_3end LINE/L1 151 301 601
1334 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1124:30553:45523/1 1 151 (0) L1PA3_3end#LINE/L1 151 301 (601) m_b1s551i241
E00378:188:HV 1 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 50
L1PA3_3end#LI 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
E00378:188:HV 51 ACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 100
i
L1PA3_3end#LI 201 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 250
E00378:188:HV 101 GAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTGGGACTGTAAA 150
iv
L1PA3_3end#LI 251 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA 300
E00378:188:HV 151 C 151
L1PA3_3end#LI 301 C 301
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1352 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1124:30553:45523/2 1 151 (0) C L1P1 LINE/L1 (425) 5730 5580 607
ANNOTATION EVIDENCE:
1352 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1124:30553:45523/2 1 151 0 C L1PA2_3end LINE/L1 327 477 425
1352 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1124:30553:45523/2 1 151 (0) C L1PA2_3end#LINE/L1 (425) 477 327 m_b1s551i297
E00378:188:HV 1 AGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGT 50
i
C L1PA2_3end#LI 477 AGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGT 428
E00378:188:HV 51 CTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGG 100
i
C L1PA2_3end#LI 427 CTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGG 378
E00378:188:HV 101 ATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCACCA 150
i i
C L1PA2_3end#LI 377 ATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCA 328
E00378:188:HV 151 C 151
C L1PA2_3end#LI 327 C 327
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1196 4.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1124:7628:23108/2 1 151 (0) C L1P1 LINE/L1 (891) 5255 5105 608
ANNOTATION EVIDENCE:
1196 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:1124:7628:23108/2 1 151 0 C L1P1_orf2 LINE/L1 2996 3146 148
1196 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:1124:7628:23108/2 1 151 (0) C L1P1_orf2#LINE/L1 (148) 3146 2996 m_b1s551i106
E00378:188:HV 1 AGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGG 50
i
C L1P1_orf2#LIN 3146 AGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGG 3097
E00378:188:HV 51 TTGCCTGTTCACTCTGGTGGTAGTTTCTTTTGCTGTGCAGAAGCGCTTTA 100
i v
C L1P1_orf2#LIN 3096 TTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTA 3047
E00378:188:HV 101 GTTTAATTAGATCCGATTTGTCAATTCTGTCTTTTGTTGCCAGTGCTTTT 150
v i v v
C L1P1_orf2#LIN 3046 GTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTT 2997
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2996 G 2996
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.79
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 16 19.1 0.0 0.0 E00378:188:HVMVNCCXX:3:1201:7659:66232/2 36 65 (86) + (TG)n Simple_repeat 1 30 (0) 609
ANNOTATION EVIDENCE:
16 19.09 0.00 0.00 E00378:188:HVMVNCCXX:3:1201:7659:66232/2 36 65 86 + (TG)n Simple_repeat 1 30 0
16 19.09 0.00 0.00 E00378:188:HVMVNCCXX:3:1201:7659:66232/2 36 65 (86) (TG)n#Simple_repeat 1 30 (0) m_b3s252i4
E00378:188:HV 36 TGTGTGTATCTGCGTATGAGTGTGTGTGTG 65
i v i i v
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 30
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1203:17127:26730/1 12 33 (118) + (A)n Simple_repeat 1 22 (0) 610
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:17127:26730/1 12 33 118 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:17127:26730/1 12 33 (118) (A)n#Simple_repeat 1 22 (0) m_b1s252i13
E00378:188:HV 12 AAAAAAAAAAAAAAAAAAAAAA 33
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1218 5.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1203:17127:26730/2 1 151 (0) + L1PA2 LINE/L1 5676 5826 (329) 611
ANNOTATION EVIDENCE:
1218 5.30 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:17127:26730/2 1 151 0 + L1PA2_3end LINE/L1 423 573 329
1218 5.30 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:17127:26730/2 1 151 (0) L1PA2_3end#LINE/L1 423 573 (329) m_b1s551i330
E00378:188:HV 1 TAAAGACACATGCACACGTACGTTTATTGTGGCCTTATCCACAATAGCAA 50
i i v i
L1PA2_3end#LI 423 TAAAGACACATGCACACGTATGTTTATTGCGGCATTATTCACAATAGCAA 472
E00378:188:HV 51 CGACTTGGACCCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAA 100
v v
L1PA2_3end#LI 473 AGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAA 522
E00378:188:HV 101 CTGTGGCACATATACACCATGGAATACTATGCAGCCATAACAAATGATGA 150
v v
L1PA2_3end#LI 523 ATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGA 572
E00378:188:HV 151 G 151
L1PA2_3end#LI 573 G 573
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1126 10.1 0.0 0.0 E00378:188:HVMVNCCXX:3:1203:32157:46683/1 4 151 (0) + AluSx SINE/Alu 68 215 (97) 612
ANNOTATION EVIDENCE:
1126 10.14 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:32157:46683/1 4 151 0 + AluSx SINE/Alu 68 215 97
1126 10.14 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:32157:46683/1 4 151 (0) AluSx#SINE/Alu 68 215 (97) m_b4s356i29
E00378:188:HV 4 AGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCT 53
i v i i i
AluSx#SINE/Al 68 AGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCT 117
E00378:188:HV 54 ACAAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCC 103
v i i v iv i
AluSx#SINE/Al 118 ACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCC 167
E00378:188:HV 104 AGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTAGAACCTGGGAGGCG 151
i v i
AluSx#SINE/Al 168 AGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCG 215
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.79
Transitions / transversions = 2.00 (10/5)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 39 70 (81) + (TG)n Simple_repeat 1 32 (0) 613
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 39 70 81 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 39 70 (81) (TG)n#Simple_repeat 1 32 (0) m_b4s252i61
E00378:188:HV 39 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 70
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 71 83 (68) + (TGTATG)n Simple_repeat 1 41 (0) 614
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 39 83 68 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 39 83 (68) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i60
E00378:188:HV 39 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 83
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 302 9.6 3.7 0.0 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 98 149 (2) C 7SLRNA srpRNA (11) 309 256 615
ANNOTATION EVIDENCE:
302 9.62 3.71 0.00 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 98 149 2 C 7SLRNA SINE/Alu 256 309 11
302 9.62 3.71 0.00 E00378:188:HVMVNCCXX:3:1203:32157:46683/2 98 149 (2) C 7SLRNA#SINE/Alu (11) 309 256 m_b4s502i5
E00378:188:HV 98 TTTTTTTTT--GAGACGGACTCTCGCTCTGTTGCCCGGGCTGGAGTGCGG 145
-- iv v i i
C 7SLRNA#SINE/A 309 TTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGGAGTGCAG 260
E00378:188:HV 146 TGGC 149
C 7SLRNA#SINE/A 259 TGGC 256
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.35
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1)
+ 1200 6.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1203:5761:10310/1 1 151 (0) + L1P3 LINE/L1 2895 3045 (3101) 616
ANNOTATION EVIDENCE:
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:5761:10310/1 1 151 0 + L1P3_orf2 LINE/L1 786 936 2358
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:3:1203:5761:10310/1 1 151 (0) L1P3_orf2#LINE/L1 786 936 (2358) m_b7s551i29
E00378:188:HV 1 AAATAATGAAATGAAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGA 50
i v i? i
L1P3_orf2#LIN 786 AAATAACGAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGA 835
E00378:188:HV 51 ACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 100
i
L1P3_orf2#LIN 836 ACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 885
E00378:188:HV 101 AGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATC 150
? v i
L1P3_orf2#LIN 886 AGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATC 935
E00378:188:HV 151 T 151
L1P3_orf2#LIN 936 T 936
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.95
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 909 7.4 7.5 0.7 E00378:188:HVMVNCCXX:3:1203:5761:10310/2 1 150 (1) C L1P3 LINE/L1 (2823) 3323 3163 617
ANNOTATION EVIDENCE:
909 7.38 7.45 0.67 E00378:188:HVMVNCCXX:3:1203:5761:10310/2 1 150 1 C L1P3_orf2 LINE/L1 1054 1214 2080
909 7.38 7.45 0.67 E00378:188:HVMVNCCXX:3:1203:5761:10310/2 1 150 (1) C L1P3_orf2#LINE/L1 (2080) 1214 1054 m_b6s551i205
E00378:188:HV 1 GTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCTATTTG 50
iv i v
C L1P3_orf2#LIN 1214 GTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTG 1165
E00378:188:HV 51 ATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----TCTGTTT 88
-------- v ---- i
C L1P3_orf2#LIN 1164 ATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCTATTT 1115
E00378:188:HV 89 TGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAA 138
i v - i
C L1P3_orf2#LIN 1114 TGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAG 1066
E00378:188:HV 139 GGTTTTTTTTGT 150
iv
C L1P3_orf2#LIN 1065 GGTTTTTCGTGT 1054
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.12
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.02 (3 / 149), avg. gap size = 4.33 (13 / 3)
+ 1346 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1204:17777:24726/1 1 151 (0) C L1P2 LINE/L1 (523) 5632 5482 618
ANNOTATION EVIDENCE:
1346 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1204:17777:24726/1 1 151 0 C L1PA4_3end LINE/L1 229 379 523
1346 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1204:17777:24726/1 1 151 (0) C L1PA4_3end#LINE/L1 (523) 379 229 m_b1s551i268
E00378:188:HV 1 GGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCAC 50
i i
C L1PA4_3end#LI 379 GGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGC 330
E00378:188:HV 51 CACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTG 100
C L1PA4_3end#LI 329 CACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTG 280
E00378:188:HV 101 TAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTG 150
vi
C L1PA4_3end#LI 279 TAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTG 230
E00378:188:HV 151 A 151
C L1PA4_3end#LI 229 A 229
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1269 0.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1204:17777:24726/2 1 151 (0) + L1P1 LINE/L1 5239 5389 (757) 619
ANNOTATION EVIDENCE:
1269 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:1204:17777:24726/2 1 151 0 + L1P1_orf2 LINE/L1 3130 3280 14
1269 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:1204:17777:24726/2 1 151 (0) L1P1_orf2#LINE/L1 3130 3280 (14) m_b1s551i156
E00378:188:HV 1 TCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAAT 50
L1P1_orf2#LIN 3130 TCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAAT 3179
E00378:188:HV 51 TTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGGCATGA 100
i
L1P1_orf2#LIN 3180 TTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGA 3229
E00378:188:HV 101 ACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAA 150
L1P1_orf2#LIN 3230 ACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAA 3279
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3280 A 3280
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 918 15.4 0.0 1.3 E00378:188:HVMVNCCXX:3:1204:22313:34483/1 1 151 (0) + AluSx SINE/Alu 95 243 (69) 620
ANNOTATION EVIDENCE:
918 15.43 0.00 1.32 E00378:188:HVMVNCCXX:3:1204:22313:34483/1 1 151 0 + AluSx SINE/Alu 95 243 69
918 15.43 0.00 1.32 E00378:188:HVMVNCCXX:3:1204:22313:34483/1 1 151 (0) AluSx#SINE/Alu 95 243 (69) m_b5s356i11
E00378:188:HV 1 CAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGG 50
i v i -- i
AluSx#SINE/Al 95 CAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGG 142
E00378:188:HV 51 CATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGA 100
i v i v v vi i i
AluSx#SINE/Al 143 CGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
E00378:188:HV 101 CAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGATATAGCACC 150
v i iivv v v v i
AluSx#SINE/Al 193 GAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCC 242
E00378:188:HV 151 A 151
AluSx#SINE/Al 243 A 243
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 11.36
Transitions / transversions = 1.09 (12/11)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 183 34.9 8.0 3.1 E00378:188:HVMVNCCXX:3:1204:6644:13211/1 1 130 (21) C MIRb SINE/MIR (116) 152 16 621
ANNOTATION EVIDENCE:
183 34.93 8.03 3.08 E00378:188:HVMVNCCXX:3:1204:6644:13211/1 1 130 21 C MIRb SINE/MIR 16 152 116
183 34.93 8.03 3.08 E00378:188:HVMVNCCXX:3:1204:6644:13211/1 1 130 (21) C MIRb#SINE/MIR (116) 152 16 m_b4s601i39
E00378:188:HV 1 CTTCACTCTACTGATGAGGGTACGAAGGCCCTAGATGACATAAGGCAAGT 50
ii i i v iv vi i - - vi v i i v
C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTC-AGA-GAGGTTAAGTAACT 105
E00378:188:HV 51 TTTTTACCAGA----AAAGTTA--AGGCTGTGGTACTGGGATTTGAATTT 94
viii -- i---- v i -- i iv ii vi i i iii
C MIRb#SINE/MIR 104 TGCCCA--AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57
E00378:188:HV 95 ---TCTGTTTGACTTCAAAGCC--TTTTGTTTTTACTATAC 130
--- i i -- vi v ii ii
C MIRb#SINE/MIR 56 AGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCAC 16
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 48.02
Transitions / transversions = 2.67 (32/12)
Gap_init rate = 0.06 (8 / 129), avg. gap size = 1.88 (15 / 8)
+ 1248 8.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1204:6644:13211/2 1 151 (0) + AluSx SINE/Alu 92 242 (70) 622
ANNOTATION EVIDENCE:
1248 7.95 0.00 0.00 E00378:188:HVMVNCCXX:3:1204:6644:13211/2 1 151 0 + AluSx SINE/Alu 92 242 70
1248 7.95 0.00 0.00 E00378:188:HVMVNCCXX:3:1204:6644:13211/2 1 151 (0) AluSx#SINE/Alu 92 242 (70) m_b4s356i19
E00378:188:HV 1 GGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCAG 50
i i i i i
AluSx#SINE/Al 92 GGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGG 141
E00378:188:HV 51 GGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGG 100
v iv i i
AluSx#SINE/Al 142 GCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGG 191
E00378:188:HV 101 AGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGC 150
i i
AluSx#SINE/Al 192 AGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGC 241
E00378:188:HV 151 C 151
AluSx#SINE/Al 242 C 242
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 247 26.2 0.0 0.0 E00378:188:HVMVNCCXX:3:1205:11150:4104/1 1 61 (90) C L1M5 LINE/L1 (372) 5801 5741 623
ANNOTATION EVIDENCE:
247 26.23 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11150:4104/1 1 61 90 C L1ME3A_3end LINE/L1 488 548 372
247 26.23 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11150:4104/1 1 61 (90) C L1ME3A_3end#LINE/L1 (372) 548 488 m_b1s551i523
E00378:188:HV 1 TATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTACTATTGT 50
iii i ii i ii iv v i i v
C L1ME3A_3end#L 548 TATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGA 499
E00378:188:HV 51 TGGACATTTAG 61
i
C L1ME3A_3end#L 498 TGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.85
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1205:11150:4104/1 123 144 (7) + (T)n Simple_repeat 1 22 (0) 624
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11150:4104/1 123 144 7 + (T)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11150:4104/1 123 144 (7) (T)n#Simple_repeat 1 22 (0) m_b1s252i12
E00378:188:HV 123 TTTTTTTTTTTTTTTTTTTTTT 144
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1105 12.1 0.0 1.3 E00378:188:HVMVNCCXX:3:1205:11150:4104/2 1 151 (0) + AluSx SINE/Alu 124 272 (40) 625
ANNOTATION EVIDENCE:
1105 12.08 0.00 1.32 E00378:188:HVMVNCCXX:3:1205:11150:4104/2 1 151 0 + AluSx SINE/Alu 124 272 40
1105 12.08 0.00 1.32 E00378:188:HVMVNCCXX:3:1205:11150:4104/2 1 151 (0) AluSx#SINE/Alu 124 272 (40) m_b2s356i7
E00378:188:HV 1 AATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTAC 50
i i i v i
AluSx#SINE/Al 124 AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTAC 173
E00378:188:HV 51 TCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGATTGC 100
i i i i i i i
AluSx#SINE/Al 174 TCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGC 223
E00378:188:HV 101 AGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAAGCGA 150
i ii --i ii
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGAGCGA 271
E00378:188:HV 151 G 151
AluSx#SINE/Al 272 G 272
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.05
Transitions / transversions = 17.00 (17/1)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 247 26.2 0.0 0.0 E00378:188:HVMVNCCXX:3:1205:11759:3120/1 1 61 (90) C L1M5 LINE/L1 (372) 5801 5741 626
ANNOTATION EVIDENCE:
247 26.23 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11759:3120/1 1 61 90 C L1ME3A_3end LINE/L1 488 548 372
247 26.23 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11759:3120/1 1 61 (90) C L1ME3A_3end#LINE/L1 (372) 548 488 m_b1s551i524
E00378:188:HV 1 TATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTACTATTGT 50
iii i ii i ii iv v i i v
C L1ME3A_3end#L 548 TATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGA 499
E00378:188:HV 51 TGGACATTTAG 61
i
C L1ME3A_3end#L 498 TGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.85
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 21 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1205:11759:3120/1 123 145 (6) + (T)n Simple_repeat 1 23 (0) 627
ANNOTATION EVIDENCE:
21 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11759:3120/1 123 145 6 + (T)n Simple_repeat 1 23 0
21 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:11759:3120/1 123 145 (6) (T)n#Simple_repeat 1 23 (0) m_b1s252i11
E00378:188:HV 123 TTTTTTTTTTTTTTTTTTTTTTT 145
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 1105 12.1 0.0 1.3 E00378:188:HVMVNCCXX:3:1205:11759:3120/2 1 151 (0) + AluSx SINE/Alu 124 272 (40) 628
ANNOTATION EVIDENCE:
1105 12.08 0.00 1.32 E00378:188:HVMVNCCXX:3:1205:11759:3120/2 1 151 0 + AluSx SINE/Alu 124 272 40
1105 12.08 0.00 1.32 E00378:188:HVMVNCCXX:3:1205:11759:3120/2 1 151 (0) AluSx#SINE/Alu 124 272 (40) m_b2s356i8
E00378:188:HV 1 AATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTAC 50
i i i v i
AluSx#SINE/Al 124 AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTAC 173
E00378:188:HV 51 TCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGATTGC 100
i i i i i i i
AluSx#SINE/Al 174 TCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGC 223
E00378:188:HV 101 AGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAAGCGA 150
i ii --i ii
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGAGCGA 271
E00378:188:HV 151 G 151
AluSx#SINE/Al 272 G 272
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.05
Transitions / transversions = 17.00 (17/1)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1030 9.6 0.7 0.0 E00378:188:HVMVNCCXX:3:1205:23115:8200/1 15 149 (2) + AluY SINE/Alu 1 136 (175) 629
ANNOTATION EVIDENCE:
1030 9.63 0.73 0.00 E00378:188:HVMVNCCXX:3:1205:23115:8200/1 15 149 2 + AluY SINE/Alu 1 136 175
1030 9.63 0.73 0.00 E00378:188:HVMVNCCXX:3:1205:23115:8200/1 15 149 (2) AluY#SINE/Alu 1 136 (175) m_b2s357i79
E00378:188:HV 15 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 64
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 65 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 114
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 115 TGAAACCCCATCTCTACTAAAAACACAAAAA-TTAG 149
i i -
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAG 136
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.46
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1)
+ 1190 7.3 0.0 0.7 E00378:188:HVMVNCCXX:3:1205:23115:8200/2 1 151 (0) C AluY SINE/Alu (28) 283 134 630
ANNOTATION EVIDENCE:
1190 7.33 0.00 0.66 E00378:188:HVMVNCCXX:3:1205:23115:8200/2 1 151 0 C AluY SINE/Alu 134 283 28
1190 7.33 0.00 0.66 E00378:188:HVMVNCCXX:3:1205:23115:8200/2 1 151 (0) C AluY#SINE/Alu (28) 283 134 m_b2s356i83
E00378:188:HV 1 TTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGAT 50
i ii
C AluY#SINE/Alu 283 TTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGAT 234
E00378:188:HV 51 CTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCT 100
v i - i i i i
C AluY#SINE/Alu 233 CTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCC 185
E00378:188:HV 101 TCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCT 150
iv
C AluY#SINE/Alu 184 TCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCT 135
E00378:188:HV 151 A 151
C AluY#SINE/Alu 134 A 134
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.84
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 331 4.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 1 46 (105) + L1PA2 LINE/L1 6108 6153 (2) 631
ANNOTATION EVIDENCE:
331 4.35 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 1 46 105 + L1PA2_3end LINE/L1 855 900 2
331 4.35 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 1 46 (105) L1PA2_3end#LINE/L1 855 900 (2) m_b1s551i484
E00378:188:HV 1 AATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 46
i v
L1PA2_3end#LI 855 AATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.48
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 40 128 (23) C L1M5 LINE/L1 (293) 5831 5741 632 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 40 128 23 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 40 128 (23) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i485
E00378:188:HV 40 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 89
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 90 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 128
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 61 128 23 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:1205:5041:60220/1 61 128 (23) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i486
E00378:188:HV 61 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 110
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 111 CTATTGTTGGACATTTAG 128
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 578 8.6 0.0 2.4 E00378:188:HVMVNCCXX:3:1205:5041:60220/2 1 83 (68) + AluSx SINE/Alu 224 304 (8) 633
ANNOTATION EVIDENCE:
578 8.64 0.00 2.41 E00378:188:HVMVNCCXX:3:1205:5041:60220/2 1 83 68 + AluSx SINE/Alu 224 304 8
578 8.64 0.00 2.41 E00378:188:HVMVNCCXX:3:1205:5041:60220/2 1 83 (68) AluSx#SINE/Alu 224 304 (8) m_b2s357i2
E00378:188:HV 1 AGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAAGCGA 50
i ii --i ii
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGAGCGA 271
E00378:188:HV 51 GACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA 83
i
AluSx#SINE/Al 272 GACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.19
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2)
+ 235 28.8 15.4 0.0 E00378:188:HVMVNCCXX:3:1206:28432:25112/1 18 149 (2) C MIR SINE/MIR (0) 262 107 634
ANNOTATION EVIDENCE:
235 28.79 15.38 0.00 E00378:188:HVMVNCCXX:3:1206:28432:25112/1 18 149 2 C MIR SINE/MIR 107 262 0
235 28.79 15.38 0.00 E00378:188:HVMVNCCXX:3:1206:28432:25112/1 18 149 (2) C MIR#SINE/MIR (0) 262 107 m_b6s601i25
E00378:188:HV 18 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 60
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
E00378:188:HV 61 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 95
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
E00378:188:HV 96 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 143
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
E00378:188:HV 144 TGAGGT 149
v
C MIR#SINE/MIR 112 AGAGGT 107
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.06
Transitions / transversions = 1.53 (23/15)
Gap_init rate = 0.04 (5 / 131), avg. gap size = 4.80 (24 / 5)
+ 250 24.6 6.2 3.9 E00378:188:HVMVNCCXX:3:1208:12956:28083/1 3 129 (22) + L1ME4c LINE/L1 5657 5786 (297) 635
ANNOTATION EVIDENCE:
250 24.59 6.15 3.94 E00378:188:HVMVNCCXX:3:1208:12956:28083/1 3 129 22 + L1ME4c_3end LINE/L1 404 533 297
250 24.59 6.15 3.94 E00378:188:HVMVNCCXX:3:1208:12956:28083/1 3 129 (22) L1ME4c_3end#LINE/L1 404 533 (297) m_b2s551i28
E00378:188:HV 3 AAGAAATAATTTAAAATATGAGAAAAAAAAACCCTTAGACA----AATGA 48
i i ----- ii v iv vi ----i v
L1ME4c_3end#L 404 AGGAAATAATTCAAAA-----GAAGGAAAAAGCTATATGCACGAAGATGT 448
E00378:188:HV 49 TCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCTAAATTT 96
iiiv i vi --i v i v i v
L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498
E00378:188:HV 97 CTGACAATAAAA-AATG-TCAAGTAAATTATGGTA 129
ii iii- - i
L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTA 533
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 1332 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:17015:13984/1 1 151 (0) + L1P3 LINE/L1 3481 3631 (2515) 636
ANNOTATION EVIDENCE:
1332 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:17015:13984/1 1 151 0 + L1P3_orf2 LINE/L1 1372 1522 1772
1332 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:17015:13984/1 1 151 (0) L1P3_orf2#LINE/L1 1372 1522 (1772) m_b6s551i109
E00378:188:HV 1 ATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAGA 50
L1P3_orf2#LIN 1372 ATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAGA 1421
E00378:188:HV 51 GGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTACCAT 100
v i
L1P3_orf2#LIN 1422 CGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTACCAT 1471
E00378:188:HV 101 TCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCCTAAC 150
i
L1P3_orf2#LIN 1472 TCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCCTAAC 1521
E00378:188:HV 151 T 151
L1P3_orf2#LIN 1522 T 1522
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 996 7.5 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:17015:13984/2 15 147 (4) C L1P3 LINE/L1 (2248) 3898 3766 637
ANNOTATION EVIDENCE:
996 7.52 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:17015:13984/2 15 147 4 C L1P3_orf2 LINE/L1 1657 1789 1505
996 7.52 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:17015:13984/2 15 147 (4) C L1P3_orf2#LINE/L1 (1505) 1789 1657 m_b6s551i34
E00378:188:HV 15 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 64
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 65 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 114
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 115 TTGATAGTGGTGGATAAGCGTTTTGATGTGCTG 147
v v
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGCTTTTTGATGTGCTG 1657
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.72
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
+ 594 2.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:28767:30791/1 1 74 (77) + L1PA2 LINE/L1 6080 6153 (2) 638
ANNOTATION EVIDENCE:
594 2.70 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28767:30791/1 1 74 77 + L1PA2_3end LINE/L1 827 900 2
594 2.70 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28767:30791/1 1 74 (77) L1PA2_3end#LINE/L1 827 900 (2) m_b1s551i451
E00378:188:HV 1 CATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAA 50
L1PA2_3end#LI 827 CATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAA 876
E00378:188:HV 51 CTTAAAGTGTAATAAAAAAAATAA 74
i v
L1PA2_3end#LI 877 CTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.75
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 881 12.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:28767:30791/2 34 151 (0) + AluSx SINE/Alu 1 118 (194) 639
ANNOTATION EVIDENCE:
881 12.71 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28767:30791/2 34 151 0 + AluSx SINE/Alu 1 118 194
881 12.71 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28767:30791/2 34 151 (0) AluSx#SINE/Alu 1 118 (194) m_b2s356i41
E00378:188:HV 34 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 83
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 84 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 133
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 134 GGTGAAACCTTGTCTCTA 151
ii
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTA 118
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.81
Transitions / transversions = 4.00 (12/3)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0)
+ 594 2.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:28940:30703/1 1 74 (77) + L1PA2 LINE/L1 6080 6153 (2) 640
ANNOTATION EVIDENCE:
594 2.70 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28940:30703/1 1 74 77 + L1PA2_3end LINE/L1 827 900 2
594 2.70 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28940:30703/1 1 74 (77) L1PA2_3end#LINE/L1 827 900 (2) m_b1s551i452
E00378:188:HV 1 CATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAA 50
L1PA2_3end#LI 827 CATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAA 876
E00378:188:HV 51 CTTAAAGTGTAATAAAAAAAATAA 74
i v
L1PA2_3end#LI 877 CTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.75
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 838 12.8 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:28940:30703/2 34 150 (1) + AluSx SINE/Alu 1 117 (195) 641
ANNOTATION EVIDENCE:
838 12.82 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28940:30703/2 34 150 1 + AluSx SINE/Alu 1 117 195
838 12.82 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:28940:30703/2 34 150 (1) AluSx#SINE/Alu 1 117 (195) m_b2s357i42
E00378:188:HV 34 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 83
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 84 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 133
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 134 GGTGAAACCTTGTCTCT 150
ii
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCT 117
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.88
Transitions / transversions = 4.00 (12/3)
Gap_init rate = 0.00 (0 / 116), avg. gap size = 0.0 (0 / 0)
+ 995 9.8 0.0 0.0 E00378:188:HVMVNCCXX:3:1208:9993:24005/1 30 151 (0) + AluY SINE/Alu 1 122 (189) 642
ANNOTATION EVIDENCE:
995 9.84 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:9993:24005/1 30 151 0 + AluY SINE/Alu 1 122 189
995 9.84 0.00 0.00 E00378:188:HVMVNCCXX:3:1208:9993:24005/1 30 151 (0) AluY#SINE/Alu 1 122 (189) m_b2s356i44
E00378:188:HV 30 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 79
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 80 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 129
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 130 TGAAACCCCATCTCTACTAAAA 151
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAA 122
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.07
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 1242 6.7 0.7 0.0 E00378:188:HVMVNCCXX:3:1209:4574:34975/2 1 150 (1) C AluY SINE/Alu (129) 182 32 643
ANNOTATION EVIDENCE:
1242 6.67 0.67 0.00 E00378:188:HVMVNCCXX:3:1209:4574:34975/2 1 150 1 C AluY SINE/Alu 32 182 129
1242 6.67 0.67 0.00 E00378:188:HVMVNCCXX:3:1209:4574:34975/2 1 150 (1) C AluY#SINE/Alu (129) 182 32 m_b2s356i59
E00378:188:HV 1 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA 50
iv
C AluY#SINE/Alu 182 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAA 133
E00378:188:HV 51 -TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGG 99
- i i ii
C AluY#SINE/Alu 132 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
E00378:188:HV 100 TCTTGATCTCCTGACCTCATGATCAGCCCGCCTTGGCCTCCCAAAGTGCT 149
i i v i
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
E00378:188:HV 150 G 150
C AluY#SINE/Alu 32 G 32
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.14
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 1275 3.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1210:29163:41216/1 1 151 (0) + L1P1 LINE/L1 4955 5105 (1041) 644
ANNOTATION EVIDENCE:
1275 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:1210:29163:41216/1 1 151 0 + L1P1_orf2 LINE/L1 2846 2996 298
1275 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:1210:29163:41216/1 1 151 (0) L1P1_orf2#LINE/L1 2846 2996 (298) m_b1s551i39
E00378:188:HV 1 TGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAA 50
v v i
L1P1_orf2#LIN 2846 TGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAA 2895
E00378:188:HV 51 GACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGG 100
i
L1P1_orf2#LIN 2896 GACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGG 2945
E00378:188:HV 101 CATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACAC 150
?
L1P1_orf2#LIN 2946 CANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACAC 2995
E00378:188:HV 151 C 151
L1P1_orf2#LIN 2996 C 2996
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1249 0.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1210:29163:41216/2 1 150 (1) C L1P LINE/L1 (731) 5424 5275 645
ANNOTATION EVIDENCE:
1249 0.67 0.00 0.00 E00378:188:HVMVNCCXX:3:1210:29163:41216/2 1 150 1 C L1PA2_3end LINE/L1 22 171 731
1249 0.67 0.00 0.00 E00378:188:HVMVNCCXX:3:1210:29163:41216/2 1 150 (1) C L1PA2_3end#LINE/L1 (731) 171 22 m_b1s551i178
E00378:188:HV 1 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTT 50
C L1PA2_3end#LI 171 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTT 122
E00378:188:HV 51 TGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCC 100
C L1PA2_3end#LI 121 TGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCC 72
E00378:188:HV 101 CACTTTTTGATGGGGTTGTGTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 150
v
C L1PA2_3end#LI 71 CACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 22
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 743 12.4 0.0 0.0 E00378:188:HVMVNCCXX:3:1211:12987:57213/1 1 105 (46) C AluSx SINE/Alu (207) 105 1 646
ANNOTATION EVIDENCE:
743 12.38 0.00 0.00 E00378:188:HVMVNCCXX:3:1211:12987:57213/1 1 105 46 C AluSx SINE/Alu 1 105 207
743 12.38 0.00 0.00 E00378:188:HVMVNCCXX:3:1211:12987:57213/1 1 105 (46) C AluSx#SINE/Alu (207) 105 1 m_b2s357i43
E00378:188:HV 1 TCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCAC 50
i i i
C AluSx#SINE/Al 105 TCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGC 56
E00378:188:HV 51 CTGGCTCTGCCTCCCAAATTGCTGAGATTACAGATGTGAGCCACTGTGCC 100
i v v v i ii i i
C AluSx#SINE/Al 55 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 6
E00378:188:HV 101 CAGCC 105
i
C AluSx#SINE/Al 5 CGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.65
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.0 (0 / 0)
+ 1225 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1211:17787:42042/2 1 151 (0) C L1P3 LINE/L1 (3013) 3133 2983 647
ANNOTATION EVIDENCE:
1225 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1211:17787:42042/2 1 151 0 C L1P3_orf2 LINE/L1 874 1024 2270
1225 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1211:17787:42042/2 1 151 (0) C L1P3_orf2#LINE/L1 (2270) 1024 874 m_b6s551i271
E00378:188:HV 1 TAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTC 50
C L1P3_orf2#LIN 1024 TAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTC 975
E00378:188:HV 51 TCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTTTCCCA 100
i i
C L1P3_orf2#LIN 974 TCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTTCCCG 925
E00378:188:HV 101 CTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTT 150
v ?
C L1P3_orf2#LIN 924 CTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTT 875
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 874 T 874
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1292 1.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1211:7233:56282/1 1 151 (0) C L1P1 LINE/L1 (795) 5351 5201 648
ANNOTATION EVIDENCE:
1292 1.32 0.00 0.00 E00378:188:HVMVNCCXX:3:1211:7233:56282/1 1 151 0 C L1P1_orf2 LINE/L1 3092 3242 52
1292 1.32 0.00 0.00 E00378:188:HVMVNCCXX:3:1211:7233:56282/1 1 151 (0) C L1P1_orf2#LINE/L1 (52) 3242 3092 m_b1s551i141
E00378:188:HV 1 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGT 50
C L1P1_orf2#LIN 3242 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGT 3193
E00378:188:HV 51 TTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCC 100
C L1P1_orf2#LIN 3192 TTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCC 3143
E00378:188:HV 101 CTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTGGC 150
i v
C L1P1_orf2#LIN 3142 CTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGC 3093
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 3092 C 3092
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 327 22.6 12.5 0.0 E00378:188:HVMVNCCXX:3:1213:30086:1749/2 18 101 (50) C L1MC4 LINE/L1 (513) 7529 7416 649
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:3:1213:30086:1749/2 18 101 50 C L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:3:1213:30086:1749/2 18 101 (50) C L1MC4a_3end#LINE/L1 (371) 2258 2163 m_b3s551i127
E00378:188:HV 18 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 62
iiv i i i i i -----
C L1MC4a_3end#L 2258 GTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGTT 2209
E00378:188:HV 63 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT----TCCTCTTCT 101
i --- i i iiii i i ---- v i
C L1MC4a_3end#L 2208 ATGCATTTTTGGCAAGAATACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 4.00 (12 / 3)
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:3:1213:30086:1749/2 18 92 59 C L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:3:1213:30086:1749/2 18 92 (59) C L1MC4_3end#LINE/L1 (513) 2276 2194 m_b3s551i128
E00378:188:HV 18 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 62
iiv i i i i -----
C L1MC4_3end#LI 2276 GTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTT 2227
E00378:188:HV 63 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT 92
i --- i ii iiii i i
C L1MC4_3end#LI 2226 ATGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 1139 8.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1214:16934:14617/1 1 151 (0) + L1PA2 LINE/L1 5940 6090 (65) 650
ANNOTATION EVIDENCE:
1139 7.95 0.00 0.00 E00378:188:HVMVNCCXX:3:1214:16934:14617/1 1 151 0 + L1PA2_3end LINE/L1 687 837 65
1139 7.95 0.00 0.00 E00378:188:HVMVNCCXX:3:1214:16934:14617/1 1 151 (0) L1PA2_3end#LINE/L1 687 837 (65) m_b1s551i394
E00378:188:HV 1 AATGAGGTCACATGGACACAGGAAGGGGAATATCACACTCTGTCGACTGT 50
i vv
L1PA2_3end#LI 687 AATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGT 736
E00378:188:HV 51 TGTGGGGTGGGGAGAGGGGGGAGGGATAGCATCAGGGAATAAACCTAATG 100
v i ii ii v
L1PA2_3end#LI 737 GGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATG 786
E00378:188:HV 101 CTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCTCATGTATACA 150
i v
L1PA2_3end#LI 787 CTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACA 836
E00378:188:HV 151 T 151
L1PA2_3end#LI 837 T 837
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.76
Transitions / transversions = 1.40 (7/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 819 18.3 0.0 1.4 E00378:188:HVMVNCCXX:3:1214:20912:59798/2 8 151 (0) C AluJb SINE/Alu (106) 206 65 651
ANNOTATION EVIDENCE:
819 18.31 0.00 1.39 E00378:188:HVMVNCCXX:3:1214:20912:59798/2 8 151 0 C AluJb SINE/Alu 65 206 106
819 18.31 0.00 1.39 E00378:188:HVMVNCCXX:3:1214:20912:59798/2 8 151 (0) C AluJb#SINE/Alu (106) 206 65 m_b5s356i17
E00378:188:HV 8 GGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACAGG 57
i i iv i i i iv i
C AluJb#SINE/Al 206 GGCTCAAGCGATCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 157
E00378:188:HV 58 CTCCCACCACAATGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGATGGG 107
v v i v i i -- v i
C AluJb#SINE/Al 156 CGCGCGCCACCACGCCCGGCTAA--TTTTTGTATTTTTTGTAGAGACGGG 109
E00378:188:HV 108 GTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAA 151
iv i v i i iv
C AluJb#SINE/Al 108 GTTTCGCCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAA 65
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 13.85
Transitions / transversions = 1.89 (17/9)
Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.00 (2 / 2)
+ 1246 7.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1216:17908:59516/1 1 151 (0) C AluSx SINE/Alu (29) 283 133 652
ANNOTATION EVIDENCE:
1246 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:1216:17908:59516/1 1 151 0 C AluSx SINE/Alu 133 283 29
1246 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:1216:17908:59516/1 1 151 (0) C AluSx#SINE/Alu (29) 283 133 m_b4s356i7
E00378:188:HV 1 TGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATC 50
i i i
C AluSx#SINE/Al 283 TGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATC 234
E00378:188:HV 51 TCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTC 100
i i
C AluSx#SINE/Al 233 TCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTC 184
E00378:188:HV 101 AGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAA 150
i i vi v i
C AluSx#SINE/Al 183 AGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAA 134
E00378:188:HV 151 T 151
C AluSx#SINE/Al 133 T 133
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 932 10.7 1.6 0.0 E00378:188:HVMVNCCXX:3:1216:17908:59516/2 31 151 (0) + AluSx SINE/Alu 1 123 (189) 653
ANNOTATION EVIDENCE:
932 10.74 1.62 0.00 E00378:188:HVMVNCCXX:3:1216:17908:59516/2 31 151 0 + AluSx SINE/Alu 1 123 189
932 10.74 1.62 0.00 E00378:188:HVMVNCCXX:3:1216:17908:59516/2 31 151 (0) AluSx#SINE/Alu 1 123 (189) m_b4s356i57
E00378:188:HV 31 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 80
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 81 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 128
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 129 GGTGAAACTCCATCTCTACTAAA 151
i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAA 123
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 120), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:1216:5944:59815/1 48 79 (72) + (CA)n Simple_repeat 1 32 (0) 654
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:1216:5944:59815/1 48 79 72 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:1216:5944:59815/1 48 79 (72) (CA)n#Simple_repeat 1 32 (0) m_b4s252i59
E00378:188:HV 48 CATACATGCACACACATACACACACACACACA 79
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:3:1216:5944:59815/2 14 106 (45) C MIRb SINE/MIR (49) 219 122 655
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:3:1216:5944:59815/2 14 106 45 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:3:1216:5944:59815/2 14 106 (45) C MIRb#SINE/MIR (49) 219 122 m_b4s601i19
E00378:188:HV 14 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 59
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 60 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 106
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1241 3.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1219:29924:57618/1 1 151 (0) + L1P1 LINE/L1 4983 5133 (1013) 656
ANNOTATION EVIDENCE:
1241 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:1219:29924:57618/1 1 151 0 + L1P1_orf2 LINE/L1 2874 3024 270
1241 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:1219:29924:57618/1 1 151 (0) L1P1_orf2#LINE/L1 2874 3024 (270) m_b1s551i57
E00378:188:HV 1 AATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAA 50
i i
L1P1_orf2#LIN 2874 AATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAA 2923
E00378:188:HV 51 AAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGC 100
?
L1P1_orf2#LIN 2924 AAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGC 2973
E00378:188:HV 101 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAAT 150
v i
L1P1_orf2#LIN 2974 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAAT 3023
E00378:188:HV 151 T 151
L1P1_orf2#LIN 3024 T 3024
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1328 0.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1219:29924:57618/2 1 151 (0) C L1P1 LINE/L1 (682) 5473 5323 657
ANNOTATION EVIDENCE:
1328 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:1219:29924:57618/2 1 151 0 C L1PA2_3end LINE/L1 70 220 682
1328 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:1219:29924:57618/2 1 151 (0) C L1PA2_3end#LINE/L1 (682) 220 70 m_b1s551i204
E00378:188:HV 1 TGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATT 50
i
C L1PA2_3end#LI 220 TGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATT 171
E00378:188:HV 51 TGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTT 100
C L1PA2_3end#LI 170 TGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTT 121
E00378:188:HV 101 GGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCC 150
C L1PA2_3end#LI 120 GGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCC 71
E00378:188:HV 151 A 151
C L1PA2_3end#LI 70 A 70
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1100 8.1 0.7 0.7 E00378:188:HVMVNCCXX:3:1220:10247:24690/1 1 150 (1) C AluY SINE/Alu (82) 229 80 658
ANNOTATION EVIDENCE:
1100 8.05 0.67 0.67 E00378:188:HVMVNCCXX:3:1220:10247:24690/1 1 150 1 C AluY SINE/Alu 80 229 82
1100 8.05 0.67 0.67 E00378:188:HVMVNCCXX:3:1220:10247:24690/1 1 150 (1) C AluY#SINE/Alu (82) 229 80 m_b2s357i86
E00378:188:HV 1 GCTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAG 50
v i - i i i i
C AluY#SINE/Alu 229 GCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAG 181
E00378:188:HV 51 CCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA-T 99
iv -
C AluY#SINE/Alu 180 CCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATT 131
E00378:188:HV 100 TTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGGTC 149
i i ii
C AluY#SINE/Alu 130 TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTC 81
E00378:188:HV 150 T 150
C AluY#SINE/Alu 80 T 80
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.59
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 610 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1220:26484:63683/1 1 76 (75) + L1PA2 LINE/L1 6078 6153 (2) 659
ANNOTATION EVIDENCE:
610 2.63 0.00 0.00 E00378:188:HVMVNCCXX:3:1220:26484:63683/1 1 76 75 + L1PA2_3end LINE/L1 825 900 2
610 2.63 0.00 0.00 E00378:188:HVMVNCCXX:3:1220:26484:63683/1 1 76 (75) L1PA2_3end#LINE/L1 825 900 (2) m_b1s551i449
E00378:188:HV 1 CACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAA 50
L1PA2_3end#LI 825 CACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAA 874
E00378:188:HV 51 AACTTAAAGTGTAATAAAAAAAATAA 76
i v
L1PA2_3end#LI 875 AACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.68
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0)
+ 626 8.2 0.0 2.3 E00378:188:HVMVNCCXX:3:1220:26484:63683/2 2 88 (63) + AluSx SINE/Alu 220 304 (8) 660
ANNOTATION EVIDENCE:
626 8.24 0.00 2.30 E00378:188:HVMVNCCXX:3:1220:26484:63683/2 2 88 63 + AluSx SINE/Alu 220 304 8
626 8.24 0.00 2.30 E00378:188:HVMVNCCXX:3:1220:26484:63683/2 2 88 (63) AluSx#SINE/Alu 220 304 (8) m_b2s357i3
E00378:188:HV 2 TTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAA 51
i ii --i ii
AluSx#SINE/Al 220 TTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGA 267
E00378:188:HV 52 GCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA 88
i
AluSx#SINE/Al 268 GCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.03
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2)
+ 1114 8.6 1.9 0.0 E00378:188:HVMVNCCXX:3:1220:8379:36364/1 1 151 (0) C L1P3 LINE/L1 (2292) 3854 3701 661
ANNOTATION EVIDENCE:
1114 8.61 1.95 0.00 E00378:188:HVMVNCCXX:3:1220:8379:36364/1 1 151 0 C L1P3_orf2 LINE/L1 1592 1745 1549
1114 8.61 1.95 0.00 E00378:188:HVMVNCCXX:3:1220:8379:36364/1 1 151 (0) C L1P3_orf2#LINE/L1 (1549) 1745 1592 m_b6s551i50
E00378:188:HV 1 ATGTTTATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAA 50
i i i i i
C L1P3_orf2#LIN 1745 ACGTTTATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAA 1696
E00378:188:HV 51 GCTGACTTGATAGTGGTGGATAAGCGTTTTGATG---TGCTGGATTCAGT 97
i v v --- i
C L1P3_orf2#LIN 1695 GCCGACTTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGT 1646
E00378:188:HV 98 TTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCATCACGGATAAT 147
i i v v
C L1P3_orf2#LIN 1645 TTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATCAGGGATATT 1596
E00378:188:HV 148 GGCC 151
C L1P3_orf2#LIN 1595 GGCC 1592
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.86
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1082 6.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1220:8379:36364/2 1 151 (0) + L1P3 LINE/L1 3274 3424 (2722) 662
ANNOTATION EVIDENCE:
1082 6.62 0.00 0.00 E00378:188:HVMVNCCXX:3:1220:8379:36364/2 1 151 0 + L1P3_orf2 LINE/L1 1165 1315 1979
1082 6.62 0.00 0.00 E00378:188:HVMVNCCXX:3:1220:8379:36364/2 1 151 (0) L1P3_orf2#LINE/L1 1165 1315 (1979) m_b6s551i173
E00378:188:HV 1 CAAATAGACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCCAC 50
v i vi
L1P3_orf2#LIN 1165 CAAATAGACACAATAAAAAATGATAAAGGGGATATCACCACTGATCCCAC 1214
E00378:188:HV 51 AGAAATACAAACTACCATCAGAGAATACTATAAATACCTCTATGCAAATA 100
i i
L1P3_orf2#LIN 1215 AGAAATACAAACTACCATCAGAGAATACTATAAACACCTCTACGCAAATA 1264
E00378:188:HV 101 AACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAGACACATACAACCTC 150
vv i v
L1P3_orf2#LIN 1265 AACTAGAAAATCTAGAAGAAATGGATAAATTCCTGGACACATACACCCTC 1314
E00378:188:HV 151 C 151
L1P3_orf2#LIN 1315 C 1315
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.29
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1276 4.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1221:7638:10503/1 1 151 (0) C L1P1 LINE/L1 (394) 5761 5611 663
ANNOTATION EVIDENCE:
1276 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:1221:7638:10503/1 1 151 0 C L1PA2_3end LINE/L1 358 508 394
1276 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:1221:7638:10503/1 1 151 (0) C L1PA2_3end#LINE/L1 (394) 508 358 m_b1s551i304
E00378:188:HV 1 CTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAAT 50
C L1PA2_3end#LI 508 CTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAAT 459
E00378:188:HV 51 AATGCCACAATAAACATACGTGTGCATGTGTCTTTGTAGCGGCATGATTT 100
i i i
C L1PA2_3end#LI 458 AATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTT 409
E00378:188:HV 101 ATAGTCCTTTGGATATATACCCAGTAATGGGATGGCTGGGTCGAATCATA 150
i i vi
C L1PA2_3end#LI 408 ATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTA 359
E00378:188:HV 151 T 151
C L1PA2_3end#LI 358 T 358
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.19
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1269 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:1221:7638:10503/2 1 151 (0) + L1P1 LINE/L1 5335 5485 (670) 664
ANNOTATION EVIDENCE:
1269 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1221:7638:10503/2 1 151 0 + L1PA2_3end LINE/L1 82 232 670
1269 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:1221:7638:10503/2 1 151 (0) L1PA2_3end#LINE/L1 82 232 (670) m_b1s551i212
E00378:188:HV 1 ATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACAT 50
L1PA2_3end#LI 82 ATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACAT 131
E00378:188:HV 51 GAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCA 100
L1PA2_3end#LI 132 GAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCA 181
E00378:188:HV 101 CAATGAAATACCATCTCACCCCAGTTAGAATGGCAGTCATTAAAAAGTCA 150
i v i
L1PA2_3end#LI 182 CAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCA 231
E00378:188:HV 151 G 151
L1PA2_3end#LI 232 G 232
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 600 19.1 7.3 0.0 E00378:188:HVMVNCCXX:3:1223:1783:8200/2 2 116 (35) C L1MC4 LINE/L1 (157) 7885 7762 665
ANNOTATION EVIDENCE:
600 19.13 7.26 0.00 E00378:188:HVMVNCCXX:3:1223:1783:8200/2 2 116 35 C L1MC4_3end LINE/L1 2509 2632 157
600 19.13 7.26 0.00 E00378:188:HVMVNCCXX:3:1223:1783:8200/2 2 116 (35) C L1MC4_3end#LINE/L1 (157) 2632 2509 m_b3s551i31
E00378:188:HV 2 TTTGAGATGAAATCGCACACGTGATGCTCCTT---------ATACTTCAG 42
vv i i v i ? i ---------
C L1MC4_3end#LI 2632 TTTGAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAATACTTCAG 2583
E00378:188:HV 43 TGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAAT 92
i i i iv ii iiv i i
C L1MC4_3end#LI 2582 TGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAAT 2533
E00378:188:HV 93 CATCAAAATCAGGAAGTTAACATT 116
i i
C L1MC4_3end#LI 2532 TATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.91
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.01 (1 / 114), avg. gap size = 9.00 (9 / 1)
+ 1247 4.7 0.0 0.0 E00378:188:HVMVNCCXX:3:1223:23348:45593/1 1 150 (1) + L1P3 LINE/L1 2876 3025 (3121) 666
ANNOTATION EVIDENCE:
1247 4.67 0.00 0.00 E00378:188:HVMVNCCXX:3:1223:23348:45593/1 1 150 1 + L1P3_orf2 LINE/L1 767 916 2378
1247 4.67 0.00 0.00 E00378:188:HVMVNCCXX:3:1223:23348:45593/1 1 150 (1) L1P3_orf2#LINE/L1 767 916 (2378) m_b7s551i33
E00378:188:HV 1 TCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAAGTAAG 50
i i v i?
L1P3_orf2#LIN 767 TCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAAANAAG 816
E00378:188:HV 51 TTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGA 100
i i
L1P3_orf2#LIN 817 TTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGA 866
E00378:188:HV 101 CACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACA 150
L1P3_orf2#LIN 867 CACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACA 916
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.88
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 795 7.1 4.1 7.3 E00378:188:HVMVNCCXX:3:1223:23348:45593/2 1 151 (0) C L1P3 LINE/L1 (2883) 3263 3118 667
ANNOTATION EVIDENCE:
795 7.14 4.11 7.28 E00378:188:HVMVNCCXX:3:1223:23348:45593/2 1 151 0 C L1P3_orf2 LINE/L1 1009 1154 2140
795 7.14 4.11 7.28 E00378:188:HVMVNCCXX:3:1223:23348:45593/2 1 151 (0) C L1P3_orf2#LINE/L1 (2140) 1154 1009 m_b6s551i222
E00378:188:HV 1 CTTCTC-TCTTTATTAGTCTTGCTAGCGG----TCTGTTTTGTTAATCTT 45
i - v ---- i
C L1P3_orf2#LIN 1154 CTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTT 1105
E00378:188:HV 46 TTCAAAAAATCAGCTCCTGGAGTAATTGATTTTTTTGAAAGGTTTTTTTT 95
i v v - i i--
C L1P3_orf2#LIN 1104 TTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC-- 1058
E00378:188:HV 96 GTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTT 144
-------- -i v
C L1P3_orf2#LIN 1057 --------GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTT 1016
E00378:188:HV 145 CTTGTCT 151
C L1P3_orf2#LIN 1015 CTTGTCT 1009
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.82
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.21 (17 / 14)
+ 1282 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:1223:25053:4772/1 1 151 (0) + L1P1 LINE/L1 4903 5053 (1093) 668
ANNOTATION EVIDENCE:
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1223:25053:4772/1 1 151 0 + L1P1_orf2 LINE/L1 2794 2944 350
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:1223:25053:4772/1 1 151 (0) L1P1_orf2#LINE/L1 2794 2944 (350) m_b1s551i21
E00378:188:HV 1 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 50
L1P1_orf2#LIN 2794 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 2843
E00378:188:HV 51 ACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTA 100
v v i
L1P1_orf2#LIN 2844 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 2893
E00378:188:HV 101 AAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 150
i
L1P1_orf2#LIN 2894 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 2943
E00378:188:HV 151 G 151
L1P1_orf2#LIN 2944 G 2944
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1301 1.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1223:25053:4772/2 1 151 (0) C L1P1 LINE/L1 (935) 5211 5061 669
ANNOTATION EVIDENCE:
1301 1.32 0.00 0.00 E00378:188:HVMVNCCXX:3:1223:25053:4772/2 1 151 0 C L1P1_orf2 LINE/L1 2952 3102 192
1301 1.32 0.00 0.00 E00378:188:HVMVNCCXX:3:1223:25053:4772/2 1 151 (0) C L1P1_orf2#LINE/L1 (192) 3102 2952 m_b1s551i88
E00378:188:HV 1 TGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGC 50
C L1P1_orf2#LIN 3102 TGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGC 3053
E00378:188:HV 51 TCTTTAGTTTAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATT 100
i v
C L1P1_orf2#LIN 3052 TCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATT 3003
E00378:188:HV 101 GCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAAT 150
C L1P1_orf2#LIN 3002 GCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAAT 2953
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2952 G 2952
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:3:1224:19806:71629/1 16 104 (47) C L1M5 LINE/L1 (293) 5831 5741 670
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:1224:19806:71629/1 16 104 47 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:1224:19806:71629/1 16 104 (47) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i502
E00378:188:HV 16 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 65
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 66 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 104
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:1224:19806:71629/1 37 104 47 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:1224:19806:71629/1 37 104 (47) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i503
E00378:188:HV 37 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 86
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 87 CTATTGTTGGACATTTAG 104
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1112 9.5 0.0 1.3 E00378:188:HVMVNCCXX:3:1224:19806:71629/2 1 150 (1) + AluSx SINE/Alu 157 304 (8) 671
ANNOTATION EVIDENCE:
1112 9.46 0.00 1.33 E00378:188:HVMVNCCXX:3:1224:19806:71629/2 1 150 1 + AluSx SINE/Alu 157 304 8
1112 9.46 0.00 1.33 E00378:188:HVMVNCCXX:3:1224:19806:71629/2 1 150 (1) AluSx#SINE/Alu 157 304 (8) m_b2s357i16
E00378:188:HV 1 CCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACT 50
i i i i
AluSx#SINE/Al 157 CCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC 206
E00378:188:HV 51 CAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCC 100
i i i i ii
AluSx#SINE/Al 207 CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCC 256
E00378:188:HV 101 TGGGTTTGACGAAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA 150
--i ii i
AluSx#SINE/Al 257 TGGG--CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 585 10.3 0.0 0.0 E00378:188:HVMVNCCXX:3:1224:7628:21069/2 73 150 (1) + AluY SINE/Alu 1 78 (233) 672
ANNOTATION EVIDENCE:
585 10.26 0.00 0.00 E00378:188:HVMVNCCXX:3:1224:7628:21069/2 73 150 1 + AluY SINE/Alu 1 78 233
585 10.26 0.00 0.00 E00378:188:HVMVNCCXX:3:1224:7628:21069/2 73 150 (1) AluY#SINE/Alu 1 78 (233) m_b2s357i65
E00378:188:HV 73 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 122
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 123 GGCGGGCTGATCATGAGGTCAGGAGATC 150
v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATC 78
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.65
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 1260 3.3 1.3 0.0 E00378:188:HVMVNCCXX:3:2101:18101:30773/1 1 151 (0) C L1P3 LINE/L1 (2442) 3704 3552 673
ANNOTATION EVIDENCE:
1260 3.31 1.30 0.00 E00378:188:HVMVNCCXX:3:2101:18101:30773/1 1 151 0 C L1P3_orf2 LINE/L1 1443 1595 1699
1260 3.31 1.30 0.00 E00378:188:HVMVNCCXX:3:2101:18101:30773/1 1 151 (0) C L1P3_orf2#LINE/L1 (1699) 1595 1443 m_b6s551i91
E00378:188:HV 1 GGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAG 48
i-- v
C L1P3_orf2#LIN 1595 GGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAG 1546
E00378:188:HV 49 GATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTA 98
v i
C L1P3_orf2#LIN 1545 GATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTA 1496
E00378:188:HV 99 TTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCC 148
i
C L1P3_orf2#LIN 1495 TTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTC 1446
E00378:188:HV 149 TGG 151
C L1P3_orf2#LIN 1445 TGG 1443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1350 1.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2101:18101:30773/2 1 151 (0) + L1P3 LINE/L1 3447 3597 (2549) 674
ANNOTATION EVIDENCE:
1350 1.32 0.00 0.00 E00378:188:HVMVNCCXX:3:2101:18101:30773/2 1 151 0 + L1P3_orf2 LINE/L1 1338 1488 1806
1350 1.32 0.00 0.00 E00378:188:HVMVNCCXX:3:2101:18101:30773/2 1 151 (0) L1P3_orf2#LINE/L1 1338 1488 (1806) m_b6s551i125
E00378:188:HV 1 CGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTA 50
L1P3_orf2#LIN 1338 CGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTA 1387
E00378:188:HV 51 ATAGCCTACCAACCAAAAAAAGCCCAGGACCAGAGGGATTCACAGCCGAA 100
v
L1P3_orf2#LIN 1388 ATAGCCTACCAACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGAA 1437
E00378:188:HV 101 TTCTACCAGGGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATT 150
i
L1P3_orf2#LIN 1438 TTCTACCAGAGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATT 1487
E00378:188:HV 151 C 151
L1P3_orf2#LIN 1488 C 1488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1139 7.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2101:23997:38667/1 1 151 (0) + L1PA2 LINE/L1 5927 6077 (78) 675
ANNOTATION EVIDENCE:
1139 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:2101:23997:38667/1 1 151 0 + L1PA2_3end LINE/L1 674 824 78
1139 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:2101:23997:38667/1 1 151 (0) L1PA2_3end#LINE/L1 674 824 (78) m_b1s551i389
E00378:188:HV 1 GTGGGAATTGAACAATGAGGTCACATGGACACAGGAAGGGGAATATCACA 50
i
L1PA2_3end#LI 674 GTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACA 723
E00378:188:HV 51 CTCTGTCGACTGTTGTGGGGTGGGGAGAGGGGGGAGGGATAGCATCAGGG 100
vv v i ii i
L1PA2_3end#LI 724 CTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGA 773
E00378:188:HV 101 AATAAACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATG 150
i v i
L1PA2_3end#LI 774 GATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATG 823
E00378:188:HV 151 G 151
L1PA2_3end#LI 824 G 824
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.04
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1139 7.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2101:24383:38878/1 1 151 (0) + L1PA2 LINE/L1 5927 6077 (78) 676
ANNOTATION EVIDENCE:
1139 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:2101:24383:38878/1 1 151 0 + L1PA2_3end LINE/L1 674 824 78
1139 7.28 0.00 0.00 E00378:188:HVMVNCCXX:3:2101:24383:38878/1 1 151 (0) L1PA2_3end#LINE/L1 674 824 (78) m_b1s551i390
E00378:188:HV 1 GTGGGAATTGAACAATGAGGTCACATGGACACAGGAAGGGGAATATCACA 50
i
L1PA2_3end#LI 674 GTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACA 723
E00378:188:HV 51 CTCTGTCGACTGTTGTGGGGTGGGGAGAGGGGGGAGGGATAGCATCAGGG 100
vv v i ii i
L1PA2_3end#LI 724 CTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGA 773
E00378:188:HV 101 AATAAACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATG 150
i v i
L1PA2_3end#LI 774 GATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATG 823
E00378:188:HV 151 G 151
L1PA2_3end#LI 824 G 824
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.04
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 181 29.5 16.4 0.0 E00378:188:HVMVNCCXX:3:2103:14529:42763/2 1 112 (39) + MIR SINE/MIR 129 262 (0) 677
ANNOTATION EVIDENCE:
181 29.46 16.42 0.00 E00378:188:HVMVNCCXX:3:2103:14529:42763/2 1 112 39 + MIR SINE/MIR 129 262 0
181 29.46 16.42 0.00 E00378:188:HVMVNCCXX:3:2103:14529:42763/2 1 112 (39) MIR#SINE/MIR 129 262 (0) m_b6s601i15
E00378:188:HV 1 TCATTTATAAATTGAAGGAAATAATAGAATCTAAGTGACAGAAGTAT--- 47
i i v ii iv v i vv v i iiv i ---
MIR#SINE/MIR 129 TCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGT 178
E00378:188:HV 48 AAGAATTAAG------AATAAACATAAA-------------TGCCAGGCA 78
i i i------ v ii ------------- v
MIR#SINE/MIR 179 GAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCA 228
E00378:188:HV 79 CACCGTATATACTCAACAAGTGTTAGCTATTTTT 112
iv viii i i v
MIR#SINE/MIR 229 CATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 37.24
Transitions / transversions = 1.75 (21/12)
Gap_init rate = 0.03 (3 / 111), avg. gap size = 7.33 (22 / 3)
+ 248 5.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2103:30634:46261/1 1 36 (115) + L1P3 LINE/L1 3863 3898 (2248) 678
ANNOTATION EVIDENCE:
248 5.56 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:30634:46261/1 1 36 115 + L1P3_orf2 LINE/L1 1754 1789 1505
248 5.56 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:30634:46261/1 1 36 (115) L1P3_orf2#LINE/L1 1754 1789 (1505) m_b6s551i1
E00378:188:HV 1 ACATAAACAGAACGAATGACAAAAACTACATGATTA 36
v i
L1P3_orf2#LIN 1754 ACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.78
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 887 8.1 0.0 0.0 E00378:188:HVMVNCCXX:3:2103:30634:46261/1 39 149 (2) + AluSx SINE/Alu 14 124 (188) 679
ANNOTATION EVIDENCE:
887 8.11 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:30634:46261/1 39 149 2 + AluSx SINE/Alu 14 124 188
887 8.11 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:30634:46261/1 39 149 (2) AluSx#SINE/Alu 14 124 (188) m_b6s357i13
E00378:188:HV 39 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 88
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 89 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCAT 138
i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
E00378:188:HV 139 CTCTACGAAAA 149
v
AluSx#SINE/Al 114 CTCTACTAAAA 124
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.17
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.0 (0 / 0)
+ 640 5.1 0.0 0.0 E00378:188:HVMVNCCXX:3:2103:3305:27116/1 1 78 (73) + AluSx SINE/Alu 214 291 (21) 680
ANNOTATION EVIDENCE:
640 5.13 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:3305:27116/1 1 78 73 + AluSx SINE/Alu 214 291 21
640 5.13 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:3305:27116/1 1 78 (73) AluSx#SINE/Alu 214 291 (21) m_b4s357i16
E00378:188:HV 1 CGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCAA 50
i i i
AluSx#SINE/Al 214 CGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGA 263
E00378:188:HV 51 CAGAGCGAGATTCCGTCTCAAAAAAAAA 78
i
AluSx#SINE/Al 264 CAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.14
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2103:3305:27116/1 106 137 (14) + (CA)n Simple_repeat 1 32 (0) 681
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:3305:27116/1 106 137 14 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2103:3305:27116/1 106 137 (14) (CA)n#Simple_repeat 1 32 (0) m_b4s252i58
E00378:188:HV 106 CATACATGCACACACATACACACACACACACA 137
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 250 30.8 1.3 0.0 E00378:188:HVMVNCCXX:3:2103:3305:27116/2 3 80 (71) C MIRb SINE/MIR (68) 200 122 682
ANNOTATION EVIDENCE:
250 30.77 1.26 0.00 E00378:188:HVMVNCCXX:3:2103:3305:27116/2 3 80 71 C MIRb SINE/MIR 122 200 68
250 30.77 1.26 0.00 E00378:188:HVMVNCCXX:3:2103:3305:27116/2 3 80 (71) C MIRb#SINE/MIR (68) 200 122 m_b4s601i27
E00378:188:HV 3 TTATTTTCTCTAATCCTCACAGTTATCTGGCCAGGTAAGTGATA-TATCT 51
i iv i iiv i iv v i iv - i
C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCC 151
E00378:188:HV 52 TCACTCTACTGATGAGGGTACGAAGGCCC 80
i i i v iv vi i
C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 41.70
Transitions / transversions = 2.00 (16/8)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1)
+ 739 10.6 0.0 1.9 E00378:188:HVMVNCCXX:3:2104:7608:59323/1 1 106 (45) + AluSx SINE/Alu 201 304 (8) 683
ANNOTATION EVIDENCE:
739 10.58 0.00 1.89 E00378:188:HVMVNCCXX:3:2104:7608:59323/1 1 106 45 + AluSx SINE/Alu 201 304 8
739 10.58 0.00 1.89 E00378:188:HVMVNCCXX:3:2104:7608:59323/1 1 106 (45) AluSx#SINE/Alu 201 304 (8) m_b2s357i9
E00378:188:HV 1 TGAACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACT 50
i i i i i ii
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
E00378:188:HV 51 CCAGCCTGGGTTTGACGAAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAA 100
--i ii i
AluSx#SINE/Al 251 CCAGCCTGGG--CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298
E00378:188:HV 101 AAAAAA 106
AluSx#SINE/Al 299 AAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.74
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.00 (2 / 2)
+ 1251 4.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2104:7608:59323/2 1 150 (1) + L1PA2 LINE/L1 5854 6003 (152) 684
ANNOTATION EVIDENCE:
1251 4.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2104:7608:59323/2 1 150 1 + L1PA2_3end LINE/L1 601 750 152
1251 4.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2104:7608:59323/2 1 150 (1) L1PA2_3end#LINE/L1 601 750 (152) m_b1s551i385
E00378:188:HV 1 AAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGAAAAAACCAA 50
i v
L1PA2_3end#LI 601 AAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 650
E00378:188:HV 51 ACACCGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATG 100
i
L1PA2_3end#LI 651 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATG 700
E00378:188:HV 101 GACACAGGAAGGGGAATATCACACTCTGTGGACTGGTGTGGGGTGGGGGG 150
v vv
L1PA2_3end#LI 701 GACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTGGGGGG 750
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.11
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2104:8552:38913/2 51 95 (56) + MIR SINE/MIR 218 262 (0) 685
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:3:2104:8552:38913/2 51 95 56 + MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:3:2104:8552:38913/2 51 95 (56) MIR#SINE/MIR 218 262 (0) m_b6s601i12
E00378:188:HV 51 AATGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTATTTTT 95
i v iv viii i i v
MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 204 34.1 7.9 3.0 E00378:188:HVMVNCCXX:3:2105:10135:20067/1 19 151 (0) + MIRb SINE/MIR 16 155 (113) 686
ANNOTATION EVIDENCE:
204 34.11 7.86 3.01 E00378:188:HVMVNCCXX:3:2105:10135:20067/1 19 151 0 + MIRb SINE/MIR 16 155 113
204 34.11 7.86 3.01 E00378:188:HVMVNCCXX:3:2105:10135:20067/1 19 151 (0) MIRb#SINE/MIR 16 155 (113) m_b4s601i36
E00378:188:HV 19 GTATAGTAAAAACAAAA--GGCTTTGAAGTCAAACAGA---AAATTCAAA 63
ii ii v iv -- i i ---iii i
MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA 65
E00378:188:HV 64 TCCCAGTACCACAGCCT--TAACTTT----TCTGGTAAAAAACTTGCCTT 107
i iv ii vi i -- i v ----i -- iiiv v i i v
MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCT--TGGGCAAGTTACTTA 113
E00378:188:HV 108 ATGTCATCTAGGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA 151
iv - - i iv vi v i i ii
MIRb#SINE/MIR 114 ACCTC-TCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 46.34
Transitions / transversions = 2.67 (32/12)
Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.88 (15 / 8)
+ 204 34.1 7.9 3.0 E00378:188:HVMVNCCXX:3:2105:10257:19891/1 19 151 (0) + MIRb SINE/MIR 16 155 (113) 687
ANNOTATION EVIDENCE:
204 34.11 7.86 3.01 E00378:188:HVMVNCCXX:3:2105:10257:19891/1 19 151 0 + MIRb SINE/MIR 16 155 113
204 34.11 7.86 3.01 E00378:188:HVMVNCCXX:3:2105:10257:19891/1 19 151 (0) MIRb#SINE/MIR 16 155 (113) m_b4s601i37
E00378:188:HV 19 GTATAGTAAAAACAAAA--GGCTTTGAAGTCAAACAGA---AAATTCAAA 63
ii ii v iv -- i i ---iii i
MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA 65
E00378:188:HV 64 TCCCAGTACCACAGCCT--TAACTTT----TCTGGTAAAAAACTTGCCTT 107
i iv ii vi i -- i v ----i -- iiiv v i i v
MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCT--TGGGCAAGTTACTTA 113
E00378:188:HV 108 ATGTCATCTAGGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA 151
iv - - i iv vi v i i ii
MIRb#SINE/MIR 114 ACCTC-TCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 46.34
Transitions / transversions = 2.67 (32/12)
Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.88 (15 / 8)
+ 1228 2.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2105:3671:63331/1 3 151 (0) + L1P1 LINE/L1 4976 5124 (1022) 688
ANNOTATION EVIDENCE:
1228 2.68 0.00 0.00 E00378:188:HVMVNCCXX:3:2105:3671:63331/1 3 151 0 + L1P1_orf2 LINE/L1 2867 3015 279
1228 2.68 0.00 0.00 E00378:188:HVMVNCCXX:3:2105:3671:63331/1 3 151 (0) L1P1_orf2#LINE/L1 2867 3015 (279) m_b1s551i50
E00378:188:HV 3 ATAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAA 52
v i i
L1P1_orf2#LIN 2867 ATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAA 2916
E00378:188:HV 53 ACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGG 102
?
L1P1_orf2#LIN 2917 ACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGG 2966
E00378:188:HV 103 CATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAA 151
L1P1_orf2#LIN 2967 CATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAA 3015
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1299 0.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2105:3671:63331/2 1 151 (0) C L1P1 LINE/L1 (840) 5306 5156 689
ANNOTATION EVIDENCE:
1299 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:2105:3671:63331/2 1 151 0 C L1P1_orf2 LINE/L1 3047 3197 97
1299 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:2105:3671:63331/2 1 151 (0) C L1P1_orf2#LINE/L1 (97) 3197 3047 m_b1s551i125
E00378:188:HV 1 TTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATAT 50
C L1P1_orf2#LIN 3197 TTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATAT 3148
E00378:188:HV 51 TAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAG 100
i
C L1P1_orf2#LIN 3147 TAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAG 3098
E00378:188:HV 101 GTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTT 150
C L1P1_orf2#LIN 3097 GTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTT 3048
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 3047 A 3047
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1082 6.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2105:7953:47193/1 1 151 (0) C L1P3 LINE/L1 (2722) 3424 3274 690
ANNOTATION EVIDENCE:
1082 6.62 0.00 0.00 E00378:188:HVMVNCCXX:3:2105:7953:47193/1 1 151 0 C L1P3_orf2 LINE/L1 1165 1315 1979
1082 6.62 0.00 0.00 E00378:188:HVMVNCCXX:3:2105:7953:47193/1 1 151 (0) C L1P3_orf2#LINE/L1 (1979) 1315 1165 m_b6s551i172
E00378:188:HV 1 GGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCTAGT 50
v i vv
C L1P3_orf2#LIN 1315 GGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCTAGT 1266
E00378:188:HV 51 TTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTTC 100
i i
C L1P3_orf2#LIN 1265 TTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTC 1216
E00378:188:HV 101 TGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCTATTT 150
iv i v
C L1P3_orf2#LIN 1215 TGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTT 1166
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 1165 G 1165
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.29
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 804 5.7 8.5 7.3 E00378:188:HVMVNCCXX:3:2105:7953:47193/2 1 151 (0) + L1P3 LINE/L1 3128 3280 (2866) 691
ANNOTATION EVIDENCE:
804 5.72 8.50 7.28 E00378:188:HVMVNCCXX:3:2105:7953:47193/2 1 151 0 + L1P3_orf2 LINE/L1 1019 1171 2123
804 5.72 8.50 7.28 E00378:188:HVMVNCCXX:3:2105:7953:47193/2 1 151 (0) L1P3_orf2#LINE/L1 1019 1171 (2123) m_b6s551i216
E00378:188:HV 1 TAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAGACACACACACACAAA 49
v i- ----------i
L1P3_orf2#LIN 1019 TAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGACAC----------G 1058
E00378:188:HV 50 AAAAACCTTTCAAAAAAATCAATTAATCCAGGAGCTGATTTTTTGAAAAG 99
i - v i
L1P3_orf2#LIN 1059 AAAAACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTGAAAAG 1107
E00378:188:HV 100 ATTAACAAAACAGA----CCGCTAGCAAGACTAATAAAGA--------GA 137
i ---- v --------
L1P3_orf2#LIN 1108 ATTAACAAAATAGATAGACCGCTAGCCAGACTAATAAAGAAGAAAAGAGA 1157
E00378:188:HV 138 GAAGAATCAAATAG 151
L1P3_orf2#LIN 1158 GAAGAATCAAATAG 1171
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 984 14.1 0.0 1.3 E00378:188:HVMVNCCXX:3:2106:10977:8657/1 1 151 (0) + AluSx SINE/Alu 79 227 (85) 692
ANNOTATION EVIDENCE:
984 14.10 0.00 1.32 E00378:188:HVMVNCCXX:3:2106:10977:8657/1 1 151 0 + AluSx SINE/Alu 79 227 85
984 14.10 0.00 1.32 E00378:188:HVMVNCCXX:3:2106:10977:8657/1 1 151 (0) AluSx#SINE/Alu 79 227 (85) m_b5s356i13
E00378:188:HV 1 TTGGGACCAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATAC 50
i i i v i
AluSx#SINE/Al 79 TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC 128
E00378:188:HV 51 AAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCA 100
-- i i v i v v vi i i
AluSx#SINE/Al 129 AAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCG 176
E00378:188:HV 101 GGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGT 150
v i iivv
AluSx#SINE/Al 177 GGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGT 226
E00378:188:HV 151 G 151
AluSx#SINE/Al 227 G 227
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.81
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 984 14.1 0.0 1.3 E00378:188:HVMVNCCXX:3:2106:11292:8710/1 1 151 (0) + AluSx SINE/Alu 79 227 (85) 693
ANNOTATION EVIDENCE:
984 14.10 0.00 1.32 E00378:188:HVMVNCCXX:3:2106:11292:8710/1 1 151 0 + AluSx SINE/Alu 79 227 85
984 14.10 0.00 1.32 E00378:188:HVMVNCCXX:3:2106:11292:8710/1 1 151 (0) AluSx#SINE/Alu 79 227 (85) m_b5s356i14
E00378:188:HV 1 TTGGGACCAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATAC 50
i i i v i
AluSx#SINE/Al 79 TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC 128
E00378:188:HV 51 AAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCA 100
-- i i v i v v vi i i
AluSx#SINE/Al 129 AAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCG 176
E00378:188:HV 101 GGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGT 150
v i iivv
AluSx#SINE/Al 177 GGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGT 226
E00378:188:HV 151 G 151
AluSx#SINE/Al 227 G 227
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.81
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 255 28.2 4.5 0.0 E00378:188:HVMVNCCXX:3:2106:14580:7374/2 63 147 (4) + MIRb SINE/MIR 122 210 (58) 694
ANNOTATION EVIDENCE:
255 28.24 4.50 0.00 E00378:188:HVMVNCCXX:3:2106:14580:7374/2 63 147 4 + MIRb SINE/MIR 122 210 58
255 28.24 4.50 0.00 E00378:188:HVMVNCCXX:3:2106:14580:7374/2 63 147 (4) MIRb#SINE/MIR 122 210 (58) m_b4s601i22
E00378:188:HV 63 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 111
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
E00378:188:HV 112 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAA 147
vi i vii --- v iv i
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAA 210
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.65
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 84), avg. gap size = 2.00 (4 / 2)
+ 790 11.0 1.8 0.0 E00378:188:HVMVNCCXX:3:2107:23145:42604/2 1 109 (42) C AluSx SINE/Alu (201) 111 1 695
ANNOTATION EVIDENCE:
790 11.01 1.80 0.00 E00378:188:HVMVNCCXX:3:2107:23145:42604/2 1 109 42 C AluSx SINE/Alu 1 111 201
790 11.01 1.80 0.00 E00378:188:HVMVNCCXX:3:2107:23145:42604/2 1 109 (42) C AluSx#SINE/Alu (201) 111 1 m_b4s357i46
E00378:188:HV 1 GGAGTTTCACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTG 48
i i v i i--
C AluSx#SINE/Al 111 GGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTG 62
E00378:188:HV 49 ATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCAC 98
i i i i i
C AluSx#SINE/Al 61 ATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 12
E00378:188:HV 99 TGCACCCGGCC 109
i i
C AluSx#SINE/Al 11 CGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.48
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.01 (1 / 108), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2109:11911:34606/1 37 68 (83) + (CA)n Simple_repeat 1 32 (0) 696
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2109:11911:34606/1 37 68 83 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2109:11911:34606/1 37 68 (83) (CA)n#Simple_repeat 1 32 (0) m_b4s252i57
E00378:188:HV 37 CATACATGCACACACATACACACACACACACA 68
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 779 6.4 8.5 7.3 E00378:188:HVMVNCCXX:3:2109:7567:30457/1 1 151 (0) C L1P3 LINE/L1 (2861) 3285 3133 697
ANNOTATION EVIDENCE:
779 6.43 8.50 7.28 E00378:188:HVMVNCCXX:3:2109:7567:30457/1 1 151 0 C L1P3_orf2 LINE/L1 1024 1176 2118
779 6.43 8.50 7.28 E00378:188:HVMVNCCXX:3:2109:7567:30457/1 1 151 (0) C L1P3_orf2#LINE/L1 (2118) 1176 1024 m_b6s551i214
E00378:188:HV 1 TGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCG 42
v -------- v
C L1P3_orf2#LIN 1176 TGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCG 1127
E00378:188:HV 43 G----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTG 88
---- i i v
C L1P3_orf2#LIN 1126 GTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTG 1077
E00378:188:HV 89 ATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-C 137
- i i---------- -i
C L1P3_orf2#LIN 1076 A-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGT 1038
E00378:188:HV 138 TCAGCTCTGATCTT 151
v
C L1P3_orf2#LIN 1037 TCTGCTCTGATCTT 1024
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1256 4.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2109:7567:30457/2 1 151 (0) + L1P3 LINE/L1 2869 3019 (3127) 698
ANNOTATION EVIDENCE:
1256 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:2109:7567:30457/2 1 151 0 + L1P3_orf2 LINE/L1 760 910 2384
1256 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:2109:7567:30457/2 1 151 (0) L1P3_orf2#LINE/L1 760 910 (2384) m_b7s551i38
E00378:188:HV 1 AACCTGCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAAT 50
i i v
L1P3_orf2#LIN 760 AACCTGCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAAT 809
E00378:188:HV 51 AAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATC 100
i? i i
L1P3_orf2#LIN 810 AAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATC 859
E00378:188:HV 101 TCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAAT 150
L1P3_orf2#LIN 860 TCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAAT 909
E00378:188:HV 151 G 151
L1P3_orf2#LIN 910 G 910
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 340 26.1 3.5 0.0 E00378:188:HVMVNCCXX:3:2110:17391:20049/2 3 124 (27) + MIRb SINE/MIR 60 187 (75) 699
ANNOTATION EVIDENCE:
331 29.51 4.69 0.00 E00378:188:HVMVNCCXX:3:2110:17391:20049/2 3 124 27 + MIR SINE/MIR 60 187 75
331 29.51 4.69 0.00 E00378:188:HVMVNCCXX:3:2110:17391:20049/2 3 124 (27) MIR#SINE/MIR 60 187 (75) m_b6s601i46
E00378:188:HV 3 CTCGAGTCAACCACTTGTTAGCTCTGTGGCAT-AAGCAAGTTACTTTACC 51
i iv vi ii v i v -ii v
MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109
E00378:188:HV 52 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGAAAATAATAGAATC 99
v iv i v -- i i v ii v v i
MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACC 159
E00378:188:HV 100 TAAGTGACAGAAGTAT---AAGAATTAA 124
vv v i iiv i ---i i
MIR#SINE/MIR 160 TACCTCATAGGGTTGTTGTGAGGATTAA 187
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.54
Transitions / transversions = 1.40 (21/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
340 25.00 3.16 0.00 E00378:188:HVMVNCCXX:3:2110:17391:20049/2 3 94 57 + MIRb SINE/MIR 67 161 107
340 25.00 3.16 0.00 E00378:188:HVMVNCCXX:3:2110:17391:20049/2 3 94 (57) MIRb#SINE/MIR 67 161 (107) m_b6s601i45
E00378:188:HV 3 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 51
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 52 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGAAAATAATA 94
v i i v -- i i v ii v
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 31.17
Transitions / transversions = 1.56 (14/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 330 27.1 3.5 0.0 E00378:188:HVMVNCCXX:3:2110:18304:19522/2 3 124 (27) + MIRb SINE/MIR 60 187 (75) 700
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:3:2110:18304:19522/2 3 124 27 + MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:3:2110:18304:19522/2 3 124 (27) MIR#SINE/MIR 60 187 (75) m_b6s601i48
E00378:188:HV 3 CTCGAGTCAACCACTTGTTAGCTCTGTGGCAT-AAGCAAGTTACTTTACC 51
i iv vi ii v i v -ii v
MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109
E00378:188:HV 52 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATAGAATC 99
v iv i v -- i i v ii iv v i
MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACC 159
E00378:188:HV 100 TAAGTGACAGAAGTAT---AAGAATTAA 124
vv v i iiv i ---i i
MIR#SINE/MIR 160 TACCTCATAGGGTTGTTGTGAGGATTAA 187
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:2110:18304:19522/2 3 94 57 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:2110:18304:19522/2 3 94 (57) MIRb#SINE/MIR 67 161 (107) m_b6s601i47
E00378:188:HV 3 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 51
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 52 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 94
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1097 6.6 3.2 0.0 E00378:188:HVMVNCCXX:3:2110:18670:16744/1 1 151 (0) + L1P3 LINE/L1 3653 3808 (2338) 701
ANNOTATION EVIDENCE:
1097 6.62 3.20 0.00 E00378:188:HVMVNCCXX:3:2110:18670:16744/1 1 151 0 + L1P3_orf2 LINE/L1 1544 1699 1595
1097 6.62 3.20 0.00 E00378:188:HVMVNCCXX:3:2110:18670:16744/1 1 151 (0) L1P3_orf2#LINE/L1 1544 1699 (1595) m_b6s551i59
E00378:188:HV 1 TCCTGATTCCAAAACCTGGCAGAGACACAA--GAAAAAGAAAATTTCAGG 48
v --i
L1P3_orf2#LIN 1544 TCCTGATACCAAAACCTGGCAGAGACACAACAAAAAAAGAAAATTTCAGG 1593
E00378:188:HV 49 CCATTATCCGTGATGAACATCGATGTGAAAATCCTCGATAAAATACTGGC 98
v v i i
L1P3_orf2#LIN 1594 CCAATATCCCTGATGAACATCGATGCGAAAATCCTCAATAAAATACTGGC 1643
E00378:188:HV 99 AAACTGAATCCAGCA---CATCAAAACGCTTATCCACCACTATCAAGTCA 145
i --- v v i
L1P3_orf2#LIN 1644 AAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCACGATCAAGTCG 1693
E00378:188:HV 146 GCTTCA 151
L1P3_orf2#LIN 1694 GCTTCA 1699
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 805 8.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2110:18670:16744/2 1 100 (51) C AluSx SINE/Alu (199) 113 14 702
ANNOTATION EVIDENCE:
805 8.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2110:18670:16744/2 1 100 51 C AluSx SINE/Alu 14 113 199
805 8.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2110:18670:16744/2 1 100 (51) C AluSx#SINE/Alu (199) 113 14 m_b6s357i15
E00378:188:HV 1 ATGGAGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGG 50
i i i
C AluSx#SINE/Al 113 ACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGG 64
E00378:188:HV 51 TGATCCACCCACCTTGTCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCC 100
i i i v i
C AluSx#SINE/Al 63 TGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.60
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0)
+ 322 8.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2110:18670:16744/2 103 151 (0) C L1P3 LINE/L1 (2248) 3898 3850 703
ANNOTATION EVIDENCE:
322 8.16 0.00 0.00 E00378:188:HVMVNCCXX:3:2110:18670:16744/2 103 151 0 C L1P3_orf2 LINE/L1 1741 1789 1505
322 8.16 0.00 0.00 E00378:188:HVMVNCCXX:3:2110:18670:16744/2 103 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1741 m_b6s551i4
E00378:188:HV 103 TAATCATGTAGTTTGTGTCATTCGTTCTGTTTATGTGATGGATTATGTT 151
i v v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTT 1741
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.61
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2110:21734:59464/2 9 40 (111) + (CA)n Simple_repeat 1 32 (0) 704
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2110:21734:59464/2 9 40 111 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2110:21734:59464/2 9 40 (111) (CA)n#Simple_repeat 1 32 (0) m_b4s252i56
E00378:188:HV 9 CATACATGCACACACATACACACACACACACA 40
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 798 15.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2112:22729:60765/2 1 151 (0) C L1P1 LINE/L1 (1007) 5139 4989 705
ANNOTATION EVIDENCE:
798 15.23 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:22729:60765/2 1 151 0 C L1P1_orf2 LINE/L1 2880 3030 264
798 15.23 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:22729:60765/2 1 151 (0) C L1P1_orf2#LINE/L1 (264) 3030 2880 m_b1s551i68
E00378:188:HV 1 TTGGTCAAGTCTGTTTTTTGTTGCCAGTGGTGTTGGTGTTTTAGACATGA 50
v v i vi v v v
C L1P1_orf2#LIN 3030 TTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGA 2981
E00378:188:HV 51 AGGCCTGGCCCTTGCCTATGTCCTGGATGGTAATGCCTAGGTTTTCTTCT 100
v v v i ?
C L1P1_orf2#LIN 2980 AGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCT 2931
E00378:188:HV 101 AGGGTGGTTATGGTTGTAGGTCTATTGTTTAGGTCTTTATTCTAGGTTGA 150
vv v vi i v i vv
C L1P1_orf2#LIN 2930 AGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGA 2881
E00378:188:HV 151 A 151
C L1P1_orf2#LIN 2880 A 2880
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.60
Transitions / transversions = 0.38 (6/16)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1241 3.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2112:24819:6267/1 1 151 (0) + L1PA2 LINE/L1 5889 6039 (116) 706
ANNOTATION EVIDENCE:
1241 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:24819:6267/1 1 151 0 + L1PA2_3end LINE/L1 636 786 116
1241 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:24819:6267/1 1 151 (0) L1PA2_3end#LINE/L1 636 786 (116) m_b1s551i387
E00378:188:HV 1 AGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAA 50
v i
L1PA2_3end#LI 636 AGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAA 685
E00378:188:HV 51 CAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGTGGACTG 100
v
L1PA2_3end#LI 686 CAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTG 735
E00378:188:HV 101 TTGTGGGGTGGGGGGAGGGGGGAGGGATAGCAGTGGGAGATATACCTAAT 150
v v
L1PA2_3end#LI 736 TGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAAT 785
E00378:188:HV 151 G 151
L1PA2_3end#LI 786 G 786
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1010 14.8 0.0 0.0 E00378:188:HVMVNCCXX:3:2112:24819:6267/2 1 149 (2) + AluSx SINE/Alu 82 230 (82) 707
ANNOTATION EVIDENCE:
1010 14.77 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:24819:6267/2 1 149 2 + AluSx SINE/Alu 82 230 82
1010 14.77 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:24819:6267/2 1 149 (2) AluSx#SINE/Alu 82 230 (82) m_b2s357i28
E00378:188:HV 1 AAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAAAGACAAA 50
i ii i v v
AluSx#SINE/Al 82 AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAA 131
E00378:188:HV 51 AATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTGCTCAGGAAG 100
i i i v i i i i
AluSx#SINE/Al 132 AATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGG 181
E00378:188:HV 101 CTGAGGCCGGAGAATCACTTGACCTCAGGACGCAGAGATTGCAGTGAGC 149
v i v i i v i i
AluSx#SINE/Al 182 CTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGC 230
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.01
Transitions / transversions = 2.67 (16/6)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1127 13.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2112:7811:38051/2 1 151 (0) C AluSx SINE/Alu (69) 243 93 708
ANNOTATION EVIDENCE:
1127 13.25 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:7811:38051/2 1 151 0 C AluSx SINE/Alu 93 243 69
1127 13.25 0.00 0.00 E00378:188:HVMVNCCXX:3:2112:7811:38051/2 1 151 (0) C AluSx#SINE/Alu (69) 243 93 m_b2s356i20
E00378:188:HV 1 TGGCATGATCTCAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAGTGATT 50
ii i i i i i i
C AluSx#SINE/Al 243 TGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATT 194
E00378:188:HV 51 CTCCTGCCGCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCAC 100
v i i i v i
C AluSx#SINE/Al 193 CTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCAC 144
E00378:188:HV 101 ACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTGG 150
i i v i ii
C AluSx#SINE/Al 143 GCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG 94
E00378:188:HV 151 C 151
C AluSx#SINE/Al 93 C 93
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.39
Transitions / transversions = 5.67 (17/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1115 2.7 2.0 1.3 E00378:188:HVMVNCCXX:3:2113:17553:8200/2 1 151 (0) C L1P3 LINE/L1 (2987) 3159 3008 709
ANNOTATION EVIDENCE:
1115 2.69 1.98 1.32 E00378:188:HVMVNCCXX:3:2113:17553:8200/2 1 151 0 C L1P3_orf2 LINE/L1 899 1050 2244
1115 2.69 1.98 1.32 E00378:188:HVMVNCCXX:3:2113:17553:8200/2 1 151 (0) C L1P3_orf2#LINE/L1 (2244) 1050 899 m_b6s551i265
E00378:188:HV 1 TATCTCCTTCA---CTGAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCT 47
--- --
C L1P3_orf2#LIN 1050 TATCTCCTTCAGTTCT--GCTCTGATCTTAGTTATTTCTTGTCTTCTGCT 1003
E00378:188:HV 48 AGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATG 97
C L1P3_orf2#LIN 1002 AGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATG 953
E00378:188:HV 98 TTAGGGTGTTGATTTTAGATCTTTCCCACTTTGTCCTGTGGGCATTTAGT 147
i i v ?
C L1P3_orf2#LIN 952 TTAGGGTGTCGATTTTAGATCTTTCCCGCTTTCTCNTGTGGGCATTTAGT 903
E00378:188:HV 148 GCTA 151
C L1P3_orf2#LIN 902 GCTA 899
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.82
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.67 (5 / 3)
+ 776 12.8 0.0 0.0 E00378:188:HVMVNCCXX:3:2113:31091:28910/2 1 109 (42) C AluSx SINE/Alu (203) 109 1 710
ANNOTATION EVIDENCE:
776 12.84 0.00 0.00 E00378:188:HVMVNCCXX:3:2113:31091:28910/2 1 109 42 C AluSx SINE/Alu 1 109 203
776 12.84 0.00 0.00 E00378:188:HVMVNCCXX:3:2113:31091:28910/2 1 109 (42) C AluSx#SINE/Alu (203) 109 1 m_b5s357i53
E00378:188:HV 1 GGTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAGTGAT 50
v i i i i
C AluSx#SINE/Al 109 GGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT 60
E00378:188:HV 51 CTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCAGTG 100
i i i i i vi
C AluSx#SINE/Al 59 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
E00378:188:HV 101 CACCCAGCC 109
i i
C AluSx#SINE/Al 9 CGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.56
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0)
+ 544 12.8 0.0 6.9 E00378:188:HVMVNCCXX:3:2114:10855:61292/1 3 103 (48) + AluSx SINE/Alu 211 304 (8) 711
ANNOTATION EVIDENCE:
544 12.76 0.00 6.93 E00378:188:HVMVNCCXX:3:2114:10855:61292/1 3 103 48 + AluSx SINE/Alu 211 304 8
544 12.76 0.00 6.93 E00378:188:HVMVNCCXX:3:2114:10855:61292/1 3 103 (48) AluSx#SINE/Alu 211 304 (8) m_b5s357i7
E00378:188:HV 3 AGGCGGAGGTTGCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCA 52
v v v i --
AluSx#SINE/Al 211 AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG-- 258
E00378:188:HV 53 GCCTGGGTGATGGAGTGAGACTCCATCTCAAAAAAACACAAAAACAAAAA 102
----- i ii i i v v v
AluSx#SINE/Al 259 -----GGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAA 303
E00378:188:HV 103 A 103
AluSx#SINE/Al 304 A 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.52
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7)
+ 1153 8.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2114:1641:40583/1 1 150 (1) C AluSx SINE/Alu (26) 286 137 712
ANNOTATION EVIDENCE:
1153 8.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2114:1641:40583/1 1 150 1 C AluSx SINE/Alu 137 286 26
1153 8.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2114:1641:40583/1 1 150 (1) C AluSx#SINE/Alu (26) 286 137 m_b4s357i33
E00378:188:HV 1 TTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCG 50
i i i
C AluSx#SINE/Al 286 TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCG 237
E00378:188:HV 51 ATCTCAGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGC 100
i i i
C AluSx#SINE/Al 236 ATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGC 187
E00378:188:HV 101 CTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGGC 150
i i vi v i
C AluSx#SINE/Al 186 CTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGC 137
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 327 22.6 12.5 0.0 E00378:188:HVMVNCCXX:3:2115:14103:16428/1 61 144 (7) + L1MC4 LINE/L1 7416 7529 (513) 713
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/1 61 144 7 + L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/1 61 144 (7) L1MC4a_3end#LINE/L1 2163 2258 (371) m_b3s551i129
E00378:188:HV 61 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 101
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
E00378:188:HV 102 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGGAC 144
--- i i i i i vii
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAATTGAGGGAC 2258
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.05 (4 / 83), avg. gap size = 3.00 (12 / 4)
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/1 70 144 7 + L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/1 70 144 (7) L1MC4_3end#LINE/L1 2194 2276 (513) m_b3s551i130
E00378:188:HV 70 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 111
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
E00378:188:HV 112 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC 144
i i i vii
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGAC 2276
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 534 17.5 8.5 0.0 E00378:188:HVMVNCCXX:3:2115:14103:16428/2 3 99 (52) C L1MC4 LINE/L1 (175) 7867 7762 714
ANNOTATION EVIDENCE:
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/2 3 99 52 C L1MC4_3end LINE/L1 2509 2614 175
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/2 3 99 (52) C L1MC4_3end#LINE/L1 (175) 2614 2509 m_b3s551i42
E00378:188:HV 3 ACGTGATGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAAC 43
i ? i --------- i i
C L1MC4_3end#LI 2614 ACATNATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAAC 2565
E00378:188:HV 44 AAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAAATCAGGAAGTT 93
i iv ii iiv i i i i
C L1MC4_3end#LI 2564 AAGGACATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGAAATT 2515
E00378:188:HV 94 AACATT 99
C L1MC4_3end#LI 2514 AACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.80
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 96), avg. gap size = 9.00 (9 / 1)
+ 281 14.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2115:14103:16428/2 104 151 (0) C L1MC4 LINE/L1 (393) 7649 7602 714
ANNOTATION EVIDENCE:
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/2 104 151 0 C L1MC4_3end LINE/L1 2349 2396 393
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:3:2115:14103:16428/2 104 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2349 m_b3s551i43
E00378:188:HV 104 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACA 151
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACA 2349
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.97
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 327 22.6 12.5 0.0 E00378:188:HVMVNCCXX:3:2115:14438:16938/1 61 144 (7) + L1MC4 LINE/L1 7416 7529 (513) 715
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/1 61 144 7 + L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/1 61 144 (7) L1MC4a_3end#LINE/L1 2163 2258 (371) m_b3s551i131
E00378:188:HV 61 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 101
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
E00378:188:HV 102 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGGAC 144
--- i i i i i vii
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAATTGAGGGAC 2258
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.05 (4 / 83), avg. gap size = 3.00 (12 / 4)
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/1 70 144 7 + L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/1 70 144 (7) L1MC4_3end#LINE/L1 2194 2276 (513) m_b3s551i132
E00378:188:HV 70 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 111
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
E00378:188:HV 112 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC 144
i i i vii
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGAC 2276
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 534 17.5 8.5 0.0 E00378:188:HVMVNCCXX:3:2115:14438:16938/2 3 99 (52) C L1MC4 LINE/L1 (175) 7867 7762 716
ANNOTATION EVIDENCE:
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/2 3 99 52 C L1MC4_3end LINE/L1 2509 2614 175
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/2 3 99 (52) C L1MC4_3end#LINE/L1 (175) 2614 2509 m_b3s551i44
E00378:188:HV 3 ACGTGATGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAAC 43
i ? i --------- i i
C L1MC4_3end#LI 2614 ACATNATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAAC 2565
E00378:188:HV 44 AAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAAATCAGGAAGTT 93
i iv ii iiv i i i i
C L1MC4_3end#LI 2564 AAGGACATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGAAATT 2515
E00378:188:HV 94 AACATT 99
C L1MC4_3end#LI 2514 AACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.80
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 96), avg. gap size = 9.00 (9 / 1)
+ 281 14.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2115:14438:16938/2 104 151 (0) C L1MC4 LINE/L1 (393) 7649 7602 716
ANNOTATION EVIDENCE:
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/2 104 151 0 C L1MC4_3end LINE/L1 2349 2396 393
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:3:2115:14438:16938/2 104 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2349 m_b3s551i45
E00378:188:HV 104 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACA 151
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACA 2349
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.97
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 633 19.9 6.4 0.8 E00378:188:HVMVNCCXX:3:2116:13464:25235/1 1 132 (19) + L1MC4 LINE/L1 7772 7911 (131) 717
ANNOTATION EVIDENCE:
633 19.85 6.43 0.76 E00378:188:HVMVNCCXX:3:2116:13464:25235/1 1 132 19 + L1MC4_3end LINE/L1 2519 2658 131
633 19.85 6.43 0.76 E00378:188:HVMVNCCXX:3:2116:13464:25235/1 1 132 (19) L1MC4_3end#LINE/L1 2519 2658 (131) m_b3s551i20
E00378:188:HV 1 TCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGTATCCTTGTTT 50
i i i vii ii vi i i
L1MC4_3end#LI 2519 TCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAATGTCCTTGTTC 2568
E00378:188:HV 51 TTAGGAAATATACACTGAAGTAT---------AAGGAGCATCACGTGTGC 91
i --------- i ? i v
L1MC4_3end#LI 2569 TTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCATNATGTCTGC 2618
E00378:188:HV 92 GATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTAT 132
i i vv - i vi i i
L1MC4_3end#LI 2619 AACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.08
Transitions / transversions = 3.17 (19/6)
Gap_init rate = 0.02 (2 / 131), avg. gap size = 5.00 (10 / 2)
+ 844 3.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2116:2361:47070/1 1 99 (52) + L1PA2 LINE/L1 6055 6153 (2) 718
ANNOTATION EVIDENCE:
844 3.03 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2361:47070/1 1 99 52 + L1PA2_3end LINE/L1 802 900 2
844 3.03 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2361:47070/1 1 99 (52) L1PA2_3end#LINE/L1 802 900 (2) m_b1s551i443
E00378:188:HV 1 GTGGGTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAACCTG 50
i
L1PA2_3end#LI 802 GTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTG 851
E00378:188:HV 51 CACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 99
i v
L1PA2_3end#LI 852 CACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.15
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0)
+ 1103 12.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2116:2361:47070/2 1 148 (3) + AluSx SINE/Alu 113 260 (52) 719
ANNOTATION EVIDENCE:
1103 12.16 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2361:47070/2 1 148 3 + AluSx SINE/Alu 113 260 52
1103 12.16 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2361:47070/2 1 148 (3) AluSx#SINE/Alu 113 260 (52) m_b2s357i23
E00378:188:HV 1 TCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTA 50
i v i i i v i
AluSx#SINE/Al 113 TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTA 162
E00378:188:HV 51 ATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAG 100
i i i i i
AluSx#SINE/Al 163 ATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAG 212
E00378:188:HV 101 GCAGAGATTGCAGTGAGCTGAGGTCATGCCACTGCACTCCAGCCTGGG 148
i i i i ii
AluSx#SINE/Al 213 GCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.73
Transitions / transversions = 8.00 (16/2)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 844 3.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2116:2575:46244/1 1 99 (52) + L1PA2 LINE/L1 6055 6153 (2) 720
ANNOTATION EVIDENCE:
844 3.03 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2575:46244/1 1 99 52 + L1PA2_3end LINE/L1 802 900 2
844 3.03 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2575:46244/1 1 99 (52) L1PA2_3end#LINE/L1 802 900 (2) m_b1s551i444
E00378:188:HV 1 GTGGGTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAACCTG 50
i
L1PA2_3end#LI 802 GTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTG 851
E00378:188:HV 51 CACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 99
i v
L1PA2_3end#LI 852 CACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.15
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0)
+ 1095 12.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2116:2575:46244/2 1 148 (3) + AluSx SINE/Alu 113 260 (52) 721
ANNOTATION EVIDENCE:
1095 12.16 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2575:46244/2 1 148 3 + AluSx SINE/Alu 113 260 52
1095 12.16 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:2575:46244/2 1 148 (3) AluSx#SINE/Alu 113 260 (52) m_b2s357i24
E00378:188:HV 1 TCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTA 50
i v i i i v i
AluSx#SINE/Al 113 TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTA 162
E00378:188:HV 51 ATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAG 100
i i i i i
AluSx#SINE/Al 163 ATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAG 212
E00378:188:HV 101 GCAGAGATTGCAGTGAGCTGAGATCATGCGACTGCACTCCAGCCTGGG 148
i i i ii v
AluSx#SINE/Al 213 GCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.71
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 993 8.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2116:7608:41110/1 31 151 (0) + AluSx SINE/Alu 14 134 (178) 722
ANNOTATION EVIDENCE:
993 8.26 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:7608:41110/1 31 151 0 + AluSx SINE/Alu 14 134 178
993 8.26 0.00 0.00 E00378:188:HVMVNCCXX:3:2116:7608:41110/1 31 151 (0) AluSx#SINE/Alu 14 134 (178) m_b6s356i19
E00378:188:HV 31 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 80
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 81 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCAT 130
i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
E00378:188:HV 131 CTCTACGAAAAATAAAAAAAT 151
v v
AluSx#SINE/Al 114 CTCTACTAAAAATACAAAAAT 134
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.69
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0)
+ 1033 13.3 0.0 0.7 E00378:188:HVMVNCCXX:3:2116:7608:41110/2 1 151 (0) C AluSx SINE/Alu (27) 285 136 723
ANNOTATION EVIDENCE:
1033 13.34 0.00 0.66 E00378:188:HVMVNCCXX:3:2116:7608:41110/2 1 151 0 C AluSx SINE/Alu 136 285 27
1033 13.34 0.00 0.66 E00378:188:HVMVNCCXX:3:2116:7608:41110/2 1 151 (0) C AluSx#SINE/Alu (27) 285 136 m_b6s356i5
E00378:188:HV 1 TTTGAGATGGAGTTTCGCTCATGTCTCCCAGGCTGGAGTGCAATGGTGTG 50
i i - v i i i
C AluSx#SINE/Al 285 TTTGAGACGGAGTCTCGCTC-TGTCGCCCAGGCTGGAGTGCAGTGGCGCG 237
E00378:188:HV 51 ATCTCGGTTCACTTCAGCCTCTACCTCCTCGGTTCAAGCAATTCTCCTGC 100
i v i ii iv i
C AluSx#SINE/Al 236 ATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGC 187
E00378:188:HV 101 CTCATCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCCAGC 150
v i vi i i
C AluSx#SINE/Al 186 CTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGC 137
E00378:188:HV 151 T 151
C AluSx#SINE/Al 136 T 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.66
Transitions / transversions = 3.00 (15/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1272 3.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2117:16812:66478/2 1 151 (0) C L1P1 LINE/L1 (1123) 5023 4873 724
ANNOTATION EVIDENCE:
1272 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2117:16812:66478/2 1 151 0 C L1P1_orf2 LINE/L1 2764 2914 380
1272 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2117:16812:66478/2 1 151 (0) C L1P1_orf2#LINE/L1 (380) 2914 2764 m_b1s551i4
E00378:188:HV 1 TAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTATCA 50
i i v v
C L1P1_orf2#LIN 2914 TAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAA 2865
E00378:188:HV 51 GGTGTAAGGCAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTT 100
v
C L1P1_orf2#LIN 2864 GGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTT 2815
E00378:188:HV 101 TTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTT 150
C L1P1_orf2#LIN 2814 TTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTT 2765
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2764 T 2764
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.77
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 948 13.6 0.0 1.3 E00378:188:HVMVNCCXX:3:2117:22475:11804/1 1 149 (2) + AluSx SINE/Alu 87 233 (79) 725
ANNOTATION EVIDENCE:
948 13.60 0.00 1.34 E00378:188:HVMVNCCXX:3:2117:22475:11804/1 1 149 2 + AluSx SINE/Alu 87 233 79
948 13.60 0.00 1.34 E00378:188:HVMVNCCXX:3:2117:22475:11804/1 1 149 (2) AluSx#SINE/Alu 87 233 (79) m_b5s357i37
E00378:188:HV 1 AGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAAT 50
i v i --
AluSx#SINE/Al 87 AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--T 134
E00378:188:HV 51 TAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTG 100
i i v i v v vi i i
AluSx#SINE/Al 135 TAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTG 184
E00378:188:HV 101 AGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGA 149
v i iivv v
AluSx#SINE/Al 185 AGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGA 233
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.87
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 1.00 (2 / 2)
+ 1295 2.0 0.0 0.7 E00378:188:HVMVNCCXX:3:2118:14367:24515/1 1 151 (0) + L1PA3 LINE/L1 5792 5941 (214) 726
ANNOTATION EVIDENCE:
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:3:2118:14367:24515/1 1 151 0 + L1PA3_3end LINE/L1 539 688 214
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:3:2118:14367:24515/1 1 151 (0) L1PA3_3end#LINE/L1 539 688 (214) m_b1s551i366
E00378:188:HV 1 CCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTT 50
-
L1PA3_3end#LI 539 CCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT- 587
E00378:188:HV 51 AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAG 100
i
L1PA3_3end#LI 588 AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAG 637
E00378:188:HV 101 AAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAACA 150
v i
L1PA3_3end#LI 638 AACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACA 687
E00378:188:HV 151 A 151
L1PA3_3end#LI 688 A 688
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 991 2.5 0.8 0.0 E00378:188:HVMVNCCXX:3:2118:14367:24515/2 1 118 (33) C L1PA2 LINE/L1 (43) 6112 5994 727
ANNOTATION EVIDENCE:
991 2.54 0.84 0.00 E00378:188:HVMVNCCXX:3:2118:14367:24515/2 1 118 33 C L1PA2_3end LINE/L1 741 859 43
991 2.54 0.84 0.00 E00378:188:HVMVNCCXX:3:2118:14367:24515/2 1 118 (33) C L1PA2_3end#LINE/L1 (43) 859 741 m_b1s551i412
E00378:188:HV 1 ACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCT 50
i
C L1PA2_3end#LI 859 ACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCT 810
E00378:188:HV 51 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 100
C L1PA2_3end#LI 809 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 760
E00378:188:HV 101 CTCCCCCC-CACCGCACCC 118
- v v
C L1PA2_3end#LI 759 CTCCCCCCTCCCCCCACCC 741
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.80
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1)
+ 1295 2.0 0.0 0.7 E00378:188:HVMVNCCXX:3:2118:14905:24392/1 1 151 (0) + L1PA3 LINE/L1 5792 5941 (214) 728
ANNOTATION EVIDENCE:
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:3:2118:14905:24392/1 1 151 0 + L1PA3_3end LINE/L1 539 688 214
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:3:2118:14905:24392/1 1 151 (0) L1PA3_3end#LINE/L1 539 688 (214) m_b1s551i367
E00378:188:HV 1 CCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTT 50
-
L1PA3_3end#LI 539 CCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT- 587
E00378:188:HV 51 AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAG 100
i
L1PA3_3end#LI 588 AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAG 637
E00378:188:HV 101 AAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAACA 150
v i
L1PA3_3end#LI 638 AACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACA 687
E00378:188:HV 151 A 151
L1PA3_3end#LI 688 A 688
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 960 5.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2118:14905:24392/2 1 120 (31) C L1PA3 LINE/L1 (43) 6112 5993 729
ANNOTATION EVIDENCE:
960 5.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:14905:24392/2 1 120 31 C L1PA3_3end LINE/L1 740 859 43
960 5.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:14905:24392/2 1 120 (31) C L1PA3_3end#LINE/L1 (43) 859 740 m_b1s551i413
E00378:188:HV 1 ACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCT 50
v i
C L1PA3_3end#LI 859 ACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCT 810
E00378:188:HV 51 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 100
C L1PA3_3end#LI 809 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 760
E00378:188:HV 101 ATCCCCACCCCCCCCCCCCC 120
v v i v
C L1PA3_3end#LI 759 CTCCCCCCTCCCCCCACCCC 740
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.38
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0)
+ 240 29.7 7.1 0.0 E00378:188:HVMVNCCXX:3:2118:15625:63402/1 28 118 (33) + L1MC4 LINE/L1 6504 6601 (1441) 730
ANNOTATION EVIDENCE:
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:3:2118:15625:63402/1 28 118 33 + L1MC4_3end LINE/L1 1251 1348 1441
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:3:2118:15625:63402/1 28 118 (33) L1MC4_3end#LINE/L1 1251 1348 (1441) m_b3s551i148
E00378:188:HV 28 TTTTTAACTGCTAGTAAAGCAATTTATAAATTTGGACAGAAAAAAAG--- 74
i v iii vi vi v i v v iiii i ---
L1MC4_3end#LI 1251 TTTCTCACTGTCGGAGAAGGGAGTTACAAATATGGAAAGGGGGAAGGCTA 1300
E00378:188:HV 75 --ATAAACTGTGTGATGTTGGCTTGGATTTGAAGATATC--TATCAAC 118
-- i iv i v v i i -- v
L1MC4_3end#LI 1301 GAATGAACCCTGTGGTGTTGGATTGGAATTGGAGGTATCGGTATGAAC 1348
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.16
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 606 18.5 7.0 0.8 E00378:188:HVMVNCCXX:3:2118:15625:63402/2 1 120 (31) C L1MC4 LINE/L1 (153) 7889 7762 731
ANNOTATION EVIDENCE:
606 18.48 7.03 0.83 E00378:188:HVMVNCCXX:3:2118:15625:63402/2 1 120 31 C L1MC4_3end LINE/L1 2509 2636 153
606 18.48 7.03 0.83 E00378:188:HVMVNCCXX:3:2118:15625:63402/2 1 120 (31) C L1MC4_3end#LINE/L1 (153) 2636 2509 m_b3s551i30
E00378:188:HV 1 ACCATTTTGAGATGAAATCGCACACGTGATGCTCCTT---------ATAC 41
- vv i i v i ? i ---------
C L1MC4_3end#LI 2636 ACCA-TTTGAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAATAC 2588
E00378:188:HV 42 TTCAGTGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGT 91
i i i iv ii iiv i
C L1MC4_3end#LI 2587 TTCAGTGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCACAGT 2538
E00378:188:HV 92 ATAATCATCAAAATCAGGAAGTTAACATT 120
i i i
C L1MC4_3end#LI 2537 ACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.03
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.02 (2 / 119), avg. gap size = 5.00 (10 / 2)
+ 1275 3.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2118:21623:25763/1 1 151 (0) C L1P1 LINE/L1 (1053) 5093 4943 732
ANNOTATION EVIDENCE:
1275 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:21623:25763/1 1 151 0 C L1P1_orf2 LINE/L1 2834 2984 310
1275 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:21623:25763/1 1 151 (0) C L1P1_orf2#LINE/L1 (310) 2984 2834 m_b1s551i32
E00378:188:HV 1 ATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTTTTC 50
?
C L1P1_orf2#LIN 2984 ATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTC 2935
E00378:188:HV 51 TTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATC 100
i
C L1P1_orf2#LIN 2934 TTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATC 2885
E00378:188:HV 101 TTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTCAGCTTT 150
i v v
C L1P1_orf2#LIN 2884 TTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTT 2835
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 2834 C 2834
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1345 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2118:3569:5423/1 1 151 (0) C L1P1 LINE/L1 (418) 5737 5587 733
ANNOTATION EVIDENCE:
1345 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:3569:5423/1 1 151 0 C L1PA2_3end LINE/L1 334 484 418
1345 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:3569:5423/1 1 151 (0) C L1PA2_3end#LINE/L1 (418) 484 334 m_b1s551i299
E00378:188:HV 1 GGTCCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTG 50
i i
C L1PA2_3end#LI 484 GGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTG 435
E00378:188:HV 51 CATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAG 100
i
C L1PA2_3end#LI 434 CATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAG 385
E00378:188:HV 101 TAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGA 150
i
C L1PA2_3end#LI 384 TAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGA 335
E00378:188:HV 151 A 151
C L1PA2_3end#LI 334 A 334
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1329 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2118:3569:5423/2 1 150 (1) + L1P1 LINE/L1 5320 5469 (686) 734
ANNOTATION EVIDENCE:
1329 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:3569:5423/2 1 150 1 + L1PA2_3end LINE/L1 67 216 686
1329 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:3569:5423/2 1 150 (1) L1PA2_3end#LINE/L1 67 216 (686) m_b1s551i203
E00378:188:HV 1 AAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGC 50
L1PA2_3end#LI 67 AAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGC 116
E00378:188:HV 51 AGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAA 100
L1PA2_3end#LI 117 AGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAA 166
E00378:188:HV 101 TGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCA 150
L1PA2_3end#LI 167 TGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCA 216
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1190 4.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2118:9506:43624/1 1 151 (0) C L1P3 LINE/L1 (3003) 3143 2993 735
ANNOTATION EVIDENCE:
1190 3.97 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:9506:43624/1 1 151 0 C L1P3_orf2 LINE/L1 884 1034 2260
1190 3.97 0.00 0.00 E00378:188:HVMVNCCXX:3:2118:9506:43624/1 1 151 (0) C L1P3_orf2#LINE/L1 (2260) 1034 884 m_b6s551i268
E00378:188:HV 1 GCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTG 50
C L1P3_orf2#LIN 1034 GCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTG 985
E00378:188:HV 51 CTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAG 100
i
C L1P3_orf2#LIN 984 CTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAG 935
E00378:188:HV 101 ATCTTTCCCACTTTGTCCTGTGGGCATTTAGTGATATAAACTTCCCTCTA 150
i v ? v i
C L1P3_orf2#LIN 934 ATCTTTCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTA 885
E00378:188:HV 151 A 151
C L1P3_orf2#LIN 884 A 884
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.16
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1299 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2119:12489:53293/1 1 151 (0) + L1P3 LINE/L1 3464 3614 (2532) 736
ANNOTATION EVIDENCE:
1299 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:2119:12489:53293/1 1 151 0 + L1P3_orf2 LINE/L1 1355 1505 1789
1299 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:2119:12489:53293/1 1 151 (0) L1P3_orf2#LINE/L1 1355 1505 (1789) m_b6s551i116
E00378:188:HV 1 CAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAA 50
L1P3_orf2#LIN 1355 CAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAA 1404
E00378:188:HV 51 AAAAGCCCAGGACCAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAA 100
v i
L1P3_orf2#LIN 1405 AAAAGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGAGGTACAA 1454
E00378:188:HV 101 AGACGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAG 150
v
L1P3_orf2#LIN 1455 AGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAG 1504
E00378:188:HV 151 A 151
L1P3_orf2#LIN 1505 A 1505
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 412 10.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2119:12489:53293/2 1 56 (95) C AluSx SINE/Alu (243) 69 14 737
ANNOTATION EVIDENCE:
412 10.71 0.00 0.00 E00378:188:HVMVNCCXX:3:2119:12489:53293/2 1 56 95 C AluSx SINE/Alu 14 69 243
412 10.71 0.00 0.00 E00378:188:HVMVNCCXX:3:2119:12489:53293/2 1 56 (95) C AluSx#SINE/Alu (243) 69 14 m_b6s357i25
E00378:188:HV 1 CTCAGGTGATCCACCCACCTTGTCCTCCCAGAGTGCTGAGATTACAGGCG 50
i i i v i i
C AluSx#SINE/Al 69 CTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCG 20
E00378:188:HV 51 TGAGCC 56
C AluSx#SINE/Al 19 TGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.18
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 690 7.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2119:12489:53293/2 59 150 (1) C L1P3 LINE/L1 (2248) 3898 3807 738
ANNOTATION EVIDENCE:
690 7.61 0.00 0.00 E00378:188:HVMVNCCXX:3:2119:12489:53293/2 59 150 1 C L1P3_orf2 LINE/L1 1698 1789 1505
690 7.61 0.00 0.00 E00378:188:HVMVNCCXX:3:2119:12489:53293/2 59 150 (1) C L1P3_orf2#LINE/L1 (1505) 1789 1698 m_b6s551i18
E00378:188:HV 59 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 108
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 109 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATG 150
i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATG 1698
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0)
+ 1242 4.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2120:10815:48881/2 1 151 (0) C L1P3 LINE/L1 (3059) 3087 2937 739
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:3:2120:10815:48881/2 1 151 0 C L1P3_orf2 LINE/L1 828 978 2316
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:3:2120:10815:48881/2 1 151 (0) C L1P3_orf2#LINE/L1 (2316) 978 828 m_b7s551i13
E00378:188:HV 1 CTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTTT 50
i
C L1P3_orf2#LIN 978 CTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTT 929
E00378:188:HV 51 CCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACT 100
i v ?
C L1P3_orf2#LIN 928 CCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACT 879
E00378:188:HV 101 GCTTTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATT 150
i i
C L1P3_orf2#LIN 878 GCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATT 829
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 828 G 828
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 30 61 (90) + (TG)n Simple_repeat 1 32 (0) 740
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 30 61 90 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 30 61 (90) (TG)n#Simple_repeat 1 32 (0) m_b4s252i55
E00378:188:HV 30 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 61
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 62 74 (77) + (TGTATG)n Simple_repeat 1 41 (0) 741
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 30 74 77 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 30 74 (77) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i54
E00378:188:HV 30 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 74
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 434 8.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 89 149 (2) C AluSx SINE/Alu (21) 291 231 742
ANNOTATION EVIDENCE:
434 8.20 0.00 0.00 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 89 149 2 C AluSx SINE/Alu 231 291 21
434 8.20 0.00 0.00 E00378:188:HVMVNCCXX:3:2121:10967:61099/2 89 149 (2) C AluSx#SINE/Alu (21) 291 231 m_b4s357i8
E00378:188:HV 89 TTTTTTTTTTAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCCGTG 138
v i i i v
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 139 GCGCGATCTCG 149
C AluSx#SINE/Al 241 GCGCGATCTCG 231
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.05
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 317 24.6 4.0 0.0 E00378:188:HVMVNCCXX:3:2121:15514:40214/2 8 119 (32) + MIRb SINE/MIR 70 187 (75) 743
ANNOTATION EVIDENCE:
307 28.57 5.09 0.00 E00378:188:HVMVNCCXX:3:2121:15514:40214/2 8 119 32 + MIR SINE/MIR 70 187 75
307 28.57 5.09 0.00 E00378:188:HVMVNCCXX:3:2121:15514:40214/2 8 119 (32) MIR#SINE/MIR 70 187 (75) m_b6s601i43
E00378:188:HV 8 CCACTTGTTAGCTCTGTGGCAT-AAGCAAGTTACTTTACCTCACTAAGTC 56
ii v i v -ii v v iv i
MIR#SINE/MIR 70 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCC 119
E00378:188:HV 57 ACAGTTT--TCATTTATAAATTGAAGGAAATAATAGAATCTAAGTGACAG 104
v -- i i v ii iv v i vv v i
MIR#SINE/MIR 120 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAG 169
E00378:188:HV 105 AAGTAT---AAGAATTAA 119
iiv i ---i i
MIR#SINE/MIR 170 GGTTGTTGTGAGGATTAA 187
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.99
Transitions / transversions = 1.46 (19/13)
Gap_init rate = 0.03 (3 / 111), avg. gap size = 2.00 (6 / 3)
317 23.17 3.53 0.00 E00378:188:HVMVNCCXX:3:2121:15514:40214/2 8 89 62 + MIRb SINE/MIR 77 161 107
317 23.17 3.53 0.00 E00378:188:HVMVNCCXX:3:2121:15514:40214/2 8 89 (62) MIRb#SINE/MIR 77 161 (107) m_b6s601i42
E00378:188:HV 8 CCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACCTCACTAAGTC 56
ii v i v- ii v v i i
MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCC 126
E00378:188:HV 57 ACAGTTT--TCATTTATAAATTGAAGGAAATAATA 89
v -- i i v ii iv
MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 28.42
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2)
+ 213 34.3 7.7 2.7 E00378:188:HVMVNCCXX:3:2121:17391:7181/1 1 147 (4) + MIRb SINE/MIR 17 171 (97) 744
ANNOTATION EVIDENCE:
213 34.26 7.74 2.72 E00378:188:HVMVNCCXX:3:2121:17391:7181/1 1 147 4 + MIRb SINE/MIR 17 171 97
213 34.26 7.74 2.72 E00378:188:HVMVNCCXX:3:2121:17391:7181/1 1 147 (4) MIRb#SINE/MIR 17 171 (97) m_b4s601i32
E00378:188:HV 1 TATAGTAAAAACAAAA--GGCTTTGAAGTCAAACAGA---AAATTCAAAT 45
ii ii v iv -- i i ---iii i
MIRb#SINE/MIR 17 TGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAAT 66
E00378:188:HV 46 CCCAGTACCACAGCCT--TAACTTT----TCTGGTAAAAAACTTGCCTTA 89
i iv ii vi i -- i v ----i -- iiiv v i i v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCT--TGGGCAAGTTACTTAA 114
E00378:188:HV 90 TGTCATCTAGGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCAC 138
iv - - i iv vi v i i ii - vi
MIRb#SINE/MIR 115 CCTC-TCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 162
E00378:188:HV 139 TTGCCTGGC 147
i i v
MIRb#SINE/MIR 163 CTACCTCGC 171
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 46.75
Transitions / transversions = 2.50 (35/14)
Gap_init rate = 0.06 (9 / 146), avg. gap size = 1.78 (16 / 9)
+ 1009 6.7 0.7 0.0 E00378:188:HVMVNCCXX:3:2121:26321:60624/2 3 151 (0) C L1P3 LINE/L1 (2980) 3166 3017 745
ANNOTATION EVIDENCE:
1009 6.71 0.67 0.00 E00378:188:HVMVNCCXX:3:2121:26321:60624/2 3 151 0 C L1P3_orf2 LINE/L1 908 1057 2237
1009 6.71 0.67 0.00 E00378:188:HVMVNCCXX:3:2121:26321:60624/2 3 151 (0) C L1P3_orf2#LINE/L1 (2237) 1057 908 m_b6s551i262
E00378:188:HV 3 GTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTT 51
-i v
C L1P3_orf2#LIN 1057 GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTT 1008
E00378:188:HV 52 CTGCTAGCTTTTGGTTTTGTTTGCTCTTGCTTCTCTAGTTCTTTTGATTG 101
iv i
C L1P3_orf2#LIN 1007 CTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTG 958
E00378:188:HV 102 TGATGTTAGGGTGTTGATTTTAGATCTTTCCCACTTTGTGCTGTGGGCAT 151
i i v v?
C L1P3_orf2#LIN 957 TGATGTTAGGGTGTCGATTTTAGATCTTTCCCGCTTTCTCNTGTGGGCAT 908
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 897 16.1 0.0 1.3 E00378:188:HVMVNCCXX:3:2122:26342:56299/2 1 151 (0) + AluSx SINE/Alu 97 245 (67) 746
ANNOTATION EVIDENCE:
897 16.10 0.00 1.32 E00378:188:HVMVNCCXX:3:2122:26342:56299/2 1 151 0 + AluSx SINE/Alu 97 245 67
897 16.10 0.00 1.32 E00378:188:HVMVNCCXX:3:2122:26342:56299/2 1 151 (0) AluSx#SINE/Alu 97 245 (67) m_b5s356i9
E00378:188:HV 1 ACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCA 50
i v i -- i i
AluSx#SINE/Al 97 ACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCG 144
E00378:188:HV 51 TTGTGGGGTGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGAGA 100
v v i v vi i i
AluSx#SINE/Al 145 TGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGA 194
E00378:188:HV 101 ATTGCTTGAACCTACTAGGCGGAGGTTGCAGGGAGCAGGTATAGCACCAC 150
i iivv v v iv v i
AluSx#SINE/Al 195 ATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCAC 244
E00378:188:HV 151 T 151
AluSx#SINE/Al 245 T 245
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 12.14
Transitions / transversions = 1.18 (13/11)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1329 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2122:28260:57934/1 1 151 (0) C L1P1 LINE/L1 (693) 5462 5312 747
ANNOTATION EVIDENCE:
1329 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2122:28260:57934/1 1 151 0 C L1PA2_3end LINE/L1 59 209 693
1329 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2122:28260:57934/1 1 151 (0) C L1PA2_3end#LINE/L1 (693) 209 59 m_b1s551i199
E00378:188:HV 1 CTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCT 50
C L1PA2_3end#LI 209 CTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCT 160
E00378:188:HV 51 GATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAA 100
C L1PA2_3end#LI 159 GATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAA 110
E00378:188:HV 101 TGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATG 150
C L1PA2_3end#LI 109 TGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATG 60
E00378:188:HV 151 G 151
C L1PA2_3end#LI 59 G 59
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1242 3.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2122:28260:57934/2 1 151 (0) + L1P1 LINE/L1 5043 5193 (953) 748
ANNOTATION EVIDENCE:
1242 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2122:28260:57934/2 1 151 0 + L1P1_orf2 LINE/L1 2934 3084 210
1242 3.31 0.00 0.00 E00378:188:HVMVNCCXX:3:2122:28260:57934/2 1 151 (0) L1P1_orf2#LINE/L1 2934 3084 (210) m_b1s551i83
E00378:188:HV 1 AGAAAACCTAGGCATTACCGTTCAGGACATAGGCATGGGCAAGGACTTCA 50
? i
L1P1_orf2#LIN 2934 AGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCA 2983
E00378:188:HV 51 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGG 100
v i
L1P1_orf2#LIN 2984 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 3033
E00378:188:HV 101 GATCTAATAAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 150
v
L1P1_orf2#LIN 3034 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 3083
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3084 A 3084
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1113 3.1 0.0 0.0 E00378:188:HVMVNCCXX:3:2123:16062:1432/1 22 151 (0) C L1PA2 LINE/L1 (2) 6153 6024 749
ANNOTATION EVIDENCE:
1113 3.08 0.00 0.00 E00378:188:HVMVNCCXX:3:2123:16062:1432/1 22 151 0 C L1PA2_3end LINE/L1 771 900 2
1113 3.08 0.00 0.00 E00378:188:HVMVNCCXX:3:2123:16062:1432/1 22 151 (0) C L1PA2_3end#LINE/L1 (2) 900 771 m_b1s551i431
E00378:188:HV 22 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 71
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 72 AGGGTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 121
v i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
E00378:188:HV 122 AACTCGTCATCTAGCATTAGGTATATCTCC 151
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCTCC 771
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.42
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 129), avg. gap size = 0.0 (0 / 0)
+ 1256 2.7 0.0 0.7 E00378:188:HVMVNCCXX:3:2123:16062:1432/2 2 151 (0) + L1PA3 LINE/L1 5794 5942 (213) 750
ANNOTATION EVIDENCE:
1256 2.69 0.00 0.67 E00378:188:HVMVNCCXX:3:2123:16062:1432/2 2 151 0 + L1PA3_3end LINE/L1 541 689 213
1256 2.69 0.00 0.67 E00378:188:HVMVNCCXX:3:2123:16062:1432/2 2 151 (0) L1PA3_3end#LINE/L1 541 689 (213) m_b1s551i368
E00378:188:HV 2 ATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAG 51
-
L1PA3_3end#LI 541 ATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AG 589
E00378:188:HV 52 GGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAA 101
i
L1PA3_3end#LI 590 GGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAA 639
E00378:188:HV 102 GAAAAAACCAAACACGGCATGTTCTCACTCATAGGTGGGAATTGAACAAT 151
v v i
L1PA3_3end#LI 640 CAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAAT 689
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.74
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 1165 4.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2123:3955:2821/2 2 151 (0) C L1P3 LINE/L1 (3000) 3146 2997 751
ANNOTATION EVIDENCE:
1165 4.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2123:3955:2821/2 2 151 0 C L1P3_orf2 LINE/L1 888 1037 2257
1165 4.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2123:3955:2821/2 2 151 (0) C L1P3_orf2#LINE/L1 (2257) 1037 888 m_b6s551i266
E00378:188:HV 2 TCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGT 51
v
C L1P3_orf2#LIN 1037 TCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGT 988
E00378:188:HV 52 TTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTT 101
i
C L1P3_orf2#LIN 987 TTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTT 938
E00378:188:HV 102 TAGATCTTTCCCACTTTGTCCTGTGGGCATTTAGGGCTATAAATTTCCCT 151
i v ? v
C L1P3_orf2#LIN 937 TAGATCTTTCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCT 888
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.18
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 570 11.5 0.0 2.2 E00378:188:HVMVNCCXX:3:2124:17797:21491/1 63 151 (0) C AluSx SINE/Alu (8) 304 218 752
ANNOTATION EVIDENCE:
570 11.50 0.00 2.25 E00378:188:HVMVNCCXX:3:2124:17797:21491/1 63 151 0 C AluSx SINE/Alu 218 304 8
570 11.50 0.00 2.25 E00378:188:HVMVNCCXX:3:2124:17797:21491/1 63 151 (0) C AluSx#SINE/Alu (8) 304 218 m_b2s357i4
E00378:188:HV 63 TTTTTTTTTTTTTTTTTTTTTTTAGACAGAGTCTCGCTTCGTCCAACCCC 112
v i ii --i v
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTC--GCCCA 257
E00378:188:HV 113 GGCTGGAGTGCAGTGGCATGATCTCAGCTCACTGCAATC 151
ii i i
C AluSx#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACC 218
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.64
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2)
+ 1091 11.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2124:17797:21491/2 1 145 (6) + AluSx SINE/Alu 116 260 (52) 753
ANNOTATION EVIDENCE:
1091 11.72 0.00 0.00 E00378:188:HVMVNCCXX:3:2124:17797:21491/2 1 145 6 + AluSx SINE/Alu 116 260 52
1091 11.72 0.00 0.00 E00378:188:HVMVNCCXX:3:2124:17797:21491/2 1 145 (6) AluSx#SINE/Alu 116 260 (52) m_b2s357i20
E00378:188:HV 1 CTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATC 50
i v i i i v i
AluSx#SINE/Al 116 CTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATC 165
E00378:188:HV 51 CCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCA 100
i i i i i i
AluSx#SINE/Al 166 CCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCG 215
E00378:188:HV 101 GAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGG 145
i i ii
AluSx#SINE/Al 216 GAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.09
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 144), avg. gap size = 0.0 (0 / 0)
+ 470 13.8 2.2 2.2 E00378:188:HVMVNCCXX:3:2124:17969:21087/1 63 151 (0) C AluSx SINE/Alu (6) 306 218 754
ANNOTATION EVIDENCE:
470 13.79 2.25 2.25 E00378:188:HVMVNCCXX:3:2124:17969:21087/1 63 151 0 C AluSx SINE/Alu 218 306 6
470 13.79 2.25 2.25 E00378:188:HVMVNCCXX:3:2124:17969:21087/1 63 151 (0) C AluSx#SINE/Alu (6) 306 218 m_b2s357i5
E00378:188:HV 63 TTTTTTTTTTTTTTTTTTTTTTTTGT--CAGAGTCTCGCTTCGTCAAACC 110
v-- i ii i--
C AluSx#SINE/Al 306 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CC 259
E00378:188:HV 111 CAGGCTGGAGGGCAGTGGCATGGTCTCAGCTCCCTGCAATC 151
v ii i i v i
C AluSx#SINE/Al 258 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACC 218
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.21
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.33 (4 / 3)
+ 1091 11.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2124:17969:21087/2 1 145 (6) + AluSx SINE/Alu 116 260 (52) 755
ANNOTATION EVIDENCE:
1091 11.72 0.00 0.00 E00378:188:HVMVNCCXX:3:2124:17969:21087/2 1 145 6 + AluSx SINE/Alu 116 260 52
1091 11.72 0.00 0.00 E00378:188:HVMVNCCXX:3:2124:17969:21087/2 1 145 (6) AluSx#SINE/Alu 116 260 (52) m_b2s357i21
E00378:188:HV 1 CTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATC 50
i v i i i v i
AluSx#SINE/Al 116 CTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATC 165
E00378:188:HV 51 CCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCA 100
i i i i i i
AluSx#SINE/Al 166 CCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCG 215
E00378:188:HV 101 GAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGG 145
i i ii
AluSx#SINE/Al 216 GAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.09
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 144), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2124:9567:28751/1 87 131 (20) C MIR SINE/MIR (0) 262 218 756
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:3:2124:9567:28751/1 87 131 20 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:3:2124:9567:28751/1 87 131 (20) C MIR#SINE/MIR (0) 262 218 m_b6s601i4
E00378:188:HV 87 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 131
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 296 26.3 8.6 0.0 E00378:188:HVMVNCCXX:3:2124:9567:28751/2 1 151 (0) + MIRb SINE/MIR 72 247 (15) 757
ANNOTATION EVIDENCE:
287 29.14 14.21 0.00 E00378:188:HVMVNCCXX:3:2124:9567:28751/2 1 151 0 + MIR SINE/MIR 72 247 15
287 29.14 14.21 0.00 E00378:188:HVMVNCCXX:3:2124:9567:28751/2 1 151 (0) MIR#SINE/MIR 72 247 (15) m_b6s601i39
E00378:188:HV 1 ACTTGTTAGCTCTGTGGCAT-AAGCAAGTTACTTTACCTCACTAAGTCAC 49
ii v i v -ii v v iv i v
MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121
E00378:188:HV 50 AGTTT--TCATTTATAAATTGAAGGAAATAATAGAATCTAAGTGACAGAA 97
-- i i v ii iv v i vv v i ii
MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGG 171
E00378:188:HV 98 GTAT---AAGAATTAAG------AATAAACATAAA-------------TG 125
v i ---i i i------ v ii -------------
MIR#SINE/MIR 172 TTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTG 221
E00378:188:HV 126 CCAGGCACACCGTATATACTCAACAA 151
v iv viii i
MIR#SINE/MIR 222 CCTGGCACATAGTAAGCGCTCAATAA 247
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.91
Transitions / transversions = 1.59 (27/17)
Gap_init rate = 0.03 (5 / 150), avg. gap size = 5.00 (25 / 5)
296 23.75 3.61 0.00 E00378:188:HVMVNCCXX:3:2124:9567:28751/2 1 80 71 + MIRb SINE/MIR 79 161 107
296 23.75 3.61 0.00 E00378:188:HVMVNCCXX:3:2124:9567:28751/2 1 80 (71) MIRb#SINE/MIR 79 161 (107) m_b6s601i38
E00378:188:HV 1 ACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACCTCACTAAGTCAC 49
ii v i v- ii v v i i v
MIRb#SINE/MIR 79 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128
E00378:188:HV 50 AGTTT--TCATTTATAAATTGAAGGAAATAATA 80
-- i i v ii iv
MIRb#SINE/MIR 129 AGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 29.32
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.50 (3 / 2)
+ 1187 7.3 0.0 0.7 E00378:188:HVMVNCCXX:3:2201:16031:5212/2 1 151 (0) + AluY SINE/Alu 139 288 (23) 758
ANNOTATION EVIDENCE:
1187 7.33 0.00 0.66 E00378:188:HVMVNCCXX:3:2201:16031:5212/2 1 151 0 + AluY SINE/Alu 139 288 23
1187 7.33 0.00 0.66 E00378:188:HVMVNCCXX:3:2201:16031:5212/2 1 151 (0) AluY#SINE/Alu 139 288 (23) m_b2s356i85
E00378:188:HV 1 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCA 50
i
AluY#SINE/Alu 139 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCA 188
E00378:188:HV 51 GGAGAACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCA 100
i i i - i v i
AluY#SINE/Alu 189 GGAGAATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCG 237
E00378:188:HV 101 TGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCTCCTCAAAAAA 150
i i vi
AluY#SINE/Alu 238 CGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAA 287
E00378:188:HV 151 A 151
AluY#SINE/Alu 288 A 288
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.48
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 490 13.6 0.0 7.4 E00378:188:HVMVNCCXX:3:2202:10409:73211/1 57 151 (0) C AluSx SINE/Alu (8) 304 217 759
ANNOTATION EVIDENCE:
490 13.63 0.00 7.37 E00378:188:HVMVNCCXX:3:2202:10409:73211/1 57 151 0 C AluSx SINE/Alu 217 304 8
490 13.63 0.00 7.37 E00378:188:HVMVNCCXX:3:2202:10409:73211/1 57 151 (0) C AluSx#SINE/Alu (8) 304 217 m_b5s357i5
E00378:188:HV 57 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 106
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 107 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCT 151
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCT 217
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.21
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.07 (7 / 94), avg. gap size = 1.00 (7 / 7)
+ 1077 12.1 0.0 1.3 E00378:188:HVMVNCCXX:3:2202:10409:73211/2 1 151 (0) + AluSx SINE/Alu 23 171 (141) 760
ANNOTATION EVIDENCE:
1077 12.08 0.00 1.32 E00378:188:HVMVNCCXX:3:2202:10409:73211/2 1 151 0 + AluSx SINE/Alu 23 171 141
1077 12.08 0.00 1.32 E00378:188:HVMVNCCXX:3:2202:10409:73211/2 1 151 (0) AluSx#SINE/Alu 23 171 (141) m_b5s356i24
E00378:188:HV 1 CTGTAATCCCAACACTTTGGGAGGCCAAGGTGGGCAGATCACTTGAGGTC 50
i i i i i
AluSx#SINE/Al 23 CTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTC 72
E00378:188:HV 51 AGGAGTTTGGGACCAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAA 100
i i i v i
AluSx#SINE/Al 73 AGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAA 122
E00378:188:HV 101 AAATACAAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGC 150
-- i i v i v v vi
AluSx#SINE/Al 123 AAATACAAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGC 170
E00378:188:HV 151 T 151
AluSx#SINE/Al 171 T 171
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.64
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1256 0.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2202:32004:2962/1 1 151 (0) C L1P1 LINE/L1 (710) 5445 5295 761
ANNOTATION EVIDENCE:
1256 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:2202:32004:2962/1 1 151 0 C L1PA2_3end LINE/L1 42 192 710
1256 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:2202:32004:2962/1 1 151 (0) C L1PA2_3end#LINE/L1 (710) 192 42 m_b1s551i188
E00378:188:HV 1 GTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATG 50
C L1PA2_3end#LI 192 GTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATG 143
E00378:188:HV 51 AGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAG 100
C L1PA2_3end#LI 142 AGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAG 93
E00378:188:HV 101 TGTCTGTTCATGTCCTTCGCCCACTGTTTGATGGGGTTGTTTGTTTTTTT 150
v
C L1PA2_3end#LI 92 TGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTT 43
E00378:188:HV 151 C 151
C L1PA2_3end#LI 42 C 42
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1127 6.1 0.0 0.0 E00378:188:HVMVNCCXX:3:2202:32004:2962/2 1 148 (3) + L1P1 LINE/L1 5060 5207 (939) 762
ANNOTATION EVIDENCE:
1127 6.08 0.00 0.00 E00378:188:HVMVNCCXX:3:2202:32004:2962/2 1 148 3 + L1P1_orf2 LINE/L1 2951 3098 196
1127 6.08 0.00 0.00 E00378:188:HVMVNCCXX:3:2202:32004:2962/2 1 148 (3) L1P1_orf2#LINE/L1 2951 3098 (196) m_b1s551i87
E00378:188:HV 1 CCATTCAGGACATAGGCATGGGGAAGGACTTCATGTCTAAAACACCAAAA 50
v
L1P1_orf2#LIN 2951 CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAA 3000
E00378:188:HV 51 GCAATGGCAACAAAAGACAGAATAGGCGAATGGGATCTAATTAAACTAAA 100
v i v i i
L1P1_orf2#LIN 3001 GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 3050
E00378:188:HV 101 GAGCGTCTGCACAGCAAAAGAAACTACCATCAGAGTAAACAGACAACC 148
v i i
L1P1_orf2#LIN 3051 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACC 3098
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.36
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 600 12.9 0.0 0.0 E00378:188:HVMVNCCXX:3:2203:10784:48406/1 67 151 (0) + AluY SINE/Alu 1 85 (226) 763
ANNOTATION EVIDENCE:
600 12.94 0.00 0.00 E00378:188:HVMVNCCXX:3:2203:10784:48406/1 67 151 0 + AluY SINE/Alu 1 85 226
600 12.94 0.00 0.00 E00378:188:HVMVNCCXX:3:2203:10784:48406/1 67 151 (0) AluY#SINE/Alu 1 85 (226) m_b4s357i58
E00378:188:HV 67 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 116
i i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 117 AGCAGGCAGATCACAAGGTCAGGAGTTTGAGAACA 151
i i i i v i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCA 85
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.61
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2203:10784:48406/2 67 98 (53) + (TG)n Simple_repeat 1 32 (0) 764
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2203:10784:48406/2 67 98 53 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2203:10784:48406/2 67 98 (53) (TG)n#Simple_repeat 1 32 (0) m_b4s252i53
E00378:188:HV 67 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 98
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:3:2203:10784:48406/2 99 111 (40) + (TGTATG)n Simple_repeat 1 41 (0) 765
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:3:2203:10784:48406/2 67 111 40 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:3:2203:10784:48406/2 67 111 (40) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i52
E00378:188:HV 67 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 111
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 958 13.5 0.0 1.3 E00378:188:HVMVNCCXX:3:2203:9638:15443/1 1 150 (1) + AluSx SINE/Alu 86 233 (79) 766
ANNOTATION EVIDENCE:
958 13.51 0.00 1.33 E00378:188:HVMVNCCXX:3:2203:9638:15443/1 1 150 1 + AluSx SINE/Alu 86 233 79
958 13.51 0.00 1.33 E00378:188:HVMVNCCXX:3:2203:9638:15443/1 1 150 (1) AluSx#SINE/Alu 86 233 (79) m_b5s357i40
E00378:188:HV 1 CAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAA 50
i v i --
AluSx#SINE/Al 86 CAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA-- 133
E00378:188:HV 51 TTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCT 100
i i v i v v vi i i
AluSx#SINE/Al 134 TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCT 183
E00378:188:HV 101 GAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGA 150
v i iivv v
AluSx#SINE/Al 184 GAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGA 233
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.80
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 871 8.2 7.6 0.7 E00378:188:HVMVNCCXX:3:2205:18345:6091/1 5 151 (0) + L1P3 LINE/L1 3163 3320 (2826) 767
ANNOTATION EVIDENCE:
871 8.22 7.59 0.68 E00378:188:HVMVNCCXX:3:2205:18345:6091/1 5 151 0 + L1P3_orf2 LINE/L1 1054 1211 2083
871 8.22 7.59 0.68 E00378:188:HVMVNCCXX:3:2205:18345:6091/1 5 151 (0) L1P3_orf2#LINE/L1 1054 1211 (2083) m_b6s551i206
E00378:188:HV 5 ACAAAAAAAACCTTTCAAAAAAATCAATTAATCCAGGAGCTGATTTTTTG 54
vi i - v i
L1P3_orf2#LIN 1054 ACACGAAAAACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTG 1102
E00378:188:HV 55 AAAAGATTAACAAAACAGA----CCGCTAGCAAGACTAATAAAGA----- 95
i ---- v -----
L1P3_orf2#LIN 1103 AAAAGATTAACAAAATAGATAGACCGCTAGCCAGACTAATAAAGAAGAAA 1152
E00378:188:HV 96 ---GAGAAGAATCAAATAGACTCAATAAAAAATGATAAAGAGGGTAATAC 142
--- v i i vi
L1P3_orf2#LIN 1153 AGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATCAC 1202
E00378:188:HV 143 CACTGATCC 151
L1P3_orf2#LIN 1203 CACTGATCC 1211
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.04
Transitions / transversions = 1.40 (7/5)
Gap_init rate = 0.03 (4 / 146), avg. gap size = 3.25 (13 / 4)
+ 1005 5.3 7.4 0.0 E00378:188:HVMVNCCXX:3:2205:18345:6091/2 1 151 (0) C L1P3 LINE/L1 (2766) 3380 3218 768
ANNOTATION EVIDENCE:
1005 5.30 7.36 0.00 E00378:188:HVMVNCCXX:3:2205:18345:6091/2 1 151 0 C L1P3_orf2 LINE/L1 1109 1271 2023
1005 5.30 7.36 0.00 E00378:188:HVMVNCCXX:3:2205:18345:6091/2 1 151 (0) C L1P3_orf2#LINE/L1 (2023) 1271 1109 m_b6s551i187
E00378:188:HV 1 TCTAGTTTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTG 50
i i
C L1P3_orf2#LIN 1271 TCTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTG 1222
E00378:188:HV 51 TATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGT 100
iv i v
C L1P3_orf2#LIN 1221 TATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGT 1172
E00378:188:HV 101 CTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG---- 138
-------- v ----
C L1P3_orf2#LIN 1171 CTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTA 1122
E00378:188:HV 139 TCTGTTTTGTTAA 151
i
C L1P3_orf2#LIN 1121 TCTATTTTGTTAA 1109
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1272 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2205:31629:38526/1 1 149 (2) C L1P LINE/L1 (732) 5423 5275 769
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2205:31629:38526/1 1 149 2 C L1HS_3end LINE/L1 22 170 732
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2205:31629:38526/1 1 149 (2) C L1HS_3end#LINE/L1 (732) 170 22 m_b1s551i179
E00378:188:HV 1 TGCATTTCTCTGATGGCCAGTGATGATGAGCATTTCTTCATGTGTTTTTT 50
C L1HS_3end#LIN 170 TGCATTTCTCTGATGGCCAGTGATGATGAGCATTTCTTCATGTGTTTTTT 121
E00378:188:HV 51 GGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCC 100
C L1HS_3end#LIN 120 GGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCC 71
E00378:188:HV 101 ACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 149
C L1HS_3end#LIN 70 ACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 22
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1156 6.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2205:31629:38526/2 1 151 (0) + L1P1 LINE/L1 5024 5174 (972) 770
ANNOTATION EVIDENCE:
1156 5.96 0.00 0.00 E00378:188:HVMVNCCXX:3:2205:31629:38526/2 1 151 0 + L1P1_orf2 LINE/L1 2915 3065 229
1156 5.96 0.00 0.00 E00378:188:HVMVNCCXX:3:2205:31629:38526/2 1 151 (0) L1P1_orf2#LINE/L1 2915 3065 (229) m_b1s551i76
E00378:188:HV 1 AAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAAGACATA 50
? i
L1P1_orf2#LIN 2915 AAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATA 2964
E00378:188:HV 51 GGCATGGGCAAGGACTTCATGGCTAAAACACCAAAAGCAATGGCAGCAAA 100
v i
L1P1_orf2#LIN 2965 GGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAA 3014
E00378:188:HV 101 AGACAGAATTGACAAATGGGAGCTAATGAAACTAAAGAACTTCTGCACAG 150
v i v v i
L1P1_orf2#LIN 3015 AGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG 3064
E00378:188:HV 151 C 151
L1P1_orf2#LIN 3065 C 3065
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.54
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1096 6.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2206:12063:13351/1 1 151 (0) C L1P3 LINE/L1 (2731) 3415 3265 771
ANNOTATION EVIDENCE:
1096 6.62 0.00 0.00 E00378:188:HVMVNCCXX:3:2206:12063:13351/1 1 151 0 C L1P3_orf2 LINE/L1 1156 1306 1988
1096 6.62 0.00 0.00 E00378:188:HVMVNCCXX:3:2206:12063:13351/1 1 151 (0) C L1P3_orf2#LINE/L1 (1988) 1306 1156 m_b6s551i176
E00378:188:HV 1 ATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCTAGCTTATTTGCA 50
i vv i i
C L1P3_orf2#LIN 1306 ATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCG 1257
E00378:188:HV 51 TAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATC 100
i
C L1P3_orf2#LIN 1256 TAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATC 1207
E00378:188:HV 101 AGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCTATTTGATTCTTCT 150
iv i v
C L1P3_orf2#LIN 1206 AGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCT 1157
E00378:188:HV 151 C 151
C L1P3_orf2#LIN 1156 C 1156
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.30
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1145 8.7 0.7 0.7 E00378:188:HVMVNCCXX:3:2207:29193:13527/1 1 151 (0) + AluY SINE/Alu 109 259 (52) 772
ANNOTATION EVIDENCE:
1145 8.67 0.66 0.66 E00378:188:HVMVNCCXX:3:2207:29193:13527/1 1 151 0 + AluY SINE/Alu 109 259 52
1145 8.67 0.66 0.66 E00378:188:HVMVNCCXX:3:2207:29193:13527/1 1 151 (0) AluY#SINE/Alu 109 259 (52) m_b2s356i75
E00378:188:HV 1 CATCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCT 49
i i - vi
AluY#SINE/Alu 109 CGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCT 158
E00378:188:HV 50 GTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAACCTGG 99
i i i i
AluY#SINE/Alu 159 GTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGG 208
E00378:188:HV 100 GGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCATTCCAGCCTG 149
- i v ii i
AluY#SINE/Alu 209 G-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 257
E00378:188:HV 150 GG 151
AluY#SINE/Alu 258 GG 259
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 271 25.9 4.9 1.5 E00378:188:HVMVNCCXX:3:2207:29193:13527/2 1 137 (14) + L1ME4c LINE/L1 5726 5867 (216) 773
ANNOTATION EVIDENCE:
271 25.93 4.93 1.46 E00378:188:HVMVNCCXX:3:2207:29193:13527/2 1 137 14 + L1ME4c_3end LINE/L1 473 614 216
271 25.93 4.93 1.46 E00378:188:HVMVNCCXX:3:2207:29193:13527/2 1 137 (14) L1ME4c_3end#LINE/L1 473 614 (216) m_b2s551i4
E00378:188:HV 1 CGGAAAATAGAAAAGAATCTAAATTTCTGACAATAAAA-AATG-TCAAGT 48
i v i v i v ii iii- - i
L1ME4c_3end#L 473 CGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGT 522
E00378:188:HV 49 AAATTATGGTA--TTTAT--GACAGAAAAATGGTGAAGCCATTAAAAAGT 94
-- i? i-- ii v - vi v vv
L1ME4c_3end#L 523 AAATTATGGTACATCNACTCGATGGAATA-TTATGCAGCCATTAAAAATG 571
E00378:188:HV 95 ATGACTATCAAGAAAA-GCAACTACCTGGAAAAATACTTATAAT 137
i i v vv - i i v v - ii i
L1ME4c_3end#L 572 ATAATTATGAAGACTATGTAGCAACATGGAAAA-TGTTTATGAT 614
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.81
Transitions / transversions = 1.62 (21/13)
Gap_init rate = 0.05 (7 / 136), avg. gap size = 1.29 (9 / 7)
+ 485 5.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2208:12845:3559/1 1 60 (91) + AluSx SINE/Alu 232 291 (21) 774
ANNOTATION EVIDENCE:
485 5.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:12845:3559/1 1 60 91 + AluSx SINE/Alu 232 291 21
485 5.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:12845:3559/1 1 60 (91) AluSx#SINE/Alu 232 291 (21) m_b4s357i6
E00378:188:HV 1 GAGATCGCGCCACTGCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCT 50
i i i
AluSx#SINE/Al 232 GAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT 281
E00378:188:HV 51 CAAAAAAAAA 60
AluSx#SINE/Al 282 CAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2208:12845:3559/1 88 119 (32) + (CA)n Simple_repeat 1 32 (0) 775
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:12845:3559/1 88 119 32 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:12845:3559/1 88 119 (32) (CA)n#Simple_repeat 1 32 (0) m_b4s252i51
E00378:188:HV 88 CATACATGCACACACATACACACACACACACA 119
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1281 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2208:13149:55772/2 1 151 (0) C L1P1 LINE/L1 (1098) 5048 4898 776
ANNOTATION EVIDENCE:
1281 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:13149:55772/2 1 151 0 C L1P1_orf2 LINE/L1 2789 2939 355
1281 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:13149:55772/2 1 151 (0) C L1P1_orf2#LINE/L1 (355) 2939 2789 m_b1s551i15
E00378:188:HV 1 TTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAAT 50
i
C L1P1_orf2#LIN 2939 TTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAAT 2890
E00378:188:HV 51 CCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTCA 100
i v v
C L1P1_orf2#LIN 2889 CCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCA 2840
E00378:188:HV 101 GCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGG 150
C L1P1_orf2#LIN 2839 GCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGG 2790
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2789 G 2789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 878 10.6 0.0 1.6 E00378:188:HVMVNCCXX:3:2208:16944:27398/1 1 125 (26) + AluSx SINE/Alu 182 304 (8) 777
ANNOTATION EVIDENCE:
878 10.57 0.00 1.60 E00378:188:HVMVNCCXX:3:2208:16944:27398/1 1 125 26 + AluSx SINE/Alu 182 304 8
878 10.57 0.00 1.60 E00378:188:HVMVNCCXX:3:2208:16944:27398/1 1 125 (26) AluSx#SINE/Alu 182 304 (8) m_b2s357i11
E00378:188:HV 1 CTGAGGCAGGAGAACCACTTGAACTCAGGAGGCAGAGATTGCAGTGAGCT 50
i i i i i i i
AluSx#SINE/Al 182 CTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCC 231
E00378:188:HV 51 GAGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAAGCGAGACTCTGT 100
ii --i ii i
AluSx#SINE/Al 232 GAGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGAGCGAGACTCCGT 279
E00378:188:HV 101 CTCAAAAAAAAAAAAAAAAAAAAAA 125
AluSx#SINE/Al 280 CTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.95
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.00 (2 / 2)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:3:2208:16944:27398/2 26 114 (37) C L1M5 LINE/L1 (293) 5831 5741 778
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:2208:16944:27398/2 26 114 37 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:2208:16944:27398/2 26 114 (37) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i490
E00378:188:HV 26 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 75
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 76 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 114
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:16944:27398/2 47 114 37 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:2208:16944:27398/2 47 114 (37) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i491
E00378:188:HV 47 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 96
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 97 CTATTGTTGGACATTTAG 114
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1297 2.0 0.0 0.7 E00378:188:HVMVNCCXX:3:2209:14204:35098/1 1 151 (0) C L1PA2 LINE/L1 (179) 5976 5827 779
ANNOTATION EVIDENCE:
1297 2.00 0.00 0.66 E00378:188:HVMVNCCXX:3:2209:14204:35098/1 1 151 0 C L1PA2_3end LINE/L1 574 723 179
1297 2.00 0.00 0.66 E00378:188:HVMVNCCXX:3:2209:14204:35098/1 1 151 (0) C L1PA2_3end#LINE/L1 (179) 723 574 m_b1s551i383
E00378:188:HV 1 TGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCAC 50
C L1PA2_3end#LI 723 TGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCAC 674
E00378:188:HV 51 CTATGAGTGAGAACATGCGGTGTTTGGTTTTTTCTTCTTGCGACAGTTTA 100
i v i
C L1PA2_3end#LI 673 CTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTA 624
E00378:188:HV 101 CTGAGAATGATGATTTCCAATTTCATCCATGTCCCTAACAAAGGACATGA 150
-
C L1PA2_3end#LI 623 CTGAGAATGATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGACATGA 575
E00378:188:HV 151 A 151
C L1PA2_3end#LI 574 A 574
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1358 2.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2209:14204:35098/2 1 151 (0) + L1P1 LINE/L1 5586 5736 (419) 780
ANNOTATION EVIDENCE:
1358 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:2209:14204:35098/2 1 151 0 + L1PA2_3end LINE/L1 333 483 419
1358 1.99 0.00 0.00 E00378:188:HVMVNCCXX:3:2209:14204:35098/2 1 151 (0) L1PA2_3end#LINE/L1 333 483 (419) m_b1s551i298
E00378:188:HV 1 ATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAGCCATCCCAT 50
i
L1PA2_3end#LI 333 ATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCAT 382
E00378:188:HV 51 TACTGGGTATATACCCAAAGGACTATAAATCATGCCGCTATAAAGACACA 100
i
L1PA2_3end#LI 383 TACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACA 432
E00378:188:HV 101 TGCACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAA 150
i
L1PA2_3end#LI 433 TGCACACGTATGTTTATTGCGGCATTATTCACAATAGCAAAGACTTGGAA 482
E00378:188:HV 151 C 151
L1PA2_3end#LI 483 C 483
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:3:2211:20263:19715/1 6 97 (54) C MIRb SINE/MIR (107) 161 67 781
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:2211:20263:19715/1 6 97 54 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:3:2211:20263:19715/1 6 97 (54) C MIRb#SINE/MIR (107) 161 67 m_b6s601i72
E00378:188:HV 6 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 53
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 54 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 97
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 16 5.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2211:20263:19715/2 1 20 (131) + (A)n Simple_repeat 1 20 (0) 782
ANNOTATION EVIDENCE:
16 5.27 0.00 0.00 E00378:188:HVMVNCCXX:3:2211:20263:19715/2 1 20 131 + (A)n Simple_repeat 1 20 0
16 5.27 0.00 0.00 E00378:188:HVMVNCCXX:3:2211:20263:19715/2 1 20 (131) (A)n#Simple_repeat 1 20 (0) m_b6s252i15
E00378:188:HV 1 AAAAAAAAAAAAAAAAAGAA 20
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 635 18.0 6.9 0.8 E00378:188:HVMVNCCXX:3:2212:14407:55737/1 1 123 (28) C L1MC4 LINE/L1 (150) 7892 7762 783
ANNOTATION EVIDENCE:
635 18.04 6.87 0.81 E00378:188:HVMVNCCXX:3:2212:14407:55737/1 1 123 28 C L1MC4_3end LINE/L1 2509 2639 150
635 18.04 6.87 0.81 E00378:188:HVMVNCCXX:3:2212:14407:55737/1 1 123 (28) C L1MC4_3end#LINE/L1 (150) 2639 2509 m_b3s551i29
E00378:188:HV 1 TGAACCATTTTGAGATGAAATCGCACACGTGATGCTCCTT---------A 41
- vv i i v i ? i ---------
C L1MC4_3end#LI 2639 TGAACCA-TTTGAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAA 2591
E00378:188:HV 42 TACTTCAGTGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCAC 91
i i i iv ii iiv i
C L1MC4_3end#LI 2590 TACTTCAGTGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCAC 2541
E00378:188:HV 92 AGTATAATCATCAAAATCAGGAAGTTAACATT 123
i i i
C L1MC4_3end#LI 2540 AGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.41
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.02 (2 / 122), avg. gap size = 5.00 (10 / 2)
+ 240 29.7 7.1 0.0 E00378:188:HVMVNCCXX:3:2212:14407:55737/2 36 126 (25) + L1MC4 LINE/L1 6504 6601 (1441) 784
ANNOTATION EVIDENCE:
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:3:2212:14407:55737/2 36 126 25 + L1MC4_3end LINE/L1 1251 1348 1441
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:3:2212:14407:55737/2 36 126 (25) L1MC4_3end#LINE/L1 1251 1348 (1441) m_b3s551i153
E00378:188:HV 36 TTTTTAACTGCTAGTAAAGCAATTTATAAATTTGGACAGAAAAAAAG--- 82
i v iii vi vi v i v v iiii i ---
L1MC4_3end#LI 1251 TTTCTCACTGTCGGAGAAGGGAGTTACAAATATGGAAAGGGGGAAGGCTA 1300
E00378:188:HV 83 --ATAAACTGTGTGATGTTGGCTTGGATTTGAAGATATC--TATCAAC 126
-- i iv i v v i i -- v
L1MC4_3end#LI 1301 GAATGAACCCTGTGGTGTTGGATTGGAATTGGAGGTATCGGTATGAAC 1348
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.16
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 932 4.3 0.7 7.3 E00378:188:HVMVNCCXX:3:2212:16802:13685/1 1 151 (0) C L1P3 LINE/L1 (2939) 3207 3067 785
ANNOTATION EVIDENCE:
932 4.28 0.71 7.28 E00378:188:HVMVNCCXX:3:2212:16802:13685/1 1 151 0 C L1P3_orf2 LINE/L1 958 1098 2196
932 4.28 0.71 7.28 E00378:188:HVMVNCCXX:3:2212:16802:13685/1 1 151 (0) C L1P3_orf2#LINE/L1 (2196) 1098 958 m_b6s551i248
E00378:188:HV 1 AAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGT 50
i v - i i--------
C L1P3_orf2#LIN 1098 AAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC-------- 1058
E00378:188:HV 51 GTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTC 99
-- -i v
C L1P3_orf2#LIN 1057 --GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTC 1010
E00378:188:HV 100 TTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAAT 149
C L1P3_orf2#LIN 1009 TTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAAT 960
E00378:188:HV 150 TG 151
C L1P3_orf2#LIN 959 TG 958
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 919 4.3 0.7 7.3 E00378:188:HVMVNCCXX:3:2212:16863:13685/1 1 150 (1) C L1P3 LINE/L1 (2939) 3207 3068 786
ANNOTATION EVIDENCE:
919 4.32 0.72 7.33 E00378:188:HVMVNCCXX:3:2212:16863:13685/1 1 150 1 C L1P3_orf2 LINE/L1 959 1098 2196
919 4.32 0.72 7.33 E00378:188:HVMVNCCXX:3:2212:16863:13685/1 1 150 (1) C L1P3_orf2#LINE/L1 (2196) 1098 959 m_b6s551i249
E00378:188:HV 1 AAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGT 50
i v - i i--------
C L1P3_orf2#LIN 1098 AAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC-------- 1058
E00378:188:HV 51 GTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTC 99
-- -i v
C L1P3_orf2#LIN 1057 --GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTC 1010
E00378:188:HV 100 TTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAAT 149
C L1P3_orf2#LIN 1009 TTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAAT 960
E00378:188:HV 150 T 150
C L1P3_orf2#LIN 959 T 959
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.77
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.00 (12 / 12)
+ 255 24.2 6.2 4.0 E00378:188:HVMVNCCXX:3:2212:30847:18502/1 27 151 (0) C L1ME4c LINE/L1 (297) 5786 5659 787
ANNOTATION EVIDENCE:
255 24.17 6.25 4.00 E00378:188:HVMVNCCXX:3:2212:30847:18502/1 27 151 0 C L1ME4c_3end LINE/L1 406 533 297
255 24.17 6.25 4.00 E00378:188:HVMVNCCXX:3:2212:30847:18502/1 27 151 (0) C L1ME4c_3end#LINE/L1 (297) 533 406 m_b2s551i25
E00378:188:HV 27 TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTT 74
i - -iii ii v i v
C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484
E00378:188:HV 75 TCTATTTTC--CTACAATAAACATTATTGCAATGATCATT----TGTCTA 118
i v i-- iv i viii v i---- iv
C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434
E00378:188:HV 119 AGGGTTTTTTTTTCTCATATTTTAAATTATTTC 151
vi v ii ----- i
C L1ME4c_3end#L 433 TAGCTTTTTCCTTC-----TTTTGAATTATTTC 406
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.91
Transitions / transversions = 2.22 (20/9)
Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.44 (13 / 9)
+ 1258 4.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2212:31994:71295/1 1 151 (0) C L1P3 LINE/L1 (3128) 3018 2868 788
ANNOTATION EVIDENCE:
1258 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:2212:31994:71295/1 1 151 0 C L1P3_orf2 LINE/L1 759 909 2385
1258 4.64 0.00 0.00 E00378:188:HVMVNCCXX:3:2212:31994:71295/1 1 151 (0) C L1P3_orf2#LINE/L1 (2385) 909 759 m_b7s551i40
E00378:188:HV 1 ATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGA 50
C L1P3_orf2#LIN 909 ATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGA 860
E00378:188:HV 51 GATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTT 100
i i ?i
C L1P3_orf2#LIN 859 GATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTT 810
E00378:188:HV 101 ATTTCTGCCTTCATTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTT 150
v i i
C L1P3_orf2#LIN 809 ATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTT 760
E00378:188:HV 151 G 151
C L1P3_orf2#LIN 759 G 759
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 31 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2213:13342:44116/1 94 122 (29) + (T)n Simple_repeat 1 29 (0) 789
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2213:13342:44116/1 94 122 29 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2213:13342:44116/1 94 122 (29) (T)n#Simple_repeat 1 29 (0) c_b6s251i11
E00378:188:HV 94 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 122
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 838 8.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2213:13342:44116/2 1 112 (39) + L1P3 LINE/L1 3787 3898 (2248) 790
ANNOTATION EVIDENCE:
838 8.04 0.00 0.00 E00378:188:HVMVNCCXX:3:2213:13342:44116/2 1 112 39 + L1P3_orf2 LINE/L1 1678 1789 1505
838 8.04 0.00 0.00 E00378:188:HVMVNCCXX:3:2213:13342:44116/2 1 112 (39) L1P3_orf2#LINE/L1 1678 1789 (1505) m_b6s551i25
E00378:188:HV 1 CACCACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCAT 50
v i i i i
L1P3_orf2#LIN 1678 CACCACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACAT 1727
E00378:188:HV 51 ACACAAATCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAA 100
i i v
L1P3_orf2#LIN 1728 ACGCAAATCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAA 1777
E00378:188:HV 101 ACTACATGATTA 112
i
L1P3_orf2#LIN 1778 ACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.88
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
+ 1171 9.9 0.7 0.0 E00378:188:HVMVNCCXX:3:2213:19451:2346/2 1 151 (0) + AluY SINE/Alu 7 158 (153) 791
ANNOTATION EVIDENCE:
1171 9.93 0.66 0.00 E00378:188:HVMVNCCXX:3:2213:19451:2346/2 1 151 0 + AluY SINE/Alu 7 158 153
1171 9.93 0.66 0.00 E00378:188:HVMVNCCXX:3:2213:19451:2346/2 1 151 (0) AluY#SINE/Alu 7 158 (153) m_b2s356i53
E00378:188:HV 1 GCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAAGGCGGG 50
ii i i i
AluY#SINE/Alu 7 GCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGG 56
E00378:188:HV 51 CTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGGTGAAAC 100
v i i ii
AluY#SINE/Alu 57 CGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAAC 106
E00378:188:HV 101 CCCATCTCTACTAAAAACACAAAAAG-TAGATGGGCGTGGTGGCGGGCGC 149
i i i- vi
AluY#SINE/Alu 107 CCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGC 156
E00378:188:HV 150 CT 151
AluY#SINE/Alu 157 CT 158
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.39
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 803 14.6 0.0 4.9 E00378:188:HVMVNCCXX:3:2214:10135:15391/1 6 149 (2) C AluSx SINE/Alu (8) 304 168 792
ANNOTATION EVIDENCE:
803 14.60 0.00 4.86 E00378:188:HVMVNCCXX:3:2214:10135:15391/1 6 149 2 C AluSx SINE/Alu 168 304 8
803 14.60 0.00 4.86 E00378:188:HVMVNCCXX:3:2214:10135:15391/1 6 149 (2) C AluSx#SINE/Alu (8) 304 168 m_b5s357i31
E00378:188:HV 6 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 55
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 56 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 105
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 106 TAGTAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCT 149
vvii i v i i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCT 168
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.65
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.00 (7 / 7)
+ 552 13.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2214:10135:15391/2 75 151 (0) + AluSx SINE/Alu 1 77 (235) 793
ANNOTATION EVIDENCE:
552 12.99 0.00 0.00 E00378:188:HVMVNCCXX:3:2214:10135:15391/2 75 151 0 + AluSx SINE/Alu 1 77 235
552 12.99 0.00 0.00 E00378:188:HVMVNCCXX:3:2214:10135:15391/2 75 151 (0) AluSx#SINE/Alu 1 77 (235) m_b5s357i64
E00378:188:HV 75 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 124
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 125 GGTGGGCAGATCACTTGAGGTCAGGAG 151
i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAG 77
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 829 12.9 0.0 0.0 E00378:188:HVMVNCCXX:3:2216:24769:71295/2 1 116 (35) C AluSx SINE/Alu (196) 116 1 794
ANNOTATION EVIDENCE:
829 12.93 0.00 0.00 E00378:188:HVMVNCCXX:3:2216:24769:71295/2 1 116 35 C AluSx SINE/Alu 1 116 196
829 12.93 0.00 0.00 E00378:188:HVMVNCCXX:3:2216:24769:71295/2 1 116 (35) C AluSx#SINE/Alu (196) 116 1 m_b5s357i52
E00378:188:HV 1 GAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTC 50
i v i i i
C AluSx#SINE/Al 116 GAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTC 67
E00378:188:HV 51 AAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGA 100
i i i i i i
C AluSx#SINE/Al 66 AGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA 17
E00378:188:HV 101 GCCAGTGCACCCAGCC 116
vi i i
C AluSx#SINE/Al 16 GCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.24
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0)
+ 1182 9.3 0.7 0.0 E00378:188:HVMVNCCXX:3:2217:10033:29103/1 2 151 (0) + AluY SINE/Alu 6 156 (155) 795
ANNOTATION EVIDENCE:
1182 9.33 0.67 0.00 E00378:188:HVMVNCCXX:3:2217:10033:29103/1 2 151 0 + AluY SINE/Alu 6 156 155
1182 9.33 0.67 0.00 E00378:188:HVMVNCCXX:3:2217:10033:29103/1 2 151 (0) AluY#SINE/Alu 6 156 (155) m_b2s356i52
E00378:188:HV 2 GGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAAGGCGG 51
ii i i i
AluY#SINE/Alu 6 GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGG 55
E00378:188:HV 52 GCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGGTGAAA 101
v i i ii
AluY#SINE/Alu 56 GCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAA 105
E00378:188:HV 102 CCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCG 150
i i - vi
AluY#SINE/Alu 106 CCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCG 155
E00378:188:HV 151 C 151
AluY#SINE/Alu 156 C 156
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.70
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 255 26.1 5.0 1.5 E00378:188:HVMVNCCXX:3:2218:9973:11382/1 8 143 (8) + L1ME4c LINE/L1 5727 5867 (216) 796
ANNOTATION EVIDENCE:
255 26.12 4.97 1.47 E00378:188:HVMVNCCXX:3:2218:9973:11382/1 8 143 8 + L1ME4c_3end LINE/L1 474 614 216
255 26.12 4.97 1.47 E00378:188:HVMVNCCXX:3:2218:9973:11382/1 8 143 (8) L1ME4c_3end#LINE/L1 474 614 (216) m_b2s551i6
E00378:188:HV 8 GGAAAATAGAAAAGAATCTAAATTTCTGACAATAAAA-AATG-TCAAGTA 55
i v i v i v ii iii- - i
L1ME4c_3end#L 474 GAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTA 523
E00378:188:HV 56 AATTATGGTA--TTTAT--GACAGAAAAATGGTGAAGCCATTAAAAAGTA 101
-- i? i-- ii v - vi v vv
L1ME4c_3end#L 524 AATTATGGTACATCNACTCGATGGAATA-TTATGCAGCCATTAAAAATGA 572
E00378:188:HV 102 TGACTATCAAGAAAA-GCAACTACCTGGAAAAATACTTATAAT 143
i i v vv - i i v v - ii i
L1ME4c_3end#L 573 TAATTATGAAGACTATGTAGCAACATGGAAAA-TGTTTATGAT 614
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.12
Transitions / transversions = 1.62 (21/13)
Gap_init rate = 0.05 (7 / 135), avg. gap size = 1.29 (9 / 7)
+ 1030 9.6 0.7 0.0 E00378:188:HVMVNCCXX:3:2219:26017:58163/1 16 150 (1) + AluY SINE/Alu 1 136 (175) 797
ANNOTATION EVIDENCE:
1030 9.63 0.73 0.00 E00378:188:HVMVNCCXX:3:2219:26017:58163/1 16 150 1 + AluY SINE/Alu 1 136 175
1030 9.63 0.73 0.00 E00378:188:HVMVNCCXX:3:2219:26017:58163/1 16 150 (1) AluY#SINE/Alu 1 136 (175) m_b2s357i77
E00378:188:HV 16 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 65
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 66 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 115
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 116 TGAAACCCCATCTCTACTAAAAACACAAAAA-TTAG 150
i i -
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAG 136
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.46
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1)
+ 545 7.1 0.0 0.0 E00378:188:HVMVNCCXX:3:2219:26017:58163/2 82 151 (0) C AluSx SINE/Alu (14) 298 229 798
ANNOTATION EVIDENCE:
545 7.14 0.00 0.00 E00378:188:HVMVNCCXX:3:2219:26017:58163/2 82 151 0 C AluSx SINE/Alu 229 298 14
545 7.14 0.00 0.00 E00378:188:HVMVNCCXX:3:2219:26017:58163/2 82 151 (0) C AluSx#SINE/Alu (14) 298 229 m_b2s357i111
E00378:188:HV 82 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 131
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 132 TGCAGTGGCATGATCTCGGC 151
ii
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGC 229
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.74
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 1285 2.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2220:8968:59218/1 1 150 (1) + L1PA2 LINE/L1 5962 6111 (44) 799
ANNOTATION EVIDENCE:
1285 2.67 0.00 0.00 E00378:188:HVMVNCCXX:3:2220:8968:59218/1 1 150 1 + L1PA2_3end LINE/L1 709 858 44
1285 2.67 0.00 0.00 E00378:188:HVMVNCCXX:3:2220:8968:59218/1 1 150 (1) L1PA2_3end#LINE/L1 709 858 (44) m_b1s551i403
E00378:188:HV 1 AAGGGGAATCTCACACTCTGTGGACTGTTGTGGGGTGGGGGGAGGGGGGA 50
v v v
L1PA2_3end#LI 709 AAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGGA 758
E00378:188:HV 51 GGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTG 100
L1PA2_3end#LI 759 GGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTG 808
E00378:188:HV 101 CAGCACACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATG 150
i
L1PA2_3end#LI 809 CAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATG 858
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 E00378:188:HVMVNCCXX:3:2220:8968:59218/2 8 29 (122) + (A)n Simple_repeat 1 22 (0) 800
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2220:8968:59218/2 8 29 122 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 E00378:188:HVMVNCCXX:3:2220:8968:59218/2 8 29 (122) (A)n#Simple_repeat 1 22 (0) m_b1s252i10
E00378:188:HV 8 AAAAAAAAAAAAAAAAAAAAAA 29
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1307 2.6 0.0 0.0 E00378:188:HVMVNCCXX:3:2221:5274:57600/1 1 151 (0) + L1P1 LINE/L1 4878 5028 (1118) 801
ANNOTATION EVIDENCE:
1307 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:2221:5274:57600/1 1 151 0 + L1P1_orf2 LINE/L1 2769 2919 375
1307 2.65 0.00 0.00 E00378:188:HVMVNCCXX:3:2221:5274:57600/1 1 151 (0) L1P1_orf2#LINE/L1 2769 2919 (375) m_b1s551i8
E00378:188:HV 1 CAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACT 50
L1P1_orf2#LIN 2769 CAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACT 2818
E00378:188:HV 51 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTGAT 100
v
L1P1_orf2#LIN 2819 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 2868
E00378:188:HV 101 AGAAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAAC 150
v i i
L1P1_orf2#LIN 2869 ACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAAC 2918
E00378:188:HV 151 C 151
L1P1_orf2#LIN 2919 C 2919
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1242 2.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2221:5274:57600/2 1 150 (1) C L1P1 LINE/L1 (850) 5296 5147 802
ANNOTATION EVIDENCE:
1242 2.67 0.00 0.00 E00378:188:HVMVNCCXX:3:2221:5274:57600/2 1 150 1 C L1P1_orf2 LINE/L1 3038 3187 107
1242 2.67 0.00 0.00 E00378:188:HVMVNCCXX:3:2221:5274:57600/2 1 150 (1) C L1P1_orf2#LINE/L1 (107) 3187 3038 m_b1s551i121
E00378:188:HV 1 TCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTG 50
C L1P1_orf2#LIN 3187 TCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTG 3138
E00378:188:HV 51 TCAGATGAGTAGGTTACGAAAATTTTCTCCCTTTTTGTAGGTTGCCTGTT 100
i v i
C L1P1_orf2#LIN 3137 TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTT 3088
E00378:188:HV 101 CACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTATTTTAATTA 150
v
C L1P1_orf2#LIN 3087 CACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTA 3038
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:3:2222:15057:39669/1 25 117 (34) + MIRb SINE/MIR 122 219 (49) 803
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:3:2222:15057:39669/1 25 117 34 + MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:3:2222:15057:39669/1 25 117 (34) MIRb#SINE/MIR 122 219 (49) m_b4s601i13
E00378:188:HV 25 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 73
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
E00378:188:HV 74 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAAA-GTCTAGC 117
vi i vii --- v iv i i- ii
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 276 27.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2222:19654:54664/2 1 132 (19) C L1PREC2 LINE/L1 (2755) 3391 3260 804
ANNOTATION EVIDENCE:
276 27.27 0.00 0.00 E00378:188:HVMVNCCXX:3:2222:19654:54664/2 1 132 19 C L1PREC2_orf2 LINE/L1 1151 1282 2012
276 27.27 0.00 0.00 E00378:188:HVMVNCCXX:3:2222:19654:54664/2 1 132 (19) C L1PREC2_orf2#LINE/L1 (2012) 1282 1151 m_b6s551i204
E00378:188:HV 1 CTTCTAGGTGTTTTGGTGTATGTGCATAGAGGTATTTATGGTTGTCTCTG 50
v i i v i i i i v
C L1PREC2_orf2# 1282 CTTCTAGGTTTTCTAGTTTGTGTGCATAGAGGTGTTCATAGTAGTCTCTG 1233
E00378:188:HV 51 GGGTTTGTGTTTGTGTCTGTGGGATCAGTGGGATTAGGCTCTTTATCATT 100
iv v i v v i v i v v vv i i
C L1PREC2_orf2# 1232 ATGGTTATTTGTATTTCTGTGGGGTCAGTGGTAATATCCCCTTTGTCATT 1183
E00378:188:HV 101 GTTTTTTGTGTGGGTTTGGGGTTTCTGTCGTT 132
vi vv vvi ivi v v
C L1PREC2_orf2# 1182 TCTGATTGTGTTTATTTGGATCTTCTCTCTTT 1151
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.06
Transitions / transversions = 0.80 (16/20)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 1339 0.7 0.0 0.0 E00378:188:HVMVNCCXX:3:2223:25652:45962/1 1 151 (0) C L1P1 LINE/L1 (854) 5292 5142 805
ANNOTATION EVIDENCE:
1339 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:2223:25652:45962/1 1 151 0 C L1P1_orf2 LINE/L1 3033 3183 111
1339 0.66 0.00 0.00 E00378:188:HVMVNCCXX:3:2223:25652:45962/1 1 151 (0) C L1P1_orf2#LINE/L1 (111) 3183 3033 m_b1s551i117
E00378:188:HV 1 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAG 50
C L1P1_orf2#LIN 3183 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAG 3134
E00378:188:HV 51 ATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACT 100
i
C L1P1_orf2#LIN 3133 ATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACT 3084
E00378:188:HV 101 CTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATC 150
C L1P1_orf2#LIN 3083 CTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATC 3034
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 3033 C 3033
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1200 5.4 0.0 0.0 E00378:188:HVMVNCCXX:3:2223:29193:41866/1 1 149 (2) C L1P3 LINE/L1 (2548) 3598 3450 806
ANNOTATION EVIDENCE:
1200 5.37 0.00 0.00 E00378:188:HVMVNCCXX:3:2223:29193:41866/1 1 149 2 C L1P3_orf2 LINE/L1 1341 1489 1805
1200 5.37 0.00 0.00 E00378:188:HVMVNCCXX:3:2223:29193:41866/1 1 149 (2) C L1P3_orf2#LINE/L1 (1805) 1489 1341 m_b6s551i124
E00378:188:HV 1 GGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAG 50
i
C L1P3_orf2#LIN 1489 GGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAG 1440
E00378:188:HV 51 AATTCGGCCGTGAATCCCTCTGGTCCTGGGCTTTTTTTGGTTGTTAGGCT 100
i v v
C L1P3_orf2#LIN 1439 AATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCT 1390
E00378:188:HV 101 ATTAATTTCTGCTTCAATTTCAGGACTTGGTATTGGTCTATTCAGGGAT 149
v i i v
C L1P3_orf2#LIN 1389 ATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGAT 1341
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.58
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 804 7.3 3.5 7.5 E00378:188:HVMVNCCXX:3:2223:29193:41866/2 1 147 (4) + L1P1 LINE/L1 3116 3256 (2890) 807
ANNOTATION EVIDENCE:
804 7.35 3.54 7.48 E00378:188:HVMVNCCXX:3:2223:29193:41866/2 1 147 4 + L1P1_orf2 LINE/L1 1007 1147 2147
804 7.35 3.54 7.48 E00378:188:HVMVNCCXX:3:2223:29193:41866/2 1 147 (4) L1P1_orf2#LINE/L1 1007 1147 (2147) m_b6s551i225
E00378:188:HV 1 GAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAGACA 49
i v i- i
L1P1_orf2#LIN 1007 GAAGGCAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAAATAGAGACA 1056
E00378:188:HV 50 CACACACACAAAAAAAACCTTTCAAAAAAATCAATTAATCCAGGCGCTGA 99
---------- i - v v i
L1P1_orf2#LIN 1057 CA----------AAAAACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGG 1095
E00378:188:HV 100 TTTTTTGAAAAGATCAACAAAA----CAGACCGCTAGCAAGACTAATAAA 145
i ----i
L1P1_orf2#LIN 1096 TTTTTTGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAA 1145
E00378:188:HV 146 GA 147
L1P1_orf2#LIN 1146 GA 1147
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.80
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.09 (13 / 146), avg. gap size = 1.23 (16 / 13)
+ 21 4.2 0.0 0.0 E00378:188:HVMVNCCXX:3:2224:14133:43659/1 1 25 (126) + (A)n Simple_repeat 1 25 (0) 808
ANNOTATION EVIDENCE:
21 4.17 0.00 0.00 E00378:188:HVMVNCCXX:3:2224:14133:43659/1 1 25 126 + (A)n Simple_repeat 1 25 0
21 4.17 0.00 0.00 E00378:188:HVMVNCCXX:3:2224:14133:43659/1 1 25 (126) (A)n#Simple_repeat 1 25 (0) m_b6s252i14
E00378:188:HV 1 AAAAAAAAAAAAAAAAAAAAAAGAA 25
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 324 27.9 14.0 0.0 E00378:188:HVMVNCCXX:3:2224:14133:43659/2 5 151 (0) C MIR SINE/MIR (0) 262 92 809
ANNOTATION EVIDENCE:
324 27.89 14.04 0.00 E00378:188:HVMVNCCXX:3:2224:14133:43659/2 5 151 0 C MIR SINE/MIR 92 262 0
324 27.89 14.04 0.00 E00378:188:HVMVNCCXX:3:2224:14133:43659/2 5 151 (0) C MIR#SINE/MIR (0) 262 92 m_b6s601i33
E00378:188:HV 5 AAAAATAGCTAACACTTGTTGAGTATCTACGGTGTGCCTGGCA------- 47
v i i iiii vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
E00378:188:HV 48 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 82
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
E00378:188:HV 83 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 130
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
E00378:188:HV 131 TGAGGTAAAGTAACTTGCTTA 151
v v ii
C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCA 92
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.89
Transitions / transversions = 1.73 (26/15)
Gap_init rate = 0.03 (5 / 146), avg. gap size = 4.80 (24 / 5)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:3:2224:24150:61503/1 6 94 (57) C L1M5 LINE/L1 (293) 5831 5741 810
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:2224:24150:61503/1 6 94 57 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:3:2224:24150:61503/1 6 94 (57) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i510
E00378:188:HV 6 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 55
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 56 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 94
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:2224:24150:61503/1 27 94 57 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:3:2224:24150:61503/1 27 94 (57) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i511
E00378:188:HV 27 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 76
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 77 CTATTGTTGGACATTTAG 94
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1137 11.3 0.0 0.0 E00378:188:HVMVNCCXX:3:2224:24150:61503/2 1 150 (1) + AluSx SINE/Alu 81 230 (82) 811
ANNOTATION EVIDENCE:
1137 11.33 0.00 0.00 E00378:188:HVMVNCCXX:3:2224:24150:61503/2 1 150 1 + AluSx SINE/Alu 81 230 82
1137 11.33 0.00 0.00 E00378:188:HVMVNCCXX:3:2224:24150:61503/2 1 150 (1) AluSx#SINE/Alu 81 230 (82) m_b2s357i29
E00378:188:HV 1 GAAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAAATACAA 50
i ii i v
AluSx#SINE/Al 81 GAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAA 130
E00378:188:HV 51 AAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTACTCAGGAA 100
i i i v i i i
AluSx#SINE/Al 131 AAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG 180
E00378:188:HV 101 GCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGATTGCAGTGAGC 150
i i i i i
AluSx#SINE/Al 181 GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGC 230
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.24
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 616 14.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:19705:43571/1 61 151 (0) + AluSx SINE/Alu 1 91 (221) 812
ANNOTATION EVIDENCE:
616 14.29 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19705:43571/1 61 151 0 + AluSx SINE/Alu 1 91 221
616 14.29 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19705:43571/1 61 151 (0) AluSx#SINE/Alu 1 91 (221) m_b2s357i48
E00378:188:HV 61 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 110
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 111 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCT 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCT 91
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.90
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0)
+ 1155 12.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:19705:43571/2 1 151 (0) C AluSx SINE/Alu (64) 248 98 813
ANNOTATION EVIDENCE:
1155 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19705:43571/2 1 151 0 C AluSx SINE/Alu 98 248 64
1155 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19705:43571/2 1 151 (0) C AluSx#SINE/Alu (64) 248 98 m_b2s356i17
E00378:188:HV 1 TGCAGTGGCATGATCTCAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAG 50
ii i i i i i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAG 199
E00378:188:HV 51 TGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACC 100
i i i i v i
C AluSx#SINE/Al 198 CGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCC 149
E00378:188:HV 101 ACCACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCAT 150
i i v i ii
C AluSx#SINE/Al 148 ACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT 99
E00378:188:HV 151 G 151
C AluSx#SINE/Al 98 G 98
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 616 14.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:19816:43800/1 61 151 (0) + AluSx SINE/Alu 1 91 (221) 814
ANNOTATION EVIDENCE:
616 14.29 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19816:43800/1 61 151 0 + AluSx SINE/Alu 1 91 221
616 14.29 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19816:43800/1 61 151 (0) AluSx#SINE/Alu 1 91 (221) m_b2s357i49
E00378:188:HV 61 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 110
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 111 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCT 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCT 91
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.90
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0)
+ 1155 12.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:19816:43800/2 1 151 (0) C AluSx SINE/Alu (64) 248 98 815
ANNOTATION EVIDENCE:
1155 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19816:43800/2 1 151 0 C AluSx SINE/Alu 98 248 64
1155 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19816:43800/2 1 151 (0) C AluSx#SINE/Alu (64) 248 98 m_b2s356i18
E00378:188:HV 1 TGCAGTGGCATGATCTCAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAG 50
ii i i i i i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAG 199
E00378:188:HV 51 TGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACC 100
i i i i v i
C AluSx#SINE/Al 198 CGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCC 149
E00378:188:HV 101 ACCACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCAT 150
i i v i ii
C AluSx#SINE/Al 148 ACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT 99
E00378:188:HV 151 G 151
C AluSx#SINE/Al 98 G 98
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 616 14.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:19877:44011/1 61 151 (0) + AluSx SINE/Alu 1 91 (221) 816
ANNOTATION EVIDENCE:
616 14.29 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19877:44011/1 61 151 0 + AluSx SINE/Alu 1 91 221
616 14.29 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19877:44011/1 61 151 (0) AluSx#SINE/Alu 1 91 (221) m_b2s357i50
E00378:188:HV 61 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 110
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 111 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCT 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCT 91
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.90
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0)
+ 1155 12.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:19877:44011/2 1 151 (0) C AluSx SINE/Alu (64) 248 98 817
ANNOTATION EVIDENCE:
1155 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19877:44011/2 1 151 0 C AluSx SINE/Alu 98 248 64
1155 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:19877:44011/2 1 151 (0) C AluSx#SINE/Alu (64) 248 98 m_b2s356i19
E00378:188:HV 1 TGCAGTGGCATGATCTCAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAG 50
ii i i i i i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAG 199
E00378:188:HV 51 TGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACC 100
i i i i v i
C AluSx#SINE/Al 198 CGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCC 149
E00378:188:HV 101 ACCACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCAT 150
i i v i ii
C AluSx#SINE/Al 148 ACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT 99
E00378:188:HV 151 G 151
C AluSx#SINE/Al 98 G 98
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 871 13.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1102:32258:64720/1 1 124 (27) C AluSx SINE/Alu (188) 124 1 818
ANNOTATION EVIDENCE:
871 13.71 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:32258:64720/1 1 124 27 C AluSx SINE/Alu 1 124 188
871 13.71 0.00 0.00 E00378:188:HVMVNCCXX:4:1102:32258:64720/1 1 124 (27) C AluSx#SINE/Alu (188) 124 1 m_b2s357i37
E00378:188:HV 1 TTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTC 50
v i ii i
C AluSx#SINE/Al 124 TTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTC 75
E00378:188:HV 51 CCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGATTAC 100
i i i v v v i
C AluSx#SINE/Al 74 CTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTAC 25
E00378:188:HV 101 AGATGTGAGCCACTGTGCCCAGCC 124
ii i i i
C AluSx#SINE/Al 24 AGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.23
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0)
+ 376 21.1 20.6 0.0 E00378:188:HVMVNCCXX:4:1104:14083:16955/1 1 104 (47) C L1MC4 LINE/L1 (465) 7577 7447 819
ANNOTATION EVIDENCE:
376 21.15 20.61 0.00 E00378:188:HVMVNCCXX:4:1104:14083:16955/1 1 104 47 C L1MC4_3end LINE/L1 2194 2324 465
376 21.15 20.61 0.00 E00378:188:HVMVNCCXX:4:1104:14083:16955/1 1 104 (47) C L1MC4_3end#LINE/L1 (465) 2324 2194 m_b3s551i114
E00378:188:HV 1 CATGACCTTCATATATTTGAATAGTACAG-------------------GT 31
? v i v v -------------------
C L1MC4_3end#LI 2324 CATGACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGT 2275
E00378:188:HV 32 CCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTAT 76
iiv i i i i -----
C L1MC4_3end#LI 2274 CCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTAT 2225
E00378:188:HV 77 AC---TTTGACGAGAATGTTGCAAAAGTAAT 104
i --- i ii iiii i i
C L1MC4_3end#LI 2224 GCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.04
Transitions / transversions = 4.25 (17/4)
Gap_init rate = 0.03 (3 / 103), avg. gap size = 9.00 (27 / 3)
+ 1289 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1104:16224:22880/1 1 151 (0) C L1P1 LINE/L1 (954) 5192 5042 820
ANNOTATION EVIDENCE:
1289 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1104:16224:22880/1 1 151 0 C L1P1_orf2 LINE/L1 2933 3083 211
1289 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1104:16224:22880/1 1 151 (0) C L1P1_orf2#LINE/L1 (211) 3083 2933 m_b1s551i82
E00378:188:HV 1 CTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATC 50
C L1P1_orf2#LIN 3083 CTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATC 3034
E00378:188:HV 51 CCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACA 100
i v
C L1P1_orf2#LIN 3033 CCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACA 2984
E00378:188:HV 101 TGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTTTTCT 150
?
C L1P1_orf2#LIN 2983 TGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCT 2934
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2933 T 2933
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 236 10.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1104:26849:50181/2 3 32 (119) + SVA_A Retroposon/SVA 407 436 (951) 821
ANNOTATION EVIDENCE:
236 10.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1104:26849:50181/2 3 32 119 + SVA_A Retroposon/SVA 407 436 951
236 10.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1104:26849:50181/2 3 32 (119) SVA_A#Retroposon/SVA 407 436 (951) m_b5s502i8
E00378:188:HV 3 CCTTGGCCTCCCAAAGTGTTGGGATTACAG 32
i i i
SVA_A#Retropo 407 CCTTGGCCTCCCAAAGTGCTAGGATTGCAG 436
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.16
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 993 4.9 1.0 0.1 E00378:188:HVMVNCCXX:4:1105:10612:35168/1 1 148 (3) + L1P3 LINE/L1 3036 3186 (2954) 822
ANNOTATION EVIDENCE:
993 2.31 0.76 0.00 E00378:188:HVMVNCCXX:4:1105:10612:35168/1 1 130 21 + L1P3_orf2 LINE/L1 927 1057 2237
993 2.31 0.76 0.00 E00378:188:HVMVNCCXX:4:1105:10612:35168/1 1 130 (21) L1P3_orf2#LINE/L1 927 1057 (2237) m_b6s551i256
E00378:188:HV 1 GGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTAGAGA 50
i
L1P3_orf2#LIN 927 GGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTAGAGA 976
E00378:188:HV 51 AGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAG 100
L1P3_orf2#LIN 977 AGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAG 1026
E00378:188:HV 101 ATCAGAGCTGAG-TGAAGGAGATAGAGACAC 130
v i-
L1P3_orf2#LIN 1027 ATCAGAGCAGAACTGAAGGAGATAGAGACAC 1057
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.63
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 129), avg. gap size = 1.00 (1 / 1)
372 23.97 2.67 0.68 E00378:188:HVMVNCCXX:4:1105:10612:35168/1 2 148 3 + L1M3_orf2 LINE/L1 928 1077 2211
372 23.97 2.67 0.68 E00378:188:HVMVNCCXX:4:1105:10612:35168/1 2 148 (3) L1M3_orf2#LINE/L1 928 1077 (2211) m_b6s551i257
E00378:188:HV 2 GAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTAGAGAA 51
v v v v i vi v i i
L1M3_orf2#LIN 928 GAAAGATCTCAAATAAACAACCTAACTTTACACCTCAAGGAACTAGAAAA 977
E00378:188:HV 52 GCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGA 101
iv i v vi v i iv i iv
L1M3_orf2#LIN 978 AGAAGAACAAACTAAGCCCAAAGTTAGCAGAAGGAAGGAAATAATAAAGA 1027
E00378:188:HV 102 TCAGAGCTGAG-TGAAGGAGATAGAGAC---ACACACACACAAAAAAAAC 147
i v i- i v i ?--- v v - i i i
L1M3_orf2#LIN 1028 TTAGAGCAGAAATAAATGAAATAGAGANTAGAAAAACA-ATAGAAAAAAT 1076
E00378:188:HV 148 C 148
L1M3_orf2#LIN 1077 C 1077
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.44
Transitions / transversions = 1.12 (18/16)
Gap_init rate = 0.02 (3 / 146), avg. gap size = 1.67 (5 / 3)
+ 1260 2.0 1.3 0.0 E00378:188:HVMVNCCXX:4:1105:10612:35168/2 1 151 (0) C L1P3 LINE/L1 (2574) 3572 3420 823
ANNOTATION EVIDENCE:
1260 1.99 1.30 0.00 E00378:188:HVMVNCCXX:4:1105:10612:35168/2 1 151 0 C L1P3_orf2 LINE/L1 1311 1463 1831
1260 1.99 1.30 0.00 E00378:188:HVMVNCCXX:4:1105:10612:35168/2 1 151 (0) C L1P3_orf2#LINE/L1 (1831) 1463 1311 m_b6s551i132
E00378:188:HV 1 AGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTGAATCCCTCTGGTCC 50
i v
C L1P3_orf2#LIN 1463 AGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCC 1414
E00378:188:HV 51 TGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAAC 100
C L1P3_orf2#LIN 1413 TGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAAC 1364
E00378:188:HV 101 TTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGCTTTAG--TTGGG 148
v --
C L1P3_orf2#LIN 1363 TTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGGTTTAGTCTTGGG 1314
E00378:188:HV 149 AGG 151
C L1P3_orf2#LIN 1313 AGG 1311
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 847 9.3 0.0 0.8 E00378:188:HVMVNCCXX:4:1106:10013:47632/2 1 119 (32) + AluY SINE/Alu 180 297 (14) 824
ANNOTATION EVIDENCE:
847 9.32 0.00 0.84 E00378:188:HVMVNCCXX:4:1106:10013:47632/2 1 119 32 + AluY SINE/Alu 180 297 14
847 9.32 0.00 0.84 E00378:188:HVMVNCCXX:4:1106:10013:47632/2 1 119 (32) AluY#SINE/Alu 180 297 (14) m_b2s357i97
E00378:188:HV 1 GCTGAAGCAGGAGAACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAG 50
i i i i - i v
AluY#SINE/Alu 180 GCTGAGGCAGGAGAATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAG 228
E00378:188:HV 51 CCGAGATCATGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCGT 100
ii i
AluY#SINE/Alu 229 CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT 278
E00378:188:HV 101 CTCAAAAAAAGAAATAAAA 119
i v
AluY#SINE/Alu 279 CTCAAAAAAAAAAAAAAAA 297
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.75
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 1.00 (1 / 1)
+ 576 17.0 15.6 0.0 E00378:188:HVMVNCCXX:4:1107:20090:38192/2 17 151 (0) C L1MC4 LINE/L1 (393) 7649 7490 825
ANNOTATION EVIDENCE:
576 17.04 15.63 0.00 E00378:188:HVMVNCCXX:4:1107:20090:38192/2 17 151 0 C L1MC4_3end LINE/L1 2237 2396 393
576 17.04 15.63 0.00 E00378:188:HVMVNCCXX:4:1107:20090:38192/2 17 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2237 m_b3s551i94
E00378:188:HV 17 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 66
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 67 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 110
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
E00378:188:HV 111 G-------------------GTCCCTTGCTCTGAGTTTGTCTGATGTTTC 141
------------------- iiv i i
C L1MC4_3end#LI 2296 GGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTTC 2247
E00378:188:HV 142 CTTATGATTA 151
i
C L1MC4_3end#LI 2246 CTCATGATTA 2237
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.78
Transitions / transversions = 1.20 (12/10)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 12.50 (25 / 2)
+ 576 17.0 15.6 0.0 E00378:188:HVMVNCCXX:4:1107:21572:38051/2 17 151 (0) C L1MC4 LINE/L1 (393) 7649 7490 826
ANNOTATION EVIDENCE:
576 17.04 15.63 0.00 E00378:188:HVMVNCCXX:4:1107:21572:38051/2 17 151 0 C L1MC4_3end LINE/L1 2237 2396 393
576 17.04 15.63 0.00 E00378:188:HVMVNCCXX:4:1107:21572:38051/2 17 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2237 m_b3s551i95
E00378:188:HV 17 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 66
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 67 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 110
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
E00378:188:HV 111 G-------------------GTCCCTTGCTCTGAGTTTGTCTGATGTTTC 141
------------------- iiv i i
C L1MC4_3end#LI 2296 GGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTTC 2247
E00378:188:HV 142 CTTATGATTA 151
i
C L1MC4_3end#LI 2246 CTCATGATTA 2237
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.78
Transitions / transversions = 1.20 (12/10)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 12.50 (25 / 2)
+ 1094 12.8 0.0 1.3 E00378:188:HVMVNCCXX:4:1107:22587:29156/1 1 151 (0) C AluSx SINE/Alu (33) 279 131 827
ANNOTATION EVIDENCE:
1094 12.75 0.00 1.32 E00378:188:HVMVNCCXX:4:1107:22587:29156/1 1 151 0 C AluSx SINE/Alu 131 279 33
1094 12.75 0.00 1.32 E00378:188:HVMVNCCXX:4:1107:22587:29156/1 1 151 (0) C AluSx#SINE/Alu (33) 279 131 m_b2s356i4
E00378:188:HV 1 ACAGAGTCTCGCTTCGTCAAACCCAGGCTGGAGTGCAGTGGCATGATCTC 50
i ii i-- ii
C AluSx#SINE/Al 279 ACGGAGTCTCGCTCTGTCG--CCCAGGCTGGAGTGCAGTGGCGCGATCTC 232
E00378:188:HV 51 AGCTCACTGCAATCTCTGCCTCCTGAGTTCAAGTGATTCTCCTGCCTCAG 100
i i i i i i
C AluSx#SINE/Al 231 GGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAG 182
E00378:188:HV 101 CTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCACACCCAGCTAATT 150
i i i v i i i
C AluSx#SINE/Al 181 CCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATT 132
E00378:188:HV 151 T 151
C AluSx#SINE/Al 131 T 131
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.12
Transitions / transversions = 18.00 (18/1)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 354 21.6 20.9 0.0 E00378:188:HVMVNCCXX:4:1107:3001:13263/2 1 102 (49) C L1MC4 LINE/L1 (467) 7575 7447 828
ANNOTATION EVIDENCE:
354 21.57 20.93 0.00 E00378:188:HVMVNCCXX:4:1107:3001:13263/2 1 102 49 C L1MC4_3end LINE/L1 2194 2322 467
354 21.57 20.93 0.00 E00378:188:HVMVNCCXX:4:1107:3001:13263/2 1 102 (49) C L1MC4_3end#LINE/L1 (467) 2322 2194 m_b3s551i116
E00378:188:HV 1 TGACCTTCATATATTTGAATAGTACAG-------------------GTCC 31
? v i v v -------------------
C L1MC4_3end#LI 2322 TGACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGTCC 2273
E00378:188:HV 32 CTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTATAC 76
iiv i i i i ----- i
C L1MC4_3end#LI 2272 CTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTATGC 2223
E00378:188:HV 77 ---TTTGACGAGAATGTTGCAAAAGTAAT 102
--- i ii iiii i i
C L1MC4_3end#LI 2222 ATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.66
Transitions / transversions = 4.25 (17/4)
Gap_init rate = 0.03 (3 / 101), avg. gap size = 9.00 (27 / 3)
+ 1255 1.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1107:6360:14758/1 1 151 (0) C L1P1 LINE/L1 (822) 5324 5174 829
ANNOTATION EVIDENCE:
1255 1.32 0.00 0.00 E00378:188:HVMVNCCXX:4:1107:6360:14758/1 1 151 0 C L1P1_orf2 LINE/L1 3065 3215 79
1255 1.32 0.00 0.00 E00378:188:HVMVNCCXX:4:1107:6360:14758/1 1 151 (0) C L1P1_orf2#LINE/L1 (79) 3215 3065 m_b1s551i131
E00378:188:HV 1 CACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 50
C L1P1_orf2#LIN 3215 CACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 3166
E00378:188:HV 51 ATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAA 100
C L1P1_orf2#LIN 3165 ATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAA 3116
E00378:188:HV 101 TTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGGAGTTTCTTTT 150
i v
C L1P1_orf2#LIN 3115 TTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTT 3066
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 3065 G 3065
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1259 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1107:6360:14758/2 1 151 (0) + L1P1 LINE/L1 4989 5139 (1007) 830
ANNOTATION EVIDENCE:
1259 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1107:6360:14758/2 1 151 0 + L1P1_orf2 LINE/L1 2880 3030 264
1259 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1107:6360:14758/2 1 151 (0) L1P1_orf2#LINE/L1 2880 3030 (264) m_b1s551i60
E00378:188:HV 1 TTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCC 50
i
L1P1_orf2#LIN 2880 TTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCC 2929
E00378:188:HV 51 TAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGAC 100
?
L1P1_orf2#LIN 2930 TAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGAC 2979
E00378:188:HV 101 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAA 150
v i
L1P1_orf2#LIN 2980 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA 3029
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3030 A 3030
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1145 8.0 0.7 0.0 E00378:188:HVMVNCCXX:4:1108:13393:55737/2 1 150 (1) C AluY SINE/Alu (111) 200 50 831
ANNOTATION EVIDENCE:
1145 8.00 0.67 0.00 E00378:188:HVMVNCCXX:4:1108:13393:55737/2 1 150 1 C AluY SINE/Alu 50 200 111
1145 8.00 0.67 0.00 E00378:188:HVMVNCCXX:4:1108:13393:55737/2 1 150 (1) C AluY#SINE/Alu (111) 200 50 m_b2s357i85
E00378:188:HV 1 ATGCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCC 50
i i i
C AluY#SINE/Alu 200 ACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCC 151
E00378:188:HV 51 GCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCA 99
iv - i i
C AluY#SINE/Alu 150 GCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCA 101
E00378:188:HV 100 CCACGTTAGCCAGGATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCC 149
ii i i v
C AluY#SINE/Alu 100 CCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 51
E00378:188:HV 150 T 150
C AluY#SINE/Alu 50 T 50
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 1164 7.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1109:1458:16990/1 1 151 (0) + L1P3 LINE/L1 2900 3050 (3096) 832
ANNOTATION EVIDENCE:
1164 7.28 0.00 0.00 E00378:188:HVMVNCCXX:4:1109:1458:16990/1 1 151 0 + L1P3_orf2 LINE/L1 791 941 2353
1164 7.28 0.00 0.00 E00378:188:HVMVNCCXX:4:1109:1458:16990/1 1 151 (0) L1P3_orf2#LINE/L1 791 941 (2353) m_b7s551i26
E00378:188:HV 1 ATGAAATGAAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAA 50
i v i? i
L1P3_orf2#LIN 791 ACGAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGAACAAA 840
E00378:188:HV 51 GACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGG 100
i
L1P3_orf2#LIN 841 GACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGG 890
E00378:188:HV 101 GAACTTTATAGCACTAAATGCCCACAGGACAAAGTAGGAAAGATCTAAAA 150
v ? v ii
L1P3_orf2#LIN 891 GAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAA 940
E00378:188:HV 151 T 151
L1P3_orf2#LIN 941 T 941
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.29
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 882 5.7 0.7 7.3 E00378:188:HVMVNCCXX:4:1109:1458:16990/2 1 151 (0) C L1P3 LINE/L1 (2916) 3230 3090 833
ANNOTATION EVIDENCE:
882 5.72 0.71 7.28 E00378:188:HVMVNCCXX:4:1109:1458:16990/2 1 151 0 C L1P3_orf2 LINE/L1 981 1121 2173
882 5.72 0.71 7.28 E00378:188:HVMVNCCXX:4:1109:1458:16990/2 1 151 (0) C L1P3_orf2#LINE/L1 (2173) 1121 981 m_b6s551i238
E00378:188:HV 1 TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTT 50
i i v -
C L1P3_orf2#LIN 1121 TCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTT 1073
E00378:188:HV 51 TTTGAAATGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGC 99
iv i---------- -i v
C L1P3_orf2#LIN 1072 TTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGC 1033
E00378:188:HV 100 TCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCT 149
C L1P3_orf2#LIN 1032 TCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCT 983
E00378:188:HV 150 CT 151
C L1P3_orf2#LIN 982 CT 981
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1360 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1110:21947:50656/1 1 151 (0) + L1P1 LINE/L1 5556 5706 (449) 834
ANNOTATION EVIDENCE:
1360 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1110:21947:50656/1 1 151 0 + L1PA3_3end LINE/L1 303 453 449
1360 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1110:21947:50656/1 1 151 (0) L1PA3_3end#LINE/L1 303 453 (449) m_b1s551i291
E00378:188:HV 1 AGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGGGATCTAGAAC 50
i
L1PA3_3end#LI 303 AGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAAC 352
E00378:188:HV 51 TGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAG 100
i
L1PA3_3end#LI 353 TAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAG 402
E00378:188:HV 101 GACTATAAATCATGCCGCTATAAAGACACATGCACACGTATGTTTATTGT 150
i i
L1PA3_3end#LI 403 GACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGC 452
E00378:188:HV 151 G 151
L1PA3_3end#LI 453 G 453
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1334 0.7 0.0 0.7 E00378:188:HVMVNCCXX:4:1110:21947:50656/2 1 151 (0) C L1PA3 LINE/L1 (279) 5876 5727 835
ANNOTATION EVIDENCE:
1334 0.66 0.00 0.66 E00378:188:HVMVNCCXX:4:1110:21947:50656/2 1 151 0 C L1PA3_3end LINE/L1 474 623 279
1334 0.66 0.00 0.66 E00378:188:HVMVNCCXX:4:1110:21947:50656/2 1 151 (0) C L1PA3_3end#LINE/L1 (279) 623 474 m_b1s551i347
E00378:188:HV 1 CTGAGAATGATGATTTCCAATTTCATCCATGTCCCTAACAAAGGACATGA 50
-
C L1PA3_3end#LI 623 CTGAGAATGATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGACATGA 575
E00378:188:HV 51 ACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCAC 100
C L1PA3_3end#LI 574 ACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCAC 525
E00378:188:HV 101 AGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGT 150
v
C L1PA3_3end#LI 524 ATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGT 475
E00378:188:HV 151 C 151
C L1PA3_3end#LI 474 C 474
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1360 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1110:21947:50726/1 1 151 (0) + L1P1 LINE/L1 5556 5706 (449) 836
ANNOTATION EVIDENCE:
1360 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1110:21947:50726/1 1 151 0 + L1PA3_3end LINE/L1 303 453 449
1360 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1110:21947:50726/1 1 151 (0) L1PA3_3end#LINE/L1 303 453 (449) m_b1s551i292
E00378:188:HV 1 AGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGGGATCTAGAAC 50
i
L1PA3_3end#LI 303 AGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAAC 352
E00378:188:HV 51 TGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAG 100
i
L1PA3_3end#LI 353 TAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAG 402
E00378:188:HV 101 GACTATAAATCATGCCGCTATAAAGACACATGCACACGTATGTTTATTGT 150
i i
L1PA3_3end#LI 403 GACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGC 452
E00378:188:HV 151 G 151
L1PA3_3end#LI 453 G 453
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1334 0.7 0.0 0.7 E00378:188:HVMVNCCXX:4:1110:21947:50726/2 1 151 (0) C L1PA3 LINE/L1 (279) 5876 5727 837
ANNOTATION EVIDENCE:
1334 0.66 0.00 0.66 E00378:188:HVMVNCCXX:4:1110:21947:50726/2 1 151 0 C L1PA3_3end LINE/L1 474 623 279
1334 0.66 0.00 0.66 E00378:188:HVMVNCCXX:4:1110:21947:50726/2 1 151 (0) C L1PA3_3end#LINE/L1 (279) 623 474 m_b1s551i348
E00378:188:HV 1 CTGAGAATGATGATTTCCAATTTCATCCATGTCCCTAACAAAGGACATGA 50
-
C L1PA3_3end#LI 623 CTGAGAATGATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGACATGA 575
E00378:188:HV 51 ACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCAC 100
C L1PA3_3end#LI 574 ACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCAC 525
E00378:188:HV 101 AGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGT 150
v
C L1PA3_3end#LI 524 ATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGT 475
E00378:188:HV 151 C 151
C L1PA3_3end#LI 474 C 474
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 327 22.6 12.5 0.0 E00378:188:HVMVNCCXX:4:1110:26098:49584/1 19 102 (49) C L1MC4 LINE/L1 (513) 7529 7416 838
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:4:1110:26098:49584/1 19 102 49 C L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:4:1110:26098:49584/1 19 102 (49) C L1MC4a_3end#LINE/L1 (371) 2258 2163 m_b3s551i121
E00378:188:HV 19 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 63
iiv i i i i i -----
C L1MC4a_3end#L 2258 GTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGTT 2209
E00378:188:HV 64 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT----TCCTCTTCT 102
i --- i i iiii i i ---- v i
C L1MC4a_3end#L 2208 ATGCATTTTTGGCAAGAATACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 4.00 (12 / 3)
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:4:1110:26098:49584/1 19 93 58 C L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:4:1110:26098:49584/1 19 93 (58) C L1MC4_3end#LINE/L1 (513) 2276 2194 m_b3s551i122
E00378:188:HV 19 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 63
iiv i i i i -----
C L1MC4_3end#LI 2276 GTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTT 2227
E00378:188:HV 64 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT 93
i --- i ii iiii i i
C L1MC4_3end#LI 2226 ATGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 700 13.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1110:7395:37260/2 52 151 (0) + AluSx SINE/Alu 1 100 (212) 839
ANNOTATION EVIDENCE:
700 13.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1110:7395:37260/2 52 151 0 + AluSx SINE/Alu 1 100 212
700 13.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1110:7395:37260/2 52 151 (0) AluSx#SINE/Alu 1 100 (212) m_b2s357i45
E00378:188:HV 52 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 101
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 102 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.05
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0)
+ 204 34.1 7.9 3.0 E00378:188:HVMVNCCXX:4:1111:13200:59165/1 10 142 (9) + MIRb SINE/MIR 16 155 (113) 840
ANNOTATION EVIDENCE:
204 34.11 7.86 3.01 E00378:188:HVMVNCCXX:4:1111:13200:59165/1 10 142 9 + MIRb SINE/MIR 16 155 113
204 34.11 7.86 3.01 E00378:188:HVMVNCCXX:4:1111:13200:59165/1 10 142 (9) MIRb#SINE/MIR 16 155 (113) m_b4s601i33
E00378:188:HV 10 GTATAGTAAAAACAAAA--GGCTTTGAAGTCAAACAGA---AAATTCAAA 54
ii ii v iv -- i i ---iii i
MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA 65
E00378:188:HV 55 TCCCAGTACCACAGCCT--TAACTTT----TCTGGTAAAAAACTTGCCTT 98
i iv ii vi i -- i v ----i -- iiiv v i i v
MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCT--TGGGCAAGTTACTTA 113
E00378:188:HV 99 ATGTCATCTAGGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA 142
iv - - i iv vi v i i ii
MIRb#SINE/MIR 114 ACCTC-TCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 46.34
Transitions / transversions = 2.67 (32/12)
Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.88 (15 / 8)
+ 946 11.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1112:30655:15707/2 1 127 (24) C AluSx SINE/Alu (185) 127 1 841
ANNOTATION EVIDENCE:
946 11.81 0.00 0.00 E00378:188:HVMVNCCXX:4:1112:30655:15707/2 1 127 24 C AluSx SINE/Alu 1 127 185
946 11.81 0.00 0.00 E00378:188:HVMVNCCXX:4:1112:30655:15707/2 1 127 (24) C AluSx#SINE/Alu (185) 127 1 m_b5s357i48
E00378:188:HV 1 TATTTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCCCAAA 50
i v i i i
C AluSx#SINE/Al 127 TATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAA 78
E00378:188:HV 51 CTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGAT 100
i i i i i
C AluSx#SINE/Al 77 CTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGAT 28
E00378:188:HV 101 TACAGGTGTGAGCCAGTGCACCCAGCC 127
i vi i i
C AluSx#SINE/Al 27 TACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 126), avg. gap size = 0.0 (0 / 0)
+ 1242 4.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1114:7030:72244/1 1 151 (0) C L1P3 LINE/L1 (3062) 3084 2934 842
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:4:1114:7030:72244/1 1 151 0 C L1P3_orf2 LINE/L1 825 975 2319
1242 3.97 0.00 0.00 E00378:188:HVMVNCCXX:4:1114:7030:72244/1 1 151 (0) C L1P3_orf2#LINE/L1 (2319) 975 825 m_b7s551i17
E00378:188:HV 1 CTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTTTCCC 50
i
C L1P3_orf2#LIN 975 CTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTTCCC 926
E00378:188:HV 51 ACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCT 100
i v ?
C L1P3_orf2#LIN 925 GCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCT 876
E00378:188:HV 101 TTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGT 150
i i
C L1P3_orf2#LIN 875 TTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGT 826
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 825 T 825
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 45 76 (75) + (TG)n Simple_repeat 1 32 (0) 843
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 45 76 75 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 45 76 (75) (TG)n#Simple_repeat 1 32 (0) m_b4s252i50
E00378:188:HV 45 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 76
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 77 89 (62) + (TGTATG)n Simple_repeat 1 41 (0) 844
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 45 89 62 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 45 89 (62) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i49
E00378:188:HV 45 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 89
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 297 8.7 4.2 0.0 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 104 149 (2) C 7SLRNA srpRNA (11) 309 262 845
ANNOTATION EVIDENCE:
297 8.70 4.17 0.00 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 104 149 2 C 7SLRNA SINE/Alu 262 309 11
297 8.70 4.17 0.00 E00378:188:HVMVNCCXX:4:1115:14215:8007/2 104 149 (2) C 7SLRNA#SINE/Alu (11) 309 262 m_b4s502i3
E00378:188:HV 104 TTTTTTTTT--GAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGC 149
-- ii v i
C 7SLRNA#SINE/A 309 TTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGGAGTGC 262
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.37
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 2.00 (2 / 1)
+ 242 20.3 0.0 9.9 E00378:188:HVMVNCCXX:4:1115:25743:21649/2 1 71 (80) + 7SLRNA srpRNA 257 320 (0) 846
ANNOTATION EVIDENCE:
242 20.31 0.00 9.86 E00378:188:HVMVNCCXX:4:1115:25743:21649/2 1 71 80 + 7SLRNA SINE/Alu 257 320 0
242 20.31 0.00 9.86 E00378:188:HVMVNCCXX:4:1115:25743:21649/2 1 71 (80) 7SLRNA#SINE/Alu 257 320 (0) m_b5s502i0
E00378:188:HV 1 CCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGACTCCATCTCA 50
------- ii iiv i i i v
7SLRNA#SINE/A 257 CCACTGCACTCCAGCCTG-------GGCAACATAGCGAGACCCCGTCTCT 299
E00378:188:HV 51 AAAAAACACAAAAACAAAAAA 71
v v v v
7SLRNA#SINE/A 300 TAAAAAAAAAAAAAAAAAAAA 320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.99
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.00 (7 / 7)
+ 1066 10.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1115:28036:25693/1 10 148 (3) C AluSx SINE/Alu (52) 260 122 847
ANNOTATION EVIDENCE:
1066 10.79 0.00 0.00 E00378:188:HVMVNCCXX:4:1115:28036:25693/1 10 148 3 C AluSx SINE/Alu 122 260 52
1066 10.79 0.00 0.00 E00378:188:HVMVNCCXX:4:1115:28036:25693/1 10 148 (3) C AluSx#SINE/Alu (52) 260 122 m_b2s357i18
E00378:188:HV 10 CCCAGGCTGGAGTGCAGTGGCATGATCTCAGCTCACTGCAATCTCTGCCT 59
ii i i i
C AluSx#SINE/Al 260 CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT 211
E00378:188:HV 60 CCTGAGTTCAAGTGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTA 109
i i i i i
C AluSx#SINE/Al 210 CCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
E00378:188:HV 110 CAGGTGCCCACCACCACACCCAGCTAATTTTTGTATTTT 148
i v i i i
C AluSx#SINE/Al 160 CAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTT 122
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.79
Transitions / transversions = 14.00 (14/1)
Gap_init rate = 0.00 (0 / 138), avg. gap size = 0.0 (0 / 0)
+ 920 3.6 0.7 6.8 E00378:188:HVMVNCCXX:4:1115:30665:69941/1 1 148 (3) + L1P3 LINE/L1 3046 3184 (2962) 848
ANNOTATION EVIDENCE:
920 3.63 0.72 6.76 E00378:188:HVMVNCCXX:4:1115:30665:69941/1 1 148 3 + L1P3_orf2 LINE/L1 937 1075 2219
920 3.63 0.72 6.76 E00378:188:HVMVNCCXX:4:1115:30665:69941/1 1 148 (3) L1P3_orf2#LINE/L1 937 1075 (2219) m_b6s551i255
E00378:188:HV 1 AAAATCAACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCA 50
i
L1P3_orf2#LIN 937 AAAATCGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCA 986
E00378:188:HV 51 AACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCTG 100
v
L1P3_orf2#LIN 987 AACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCAG 1036
E00378:188:HV 101 AG-TGAAGGAGATAGAGACACACACACACAAAAAAAACCTTTCAAAAAA 148
i- ----------i i
L1P3_orf2#LIN 1037 AACTGAAGGAGATAGAGACAC----------GAAAAACCCTTCAAAAAA 1075
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.36
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.00 (11 / 11)
+ 1183 3.3 1.3 0.0 E00378:188:HVMVNCCXX:4:1115:30665:69941/2 1 151 (0) C L1P3 LINE/L1 (2619) 3527 3375 849
ANNOTATION EVIDENCE:
1183 3.31 1.30 0.00 E00378:188:HVMVNCCXX:4:1115:30665:69941/2 1 151 0 C L1P3_orf2 LINE/L1 1266 1418 1876
1183 3.31 1.30 0.00 E00378:188:HVMVNCCXX:4:1115:30665:69941/2 1 151 (0) C L1P3_orf2#LINE/L1 (1876) 1418 1266 m_b6s551i139
E00378:188:HV 1 GGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTCAATTTC 50
C L1P3_orf2#LIN 1418 GGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTCAATTTC 1369
E00378:188:HV 51 AGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGCTTTAG-- 98
v --
C L1P3_orf2#LIN 1368 AGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGGTTTAGTC 1319
E00378:188:HV 99 TTGGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCT 148
v i vv
C L1P3_orf2#LIN 1318 TTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCT 1269
E00378:188:HV 149 AGT 151
C L1P3_orf2#LIN 1268 AGT 1266
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 937 13.7 0.0 1.4 E00378:188:HVMVNCCXX:4:1115:9019:16832/2 1 148 (3) + AluSx SINE/Alu 113 258 (54) 850
ANNOTATION EVIDENCE:
937 13.69 0.00 1.35 E00378:188:HVMVNCCXX:4:1115:9019:16832/2 1 148 3 + AluSx SINE/Alu 113 258 54
937 13.69 0.00 1.35 E00378:188:HVMVNCCXX:4:1115:9019:16832/2 1 148 (3) AluSx#SINE/Alu 113 258 (54) m_b5s357i35
E00378:188:HV 1 TCTCTACTAAAAATACAAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTG 50
-- i i v i v v
AluSx#SINE/Al 113 TCTCTACTAAAAATACAAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTG 160
E00378:188:HV 51 TAATCATAGCTGCTCAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACT 100
vi i i v i iivv
AluSx#SINE/Al 161 TAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG 210
E00378:188:HV 101 AGGCGGAGGTTGCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTG 148
v v v i
AluSx#SINE/Al 211 AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.95
Transitions / transversions = 1.00 (10/10)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 1101 4.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1116:22343:61257/1 1 131 (20) + AluSx SINE/Alu 161 291 (21) 851
ANNOTATION EVIDENCE:
1101 4.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1116:22343:61257/1 1 131 20 + AluSx SINE/Alu 161 291 21
1101 4.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1116:22343:61257/1 1 131 (20) AluSx#SINE/Alu 161 291 (21) m_b4s357i25
E00378:188:HV 1 TAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGG 50
i i
AluSx#SINE/Al 161 TAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG 210
E00378:188:HV 51 AGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGG 100
i i
AluSx#SINE/Al 211 AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
E00378:188:HV 101 CAACAGAGCGAGATTCCGTCTCAAAAAAAAA 131
i i
AluSx#SINE/Al 261 CGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.58
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 222 28.4 5.8 0.0 E00378:188:HVMVNCCXX:4:1116:22343:61257/2 68 148 (3) C MIRb SINE/MIR (49) 219 134 852
ANNOTATION EVIDENCE:
222 28.40 5.81 0.00 E00378:188:HVMVNCCXX:4:1116:22343:61257/2 68 148 3 C MIRb SINE/MIR 134 219 49
222 28.40 5.81 0.00 E00378:188:HVMVNCCXX:4:1116:22343:61257/2 68 148 (3) C MIRb#SINE/MIR (49) 219 134 m_b4s601i4
E00378:188:HV 68 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 113
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 114 CAGGTAAGTGATA-TATCTTCACTCTACTGGTGAGG 148
v i iv - ii i i v i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGG 134
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 37.58
Transitions / transversions = 2.29 (16/7)
Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.67 (5 / 3)
+ 1114 13.2 0.0 0.0 E00378:188:HVMVNCCXX:4:1116:23054:13931/2 1 151 (0) C AluSx SINE/Alu (160) 152 2 853
ANNOTATION EVIDENCE:
1114 13.25 0.00 0.00 E00378:188:HVMVNCCXX:4:1116:23054:13931/2 1 151 0 C AluSx SINE/Alu 2 152 160
1114 13.25 0.00 0.00 E00378:188:HVMVNCCXX:4:1116:23054:13931/2 1 151 (0) C AluSx#SINE/Alu (160) 152 2 m_b2s356i37
E00378:188:HV 1 CACCACCACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCA 50
i i i v i ii
C AluSx#SINE/Al 152 CGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCA 103
E00378:188:HV 51 CCATGTTGGCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCACCTG 100
i i i i
C AluSx#SINE/Al 102 CCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCG 53
E00378:188:HV 101 GCTCTGCCTCCCAAATTGCTGAGATTACAGATGTGAGCCACTGTGCCCAG 150
v v v i ii i i i
C AluSx#SINE/Al 52 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
E00378:188:HV 151 C 151
C AluSx#SINE/Al 2 C 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.71
Transitions / transversions = 4.00 (16/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1046 4.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1116:8268:70029/1 24 151 (0) C L1PA2 LINE/L1 (2) 6153 6026 854
ANNOTATION EVIDENCE:
1046 4.69 0.00 0.00 E00378:188:HVMVNCCXX:4:1116:8268:70029/1 24 151 0 C L1PA2_3end LINE/L1 773 900 2
1046 4.69 0.00 0.00 E00378:188:HVMVNCCXX:4:1116:8268:70029/1 24 151 (0) C L1PA2_3end#LINE/L1 (2) 900 773 m_b1s551i432
E00378:188:HV 24 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 73
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 74 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCCCT 123
i v
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
E00378:188:HV 124 AACTCGGCATCTAGCATTAGGTAGATCT 151
v v
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCT 773
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.10
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.0 (0 / 0)
+ 1269 2.7 0.0 0.7 E00378:188:HVMVNCCXX:4:1116:8268:70029/2 1 151 (0) + L1PA2 LINE/L1 5800 5949 (206) 855
ANNOTATION EVIDENCE:
1269 2.67 0.00 0.66 E00378:188:HVMVNCCXX:4:1116:8268:70029/2 1 151 0 + L1PA2_3end LINE/L1 547 696 206
1269 2.67 0.00 0.66 E00378:188:HVMVNCCXX:4:1116:8268:70029/2 1 151 (0) L1PA2_3end#LINE/L1 547 696 (206) m_b1s551i377
E00378:188:HV 1 TACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACAT 50
-
L1PA2_3end#LI 547 TACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACAT 595
E00378:188:HV 51 GGAGGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGAAAAA 100
v i v
L1PA2_3end#LI 596 GGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAA 645
E00378:188:HV 101 ACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGATC 150
i
L1PA2_3end#LI 646 ACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATC 695
E00378:188:HV 151 A 151
L1PA2_3end#LI 696 A 696
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1309 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:14306:12560/1 1 151 (0) C L1P1 LINE/L1 (626) 5529 5379 856
ANNOTATION EVIDENCE:
1309 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:14306:12560/1 1 151 0 C L1PA2_3end LINE/L1 126 276 626
1309 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:14306:12560/1 1 151 (0) C L1PA2_3end#LINE/L1 (626) 276 126 m_b1s551i232
E00378:188:HV 1 AAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACT 50
vi
C L1PA2_3end#LI 276 AAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACT 227
E00378:188:HV 51 TTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTT 100
i
C L1PA2_3end#LI 226 TTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTT 177
E00378:188:HV 101 TTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTG 150
C L1PA2_3end#LI 176 TTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTG 127
E00378:188:HV 151 T 151
C L1PA2_3end#LI 126 T 126
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1288 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:14306:12560/2 1 151 (0) + L1P LINE/L1 5266 5416 (739) 857
ANNOTATION EVIDENCE:
1288 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:14306:12560/2 1 151 0 + L1PA2_3end LINE/L1 13 163 739
1288 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:14306:12560/2 1 151 (0) L1PA2_3end#LINE/L1 13 163 (739) m_b1s551i171
E00378:188:HV 1 ATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCAT 50
L1PA2_3end#LI 13 ATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCAT 62
E00378:188:HV 51 CAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTT 100
L1PA2_3end#LI 63 CAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTT 112
E00378:188:HV 101 ATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGA 150
L1PA2_3end#LI 113 ATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGA 162
E00378:188:HV 151 G 151
L1PA2_3end#LI 163 G 163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 429 14.5 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:16741:46208/1 1 62 (89) C AluSx SINE/Alu (250) 62 1 858
ANNOTATION EVIDENCE:
429 14.52 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:16741:46208/1 1 62 89 C AluSx SINE/Alu 1 62 250
429 14.52 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:16741:46208/1 1 62 (89) C AluSx#SINE/Alu (250) 62 1 m_b5s357i70
E00378:188:HV 1 GATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCA 50
i i i i i
C AluSx#SINE/Al 62 GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA 13
E00378:188:HV 51 GTGCACCCAGCC 62
vi i i
C AluSx#SINE/Al 12 CCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.50
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:19745:24233/2 26 57 (94) + (CA)n Simple_repeat 1 32 (0) 859
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:19745:24233/2 26 57 94 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:19745:24233/2 26 57 (94) (CA)n#Simple_repeat 1 32 (0) m_b4s252i48
E00378:188:HV 26 CATACATGCACACACATACACACACACACACA 57
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1179 9.9 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:4127:27064/1 1 151 (0) C AluSx SINE/Alu (127) 185 35 860
ANNOTATION EVIDENCE:
1179 9.93 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:4127:27064/1 1 151 0 C AluSx SINE/Alu 35 185 127
1179 9.93 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:4127:27064/1 1 151 (0) C AluSx#SINE/Alu (127) 185 35 m_b6s356i16
E00378:188:HV 1 TCATCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCCAGCT 50
v i vi i i
C AluSx#SINE/Al 185 TCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCT 136
E00378:188:HV 51 AATTTTTTTATTTTTCGTAGAGATGGAGTTTCACCATGTTGGCCAGGCTG 100
v v i i
C AluSx#SINE/Al 135 AATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG 86
E00378:188:HV 101 GTCTTGAACTCCTGACCTCAGGTGATCCACCCACCTTGTCCTCCCAAAGT 150
i i i i v
C AluSx#SINE/Al 85 GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGT 36
E00378:188:HV 151 G 151
C AluSx#SINE/Al 35 G 35
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.72
Transitions / transversions = 2.00 (10/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 723 7.4 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:4127:27064/2 1 95 (56) + L1P3 LINE/L1 3804 3898 (2248) 861
ANNOTATION EVIDENCE:
723 7.37 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:4127:27064/2 1 95 56 + L1P3_orf2 LINE/L1 1695 1789 1505
723 7.37 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:4127:27064/2 1 95 (56) L1P3_orf2#LINE/L1 1695 1789 (1505) m_b6s551i21
E00378:188:HV 1 CTTCATCCCTGGGACGCAAGGCTGATTCAGCATACACAAATCAATAAACA 50
i i i i i
L1P3_orf2#LIN 1695 CTTCATCCCTGGGATGCAAGGCTGGTTCAACATACGCAAATCAATAAACG 1744
E00378:188:HV 51 TAATCCATCACATAAACAGAACGAATGACAAAAACTACATGATTA 95
v i
L1P3_orf2#LIN 1745 TAATCCATCACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.74
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0)
+ 415 9.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1117:4127:27064/2 98 151 (0) + AluSx SINE/Alu 14 67 (245) 862
ANNOTATION EVIDENCE:
415 9.26 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:4127:27064/2 98 151 0 + AluSx SINE/Alu 14 67 245
415 9.26 0.00 0.00 E00378:188:HVMVNCCXX:4:1117:4127:27064/2 98 151 (0) AluSx#SINE/Alu 14 67 (245) m_b6s357i28
E00378:188:HV 98 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 147
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 148 CCTG 151
AluSx#SINE/Al 64 CCTG 67
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.39
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 1281 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1118:11596:69326/1 1 151 (0) C L1P1 LINE/L1 (1097) 5049 4899 863
ANNOTATION EVIDENCE:
1281 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1118:11596:69326/1 1 151 0 C L1P1_orf2 LINE/L1 2790 2940 354
1281 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1118:11596:69326/1 1 151 (0) C L1P1_orf2#LINE/L1 (354) 2940 2790 m_b1s551i16
E00378:188:HV 1 GTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAA 50
i
C L1P1_orf2#LIN 2940 GTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAA 2891
E00378:188:HV 51 TCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTC 100
i v v
C L1P1_orf2#LIN 2890 TCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTC 2841
E00378:188:HV 101 AGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAG 150
C L1P1_orf2#LIN 2840 AGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAG 2791
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 2790 G 2790
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1178 6.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1118:17888:42569/2 1 151 (0) C L1P3 LINE/L1 (3170) 2976 2826 864
ANNOTATION EVIDENCE:
1178 6.62 0.00 0.00 E00378:188:HVMVNCCXX:4:1118:17888:42569/2 1 151 0 C L1P3_orf2 LINE/L1 717 867 2427
1178 6.62 0.00 0.00 E00378:188:HVMVNCCXX:4:1118:17888:42569/2 1 151 (0) C L1P3_orf2#LINE/L1 (2427) 867 717 m_b7s551i50
E00378:188:HV 1 GTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAAGA 50
i i
C L1P3_orf2#LIN 867 GTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGA 818
E00378:188:HV 51 ACTTACTTATTTCTGCCTTCATTTCATTATTTACCTAGTAGTCATTCAGG 100
?i v i i
C L1P3_orf2#LIN 817 ACTTNTTTATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTCAGG 768
E00378:188:HV 101 AGCAGGGTGTTCAGTTTCCGTGTAGTTGTGTGGTTTTGAGTGAGTTTCTT 150
v i i
C L1P3_orf2#LIN 767 AGCAGGTTGTTCAGTTTCCATGTAGTTGTGCGGTTTTGAGTGAGTTTCTT 718
E00378:188:HV 151 A 151
C L1P3_orf2#LIN 717 A 717
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.34
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 248 25.8 5.0 1.5 E00378:188:HVMVNCCXX:4:1118:5112:36856/2 17 150 (1) C L1ME4c LINE/L1 (216) 5867 5729 865
ANNOTATION EVIDENCE:
248 25.75 5.03 1.49 E00378:188:HVMVNCCXX:4:1118:5112:36856/2 17 150 1 C L1ME4c_3end LINE/L1 476 614 216
248 25.75 5.03 1.49 E00378:188:HVMVNCCXX:4:1118:5112:36856/2 17 150 (1) C L1ME4c_3end#LINE/L1 (216) 614 476 m_b2s551i3
E00378:188:HV 17 ATTATAAGTATTTTTCCAGGTAGTTGC-TTTTCTTGATAGTCATACTTTT 65
i ii - v v i i - vv v i i vv
C L1ME4c_3end#L 614 ATCATAAACA-TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTT 566
E00378:188:HV 66 TAATGGCTTCACCATTTTTCTGTC--ATAAA--TACCATAATTTACTTGA 111
v iv - v ii --i ?i -- i
C L1ME4c_3end#L 565 TAATGGCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAA 517
E00378:188:HV 112 -CATT-TTTTATTGTCAGAAATTTAGATTCTTTTCTATTTT 150
- -iii ii v i v i v
C L1ME4c_3end#L 516 CCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.46
Transitions / transversions = 1.54 (20/13)
Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.29 (9 / 7)
+ 522 11.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1119:10927:36311/2 1 71 (80) C AluY SINE/Alu (240) 71 1 866
ANNOTATION EVIDENCE:
522 11.27 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:10927:36311/2 1 71 80 C AluY SINE/Alu 1 71 240
522 11.27 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:10927:36311/2 1 71 (80) C AluY#SINE/Alu (240) 71 1 m_b2s357i59
E00378:188:HV 1 TGACCTCATGATCAGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTACAAG 50
i v i i i
C AluY#SINE/Alu 71 TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGG 22
E00378:188:HV 51 CGTGAGCCACCATGCCTGGCC 71
ii i
C AluY#SINE/Alu 21 CGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.13
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 1272 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1119:14022:6302/1 1 151 (0) C L1P1 LINE/L1 (712) 5443 5293 867
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14022:6302/1 1 151 0 C L1PA2_3end LINE/L1 40 190 712
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14022:6302/1 1 151 (0) C L1PA2_3end#LINE/L1 (712) 190 40 m_b1s551i183
E00378:188:HV 1 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 50
C L1PA2_3end#LI 190 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 141
E00378:188:HV 51 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 100
C L1PA2_3end#LI 140 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 91
E00378:188:HV 101 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 150
C L1PA2_3end#LI 90 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 41
E00378:188:HV 151 T 151
C L1PA2_3end#LI 40 T 40
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1266 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1119:14022:6302/2 1 151 (0) + L1P1 LINE/L1 4998 5148 (998) 868
ANNOTATION EVIDENCE:
1266 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14022:6302/2 1 151 0 + L1P1_orf2 LINE/L1 2889 3039 255
1266 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14022:6302/2 1 151 (0) L1P1_orf2#LINE/L1 2889 3039 (255) m_b1s551i63
E00378:188:HV 1 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 50
i
L1P1_orf2#LIN 2889 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 2938
E00378:188:HV 51 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 100
?
L1P1_orf2#LIN 2939 ACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 2988
E00378:188:HV 101 AAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCT 150
v i
L1P1_orf2#LIN 2989 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3038
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3039 A 3039
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1272 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1119:14905:7515/1 1 151 (0) C L1P1 LINE/L1 (712) 5443 5293 869
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14905:7515/1 1 151 0 C L1PA2_3end LINE/L1 40 190 712
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14905:7515/1 1 151 (0) C L1PA2_3end#LINE/L1 (712) 190 40 m_b1s551i184
E00378:188:HV 1 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 50
C L1PA2_3end#LI 190 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 141
E00378:188:HV 51 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 100
C L1PA2_3end#LI 140 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 91
E00378:188:HV 101 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 150
C L1PA2_3end#LI 90 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 41
E00378:188:HV 151 T 151
C L1PA2_3end#LI 40 T 40
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1266 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1119:14905:7515/2 1 151 (0) + L1P1 LINE/L1 4998 5148 (998) 870
ANNOTATION EVIDENCE:
1266 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14905:7515/2 1 151 0 + L1P1_orf2 LINE/L1 2889 3039 255
1266 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1119:14905:7515/2 1 151 (0) L1P1_orf2#LINE/L1 2889 3039 (255) m_b1s551i64
E00378:188:HV 1 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 50
i
L1P1_orf2#LIN 2889 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 2938
E00378:188:HV 51 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 100
?
L1P1_orf2#LIN 2939 ACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 2988
E00378:188:HV 101 AAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCT 150
v i
L1P1_orf2#LIN 2989 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3038
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3039 A 3039
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1309 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1120:14194:44890/1 1 151 (0) + L1P3 LINE/L1 3496 3646 (2500) 871
ANNOTATION EVIDENCE:
1309 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1120:14194:44890/1 1 151 0 + L1P3_orf2 LINE/L1 1387 1537 1757
1309 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1120:14194:44890/1 1 151 (0) L1P3_orf2#LINE/L1 1387 1537 (1757) m_b6s551i105
E00378:188:HV 1 AATAGCCTACCAACCAAAAAAAGCCCAGGACCAGAGGGATTCACAGCCGA 50
v
L1P3_orf2#LIN 1387 AATAGCCTACCAACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGA 1436
E00378:188:HV 51 ATTCTACCAGGGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTAT 100
i
L1P3_orf2#LIN 1437 ATTCTACCAGAGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTAT 1486
E00378:188:HV 101 TCCAAACAATAGAAAAAGAGGGACTCTTCCCTAACTCATTTTATGATGCC 150
i v
L1P3_orf2#LIN 1487 TCCAAACAATAGAAAAAGAGGGACTCCTCCCTAACTCATTTTATGAGGCC 1536
E00378:188:HV 151 A 151
L1P3_orf2#LIN 1537 A 1537
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1227 4.0 1.3 0.0 E00378:188:HVMVNCCXX:4:1120:14194:44890/2 1 151 (0) C L1P3 LINE/L1 (2424) 3722 3570 872
ANNOTATION EVIDENCE:
1227 3.97 1.30 0.00 E00378:188:HVMVNCCXX:4:1120:14194:44890/2 1 151 0 C L1P3_orf2 LINE/L1 1461 1613 1681
1227 3.97 1.30 0.00 E00378:188:HVMVNCCXX:4:1120:14194:44890/2 1 151 (0) C L1P3_orf2#LINE/L1 (1681) 1613 1461 m_b6s551i84
E00378:188:HV 1 ATGTTCATCACGGATAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCT 48
v v i--
C L1P3_orf2#LIN 1613 ATGTTCATCAGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCT 1564
E00378:188:HV 49 GCCAGGTTTTGGAATCAGGATGATGCTGGCATCATAAAATGAGTTAGGGA 98
v v
C L1P3_orf2#LIN 1563 GCCAGGTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGA 1514
E00378:188:HV 99 AGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACC 148
i
C L1P3_orf2#LIN 1513 GGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACC 1464
E00378:188:HV 149 AGC 151
C L1P3_orf2#LIN 1463 AGC 1461
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.08
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1178 8.6 0.7 0.0 E00378:188:HVMVNCCXX:4:1120:17229:9783/2 1 151 (0) + AluY SINE/Alu 45 196 (115) 873
ANNOTATION EVIDENCE:
1178 8.61 0.66 0.00 E00378:188:HVMVNCCXX:4:1120:17229:9783/2 1 151 0 + AluY SINE/Alu 45 196 115
1178 8.61 0.66 0.00 E00378:188:HVMVNCCXX:4:1120:17229:9783/2 1 151 (0) AluY#SINE/Alu 45 196 (115) m_b2s356i60
E00378:188:HV 1 GGCCAAGGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTA 50
i v i i
AluY#SINE/Alu 45 GGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTA 94
E00378:188:HV 51 ACGTGGTGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCGT 99
ii i i - vi
AluY#SINE/Alu 95 ACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGT 144
E00378:188:HV 100 GGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGGGGCTGAAGCAGGAGAA 149
i i
AluY#SINE/Alu 145 GGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAA 194
E00378:188:HV 150 CG 151
i
AluY#SINE/Alu 195 TG 196
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.25
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 940 4.3 0.7 7.3 E00378:188:HVMVNCCXX:4:1121:26575:42147/2 1 151 (0) C L1P3 LINE/L1 (2923) 3223 3083 874
ANNOTATION EVIDENCE:
940 4.28 0.71 7.28 E00378:188:HVMVNCCXX:4:1121:26575:42147/2 1 151 0 C L1P3_orf2 LINE/L1 974 1114 2180
940 4.28 0.71 7.28 E00378:188:HVMVNCCXX:4:1121:26575:42147/2 1 151 (0) C L1P3_orf2#LINE/L1 (2180) 1114 974 m_b6s551i241
E00378:188:HV 1 TGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAA 50
i v - i
C L1P3_orf2#LIN 1114 TGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAG 1066
E00378:188:HV 51 GGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATC 99
i---------- -i v
C L1P3_orf2#LIN 1065 GGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCTCTGATC 1026
E00378:188:HV 100 TTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTT 149
C L1P3_orf2#LIN 1025 TTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTT 976
E00378:188:HV 150 CT 151
C L1P3_orf2#LIN 975 CT 974
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1174 7.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1121:6228:56440/2 1 143 (8) C AluY SINE/Alu (168) 143 1 875
ANNOTATION EVIDENCE:
1174 6.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1121:6228:56440/2 1 143 8 C AluY SINE/Alu 1 143 168
1174 6.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1121:6228:56440/2 1 143 (8) C AluY#SINE/Alu (168) 143 1 m_b2s357i82
E00378:188:HV 1 CGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAGGTT 50
iv
C AluY#SINE/Alu 143 CGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTT 94
E00378:188:HV 51 AGCCAGGATGGTCTTGATCTCCTGATCTCATGATCCGCCCGCCTTGGCCT 100
i i i i
C AluY#SINE/Alu 93 AGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCT 44
E00378:188:HV 101 CCCAAAGTGCTGAGATTACAGGCGTGAGCCACCATGCCTGGCC 143
i ii i
C AluY#SINE/Alu 43 CCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.64
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 142), avg. gap size = 0.0 (0 / 0)
+ 1241 8.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1122:20943:6689/1 1 151 (0) C AluSx SINE/Alu (63) 249 99 876
ANNOTATION EVIDENCE:
1241 7.95 0.00 0.00 E00378:188:HVMVNCCXX:4:1122:20943:6689/1 1 151 0 C AluSx SINE/Alu 99 249 63
1241 7.95 0.00 0.00 E00378:188:HVMVNCCXX:4:1122:20943:6689/1 1 151 (0) C AluSx#SINE/Alu (63) 249 99 m_b4s356i17
E00378:188:HV 1 GTGCAGTGGCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAA 50
i i
C AluSx#SINE/Al 249 GTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAA 200
E00378:188:HV 51 GCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGC 100
i i vi
C AluSx#SINE/Al 199 GCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGC 150
E00378:188:HV 101 CACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAGGTGGAGTTTCACCA 150
v i i ii i
C AluSx#SINE/Al 149 CACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCA 100
E00378:188:HV 151 T 151
C AluSx#SINE/Al 99 T 99
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 558 10.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1122:20943:6689/2 78 151 (0) + AluY SINE/Alu 1 74 (237) 877
ANNOTATION EVIDENCE:
558 10.81 0.00 0.00 E00378:188:HVMVNCCXX:4:1122:20943:6689/2 78 151 0 + AluY SINE/Alu 1 74 237
558 10.81 0.00 0.00 E00378:188:HVMVNCCXX:4:1122:20943:6689/2 78 151 (0) AluY#SINE/Alu 1 74 (237) m_b4s357i61
E00378:188:HV 78 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 127
i i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 128 AGCAGGCAGATCACAAGGTCAGGA 151
i i i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGA 74
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.35
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 255 26.1 5.0 1.5 E00378:188:HVMVNCCXX:4:1123:25905:2346/2 13 148 (3) C L1ME4c LINE/L1 (216) 5867 5727 878
ANNOTATION EVIDENCE:
255 26.12 4.97 1.47 E00378:188:HVMVNCCXX:4:1123:25905:2346/2 13 148 3 C L1ME4c_3end LINE/L1 474 614 216
255 26.12 4.97 1.47 E00378:188:HVMVNCCXX:4:1123:25905:2346/2 13 148 (3) C L1ME4c_3end#LINE/L1 (216) 614 474 m_b2s551i5
E00378:188:HV 13 ATTATAAGTATTTTTCCAGGTAGTTGC-TTTTCTTGATAGTCATACTTTT 61
i ii - v v i i - vv v i i vv
C L1ME4c_3end#L 614 ATCATAAACA-TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTT 566
E00378:188:HV 62 TAATGGCTTCACCATTTTTCTGTC--ATAAA--TACCATAATTTACTTGA 107
v iv - v ii --i ?i -- i
C L1ME4c_3end#L 565 TAATGGCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAA 517
E00378:188:HV 108 -CATT-TTTTATTGTCAGAAATTTAGATTCTTTTCTATTTTCC 148
- -iii ii v i v i v i
C L1ME4c_3end#L 516 CCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTC 474
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.12
Transitions / transversions = 1.62 (21/13)
Gap_init rate = 0.05 (7 / 135), avg. gap size = 1.29 (9 / 7)
+ 971 14.1 0.7 0.0 E00378:188:HVMVNCCXX:4:1124:2828:3964/1 1 149 (2) C AluY SINE/Alu (161) 150 1 879
ANNOTATION EVIDENCE:
971 14.09 0.67 0.00 E00378:188:HVMVNCCXX:4:1124:2828:3964/1 1 149 2 C AluY SINE/Alu 1 150 161
971 14.09 0.67 0.00 E00378:188:HVMVNCCXX:4:1124:2828:3964/1 1 149 (2) C AluY#SINE/Alu (161) 150 1 m_b2s357i83
E00378:188:HV 1 GCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTCGAGCTGGGGTTTCA 49
iv - i v vi
C AluY#SINE/Alu 150 GCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCA 101
E00378:188:HV 50 CCACGTTATCCAGGATGTTCTTGATCTCCTGACCTCATGATCAGCCCGCC 99
ii v v i i v
C AluY#SINE/Alu 100 CCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 51
E00378:188:HV 100 TTGGCCTCCCAAAGTGCTGAGATTACAAGCGTGAGCCAGTATGCCTGGCC 149
i i i viii i
C AluY#SINE/Alu 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.13
Transitions / transversions = 2.00 (14/7)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 253 27.3 5.9 0.7 E00378:188:HVMVNCCXX:4:1201:13859:7462/1 8 151 (0) C L1ME4c LINE/L1 (226) 5857 5706 880
ANNOTATION EVIDENCE:
253 27.27 5.92 0.69 E00378:188:HVMVNCCXX:4:1201:13859:7462/1 8 151 0 C L1ME4c_3end LINE/L1 453 604 226
253 27.27 5.92 0.69 E00378:188:HVMVNCCXX:4:1201:13859:7462/1 8 151 (0) C L1ME4c_3end#LINE/L1 (226) 604 453 m_b2s551i9
E00378:188:HV 8 TTTTCCAGGTAGTTGC-TTTTCTTGATAGTCATACTTTTTAATGGCTTCA 56
v v i i - vv v i i vv v
C L1ME4c_3end#L 604 TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCA 555
E00378:188:HV 57 CCATTTTTCTGTC--ATAAA--TACCATAATTTACTTGA-CATT-TTTTA 100
iv - v ii --i ?i -- i - -iii
C L1ME4c_3end#L 554 TAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506
E00378:188:HV 101 TTGTCAGAAATTTAGATTCTTTTCTATTTTC--CTACAATAAACATTATT 148
ii v i v i v i-- iv i viii
C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456
E00378:188:HV 149 GCA 151
C L1ME4c_3end#L 455 GCA 453
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.78
Transitions / transversions = 1.53 (23/15)
Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.43 (10 / 7)
+ 281 14.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1201:16447:39827/2 1 48 (103) + L1MC4 LINE/L1 7602 7649 (393) 881
ANNOTATION EVIDENCE:
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:16447:39827/2 1 48 103 + L1MC4_3end LINE/L1 2349 2396 393
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:16447:39827/2 1 48 (103) L1MC4_3end#LINE/L1 2349 2396 (393) m_b3s551i46
E00378:188:HV 1 TGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGCAATG 48
i v vvv v i
L1MC4_3end#LI 2349 TGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.97
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 534 17.5 8.5 0.0 E00378:188:HVMVNCCXX:4:1201:16447:39827/2 53 149 (2) + L1MC4 LINE/L1 7762 7867 (175) 881
ANNOTATION EVIDENCE:
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:4:1201:16447:39827/2 53 149 2 + L1MC4_3end LINE/L1 2509 2614 175
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:4:1201:16447:39827/2 53 149 (2) L1MC4_3end#LINE/L1 2509 2614 (175) m_b3s551i47
E00378:188:HV 53 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 102
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
E00378:188:HV 103 ATCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCA 143
i i i --------- i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCA 2608
E00378:188:HV 144 TCACGT 149
? i
L1MC4_3end#LI 2609 TNATGT 2614
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.80
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 96), avg. gap size = 9.00 (9 / 1)
+ 281 14.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1201:16467:39967/2 1 48 (103) + L1MC4 LINE/L1 7602 7649 (393) 882
ANNOTATION EVIDENCE:
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:16467:39967/2 1 48 103 + L1MC4_3end LINE/L1 2349 2396 393
281 14.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:16467:39967/2 1 48 (103) L1MC4_3end#LINE/L1 2349 2396 (393) m_b3s551i48
E00378:188:HV 1 TGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGCAATG 48
i v vvv v i
L1MC4_3end#LI 2349 TGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.97
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 534 17.5 8.5 0.0 E00378:188:HVMVNCCXX:4:1201:16467:39967/2 53 149 (2) + L1MC4 LINE/L1 7762 7867 (175) 882
ANNOTATION EVIDENCE:
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:4:1201:16467:39967/2 53 149 2 + L1MC4_3end LINE/L1 2509 2614 175
534 17.53 8.49 0.00 E00378:188:HVMVNCCXX:4:1201:16467:39967/2 53 149 (2) L1MC4_3end#LINE/L1 2509 2614 (175) m_b3s551i49
E00378:188:HV 53 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 102
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
E00378:188:HV 103 ATCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCA 143
i i i --------- i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCA 2608
E00378:188:HV 144 TCACGT 149
? i
L1MC4_3end#LI 2609 TNATGT 2614
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.80
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 96), avg. gap size = 9.00 (9 / 1)
+ 330 27.1 3.5 0.0 E00378:188:HVMVNCCXX:4:1201:1681:45927/2 30 151 (0) + MIRb SINE/MIR 60 187 (75) 883
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:4:1201:1681:45927/2 30 151 0 + MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:4:1201:1681:45927/2 30 151 (0) MIR#SINE/MIR 60 187 (75) m_b6s601i60
E00378:188:HV 30 CTCGAGTCAACCACTTGTTAGCTCTGTGGCAT-AAGCAAGTTACTTTACC 78
i iv vi ii v i v -ii v
MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109
E00378:188:HV 79 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATAGAATC 126
v iv i v -- i i v ii iv v i
MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACC 159
E00378:188:HV 127 TAAGTGACAGAAGTAT---AAGAATTAA 151
vv v i iiv i ---i i
MIR#SINE/MIR 160 TACCTCATAGGGTTGTTGTGAGGATTAA 187
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:1201:1681:45927/2 30 121 30 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:1201:1681:45927/2 30 121 (30) MIRb#SINE/MIR 67 161 (107) m_b6s601i59
E00378:188:HV 30 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 78
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 79 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 121
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 504 16.9 0.0 0.0 E00378:188:HVMVNCCXX:4:1201:3559:30861/2 6 88 (63) C L1MC4 LINE/L1 (198) 7844 7762 884
ANNOTATION EVIDENCE:
504 16.87 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:3559:30861/2 6 88 63 C L1MC4_3end LINE/L1 2509 2591 198
504 16.87 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:3559:30861/2 6 88 (63) C L1MC4_3end#LINE/L1 (198) 2591 2509 m_b3s551i52
E00378:188:HV 6 ATACTTCAGTGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCA 55
i i i iv ii iiv i
C L1MC4_3end#LI 2591 ATACTTCAGTGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCA 2542
E00378:188:HV 56 CAGTATAATCATCAAAATCAGGAAGTTAACATT 88
i i i
C L1MC4_3end#LI 2541 CAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.02
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 292 16.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1201:3559:30861/2 93 146 (5) C L1MC4 LINE/L1 (393) 7649 7596 884
ANNOTATION EVIDENCE:
292 16.67 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:3559:30861/2 93 146 5 C L1MC4_3end LINE/L1 2343 2396 393
292 16.67 0.00 0.00 E00378:188:HVMVNCCXX:4:1201:3559:30861/2 93 146 (5) C L1MC4_3end#LINE/L1 (393) 2396 2343 m_b3s551i53
E00378:188:HV 93 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGG 142
i v vvv v i v
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 143 TCTT 146
i
C L1MC4_3end#LI 2346 TCCT 2343
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.75
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 1179 6.0 1.3 0.0 E00378:188:HVMVNCCXX:4:1203:13575:64070/1 1 151 (0) + L1P3 LINE/L1 3607 3759 (2387) 885
ANNOTATION EVIDENCE:
1179 5.96 1.30 0.00 E00378:188:HVMVNCCXX:4:1203:13575:64070/1 1 151 0 + L1P3_orf2 LINE/L1 1498 1650 1644
1179 5.96 1.30 0.00 E00378:188:HVMVNCCXX:4:1203:13575:64070/1 1 151 (0) L1P3_orf2#LINE/L1 1498 1650 (1644) m_b6s551i73
E00378:188:HV 1 GAAAAAGAGGGACTCTTCCCTAACTCATTTTATGATGCCAGCATCATCCT 50
i v
L1P3_orf2#LIN 1498 GAAAAAGAGGGACTCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCT 1547
E00378:188:HV 51 GATTCCAAAACCTGGCAGAGACACAA--GAAAAAGAAAATTTCAGGCCAT 98
v --i v
L1P3_orf2#LIN 1548 GATACCAAAACCTGGCAGAGACACAACAAAAAAAGAAAATTTCAGGCCAA 1597
E00378:188:HV 99 TATCCGTGATGAACATCGATGTGAAAATCCTCGATAAAATACTGGCAAAC 148
v i i
L1P3_orf2#LIN 1598 TATCCCTGATGAACATCGATGCGAAAATCCTCAATAAAATACTGGCAAAC 1647
E00378:188:HV 149 TGA 151
i
L1P3_orf2#LIN 1648 CGA 1650
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 723 6.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1203:13575:64070/2 1 89 (62) C AluSx SINE/Alu (210) 102 14 886
ANNOTATION EVIDENCE:
723 6.74 0.00 0.00 E00378:188:HVMVNCCXX:4:1203:13575:64070/2 1 89 62 C AluSx SINE/Alu 14 102 210
723 6.74 0.00 0.00 E00378:188:HVMVNCCXX:4:1203:13575:64070/2 1 89 (62) C AluSx#SINE/Alu (210) 102 14 m_b6s357i17
E00378:188:HV 1 CCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCA 50
i i i
C AluSx#SINE/Al 102 CCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCG 53
E00378:188:HV 51 CCTTGTCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCC 89
i v i
C AluSx#SINE/Al 52 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.75
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
+ 410 5.1 0.0 0.0 E00378:188:HVMVNCCXX:4:1203:13575:64070/2 92 150 (1) C L1P3 LINE/L1 (2248) 3898 3840 887
ANNOTATION EVIDENCE:
410 5.08 0.00 0.00 E00378:188:HVMVNCCXX:4:1203:13575:64070/2 92 150 1 C L1P3_orf2 LINE/L1 1731 1789 1505
410 5.08 0.00 0.00 E00378:188:HVMVNCCXX:4:1203:13575:64070/2 92 150 (1) C L1P3_orf2#LINE/L1 (1505) 1789 1731 m_b6s551i10
E00378:188:HV 92 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 141
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 142 ATTGATTTG 150
C L1P3_orf2#LIN 1739 ATTGATTTG 1731
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.65
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 1092 12.9 0.0 0.0 E00378:188:HVMVNCCXX:4:1204:19197:7462/1 5 151 (0) + AluSx SINE/Alu 1 147 (165) 888
ANNOTATION EVIDENCE:
1092 12.93 0.00 0.00 E00378:188:HVMVNCCXX:4:1204:19197:7462/1 5 151 0 + AluSx SINE/Alu 1 147 165
1092 12.93 0.00 0.00 E00378:188:HVMVNCCXX:4:1204:19197:7462/1 5 151 (0) AluSx#SINE/Alu 1 147 (165) m_b2s356i38
E00378:188:HV 5 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 54
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 55 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 104
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 105 GGTGAAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGG 151
ii i v i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGG 147
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.85
Transitions / transversions = 3.75 (15/4)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 388 3.9 0.0 0.0 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 1 51 (100) + L1PA2 LINE/L1 6103 6153 (2) 889
ANNOTATION EVIDENCE:
388 3.92 0.00 0.00 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 1 51 100 + L1PA2_3end LINE/L1 850 900 2
388 3.92 0.00 0.00 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 1 51 (100) L1PA2_3end#LINE/L1 850 900 (2) m_b1s551i475
E00378:188:HV 1 TGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATA 50
i v
L1PA2_3end#LI 850 TGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAA 899
E00378:188:HV 51 A 51
L1PA2_3end#LI 900 A 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.03
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 45 133 (18) C L1M5 LINE/L1 (293) 5831 5741 890 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 45 133 18 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 45 133 (18) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i476
E00378:188:HV 45 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 94
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 95 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 133
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 66 133 18 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:4:1204:19197:7462/2 66 133 (18) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i477
E00378:188:HV 66 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 115
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 116 CTATTGTTGGACATTTAG 133
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 597 13.8 2.1 0.0 E00378:188:HVMVNCCXX:4:1206:1215:23776/2 54 147 (4) + AluSx SINE/Alu 1 96 (216) 891
ANNOTATION EVIDENCE:
597 13.83 2.09 0.00 E00378:188:HVMVNCCXX:4:1206:1215:23776/2 54 147 4 + AluSx SINE/Alu 1 96 216
597 13.83 2.09 0.00 E00378:188:HVMVNCCXX:4:1206:1215:23776/2 54 147 (4) AluSx#SINE/Alu 1 96 (216) m_b4s357i53
E00378:188:HV 54 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGC 103
i i i i v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 104 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGGACAGCCTCGCCA 147
i i i --i i iv v
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCA 96
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.51
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.01 (1 / 93), avg. gap size = 2.00 (2 / 1)
+ 427 17.8 7.1 15.1 E00378:188:HVMVNCCXX:4:1206:23460:40934/2 1 139 (12) + L1MC4 LINE/L1 7826 7952 (90) 892
ANNOTATION EVIDENCE:
427 17.80 7.08 15.11 E00378:188:HVMVNCCXX:4:1206:23460:40934/2 1 139 12 + L1MC4_3end LINE/L1 2573 2699 90
427 17.80 7.08 15.11 E00378:188:HVMVNCCXX:4:1206:23460:40934/2 1 139 (12) L1MC4_3end#LINE/L1 2573 2699 (90) m_b3s551i9
E00378:188:HV 1 GAAATATACACTGAAGTAT---------AAGGAGCATCACGTGTGCGATT 41
i --------- i ? i v i i
L1MC4_3end#LI 2573 GAAATACACACTGAAGTATTTAGGGGTAAAGGGGCATNATGTCTGCAACT 2622
E00378:188:HV 42 TCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTATCTGCGTATGAGTG 91
vv - i vi i i -- ---------
L1MC4_3end#LI 2623 TACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT--GC--------- 2660
E00378:188:HV 92 TGTGTGTGGAGAGAGGGAATGATTAAGCAAATATGGTAAAACGTTAAC 139
--------- ? ? i v i i i
L1MC4_3end#LI 2661 ---------ANANAGAGAATGATAAAGCAAATGTGGCAAAATGTTAAC 2699
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.98
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.16 (22 / 138), avg. gap size = 1.36 (30 / 22)
+ 1151 7.4 0.7 0.0 E00378:188:HVMVNCCXX:4:1206:24180:44046/1 1 148 (3) C L1PA2 LINE/L1 (21) 6134 5986 893
ANNOTATION EVIDENCE:
1151 7.43 0.68 0.00 E00378:188:HVMVNCCXX:4:1206:24180:44046/1 1 148 3 C L1PA2_3end LINE/L1 733 881 21
1151 7.43 0.68 0.00 E00378:188:HVMVNCCXX:4:1206:24180:44046/1 1 148 (3) C L1PA2_3end#LINE/L1 (21) 881 733 m_b1s551i417
E00378:188:HV 1 TTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTAT 50
C L1PA2_3end#LI 881 TTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTAT 832
E00378:188:HV 51 ACATGTGCCATGCTGGTGTGCTGCACCCACTAACTCGTCATCTAGCATTA 100
i
C L1PA2_3end#LI 831 ACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTA 782
E00378:188:HV 101 GGTATATCTCCCAATGCTATATATTCCCGCG-CTCCCATCCCACGACGG 148
viv i v v- i i v i
C L1PA2_3end#LI 781 GGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCCACCCCACCACAG 733
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.17
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 1.00 (1 / 1)
+ 1296 2.0 0.0 0.7 E00378:188:HVMVNCCXX:4:1206:24180:44046/2 1 151 (0) + L1PA2 LINE/L1 5820 5969 (186) 894
ANNOTATION EVIDENCE:
1296 2.00 0.00 0.66 E00378:188:HVMVNCCXX:4:1206:24180:44046/2 1 151 0 + L1PA2_3end LINE/L1 567 716 186
1296 2.00 0.00 0.66 E00378:188:HVMVNCCXX:4:1206:24180:44046/2 1 151 (0) L1PA2_3end#LINE/L1 567 716 (186) m_b1s551i382
E00378:188:HV 1 TGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAAATCATC 50
-
L1PA2_3end#LI 567 TGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAATCATC 615
E00378:188:HV 51 ATTCTCAGTAAACTGTCGCAAGAAGAAAAAACCAAACACCGCATGTTCTC 100
i v i
L1PA2_3end#LI 616 ATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTC 665
E00378:188:HV 101 ACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGA 150
L1PA2_3end#LI 666 ACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGA 715
E00378:188:HV 151 A 151
L1PA2_3end#LI 716 A 716
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1327 0.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1206:3407:64456/1 1 151 (0) C L1P1 LINE/L1 (647) 5508 5358 895
ANNOTATION EVIDENCE:
1327 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:1206:3407:64456/1 1 151 0 C L1PA2_3end LINE/L1 105 255 647
1327 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:1206:3407:64456/1 1 151 (0) C L1PA2_3end#LINE/L1 (647) 255 105 m_b1s551i224
E00378:188:HV 1 TCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAA 50
i
C L1PA2_3end#LI 255 TCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAA 206
E00378:188:HV 51 CTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATG 100
C L1PA2_3end#LI 205 CTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATG 156
E00378:188:HV 101 GCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTC 150
C L1PA2_3end#LI 155 GCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTC 106
E00378:188:HV 151 T 151
C L1PA2_3end#LI 105 T 105
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1275 3.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1206:3407:64456/2 1 151 (0) + L1P1 LINE/L1 4944 5094 (1052) 896
ANNOTATION EVIDENCE:
1275 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:1206:3407:64456/2 1 151 0 + L1P1_orf2 LINE/L1 2835 2985 309
1275 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:1206:3407:64456/2 1 151 (0) L1P1_orf2#LINE/L1 2835 2985 (309) m_b1s551i33
E00378:188:HV 1 AAAGCTGAAACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAA 50
v v i
L1P1_orf2#LIN 2835 AAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAA 2884
E00378:188:HV 51 GATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAA 100
i
L1P1_orf2#LIN 2885 GATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAA 2934
E00378:188:HV 101 GAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 150
?
L1P1_orf2#LIN 2935 GAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 2984
E00378:188:HV 151 G 151
L1P1_orf2#LIN 2985 G 2985
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 620 16.8 0.0 5.6 E00378:188:HVMVNCCXX:4:1207:29670:33691/2 26 151 (0) C AluSx SINE/Alu (8) 304 186 897
ANNOTATION EVIDENCE:
620 16.80 0.00 5.56 E00378:188:HVMVNCCXX:4:1207:29670:33691/2 26 151 0 C AluSx SINE/Alu 186 304 8
620 16.80 0.00 5.56 E00378:188:HVMVNCCXX:4:1207:29670:33691/2 26 151 (0) C AluSx#SINE/Alu (8) 304 186 m_b5s357i22
E00378:188:HV 26 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 75
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 76 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 125
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 126 TAGTAGGTTCAAGGAATTGTACTGCC 151
vvii vi v v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCC 186
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 13.31
Transitions / transversions = 0.82 (9/11)
Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.00 (7 / 7)
+ 1329 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:13697:28417/1 1 151 (0) C L1P1 LINE/L1 (599) 5556 5406 898
ANNOTATION EVIDENCE:
1329 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:13697:28417/1 1 151 0 C L1PA3_3end LINE/L1 153 303 599
1329 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:13697:28417/1 1 151 (0) C L1PA3_3end#LINE/L1 (599) 303 153 m_b1s551i243
E00378:188:HV 1 TAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATC 50
vi
C L1PA3_3end#LI 303 TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATC 254
E00378:188:HV 51 CTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACT 100
i
C L1PA3_3end#LI 253 CTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACT 204
E00378:188:HV 101 GGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGC 150
C L1PA3_3end#LI 203 GGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGC 154
E00378:188:HV 151 C 151
C L1PA3_3end#LI 153 C 153
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1284 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:13697:28417/2 1 151 (0) + L1P1 LINE/L1 5231 5381 (765) 899
ANNOTATION EVIDENCE:
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:13697:28417/2 1 151 0 + L1P1_orf2 LINE/L1 3122 3272 22
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:13697:28417/2 1 151 (0) L1P1_orf2#LINE/L1 3122 3272 (22) m_b1s551i151
E00378:188:HV 1 CAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC 50
L1P1_orf2#LIN 3122 CAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC 3171
E00378:188:HV 51 AAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAA 100
L1P1_orf2#LIN 3172 AAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAA 3221
E00378:188:HV 101 GGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAC 150
L1P1_orf2#LIN 3222 GGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAC 3271
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3272 A 3272
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1329 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:14022:28593/1 1 151 (0) C L1P1 LINE/L1 (599) 5556 5406 900
ANNOTATION EVIDENCE:
1329 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:14022:28593/1 1 151 0 C L1PA3_3end LINE/L1 153 303 599
1329 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:14022:28593/1 1 151 (0) C L1PA3_3end#LINE/L1 (599) 303 153 m_b1s551i244
E00378:188:HV 1 TAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATC 50
vi
C L1PA3_3end#LI 303 TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATC 254
E00378:188:HV 51 CTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACT 100
i
C L1PA3_3end#LI 253 CTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACT 204
E00378:188:HV 101 GGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGC 150
C L1PA3_3end#LI 203 GGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGC 154
E00378:188:HV 151 C 151
C L1PA3_3end#LI 153 C 153
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1284 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:14022:28593/2 1 151 (0) + L1P1 LINE/L1 5231 5381 (765) 901
ANNOTATION EVIDENCE:
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:14022:28593/2 1 151 0 + L1P1_orf2 LINE/L1 3122 3272 22
1284 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:14022:28593/2 1 151 (0) L1P1_orf2#LINE/L1 3122 3272 (22) m_b1s551i152
E00378:188:HV 1 CAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC 50
L1P1_orf2#LIN 3122 CAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC 3171
E00378:188:HV 51 AAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAA 100
L1P1_orf2#LIN 3172 AAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAA 3221
E00378:188:HV 101 GGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAC 150
L1P1_orf2#LIN 3222 GGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAC 3271
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3272 A 3272
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 848 12.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:2514:21667/1 1 118 (33) C AluSx SINE/Alu (194) 118 1 902
ANNOTATION EVIDENCE:
848 12.71 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:2514:21667/1 1 118 33 C AluSx SINE/Alu 1 118 194
848 12.71 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:2514:21667/1 1 118 (33) C AluSx#SINE/Alu (194) 118 1 m_b2s357i41
E00378:188:HV 1 TAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGACC 50
ii i i
C AluSx#SINE/Al 118 TAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACC 69
E00378:188:HV 51 TCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGATTACAGATGT 100
i i v v v i ii
C AluSx#SINE/Al 68 TCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 19
E00378:188:HV 101 GAGCCACTGTGCCCAGCC 118
i i i
C AluSx#SINE/Al 18 GAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.81
Transitions / transversions = 4.00 (12/3)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0)
+ 572 9.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:26037:57952/1 1 83 (68) + L1P3 LINE/L1 3816 3898 (2248) 903
ANNOTATION EVIDENCE:
572 9.64 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:26037:57952/1 1 83 68 + L1P3_orf2 LINE/L1 1707 1789 1505
572 9.64 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:26037:57952/1 1 83 (68) L1P3_orf2#LINE/L1 1707 1789 (1505) m_b6s551i14
E00378:188:HV 1 GACGCAAGGCTGATTCAGCATACACAAATCAATAAACATAATCCATCACA 50
i i i i i
L1P3_orf2#LIN 1707 GATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAATCCATCACA 1756
E00378:188:HV 51 TAAACAGAACGAACGACAAAAACTACATGATTA 83
v i i
L1P3_orf2#LIN 1757 TAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.00
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 523 7.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:26037:57952/1 86 151 (0) + AluSx SINE/Alu 14 79 (233) 904
ANNOTATION EVIDENCE:
523 7.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:26037:57952/1 86 151 0 + AluSx SINE/Alu 14 79 233
523 7.58 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:26037:57952/1 86 151 (0) AluSx#SINE/Alu 14 79 (233) m_b6s357i21
E00378:188:HV 86 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 135
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 136 CCTGAGGTCAGGAGTT 151
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTT 79
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.57
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 30 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1208:26037:57952/2 17 44 (107) + (T)n Simple_repeat 1 28 (0) 905
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:26037:57952/2 17 44 107 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1208:26037:57952/2 17 44 (107) (T)n#Simple_repeat 1 28 (0) c_b6s251i10
E00378:188:HV 17 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 16 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1210:13494:36504/1 1 17 (134) + (A)n Simple_repeat 1 17 (0) 906
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:13494:36504/1 1 17 134 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:13494:36504/1 1 17 (134) (A)n#Simple_repeat 1 17 (0) m_b1s252i9
E00378:188:HV 1 AAAAAAAAAAAAAAAAA 17
(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)
+ 267 26.5 0.0 0.0 E00378:188:HVMVNCCXX:4:1210:13494:36504/1 79 146 (5) + L1M5 LINE/L1 5741 5808 (365) 907
ANNOTATION EVIDENCE:
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:13494:36504/1 79 146 5 + L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:13494:36504/1 79 146 (5) L1ME3A_3end#LINE/L1 488 555 (365) m_b1s551i520
E00378:188:HV 79 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 128
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
E00378:188:HV 129 ATAACAAAATAATATGCA 146
i iii v i
L1ME3A_3end#L 538 ACAATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 E00378:188:HVMVNCCXX:4:1210:13494:36504/2 19 107 (44) C L1M5 LINE/L1 (293) 5831 5741 908
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:4:1210:13494:36504/2 19 107 44 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 E00378:188:HVMVNCCXX:4:1210:13494:36504/2 19 107 (44) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i498
E00378:188:HV 19 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 68
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 69 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 107
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:13494:36504/2 40 107 44 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:13494:36504/2 40 107 (44) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i499
E00378:188:HV 40 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 89
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 90 CTATTGTTGGACATTTAG 107
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 463 18.4 5.8 0.0 E00378:188:HVMVNCCXX:4:1210:20618:33727/1 16 113 (38) + L1MC4 LINE/L1 7546 7649 (393) 909
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:4:1210:20618:33727/1 16 113 38 + L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:4:1210:20618:33727/1 16 113 (38) L1MC4_3end#LINE/L1 2293 2396 (393) m_b3s551i86
E00378:188:HV 16 GACCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA----- 60
i v v i v ? v i i i -----
L1MC4_3end#LI 2293 GGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTG 2342
E00378:188:HV 61 -AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 109
-i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
E00378:188:HV 110 AATG 113
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 3.00 (6 / 2)
+ 242 8.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1210:20618:33727/1 118 151 (0) + L1MC4 LINE/L1 7762 7795 (247) 909
ANNOTATION EVIDENCE:
242 8.82 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:20618:33727/1 118 151 0 + L1MC4_3end LINE/L1 2509 2542 247
242 8.82 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:20618:33727/1 118 151 (0) L1MC4_3end#LINE/L1 2509 2542 (247) m_b3s551i87
E00378:188:HV 118 AATGTTAACTTCCTGATTTTGATGATTATACTGT 151
i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGT 2542
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.71
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 571 20.8 6.7 0.8 E00378:188:HVMVNCCXX:4:1210:20618:33727/2 26 151 (0) C L1MC4 LINE/L1 (131) 7911 7778 910
ANNOTATION EVIDENCE:
571 20.79 6.71 0.79 E00378:188:HVMVNCCXX:4:1210:20618:33727/2 26 151 0 C L1MC4_3end LINE/L1 2525 2658 131
571 20.79 6.71 0.79 E00378:188:HVMVNCCXX:4:1210:20618:33727/2 26 151 (0) C L1MC4_3end#LINE/L1 (131) 2658 2525 m_b3s551i18
E00378:188:HV 26 ATACACACATCATTTTCTCTGAACCATTTTGAGATGAAATCGCACACGTG 75
i i iv i - vv i i v i ?
C L1MC4_3end#LI 2658 ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAGTTGCAGACATN 2610
E00378:188:HV 76 ATGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAACAAGGA 116
i --------- i i
C L1MC4_3end#LI 2609 ATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAACAAGGA 2560
E00378:188:HV 117 TACACTTCTGTTTAGCCACAGTATAATCATCAAAA 151
i iv ii iiv i i i
C L1MC4_3end#LI 2559 CATTCTCTTACATAACCACAGTACAATTATCAAAA 2525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.46
Transitions / transversions = 3.17 (19/6)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 5.00 (10 / 2)
+ 463 18.4 5.8 0.0 E00378:188:HVMVNCCXX:4:1210:25164:31125/1 16 113 (38) + L1MC4 LINE/L1 7546 7649 (393) 911
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:4:1210:25164:31125/1 16 113 38 + L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 E00378:188:HVMVNCCXX:4:1210:25164:31125/1 16 113 (38) L1MC4_3end#LINE/L1 2293 2396 (393) m_b3s551i88
E00378:188:HV 16 GACCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA----- 60
i v v i v ? v i i i -----
L1MC4_3end#LI 2293 GGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTG 2342
E00378:188:HV 61 -AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 109
-i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
E00378:188:HV 110 AATG 113
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 3.00 (6 / 2)
+ 242 8.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1210:25164:31125/1 118 151 (0) + L1MC4 LINE/L1 7762 7795 (247) 911
ANNOTATION EVIDENCE:
242 8.82 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:25164:31125/1 118 151 0 + L1MC4_3end LINE/L1 2509 2542 247
242 8.82 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:25164:31125/1 118 151 (0) L1MC4_3end#LINE/L1 2509 2542 (247) m_b3s551i89
E00378:188:HV 118 AATGTTAACTTCCTGATTTTGATGATTATACTGT 151
i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGT 2542
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.71
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 571 20.8 6.7 0.8 E00378:188:HVMVNCCXX:4:1210:25164:31125/2 26 151 (0) C L1MC4 LINE/L1 (131) 7911 7778 912
ANNOTATION EVIDENCE:
571 20.79 6.71 0.79 E00378:188:HVMVNCCXX:4:1210:25164:31125/2 26 151 0 C L1MC4_3end LINE/L1 2525 2658 131
571 20.79 6.71 0.79 E00378:188:HVMVNCCXX:4:1210:25164:31125/2 26 151 (0) C L1MC4_3end#LINE/L1 (131) 2658 2525 m_b3s551i19
E00378:188:HV 26 ATACACACATCATTTTCTCTGAACCATTTTGAGATGAAATCGCACACGTG 75
i i iv i - vv i i v i ?
C L1MC4_3end#LI 2658 ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAGTTGCAGACATN 2610
E00378:188:HV 76 ATGCTCCTT---------ATACTTCAGTGTATATTTCCTAAAAACAAGGA 116
i --------- i i
C L1MC4_3end#LI 2609 ATGCCCCTTTACCCCTAAATACTTCAGTGTGTATTTCCTAAGAACAAGGA 2560
E00378:188:HV 117 TACACTTCTGTTTAGCCACAGTATAATCATCAAAA 151
i iv ii iiv i i i
C L1MC4_3end#LI 2559 CATTCTCTTACATAACCACAGTACAATTATCAAAA 2525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.46
Transitions / transversions = 3.17 (19/6)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 5.00 (10 / 2)
+ 470 5.1 0.0 0.0 E00378:188:HVMVNCCXX:4:1210:27671:38280/1 3 61 (90) + AluSx SINE/Alu 240 298 (14) 913
ANNOTATION EVIDENCE:
470 5.08 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:27671:38280/1 3 61 90 + AluSx SINE/Alu 240 298 14
470 5.08 0.00 0.00 E00378:188:HVMVNCCXX:4:1210:27671:38280/1 3 61 (90) AluSx#SINE/Alu 240 298 (14) m_b2s357i114
E00378:188:HV 3 GCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 52
i
AluSx#SINE/Al 240 GCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 289
E00378:188:HV 53 GAAATAAAA 61
i v
AluSx#SINE/Al 290 AAAAAAAAA 298
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.29
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 250 24.6 6.2 3.9 E00378:188:HVMVNCCXX:4:1210:27671:38280/2 22 148 (3) + L1ME4c LINE/L1 5657 5786 (297) 914
ANNOTATION EVIDENCE:
250 24.59 6.15 3.94 E00378:188:HVMVNCCXX:4:1210:27671:38280/2 22 148 3 + L1ME4c_3end LINE/L1 404 533 297
250 24.59 6.15 3.94 E00378:188:HVMVNCCXX:4:1210:27671:38280/2 22 148 (3) L1ME4c_3end#LINE/L1 404 533 (297) m_b2s551i34
E00378:188:HV 22 AAGAAATAATTTAAAATATGAGAAAAAAAAACCCTTAGACA----AATGA 67
i i ----- ii v iv vi ----i v
L1ME4c_3end#L 404 AGGAAATAATTCAAAA-----GAAGGAAAAAGCTATATGCACGAAGATGT 448
E00378:188:HV 68 TCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCTAAATTT 115
iiiv i vi --i v i v i v
L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498
E00378:188:HV 116 CTGACAATAAAA-AATG-TCAAGTAAATTATGGTA 148
ii iii- - i
L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTA 533
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 764 14.5 0.0 5.1 E00378:188:HVMVNCCXX:4:1212:20050:33199/1 1 138 (13) + AluSx SINE/Alu 174 304 (8) 915
ANNOTATION EVIDENCE:
764 14.51 0.00 5.07 E00378:188:HVMVNCCXX:4:1212:20050:33199/1 1 138 13 + AluSx SINE/Alu 174 304 8
764 14.51 0.00 5.07 E00378:188:HVMVNCCXX:4:1212:20050:33199/1 1 138 (13) AluSx#SINE/Alu 174 304 (8) m_b5s357i26
E00378:188:HV 1 TCAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGC 50
i v i iivv
AluSx#SINE/Al 174 TCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGC 223
E00378:188:HV 51 AGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGG 100
v v v i ------- i ii
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG-------GGCGACAG 266
E00378:188:HV 101 AGTGAGACTCCATCTCAAAAAAACACAAAAACAAAAAA 138
i i v v v
AluSx#SINE/Al 267 AGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.30
Transitions / transversions = 1.11 (10/9)
Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.00 (7 / 7)
+ 1272 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1212:23236:6126/1 1 151 (0) C L1P1 LINE/L1 (753) 5393 5243 916
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:23236:6126/1 1 151 0 C L1P1_orf2 LINE/L1 3134 3284 10
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:23236:6126/1 1 151 (0) C L1P1_orf2#LINE/L1 (10) 3284 3134 m_b1s551i160
E00378:188:HV 1 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 50
C L1P1_orf2#LIN 3284 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 3235
E00378:188:HV 51 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 100
C L1P1_orf2#LIN 3234 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 3185
E00378:188:HV 101 TGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCA 150
C L1P1_orf2#LIN 3184 TGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCA 3135
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 3134 G 3134
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 3.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1212:23236:6126/2 1 151 (0) + L1P1 LINE/L1 4916 5066 (1080) 917
ANNOTATION EVIDENCE:
1274 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:23236:6126/2 1 151 0 + L1P1_orf2 LINE/L1 2807 2957 337
1274 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:23236:6126/2 1 151 (0) L1P1_orf2#LINE/L1 2807 2957 (337) m_b1s551i27
E00378:188:HV 1 GCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTC 50
L1P1_orf2#LIN 2807 GCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTC 2856
E00378:188:HV 51 CTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACAT 100
v v i i
L1P1_orf2#LIN 2857 CTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGT 2906
E00378:188:HV 101 TAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTC 150
?
L1P1_orf2#LIN 2907 TAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTC 2956
E00378:188:HV 151 A 151
L1P1_orf2#LIN 2957 A 2957
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1124 11.3 1.3 0.0 E00378:188:HVMVNCCXX:4:1212:28584:24356/1 1 151 (0) + AluSx SINE/Alu 18 170 (142) 918
ANNOTATION EVIDENCE:
1124 11.26 1.30 0.00 E00378:188:HVMVNCCXX:4:1212:28584:24356/1 1 151 0 + AluSx SINE/Alu 18 170 142
1124 11.26 1.30 0.00 E00378:188:HVMVNCCXX:4:1212:28584:24356/1 1 151 (0) AluSx#SINE/Alu 18 170 (142) m_b4s356i40
E00378:188:HV 1 CACACCTGTAATCCCAGCACTTTGGGAGGCTGAAGCAGGCAGATCAC--A 48
i i i i i --i
AluSx#SINE/Al 18 CACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTG 67
E00378:188:HV 49 AGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCT 98
i v i i i
AluSx#SINE/Al 68 AGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCT 117
E00378:188:HV 99 ACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCC 148
i i v iv i
AluSx#SINE/Al 118 ACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCC 167
E00378:188:HV 149 AGC 151
AluSx#SINE/Al 168 AGC 170
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.84
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 256 33.6 6.5 2.7 E00378:188:HVMVNCCXX:4:1212:28584:24356/2 5 151 (0) C MIRb SINE/MIR (76) 192 40 919
ANNOTATION EVIDENCE:
256 33.56 6.53 2.72 E00378:188:HVMVNCCXX:4:1212:28584:24356/2 5 151 0 C MIRb SINE/MIR 40 192 76
256 33.56 6.53 2.72 E00378:188:HVMVNCCXX:4:1212:28584:24356/2 5 151 (0) C MIRb#SINE/MIR (76) 192 40 m_b4s601i29
E00378:188:HV 5 TCTAATCCTCACAGTTATCTGGCCAGGTAAGTGATA-TATCTTCACTCTA 53
i iiv i iv v i iv - ii i i
C MIRb#SINE/MIR 192 TTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTA 143
E00378:188:HV 54 CTGATGAGGGTACGAAGGCCCTAGATGACATAAGGCAAGTTTTTTACCAG 103
v iv vi i - - vi v i i v viii --
C MIRb#SINE/MIR 142 CAGATGAGGAAACTGAGGCTC-AGA-GAGGTTAAGTAACTTGCCCA--AG 97
E00378:188:HV 104 A----AAAGTTA--AGGCTGTGGTACTGGGATTTGAATTT---TCTGTTT 144
i---- v i -- i iv ii vi i i iii--- i
C MIRb#SINE/MIR 96 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCT 47
E00378:188:HV 145 GACTTCA 151
i
C MIRb#SINE/MIR 46 GACTCCA 40
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 45.18
Transitions / transversions = 2.43 (34/14)
Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.75 (14 / 8)
+ 1218 6.7 0.0 0.7 E00378:188:HVMVNCCXX:4:1212:29498:19504/1 1 151 (0) + AluY SINE/Alu 143 292 (19) 920
ANNOTATION EVIDENCE:
1218 6.66 0.00 0.66 E00378:188:HVMVNCCXX:4:1212:29498:19504/1 1 151 0 + AluY SINE/Alu 143 292 19
1218 6.66 0.00 0.66 E00378:188:HVMVNCCXX:4:1212:29498:19504/1 1 151 (0) AluY#SINE/Alu 143 292 (19) m_b2s356i89
E00378:188:HV 1 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAG 50
i
AluY#SINE/Alu 143 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAG 192
E00378:188:HV 51 AACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCC 100
i i i - i v ii
AluY#SINE/Alu 193 AATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCC 241
E00378:188:HV 101 ACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAGAA 150
i i
AluY#SINE/Alu 242 ACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA 291
E00378:188:HV 151 A 151
AluY#SINE/Alu 292 A 292
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.79
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 248 25.8 5.0 1.5 E00378:188:HVMVNCCXX:4:1212:29498:19504/2 1 134 (17) + L1ME4c LINE/L1 5729 5867 (216) 921
ANNOTATION EVIDENCE:
248 25.75 5.03 1.49 E00378:188:HVMVNCCXX:4:1212:29498:19504/2 1 134 17 + L1ME4c_3end LINE/L1 476 614 216
248 25.75 5.03 1.49 E00378:188:HVMVNCCXX:4:1212:29498:19504/2 1 134 (17) L1ME4c_3end#LINE/L1 476 614 (216) m_b2s551i2
E00378:188:HV 1 AAAATAGAAAAGAATCTAAATTTCTGACAATAAAA-AATG-TCAAGTAAA 48
v i v i v ii iii- - i
L1ME4c_3end#L 476 AAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAA 525
E00378:188:HV 49 TTATGGTA--TTTAT--GACAGAAAAATGGTGAAGCCATTAAAAAGTATG 94
-- i? i-- ii v - vi v vv i
L1ME4c_3end#L 526 TTATGGTACATCNACTCGATGGAATA-TTATGCAGCCATTAAAAATGATA 574
E00378:188:HV 95 ACTATCAAGAAAA-GCAACTACCTGGAAAAATACTTATAAT 134
i v vv - i i v v - ii i
L1ME4c_3end#L 575 ATTATGAAGACTATGTAGCAACATGGAAAA-TGTTTATGAT 614
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.46
Transitions / transversions = 1.54 (20/13)
Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.29 (9 / 7)
+ 506 7.9 0.0 0.0 E00378:188:HVMVNCCXX:4:1212:6350:44837/2 1 63 (88) C AluSx SINE/Alu (34) 278 216 922
ANNOTATION EVIDENCE:
506 7.94 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:6350:44837/2 1 63 88 C AluSx SINE/Alu 216 278 34
506 7.94 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:6350:44837/2 1 63 (88) C AluSx#SINE/Alu (34) 278 216 m_b2s357i105
E00378:188:HV 1 CAGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATTTCGGC 50
i i ii i
C AluSx#SINE/Al 278 CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGC 229
E00378:188:HV 51 TCACTGCAACCTC 63
C AluSx#SINE/Al 228 TCACTGCAACCTC 216
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.79
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 898 11.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1212:9404:12578/1 37 151 (0) + AluY SINE/Alu 1 115 (196) 923
ANNOTATION EVIDENCE:
898 11.30 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:9404:12578/1 37 151 0 + AluY SINE/Alu 1 115 196
898 11.30 0.00 0.00 E00378:188:HVMVNCCXX:4:1212:9404:12578/1 37 151 (0) AluY#SINE/Alu 1 115 (196) m_b2s356i43
E00378:188:HV 37 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGGGGCCAA 86
i ii i i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 87 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 136
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 137 TGAAACCCCATCTCT 151
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCT 115
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.27
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.0 (0 / 0)
+ 727 8.9 0.0 1.0 E00378:188:HVMVNCCXX:4:1212:9404:12578/2 50 151 (0) C AluSx SINE/Alu (14) 298 198 924
ANNOTATION EVIDENCE:
727 8.91 0.00 0.98 E00378:188:HVMVNCCXX:4:1212:9404:12578/2 50 151 0 C AluSx SINE/Alu 198 298 14
727 8.91 0.00 0.98 E00378:188:HVMVNCCXX:4:1212:9404:12578/2 50 151 (0) C AluSx#SINE/Alu (14) 298 198 m_b2s357i100
E00378:188:HV 50 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 99
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 100 TGCAGTGGCATGATCGCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 149
ii v i - i v
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT-CCCGGGTTCAA 200
E00378:188:HV 150 GC 151
C AluSx#SINE/Al 199 GC 198
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.55
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1)
+ 817 16.2 0.0 1.4 E00378:188:HVMVNCCXX:4:1213:31467:6636/1 14 151 (0) C AluSx SINE/Alu (54) 258 123 925
ANNOTATION EVIDENCE:
817 16.17 0.00 1.45 E00378:188:HVMVNCCXX:4:1213:31467:6636/1 14 151 0 C AluSx SINE/Alu 123 258 54
817 16.17 0.00 1.45 E00378:188:HVMVNCCXX:4:1213:31467:6636/1 14 151 (0) C AluSx#SINE/Alu (54) 258 123 m_b5s356i3
E00378:188:HV 14 CAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTACAACCTCCGCCCAG 63
i v v v i ivv
C AluSx#SINE/Al 258 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCC 209
E00378:188:HV 64 TAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACA 113
ii i v i i iv
C AluSx#SINE/Al 208 CGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA 159
E00378:188:HV 114 GGCTCCCACCACAATGCCTGGCTAATTTTTTTGTATTT 151
v v i v i i --
C AluSx#SINE/Al 158 GGCGCGCGCCACCACGCCCGGCTAA--TTTTTGTATTT 123
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 12.45
Transitions / transversions = 1.20 (12/10)
Gap_init rate = 0.01 (2 / 137), avg. gap size = 1.00 (2 / 2)
+ 1321 1.3 0.0 0.7 E00378:188:HVMVNCCXX:4:1214:2575:24726/1 1 151 (0) + L1PA2 LINE/L1 5704 5853 (302) 926
ANNOTATION EVIDENCE:
1321 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:1214:2575:24726/1 1 151 0 + L1PA2_3end LINE/L1 451 600 302
1321 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:1214:2575:24726/1 1 151 (0) L1PA2_3end#LINE/L1 451 600 (302) m_b1s551i339
E00378:188:HV 1 GTGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 50
i
L1PA2_3end#LI 451 GCGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 500
E00378:188:HV 51 AATGATAGACTGGATTAAGAAACTGTGGCACATATACACCATGGAATACT 100
v
L1PA2_3end#LI 501 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 550
E00378:188:HV 101 ATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGAT 150
-
L1PA2_3end#LI 551 ATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGAT 599
E00378:188:HV 151 G 151
L1PA2_3end#LI 600 G 600
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.74
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1076 5.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1214:2575:24726/2 15 151 (0) C L1PA2 LINE/L1 (2) 6153 6017 927
ANNOTATION EVIDENCE:
1076 5.84 0.00 0.00 E00378:188:HVMVNCCXX:4:1214:2575:24726/2 15 151 0 C L1PA2_3end LINE/L1 764 900 2
1076 5.84 0.00 0.00 E00378:188:HVMVNCCXX:4:1214:2575:24726/2 15 151 (0) C L1PA2_3end#LINE/L1 (2) 900 764 m_b1s551i425
E00378:188:HV 15 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGG 64
v i v
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 65 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACGCACT 114
i v
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
E00378:188:HV 115 AACTCGTGATCTAGCATTAGGTATGTCTCCCATTGCT 151
v i v
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCTCCCAATGCT 764
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.37
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.0 (0 / 0)
+ 1278 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:1215:30766:25007/1 1 151 (0) + L1PA2 LINE/L1 5922 6072 (83) 928
ANNOTATION EVIDENCE:
1278 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1215:30766:25007/1 1 151 0 + L1PA2_3end LINE/L1 669 819 83
1278 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:1215:30766:25007/1 1 151 (0) L1PA2_3end#LINE/L1 669 819 (83) m_b1s551i388
E00378:188:HV 1 CATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATA 50
L1PA2_3end#LI 669 CATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATA 718
E00378:188:HV 51 TCACACTCTGTGGACTGTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCAT 100
v v
L1PA2_3end#LI 719 TCACACTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCAT 768
E00378:188:HV 101 TGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCA 150
i
L1PA2_3end#LI 769 TGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCA 818
E00378:188:HV 151 G 151
L1PA2_3end#LI 819 G 819
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 257 25.8 0.0 0.0 E00378:188:HVMVNCCXX:4:1215:30766:25007/2 1 66 (85) + L1M5 LINE/L1 5743 5808 (365) 929
ANNOTATION EVIDENCE:
257 25.76 0.00 0.00 E00378:188:HVMVNCCXX:4:1215:30766:25007/2 1 66 85 + L1ME3A_3end LINE/L1 490 555 365
257 25.76 0.00 0.00 E00378:188:HVMVNCCXX:4:1215:30766:25007/2 1 66 (85) L1ME3A_3end#LINE/L1 490 555 (365) m_b1s551i458
E00378:188:HV 1 AAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTACAT 50
v i i v vi ii i ii i
L1ME3A_3end#L 490 AAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCACAC 539
E00378:188:HV 51 AACAAAATAATATGCA 66
iii v i
L1ME3A_3end#L 540 AATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.54
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 548 4.2 0.0 0.0 E00378:188:HVMVNCCXX:4:1215:30766:25007/2 81 151 (0) C L1PA2 LINE/L1 (2) 6153 6083 930
ANNOTATION EVIDENCE:
548 4.23 0.00 0.00 E00378:188:HVMVNCCXX:4:1215:30766:25007/2 81 151 0 C L1PA2_3end LINE/L1 830 900 2
548 4.23 0.00 0.00 E00378:188:HVMVNCCXX:4:1215:30766:25007/2 81 151 (0) C L1PA2_3end#LINE/L1 (2) 900 830 m_b1s551i459
E00378:188:HV 81 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 130
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 131 AGGGTAGTTACATATGTATAC 151
v
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATAC 830
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.35
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 1228 4.0 1.3 0.0 E00378:188:HVMVNCCXX:4:1216:18182:37032/1 1 151 (0) C L1P3 LINE/L1 (2432) 3714 3562 931
ANNOTATION EVIDENCE:
1228 3.97 1.30 0.00 E00378:188:HVMVNCCXX:4:1216:18182:37032/1 1 151 0 C L1P3_orf2 LINE/L1 1453 1605 1689
1228 3.97 1.30 0.00 E00378:188:HVMVNCCXX:4:1216:18182:37032/1 1 151 (0) C L1P3_orf2#LINE/L1 (1689) 1605 1453 m_b6s551i86
E00378:188:HV 1 CACGGATAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTT 48
v v i--
C L1P3_orf2#LIN 1605 CAGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTT 1556
E00378:188:HV 49 TTGGAATCAGGATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCC 98
v v i
C L1P3_orf2#LIN 1555 TTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCC 1506
E00378:188:HV 99 TCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTC 148
C L1P3_orf2#LIN 1505 TCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTC 1456
E00378:188:HV 149 TTT 151
C L1P3_orf2#LIN 1455 TTT 1453
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.08
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1175 3.4 1.3 0.0 E00378:188:HVMVNCCXX:4:1216:18182:37032/2 3 151 (0) + L1P3 LINE/L1 3344 3494 (2652) 932
ANNOTATION EVIDENCE:
1175 3.36 1.32 0.00 E00378:188:HVMVNCCXX:4:1216:18182:37032/2 3 151 0 + L1P3_orf2 LINE/L1 1235 1385 1909
1175 3.36 1.32 0.00 E00378:188:HVMVNCCXX:4:1216:18182:37032/2 3 151 (0) L1P3_orf2#LINE/L1 1235 1385 (1909) m_b6s551i149
E00378:188:HV 3 GAAAATACTATAAACACCTCTACACAAATAAACTAGAAAATCTAGAAGAA 52
i i
L1P3_orf2#LIN 1235 GAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAA 1284
E00378:188:HV 53 ATGGATAAATTCCTGAACACATACAACCTCCCAA--CTAAAGCAGGAAGA 100
i v -- v
L1P3_orf2#LIN 1285 ATGGATAAATTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGA 1334
E00378:188:HV 101 AGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAA 150
L1P3_orf2#LIN 1335 AGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAA 1384
E00378:188:HV 151 T 151
L1P3_orf2#LIN 1385 T 1385
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.81
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:4:1217:16640:40970/2 27 71 (80) + MIR SINE/MIR 218 262 (0) 933
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:4:1217:16640:40970/2 27 71 80 + MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:4:1217:16640:40970/2 27 71 (80) MIR#SINE/MIR 218 262 (0) m_b6s601i10
E00378:188:HV 27 AATGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTATTTTT 71
i v iv viii i i v
MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 1133 6.1 0.0 0.7 E00378:188:HVMVNCCXX:4:1218:28432:54049/1 1 148 (3) C AluY SINE/Alu (26) 285 139 934
ANNOTATION EVIDENCE:
1133 6.12 0.00 0.68 E00378:188:HVMVNCCXX:4:1218:28432:54049/1 1 148 3 C AluY SINE/Alu 139 285 26
1133 6.12 0.00 0.68 E00378:188:HVMVNCCXX:4:1218:28432:54049/1 1 148 (3) C AluY#SINE/Alu (26) 285 139 m_b2s357i92
E00378:188:HV 1 TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATG 50
i ii
C AluY#SINE/Alu 285 TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCG 236
E00378:188:HV 51 ATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTG 100
v i - i i i
C AluY#SINE/Alu 235 ATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTG 187
E00378:188:HV 101 CTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 148
i
C AluY#SINE/Alu 186 CCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.14
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 1.00 (1 / 1)
+ 247 23.8 6.2 3.9 E00378:188:HVMVNCCXX:4:1218:30573:32373/2 11 137 (14) C L1ME4c LINE/L1 (297) 5786 5657 935
ANNOTATION EVIDENCE:
247 23.77 6.15 3.94 E00378:188:HVMVNCCXX:4:1218:30573:32373/2 11 137 14 C L1ME4c_3end LINE/L1 404 533 297
247 23.77 6.15 3.94 E00378:188:HVMVNCCXX:4:1218:30573:32373/2 11 137 (14) C L1ME4c_3end#LINE/L1 (297) 533 404 m_b2s551i32
E00378:188:HV 11 TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTT 58
i - -iii ii v i v
C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484
E00378:188:HV 59 TCTATTTTC--CTACAATAAACATTATTGCAATGATCATT----TGTCTA 102
i v i-- iv i viii v i---- iv
C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434
E00378:188:HV 103 AGGGTTTTTTTTTCTCATATTTGAAATTATTTCTT 137
vi v ii ---- - i
C L1ME4c_3end#L 433 TAGCTTTTTCCTTCT----TTTG-AATTATTTCCT 404
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.32
Transitions / transversions = 2.22 (20/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 1263 4.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1219:13900:52608/1 1 151 (0) + L1P3 LINE/L1 2873 3023 (3123) 936
ANNOTATION EVIDENCE:
1263 4.64 0.00 0.00 E00378:188:HVMVNCCXX:4:1219:13900:52608/1 1 151 0 + L1P3_orf2 LINE/L1 764 914 2380
1263 4.64 0.00 0.00 E00378:188:HVMVNCCXX:4:1219:13900:52608/1 1 151 (0) L1P3_orf2#LINE/L1 764 914 (2380) m_b7s551i37
E00378:188:HV 1 TGCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAAGT 50
i i v i?
L1P3_orf2#LIN 764 TGCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAAAN 813
E00378:188:HV 51 AAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTG 100
i i
L1P3_orf2#LIN 814 AAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTG 863
E00378:188:HV 101 GGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCC 150
L1P3_orf2#LIN 864 GGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCC 913
E00378:188:HV 151 A 151
L1P3_orf2#LIN 914 A 914
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 899 5.1 0.7 7.4 E00378:188:HVMVNCCXX:4:1219:13900:52608/2 2 150 (1) C L1P3 LINE/L1 (2916) 3230 3092 937
ANNOTATION EVIDENCE:
899 5.07 0.72 7.38 E00378:188:HVMVNCCXX:4:1219:13900:52608/2 2 150 1 C L1P3_orf2 LINE/L1 983 1121 2173
899 5.07 0.72 7.38 E00378:188:HVMVNCCXX:4:1219:13900:52608/2 2 150 (1) C L1P3_orf2#LINE/L1 (2173) 1121 983 m_b6s551i237
E00378:188:HV 2 TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTT 51
i i v -
C L1P3_orf2#LIN 1121 TCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTT 1073
E00378:188:HV 52 TTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGC 100
i i---------- -i v
C L1P3_orf2#LIN 1072 TTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGC 1033
E00378:188:HV 101 TCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCT 150
C L1P3_orf2#LIN 1032 TCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCT 983
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.57
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.08 (12 / 148), avg. gap size = 1.00 (12 / 12)
+ 218 29.2 15.6 0.0 E00378:188:HVMVNCCXX:4:1219:1529:64474/2 1 130 (21) + MIR SINE/MIR 109 262 (0) 938
ANNOTATION EVIDENCE:
218 29.23 15.58 0.00 E00378:188:HVMVNCCXX:4:1219:1529:64474/2 1 130 21 + MIR SINE/MIR 109 262 0
218 29.23 15.58 0.00 E00378:188:HVMVNCCXX:4:1219:1529:64474/2 1 130 (21) MIR#SINE/MIR 109 262 (0) m_b6s601i23
E00378:188:HV 1 CTCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATAGAAT 48
v iv i v -- i i v ii iv v i
MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTAC 158
E00378:188:HV 49 CTAAGTGACAGAAGTAT---AAGAATTAAG------AATAAACATAAA-- 87
vv v i iiv i ---i i i------ v ii --
MIR#SINE/MIR 159 CTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGC 208
E00378:188:HV 88 -----------TGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTAT 126
----------- v iv viii i i
MIR#SINE/MIR 209 GCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTAT 258
E00378:188:HV 127 TTTT 130
v
MIR#SINE/MIR 259 TATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.80
Transitions / transversions = 1.53 (23/15)
Gap_init rate = 0.04 (5 / 129), avg. gap size = 4.80 (24 / 5)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:4:1220:15219:48037/1 22 113 (38) C MIRb SINE/MIR (107) 161 67 939
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:1220:15219:48037/1 22 113 38 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:1220:15219:48037/1 22 113 (38) C MIRb#SINE/MIR (107) 161 67 m_b6s601i67
E00378:188:HV 22 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 69
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 70 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 113
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1253 3.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1220:2138:51746/1 1 151 (0) + L1P3 LINE/L1 2951 3101 (3045) 940
ANNOTATION EVIDENCE:
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:1220:2138:51746/1 1 151 0 + L1P3_orf2 LINE/L1 842 992 2302
1253 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:1220:2138:51746/1 1 151 (0) L1P3_orf2#LINE/L1 842 992 (2302) m_b7s551i5
E00378:188:HV 1 ACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGG 50
i
L1P3_orf2#LIN 842 ACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGG 891
E00378:188:HV 51 AAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAAT 100
? v i
L1P3_orf2#LIN 892 AAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAAT 941
E00378:188:HV 101 CAACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAA 150
i
L1P3_orf2#LIN 942 CGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAA 991
E00378:188:HV 151 A 151
L1P3_orf2#LIN 992 A 992
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1116 5.3 1.3 0.0 E00378:188:HVMVNCCXX:4:1220:2138:51746/2 1 151 (0) C L1P3 LINE/L1 (2667) 3479 3327 941
ANNOTATION EVIDENCE:
1116 5.30 1.30 0.00 E00378:188:HVMVNCCXX:4:1220:2138:51746/2 1 151 0 C L1P3_orf2 LINE/L1 1218 1370 1924
1116 5.30 1.30 0.00 E00378:188:HVMVNCCXX:4:1220:2138:51746/2 1 151 (0) C L1P3_orf2#LINE/L1 (1924) 1370 1218 m_b6s551i152
E00378:188:HV 1 TCAGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGCTTTAG 50
v
C L1P3_orf2#LIN 1370 TCAGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGGTTTAG 1321
E00378:188:HV 51 --TTGGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTT 98
-- v i vv
C L1P3_orf2#LIN 1320 TCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTT 1271
E00378:188:HV 99 CTAGTGTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGT 148
v i i
C L1P3_orf2#LIN 1270 CTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGT 1221
E00378:188:HV 149 ATT 151
C L1P3_orf2#LIN 1220 ATT 1218
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 26 57 (94) + (TG)n Simple_repeat 1 32 (0) 942
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 26 57 94 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 26 57 (94) (TG)n#Simple_repeat 1 32 (0) m_b4s252i47
E00378:188:HV 26 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 57
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 58 70 (81) + (TGTATG)n Simple_repeat 1 41 (0) 943
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 26 70 81 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 26 70 (81) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i46
E00378:188:HV 26 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 70
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 549 4.5 0.0 0.0 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 85 151 (0) C AluSx SINE/Alu (21) 291 225 944
ANNOTATION EVIDENCE:
549 4.48 0.00 0.00 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 85 151 0 C AluSx SINE/Alu 225 291 21
549 4.48 0.00 0.00 E00378:188:HVMVNCCXX:4:1220:25408:2786/1 85 151 (0) C AluSx#SINE/Alu (21) 291 225 m_b4s357i11
E00378:188:HV 85 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 134
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 135 GCGCGATCTCGGCTCAC 151
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCAC 225
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.24
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 941 10.7 1.6 0.0 E00378:188:HVMVNCCXX:4:1220:25408:2786/2 30 151 (0) + AluSx SINE/Alu 1 124 (188) 945
ANNOTATION EVIDENCE:
941 10.66 1.61 0.00 E00378:188:HVMVNCCXX:4:1220:25408:2786/2 30 151 0 + AluSx SINE/Alu 1 124 188
941 10.66 1.61 0.00 E00378:188:HVMVNCCXX:4:1220:25408:2786/2 30 151 (0) AluSx#SINE/Alu 1 124 (188) m_b4s356i56
E00378:188:HV 30 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 79
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 80 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 127
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 128 GGTGAAACTCCATCTCTACTAAAA 151
i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAA 124
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.96
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 121), avg. gap size = 2.00 (2 / 1)
+ 1185 11.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1222:4300:28769/1 1 151 (0) + AluSx SINE/Alu 87 237 (75) 946
ANNOTATION EVIDENCE:
1185 11.26 0.00 0.00 E00378:188:HVMVNCCXX:4:1222:4300:28769/1 1 151 0 + AluSx SINE/Alu 87 237 75
1185 11.26 0.00 0.00 E00378:188:HVMVNCCXX:4:1222:4300:28769/1 1 151 (0) AluSx#SINE/Alu 87 237 (75) m_b2s356i22
E00378:188:HV 1 AGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAAATACAAAAATTA 50
ii i v
AluSx#SINE/Al 87 AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTA 136
E00378:188:HV 51 GCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTACTCAGGAAGCTGAG 100
i i i v i i i
AluSx#SINE/Al 137 GCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAG 186
E00378:188:HV 101 GCAGGAGAATCACTTGAACTCAGGAGGCAGAGATTGCAGTGAGCTGAGAT 150
i i i i i i
AluSx#SINE/Al 187 GCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGAT 236
E00378:188:HV 151 C 151
AluSx#SINE/Al 237 C 237
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.54
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1070 2.4 0.0 0.0 E00378:188:HVMVNCCXX:4:1222:4300:28769/2 1 123 (28) + L1PA2 LINE/L1 6031 6153 (2) 947
ANNOTATION EVIDENCE:
1070 2.44 0.00 0.00 E00378:188:HVMVNCCXX:4:1222:4300:28769/2 1 123 28 + L1PA2_3end LINE/L1 778 900 2
1070 2.44 0.00 0.00 E00378:188:HVMVNCCXX:4:1222:4300:28769/2 1 123 (28) L1PA2_3end#LINE/L1 778 900 (2) m_b1s551i435
E00378:188:HV 1 TACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCAC 50
i
L1PA2_3end#LI 778 TACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCAC 827
E00378:188:HV 51 ATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAAC 100
L1PA2_3end#LI 828 ATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAAC 877
E00378:188:HV 101 TTAAAGTGTAATAAAAAAAATAA 123
i v
L1PA2_3end#LI 878 TTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.73
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0)
+ 330 27.1 3.5 0.0 E00378:188:HVMVNCCXX:4:1222:8542:1766/2 21 142 (9) + MIRb SINE/MIR 60 187 (75) 948
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:4:1222:8542:1766/2 21 142 9 + MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:4:1222:8542:1766/2 21 142 (9) MIR#SINE/MIR 60 187 (75) m_b6s601i56
E00378:188:HV 21 CTCGAGTCAACCACTTGTTAGCTCTGTGGCAT-AAGCAAGTTACTTTACC 69
i iv vi ii v i v -ii v
MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109
E00378:188:HV 70 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATAGAATC 117
v iv i v -- i i v ii iv v i
MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACC 159
E00378:188:HV 118 TAAGTGACAGAAGTAT---AAGAATTAA 142
vv v i iiv i ---i i
MIR#SINE/MIR 160 TACCTCATAGGGTTGTTGTGAGGATTAA 187
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:1222:8542:1766/2 21 112 39 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:1222:8542:1766/2 21 112 (39) MIRb#SINE/MIR 67 161 (107) m_b6s601i55
E00378:188:HV 21 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 69
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 70 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 112
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 453 15.7 0.0 0.0 E00378:188:HVMVNCCXX:4:1223:17726:24567/2 1 70 (81) C AluSx SINE/Alu (242) 70 1 949
ANNOTATION EVIDENCE:
453 15.71 0.00 0.00 E00378:188:HVMVNCCXX:4:1223:17726:24567/2 1 70 81 C AluSx SINE/Alu 1 70 242
453 15.71 0.00 0.00 E00378:188:HVMVNCCXX:4:1223:17726:24567/2 1 70 (81) C AluSx#SINE/Alu (242) 70 1 m_b2s357i56
E00378:188:HV 1 CCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGATTACAGAT 50
i i v v v i ii
C AluSx#SINE/Al 70 CCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
E00378:188:HV 51 GTGAGCCACTGTGCCCAGCC 70
i i i
C AluSx#SINE/Al 20 GTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.47
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 1239 7.3 0.0 0.0 E00378:188:HVMVNCCXX:4:1223:28381:62153/1 1 151 (0) + AluSx SINE/Alu 137 287 (25) 950
ANNOTATION EVIDENCE:
1239 7.28 0.00 0.00 E00378:188:HVMVNCCXX:4:1223:28381:62153/1 1 151 0 + AluSx SINE/Alu 137 287 25
1239 7.28 0.00 0.00 E00378:188:HVMVNCCXX:4:1223:28381:62153/1 1 151 (0) AluSx#SINE/Alu 137 287 (25) m_b4s356i6
E00378:188:HV 1 GCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAG 50
i v iv i i
AluSx#SINE/Al 137 GCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAG 186
E00378:188:HV 51 GCAGGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGAT 100
i i
AluSx#SINE/Al 187 GCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGAT 236
E00378:188:HV 101 CGCGCCACTGCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAA 150
i i i
AluSx#SINE/Al 237 CGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAA 286
E00378:188:HV 151 A 151
AluSx#SINE/Al 287 A 287
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 15 5.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1223:28381:62153/2 133 151 (0) + (TG)n Simple_repeat 1 19 (0) 951
ANNOTATION EVIDENCE:
15 5.56 0.00 0.00 E00378:188:HVMVNCCXX:4:1223:28381:62153/2 133 151 0 + (TG)n Simple_repeat 1 19 0
15 5.56 0.00 0.00 E00378:188:HVMVNCCXX:4:1223:28381:62153/2 133 151 (0) (TG)n#Simple_repeat 1 19 (0) m_b4s252i45
E00378:188:HV 133 TGTGTGTGTGTGTGTATGT 151
i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGT 19
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 871 11.0 1.7 0.0 E00378:188:HVMVNCCXX:4:1223:9343:56915/2 1 118 (33) C AluSx SINE/Alu (192) 120 1 952
ANNOTATION EVIDENCE:
871 11.02 1.66 0.00 E00378:188:HVMVNCCXX:4:1223:9343:56915/2 1 118 33 C AluSx SINE/Alu 1 120 192
871 11.02 1.66 0.00 E00378:188:HVMVNCCXX:4:1223:9343:56915/2 1 118 (33) C AluSx#SINE/Alu (192) 120 1 m_b4s357i43
E00378:188:HV 1 AGTAGAGATGGAGTTTCACCATATTGGCCAGGCTGTTCTCAAACTCCTGA 50
i i i v i
C AluSx#SINE/Al 120 AGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGA 71
E00378:188:HV 51 CCTT--GTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGT 98
i-- i i i i i
C AluSx#SINE/Al 70 CCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
E00378:188:HV 99 GTGAGCCACTGCACCCGGCC 118
i i
C AluSx#SINE/Al 20 GTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.13
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 2.00 (2 / 1)
+ 1298 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:1224:17604:51641/1 1 151 (0) C L1P1 LINE/L1 (1110) 5036 4886 953
ANNOTATION EVIDENCE:
1298 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1224:17604:51641/1 1 151 0 C L1P1_orf2 LINE/L1 2777 2927 367
1298 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:1224:17604:51641/1 1 151 (0) C L1P1_orf2#LINE/L1 (367) 2927 2777 m_b1s551i11
E00378:188:HV 1 GTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATT 50
i
C L1P1_orf2#LIN 2927 GTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATT 2878
E00378:188:HV 51 GATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATA 100
i v v
C L1P1_orf2#LIN 2877 AATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATA 2828
E00378:188:HV 101 TGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCC 150
C L1P1_orf2#LIN 2827 TGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCC 2778
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 2777 C 2777
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 471 17.9 6.8 14.6 E00378:188:HVMVNCCXX:4:2101:25631:17694/2 8 151 (0) + L1MC4 LINE/L1 7811 7942 (100) 954
ANNOTATION EVIDENCE:
471 17.89 6.82 14.58 E00378:188:HVMVNCCXX:4:2101:25631:17694/2 8 151 0 + L1MC4_3end LINE/L1 2558 2689 100
471 17.89 6.82 14.58 E00378:188:HVMVNCCXX:4:2101:25631:17694/2 8 151 (0) L1MC4_3end#LINE/L1 2558 2689 (100) m_b3s551i11
E00378:188:HV 8 TATCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGC 48
i i i --------- i
L1MC4_3end#LI 2558 TGTCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGC 2607
E00378:188:HV 49 ATCACGTGTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGT 98
? i v i i vv - i vi i i
L1MC4_3end#LI 2608 ATNATGTCTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTAT 2656
E00378:188:HV 99 ATCTGCGTATGAGTGTGTGTGTGGAGAGAGGGAATGATTAAGCAAATATG 148
-- ------------------ ? ? i v i
L1MC4_3end#LI 2657 AT--GC------------------ANANAGAGAATGATAAAGCAAATGTG 2686
E00378:188:HV 149 GTA 151
i
L1MC4_3end#LI 2687 GCA 2689
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.25
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.15 (22 / 143), avg. gap size = 1.36 (30 / 22)
+ 1333 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2101:27773:68447/1 1 150 (1) + L1P1 LINE/L1 5434 5583 (572) 955
ANNOTATION EVIDENCE:
1333 2.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2101:27773:68447/1 1 150 1 + L1PA3_3end LINE/L1 181 330 572
1333 2.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2101:27773:68447/1 1 150 (1) L1PA3_3end#LINE/L1 181 330 (572) m_b1s551i257
E00378:188:HV 1 ACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTC 50
i
L1PA3_3end#LI 181 ACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTC 230
E00378:188:HV 51 AGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTAC 100
iv
L1PA3_3end#LI 231 AGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTAC 280
E00378:188:HV 101 ACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGG 150
L1PA3_3end#LI 281 ACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGG 330
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1177 6.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2101:27773:68447/2 1 151 (0) C L1PA2 LINE/L1 (318) 5837 5687 956
ANNOTATION EVIDENCE:
1177 5.96 0.00 0.00 E00378:188:HVMVNCCXX:4:2101:27773:68447/2 1 151 0 C L1PA2_3end LINE/L1 434 584 318
1177 5.96 0.00 0.00 E00378:188:HVMVNCCXX:4:2101:27773:68447/2 1 151 (0) C L1PA2_3end#LINE/L1 (318) 584 434 m_b1s551i334
E00378:188:HV 1 AAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTA 50
C L1PA2_3end#LI 584 AAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTA 535
E00378:188:HV 51 TATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTTGTTT 100
v v v
C L1PA2_3end#LI 534 TATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTT 485
E00378:188:HV 101 GGTTCCAAGTCTTTTCGAGTGTGAATAATGCCACAATAAACATACTTTTG 150
v v v i v v
C L1PA2_3end#LI 484 GGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTG 435
E00378:188:HV 151 C 151
C L1PA2_3end#LI 434 C 434
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.59
Transitions / transversions = 0.12 (1/8)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 327 22.6 12.5 0.0 E00378:188:HVMVNCCXX:4:2101:28493:68570/1 24 107 (44) C L1MC4 LINE/L1 (513) 7529 7416 957
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:4:2101:28493:68570/1 24 107 44 C L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 E00378:188:HVMVNCCXX:4:2101:28493:68570/1 24 107 (44) C L1MC4a_3end#LINE/L1 (371) 2258 2163 m_b3s551i119
E00378:188:HV 24 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 68
iiv i i i i i -----
C L1MC4a_3end#L 2258 GTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGTT 2209
E00378:188:HV 69 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT----TCCTCTTCT 107
i --- i i iiii i i ---- v i
C L1MC4a_3end#L 2208 ATGCATTTTTGGCAAGAATACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 4.00 (12 / 3)
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:4:2101:28493:68570/1 24 98 53 C L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 E00378:188:HVMVNCCXX:4:2101:28493:68570/1 24 98 (53) C L1MC4_3end#LINE/L1 (513) 2276 2194 m_b3s551i120
E00378:188:HV 24 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 68
iiv i i i i -----
C L1MC4_3end#LI 2276 GTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTT 2227
E00378:188:HV 69 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT 98
i --- i ii iiii i i
C L1MC4_3end#LI 2226 ATGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 717 10.5 0.0 0.9 E00378:188:HVMVNCCXX:4:2101:29640:3928/1 1 106 (45) + AluY SINE/Alu 187 291 (20) 958
ANNOTATION EVIDENCE:
717 10.48 0.00 0.94 E00378:188:HVMVNCCXX:4:2101:29640:3928/1 1 106 45 + AluY SINE/Alu 187 291 20
717 10.48 0.00 0.94 E00378:188:HVMVNCCXX:4:2101:29640:3928/1 1 106 (45) AluY#SINE/Alu 187 291 (20) m_b2s357i98
E00378:188:HV 1 CAGGAGAACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGAT 50
i i i - i v
AluY#SINE/Alu 187 CAGGAGAATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGAT 235
E00378:188:HV 51 CATGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCGGCTCAAAA 100
ii i v
AluY#SINE/Alu 236 CGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAA 285
E00378:188:HV 101 AGAGAA 106
i i
AluY#SINE/Alu 286 AAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.50
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 4 35 (116) + (TG)n Simple_repeat 1 32 (0) 959
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 4 35 116 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 4 35 (116) (TG)n#Simple_repeat 1 32 (0) m_b4s252i44
E00378:188:HV 4 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 35
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 36 48 (103) + (TGTATG)n Simple_repeat 1 41 (0) 960
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 4 48 103 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 4 48 (103) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i43
E00378:188:HV 4 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 48
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 721 5.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 63 151 (0) C AluSx SINE/Alu (21) 291 203 961
ANNOTATION EVIDENCE:
721 5.62 0.00 0.00 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 63 151 0 C AluSx SINE/Alu 203 291 21
721 5.62 0.00 0.00 E00378:188:HVMVNCCXX:4:2102:15514:48089/1 63 151 (0) C AluSx#SINE/Alu (21) 291 203 m_b4s357i19
E00378:188:HV 63 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 112
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 113 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTT 151
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTT 203
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.73
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
+ 954 13.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2102:15514:48089/2 20 151 (0) + AluY SINE/Alu 1 132 (179) 962
ANNOTATION EVIDENCE:
954 13.64 0.00 0.00 E00378:188:HVMVNCCXX:4:2102:15514:48089/2 20 151 0 + AluY SINE/Alu 1 132 179
954 13.64 0.00 0.00 E00378:188:HVMVNCCXX:4:2102:15514:48089/2 20 151 (0) AluY#SINE/Alu 1 132 (179) m_b4s356i52
E00378:188:HV 20 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 69
i i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 70 AGCAGGCAGATCACAAGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGG 119
i i i i v i v v i i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
E00378:188:HV 120 TGAAACTCCATCTCTACTAAAAACACAAAAAA 151
i i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAA 132
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.19
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 929 8.9 0.0 0.8 E00378:188:HVMVNCCXX:4:2102:23419:19487/1 27 151 (0) C AluY SINE/Alu (14) 297 174 963
ANNOTATION EVIDENCE:
929 8.87 0.00 0.80 E00378:188:HVMVNCCXX:4:2102:23419:19487/1 27 151 0 C AluY SINE/Alu 174 297 14
929 8.87 0.00 0.80 E00378:188:HVMVNCCXX:4:2102:23419:19487/1 27 151 (0) C AluY#SINE/Alu (14) 297 174 m_b2s356i95
E00378:188:HV 27 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 76
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
E00378:188:HV 77 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 126
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
E00378:188:HV 127 GCCGTTCTCCTGCTTCAGCCTCCCG 151
i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCG 174
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.46
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 124), avg. gap size = 1.00 (1 / 1)
+ 702 11.2 2.0 0.0 E00378:188:HVMVNCCXX:4:2102:8420:11576/2 1 98 (53) C AluSx SINE/Alu (212) 100 1 964
ANNOTATION EVIDENCE:
702 11.22 2.00 0.00 E00378:188:HVMVNCCXX:4:2102:8420:11576/2 1 98 53 C AluSx SINE/Alu 1 100 212
702 11.22 2.00 0.00 E00378:188:HVMVNCCXX:4:2102:8420:11576/2 1 98 (53) C AluSx#SINE/Alu (212) 100 1 m_b4s357i52
E00378:188:HV 1 ATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCT 48
i v i i-- i i i
C AluSx#SINE/Al 100 ATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCC 51
E00378:188:HV 49 TCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCC 98
i i i i
C AluSx#SINE/Al 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 2.00 (2 / 1)
+ 1164 2.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2103:19654:54805/1 1 131 (20) C L1PA2 LINE/L1 (26) 6129 5999 965
ANNOTATION EVIDENCE:
1164 2.29 0.00 0.00 E00378:188:HVMVNCCXX:4:2103:19654:54805/1 1 131 20 C L1PA2_3end LINE/L1 746 876 26
1164 2.29 0.00 0.00 E00378:188:HVMVNCCXX:4:2103:19654:54805/1 1 131 (20) C L1PA2_3end#LINE/L1 (26) 876 746 m_b1s551i407
E00378:188:HV 1 TTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATG 50
C L1PA2_3end#LI 876 TTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATG 827
E00378:188:HV 51 TGCCATGCTGGTGTGCTGCACCCACTAACTCGTCATCTAGCATTAGGTAT 100
i
C L1PA2_3end#LI 826 TGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTAT 777
E00378:188:HV 101 ATCTCCCAATGCTATCCCTCCCGCCTCCTCC 131
v i
C L1PA2_3end#LI 776 ATCTCCCAATGCTATCCCTCCCCCCTCCCCC 746
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.62
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 1322 1.3 0.0 0.7 E00378:188:HVMVNCCXX:4:2103:19654:54805/2 1 151 (0) + L1PA2 LINE/L1 5696 5845 (310) 966
ANNOTATION EVIDENCE:
1322 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:2103:19654:54805/2 1 151 0 + L1PA2_3end LINE/L1 443 592 310
1322 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:2103:19654:54805/2 1 151 (0) L1PA2_3end#LINE/L1 443 592 (310) m_b1s551i335
E00378:188:HV 1 TGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAA 50
i
L1PA2_3end#LI 443 TGTTTATTGCGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAA 492
E00378:188:HV 51 TGTCCAACAATGATAGACTGGATTAAGAAACTGTGGCACATATACACCAT 100
v
L1PA2_3end#LI 493 TGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCAT 542
E00378:188:HV 101 GGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGG 150
-
L1PA2_3end#LI 543 GGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGG 591
E00378:188:HV 151 A 151
L1PA2_3end#LI 592 A 592
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.74
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1320 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2103:29031:52906/2 1 151 (0) C L1PA2 LINE/L1 (324) 5831 5681 967
ANNOTATION EVIDENCE:
1320 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2103:29031:52906/2 1 151 0 C L1PA2_3end LINE/L1 428 578 324
1320 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2103:29031:52906/2 1 151 (0) C L1PA2_3end#LINE/L1 (324) 578 428 m_b1s551i333
E00378:188:HV 1 ATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTG 50
C L1PA2_3end#LI 578 ATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTG 529
E00378:188:HV 51 CCACAGTTTCTTAATCCAGTCTATCATTTTTGGACATTTGGGTTGGTTCC 100
v v
C L1PA2_3end#LI 528 CCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCC 479
E00378:188:HV 101 AAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTG 150
i
C L1PA2_3end#LI 478 AAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTG 429
E00378:188:HV 151 T 151
C L1PA2_3end#LI 428 T 428
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 599 11.1 0.0 0.0 E00378:188:HVMVNCCXX:4:2103:3610:67058/1 71 151 (0) + AluY SINE/Alu 1 81 (230) 968
ANNOTATION EVIDENCE:
599 11.11 0.00 0.00 E00378:188:HVMVNCCXX:4:2103:3610:67058/1 71 151 0 + AluY SINE/Alu 1 81 230
599 11.11 0.00 0.00 E00378:188:HVMVNCCXX:4:2103:3610:67058/1 71 151 (0) AluY#SINE/Alu 1 81 (230) m_b2s357i67
E00378:188:HV 71 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 120
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 121 GGCGGGCTGATCATGAGGTCAGGAGATCAAG 151
v i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAG 81
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.61
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0)
+ 1168 8.0 0.0 0.7 E00378:188:HVMVNCCXX:4:2103:3610:67058/2 1 151 (0) C AluY SINE/Alu (35) 276 127 969
ANNOTATION EVIDENCE:
1168 8.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2103:3610:67058/2 1 151 0 C AluY SINE/Alu 127 276 35
1168 8.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2103:3610:67058/2 1 151 (0) C AluY#SINE/Alu (35) 276 127 m_b2s356i81
E00378:188:HV 1 GGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATCTCGGCT 50
i ii
C AluY#SINE/Alu 276 GGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCT 227
E00378:188:HV 51 CACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCCT 100
v i - i i i i
C AluY#SINE/Alu 226 CACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAGCCT 178
E00378:188:HV 101 CCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAACTTTT 150
iv i
C AluY#SINE/Alu 177 CCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTT 128
E00378:188:HV 151 T 151
C AluY#SINE/Alu 127 T 127
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2105:11606:34219/1 31 62 (89) + (CA)n Simple_repeat 1 32 (0) 970
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:11606:34219/1 31 62 89 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:11606:34219/1 31 62 (89) (CA)n#Simple_repeat 1 32 (0) m_b4s252i42
E00378:188:HV 31 CATACATGCACACACATACACACACACACACA 62
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 621 13.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2105:12946:52889/1 1 88 (63) C AluSx SINE/Alu (224) 88 1 971
ANNOTATION EVIDENCE:
621 13.64 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:12946:52889/1 1 88 63 C AluSx SINE/Alu 1 88 224
621 13.64 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:12946:52889/1 1 88 (63) C AluSx#SINE/Alu (224) 88 1 m_b5s357i62
E00378:188:HV 1 CTGGTCCCAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAA 50
i i i i i i
C AluSx#SINE/Al 88 CTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA 39
E00378:188:HV 51 AGTGTTGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 88
i i vi i i
C AluSx#SINE/Al 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.72
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0)
+ 1317 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2105:6573:29332/1 1 151 (0) + L1P1 LINE/L1 5383 5533 (622) 972
ANNOTATION EVIDENCE:
1317 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:6573:29332/1 1 151 0 + L1PA2_3end LINE/L1 130 280 622
1317 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:6573:29332/1 1 151 (0) L1PA2_3end#LINE/L1 130 280 (622) m_b1s551i233
E00378:188:HV 1 ATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAAC 50
L1PA2_3end#LI 130 ATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAAC 179
E00378:188:HV 51 CACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGT 100
i
L1PA2_3end#LI 180 CACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGT 229
E00378:188:HV 101 CAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTA 150
iv
L1PA2_3end#LI 230 CAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTA 279
E00378:188:HV 151 C 151
L1PA2_3end#LI 280 C 280
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1323 1.3 0.0 0.7 E00378:188:HVMVNCCXX:4:2105:6573:29332/2 1 151 (0) C L1PA2 LINE/L1 (309) 5846 5697 973
ANNOTATION EVIDENCE:
1323 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:2105:6573:29332/2 1 151 0 C L1PA2_3end LINE/L1 444 593 309
1323 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:2105:6573:29332/2 1 151 (0) C L1PA2_3end#LINE/L1 (309) 593 444 m_b1s551i336
E00378:188:HV 1 GTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATT 50
-
C L1PA2_3end#LI 593 GTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATT 545
E00378:188:HV 51 CCATGGTGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGA 100
v
C L1PA2_3end#LI 544 CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGA 495
E00378:188:HV 101 CATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAA 150
i
C L1PA2_3end#LI 494 CATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAA 445
E00378:188:HV 151 C 151
C L1PA2_3end#LI 444 C 444
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.74
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1317 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2105:8542:30949/1 1 151 (0) + L1P1 LINE/L1 5383 5533 (622) 974
ANNOTATION EVIDENCE:
1317 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:8542:30949/1 1 151 0 + L1PA2_3end LINE/L1 130 280 622
1317 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2105:8542:30949/1 1 151 (0) L1PA2_3end#LINE/L1 130 280 (622) m_b1s551i234
E00378:188:HV 1 ATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAAC 50
L1PA2_3end#LI 130 ATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAAC 179
E00378:188:HV 51 CACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGT 100
i
L1PA2_3end#LI 180 CACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGT 229
E00378:188:HV 101 CAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTA 150
iv
L1PA2_3end#LI 230 CAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTA 279
E00378:188:HV 151 C 151
L1PA2_3end#LI 280 C 280
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1323 1.3 0.0 0.7 E00378:188:HVMVNCCXX:4:2105:8542:30949/2 1 151 (0) C L1PA2 LINE/L1 (309) 5846 5697 975
ANNOTATION EVIDENCE:
1323 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:2105:8542:30949/2 1 151 0 C L1PA2_3end LINE/L1 444 593 309
1323 1.33 0.00 0.66 E00378:188:HVMVNCCXX:4:2105:8542:30949/2 1 151 (0) C L1PA2_3end#LINE/L1 (309) 593 444 m_b1s551i337
E00378:188:HV 1 GTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATT 50
-
C L1PA2_3end#LI 593 GTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATT 545
E00378:188:HV 51 CCATGGTGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGA 100
v
C L1PA2_3end#LI 544 CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGA 495
E00378:188:HV 101 CATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAA 150
i
C L1PA2_3end#LI 494 CATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAA 445
E00378:188:HV 151 C 151
C L1PA2_3end#LI 444 C 444
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.74
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1275 0.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2106:7710:72086/1 1 151 (0) C L1P1 LINE/L1 (822) 5324 5174 976
ANNOTATION EVIDENCE:
1275 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2106:7710:72086/1 1 151 0 C L1P1_orf2 LINE/L1 3065 3215 79
1275 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2106:7710:72086/1 1 151 (0) C L1P1_orf2#LINE/L1 (79) 3215 3065 m_b1s551i132
E00378:188:HV 1 CACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 50
C L1P1_orf2#LIN 3215 CACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTC 3166
E00378:188:HV 51 ATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAA 100
C L1P1_orf2#LIN 3165 ATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAA 3116
E00378:188:HV 101 TTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTT 150
i
C L1P1_orf2#LIN 3115 TTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTT 3066
E00378:188:HV 151 G 151
C L1P1_orf2#LIN 3065 G 3065
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1259 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2106:7710:72086/2 1 151 (0) + L1P1 LINE/L1 4989 5139 (1007) 977
ANNOTATION EVIDENCE:
1259 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2106:7710:72086/2 1 151 0 + L1P1_orf2 LINE/L1 2880 3030 264
1259 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2106:7710:72086/2 1 151 (0) L1P1_orf2#LINE/L1 2880 3030 (264) m_b1s551i61
E00378:188:HV 1 TTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCC 50
i
L1P1_orf2#LIN 2880 TTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCC 2929
E00378:188:HV 51 TAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGAC 100
?
L1P1_orf2#LIN 2930 TAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGAC 2979
E00378:188:HV 101 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAA 150
v i
L1P1_orf2#LIN 2980 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA 3029
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3030 A 3030
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 689 10.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2107:19725:67058/2 1 90 (61) C AluY SINE/Alu (221) 90 1 978
ANNOTATION EVIDENCE:
689 10.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2107:19725:67058/2 1 90 61 C AluY SINE/Alu 1 90 221
689 10.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2107:19725:67058/2 1 90 (61) C AluY#SINE/Alu (221) 90 1 m_b2s357i68
E00378:188:HV 1 CAGGATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCCTTGGCCTCCC 50
i i v i
C AluY#SINE/Alu 90 CAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCC 41
E00378:188:HV 51 AAAGTGCTGAGATTACAAGCGTGAGCCACCATGCCTGGCC 90
i i ii i
C AluY#SINE/Alu 40 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.13
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0)
+ 1148 8.7 0.7 0.7 E00378:188:HVMVNCCXX:4:2107:22130:25833/1 1 151 (0) C AluY SINE/Alu (58) 253 103 979
ANNOTATION EVIDENCE:
1148 8.67 0.66 0.66 E00378:188:HVMVNCCXX:4:2107:22130:25833/1 1 151 0 C AluY SINE/Alu 103 253 58
1148 8.67 0.66 0.66 E00378:188:HVMVNCCXX:4:2107:22130:25833/1 1 151 (0) C AluY#SINE/Alu (58) 253 103 m_b2s356i72
E00378:188:HV 1 CTGGAATGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAG 50
i ii v i - i
C AluY#SINE/Alu 253 CTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGG 205
E00378:188:HV 51 GTTCATGCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGC 100
i i i
C AluY#SINE/Alu 204 GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 155
E00378:188:HV 101 GCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGAGATGGGGT 149
iv - i i
C AluY#SINE/Alu 154 GCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 105
E00378:188:HV 150 TT 151
C AluY#SINE/Alu 104 TT 103
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 644 20.1 6.3 0.7 E00378:188:HVMVNCCXX:4:2107:9557:16850/1 1 135 (16) + L1MC4 LINE/L1 7769 7911 (131) 980
ANNOTATION EVIDENCE:
644 20.15 6.30 0.74 E00378:188:HVMVNCCXX:4:2107:9557:16850/1 1 135 16 + L1MC4_3end LINE/L1 2516 2658 131
644 20.15 6.30 0.74 E00378:188:HVMVNCCXX:4:2107:9557:16850/1 1 135 (16) L1MC4_3end#LINE/L1 2516 2658 (131) m_b3s551i22
E00378:188:HV 1 ACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGTATCCTTG 50
i i i i vii ii vi i
L1MC4_3end#LI 2516 ATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAATGTCCTTG 2565
E00378:188:HV 51 TTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCATCACGTG 91
i i --------- i ? i v
L1MC4_3end#LI 2566 TTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCATNATGTC 2615
E00378:188:HV 92 TGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTAT 135
i i vv - i vi i i
L1MC4_3end#LI 2616 TGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.59
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 5.00 (10 / 2)
+ 25 3.5 0.0 0.0 E00378:188:HVMVNCCXX:4:2108:20912:31318/1 3 32 (119) + (A)n Simple_repeat 1 30 (0) 981
ANNOTATION EVIDENCE:
25 3.45 0.00 0.00 E00378:188:HVMVNCCXX:4:2108:20912:31318/1 3 32 119 + (A)n Simple_repeat 1 30 0
25 3.45 0.00 0.00 E00378:188:HVMVNCCXX:4:2108:20912:31318/1 3 32 (119) (A)n#Simple_repeat 1 30 (0) m_b6s252i13
E00378:188:HV 3 AAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 32
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:4:2108:20912:31318/2 23 114 (37) C MIRb SINE/MIR (107) 161 67 982
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:2108:20912:31318/2 23 114 37 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:2108:20912:31318/2 23 114 (37) C MIRb#SINE/MIR (107) 161 67 m_b6s601i65
E00378:188:HV 23 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 70
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 71 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 114
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1129 4.6 1.3 0.0 E00378:188:HVMVNCCXX:4:2108:6400:12894/1 1 151 (0) C L1P3 LINE/L1 (2671) 3475 3323 983
ANNOTATION EVIDENCE:
1129 4.64 1.30 0.00 E00378:188:HVMVNCCXX:4:2108:6400:12894/1 1 151 0 C L1P3_orf2 LINE/L1 1214 1366 1928
1129 4.64 1.30 0.00 E00378:188:HVMVNCCXX:4:2108:6400:12894/1 1 151 (0) C L1P3_orf2#LINE/L1 (1928) 1366 1214 m_b6s551i153
E00378:188:HV 1 AACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGCTTTAG--TT 48
v --
C L1P3_orf2#LIN 1366 AACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCTGGTTTAGTCTT 1317
E00378:188:HV 49 GGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCTAG 98
v i vv
C L1P3_orf2#LIN 1316 GGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCTAG 1267
E00378:188:HV 99 TTTATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTT 148
i i
C L1P3_orf2#LIN 1266 TTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTT 1217
E00378:188:HV 149 CTG 151
C L1P3_orf2#LIN 1216 CTG 1214
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1051 4.2 0.7 0.0 E00378:188:HVMVNCCXX:4:2108:6400:12894/2 1 142 (9) + L1P3 LINE/L1 3024 3166 (2980) 984
ANNOTATION EVIDENCE:
1051 4.23 0.70 0.00 E00378:188:HVMVNCCXX:4:2108:6400:12894/2 1 142 9 + L1P3_orf2 LINE/L1 915 1057 2237
1051 4.23 0.70 0.00 E00378:188:HVMVNCCXX:4:2108:6400:12894/2 1 142 (9) L1P3_orf2#LINE/L1 915 1057 (2237) m_b6s551i259
E00378:188:HV 1 CAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAA 50
? v i i
L1P3_orf2#LIN 915 CANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAA 964
E00378:188:HV 51 AAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAA 100
L1P3_orf2#LIN 965 AAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAA 1014
E00378:188:HV 101 GAAATAACTAAGATCAGAGCGGAG-TGAAGGAGATAGAGACAC 142
i i-
L1P3_orf2#LIN 1015 GAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGACAC 1057
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.31
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.01 (1 / 141), avg. gap size = 1.00 (1 / 1)
+ 1340 1.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:16447:49074/1 1 151 (0) C L1P1 LINE/L1 (331) 5824 5674 985
ANNOTATION EVIDENCE:
1340 1.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16447:49074/1 1 151 0 C L1PA2_3end LINE/L1 421 571 331
1340 1.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16447:49074/1 1 151 (0) C L1PA2_3end#LINE/L1 (331) 571 421 m_b1s551i327
E00378:188:HV 1 CATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGT 50
v
C L1PA2_3end#LI 571 CATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATT 522
E00378:188:HV 51 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 100
C L1PA2_3end#LI 521 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 472
E00378:188:HV 101 TGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTAT 150
i
C L1PA2_3end#LI 471 TGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTAT 422
E00378:188:HV 151 A 151
C L1PA2_3end#LI 421 A 421
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.73
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1295 0.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:16447:49074/2 1 151 (0) + L1P1 LINE/L1 5195 5345 (801) 986
ANNOTATION EVIDENCE:
1295 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16447:49074/2 1 151 0 + L1P1_orf2 LINE/L1 3086 3236 58
1295 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16447:49074/2 1 151 (0) L1P1_orf2#LINE/L1 3086 3236 (58) m_b1s551i138
E00378:188:HV 1 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCT 50
i
L1P1_orf2#LIN 3086 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCT 3135
E00378:188:HV 51 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 100
L1P1_orf2#LIN 3136 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 3185
E00378:188:HV 101 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAC 150
L1P1_orf2#LIN 3186 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAC 3235
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3236 A 3236
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1320 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:16467:49179/1 1 151 (0) C L1P1 LINE/L1 (331) 5824 5674 987
ANNOTATION EVIDENCE:
1320 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16467:49179/1 1 151 0 C L1PA2_3end LINE/L1 421 571 331
1320 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16467:49179/1 1 151 (0) C L1PA2_3end#LINE/L1 (331) 571 421 m_b1s551i328
E00378:188:HV 1 CATCATTTTTTATGGCTGCATAGTATTCCATGGGGTATATGTGCCACAGT 50
v v
C L1PA2_3end#LI 571 CATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATT 522
E00378:188:HV 51 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 100
C L1PA2_3end#LI 521 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 472
E00378:188:HV 101 TGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTAT 150
i
C L1PA2_3end#LI 471 TGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTAT 422
E00378:188:HV 151 A 151
C L1PA2_3end#LI 421 A 421
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1274 1.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:16467:49179/2 1 151 (0) + L1P1 LINE/L1 5195 5345 (801) 988
ANNOTATION EVIDENCE:
1274 1.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16467:49179/2 1 151 0 + L1P1_orf2 LINE/L1 3086 3236 58
1274 1.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:16467:49179/2 1 151 (0) L1P1_orf2#LINE/L1 3086 3236 (58) m_b1s551i139
E00378:188:HV 1 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCT 50
i
L1P1_orf2#LIN 3086 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCT 3135
E00378:188:HV 51 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 100
L1P1_orf2#LIN 3136 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 3185
E00378:188:HV 101 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATAAACAGAC 150
i
L1P1_orf2#LIN 3186 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAC 3235
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3236 A 3236
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 37 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:24799:30316/1 115 148 (3) + (T)n Simple_repeat 1 34 (0) 989
ANNOTATION EVIDENCE:
37 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:24799:30316/1 115 148 3 + (T)n Simple_repeat 1 34 0
37 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:24799:30316/1 115 148 (3) (T)n#Simple_repeat 1 34 (0) c_b6s251i9
E00378:188:HV 115 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 148
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 341 6.1 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:24799:30316/2 1 49 (102) + L1P3 LINE/L1 3850 3898 (2248) 990
ANNOTATION EVIDENCE:
341 6.12 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:24799:30316/2 1 49 102 + L1P3_orf2 LINE/L1 1741 1789 1505
341 6.12 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:24799:30316/2 1 49 (102) L1P3_orf2#LINE/L1 1741 1789 (1505) m_b6s551i5
E00378:188:HV 1 AACATAATCCATCACATAAACAGAACGAATGACAAAAACTACATGATTA 49
i v i
L1P3_orf2#LIN 1741 AACGTAATCCATCACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.42
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 844 8.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2109:24799:30316/2 52 151 (0) + AluSx SINE/Alu 14 113 (199) 991
ANNOTATION EVIDENCE:
844 8.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:24799:30316/2 52 151 0 + AluSx SINE/Alu 14 113 199
844 8.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2109:24799:30316/2 52 151 (0) AluSx#SINE/Alu 14 113 (199) m_b6s356i22
E00378:188:HV 52 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 101
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 102 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCAT 151
i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.60
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0)
+ 15 10.7 3.3 0.0 E00378:188:HVMVNCCXX:4:2109:7831:67023/1 120 149 (2) + (TTTATT)n Simple_repeat 1 31 (0) 992
ANNOTATION EVIDENCE:
15 10.73 3.33 0.00 E00378:188:HVMVNCCXX:4:2109:7831:67023/1 120 149 2 + (TTTATT)n Simple_repeat 1 31 0
15 10.73 3.33 0.00 E00378:188:HVMVNCCXX:4:2109:7831:67023/1 120 149 (2) (TTTATT)n#Simple_repeat 1 31 (0) m_b2s252i6
E00378:188:HV 120 TTTATTTTT-TTTTTATTTTTACTTGAATTT 149
- i vv
(TTTATT)n#Sim 1 TTTATTTTTATTTTTATTTTTATTTTTATTT 31
Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1)
+ 296 10.2 3.9 0.0 E00378:188:HVMVNCCXX:4:2109:7831:67023/2 102 150 (1) C 7SLRNA srpRNA (4) 316 266 993
ANNOTATION EVIDENCE:
296 10.20 3.92 0.00 E00378:188:HVMVNCCXX:4:2109:7831:67023/2 102 150 1 C 7SLRNA SINE/Alu 266 316 4
296 10.20 3.92 0.00 E00378:188:HVMVNCCXX:4:2109:7831:67023/2 102 150 (1) C 7SLRNA#SINE/Alu (4) 316 266 m_b2s502i3
E00378:188:HV 102 TTTTATTTCTTTTTTT--GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 149
v i -- i v i
C 7SLRNA#SINE/A 316 TTTTTTTTTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGG 267
E00378:188:HV 150 A 150
C 7SLRNA#SINE/A 266 A 266
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.04
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.02 (1 / 48), avg. gap size = 2.00 (2 / 1)
+ 776 17.1 0.0 1.4 E00378:188:HVMVNCCXX:4:2110:26687:58444/1 9 150 (1) C AluSx SINE/Alu (8) 304 165 994
ANNOTATION EVIDENCE:
776 17.14 0.00 1.41 E00378:188:HVMVNCCXX:4:2110:26687:58444/1 9 150 1 C AluSx SINE/Alu 165 304 8
776 17.14 0.00 1.41 E00378:188:HVMVNCCXX:4:2110:26687:58444/1 9 150 (1) C AluSx#SINE/Alu (8) 304 165 m_b2s357i13
E00378:188:HV 9 TTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTTCGTCAAACCCA 58
i ii i--
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCA 257
E00378:188:HV 59 GGCTGGGGGGCAGTGGCATGATCTCAGCTCCCTGCAATCTCTGCCTCCTT 108
i v ii i v i i iv
C AluSx#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCG 207
E00378:188:HV 109 GGGTGAAGTGGTTTTCCTGCCCCAGCTTCCTGGGTGGCTGGG 150
v v i i i i i i i i
C AluSx#SINE/Al 206 GGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGG 165
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 12.48
Transitions / transversions = 3.80 (19/5)
Gap_init rate = 0.01 (2 / 141), avg. gap size = 1.00 (2 / 2)
+ 474 15.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2110:26687:58444/2 79 150 (1) + AluSx SINE/Alu 1 72 (240) 995
ANNOTATION EVIDENCE:
474 15.28 0.00 0.00 E00378:188:HVMVNCCXX:4:2110:26687:58444/2 79 150 1 + AluSx SINE/Alu 1 72 240
474 15.28 0.00 0.00 E00378:188:HVMVNCCXX:4:2110:26687:58444/2 79 150 (1) AluSx#SINE/Alu 1 72 (240) m_b2s357i54
E00378:188:HV 79 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 128
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 129 GCCAGGTGGATCACCTGAGGTC 150
v i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTC 72
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.22
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 456 22.2 7.7 0.9 E00378:188:HVMVNCCXX:4:2110:30259:18713/2 1 109 (42) + L1MC4 LINE/L1 7795 7911 (131) 996
ANNOTATION EVIDENCE:
456 22.22 7.70 0.92 E00378:188:HVMVNCCXX:4:2110:30259:18713/2 1 109 42 + L1MC4_3end LINE/L1 2542 2658 131
456 22.22 7.70 0.92 E00378:188:HVMVNCCXX:4:2110:30259:18713/2 1 109 (42) L1MC4_3end#LINE/L1 2542 2658 (131) m_b3s551i14
E00378:188:HV 1 TGGCTAAACAGAAGTGTATCCTTGTTTTTAGGAAATATACACTGAAGTAT 50
i vii ii vi i i i
L1MC4_3end#LI 2542 TGGTTATGTAAGAGAATGTCCTTGTTCTTAGGAAATACACACTGAAGTAT 2591
E00378:188:HV 51 ---------AAGGAGCATCACGTGTGCGATTTCATCTCAAAATGGTTCAG 91
--------- i ? i v i i vv -
L1MC4_3end#LI 2592 TTAGGGGTAAAGGGGCATNATGTCTGCAACTTACTCTCAAA-TGGTTCAG 2640
E00378:188:HV 92 AGAAAATGATGTGTGTAT 109
i vi i i
L1MC4_3end#LI 2641 AAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.38
Transitions / transversions = 2.83 (17/6)
Gap_init rate = 0.02 (2 / 108), avg. gap size = 5.00 (10 / 2)
+ 489 12.1 0.0 0.0 E00378:188:HVMVNCCXX:4:2110:6644:45101/1 1 66 (85) C AluY SINE/Alu (245) 66 1 997
ANNOTATION EVIDENCE:
489 12.12 0.00 0.00 E00378:188:HVMVNCCXX:4:2110:6644:45101/1 1 66 85 C AluY SINE/Alu 1 66 245
489 12.12 0.00 0.00 E00378:188:HVMVNCCXX:4:2110:6644:45101/1 1 66 (85) C AluY#SINE/Alu (245) 66 1 m_b4s357i63
E00378:188:HV 1 TTGTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGA 50
i i i i i i
C AluY#SINE/Alu 66 TCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA 17
E00378:188:HV 51 GCCACTGCACCCGGCC 66
i i
C AluY#SINE/Alu 16 GCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.64
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 1090 12.8 0.0 1.3 E00378:188:HVMVNCCXX:4:2111:31903:45048/2 1 151 (0) C AluSx SINE/Alu (40) 272 124 998
ANNOTATION EVIDENCE:
1090 12.75 0.00 1.32 E00378:188:HVMVNCCXX:4:2111:31903:45048/2 1 151 0 C AluSx SINE/Alu 124 272 40
1090 12.75 0.00 1.32 E00378:188:HVMVNCCXX:4:2111:31903:45048/2 1 151 (0) C AluSx#SINE/Alu (40) 272 124 m_b2s356i6
E00378:188:HV 1 CTCGCTTCGTCAAACCCAGGCTGGAGTGCAGTGGCATGATCTCAGCTCAC 50
ii i-- ii i
C AluSx#SINE/Al 272 CTCGCTCTGTCG--CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCAC 225
E00378:188:HV 51 TGCAATCTCTGCCTCCTGAGTTCAAGTGATTCTCCTGCCTCAGCTTCCTG 100
i i i i i i i
C AluSx#SINE/Al 224 TGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCG 175
E00378:188:HV 101 AGTAGCTGGGATTACAGGTGCCCACCACCATACCCAGCTAATTTTTGTAT 150
i v i ii i
C AluSx#SINE/Al 174 AGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTAT 125
E00378:188:HV 151 T 151
C AluSx#SINE/Al 124 T 124
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.72
Transitions / transversions = 18.00 (18/1)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 951 9.0 0.0 0.7 E00378:188:HVMVNCCXX:4:2112:9891:9730/2 16 150 (1) C AluY SINE/Alu (14) 297 164 999
ANNOTATION EVIDENCE:
951 8.96 0.00 0.74 E00378:188:HVMVNCCXX:4:2112:9891:9730/2 16 150 1 C AluY SINE/Alu 164 297 14
951 8.96 0.00 0.74 E00378:188:HVMVNCCXX:4:2112:9891:9730/2 16 150 (1) C AluY#SINE/Alu (14) 297 164 m_b2s357i96
E00378:188:HV 16 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 65
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
E00378:188:HV 66 TGCAGTGGCGTGATCTCGGCTCGCTGCAACCTCCACCTCCCCATGTTCAT 115
i i v i - iv i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
E00378:188:HV 116 GCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGG 150
i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGG 164
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.58
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1)
+ 982 14.1 0.0 1.3 E00378:188:HVMVNCCXX:4:2113:11069:34342/1 1 151 (0) + AluSx SINE/Alu 73 221 (91) 1000
ANNOTATION EVIDENCE:
982 14.10 0.00 1.32 E00378:188:HVMVNCCXX:4:2113:11069:34342/1 1 151 0 + AluSx SINE/Alu 73 221 91
982 14.10 0.00 1.32 E00378:188:HVMVNCCXX:4:2113:11069:34342/1 1 151 (0) AluSx#SINE/Alu 73 221 (91) m_b5s356i16
E00378:188:HV 1 AGGAGTTTGGGACCAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAA 50
i i i v i
AluSx#SINE/Al 73 AGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAA 122
E00378:188:HV 51 AAATACAAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGC 100
-- i i v i v v vi
AluSx#SINE/Al 123 AAATACAAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGC 170
E00378:188:HV 101 TGCTCAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGT 150
i i v i iivv
AluSx#SINE/Al 171 TACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGT 220
E00378:188:HV 151 T 151
AluSx#SINE/Al 221 T 221
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.81
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 668 15.6 0.0 5.4 E00378:188:HVMVNCCXX:4:2113:11069:34342/2 22 150 (1) C AluSx SINE/Alu (8) 304 183 1001
ANNOTATION EVIDENCE:
668 15.58 0.00 5.43 E00378:188:HVMVNCCXX:4:2113:11069:34342/2 22 150 1 C AluSx SINE/Alu 183 304 8
668 15.58 0.00 5.43 E00378:188:HVMVNCCXX:4:2113:11069:34342/2 22 150 (1) C AluSx#SINE/Alu (8) 304 183 m_b5s357i23
E00378:188:HV 22 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 71
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 72 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 121
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 122 TAGTAGTTTCAAGCAATTGTCCTGCCTCA 150
vvii v i v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCA 183
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.98
Transitions / transversions = 0.90 (9/10)
Gap_init rate = 0.05 (7 / 128), avg. gap size = 1.00 (7 / 7)
+ 1301 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2114:11393:42323/1 1 151 (0) + L1P1 LINE/L1 5304 5454 (701) 1002
ANNOTATION EVIDENCE:
1301 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2114:11393:42323/1 1 151 0 + L1PA2_3end LINE/L1 51 201 701
1301 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2114:11393:42323/1 1 151 (0) L1PA2_3end#LINE/L1 51 201 (701) m_b1s551i192
E00378:188:HV 1 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 50
L1PA2_3end#LI 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
E00378:188:HV 51 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 100
L1PA2_3end#LI 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 150
E00378:188:HV 101 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 150
L1PA2_3end#LI 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
E00378:188:HV 151 A 151
L1PA2_3end#LI 201 A 201
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1193 6.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2114:11393:42323/2 1 151 (0) C L1P2 LINE/L1 (337) 5818 5668 1003
ANNOTATION EVIDENCE:
1193 5.96 0.00 0.00 E00378:188:HVMVNCCXX:4:2114:11393:42323/2 1 151 0 C L1PA4_3end LINE/L1 415 565 337
1193 5.96 0.00 0.00 E00378:188:HVMVNCCXX:4:2114:11393:42323/2 1 151 (0) C L1PA4_3end#LINE/L1 (337) 565 415 m_b1s551i321
E00378:188:HV 1 TTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGTTTCTTA 50
v
C L1PA4_3end#LI 565 TTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTA 516
E00378:188:HV 51 TTCCAGTCTATCATTGTTGGACATTTGGCTTGGTTGCAAGTCTTTGCTGT 100
v v v i
C L1PA4_3end#LI 515 ATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTAT 466
E00378:188:HV 101 TGTCGACAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCAGC 150
vi i i
C L1PA4_3end#LI 465 TGTGAATAGTGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGC 416
E00378:188:HV 151 A 151
C L1PA4_3end#LI 415 A 415
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.57
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1136 4.6 1.3 0.0 E00378:188:HVMVNCCXX:4:2114:23876:8675/1 1 151 (0) + L1P3 LINE/L1 3328 3480 (2666) 1004
ANNOTATION EVIDENCE:
1136 4.64 1.30 0.00 E00378:188:HVMVNCCXX:4:2114:23876:8675/1 1 151 0 + L1P3_orf2 LINE/L1 1219 1371 1923
1136 4.64 1.30 0.00 E00378:188:HVMVNCCXX:4:2114:23876:8675/1 1 151 (0) L1P3_orf2#LINE/L1 1219 1371 (1923) m_b6s551i151
E00378:188:HV 1 ATACAAACTACCATCAGAGAATACTATAAATACCTCTATGCAAATAAACT 50
i i
L1P3_orf2#LIN 1219 ATACAAACTACCATCAGAGAATACTATAAACACCTCTACGCAAATAAACT 1268
E00378:188:HV 51 AGAAAATCTAGAAGAAAGTGATAAATTCCTAGACACATACAACCTCCCAA 100
vv i v
L1P3_orf2#LIN 1269 AGAAAATCTAGAAGAAATGGATAAATTCCTGGACACATACACCCTCCCAA 1318
E00378:188:HV 101 --CTAAAGCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCT 148
-- v
L1P3_orf2#LIN 1319 GACTAAACCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCT 1368
E00378:188:HV 149 GAA 151
L1P3_orf2#LIN 1369 GAA 1371
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1335 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2114:23876:8675/2 1 151 (0) C L1P3 LINE/L1 (2510) 3636 3486 1005
ANNOTATION EVIDENCE:
1335 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2114:23876:8675/2 1 151 0 C L1P3_orf2 LINE/L1 1377 1527 1767
1335 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2114:23876:8675/2 1 151 (0) C L1P3_orf2#LINE/L1 (1767) 1527 1377 m_b6s551i108
E00378:188:HV 1 AAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 50
i
C L1P3_orf2#LIN 1527 AAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 1478
E00378:188:HV 51 GAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTG 100
i
C L1P3_orf2#LIN 1477 GAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTG 1428
E00378:188:HV 101 AATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGC 150
v
C L1P3_orf2#LIN 1427 AATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGC 1378
E00378:188:HV 151 C 151
C L1P3_orf2#LIN 1377 C 1377
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 803 12.3 0.0 0.8 E00378:188:HVMVNCCXX:4:2116:11180:3805/1 1 131 (20) + AluSx SINE/Alu 183 312 (0) 1006
ANNOTATION EVIDENCE:
803 12.30 0.00 0.76 E00378:188:HVMVNCCXX:4:2116:11180:3805/1 1 131 20 + AluSx SINE/Alu 183 312 0
803 12.30 0.00 0.76 E00378:188:HVMVNCCXX:4:2116:11180:3805/1 1 131 (20) AluSx#SINE/Alu 183 312 (0) m_b6s357i4
E00378:188:HV 1 TGAGGCAGGAGAATTGCTTGAACCGAGGAGGTAGAGGCTGAAGTGAACCG 50
i vi ii i v i
AluSx#SINE/Al 183 TGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG 232
E00378:188:HV 51 AGATCACACCATTGCACTCCAGCCTGGGAGACATGAGCGAAACTCCAGCT 100
i i i v - i iv
AluSx#SINE/Al 233 AGATCGCGCCACTGCACTCCAGCCTGGGCGACA-GAGCGAGACTCCGTCT 281
E00378:188:HV 101 CAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 131
i
AluSx#SINE/Al 282 CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.60
Transitions / transversions = 3.00 (12/4)
Gap_init rate = 0.01 (1 / 130), avg. gap size = 1.00 (1 / 1)
+ 330 27.1 3.5 0.0 E00378:188:HVMVNCCXX:4:2116:11180:3805/2 2 123 (28) C MIRb SINE/MIR (75) 187 60 1007
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:4:2116:11180:3805/2 2 123 28 C MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 E00378:188:HVMVNCCXX:4:2116:11180:3805/2 2 123 (28) C MIR#SINE/MIR (75) 187 60 m_b6s601i57
E00378:188:HV 2 TTAATTCTT---ATACTTCTGTCACTTAGATTCTATTATTTCCTTCAATT 48
i i--- i vii i v vv i v vi ii v
C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTT 138
E00378:188:HV 49 TATAAATGA--AAACTGTGACTTAGTGAGGTAAAGTAACTTGCTT-ATGC 95
i i -- v i vi v v ii- v i
C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88
E00378:188:HV 96 CACAGAGCTAACAAGTGGTTGACTCGAG 123
v ii iv vi i
C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAGCCGGG 60
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:2116:11180:3805/2 32 123 28 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:2116:11180:3805/2 32 123 (28) C MIRb#SINE/MIR (107) 161 67 m_b6s601i58
E00378:188:HV 32 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 79
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
E00378:188:HV 80 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 123
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 1340 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2116:19583:39282/1 1 151 (0) + L1P2 LINE/L1 5480 5630 (525) 1008
ANNOTATION EVIDENCE:
1340 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2116:19583:39282/1 1 151 0 + L1PA4_3end LINE/L1 227 377 525
1340 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2116:19583:39282/1 1 151 (0) L1PA4_3end#LINE/L1 227 377 (525) m_b1s551i267
E00378:188:HV 1 AGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTT 50
iv
L1PA4_3end#LI 227 AGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTT 276
E00378:188:HV 51 TTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGT 100
L1PA4_3end#LI 277 TTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGT 326
E00378:188:HV 101 GTGGTGATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAGCCA 150
i i
L1PA4_3end#LI 327 GTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCA 376
E00378:188:HV 151 T 151
L1PA4_3end#LI 377 T 377
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1289 2.0 0.0 0.7 E00378:188:HVMVNCCXX:4:2116:19583:39282/2 1 151 (0) C L1PA3 LINE/L1 (209) 5946 5797 1009
ANNOTATION EVIDENCE:
1289 2.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2116:19583:39282/2 1 151 0 C L1PA3_3end LINE/L1 544 693 209
1289 2.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2116:19583:39282/2 1 151 (0) C L1PA3_3end#LINE/L1 (209) 693 544 m_b1s551i372
E00378:188:HV 1 TCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTTT 50
i
C L1PA3_3end#LI 693 TCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTT 644
E00378:188:HV 51 TTTCTTCTTGCGACAGTTTACTGAGAATGATGATTTCCAATTTCATCCAT 100
v i
C L1PA3_3end#LI 643 TTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCAT 594
E00378:188:HV 101 GTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATT 150
-
C L1PA3_3end#LI 593 GTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATT 545
E00378:188:HV 151 C 151
C L1PA3_3end#LI 544 C 544
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 902 13.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2116:19613:36592/2 1 127 (24) C AluSx SINE/Alu (185) 127 1 1010
ANNOTATION EVIDENCE:
902 13.39 0.00 0.00 E00378:188:HVMVNCCXX:4:2116:19613:36592/2 1 127 24 C AluSx SINE/Alu 1 127 185
902 13.39 0.00 0.00 E00378:188:HVMVNCCXX:4:2116:19613:36592/2 1 127 (24) C AluSx#SINE/Alu (185) 127 1 m_b2s357i36
E00378:188:HV 1 TATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAA 50
v i ii i
C AluSx#SINE/Al 127 TATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAA 78
E00378:188:HV 51 CTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGAT 100
i i i v v v i
C AluSx#SINE/Al 77 CTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGAT 28
E00378:188:HV 101 TACAGATGTGAGCCACTGTGCCCAGCC 127
ii i i i
C AluSx#SINE/Al 27 TACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.99
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 126), avg. gap size = 0.0 (0 / 0)
+ 1217 5.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2116:20801:28910/1 1 151 (0) + L1P3 LINE/L1 2828 2978 (3168) 1011
ANNOTATION EVIDENCE:
1217 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2116:20801:28910/1 1 151 0 + L1P3_orf2 LINE/L1 719 869 2425
1217 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2116:20801:28910/1 1 151 (0) L1P3_orf2#LINE/L1 719 869 (2425) m_b7s551i49
E00378:188:HV 1 AGAAACTCACTCAAAACCACACAACTACATGGAAACTGAACAACCTGCTC 50
i
L1P3_orf2#LIN 719 AGAAACTCACTCAAAACCGCACAACTACATGGAAACTGAACAACCTGCTC 768
E00378:188:HV 51 CTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAAGTAAGTT 100
i i v i?
L1P3_orf2#LIN 769 CTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAAANAAGTT 818
E00378:188:HV 101 CTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGGACA 150
i i
L1P3_orf2#LIN 819 CTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGGACA 868
E00378:188:HV 151 C 151
L1P3_orf2#LIN 869 C 869
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 932 5.0 0.7 7.3 E00378:188:HVMVNCCXX:4:2116:20801:28910/2 1 151 (0) C L1P3 LINE/L1 (2930) 3216 3076 1012
ANNOTATION EVIDENCE:
932 5.00 0.71 7.28 E00378:188:HVMVNCCXX:4:2116:20801:28910/2 1 151 0 C L1P3_orf2 LINE/L1 967 1107 2187
932 5.00 0.71 7.28 E00378:188:HVMVNCCXX:4:2116:20801:28910/2 1 151 (0) C L1P3_orf2#LINE/L1 (2187) 1107 967 m_b6s551i245
E00378:188:HV 1 CTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTT 50
i v - i
C L1P3_orf2#LIN 1107 CTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTT 1059
E00378:188:HV 51 TTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGCTA 99
i---------- -i v i
C L1P3_orf2#LIN 1058 C----------GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTA 1019
E00378:188:HV 100 TTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGT 149
C L1P3_orf2#LIN 1018 TTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGT 969
E00378:188:HV 150 TC 151
C L1P3_orf2#LIN 968 TC 967
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1100 8.0 1.9 0.0 E00378:188:HVMVNCCXX:4:2117:27580:5247/1 1 151 (0) + L1P3 LINE/L1 3744 3897 (2249) 1013
ANNOTATION EVIDENCE:
1100 7.95 1.95 0.00 E00378:188:HVMVNCCXX:4:2117:27580:5247/1 1 151 0 + L1P3_orf2 LINE/L1 1635 1788 1506
1100 7.95 1.95 0.00 E00378:188:HVMVNCCXX:4:2117:27580:5247/1 1 151 (0) L1P3_orf2#LINE/L1 1635 1788 (1506) m_b6s551i38
E00378:188:HV 1 AATACTGGCAAACTGAATCCAGCA---CATCAAAACGCTTATCCACCACT 47
i --- v v
L1P3_orf2#LIN 1635 AATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCACG 1684
E00378:188:HV 48 ATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCATACACAAA 97
i i i i i
L1P3_orf2#LIN 1685 ATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACATACGCAAA 1734
E00378:188:HV 98 TCAATAAACATAATCTATCACATAAACAGAACGAATGACAAAAACTACAT 147
i i v i
L1P3_orf2#LIN 1735 TCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAACCACAT 1784
E00378:188:HV 148 GATT 151
L1P3_orf2#LIN 1785 GATT 1788
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.81
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1103 11.9 0.0 0.0 E00378:188:HVMVNCCXX:4:2117:27580:5247/2 1 151 (0) C AluSx SINE/Alu (86) 226 76 1014
ANNOTATION EVIDENCE:
1103 11.92 0.00 0.00 E00378:188:HVMVNCCXX:4:2117:27580:5247/2 1 151 0 C AluSx SINE/Alu 76 226 86
1103 11.92 0.00 0.00 E00378:188:HVMVNCCXX:4:2117:27580:5247/2 1 151 (0) C AluSx#SINE/Alu (86) 226 76 m_b6s356i14
E00378:188:HV 1 ACTTCAGCCTCTACCTCCTCGGTTCAAGCAATTCTCCTGCCTCATCCTCC 50
v i ii iv i v
C AluSx#SINE/Al 226 ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCC 177
E00378:188:HV 51 TGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCCAGCTAATTTTTTT 100
i vi i i v
C AluSx#SINE/Al 176 CGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGT 127
E00378:188:HV 101 ATTTTTCGTAGAGATGGAGTTTCACCATGTTGGCCAGGCTGGTCTTGAAC 150
v i i i
C AluSx#SINE/Al 126 ATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAAC 77
E00378:188:HV 151 T 151
C AluSx#SINE/Al 76 T 76
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.79
Transitions / transversions = 2.00 (12/6)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1232 6.0 0.0 0.7 E00378:188:HVMVNCCXX:4:2117:7933:35801/2 1 151 (0) + AluY SINE/Alu 139 288 (23) 1015
ANNOTATION EVIDENCE:
1232 6.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2117:7933:35801/2 1 151 0 + AluY SINE/Alu 139 288 23
1232 6.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2117:7933:35801/2 1 151 (0) AluY#SINE/Alu 139 288 (23) m_b2s356i86
E00378:188:HV 1 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCA 50
i
AluY#SINE/Alu 139 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCA 188
E00378:188:HV 51 GGAGAACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCA 100
i i i - i v i
AluY#SINE/Alu 189 GGAGAATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCG 237
E00378:188:HV 101 TGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAA 150
i i
AluY#SINE/Alu 238 CGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAA 287
E00378:188:HV 151 A 151
AluY#SINE/Alu 288 A 288
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.08
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 702 7.9 0.0 0.0 E00378:188:HVMVNCCXX:4:2118:13971:73159/1 63 151 (0) C AluSx SINE/Alu (14) 298 210 1016
ANNOTATION EVIDENCE:
702 7.87 0.00 0.00 E00378:188:HVMVNCCXX:4:2118:13971:73159/1 63 151 0 C AluSx SINE/Alu 210 298 14
702 7.87 0.00 0.00 E00378:188:HVMVNCCXX:4:2118:13971:73159/1 63 151 (0) C AluSx#SINE/Alu (14) 298 210 m_b2s357i102
E00378:188:HV 63 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 112
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
E00378:188:HV 113 TGCAGTGGCATGANCTCGGCTCACTGCAACCTCCACCTC 151
ii ? i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.86
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
+ 1210 8.0 0.7 0.0 E00378:188:HVMVNCCXX:4:2118:13971:73159/2 1 151 (0) + AluY SINE/Alu 43 194 (117) 1017
ANNOTATION EVIDENCE:
1210 7.95 0.66 0.00 E00378:188:HVMVNCCXX:4:2118:13971:73159/2 1 151 0 + AluY SINE/Alu 43 194 117
1210 7.95 0.66 0.00 E00378:188:HVMVNCCXX:4:2118:13971:73159/2 1 151 (0) AluY#SINE/Alu 43 194 (117) c_b2s352i3
E00378:188:HV 1 GNGGCCAAGGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGC 50
? i v i i
AluY#SINE/Alu 43 GAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGC 92
E00378:188:HV 51 TAACGTGGTGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGC 99
ii i i - vi
AluY#SINE/Alu 93 TAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGC 142
E00378:188:HV 100 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAG 149
i
AluY#SINE/Alu 143 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAG 192
E00378:188:HV 150 AA 151
AluY#SINE/Alu 193 AA 194
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.84
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 240 29.7 7.1 0.0 E00378:188:HVMVNCCXX:4:2118:20101:43835/1 29 119 (32) C L1MC4 LINE/L1 (1441) 6601 6504 1018
ANNOTATION EVIDENCE:
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:4:2118:20101:43835/1 29 119 32 C L1MC4_3end LINE/L1 1251 1348 1441
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:4:2118:20101:43835/1 29 119 (32) C L1MC4_3end#LINE/L1 (1441) 1348 1251 m_b3s551i150
E00378:188:HV 29 GTTGATA--GATATCTTCAAATCCAAGCCAACATCACACAGTTTAT---- 72
v -- i i v v i vi i ----
C L1MC4_3end#LI 1348 GTTCATACCGATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTA 1299
E00378:188:HV 73 -CTTTTTTTCTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAA 119
- i iiii v v i v iv iv iii v i
C L1MC4_3end#LI 1298 GCCTTCCCCCTTTCCATATTTGTAACTCCCTTCTCCGACAGTGAGAAA 1251
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.16
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2118:29528:7181/1 42 73 (78) + (CA)n Simple_repeat 1 32 (0) 1019
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2118:29528:7181/1 42 73 78 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2118:29528:7181/1 42 73 (78) (CA)n#Simple_repeat 1 32 (0) m_b4s252i41
E00378:188:HV 42 CATACATGCACACACATACACACACACACACA 73
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 E00378:188:HVMVNCCXX:4:2118:29528:7181/2 57 149 (2) C MIRb SINE/MIR (49) 219 122 1020
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:4:2118:29528:7181/2 57 149 2 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 E00378:188:HVMVNCCXX:4:2118:29528:7181/2 57 149 (2) C MIRb#SINE/MIR (49) 219 122 m_b4s601i6
E00378:188:HV 57 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 102
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 103 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 149
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1145 12.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2119:14894:54190/1 1 151 (0) + AluSx SINE/Alu 105 255 (57) 1021
ANNOTATION EVIDENCE:
1145 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:14894:54190/1 1 151 0 + AluSx SINE/Alu 105 255 57
1145 12.58 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:14894:54190/1 1 151 (0) AluSx#SINE/Alu 105 255 (57) m_b2s356i12
E00378:188:HV 1 AAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGG 50
ii i v i i i v
AluSx#SINE/Al 105 AAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCG 154
E00378:188:HV 51 CACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAA 100
i i i i
AluSx#SINE/Al 155 CGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAA 204
E00378:188:HV 101 CTCAGGAGGCAGAGATTGCAGTGAGCGGAGATCATGCCACTGCACTCCAG 150
i i i i v ii
AluSx#SINE/Al 205 CCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAG 254
E00378:188:HV 151 C 151
AluSx#SINE/Al 255 C 255
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.32
Transitions / transversions = 5.33 (16/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 327 4.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 1 45 (106) + L1PA2 LINE/L1 6109 6153 (2) 1022
ANNOTATION EVIDENCE:
327 4.44 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 1 45 106 + L1PA2_3end LINE/L1 856 900 2
327 4.44 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 1 45 (106) L1PA2_3end#LINE/L1 856 900 (2) m_b1s551i487
E00378:188:HV 1 ATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 45
i v
L1PA2_3end#LI 856 ATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.59
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 249 28.6 0.0 0.3 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 39 127 (24) C L1M5 LINE/L1 (293) 5831 5741 1023 *
ANNOTATION EVIDENCE:
228 30.68 0.00 1.12 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 39 127 24 C L1ME4a_3end LINE/L1 491 578 293
228 30.68 0.00 1.12 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 39 127 (24) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i488
E00378:188:HV 39 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 88
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 89 ACAGGTGATATATCCATTTTACTATTGTTGGACATTTAG 127
i iv v v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.43
Transitions / transversions = 2.12 (17/8)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
249 27.94 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 60 127 24 C L1ME3A_3end LINE/L1 488 555 365
249 27.94 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:14894:54190/2 60 127 (24) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i489
E00378:188:HV 60 TGCATATTATTTTGTTATGTAGACATATTACAGGTGATATATCCATTTTA 109
i v iii i ii i ii iv v v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
E00378:188:HV 110 CTATTGTTGGACATTTAG 127
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.18
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1258 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2119:20567:9976/2 1 151 (0) + L1P1 LINE/L1 5022 5172 (974) 1024
ANNOTATION EVIDENCE:
1258 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:20567:9976/2 1 151 0 + L1P1_orf2 LINE/L1 2913 3063 231
1258 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2119:20567:9976/2 1 151 (0) L1P1_orf2#LINE/L1 2913 3063 (231) m_b1s551i73
E00378:188:HV 1 TAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACA 50
?
L1P1_orf2#LIN 2913 TAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACA 2962
E00378:188:HV 51 TAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACA 100
L1P1_orf2#LIN 2963 TAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACA 3012
E00378:188:HV 101 AAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTGCTGCAC 150
v i v
L1P1_orf2#LIN 3013 AAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCAC 3062
E00378:188:HV 151 A 151
L1P1_orf2#LIN 3063 A 3063
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1295 2.0 0.0 0.7 E00378:188:HVMVNCCXX:4:2121:2432:57073/1 1 151 (0) + L1PA2 LINE/L1 5809 5958 (197) 1025
ANNOTATION EVIDENCE:
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2121:2432:57073/1 1 151 0 + L1PA2_3end LINE/L1 556 705 197
1295 2.00 0.00 0.66 E00378:188:HVMVNCCXX:4:2121:2432:57073/1 1 151 (0) L1PA2_3end#LINE/L1 556 705 (197) m_b1s551i378
E00378:188:HV 1 GCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAAT 50
-
L1PA2_3end#LI 556 GCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAAT 604
E00378:188:HV 51 TGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGAAAAAACCAAACAC 100
i v
L1PA2_3end#LI 605 TGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACAC 654
E00378:188:HV 101 CGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACA 150
i
L1PA2_3end#LI 655 CGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACA 704
E00378:188:HV 151 C 151
L1PA2_3end#LI 705 C 705
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 627 6.9 0.0 0.0 E00378:188:HVMVNCCXX:4:2121:2432:57073/2 64 150 (1) C L1PA2 LINE/L1 (2) 6153 6067 1026
ANNOTATION EVIDENCE:
627 6.90 0.00 0.00 E00378:188:HVMVNCCXX:4:2121:2432:57073/2 64 150 1 C L1PA2_3end LINE/L1 814 900 2
627 6.90 0.00 0.00 E00378:188:HVMVNCCXX:4:2121:2432:57073/2 64 150 (1) C L1PA2_3end#LINE/L1 (2) 900 814 m_b1s551i448
E00378:188:HV 64 TTGTTTTTTTTATTACACTTTAAGTTTTAGGGGACATGTGCACATTGTGC 113
v i v
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
E00378:188:HV 114 AGGTTAGTTACATATGTATACATGTGCCAATCTTGTG 150
vv v
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTG 814
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.25
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0)
+ 1117 10.9 1.3 0.0 E00378:188:HVMVNCCXX:4:2122:10724:49531/1 5 151 (0) C AluSx SINE/Alu (161) 151 3 1027
ANNOTATION EVIDENCE:
1117 10.88 1.34 0.00 E00378:188:HVMVNCCXX:4:2122:10724:49531/1 5 151 0 C AluSx SINE/Alu 3 151 161
1117 10.88 1.34 0.00 E00378:188:HVMVNCCXX:4:2122:10724:49531/1 5 151 (0) C AluSx#SINE/Alu (161) 151 3 m_b4s356i44
E00378:188:HV 5 GCCACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAGATGGAGTTTCAC 54
v i i i i
C AluSx#SINE/Al 151 GCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 102
E00378:188:HV 55 CATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGC 102
i v i i-- i i
C AluSx#SINE/Al 101 CATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGC 52
E00378:188:HV 103 TTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGG 151
i i i i i
C AluSx#SINE/Al 51 CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.62
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 146), avg. gap size = 2.00 (2 / 1)
+ 1207 8.1 0.7 0.0 E00378:188:HVMVNCCXX:4:2122:20172:58901/1 3 151 (0) + AluY SINE/Alu 11 160 (151) 1028
ANNOTATION EVIDENCE:
1207 8.05 0.67 0.00 E00378:188:HVMVNCCXX:4:2122:20172:58901/1 3 151 0 + AluY SINE/Alu 11 160 151
1207 8.05 0.67 0.00 E00378:188:HVMVNCCXX:4:2122:20172:58901/1 3 151 (0) AluY#SINE/Alu 11 160 (151) m_b2s356i54
E00378:188:HV 3 GGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAAGGCGGGCTGA 52
i i i v
AluY#SINE/Alu 11 GGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA 60
E00378:188:HV 53 TCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGGTGAAACCCCA 102
i i ii i
AluY#SINE/Alu 61 TCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCG 110
E00378:188:HV 103 TCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCTGT 151
i - vi
AluY#SINE/Alu 111 TCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGT 160
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.59
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 1113 9.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2123:1692:41620/2 1 146 (5) + AluSx SINE/Alu 36 181 (131) 1029
ANNOTATION EVIDENCE:
1113 9.59 0.00 0.00 E00378:188:HVMVNCCXX:4:2123:1692:41620/2 1 146 5 + AluSx SINE/Alu 36 181 131
1113 9.59 0.00 0.00 E00378:188:HVMVNCCXX:4:2123:1692:41620/2 1 146 (5) AluSx#SINE/Alu 36 181 (131) m_b6s357i11
E00378:188:HV 1 ACTTTGGGAGGACAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCAAGAC 50
v i i i i
AluSx#SINE/Al 36 ACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGAC 85
E00378:188:HV 51 CAGCCTGGCCAACATGGTGAAACTCCATCTCTACGAAAAATAAAAAAATT 100
i i v v
AluSx#SINE/Al 86 CAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATT 135
E00378:188:HV 101 AGCTGGGCATGGTGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGG 146
i i iv i
AluSx#SINE/Al 136 AGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGG 181
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0)
+ 1282 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2124:1996:52942/1 1 151 (0) + L1P1 LINE/L1 4903 5053 (1093) 1030
ANNOTATION EVIDENCE:
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2124:1996:52942/1 1 151 0 + L1P1_orf2 LINE/L1 2794 2944 350
1282 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2124:1996:52942/1 1 151 (0) L1P1_orf2#LINE/L1 2794 2944 (350) m_b1s551i22
E00378:188:HV 1 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 50
L1P1_orf2#LIN 2794 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 2843
E00378:188:HV 51 ACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTA 100
v v i
L1P1_orf2#LIN 2844 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 2893
E00378:188:HV 101 AAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 150
i
L1P1_orf2#LIN 2894 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 2943
E00378:188:HV 151 G 151
L1P1_orf2#LIN 2944 G 2944
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1279 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2124:1996:52942/2 1 151 (0) C L1P1 LINE/L1 (902) 5244 5094 1031
ANNOTATION EVIDENCE:
1279 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2124:1996:52942/2 1 151 0 C L1P1_orf2 LINE/L1 2985 3135 159
1279 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2124:1996:52942/2 1 151 (0) C L1P1_orf2#LINE/L1 (159) 3135 2985 m_b1s551i96
E00378:188:HV 1 AGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCA 50
i
C L1P1_orf2#LIN 3135 AGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCA 3086
E00378:188:HV 51 CTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGA 100
C L1P1_orf2#LIN 3085 CTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGA 3036
E00378:188:HV 101 TCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGA 150
i v
C L1P1_orf2#LIN 3035 TCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGA 2986
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 2985 C 2985
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 747 13.2 0.0 0.0 E00378:188:HVMVNCCXX:4:2124:20780:1168/2 2 107 (44) C AluSx SINE/Alu (206) 106 1 1032
ANNOTATION EVIDENCE:
747 13.21 0.00 0.00 E00378:188:HVMVNCCXX:4:2124:20780:1168/2 2 107 44 C AluSx SINE/Alu 1 106 206
747 13.21 0.00 0.00 E00378:188:HVMVNCCXX:4:2124:20780:1168/2 2 107 (44) C AluSx#SINE/Alu (206) 106 1 m_b5s357i55
E00378:188:HV 2 TTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAGTGATCTG 51
v i i i i i
C AluSx#SINE/Al 106 TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCG 57
E00378:188:HV 52 CCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGCAC 101
i i i i vi i
C AluSx#SINE/Al 56 CCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGC 7
E00378:188:HV 102 CCAGCC 107
i
C AluSx#SINE/Al 6 CCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.76
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0)
+ 234 25.2 16.6 1.5 E00378:188:HVMVNCCXX:4:2201:10531:28136/1 1 133 (18) + MIR SINE/MIR 103 259 (3) 1033
ANNOTATION EVIDENCE:
234 25.19 16.56 1.50 E00378:188:HVMVNCCXX:4:2201:10531:28136/1 1 133 18 + MIR SINE/MIR 103 259 3
234 25.19 16.56 1.50 E00378:188:HVMVNCCXX:4:2201:10531:28136/1 1 133 (18) MIR#SINE/MIR 103 259 (3) m_b6s601i27
E00378:188:HV 1 CTTTACCTCACTAAGTCACAGTTT--TCATTTATAAA-TGGAAGGA-AAT 46
v v iv i v -- i i - -- -
MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG--GGATAAT 150
E00378:188:HV 47 AATAGAATCTAAGTGACAGAAGTAT---AAGAATTAAG------AATAAA 87
v i vv v i iiv i ---i i i------ v
MIR#SINE/MIR 151 AATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACA 200
E00378:188:HV 88 CATAAA-------------TGCCAGGCACACCGTATATACTCAACAAGTG 124
ii ------------- v iv viii i i
MIR#SINE/MIR 201 TGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 250
E00378:188:HV 125 TTAGCTATT 133
MIR#SINE/MIR 251 TTAGCTATT 259
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 30.19
Transitions / transversions = 1.54 (20/13)
Gap_init rate = 0.06 (8 / 132), avg. gap size = 3.50 (28 / 8)
+ 1056 4.6 7.4 0.0 E00378:188:HVMVNCCXX:4:2201:29924:39124/2 1 151 (0) C L1P3 LINE/L1 (2792) 3354 3192 1034
ANNOTATION EVIDENCE:
1056 4.64 7.36 0.00 E00378:188:HVMVNCCXX:4:2201:29924:39124/2 1 151 0 C L1P3_orf2 LINE/L1 1083 1245 2049
1056 4.64 7.36 0.00 E00378:188:HVMVNCCXX:4:2201:29924:39124/2 1 151 (0) C L1P3_orf2#LINE/L1 (2049) 1245 1083 m_b6s551i195
E00378:188:HV 1 ATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTAT 50
iv
C L1P3_orf2#LIN 1245 ATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATAT 1196
E00378:188:HV 51 CCTCTTTATCATTTTTTATTGAGTCTATTTGATTCTTCTC--------TC 92
i v --------
C L1P3_orf2#LIN 1195 CCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCTTC 1146
E00378:188:HV 93 TTTATTAGTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAA 138
v ---- i
C L1P3_orf2#LIN 1145 TTTATTAGTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAA 1096
E00378:188:HV 139 TCAGCTCCTGGAT 151
i
C L1P3_orf2#LIN 1095 CCAGCTCCTGGAT 1083
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.80
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1335 0.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2202:23632:22563/1 1 151 (0) C L1P1 LINE/L1 (646) 5509 5359 1035
ANNOTATION EVIDENCE:
1335 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2202:23632:22563/1 1 151 0 C L1PA2_3end LINE/L1 106 256 646
1335 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2202:23632:22563/1 1 151 (0) C L1PA2_3end#LINE/L1 (646) 256 106 m_b1s551i226
E00378:188:HV 1 ATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTA 50
i
C L1PA2_3end#LI 256 ATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTA 207
E00378:188:HV 51 ACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGAT 100
C L1PA2_3end#LI 206 ACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGAT 157
E00378:188:HV 101 GGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGT 150
C L1PA2_3end#LI 156 GGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGT 107
E00378:188:HV 151 C 151
C L1PA2_3end#LI 106 C 106
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1272 0.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2202:23632:22563/2 1 151 (0) + L1P1 LINE/L1 5294 5444 (711) 1036
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2202:23632:22563/2 1 151 0 + L1PA2_3end LINE/L1 41 191 711
1272 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2202:23632:22563/2 1 151 (0) L1PA2_3end#LINE/L1 41 191 (711) m_b1s551i187
E00378:188:HV 1 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGA 50
L1PA2_3end#LI 41 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGA 90
E00378:188:HV 51 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 100
L1PA2_3end#LI 91 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 140
E00378:188:HV 101 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 150
L1PA2_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190
E00378:188:HV 151 A 151
L1PA2_3end#LI 191 A 191
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 863 14.6 0.0 1.4 E00378:188:HVMVNCCXX:4:2202:30716:29455/1 13 151 (0) C AluSx SINE/Alu (54) 258 122 1037
ANNOTATION EVIDENCE:
863 14.60 0.00 1.44 E00378:188:HVMVNCCXX:4:2202:30716:29455/1 13 151 0 C AluSx SINE/Alu 122 258 54
863 14.60 0.00 1.44 E00378:188:HVMVNCCXX:4:2202:30716:29455/1 13 151 (0) C AluSx#SINE/Alu (54) 258 122 m_b5s356i4
E00378:188:HV 13 CAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCCTAG 62
i v v v vv
C AluSx#SINE/Al 258 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCC 209
E00378:188:HV 63 TAGGTTCAAGCAATTGTCCTGCCTCAGCCTCCTGAGCAGCTATGATTACA 112
ii i v i i iv
C AluSx#SINE/Al 208 CGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA 159
E00378:188:HV 113 GGCTCCCACCACAATGCCTGGCTAATTTTTTTGTATTTT 151
v v i v i i --
C AluSx#SINE/Al 158 GGCGCGCGCCACCACGCCCGGCTAA--TTTTTGTATTTT 122
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 10.65
Transitions / transversions = 1.00 (10/10)
Gap_init rate = 0.01 (2 / 138), avg. gap size = 1.00 (2 / 2)
+ 568 18.4 15.1 0.0 E00378:188:HVMVNCCXX:4:2202:4888:4649/2 5 145 (6) C L1MC4 LINE/L1 (393) 7649 7484 1038
ANNOTATION EVIDENCE:
568 18.44 15.06 0.00 E00378:188:HVMVNCCXX:4:2202:4888:4649/2 5 145 6 C L1MC4_3end LINE/L1 2231 2396 393
568 18.44 15.06 0.00 E00378:188:HVMVNCCXX:4:2202:4888:4649/2 5 145 (6) C L1MC4_3end#LINE/L1 (393) 2396 2231 m_b3s551i100
E00378:188:HV 5 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 54
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
E00378:188:HV 55 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 98
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
E00378:188:HV 99 G-------------------GTCCCTTGCTCTGAGTTTGTCTGATGTTTC 129
------------------- iiv i i
C L1MC4_3end#LI 2296 GGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTTC 2247
E00378:188:HV 130 CTTATTATTAAATTTA 145
i v i i
C L1MC4_3end#LI 2246 CTCATGATTAGATTCA 2231
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.72
Transitions / transversions = 1.27 (14/11)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 12.50 (25 / 2)
+ 1276 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2203:18355:30861/1 1 151 (0) C L1P1 LINE/L1 (930) 5216 5066 1039
ANNOTATION EVIDENCE:
1276 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2203:18355:30861/1 1 151 0 C L1P1_orf2 LINE/L1 2957 3107 187
1276 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2203:18355:30861/1 1 151 (0) C L1P1_orf2#LINE/L1 (187) 3107 2957 m_b1s551i89
E00378:188:HV 1 CATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCA 50
i
C L1P1_orf2#LIN 3107 CATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCA 3058
E00378:188:HV 51 GAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTG 100
i v
C L1P1_orf2#LIN 3057 GAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTG 3008
E00378:188:HV 101 CCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCC 150
C L1P1_orf2#LIN 3007 CCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCC 2958
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2957 T 2957
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1209 5.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2203:21633:61503/2 1 151 (0) C L1P3 LINE/L1 (3170) 2976 2826 1040
ANNOTATION EVIDENCE:
1209 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2203:21633:61503/2 1 151 0 C L1P3_orf2 LINE/L1 717 867 2427
1209 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2203:21633:61503/2 1 151 (0) C L1P3_orf2#LINE/L1 (2427) 867 717 m_b7s551i51
E00378:188:HV 1 GTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAAGA 50
i i
C L1P3_orf2#LIN 867 GTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGA 818
E00378:188:HV 51 ACTTAGTTATTTCTGCCTTCATTTCATTATTTACCTAGTAGTCATTCAGG 100
?v v i i
C L1P3_orf2#LIN 817 ACTTNTTTATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTCAGG 768
E00378:188:HV 101 AGCAGGTTGTTCAGTTTCCATGTAGTTGTGTGGTTTTGAGTGAGTTTCTT 150
i
C L1P3_orf2#LIN 767 AGCAGGTTGTTCAGTTTCCATGTAGTTGTGCGGTTTTGAGTGAGTTTCTT 718
E00378:188:HV 151 A 151
C L1P3_orf2#LIN 717 A 717
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.93
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1243 7.3 0.7 0.0 E00378:188:HVMVNCCXX:4:2203:5416:29050/1 1 151 (0) + AluY SINE/Alu 25 176 (135) 1041
ANNOTATION EVIDENCE:
1243 7.28 0.66 0.00 E00378:188:HVMVNCCXX:4:2203:5416:29050/1 1 151 0 + AluY SINE/Alu 25 176 135
1243 7.28 0.66 0.00 E00378:188:HVMVNCCXX:4:2203:5416:29050/1 1 151 (0) AluY#SINE/Alu 25 176 (135) m_b2s356i58
E00378:188:HV 1 GTAATCTCAGCACTTTGGGAGGCCAAGGCGGGCTGATCATGAGGTCAGGA 50
i i v i
AluY#SINE/Alu 25 GTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGA 74
E00378:188:HV 51 GATCAAGACCATCCTGGCTAACGTGGTGAAACCCCATCTCTACTAAAAAC 100
i ii i i
AluY#SINE/Alu 75 GATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAAT 124
E00378:188:HV 101 ACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTC 149
- vi
AluY#SINE/Alu 125 ACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTC 174
E00378:188:HV 150 GG 151
AluY#SINE/Alu 175 GG 176
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.81
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1334 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2204:30097:3805/1 1 151 (0) + L1P1 LINE/L1 5450 5600 (555) 1042
ANNOTATION EVIDENCE:
1334 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2204:30097:3805/1 1 151 0 + L1PA3_3end LINE/L1 197 347 555
1334 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2204:30097:3805/1 1 151 (0) L1PA3_3end#LINE/L1 197 347 (555) m_b1s551i262
E00378:188:HV 1 TCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGC 50
i
L1PA3_3end#LI 197 TCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGC 246
E00378:188:HV 51 TGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTGGGACTG 100
iv
L1PA3_3end#LI 247 TGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTG 296
E00378:188:HV 101 TAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGGGATC 150
i
L1PA3_3end#LI 297 TAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATC 346
E00378:188:HV 151 T 151
L1PA3_3end#LI 347 T 347
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1212 5.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2204:30097:3805/2 1 151 (0) C L1P1 LINE/L1 (332) 5823 5673 1043
ANNOTATION EVIDENCE:
1212 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2204:30097:3805/2 1 151 0 C L1PA2_3end LINE/L1 420 570 332
1212 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2204:30097:3805/2 1 151 (0) C L1PA2_3end#LINE/L1 (332) 570 420 m_b1s551i325
E00378:188:HV 1 ATTGTTTTTTATGGCTGGAGAGTATTCCATGGTGTGTATGTGCCACAGTT 50
ii v v i v
C L1PA2_3end#LI 570 ATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTT 521
E00378:188:HV 51 TCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTT 100
C L1PA2_3end#LI 520 TCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTT 471
E00378:188:HV 101 GCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCGTTATA 150
i v
C L1PA2_3end#LI 470 GCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATA 421
E00378:188:HV 151 G 151
C L1PA2_3end#LI 420 G 420
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 596 17.3 15.2 0.0 E00378:188:HVMVNCCXX:4:2205:14610:32109/1 2 140 (11) + L1MC4 LINE/L1 7486 7649 (393) 1044
ANNOTATION EVIDENCE:
596 17.27 15.25 0.00 E00378:188:HVMVNCCXX:4:2205:14610:32109/1 2 140 11 + L1MC4_3end LINE/L1 2233 2396 393
596 17.27 15.25 0.00 E00378:188:HVMVNCCXX:4:2205:14610:32109/1 2 140 (11) L1MC4_3end#LINE/L1 2233 2396 (393) m_b3s551i97
E00378:188:HV 2 AATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGGAC------ 45
i i i i vii ------
L1MC4_3end#LI 2233 AATCTAATCATGAGGAAACATCAGACAAACCCAAATTGAGGGACATTCTA 2282
E00378:188:HV 46 -------------CTGTACTATTCAAATATATGAAGGTCATGATAAATAA 82
------------- v v i v ? v i i
L1MC4_3end#LI 2283 CAAAATAACTGGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAA 2332
E00378:188:HV 83 AAAAA------AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACAC 126
i ------i i v vvv
L1MC4_3end#LI 2333 AGAAAGACTGAGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGAC 2382
E00378:188:HV 127 ACCTAAATGCAATG 140
v i
L1MC4_3end#LI 2383 AACTAAATGCAACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.15
Transitions / transversions = 1.30 (13/10)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 8.33 (25 / 3)
+ 231 23.1 0.0 0.0 E00378:188:HVMVNCCXX:4:2205:14610:32109/2 74 125 (26) C L1MC4 LINE/L1 (90) 7952 7901 1045
ANNOTATION EVIDENCE:
231 23.08 0.00 0.00 E00378:188:HVMVNCCXX:4:2205:14610:32109/2 74 125 26 C L1MC4_3end LINE/L1 2648 2699 90
231 23.08 0.00 0.00 E00378:188:HVMVNCCXX:4:2205:14610:32109/2 74 125 (26) C L1MC4_3end#LINE/L1 (90) 2699 2648 m_b3s551i1
E00378:188:HV 74 GTTAACGTTTTACCATATTTGCTTAATCATTCCCTCTCTCCACACACACA 123
i i i v i ? ? v i i i
C L1MC4_3end#LI 2699 GTTAACATTTTGCCACATTTGCTTTATCATTCTCTNTNTGCATATACATA 2650
E00378:188:HV 124 CT 125
i
C L1MC4_3end#LI 2649 TT 2648
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.40
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 944 6.1 7.5 0.0 E00378:188:HVMVNCCXX:4:2205:5284:11312/1 1 147 (4) C L1P3 LINE/L1 (2809) 3337 3179 1046
ANNOTATION EVIDENCE:
944 6.12 7.54 0.00 E00378:188:HVMVNCCXX:4:2205:5284:11312/1 1 147 4 C L1P3_orf2 LINE/L1 1070 1228 2066
944 6.12 7.54 0.00 E00378:188:HVMVNCCXX:4:2205:5284:11312/1 1 147 (4) C L1P3_orf2#LINE/L1 (2066) 1228 1070 m_b6s551i201
E00378:188:HV 1 TAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTT 50
iv i
C L1P3_orf2#LIN 1228 TAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTT 1179
E00378:188:HV 51 ATTGAGTCTATTTGATTTTTCTC--------TCTTTATTAGTCTTGCTAG 92
v i -------- v
C L1P3_orf2#LIN 1178 ATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAG 1129
E00378:188:HV 93 CGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAAT 138
---- i i v
C L1P3_orf2#LIN 1128 CGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCAT 1079
E00378:188:HV 139 TGATTTTTT 147
C L1P3_orf2#LIN 1078 TGATTTTTT 1070
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.40
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (2 / 146), avg. gap size = 6.00 (12 / 2)
+ 1258 3.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2205:5284:11312/2 1 151 (0) + L1P3 LINE/L1 2948 3098 (3048) 1047
ANNOTATION EVIDENCE:
1258 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:2205:5284:11312/2 1 151 0 + L1P3_orf2 LINE/L1 839 989 2305
1258 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:2205:5284:11312/2 1 151 (0) L1P3_orf2#LINE/L1 839 989 (2305) m_b7s551i7
E00378:188:HV 1 AAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGA 50
i
L1P3_orf2#LIN 839 AAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGA 888
E00378:188:HV 51 GGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAA 100
? v i
L1P3_orf2#LIN 889 GGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAA 938
E00378:188:HV 101 AATCAACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAA 150
i
L1P3_orf2#LIN 939 AATCGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAA 988
E00378:188:HV 151 C 151
L1P3_orf2#LIN 989 C 989
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 330 26.1 3.2 0.0 E00378:188:HVMVNCCXX:4:2207:12023:23513/1 31 122 (29) + MIRb SINE/MIR 67 161 (107) 1048
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:2207:12023:23513/1 31 122 29 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 E00378:188:HVMVNCCXX:4:2207:12023:23513/1 31 122 (29) MIRb#SINE/MIR 67 161 (107) m_b6s601i63
E00378:188:HV 31 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 79
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
E00378:188:HV 80 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 122
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 656 6.2 0.0 0.0 E00378:188:HVMVNCCXX:4:2208:14468:48423/1 1 81 (70) + AluSx SINE/Alu 218 298 (14) 1049
ANNOTATION EVIDENCE:
656 6.17 0.00 0.00 E00378:188:HVMVNCCXX:4:2208:14468:48423/1 1 81 70 + AluSx SINE/Alu 218 298 14
656 6.17 0.00 0.00 E00378:188:HVMVNCCXX:4:2208:14468:48423/1 1 81 (70) AluSx#SINE/Alu 218 298 (14) m_b2s357i107
E00378:188:HV 1 GGTTGCAGTGAGCCGAGATCATGCCACTGCATTCCAGCCTGGGCGACAGA 50
ii i
AluSx#SINE/Al 218 GGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGA 267
E00378:188:HV 51 GCGAGACTCCGTCTCAAAAAAAGAAATAAAA 81
i v
AluSx#SINE/Al 268 GCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.07
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0)
+ 958 7.8 0.0 0.0 E00378:188:HVMVNCCXX:4:2208:27285:53610/1 23 151 (0) C L1P3 LINE/L1 (2248) 3898 3770 1050
ANNOTATION EVIDENCE:
958 7.75 0.00 0.00 E00378:188:HVMVNCCXX:4:2208:27285:53610/1 23 151 0 C L1P3_orf2 LINE/L1 1661 1789 1505
958 7.75 0.00 0.00 E00378:188:HVMVNCCXX:4:2208:27285:53610/1 23 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1661 m_b6s551i31
E00378:188:HV 23 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 72
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 73 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 122
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
E00378:188:HV 123 TTGATAGTGGTGGATAAGCGTTTTGATGT 151
v v
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGCTTTTTGATGT 1661
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.90
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 128), avg. gap size = 0.0 (0 / 0)
+ 1224 4.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2208:27285:53610/2 1 151 (0) + L1P3 LINE/L1 3465 3615 (2531) 1051
ANNOTATION EVIDENCE:
1224 4.64 0.00 0.00 E00378:188:HVMVNCCXX:4:2208:27285:53610/2 1 151 0 + L1P3_orf2 LINE/L1 1356 1506 1788
1224 4.64 0.00 0.00 E00378:188:HVMVNCCXX:4:2208:27285:53610/2 1 151 (0) L1P3_orf2#LINE/L1 1356 1506 (1788) m_b6s551i115
E00378:188:HV 1 AATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAA 50
L1P3_orf2#LIN 1356 AATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAA 1405
E00378:188:HV 51 AAAGCCCAGGACCAGAGGGATTCACAGCCGAATTCTACCAGGGGGACAAG 100
v i v i
L1P3_orf2#LIN 1406 AAAGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGAGGTACAAA 1455
E00378:188:HV 101 GAGGGGCTGGTACCATTCCTTCTGAAACTATTCGAAACAATAGAAAACGA 150
i v v
L1P3_orf2#LIN 1456 GAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGA 1505
E00378:188:HV 151 G 151
L1P3_orf2#LIN 1506 G 1506
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.79
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1310 2.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:18832:9853/1 1 151 (0) C L1P1 LINE/L1 (1135) 5011 4861 1052
ANNOTATION EVIDENCE:
1310 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:18832:9853/1 1 151 0 C L1P1_orf2 LINE/L1 2752 2902 392
1310 1.99 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:18832:9853/1 1 151 (0) C L1P1_orf2#LINE/L1 (392) 2902 2752 m_b1s551i1
E00378:188:HV 1 TTAAGTCTTTAATCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAG 50
i v v
C L1P1_orf2#LIN 2902 TTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAG 2853
E00378:188:HV 51 GGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCA 100
C L1P1_orf2#LIN 2852 GGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCA 2803
E00378:188:HV 101 TTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGT 150
C L1P1_orf2#LIN 2802 TTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGT 2753
E00378:188:HV 151 C 151
C L1P1_orf2#LIN 2752 C 2752
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 42 73 (78) + (TG)n Simple_repeat 1 32 (0) 1053
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 42 73 78 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 42 73 (78) (TG)n#Simple_repeat 1 32 (0) m_b4s252i40
E00378:188:HV 42 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 73
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 74 86 (65) + (TGTATG)n Simple_repeat 1 41 (0) 1054
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 42 86 65 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 42 86 (65) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i39
E00378:188:HV 42 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 86
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 400 5.9 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 101 151 (0) C AluSx SINE/Alu (21) 291 241 1055
ANNOTATION EVIDENCE:
400 5.88 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 101 151 0 C AluSx SINE/Alu 241 291 21
400 5.88 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30787:15057/1 101 151 (0) C AluSx#SINE/Alu (21) 291 241 m_b4s357i0
E00378:188:HV 101 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 150
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 151 G 151
C AluSx#SINE/Al 241 G 241
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.30
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 42 73 (78) + (TG)n Simple_repeat 1 32 (0) 1056
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 42 73 78 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 42 73 (78) (TG)n#Simple_repeat 1 32 (0) m_b4s252i38
E00378:188:HV 42 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 73
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 74 86 (65) + (TGTATG)n Simple_repeat 1 41 (0) 1057
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 42 86 65 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 42 86 (65) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i37
E00378:188:HV 42 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 86
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 400 5.9 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 101 151 (0) C AluSx SINE/Alu (21) 291 241 1058
ANNOTATION EVIDENCE:
400 5.88 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 101 151 0 C AluSx SINE/Alu 241 291 21
400 5.88 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:30797:15039/1 101 151 (0) C AluSx#SINE/Alu (21) 291 241 m_b4s357i1
E00378:188:HV 101 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 150
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
E00378:188:HV 151 G 151
C AluSx#SINE/Al 241 G 241
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.30
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 1073 7.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:32532:4368/1 1 151 (0) C L1P3 LINE/L1 (2736) 3410 3260 1059
ANNOTATION EVIDENCE:
1073 7.28 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:32532:4368/1 1 151 0 C L1P3_orf2 LINE/L1 1151 1301 1993
1073 7.28 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:32532:4368/1 1 151 (0) C L1P3_orf2#LINE/L1 (1993) 1301 1151 m_b6s551i177
E00378:188:HV 1 TCTAGGAATTCATCACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAG 50
i i vv i
C L1P3_orf2#LIN 1301 TCCAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAG 1252
E00378:188:HV 51 GTATTTATAGTATTCTCCGATGGTAGTTTGTATTTCTGTGGGATCAGTGG 100
i i
C L1P3_orf2#LIN 1251 GTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGG 1202
E00378:188:HV 101 TATTATCCTCTTTATCATTTTTTATTGAGTCTATTTGATTCTTCTCTCTT 150
iv i v
C L1P3_orf2#LIN 1201 TGATATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTT 1152
E00378:188:HV 151 T 151
C L1P3_orf2#LIN 1151 T 1151
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.04
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1199 5.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2209:32532:4368/2 1 151 (0) + L1P3 LINE/L1 2945 3095 (3051) 1060
ANNOTATION EVIDENCE:
1199 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:32532:4368/2 1 151 0 + L1P3_orf2 LINE/L1 836 986 2308
1199 5.30 0.00 0.00 E00378:188:HVMVNCCXX:4:2209:32532:4368/2 1 151 (0) L1P3_orf2#LINE/L1 836 986 (2308) m_b7s551i9
E00378:188:HV 1 ACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 50
i
L1P3_orf2#LIN 836 ACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 885
E00378:188:HV 51 AGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATC 100
? v i
L1P3_orf2#LIN 886 AGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATC 935
E00378:188:HV 101 CAAAATCAACACCCTAACATCACAATTAAAAGAACTAAAGAAGCAAAAGC 150
i i i i
L1P3_orf2#LIN 936 TAAAATCGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGC 985
E00378:188:HV 151 A 151
L1P3_orf2#LIN 986 A 986
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1041 13.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2210:16549:23126/1 2 151 (0) C AluSx SINE/Alu (47) 265 116 1061
ANNOTATION EVIDENCE:
1041 13.33 0.00 0.00 E00378:188:HVMVNCCXX:4:2210:16549:23126/1 2 151 0 C AluSx SINE/Alu 116 265 47
1041 13.33 0.00 0.00 E00378:188:HVMVNCCXX:4:2210:16549:23126/1 2 151 (0) C AluSx#SINE/Alu (47) 265 116 m_b6s356i11
E00378:188:HV 2 TGTCTCCCAGGCTGGAGTGCAATGGTGTGATCTCGGTTCACTTCAGCCTC 51
v i i i i v i
C AluSx#SINE/Al 265 TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTC 216
E00378:188:HV 52 TACCTCCTCGGTTCAAGCAATTCTCCTGCCTCATCCTCCTGAGTAGCTGG 101
ii iv i v i
C AluSx#SINE/Al 215 CGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGG 166
E00378:188:HV 102 GATTACAGGCGCCTGCCACCATGCCCAGCTAATTTTTTTATTTTTCGTAG 151
vi i i v v
C AluSx#SINE/Al 165 GATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAG 116
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.31
Transitions / transversions = 1.86 (13/7)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1068 7.3 3.2 0.0 E00378:188:HVMVNCCXX:4:2210:16549:23126/2 2 151 (0) + L1P3 LINE/L1 3623 3777 (2369) 1062
ANNOTATION EVIDENCE:
1068 7.33 3.22 0.00 E00378:188:HVMVNCCXX:4:2210:16549:23126/2 2 151 0 + L1P3_orf2 LINE/L1 1514 1668 1626
1068 7.33 3.22 0.00 E00378:188:HVMVNCCXX:4:2210:16549:23126/2 2 151 (0) L1P3_orf2#LINE/L1 1514 1668 (1626) m_b6s551i70
E00378:188:HV 2 TCCCTAACTCATTTTATGATGCCAGCATCATCCTGATTCCAAAACCTGGC 51
v v
L1P3_orf2#LIN 1514 TCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAACCTGGC 1563
E00378:188:HV 52 AGAGACACAA--GAAAAAGAAAATTTCAGGCCATTATCCGTGATGAACAT 99
--i v v
L1P3_orf2#LIN 1564 AGAGACACAACAAAAAAAGAAAATTTCAGGCCAATATCCCTGATGAACAT 1613
E00378:188:HV 100 CGATGTGAAAATCCACGATAAAGTACTGGCAAACTGAATCGAGCA---CA 146
i v i i i v ---
L1P3_orf2#LIN 1614 CGATGCGAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACA 1663
E00378:188:HV 147 TCAAA 151
L1P3_orf2#LIN 1664 TCAAA 1668
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.40
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 2.50 (5 / 2)
+ 252 28.5 14.9 0.0 E00378:188:HVMVNCCXX:4:2210:27864:22089/1 15 151 (0) C MIR SINE/MIR (0) 262 102 1063
ANNOTATION EVIDENCE:
252 28.47 14.91 0.00 E00378:188:HVMVNCCXX:4:2210:27864:22089/1 15 151 0 C MIR SINE/MIR 102 262 0
252 28.47 14.91 0.00 E00378:188:HVMVNCCXX:4:2210:27864:22089/1 15 151 (0) C MIR#SINE/MIR (0) 262 102 m_b6s601i28
E00378:188:HV 15 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 57
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
E00378:188:HV 58 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 92
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
E00378:188:HV 93 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 140
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
E00378:188:HV 141 TGAGGTAAAGT 151
v v
C MIR#SINE/MIR 112 AGAGGTTAAGT 102
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.46
Transitions / transversions = 1.44 (23/16)
Gap_init rate = 0.04 (5 / 136), avg. gap size = 4.80 (24 / 5)
+ 237 29.7 7.1 0.0 E00378:188:HVMVNCCXX:4:2211:25875:41391/2 27 117 (34) C L1MC4 LINE/L1 (1441) 6601 6504 1064
ANNOTATION EVIDENCE:
237 29.67 7.14 0.00 E00378:188:HVMVNCCXX:4:2211:25875:41391/2 27 117 34 C L1MC4_3end LINE/L1 1251 1348 1441
237 29.67 7.14 0.00 E00378:188:HVMVNCCXX:4:2211:25875:41391/2 27 117 (34) C L1MC4_3end#LINE/L1 (1441) 1348 1251 m_b3s551i152
E00378:188:HV 27 GTTGATA--GATATCTTCAAATCCAAGCCAACATCACACAGTTGAT---- 70
v -- i i v v i vi v ----
C L1MC4_3end#LI 1348 GTTCATACCGATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTA 1299
E00378:188:HV 71 -CTTTTTTTCTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAA 117
- i iiii v v i v iv iv iii v i
C L1MC4_3end#LI 1298 GCCTTCCCCCTTTCCATATTTGTAACTCCCTTCTCCGACAGTGAGAAA 1251
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.86
Transitions / transversions = 1.45 (16/11)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 628 15.3 0.0 5.9 E00378:188:HVMVNCCXX:4:2212:24342:22493/2 34 151 (0) C AluSx SINE/Alu (8) 304 194 1065
ANNOTATION EVIDENCE:
628 15.32 0.00 5.93 E00378:188:HVMVNCCXX:4:2212:24342:22493/2 34 151 0 C AluSx SINE/Alu 194 304 8
628 15.32 0.00 5.93 E00378:188:HVMVNCCXX:4:2212:24342:22493/2 34 151 (0) C AluSx#SINE/Alu (8) 304 194 m_b5s357i14
E00378:188:HV 34 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 83
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 84 CTGCAGGCTGGAGTGCAGTGGTGCGATATCTGCTCGCTGCAACCTCCGCC 133
--- i v v i
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 134 TAGTAGGTTCAAGCAATT 151
vvii i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATT 194
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.15
Transitions / transversions = 1.43 (10/7)
Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.00 (7 / 7)
+ 1225 6.0 0.0 0.7 E00378:188:HVMVNCCXX:4:2212:25581:49285/2 2 151 (0) C AluY SINE/Alu (23) 288 140 1066
ANNOTATION EVIDENCE:
1225 6.04 0.00 0.67 E00378:188:HVMVNCCXX:4:2212:25581:49285/2 2 151 0 C AluY SINE/Alu 140 288 23
1225 6.04 0.00 0.67 E00378:188:HVMVNCCXX:4:2212:25581:49285/2 2 151 (0) C AluY#SINE/Alu (23) 288 140 m_b2s356i87
E00378:188:HV 2 TTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGC 51
i
C AluY#SINE/Alu 288 TTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGC 239
E00378:188:HV 52 ATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGTTCTC 101
ii v i - i i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTC 190
E00378:188:HV 102 CTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCC 151
i
C AluY#SINE/Alu 189 CTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCC 140
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.10
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 589 17.1 0.0 5.9 E00378:188:HVMVNCCXX:4:2212:25986:22915/2 34 151 (0) C AluSx SINE/Alu (8) 304 194 1067
ANNOTATION EVIDENCE:
589 17.11 0.00 5.93 E00378:188:HVMVNCCXX:4:2212:25986:22915/2 34 151 0 C AluSx SINE/Alu 194 304 8
589 17.11 0.00 5.93 E00378:188:HVMVNCCXX:4:2212:25986:22915/2 34 151 (0) C AluSx#SINE/Alu (8) 304 194 m_b5s357i15
E00378:188:HV 34 TTTTTTGTTTTTGTGTTTTTTTAAGATGGAGGCTCACTCCATCACCCAGG 83
v v v i i v i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 84 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 133
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 134 TAGTAGGTTCAAGCAATT 151
vvii i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATT 194
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 13.27
Transitions / transversions = 1.11 (10/9)
Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.00 (7 / 7)
+ 1296 0.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2212:5396:40196/1 1 151 (0) C L1P1 LINE/L1 (838) 5308 5158 1068
ANNOTATION EVIDENCE:
1296 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2212:5396:40196/1 1 151 0 C L1P1_orf2 LINE/L1 3049 3199 95
1296 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2212:5396:40196/1 1 151 (0) C L1P1_orf2#LINE/L1 (95) 3199 3049 m_b1s551i126
E00378:188:HV 1 TGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGAT 50
C L1P1_orf2#LIN 3199 TGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGAT 3150
E00378:188:HV 51 ATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGT 100
i
C L1P1_orf2#LIN 3149 ATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGT 3100
E00378:188:HV 101 AGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCT 150
C L1P1_orf2#LIN 3099 AGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCT 3050
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 3049 T 3049
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1297 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2212:5396:40196/2 1 151 (0) + L1P1 LINE/L1 4873 5023 (1123) 1069
ANNOTATION EVIDENCE:
1297 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2212:5396:40196/2 1 151 0 + L1P1_orf2 LINE/L1 2764 2914 380
1297 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2212:5396:40196/2 1 151 (0) L1P1_orf2#LINE/L1 2764 2914 (380) m_b1s551i3
E00378:188:HV 1 AAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGA 50
L1P1_orf2#LIN 2764 AAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGA 2813
E00378:188:HV 51 AAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACAC 100
L1P1_orf2#LIN 2814 AAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACAC 2863
E00378:188:HV 101 CTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCT 150
v v i i
L1P1_orf2#LIN 2864 CTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCT 2913
E00378:188:HV 151 A 151
L1P1_orf2#LIN 2914 A 2914
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 843 6.6 0.7 7.5 E00378:188:HVMVNCCXX:4:2213:18873:45048/1 5 151 (0) C L1P3 LINE/L1 (2916) 3230 3094 1070
ANNOTATION EVIDENCE:
843 6.61 0.73 7.48 E00378:188:HVMVNCCXX:4:2213:18873:45048/1 5 151 0 C L1P3_orf2 LINE/L1 985 1121 2173
843 6.61 0.73 7.48 E00378:188:HVMVNCCXX:4:2213:18873:45048/1 5 151 (0) C L1P3_orf2#LINE/L1 (2173) 1121 985 m_b6s551i235
E00378:188:HV 5 TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTACTGGATTAATTGATTTT 54
i i v v -
C L1P3_orf2#LIN 1121 TCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTT 1073
E00378:188:HV 55 TTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGC 103
i i---------- -i v
C L1P3_orf2#LIN 1072 TTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGC 1033
E00378:188:HV 104 TCTGAGCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTG 151
v
C L1P3_orf2#LIN 1032 TCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTG 985
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.21
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.08 (12 / 146), avg. gap size = 1.00 (12 / 12)
+ 1065 8.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2213:18873:45048/2 1 151 (0) + L1P3 LINE/L1 2945 3095 (3051) 1071
ANNOTATION EVIDENCE:
1065 8.61 0.00 0.00 E00378:188:HVMVNCCXX:4:2213:18873:45048/2 1 151 0 + L1P3_orf2 LINE/L1 836 986 2308
1065 8.61 0.00 0.00 E00378:188:HVMVNCCXX:4:2213:18873:45048/2 1 151 (0) L1P3_orf2#LINE/L1 836 986 (2308) m_b7s551i10
E00378:188:HV 1 ACAAAGACACAATGTACCAGAATCTCTGGGACACCGCTAAAGGAGTGGGT 50
i v v vv
L1P3_orf2#LIN 836 ACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTT 885
E00378:188:HV 51 AGAGGGAAATTTATAGCACTAAAGGCCCACAGGACAAAGTGGGGAAGATC 100
v ? v i i
L1P3_orf2#LIN 886 AGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATC 935
E00378:188:HV 101 TAAAATCAACACCCTAACATCACAATTAAAAGAACGAGATAAGCAAGAGC 150
i v v
L1P3_orf2#LIN 936 TAAAATCGACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGC 985
E00378:188:HV 151 A 151
L1P3_orf2#LIN 986 A 986
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.48
Transitions / transversions = 0.50 (4/8)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1303 2.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2213:3863:60993/1 1 151 (0) C L1P1 LINE/L1 (335) 5820 5670 1072
ANNOTATION EVIDENCE:
1303 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2213:3863:60993/1 1 151 0 C L1PA2_3end LINE/L1 417 567 335
1303 2.65 0.00 0.00 E00378:188:HVMVNCCXX:4:2213:3863:60993/1 1 151 (0) C L1PA2_3end#LINE/L1 (335) 567 417 m_b1s551i323
E00378:188:HV 1 ATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGTTGCT 50
v v
C L1PA2_3end#LI 567 ATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCT 518
E00378:188:HV 51 TAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCT 100
C L1PA2_3end#LI 517 TAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCT 468
E00378:188:HV 101 ATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCG 150
i i
C L1PA2_3end#LI 467 ATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCA 418
E00378:188:HV 151 G 151
C L1PA2_3end#LI 417 G 417
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1299 3.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2213:3863:60993/2 1 151 (0) + L1P1 LINE/L1 5463 5613 (542) 1073
ANNOTATION EVIDENCE:
1299 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:2213:3863:60993/2 1 151 0 + L1PA3_3end LINE/L1 210 360 542
1299 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:2213:3863:60993/2 1 151 (0) L1PA3_3end#LINE/L1 210 360 (542) m_b1s551i264
E00378:188:HV 1 AATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTG 50
i
L1PA3_3end#LI 210 AATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTG 259
E00378:188:HV 51 GAGAAATAGGAATCCTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAA 100
iv
L1PA3_3end#LI 260 GAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAA 309
E00378:188:HV 101 CCATTGTGGAAGTCAGTGTGGTGATTCCTCAGGGATCTAGAACTGGAAAT 150
i i
L1PA3_3end#LI 310 CCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAAT 359
E00378:188:HV 151 A 151
L1PA3_3end#LI 360 A 360
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 428 3.1 0.0 0.3 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 1 59 (92) C L1PA3 LINE/L1 (93) 6062 6004 1074
ANNOTATION EVIDENCE:
307 15.51 0.00 1.69 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 1 59 92 C L1PA6_3end LINE/L1 751 808 93
307 15.51 0.00 1.69 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 1 59 (92) C L1PA6_3end#LINE/L1 (93) 808 751 m_b1s551i420
E00378:188:HV 1 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTAGCG 50
ii i - v i v v
C L1PA6_3end#LI 808 GCACCCATCAACTCGTCATTTA-CATTAGGTATTTCTCCTAATGCTATCC 760
E00378:188:HV 51 CTGCACCAG 59
v v
C L1PA6_3end#LI 759 CTCCCCCAG 751
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.42
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)
428 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 1 47 104 C L1PA3_3end LINE/L1 763 809 93
428 0.00 0.00 0.00 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 1 47 (104) C L1PA3_3end#LINE/L1 (93) 809 763 m_b1s551i421
E00378:188:HV 1 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTA 47
C L1PA3_3end#LI 809 GCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTA 763
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 11 23.0 0.0 8.2 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 65 117 (34) + G-rich Low_complexity 1 49 (0) 1075
ANNOTATION EVIDENCE:
11 23.00 0.00 8.16 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 65 117 34 + (CGGGTGG)n Simple_repeat 1 49 0
11 23.00 0.00 8.16 E00378:188:HVMVNCCXX:4:2214:12966:62734/1 65 117 (34) (CGGGTGG)n#Simple_repeat 1 49 (0) m_b1s252i8
E00378:188:HV 65 CGGGCGGCGAGTGTCGGGCCAGGGGTGGTCGCGGGCTGCGGGGTGGCTGG 114
i i v --v v - v - vv v
(CGGGTGG)n#Si 1 CGGGTGGCGGGTGGCGGG--TGGCG-GGTGGCGGG-TGGCGGGTGGCGGG 46
E00378:188:HV 115 TGG 117
(CGGGTGG)n#Si 47 TGG 49
Matrix = Unknown
Transitions / transversions = 0.29 (2/7)
Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4)
+ 1180 7.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2214:12966:62734/2 1 149 (2) + L1P1 LINE/L1 5599 5747 (408) 1076
ANNOTATION EVIDENCE:
1180 7.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2214:12966:62734/2 1 149 2 + L1PA2_3end LINE/L1 346 494 408
1180 7.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2214:12966:62734/2 1 149 (2) L1PA2_3end#LINE/L1 346 494 (408) m_b1s551i302
E00378:188:HV 1 CTAGAACTGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATA 50
i
L1PA2_3end#LI 346 CTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATA 395
E00378:188:HV 51 CCCAAAGGACTATAAATCATGCCGCTATAAAGACACATGCACACGTATGT 100
i
L1PA2_3end#LI 396 CCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGT 445
E00378:188:HV 101 GTATTGTGGCTTTATTCGCAATGGCAATGGCTTGGAACCACTCCAAATG 149
v i v i i v i vi
L1PA2_3end#LI 446 TTATTGCGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATG 494
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.13
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1154 11.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2214:31527:41585/1 1 151 (0) + AluSx SINE/Alu 24 174 (138) 1077
ANNOTATION EVIDENCE:
1154 11.26 0.00 0.00 E00378:188:HVMVNCCXX:4:2214:31527:41585/1 1 151 0 + AluSx SINE/Alu 24 174 138
1154 11.26 0.00 0.00 E00378:188:HVMVNCCXX:4:2214:31527:41585/1 1 151 (0) AluSx#SINE/Alu 24 174 (138) m_b2s356i33
E00378:188:HV 1 TGTAATCTCAGCAATTTGGGAGGCAGAGCCAGGTGGATCACCTGAGGTCG 50
i v v v i i i
AluSx#SINE/Al 24 TGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA 73
E00378:188:HV 51 GGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAA 100
i ii i v
AluSx#SINE/Al 74 GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAA 123
E00378:188:HV 101 AATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTAC 150
i i i v i
AluSx#SINE/Al 124 AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTAC 173
E00378:188:HV 151 T 151
AluSx#SINE/Al 174 T 174
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.46
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 234 29.5 0.0 1.1 E00378:188:HVMVNCCXX:4:2214:31527:41585/2 1 89 (62) C L1M5 LINE/L1 (293) 5831 5744 1078
ANNOTATION EVIDENCE:
234 29.54 0.00 1.12 E00378:188:HVMVNCCXX:4:2214:31527:41585/2 1 89 62 C L1ME4a_3end LINE/L1 491 578 293
234 29.54 0.00 1.12 E00378:188:HVMVNCCXX:4:2214:31527:41585/2 1 89 (62) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i514
E00378:188:HV 1 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATATAGACATATT 50
i- ? v vi v iii ii i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
E00378:188:HV 51 ACAGGTTATATATCCATTTTACTATTGTTGAACATTTAG 89
i iv v v ? iiv i
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
+ 240 29.7 7.1 0.0 E00378:188:HVMVNCCXX:4:2215:2412:58409/1 29 119 (32) C L1MC4 LINE/L1 (1441) 6601 6504 1079
ANNOTATION EVIDENCE:
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:4:2215:2412:58409/1 29 119 32 C L1MC4_3end LINE/L1 1251 1348 1441
240 29.67 7.14 0.00 E00378:188:HVMVNCCXX:4:2215:2412:58409/1 29 119 (32) C L1MC4_3end#LINE/L1 (1441) 1348 1251 m_b3s551i151
E00378:188:HV 29 GTTGATA--GATATCTTCAAATCCAAGCCAACATCACACAGTTTAT---- 72
v -- i i v v i vi i ----
C L1MC4_3end#LI 1348 GTTCATACCGATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTA 1299
E00378:188:HV 73 -CTTTTTTTCTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAA 119
- i iiii v v i v iv iv iii v i
C L1MC4_3end#LI 1298 GCCTTCCCCCTTTCCATATTTGTAACTCCCTTCTCCGACAGTGAGAAA 1251
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.16
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 16 19.1 0.0 0.0 E00378:188:HVMVNCCXX:4:2215:26139:65898/1 43 72 (79) + (TG)n Simple_repeat 1 30 (0) 1080
ANNOTATION EVIDENCE:
16 19.09 0.00 0.00 E00378:188:HVMVNCCXX:4:2215:26139:65898/1 43 72 79 + (TG)n Simple_repeat 1 30 0
16 19.09 0.00 0.00 E00378:188:HVMVNCCXX:4:2215:26139:65898/1 43 72 (79) (TG)n#Simple_repeat 1 30 (0) m_b3s252i3
E00378:188:HV 43 TGTGTGTATCTGCGTATGAGTGTGTGTGTG 72
i v i i v
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 30
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1002 11.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2215:2909:19926/2 2 134 (17) C AluSx SINE/Alu (179) 133 1 1081
ANNOTATION EVIDENCE:
1002 11.28 0.00 0.00 E00378:188:HVMVNCCXX:4:2215:2909:19926/2 2 134 17 C AluSx SINE/Alu 1 133 179
1002 11.28 0.00 0.00 E00378:188:HVMVNCCXX:4:2215:2909:19926/2 2 134 (17) C AluSx#SINE/Alu (179) 133 1 m_b5s357i47
E00378:188:HV 2 TTTTTGTATTTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGT 51
i v i
C AluSx#SINE/Al 133 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGT 84
E00378:188:HV 52 CCCAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGT 101
i i i i i i i
C AluSx#SINE/Al 83 CTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC 34
E00378:188:HV 102 TGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 134
i vi i i
C AluSx#SINE/Al 33 TGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.41
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
+ 1228 2.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2215:4807:13791/2 1 149 (2) C L1P1 LINE/L1 (1022) 5124 4976 1082
ANNOTATION EVIDENCE:
1228 2.68 0.00 0.00 E00378:188:HVMVNCCXX:4:2215:4807:13791/2 1 149 2 C L1P1_orf2 LINE/L1 2867 3015 279
1228 2.68 0.00 0.00 E00378:188:HVMVNCCXX:4:2215:4807:13791/2 1 149 (2) C L1P1_orf2#LINE/L1 (279) 3015 2867 m_b1s551i52
E00378:188:HV 1 TTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGC 50
C L1P1_orf2#LIN 3015 TTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGC 2966
E00378:188:HV 51 CTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTT 100
?
C L1P1_orf2#LIN 2965 CTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTT 2916
E00378:188:HV 101 TTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTAT 149
i i v
C L1P1_orf2#LIN 2915 TTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTAT 2867
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1200 6.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2217:13595:61819/2 1 151 (0) C L1P1 LINE/L1 (1085) 5061 4911 1083
ANNOTATION EVIDENCE:
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:4:2217:13595:61819/2 1 151 0 C L1P1_orf2 LINE/L1 2802 2952 342
1200 5.96 0.00 0.00 E00378:188:HVMVNCCXX:4:2217:13595:61819/2 1 151 (0) C L1P1_orf2#LINE/L1 (342) 2952 2802 m_b1s551i26
E00378:188:HV 1 GGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGT 50
? i
C L1P1_orf2#LIN 2952 GGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGT 2903
E00378:188:HV 51 TTAAGTCTTTAATCCATCTTGGATTGATTTTTCTATCAGGGGTAAGGAAG 100
i i v v v
C L1P1_orf2#LIN 2902 TTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAG 2853
E00378:188:HV 101 GGATCCAGTTTCGGCTTTCTACATATGGCGAGCCAGTTTTCCCAGCACCA 150
i v
C L1P1_orf2#LIN 2852 GGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCA 2803
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2802 T 2802
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.89
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1117 6.0 3.2 0.0 E00378:188:HVMVNCCXX:4:2218:19106:72069/1 1 151 (0) C L1P3 LINE/L1 (2358) 3788 3633 1084
ANNOTATION EVIDENCE:
1117 5.96 3.20 0.00 E00378:188:HVMVNCCXX:4:2218:19106:72069/1 1 151 0 C L1P3_orf2 LINE/L1 1524 1679 1615
1117 5.96 3.20 0.00 E00378:188:HVMVNCCXX:4:2218:19106:72069/1 1 151 (0) C L1P3_orf2#LINE/L1 (1615) 1679 1524 m_b6s551i67
E00378:188:HV 1 TGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATC 47
v --- i i
C L1P3_orf2#LIN 1679 TGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATT 1630
E00378:188:HV 48 GAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCTT 97
i v v
C L1P3_orf2#LIN 1629 GAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCTT 1580
E00378:188:HV 98 TTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATCA 145
i-- v v
C L1P3_orf2#LIN 1579 TTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCA 1530
E00378:188:HV 146 TAAAAT 151
C L1P3_orf2#LIN 1529 TAAAAT 1524
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 1221 2.7 1.3 0.0 E00378:188:HVMVNCCXX:4:2218:19106:72069/2 2 151 (0) + L1P3 LINE/L1 3397 3548 (2598) 1085
ANNOTATION EVIDENCE:
1221 2.67 1.31 0.00 E00378:188:HVMVNCCXX:4:2218:19106:72069/2 2 151 0 + L1P3_orf2 LINE/L1 1288 1439 1855
1221 2.67 1.31 0.00 E00378:188:HVMVNCCXX:4:2218:19106:72069/2 2 151 (0) L1P3_orf2#LINE/L1 1288 1439 (1855) m_b6s551i135
E00378:188:HV 2 GATAAATTCCTAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGT 49
i v -- v
L1P3_orf2#LIN 1288 GATAAATTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGT 1337
E00378:188:HV 50 CGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTA 99
L1P3_orf2#LIN 1338 CGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTA 1387
E00378:188:HV 100 ATAGCCTACCAACCAAAAAAAGCCCAGGACCAGAGGGATTCACAGCCGAA 149
v
L1P3_orf2#LIN 1388 ATAGCCTACCAACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGAA 1437
E00378:188:HV 150 TT 151
L1P3_orf2#LIN 1438 TT 1439
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2218:19745:8693/1 30 61 (90) + (CA)n Simple_repeat 1 32 (0) 1086
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2218:19745:8693/1 30 61 90 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 E00378:188:HVMVNCCXX:4:2218:19745:8693/1 30 61 (90) (CA)n#Simple_repeat 1 32 (0) m_b4s252i36
E00378:188:HV 30 CATACATGCACACACATACACACACACACACA 61
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 239 30.1 5.1 0.0 E00378:188:HVMVNCCXX:4:2218:19745:8693/2 7 99 (52) C MIRb SINE/MIR (49) 219 122 1087
ANNOTATION EVIDENCE:
239 30.11 5.11 0.00 E00378:188:HVMVNCCXX:4:2218:19745:8693/2 7 99 52 C MIRb SINE/MIR 122 219 49
239 30.11 5.11 0.00 E00378:188:HVMVNCCXX:4:2218:19745:8693/2 7 99 (52) C MIRb#SINE/MIR (49) 219 122 m_b4s601i20
E00378:188:HV 7 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 52
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
E00378:188:HV 53 CACGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 99
v v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.18
Transitions / transversions = 1.80 (18/10)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 764 10.5 1.9 0.0 E00378:188:HVMVNCCXX:4:2219:14641:18379/1 47 151 (0) + AluSx SINE/Alu 1 107 (205) 1088
ANNOTATION EVIDENCE:
764 10.48 1.86 0.00 E00378:188:HVMVNCCXX:4:2219:14641:18379/1 47 151 0 + AluSx SINE/Alu 1 107 205
764 10.48 1.86 0.00 E00378:188:HVMVNCCXX:4:2219:14641:18379/1 47 151 (0) AluSx#SINE/Alu 1 107 (205) m_b4s357i48
E00378:188:HV 47 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 96
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
E00378:188:HV 97 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 144
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
E00378:188:HV 145 GGTGAAA 151
AluSx#SINE/Al 101 GGTGAAA 107
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.65
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 104), avg. gap size = 2.00 (2 / 1)
+ 19 4.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2219:14641:18379/2 86 109 (42) + (TG)n Simple_repeat 1 24 (0) 1089
ANNOTATION EVIDENCE:
19 4.35 0.00 0.00 E00378:188:HVMVNCCXX:4:2219:14641:18379/2 86 109 42 + (TG)n Simple_repeat 1 24 0
19 4.35 0.00 0.00 E00378:188:HVMVNCCXX:4:2219:14641:18379/2 86 109 (42) (TG)n#Simple_repeat 1 24 (0) m_b4s252i35
E00378:188:HV 86 TGTGTGTGTGTGTGTATGTGTGTG 109
i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 1135 11.9 0.0 0.0 E00378:188:HVMVNCCXX:4:2219:28909:35397/2 1 151 (0) C AluSx SINE/Alu (101) 211 61 1090
ANNOTATION EVIDENCE:
1135 11.92 0.00 0.00 E00378:188:HVMVNCCXX:4:2219:28909:35397/2 1 151 0 C AluSx SINE/Alu 61 211 101
1135 11.92 0.00 0.00 E00378:188:HVMVNCCXX:4:2219:28909:35397/2 1 151 (0) C AluSx#SINE/Alu (101) 211 61 m_b2s356i27
E00378:188:HV 1 TCCTGAGTTCAAGTGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATT 50
i i i i i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATT 162
E00378:188:HV 51 ACAGGTGCCCACCACCACACCCAGCTAATTTTTGTATTTTAAATAGAGAC 100
i v i i i v i
C AluSx#SINE/Al 161 ACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGAC 112
E00378:188:HV 101 AAGGTTTCACCATCTTGCCCAGGCTGGTTTCGAACTCCGGACCTCAGGTG 150
ii v v i v
C AluSx#SINE/Al 111 GGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTG 62
E00378:188:HV 151 A 151
C AluSx#SINE/Al 61 A 61
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.54
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1237 3.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2219:29488:5141/2 1 151 (0) C L1P1 LINE/L1 (930) 5216 5066 1091
ANNOTATION EVIDENCE:
1237 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:2219:29488:5141/2 1 151 0 C L1P1_orf2 LINE/L1 2957 3107 187
1237 3.31 0.00 0.00 E00378:188:HVMVNCCXX:4:2219:29488:5141/2 1 151 (0) C L1P1_orf2#LINE/L1 (187) 3107 2957 m_b1s551i90
E00378:188:HV 1 CATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCA 50
i
C L1P1_orf2#LIN 3107 CATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCA 3058
E00378:188:HV 51 GAAGCTCTTTGGTTTAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTG 100
i i v
C L1P1_orf2#LIN 3057 GAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTG 3008
E00378:188:HV 101 CCATTGCTTTTGGAGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCC 150
v
C L1P1_orf2#LIN 3007 CCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCC 2958
E00378:188:HV 151 T 151
C L1P1_orf2#LIN 2957 T 2957
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1122 6.0 3.2 0.0 E00378:188:HVMVNCCXX:4:2220:17482:63595/1 1 151 (0) + L1P3 LINE/L1 3631 3786 (2360) 1092
ANNOTATION EVIDENCE:
1122 5.96 3.20 0.00 E00378:188:HVMVNCCXX:4:2220:17482:63595/1 1 151 0 + L1P3_orf2 LINE/L1 1522 1677 1617
1122 5.96 3.20 0.00 E00378:188:HVMVNCCXX:4:2220:17482:63595/1 1 151 (0) L1P3_orf2#LINE/L1 1522 1677 (1617) m_b6s551i69
E00378:188:HV 1 TCATTTTATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACAC 50
v v
L1P3_orf2#LIN 1522 TCATTTTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGAGACAC 1571
E00378:188:HV 51 AA--GAAAAAGAAAATTTCAGGCCATTATCCGTGATGAACATCGATGTGA 98
--i v v i
L1P3_orf2#LIN 1572 AACAAAAAAAGAAAATTTCAGGCCAATATCCCTGATGAACATCGATGCGA 1621
E00378:188:HV 99 AAATCCTCGATAAAATACTGGCAAACTGAATCCAGCA---CATCAAAACG 145
i i --- v
L1P3_orf2#LIN 1622 AAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAG 1671
E00378:188:HV 146 CTTATC 151
L1P3_orf2#LIN 1672 CTTATC 1677
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 896 8.0 0.0 0.0 E00378:188:HVMVNCCXX:4:2220:17482:63595/2 1 112 (39) C AluSx SINE/Alu (187) 125 14 1093
ANNOTATION EVIDENCE:
896 8.04 0.00 0.00 E00378:188:HVMVNCCXX:4:2220:17482:63595/2 1 112 39 C AluSx SINE/Alu 14 125 187
896 8.04 0.00 0.00 E00378:188:HVMVNCCXX:4:2220:17482:63595/2 1 112 (39) C AluSx#SINE/Alu (187) 125 14 m_b6s357i12
E00378:188:HV 1 TTTTTCGTAGAGATGGAGTTTCACCATGTTGGCCAGGCTGGTCTTGAACT 50
v i i i
C AluSx#SINE/Al 125 TTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACT 76
E00378:188:HV 51 CCTGACCTCAGGTGATCCACCCACCTTGTCCTCCCAAAGTGCTGAGATTA 100
i i i v i
C AluSx#SINE/Al 75 CCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA 26
E00378:188:HV 101 CAGGCGTGAGCC 112
C AluSx#SINE/Al 25 CAGGCGTGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.14
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
+ 259 5.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2220:17482:63595/2 115 151 (0) C L1P3 LINE/L1 (2248) 3898 3862 1094
ANNOTATION EVIDENCE:
259 5.41 0.00 0.00 E00378:188:HVMVNCCXX:4:2220:17482:63595/2 115 151 0 C L1P3_orf2 LINE/L1 1753 1789 1505
259 5.41 0.00 0.00 E00378:188:HVMVNCCXX:4:2220:17482:63595/2 115 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1753 m_b6s551i0
E00378:188:HV 115 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTG 151
i v
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTG 1753
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.62
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2221:2879:28945/2 81 125 (26) C MIR SINE/MIR (0) 262 218 1095
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:4:2221:2879:28945/2 81 125 26 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:4:2221:2879:28945/2 81 125 (26) C MIR#SINE/MIR (0) 262 218 m_b6s601i8
E00378:188:HV 81 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 125
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 E00378:188:HVMVNCCXX:4:2221:3468:28874/2 81 125 (26) C MIR SINE/MIR (0) 262 218 1096
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:4:2221:3468:28874/2 81 125 26 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 E00378:188:HVMVNCCXX:4:2221:3468:28874/2 81 125 (26) C MIR#SINE/MIR (0) 262 218 m_b6s601i9
E00378:188:HV 81 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 125
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 16 19.1 0.0 0.0 E00378:188:HVMVNCCXX:4:2221:4980:59868/1 103 132 (19) + (CA)n Simple_repeat 1 30 (0) 1097
ANNOTATION EVIDENCE:
16 19.09 0.00 0.00 E00378:188:HVMVNCCXX:4:2221:4980:59868/1 103 132 19 + (CA)n Simple_repeat 1 30 0
16 19.09 0.00 0.00 E00378:188:HVMVNCCXX:4:2221:4980:59868/1 103 132 (19) (CA)n#Simple_repeat 1 30 (0) m_b3s252i2
E00378:188:HV 103 CACACACACACTCATACGCAGATACACACA 132
v i i v i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACA 30
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 563 18.0 18.0 0.0 E00378:188:HVMVNCCXX:4:2221:4980:59868/2 2 151 (0) + L1MC4 LINE/L1 7461 7643 (399) 1098
ANNOTATION EVIDENCE:
563 18.00 18.03 0.00 E00378:188:HVMVNCCXX:4:2221:4980:59868/2 2 151 0 + L1MC4_3end LINE/L1 2208 2390 399
563 18.00 18.03 0.00 E00378:188:HVMVNCCXX:4:2221:4980:59868/2 2 151 (0) L1MC4_3end#LINE/L1 2208 2390 (399) m_b3s551i103
E00378:188:HV 2 ATTCTCGTCAAA---GTATAA-----ATTTAATCATAAGGAAACATCAGA 43
ii i --- i ----- i i
L1MC4_3end#LI 2208 ATTCCTGCCAAAAATGCATAACCTGAATCTAATCATGAGGAAACATCAGA 2257
E00378:188:HV 44 CAAACTCAGAGCAAGGGAC-------------------CTGTACTATTCA 74
i i vii ------------------- v
L1MC4_3end#LI 2258 CAAACCCAAATTGAGGGACATTCTACAAAATAACTGGCCTGTACTCTTCA 2307
E00378:188:HV 75 AATATATGAAGGTCATGATAAATAAAAAAA------AGAACTGTTCCAGA 118
v i v ? v i i i ------i
L1MC4_3end#LI 2308 AAAATGTCAANGTCATGAAAGACAAAGAAAGACTGAGGAACTGTTCCAGA 2357
E00378:188:HV 119 TTGAAGGAGACTAAACAGACTACACACCTAAAT 151
i v vvv v
L1MC4_3end#LI 2358 TTAAAGGAGACTAAAGAGACATGACAACTAAAT 2390
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.16
Transitions / transversions = 1.60 (16/10)
Gap_init rate = 0.03 (4 / 149), avg. gap size = 8.25 (33 / 4)
+ 781 6.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2222:17432:7392/1 2 96 (55) C AluSx SINE/Alu (204) 108 14 1099
ANNOTATION EVIDENCE:
781 6.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2222:17432:7392/1 2 96 55 C AluSx SINE/Alu 14 108 204
781 6.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2222:17432:7392/1 2 96 (55) C AluSx#SINE/Alu (204) 108 14 m_b6s357i16
E00378:188:HV 2 GTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATC 51
i
C AluSx#SINE/Al 108 GTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATC 59
E00378:188:HV 52 CACCCACCTTGTCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCC 96
i i i v i
C AluSx#SINE/Al 58 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.57
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0)
+ 365 5.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2222:17432:7392/1 99 151 (0) C L1P3 LINE/L1 (2248) 3898 3846 1100
ANNOTATION EVIDENCE:
365 5.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2222:17432:7392/1 99 151 0 C L1P3_orf2 LINE/L1 1737 1789 1505
365 5.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2222:17432:7392/1 99 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1737 m_b6s551i7
E00378:188:HV 99 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 148
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
E00378:188:HV 149 ATT 151
C L1P3_orf2#LIN 1739 ATT 1737
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.08
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 1211 4.0 1.3 0.0 E00378:188:HVMVNCCXX:4:2222:17432:7392/2 1 150 (1) + L1P3 LINE/L1 3576 3727 (2419) 1101
ANNOTATION EVIDENCE:
1211 4.00 1.31 0.00 E00378:188:HVMVNCCXX:4:2222:17432:7392/2 1 150 1 + L1P3_orf2 LINE/L1 1467 1618 1676
1211 4.00 1.31 0.00 E00378:188:HVMVNCCXX:4:2222:17432:7392/2 1 150 (1) L1P3_orf2#LINE/L1 1467 1618 (1676) m_b6s551i82
E00378:188:HV 1 ACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCC 50
i
L1P3_orf2#LIN 1467 ACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCC 1516
E00378:188:HV 51 CTAACTCATTTTATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGA 100
v v
L1P3_orf2#LIN 1517 CTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGA 1566
E00378:188:HV 101 GACACAA--GAAAAAGAAAATTTCAGGCCATTATCCGTGATGAACATCGA 148
--i v v
L1P3_orf2#LIN 1567 GACACAACAAAAAAAGAAAATTTCAGGCCAATATCCCTGATGAACATCGA 1616
E00378:188:HV 149 TG 150
L1P3_orf2#LIN 1617 TG 1618
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.11
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 239 14.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2222:6573:10169/2 1 34 (117) + SVA_A Retroposon/SVA 403 436 (951) 1102
ANNOTATION EVIDENCE:
239 14.71 0.00 0.00 E00378:188:HVMVNCCXX:4:2222:6573:10169/2 1 34 117 + SVA_A Retroposon/SVA 403 436 951
239 14.71 0.00 0.00 E00378:188:HVMVNCCXX:4:2222:6573:10169/2 1 34 (117) SVA_A#Retroposon/SVA 403 436 (951) m_b5s502i6
E00378:188:HV 1 CCCACCTTGGCCTCCCAAAGTGTTGGGATTACAG 34
ii i i i
SVA_A#Retropo 403 CCTGCCTTGGCCTCCCAAAGTGCTAGGATTGCAG 436
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.42
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 1287 0.7 0.0 0.0 E00378:188:HVMVNCCXX:4:2223:29021:52537/1 1 151 (0) C L1P1 LINE/L1 (702) 5453 5303 1103
ANNOTATION EVIDENCE:
1287 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2223:29021:52537/1 1 151 0 C L1PA2_3end LINE/L1 50 200 702
1287 0.66 0.00 0.00 E00378:188:HVMVNCCXX:4:2223:29021:52537/1 1 151 (0) C L1PA2_3end#LINE/L1 (702) 200 50 m_b1s551i190
E00378:188:HV 1 GTGAGATGGTATCTCATTGTGGTTTTGATTAGCATTTCTCTGATGGCCAG 50
v
C L1PA2_3end#LI 200 GTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAG 151
E00378:188:HV 51 TGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 100
C L1PA2_3end#LI 150 TGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 101
E00378:188:HV 101 TTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTT 150
C L1PA2_3end#LI 100 TTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTT 51
E00378:188:HV 151 G 151
C L1PA2_3end#LI 50 G 50
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 375 5.6 0.0 0.0 E00378:188:HVMVNCCXX:4:2223:5365:21262/1 1 54 (97) + L1P3 LINE/L1 3845 3898 (2248) 1104
ANNOTATION EVIDENCE:
375 5.56 0.00 0.00 E00378:188:HVMVNCCXX:4:2223:5365:21262/1 1 54 97 + L1P3_orf2 LINE/L1 1736 1789 1505
375 5.56 0.00 0.00 E00378:188:HVMVNCCXX:4:2223:5365:21262/1 1 54 (97) L1P3_orf2#LINE/L1 1736 1789 (1505) m_b6s551i8
E00378:188:HV 1 CAATAAACATAATCCATCACATAAACAGAACGAATGACAAAAACTACATG 50
i v i
L1P3_orf2#LIN 1736 CAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAACCACATG 1785
E00378:188:HV 51 ATTA 54
L1P3_orf2#LIN 1786 ATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.00
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 822 6.3 0.0 0.0 E00378:188:HVMVNCCXX:4:2223:5365:21262/1 57 151 (0) + AluSx SINE/Alu 14 108 (204) 1105
ANNOTATION EVIDENCE:
822 6.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2223:5365:21262/1 57 151 0 + AluSx SINE/Alu 14 108 204
822 6.32 0.00 0.00 E00378:188:HVMVNCCXX:4:2223:5365:21262/1 57 151 (0) AluSx#SINE/Alu 14 108 (204) m_b6s356i24
E00378:188:HV 57 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 106
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
E00378:188:HV 107 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAAC 151
i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAAC 108
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.57
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0)
+ 1045 12.7 0.0 0.7 E00378:188:HVMVNCCXX:4:2223:5365:21262/2 1 151 (0) C AluSx SINE/Alu (26) 286 137 1106
ANNOTATION EVIDENCE:
1045 12.66 0.00 0.66 E00378:188:HVMVNCCXX:4:2223:5365:21262/2 1 151 0 C AluSx SINE/Alu 137 286 26
1045 12.66 0.00 0.66 E00378:188:HVMVNCCXX:4:2223:5365:21262/2 1 151 (0) C AluSx#SINE/Alu (26) 286 137 m_b6s356i3
E00378:188:HV 1 TTTTGAGATGGAGTTTCGCTCATGTCTCCCAGGCTGGAGTGCAATGGTGT 50
i i - v i i i
C AluSx#SINE/Al 286 TTTTGAGACGGAGTCTCGCTC-TGTCGCCCAGGCTGGAGTGCAGTGGCGC 238
E00378:188:HV 51 GATCTCGGTTCACTTCAGCCTCTGCCTCCTCGGTTCAAGCAATTCTCCTG 100
i v i i iv i
C AluSx#SINE/Al 237 GATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTG 188
E00378:188:HV 101 CCTCATCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCCAG 150
v i vi i i
C AluSx#SINE/Al 187 CCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGG 138
E00378:188:HV 151 C 151
C AluSx#SINE/Al 137 C 137
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.99
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 613 15.8 0.0 5.8 E00378:188:HVMVNCCXX:4:2224:16478:35696/1 31 151 (0) C AluSx SINE/Alu (8) 304 191 1107
ANNOTATION EVIDENCE:
613 15.79 0.00 5.79 E00378:188:HVMVNCCXX:4:2224:16478:35696/1 31 151 0 C AluSx SINE/Alu 191 304 8
613 15.79 0.00 5.79 E00378:188:HVMVNCCXX:4:2224:16478:35696/1 31 151 (0) C AluSx#SINE/Alu (8) 304 191 m_b5s357i16
E00378:188:HV 31 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 80
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
E00378:188:HV 81 CTGCAGGCTGGAGTGCAGTGGGGCTATATCTGCTCACTGCAACCTCCGCC 130
--- v v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
E00378:188:HV 131 TAGTAGGTTCAAGCAATTGTC 151
vvii i v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTC 191
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 12.79
Transitions / transversions = 0.80 (8/10)
Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7)
+ 588 14.4 0.0 1.9 E00378:188:HVMVNCCXX:4:2224:19400:67234/2 46 151 (0) C AluSx SINE/Alu (8) 304 201 1108
ANNOTATION EVIDENCE:
588 14.42 0.00 1.89 E00378:188:HVMVNCCXX:4:2224:19400:67234/2 46 151 0 C AluSx SINE/Alu 201 304 8
588 14.42 0.00 1.89 E00378:188:HVMVNCCXX:4:2224:19400:67234/2 46 151 (0) C AluSx#SINE/Alu (8) 304 201 m_b2s357i8
E00378:188:HV 46 TTTTTTTTTTTTTTTTTTTTTTGAGAGAGAGTCTCGCTTCGTCAAACCCG 95
vi ii i-- i
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCA 257
E00378:188:HV 96 GGCTGGATTGCTGTGGCATGATCTCCGCTCACTGCAATCTCTGCCTCCTG 145
v v ii v i i i
C AluSx#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCG 207
E00378:188:HV 146 TGTTCA 151
v
C AluSx#SINE/Al 206 GGTTCA 201
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.87
Transitions / transversions = 2.00 (10/5)
Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.00 (2 / 2)
+ 23 7.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1102:1042:62400/1 19 48 (103) + (T)n Simple_repeat 1 30 (0) 1109
ANNOTATION EVIDENCE:
23 6.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:1042:62400/1 19 48 103 + (T)n Simple_repeat 1 30 0
23 6.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:1042:62400/1 19 48 (103) (T)n#Simple_repeat 1 30 (0) m_b6s252i11
ST-E00130:540 19 TTCTTTTTTTTTTTTGTTTTTTTTTTTTTT 48
i v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 911 7.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1102:1042:62400/2 4 122 (29) + L1P3 LINE/L1 3780 3898 (2248) 1110
ANNOTATION EVIDENCE:
911 7.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:1042:62400/2 4 122 29 + L1P3_orf2 LINE/L1 1671 1789 1505
911 7.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:1042:62400/2 4 122 (29) L1P3_orf2#LINE/L1 1671 1789 (1505) m_b6s551i29
ST-E00130:540 4 GCTTATCCACCACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGAT 53
v i i i
L1P3_orf2#LIN 1671 GCTTATCCACCACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGT 1720
ST-E00130:540 54 TCAGCATACACAAATCAATAAACATAATCCATCACATAAACAGAACGAAT 103
i i i v
L1P3_orf2#LIN 1721 TCAACATACGCAAATCAATAAACGTAATCCATCACATAAACAGAACCAAT 1770
ST-E00130:540 104 GACAAAAACTACATGATTA 122
i
L1P3_orf2#LIN 1771 GACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.52
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 1303 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1102:3884:59130/1 1 151 (0) C L1P1 LINE/L1 (664) 5491 5341 1111
ANNOTATION EVIDENCE:
1303 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:3884:59130/1 1 151 0 C L1PA2_3end LINE/L1 88 238 664
1303 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:3884:59130/1 1 151 (0) C L1PA2_3end#LINE/L1 (664) 238 88 m_b1s551i216
ST-E00130:540 1 TGTTTCCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTAT 50
i
C L1PA2_3end#LI 238 TGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTAT 189
ST-E00130:540 51 CTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCA 100
C L1PA2_3end#LI 188 CTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCA 139
ST-E00130:540 101 TTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTC 150
C L1PA2_3end#LI 138 TTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTC 89
ST-E00130:540 151 T 151
C L1PA2_3end#LI 88 T 88
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1289 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1102:3884:59130/2 1 151 (0) + L1P1 LINE/L1 5020 5170 (976) 1112
ANNOTATION EVIDENCE:
1289 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:3884:59130/2 1 151 0 + L1P1_orf2 LINE/L1 2911 3061 233
1289 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1102:3884:59130/2 1 151 (0) L1P1_orf2#LINE/L1 2911 3061 (233) m_b1s551i72
ST-E00130:540 1 CCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGA 50
?
L1P1_orf2#LIN 2911 CCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGA 2960
ST-E00130:540 51 CATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAA 100
L1P1_orf2#LIN 2961 CATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAA 3010
ST-E00130:540 101 CAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGC 150
v i
L1P1_orf2#LIN 3011 CAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGC 3060
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3061 A 3061
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1107 11.9 1.3 0.0 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/1 1 151 (0) + AluSx SINE/Alu 5 157 (155) 1113
ANNOTATION EVIDENCE:
1107 11.92 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/1 1 151 0 + AluSx SINE/Alu 5 157 155
1107 11.92 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/1 1 151 (0) AluSx#SINE/Alu 5 157 (155) m_b4s356i43
ST-E00130:540 1 GGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAAGCA 50
i i i i i i
AluSx#SINE/Al 5 GGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCG 54
ST-E00130:540 51 GGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTG 98
i --i i v i
AluSx#SINE/Al 55 GGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTG 104
ST-E00130:540 99 AAACTCCATCTCTACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGG 148
i i i i v iv
AluSx#SINE/Al 105 AAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCG 154
ST-E00130:540 149 CGC 151
AluSx#SINE/Al 155 CGC 157
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.24
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/2 106 137 (14) + (TG)n Simple_repeat 1 32 (0) 1114
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/2 106 137 14 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/2 106 137 (14) (TG)n#Simple_repeat 1 32 (0) m_b4s252i34
ST-E00130:540 106 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 137
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/2 138 150 (1) + (TGTATG)n Simple_repeat 1 41 (0) 1115
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/2 106 150 1 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:1106:14560:45663/2 106 150 (1) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i33
ST-E00130:540 106 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 150
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1108:11596:7902/1 19 50 (101) + (CA)n Simple_repeat 1 32 (0) 1116
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1108:11596:7902/1 19 50 101 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1108:11596:7902/1 19 50 (101) (CA)n#Simple_repeat 1 32 (0) m_b4s252i32
ST-E00130:540 19 CATACATGCACACACATACACACACACACACA 50
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 240 29.7 7.1 0.0 ST-E00130:540:HVYVWCCXX:1:1108:12378:58339/2 37 127 (24) C L1MC4 LINE/L1 (1441) 6601 6504 1117
ANNOTATION EVIDENCE:
240 29.67 7.14 0.00 ST-E00130:540:HVYVWCCXX:1:1108:12378:58339/2 37 127 24 C L1MC4_3end LINE/L1 1251 1348 1441
240 29.67 7.14 0.00 ST-E00130:540:HVYVWCCXX:1:1108:12378:58339/2 37 127 (24) C L1MC4_3end#LINE/L1 (1441) 1348 1251 m_b3s551i147
ST-E00130:540 37 GTTGATA--GATATCTTCAAATCCAAGCCAACATCACACAGTTTAT---- 80
v -- i i v v i vi i ----
C L1MC4_3end#LI 1348 GTTCATACCGATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTA 1299
ST-E00130:540 81 -CTTTTTTTCTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAA 127
- i iiii v v i v iv iv iii v i
C L1MC4_3end#LI 1298 GCCTTCCCCCTTTCCATATTTGTAACTCCCTTCTCCGACAGTGAGAAA 1251
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.16
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3)
+ 1272 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1109:5365:39686/1 1 151 (0) C L1P1 LINE/L1 (712) 5443 5293 1118
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5365:39686/1 1 151 0 C L1PA2_3end LINE/L1 40 190 712
1272 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5365:39686/1 1 151 (0) C L1PA2_3end#LINE/L1 (712) 190 40 m_b1s551i185
ST-E00130:540 1 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 50
C L1PA2_3end#LI 190 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 141
ST-E00130:540 51 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 100
C L1PA2_3end#LI 140 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 91
ST-E00130:540 101 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 150
C L1PA2_3end#LI 90 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 41
ST-E00130:540 151 T 151
C L1PA2_3end#LI 40 T 40
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1270 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1109:5365:39686/2 1 151 (0) + L1P1 LINE/L1 5101 5251 (895) 1119
ANNOTATION EVIDENCE:
1270 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5365:39686/2 1 151 0 + L1P1_orf2 LINE/L1 2992 3142 152
1270 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5365:39686/2 1 151 (0) L1P1_orf2#LINE/L1 2992 3142 (152) m_b1s551i100
ST-E00130:540 1 ACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCTAAT 50
v i
L1P1_orf2#LIN 2992 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3041
ST-E00130:540 51 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 100
L1P1_orf2#LIN 3042 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 3091
ST-E00130:540 101 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 150
i
L1P1_orf2#LIN 3092 GGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 3141
ST-E00130:540 151 G 151
L1P1_orf2#LIN 3142 G 3142
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1272 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1109:5883:39669/1 1 151 (0) C L1P1 LINE/L1 (712) 5443 5293 1120
ANNOTATION EVIDENCE:
1272 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5883:39669/1 1 151 0 C L1PA2_3end LINE/L1 40 190 712
1272 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5883:39669/1 1 151 (0) C L1PA2_3end#LINE/L1 (712) 190 40 m_b1s551i186
ST-E00130:540 1 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 50
C L1PA2_3end#LI 190 ATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAG 141
ST-E00130:540 51 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 100
C L1PA2_3end#LI 140 CATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTG 91
ST-E00130:540 101 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 150
C L1PA2_3end#LI 90 TCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 41
ST-E00130:540 151 T 151
C L1PA2_3end#LI 40 T 40
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1270 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1109:5883:39669/2 1 151 (0) + L1P1 LINE/L1 5101 5251 (895) 1121
ANNOTATION EVIDENCE:
1270 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5883:39669/2 1 151 0 + L1P1_orf2 LINE/L1 2992 3142 152
1270 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1109:5883:39669/2 1 151 (0) L1P1_orf2#LINE/L1 2992 3142 (152) m_b1s551i101
ST-E00130:540 1 ACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATCTAAT 50
v i
L1P1_orf2#LIN 2992 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3041
ST-E00130:540 51 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 100
L1P1_orf2#LIN 3042 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 3091
ST-E00130:540 101 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 150
i
L1P1_orf2#LIN 3092 GGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 3141
ST-E00130:540 151 G 151
L1P1_orf2#LIN 3142 G 3142
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 888 5.0 3.5 7.3 ST-E00130:540:HVYVWCCXX:1:1111:22394:22282/1 1 151 (0) + L1P3 LINE/L1 3095 3239 (2907) 1122
ANNOTATION EVIDENCE:
888 5.00 3.45 7.28 ST-E00130:540:HVYVWCCXX:1:1111:22394:22282/1 1 151 0 + L1P3_orf2 LINE/L1 986 1130 2164
888 5.00 3.45 7.28 ST-E00130:540:HVYVWCCXX:1:1111:22394:22282/1 1 151 (0) L1P3_orf2#LINE/L1 986 1130 (2164) m_b6s551i234
ST-E00130:540 1 AAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCT 50
v
L1P3_orf2#LIN 986 AAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCA 1035
ST-E00130:540 51 GAG-TGAAGGAGATAGAGACACACACACACAAAAAAAACCTTTCAAAAAA 99
i- ----------i i
L1P3_orf2#LIN 1036 GAACTGAAGGAGATAGAGACAC----------GAAAAACCCTTCAAAAAA 1075
ST-E00130:540 100 ATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAACAGA--- 146
- v i i ---
L1P3_orf2#LIN 1076 -TCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAATAGATAG 1124
ST-E00130:540 147 -CCGCT 151
-
L1P3_orf2#LIN 1125 ACCGCT 1130
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 943 6.1 7.5 0.7 ST-E00130:540:HVYVWCCXX:1:1111:22394:22282/2 1 149 (2) C L1P3 LINE/L1 (2819) 3327 3168 1123
ANNOTATION EVIDENCE:
943 6.08 7.50 0.67 ST-E00130:540:HVYVWCCXX:1:1111:22394:22282/2 1 149 2 C L1P3_orf2 LINE/L1 1059 1218 2076
943 6.08 7.50 0.67 ST-E00130:540:HVYVWCCXX:1:1111:22394:22282/2 1 149 (2) C L1P3_orf2#LINE/L1 (2076) 1218 1059 m_b6s551i203
ST-E00130:540 1 TTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCTA 50
iv i v
C L1P3_orf2#LIN 1218 TTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTA 1169
ST-E00130:540 51 TTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----TCT 88
-------- v ----
C L1P3_orf2#LIN 1168 TTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCT 1119
ST-E00130:540 89 GTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTT 138
i i v -
C L1P3_orf2#LIN 1118 ATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTT 1070
ST-E00130:540 139 GAAAGGTTTTT 149
i
C L1P3_orf2#LIN 1069 GAAGGGTTTTT 1059
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.36
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.02 (3 / 148), avg. gap size = 4.33 (13 / 3)
+ 622 15.8 0.0 5.8 ST-E00130:540:HVYVWCCXX:1:1112:18223:27398/2 1 121 (30) + AluSx SINE/Alu 191 304 (8) 1124
ANNOTATION EVIDENCE:
622 15.79 0.00 5.79 ST-E00130:540:HVYVWCCXX:1:1112:18223:27398/2 1 121 30 + AluSx SINE/Alu 191 304 8
622 15.79 0.00 5.79 ST-E00130:540:HVYVWCCXX:1:1112:18223:27398/2 1 121 (30) AluSx#SINE/Alu 191 304 (8) m_b5s357i18
ST-E00130:540 1 GACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGATATAGCA 50
v i iivv v v v i
AluSx#SINE/Al 191 GAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG 240
ST-E00130:540 51 CCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGACTCCATCTCA 100
------- i ii i i
AluSx#SINE/Al 241 CCACTGCACTCCAGCCTG-------GGCGACAGAGCGAGACTCCGTCTCA 283
ST-E00130:540 101 AAAAAACACAAAAACAAAAAA 121
v v v
AluSx#SINE/Al 284 AAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.86
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7)
+ 780 6.4 8.5 7.3 ST-E00130:540:HVYVWCCXX:1:1112:22881:52203/1 1 151 (0) C L1P3 LINE/L1 (2858) 3288 3136 1125
ANNOTATION EVIDENCE:
780 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:1:1112:22881:52203/1 1 151 0 C L1P3_orf2 LINE/L1 1027 1179 2115
780 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:1:1112:22881:52203/1 1 151 (0) C L1P3_orf2#LINE/L1 (2115) 1179 1027 m_b6s551i211
ST-E00130:540 1 TATTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTA 42
v -------- v
C L1P3_orf2#LIN 1179 TATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTA 1130
ST-E00130:540 43 GCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAA 88
---- i i v
C L1P3_orf2#LIN 1129 GCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCA 1080
ST-E00130:540 89 TTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTC 138
- i i----------
C L1P3_orf2#LIN 1079 TTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTC 1041
ST-E00130:540 139 A-CTCAGCTCTGAT 151
-i v
C L1P3_orf2#LIN 1040 AGTTCTGCTCTGAT 1027
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1236 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1112:22881:52203/2 1 151 (0) + L1P3 LINE/L1 2975 3125 (3021) 1126
ANNOTATION EVIDENCE:
1236 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1112:22881:52203/2 1 151 0 + L1P3_orf2 LINE/L1 866 1016 2278
1236 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1112:22881:52203/2 1 151 (0) L1P3_orf2#LINE/L1 866 1016 (2278) m_b6s551i275
ST-E00130:540 1 ACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCAC 50
L1P3_orf2#LIN 866 ACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCAC 915
ST-E00130:540 51 AGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAA 100
? v i i
L1P3_orf2#LIN 916 ANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAA 965
ST-E00130:540 101 AGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAG 150
L1P3_orf2#LIN 966 AGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAG 1015
ST-E00130:540 151 A 151
L1P3_orf2#LIN 1016 A 1016
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 226 25.6 5.6 1.7 ST-E00130:540:HVYVWCCXX:1:1112:29975:61679/1 2 120 (31) + L1ME4c LINE/L1 5744 5867 (216) 1127
ANNOTATION EVIDENCE:
226 25.64 5.64 1.68 ST-E00130:540:HVYVWCCXX:1:1112:29975:61679/1 2 120 31 + L1ME4c_3end LINE/L1 491 614 216
226 25.64 5.64 1.68 ST-E00130:540:HVYVWCCXX:1:1112:29975:61679/1 2 120 (31) L1ME4c_3end#LINE/L1 491 614 (216) m_b2s551i0
ST-E00130:540 2 CTAAATTTCTGACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT 47
v ii iii- - i -- i? i
L1ME4c_3end#L 491 CTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNAC 540
ST-E00130:540 48 --GACAGAAAAATGGTGAAGCCATTAAAAAGTATGACTATCAAGAAAA-G 94
-- ii v - vi v vv i i v vv -
L1ME4c_3end#L 541 TCGATGGAATA-TTATGCAGCCATTAAAAATGATAATTATGAAGACTATG 589
ST-E00130:540 95 CAACTACCTGGAAAAATACTTATAAT 120
i i v v - ii i
L1ME4c_3end#L 590 TAGCAACATGGAAAA-TGTTTATGAT 614
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.23
Transitions / transversions = 1.64 (18/11)
Gap_init rate = 0.06 (7 / 118), avg. gap size = 1.29 (9 / 7)
+ 1156 8.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:1112:29975:61679/2 1 151 (0) + AluY SINE/Alu 133 282 (29) 1128
ANNOTATION EVIDENCE:
1156 8.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:1112:29975:61679/2 1 151 0 + AluY SINE/Alu 133 282 29
1156 8.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:1112:29975:61679/2 1 151 (0) AluY#SINE/Alu 133 282 (29) m_b2s356i82
ST-E00130:540 1 TTAGATGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCT 50
vi
AluY#SINE/Alu 133 TTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCT 182
ST-E00130:540 51 GAAGCAGGAGAACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCG 100
i i i i - i v
AluY#SINE/Alu 183 GAGGCAGGAGAATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCG 231
ST-E00130:540 101 AGATCATGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACGCCGTCTC 150
ii i v
AluY#SINE/Alu 232 AGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTC 281
ST-E00130:540 151 A 151
AluY#SINE/Alu 282 A 282
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.54
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 361 5.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/1 1 52 (99) + L1P3 LINE/L1 3847 3898 (2248) 1129
ANNOTATION EVIDENCE:
361 5.77 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/1 1 52 99 + L1P3_orf2 LINE/L1 1738 1789 1505
361 5.77 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/1 1 52 (99) L1P3_orf2#LINE/L1 1738 1789 (1505) m_b6s551i6
ST-E00130:540 1 ATAAACATAATCCATCACATAAACAGAACGAATGACAAAAACTACATGAT 50
i v i
L1P3_orf2#LIN 1738 ATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAACCACATGAT 1787
ST-E00130:540 51 TA 52
L1P3_orf2#LIN 1788 TA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.16
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 828 7.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/1 55 151 (0) + AluSx SINE/Alu 14 110 (202) 1130
ANNOTATION EVIDENCE:
828 7.22 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/1 55 151 0 + AluSx SINE/Alu 14 110 202
828 7.22 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/1 55 151 (0) AluSx#SINE/Alu 14 110 (202) m_b6s356i23
ST-E00130:540 55 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 104
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 105 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTC 151
i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCC 110
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.60
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0)
+ 31 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/2 31 59 (92) + (T)n Simple_repeat 1 29 (0) 1131
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/2 31 59 92 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1113:32765:49074/2 31 59 (92) (T)n#Simple_repeat 1 29 (0) c_b6s251i8
ST-E00130:540 31 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 59
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 1314 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1116:17574:71840/1 1 151 (0) C L1P1 LINE/L1 (846) 5300 5150 1132
ANNOTATION EVIDENCE:
1314 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:17574:71840/1 1 151 0 C L1P1_orf2 LINE/L1 3041 3191 103
1314 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:17574:71840/1 1 151 (0) C L1P1_orf2#LINE/L1 (103) 3191 3041 m_b1s551i123
ST-E00130:540 1 TTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCC 50
C L1P1_orf2#LIN 3191 TTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCC 3142
ST-E00130:540 51 TTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCC 100
i
C L1P1_orf2#LIN 3141 TTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCC 3092
ST-E00130:540 101 TGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTA 150
C L1P1_orf2#LIN 3091 TGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTA 3042
ST-E00130:540 151 A 151
C L1P1_orf2#LIN 3041 A 3041
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1273 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1116:17574:71840/2 1 151 (0) + L1P1 LINE/L1 4909 5059 (1087) 1133
ANNOTATION EVIDENCE:
1273 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:17574:71840/2 1 151 0 + L1P1_orf2 LINE/L1 2800 2950 344
1273 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:17574:71840/2 1 151 (0) L1P1_orf2#LINE/L1 2800 2950 (344) m_b1s551i25
ST-E00130:540 1 AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 50
L1P1_orf2#LIN 2800 AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 2849
ST-E00130:540 51 TCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACT 100
v v i
L1P1_orf2#LIN 2850 TCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACT 2899
ST-E00130:540 101 TAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATT 150
i ?
L1P1_orf2#LIN 2900 TAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANT 2949
ST-E00130:540 151 A 151
L1P1_orf2#LIN 2950 A 2950
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1303 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1116:3995:28804/1 1 151 (0) + L1P1 LINE/L1 5338 5488 (667) 1134
ANNOTATION EVIDENCE:
1303 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:3995:28804/1 1 151 0 + L1PA2_3end LINE/L1 85 235 667
1303 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:3995:28804/1 1 151 (0) L1PA2_3end#LINE/L1 85 235 (667) m_b1s551i214
ST-E00130:540 1 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAA 50
L1PA2_3end#LI 85 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAA 134
ST-E00130:540 51 AAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAA 100
L1PA2_3end#LI 135 AAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAA 184
ST-E00130:540 101 TGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGA 150
i
L1PA2_3end#LI 185 TGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGA 234
ST-E00130:540 151 A 151
L1PA2_3end#LI 235 A 235
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1346 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1116:3995:28804/2 1 151 (0) C L1P2 LINE/L1 (520) 5635 5485 1135
ANNOTATION EVIDENCE:
1346 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:3995:28804/2 1 151 0 C L1PA4_3end LINE/L1 232 382 520
1346 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1116:3995:28804/2 1 151 (0) C L1PA4_3end#LINE/L1 (520) 382 232 m_b1s551i269
ST-E00130:540 1 ATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAAT 50
i
C L1PA4_3end#LI 382 ATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAT 333
ST-E00130:540 51 CACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACA 100
i
C L1PA4_3end#LI 332 CGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACA 283
ST-E00130:540 101 GTGTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTC 150
vi
C L1PA4_3end#LI 282 GTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTC 233
ST-E00130:540 151 C 151
C L1PA4_3end#LI 232 C 232
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 242 20.3 0.0 9.9 ST-E00130:540:HVYVWCCXX:1:1118:10176:41550/2 2 72 (79) + 7SLRNA srpRNA 257 320 (0) 1136
ANNOTATION EVIDENCE:
242 20.31 0.00 9.86 ST-E00130:540:HVYVWCCXX:1:1118:10176:41550/2 2 72 79 + 7SLRNA SINE/Alu 257 320 0
242 20.31 0.00 9.86 ST-E00130:540:HVYVWCCXX:1:1118:10176:41550/2 2 72 (79) 7SLRNA#SINE/Alu 257 320 (0) m_b5s502i1
ST-E00130:540 2 CCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGACTCCATCTCA 51
------- ii iiv i i i v
7SLRNA#SINE/A 257 CCACTGCACTCCAGCCTG-------GGCAACATAGCGAGACCCCGTCTCT 299
ST-E00130:540 52 AAAAAACACAAAAACAAAAAA 72
v v v v
7SLRNA#SINE/A 300 TAAAAAAAAAAAAAAAAAAAA 320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.99
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.00 (7 / 7)
+ 243 23.2 0.0 1.8 ST-E00130:540:HVYVWCCXX:1:1120:11099:33938/2 1 57 (94) + L1MC4 LINE/L1 7856 7911 (131) 1137
ANNOTATION EVIDENCE:
243 23.22 0.00 1.75 ST-E00130:540:HVYVWCCXX:1:1120:11099:33938/2 1 57 94 + L1MC4_3end LINE/L1 2603 2658 131
243 23.22 0.00 1.75 ST-E00130:540:HVYVWCCXX:1:1120:11099:33938/2 1 57 (94) L1MC4_3end#LINE/L1 2603 2658 (131) m_b3s551i6
ST-E00130:540 1 GGAGCATCACGTGTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATG 50
i ? i v i i vv - i vi i
L1MC4_3end#LI 2603 GGGGCATNATGTCTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATA 2651
ST-E00130:540 51 TGTGTAT 57
i
L1MC4_3end#LI 2652 TGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.53
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1)
+ 1215 6.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1121:17634:32531/2 1 151 (0) + L1PA3 LINE/L1 5956 6106 (49) 1138
ANNOTATION EVIDENCE:
1215 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1121:17634:32531/2 1 151 0 + L1PA3_3end LINE/L1 703 853 49
1215 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1121:17634:32531/2 1 151 (0) L1PA3_3end#LINE/L1 703 853 (49) m_b1s551i401
ST-E00130:540 1 CACAGGAAGGGGAATATCACACTCTGTGGACTGTTGTGGGGTGGGGAGAG 50
i v i
L1PA3_3end#LI 703 CACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGGTGGGGGGAG 752
ST-E00130:540 51 GGGGGAGGGATAGCATCAGGGGATAAACCTAATGCTAGATGACGAGTTAG 100
ii i v
L1PA3_3end#LI 753 GGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAG 802
ST-E00130:540 101 TGGGTGCAGCACACCAGCATGGCTCATGTATACATATGTAACTAACCTGC 150
i v
L1PA3_3end#LI 803 TGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGC 852
ST-E00130:540 151 A 151
L1PA3_3end#LI 853 A 853
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.59
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1223 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1121:20699:4649/1 2 151 (0) + L1P3 LINE/L1 2908 3057 (3089) 1139
ANNOTATION EVIDENCE:
1223 5.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1121:20699:4649/1 2 151 0 + L1P3_orf2 LINE/L1 799 948 2346
1223 5.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1121:20699:4649/1 2 151 (0) L1P3_orf2#LINE/L1 799 948 (2346) m_b7s551i25
ST-E00130:540 2 AAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAAT 51
i? i i
L1P3_orf2#LIN 799 AAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAAC 848
ST-E00130:540 52 GTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTA 101
L1P3_orf2#LIN 849 GTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTA 898
ST-E00130:540 102 TAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACC 151
? v i i
L1P3_orf2#LIN 899 TAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACC 948
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.27
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 924 3.6 0.7 7.3 ST-E00130:540:HVYVWCCXX:1:1121:20699:4649/2 2 151 (0) C L1P3 LINE/L1 (2957) 3189 3050 1140
ANNOTATION EVIDENCE:
924 3.59 0.72 7.33 ST-E00130:540:HVYVWCCXX:1:1121:20699:4649/2 2 151 0 C L1P3_orf2 LINE/L1 941 1080 2214
924 3.59 0.72 7.33 ST-E00130:540:HVYVWCCXX:1:1121:20699:4649/2 2 151 (0) C L1P3_orf2#LINE/L1 (2214) 1080 941 m_b6s551i254
ST-E00130:540 2 ATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTT 51
- i i----------
C L1P3_orf2#LIN 1080 ATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTT 1042
ST-E00130:540 52 CA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAAT 100
-i v
C L1P3_orf2#LIN 1041 CAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAAT 992
ST-E00130:540 101 TTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTG 150
i
C L1P3_orf2#LIN 991 TTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCG 942
ST-E00130:540 151 A 151
C L1P3_orf2#LIN 941 A 941
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.34
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.00 (12 / 12)
+ 1132 7.3 1.9 0.0 ST-E00130:540:HVYVWCCXX:1:1122:4310:20735/1 1 151 (0) C L1P3 LINE/L1 (2271) 3875 3722 1141
ANNOTATION EVIDENCE:
1132 7.28 1.95 0.00 ST-E00130:540:HVYVWCCXX:1:1122:4310:20735/1 1 151 0 C L1P3_orf2 LINE/L1 1613 1766 1528
1132 7.28 1.95 0.00 ST-E00130:540:HVYVWCCXX:1:1122:4310:20735/1 1 151 (0) C L1P3_orf2#LINE/L1 (1528) 1766 1613 m_b6s551i47
ST-E00130:540 1 GTTCTGTTTATGTGATGGATTATGTTTATTGATTTGTGTATGCTGAATCA 50
i i i i
C L1P3_orf2#LIN 1766 GTTCTGTTTATGTGATGGATTACGTTTATTGATTTGCGTATGTTGAACCA 1717
ST-E00130:540 51 GCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGGTGGATAAGCGTTT 100
i i v v
C L1P3_orf2#LIN 1716 GCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGGTGGATAAGCTTTT 1667
ST-E00130:540 101 TGATG---TGCTGGATTCAGTTTGCCAGTATTTTATCGAGGATTTTCACA 147
--- i i i
C L1P3_orf2#LIN 1666 TGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCA 1617
ST-E00130:540 148 TCGA 151
C L1P3_orf2#LIN 1616 TCGA 1613
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1168 6.0 1.3 0.0 ST-E00130:540:HVYVWCCXX:1:1122:4310:20735/2 1 151 (0) + L1P3 LINE/L1 3594 3746 (2400) 1142
ANNOTATION EVIDENCE:
1168 5.96 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:1122:4310:20735/2 1 151 0 + L1P3_orf2 LINE/L1 1485 1637 1657
1168 5.96 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:1122:4310:20735/2 1 151 (0) L1P3_orf2#LINE/L1 1485 1637 (1657) m_b6s551i76
ST-E00130:540 1 ATTCCAAACAATAGAAAAAGAGGGACTCTTCCCTAACTCATTTTATGGTG 50
i iv
L1P3_orf2#LIN 1485 ATTCCAAACAATAGAAAAAGAGGGACTCCTCCCTAACTCATTTTATGAGG 1534
ST-E00130:540 51 CCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAA--GAAAAAGAA 98
v --i
L1P3_orf2#LIN 1535 CCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAAAAAAAGAA 1584
ST-E00130:540 99 AATTTCAGGCCATTATCCGTGATGAACATCGATGTGAAAATCCTCGATAA 148
v v i i
L1P3_orf2#LIN 1585 AATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATCCTCAATAA 1634
ST-E00130:540 149 AAT 151
L1P3_orf2#LIN 1635 AAT 1637
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.57
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 796 16.6 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:1123:28929:29595/2 1 146 (5) C AluY SINE/Alu (39) 272 128 1143
ANNOTATION EVIDENCE:
796 16.55 0.00 0.68 ST-E00130:540:HVYVWCCXX:1:1123:28929:29595/2 1 146 5 C AluY SINE/Alu 128 272 39
796 16.55 0.00 0.68 ST-E00130:540:HVYVWCCXX:1:1123:28929:29595/2 1 146 (5) C AluY#SINE/Alu (39) 272 128 m_b2s357i90
ST-E00130:540 1 TCTCGATCTGTCGCCCAGGATGGAATGCAGTGGCATGATCTCGGCTAACT 50
v v i ii v
C AluY#SINE/Alu 272 TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACT 223
ST-E00130:540 51 GCAACGTCCAGCTGCCGAGGTTCATGCCGTTCTCCTGCTTGAGCCTACAG 100
vv iv v - i i i v v v
C AluY#SINE/Alu 222 GCAAGCTCCGCCTCCCG-GGTTCACGCCATTCTCCTGCCTCAGCCTCCCG 174
ST-E00130:540 101 AGTAGCTGGGACTACAGGCGACCGCGAACAGGACCATCTAATTTTT 146
v v v v v iv
C AluY#SINE/Alu 173 AGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTT 128
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 14.87
Transitions / transversions = 0.50 (8/16)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 1.00 (1 / 1)
+ 786 6.4 8.5 7.3 ST-E00130:540:HVYVWCCXX:1:1123:4249:72596/1 1 151 (0) C L1P3 LINE/L1 (2859) 3287 3135 1144
ANNOTATION EVIDENCE:
786 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:1:1123:4249:72596/1 1 151 0 C L1P3_orf2 LINE/L1 1026 1178 2116
786 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:1:1123:4249:72596/1 1 151 (0) C L1P3_orf2#LINE/L1 (2116) 1178 1026 m_b6s551i213
ST-E00130:540 1 ATTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAG 42
v -------- v
C L1P3_orf2#LIN 1178 ATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAG 1129
ST-E00130:540 43 CGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAAT 88
---- i i v
C L1P3_orf2#LIN 1128 CGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCAT 1079
ST-E00130:540 89 TGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA 138
- i i----------
C L1P3_orf2#LIN 1078 TGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCA 1040
ST-E00130:540 139 -CTCAGCTCTGATC 151
-i v
C L1P3_orf2#LIN 1039 GTTCTGCTCTGATC 1026
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1100 7.6 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:1124:11373:33814/1 1 146 (5) + AluY SINE/Alu 153 297 (14) 1145
ANNOTATION EVIDENCE:
1100 7.58 0.00 0.68 ST-E00130:540:HVYVWCCXX:1:1124:11373:33814/1 1 146 5 + AluY SINE/Alu 153 297 14
1100 7.58 0.00 0.68 ST-E00130:540:HVYVWCCXX:1:1124:11373:33814/1 1 146 (5) AluY#SINE/Alu 153 297 (14) m_b2s357i93
ST-E00130:540 1 GCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGA 50
i i i
AluY#SINE/Alu 153 GCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGA 202
ST-E00130:540 51 ACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCATTCC 100
i - i v ii i
AluY#SINE/Alu 203 ACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC 251
ST-E00130:540 101 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAGAAATAAAA 146
i v
AluY#SINE/Alu 252 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.64
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 1.00 (1 / 1)
+ 926 8.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1124:20973:72244/1 27 151 (0) C L1P3 LINE/L1 (2248) 3898 3774 1146
ANNOTATION EVIDENCE:
926 8.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1124:20973:72244/1 27 151 0 C L1P3_orf2 LINE/L1 1665 1789 1505
926 8.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1124:20973:72244/1 27 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1665 m_b6s551i30
ST-E00130:540 27 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 76
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
ST-E00130:540 77 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 126
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
ST-E00130:540 127 TTGATAGTGGTGGATAAGCGTTTTG 151
v v
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGCTTTTTG 1665
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.10
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 124), avg. gap size = 0.0 (0 / 0)
+ 1299 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1124:20973:72244/2 1 151 (0) + L1P3 LINE/L1 3516 3666 (2480) 1147
ANNOTATION EVIDENCE:
1299 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1124:20973:72244/2 1 151 0 + L1P3_orf2 LINE/L1 1407 1557 1737
1299 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1124:20973:72244/2 1 151 (0) L1P3_orf2#LINE/L1 1407 1557 (1737) m_b6s551i103
ST-E00130:540 1 AAGCCCAGGACCAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAAAG 50
v i
L1P3_orf2#LIN 1407 AAGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGAGGTACAAAG 1456
ST-E00130:540 51 AGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAG 100
L1P3_orf2#LIN 1457 AGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAG 1506
ST-E00130:540 101 GGACTCTTCCCTAACTCATTTTATGATGCCAGCATCATCCTGATTCCAAA 150
i v v
L1P3_orf2#LIN 1507 GGACTCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAA 1556
ST-E00130:540 151 A 151
L1P3_orf2#LIN 1557 A 1557
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 327 22.6 12.5 0.0 ST-E00130:540:HVYVWCCXX:1:1124:28534:60694/1 19 102 (49) C L1MC4 LINE/L1 (513) 7529 7416 1148
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 ST-E00130:540:HVYVWCCXX:1:1124:28534:60694/1 19 102 49 C L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 ST-E00130:540:HVYVWCCXX:1:1124:28534:60694/1 19 102 (49) C L1MC4a_3end#LINE/L1 (371) 2258 2163 m_b3s551i123
ST-E00130:540 19 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 63
iiv i i i i i -----
C L1MC4a_3end#L 2258 GTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGTT 2209
ST-E00130:540 64 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT----TCCTCTTCT 102
i --- i i iiii i i ---- v i
C L1MC4a_3end#L 2208 ATGCATTTTTGGCAAGAATACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 4.00 (12 / 3)
327 22.67 9.64 0.00 ST-E00130:540:HVYVWCCXX:1:1124:28534:60694/1 19 93 58 C L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 ST-E00130:540:HVYVWCCXX:1:1124:28534:60694/1 19 93 (58) C L1MC4_3end#LINE/L1 (513) 2276 2194 m_b3s551i124
ST-E00130:540 19 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 63
iiv i i i i -----
C L1MC4_3end#LI 2276 GTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTT 2227
ST-E00130:540 64 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT 93
i --- i ii iiii i i
C L1MC4_3end#LI 2226 ATGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 236 27.2 5.8 0.0 ST-E00130:540:HVYVWCCXX:1:1201:10500:14547/1 8 88 (63) + MIRb SINE/MIR 134 219 (49) 1149
ANNOTATION EVIDENCE:
236 27.16 5.81 0.00 ST-E00130:540:HVYVWCCXX:1:1201:10500:14547/1 8 88 63 + MIRb SINE/MIR 134 219 49
236 27.16 5.81 0.00 ST-E00130:540:HVYVWCCXX:1:1201:10500:14547/1 8 88 (63) MIRb#SINE/MIR 134 219 (49) m_b4s601i5
ST-E00130:540 8 CCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGCCAGATAACTGTG 56
v i i ii - vi i v vi i vii
MIRb#SINE/MIR 134 CCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTG 183
ST-E00130:540 57 AGGATTA---GAGAAAATAAACGTAAAA-GTCTAGC 88
--- v iv i i- ii
MIRb#SINE/MIR 184 AGGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.26
Transitions / transversions = 2.14 (15/7)
Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.67 (5 / 3)
+ 1293 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1201:13839:43888/1 1 151 (0) C L1P1 LINE/L1 (819) 5327 5177 1150
ANNOTATION EVIDENCE:
1293 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1201:13839:43888/1 1 151 0 C L1P1_orf2 LINE/L1 3068 3218 76
1293 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1201:13839:43888/1 1 151 (0) C L1P1_orf2#LINE/L1 (76) 3218 3068 m_b1s551i133
ST-E00130:540 1 GCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAG 50
C L1P1_orf2#LIN 3218 GCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAG 3169
ST-E00130:540 51 TTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGA 100
C L1P1_orf2#LIN 3168 TTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGA 3119
ST-E00130:540 101 AAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCT 150
i
C L1P1_orf2#LIN 3118 AAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCT 3069
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 3068 T 3068
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1281 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1201:13839:43888/2 1 151 (0) + L1P1 LINE/L1 4900 5050 (1096) 1151
ANNOTATION EVIDENCE:
1281 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1201:13839:43888/2 1 151 0 + L1P1_orf2 LINE/L1 2791 2941 353
1281 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1201:13839:43888/2 1 151 (0) L1P1_orf2#LINE/L1 2791 2941 (353) m_b1s551i17
ST-E00130:540 1 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 50
L1P1_orf2#LIN 2791 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2840
ST-E00130:540 51 GAAACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGA 100
v v i
L1P1_orf2#LIN 2841 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2890
ST-E00130:540 101 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 150
i
L1P1_orf2#LIN 2891 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2940
ST-E00130:540 151 C 151
L1P1_orf2#LIN 2941 C 2941
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1242 4.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1201:14265:40688/2 1 151 (0) C L1P3 LINE/L1 (3058) 3088 2938 1152
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1201:14265:40688/2 1 151 0 C L1P3_orf2 LINE/L1 829 979 2315
1242 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1201:14265:40688/2 1 151 (0) C L1P3_orf2#LINE/L1 (2315) 979 829 m_b7s551i12
ST-E00130:540 1 GCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTT 50
i
C L1P3_orf2#LIN 979 GCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTT 930
ST-E00130:540 51 TCCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACAC 100
i v ?
C L1P3_orf2#LIN 929 TCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACAC 880
ST-E00130:540 101 TGCTTTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTAT 150
i i
C L1P3_orf2#LIN 879 TGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCAT 830
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 829 T 829
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 767 13.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1204:24647:11312/2 1 108 (43) C AluSx SINE/Alu (204) 108 1 1153
ANNOTATION EVIDENCE:
767 12.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1204:24647:11312/2 1 108 43 C AluSx SINE/Alu 1 108 204
767 12.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1204:24647:11312/2 1 108 (43) C AluSx#SINE/Alu (204) 108 1 m_b5s357i54
ST-E00130:540 1 GTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAGTGATC 50
v i i i i
C AluSx#SINE/Al 108 GTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATC 59
ST-E00130:540 51 TGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGC 100
i i i i i vi
C AluSx#SINE/Al 58 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
ST-E00130:540 101 ACCCAGCC 108
i i
C AluSx#SINE/Al 8 GCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.62
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0)
+ 492 7.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1204:3742:4456/1 88 151 (0) C AluSx SINE/Alu (14) 298 235 1154
ANNOTATION EVIDENCE:
492 7.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1204:3742:4456/1 88 151 0 C AluSx SINE/Alu 235 298 14
492 7.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1204:3742:4456/1 88 151 (0) C AluSx#SINE/Alu (14) 298 235 m_b2s357i112
ST-E00130:540 88 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 137
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
ST-E00130:540 138 TGCAGTGGCATGAT 151
ii
C AluSx#SINE/Al 248 TGCAGTGGCGCGAT 235
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.20
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 1126 10.7 0.7 0.0 ST-E00130:540:HVYVWCCXX:1:1204:3742:4456/2 3 151 (0) + AluY SINE/Alu 1 150 (161) 1155
ANNOTATION EVIDENCE:
1126 10.74 0.67 0.00 ST-E00130:540:HVYVWCCXX:1:1204:3742:4456/2 3 151 0 + AluY SINE/Alu 1 150 161
1126 10.74 0.67 0.00 ST-E00130:540:HVYVWCCXX:1:1204:3742:4456/2 3 151 (0) AluY#SINE/Alu 1 150 (161) m_b2s356i50
ST-E00130:540 3 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 52
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 53 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 102
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
ST-E00130:540 103 TGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCGGGGTGGC 151
i i - vi v
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.52
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 594 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1205:16823:11294/1 78 151 (0) C L1PA2 LINE/L1 (2) 6153 6080 1156
ANNOTATION EVIDENCE:
594 2.70 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1205:16823:11294/1 78 151 0 C L1PA2_3end LINE/L1 827 900 2
594 2.70 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1205:16823:11294/1 78 151 (0) C L1PA2_3end#LINE/L1 (2) 900 827 m_b1s551i454
ST-E00130:540 78 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 127
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 128 AGGTTAGTTACATATGTATACATG 151
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATG 827
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.75
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 1185 5.3 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:1205:16823:11294/2 1 151 (0) + L1PA3 LINE/L1 5794 5943 (212) 1157
ANNOTATION EVIDENCE:
1185 5.34 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:1205:16823:11294/2 1 151 0 + L1PA3_3end LINE/L1 541 690 212
1185 5.34 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:1205:16823:11294/2 1 151 (0) L1PA3_3end#LINE/L1 541 690 (212) m_b1s551i369
ST-E00130:540 1 ATGGAATACTATGCAGCCATAAAAAAGGATGCGTTCATGTCCTTTGTTAG 50
v v -
L1PA3_3end#LI 541 ATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AG 589
ST-E00130:540 51 GGACATGGAGGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAA 100
v i
L1PA3_3end#LI 590 GGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAA 639
ST-E00130:540 101 GAAAAAACCAAGCACCGCATGTTCTCACTCATAGGTGGGAATTGCACAAT 150
v i i v
L1PA3_3end#LI 640 CAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAAT 689
ST-E00130:540 151 G 151
L1PA3_3end#LI 690 G 690
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.53
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1263 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1206:30462:58198/1 1 151 (0) + L1P3 LINE/L1 2953 3103 (3043) 1158
ANNOTATION EVIDENCE:
1263 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1206:30462:58198/1 1 151 0 + L1P3_orf2 LINE/L1 844 994 2300
1263 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1206:30462:58198/1 1 151 (0) L1P3_orf2#LINE/L1 844 994 (2300) m_b7s551i3
ST-E00130:540 1 ACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAA 50
i
L1P3_orf2#LIN 844 ACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAA 893
ST-E00130:540 51 ATTTATAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCA 100
? v i i
L1P3_orf2#LIN 894 ATTTATAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCG 943
ST-E00130:540 101 ACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAAT 150
L1P3_orf2#LIN 944 ACACCCTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAAT 993
ST-E00130:540 151 T 151
L1P3_orf2#LIN 994 T 994
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1015 5.3 7.4 0.0 ST-E00130:540:HVYVWCCXX:1:1206:30462:58198/2 1 151 (0) C L1P3 LINE/L1 (2803) 3343 3181 1159
ANNOTATION EVIDENCE:
1015 5.30 7.36 0.00 ST-E00130:540:HVYVWCCXX:1:1206:30462:58198/2 1 151 0 C L1P3_orf2 LINE/L1 1072 1234 2060
1015 5.30 7.36 0.00 ST-E00130:540:HVYVWCCXX:1:1206:30462:58198/2 1 151 (0) C L1P3_orf2#LINE/L1 (2060) 1234 1072 m_b6s551i198
ST-E00130:540 1 TGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCA 50
iv i
C L1P3_orf2#LIN 1234 TGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCA 1185
ST-E00130:540 51 TTTTTTATTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTCT 92
v --------
C L1P3_orf2#LIN 1184 TTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCT 1135
ST-E00130:540 93 TGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGG 138
v ---- i i
C L1P3_orf2#LIN 1134 GGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGG 1085
ST-E00130:540 139 ATTAATTGATTTT 151
v
C L1P3_orf2#LIN 1084 ATTCATTGATTTT 1072
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.50
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 285 26.1 5.6 0.7 ST-E00130:540:HVYVWCCXX:1:1208:20476:48107/1 3 137 (14) C L1ME4c LINE/L1 (246) 5837 5696 1160
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 ST-E00130:540:HVYVWCCXX:1:1208:20476:48107/1 3 137 14 C L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 ST-E00130:540:HVYVWCCXX:1:1208:20476:48107/1 3 137 (14) C L1ME4c_3end#LINE/L1 (246) 584 443 m_b2s551i17
ST-E00130:540 3 TCTTGATAGTCATACTTTTTAATGGCTTCACCATTTTTCTGTC--ATAAA 50
v i i vv v iv - v ii --i ?i
C L1ME4c_3end#L 584 TCTTCATAATTATCATTTTTAATGGCTGCATAA-TATTCCATCGAGTNGA 536
ST-E00130:540 51 --TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCT 96
-- i - -iii ii v i v
C L1ME4c_3end#L 535 TGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGT 486
ST-E00130:540 97 TTTCTATTTTC--CTACAATAAACATTATTGCAATGATCATTT 137
i v i-- iv i viii v i
C L1ME4c_3end#L 485 TTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 206 28.7 16.4 0.0 ST-E00130:540:HVYVWCCXX:1:1208:6654:18537/1 30 151 (0) C MIR SINE/MIR (0) 262 117 1161
ANNOTATION EVIDENCE:
206 28.69 16.44 0.00 ST-E00130:540:HVYVWCCXX:1:1208:6654:18537/1 30 151 0 C MIR SINE/MIR 117 262 0
206 28.69 16.44 0.00 ST-E00130:540:HVYVWCCXX:1:1208:6654:18537/1 30 151 (0) C MIR#SINE/MIR (0) 262 117 m_b6s601i21
ST-E00130:540 30 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 72
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 73 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 107
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 108 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGAC 151
v i v vi ii v i i -- v i
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 117
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.96
Transitions / transversions = 1.69 (22/13)
Gap_init rate = 0.04 (5 / 121), avg. gap size = 4.80 (24 / 5)
+ 1100 8.0 1.9 0.0 ST-E00130:540:HVYVWCCXX:1:1209:15980:4526/1 1 151 (0) C L1P3 LINE/L1 (2275) 3871 3718 1162
ANNOTATION EVIDENCE:
1100 7.95 1.95 0.00 ST-E00130:540:HVYVWCCXX:1:1209:15980:4526/1 1 151 0 C L1P3_orf2 LINE/L1 1609 1762 1532
1100 7.95 1.95 0.00 ST-E00130:540:HVYVWCCXX:1:1209:15980:4526/1 1 151 (0) C L1P3_orf2#LINE/L1 (1532) 1762 1609 m_b6s551i48
ST-E00130:540 1 TGGTTATGTGATGGATTATGTTTATTGATTTGTGTATGCTGAATCAGCCT 50
v i i i i
C L1P3_orf2#LIN 1762 TGTTTATGTGATGGATTACGTTTATTGATTTGCGTATGTTGAACCAGCCT 1713
ST-E00130:540 51 TGCGTCCCAGGGATGAAGCTGACTTGATAGTGGTGGATAAGCGTTTTGAT 100
i i v v
C L1P3_orf2#LIN 1712 TGCATCCCAGGGATGAAGCCGACTTGATCGTGGTGGATAAGCTTTTTGAT 1663
ST-E00130:540 101 G---TGCTGGATTCAGTTTGCCAGTATTTTATCGAGGATTTTCACATCGA 147
--- i i i
C L1P3_orf2#LIN 1662 GTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCATCGA 1613
ST-E00130:540 148 TGTT 151
C L1P3_orf2#LIN 1612 TGTT 1609
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.15
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1179 4.0 1.3 0.0 ST-E00130:540:HVYVWCCXX:1:1209:15980:4526/2 1 151 (0) + L1P3 LINE/L1 3360 3512 (2634) 1163
ANNOTATION EVIDENCE:
1179 3.97 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:1209:15980:4526/2 1 151 0 + L1P3_orf2 LINE/L1 1251 1403 1891
1179 3.97 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:1209:15980:4526/2 1 151 (0) L1P3_orf2#LINE/L1 1251 1403 (1891) m_b6s551i141
ST-E00130:540 1 CCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAG 50
i vv i
L1P3_orf2#LIN 1251 CCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGG 1300
ST-E00130:540 51 ACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAAT 98
v -- v
L1P3_orf2#LIN 1301 ACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAAT 1350
ST-E00130:540 99 AGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAAC 148
L1P3_orf2#LIN 1351 AGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAAC 1400
ST-E00130:540 149 CAA 151
L1P3_orf2#LIN 1401 CAA 1403
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.46
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 657 13.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1209:7578:41866/1 1 92 (59) C AluSx SINE/Alu (220) 92 1 1164
ANNOTATION EVIDENCE:
657 13.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1209:7578:41866/1 1 92 59 C AluSx SINE/Alu 1 92 220
657 13.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1209:7578:41866/1 1 92 (59) C AluSx#SINE/Alu (220) 92 1 m_b5s357i59
ST-E00130:540 1 CAGGCTGGTCCCAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTC 50
i i i i i i
C AluSx#SINE/Al 92 CAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTC 43
ST-E00130:540 51 CCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 92
i i vi i i
C AluSx#SINE/Al 42 CCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.46
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0)
+ 1354 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1210:3620:5335/1 1 151 (0) C L1P1 LINE/L1 (430) 5725 5575 1165
ANNOTATION EVIDENCE:
1354 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1210:3620:5335/1 1 151 0 C L1PA2_3end LINE/L1 322 472 430
1354 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1210:3620:5335/1 1 151 (0) C L1PA2_3end#LINE/L1 (430) 472 322 m_b1s551i296
ST-E00130:540 1 TTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTA 50
i
C L1PA2_3end#LI 472 TTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTA 423
ST-E00130:540 51 TAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGC 100
i
C L1PA2_3end#LI 422 TAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGC 373
ST-E00130:540 101 TGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCACCACACTG 150
i i
C L1PA2_3end#LI 372 TGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTG 323
ST-E00130:540 151 A 151
C L1PA2_3end#LI 322 A 322
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1300 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1210:3620:5335/2 1 151 (0) + L1P1 LINE/L1 5344 5494 (661) 1166
ANNOTATION EVIDENCE:
1300 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1210:3620:5335/2 1 151 0 + L1PA2_3end LINE/L1 91 241 661
1300 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1210:3620:5335/2 1 151 (0) L1PA2_3end#LINE/L1 91 241 (661) m_b1s551i217
ST-E00130:540 1 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 50
L1PA2_3end#LI 91 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 140
ST-E00130:540 51 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 100
L1PA2_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190
ST-E00130:540 101 ACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAAC 150
i
L1PA2_3end#LI 191 ACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAAC 240
ST-E00130:540 151 A 151
L1PA2_3end#LI 241 A 241
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 899 13.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1214:24170:56967/1 28 151 (0) + AluSx SINE/Alu 1 124 (188) 1167
ANNOTATION EVIDENCE:
899 13.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:24170:56967/1 28 151 0 + AluSx SINE/Alu 1 124 188
899 13.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:24170:56967/1 28 151 (0) AluSx#SINE/Alu 1 124 (188) m_b2s356i40
ST-E00130:540 28 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 77
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 78 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 127
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 128 GGTGAAACCTTGTCTCTATTTAAA 151
ii i v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAA 124
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.23
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0)
+ 19 4.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1214:24170:56967/2 17 39 (112) + (T)n Simple_repeat 1 23 (0) 1168
ANNOTATION EVIDENCE:
19 4.50 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:24170:56967/2 17 39 112 + (T)n Simple_repeat 1 23 0
19 4.50 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:24170:56967/2 17 39 (112) (T)n#Simple_repeat 1 23 (0) m_b2s252i5
ST-E00130:540 17 TTTTTTTTTTTTTTTATTTTTTT 39
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 24 6.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/1 43 73 (78) + (T)n Simple_repeat 1 31 (0) 1169
ANNOTATION EVIDENCE:
24 6.76 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/1 43 73 78 + (T)n Simple_repeat 1 31 0
24 6.76 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/1 43 73 (78) (T)n#Simple_repeat 1 31 (0) m_b6s252i10
ST-E00130:540 43 TTCTTTTTTTTTTTTGTTTTTTTTTTTTTTT 73
i v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 331 4.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/2 2 46 (105) + L1P3 LINE/L1 3854 3898 (2248) 1170
ANNOTATION EVIDENCE:
331 4.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/2 2 46 105 + L1P3_orf2 LINE/L1 1745 1789 1505
331 4.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/2 2 46 (105) L1P3_orf2#LINE/L1 1745 1789 (1505) m_b6s551i3
ST-E00130:540 2 TAATCCATCACATAAACAGAACGAATGACAAAAACTACATGATTA 46
v i
L1P3_orf2#LIN 1745 TAATCCATCACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.59
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 843 8.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/2 49 151 (0) + AluSx SINE/Alu 14 116 (196) 1171
ANNOTATION EVIDENCE:
843 8.74 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/2 49 151 0 + AluSx SINE/Alu 14 116 196
843 8.74 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1214:32349:32742/2 49 151 (0) AluSx#SINE/Alu 14 116 (196) m_b6s356i21
ST-E00130:540 49 GGCTCACGCCTGTAATCTCAGCACTTAGGGAGGACAAGGTGGGTGGATCA 98
i v v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 99 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCAT 148
i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
ST-E00130:540 149 CTC 151
AluSx#SINE/Al 114 CTC 116
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0)
+ 1020 11.1 1.5 0.0 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/1 17 151 (0) + AluSx SINE/Alu 1 137 (175) 1172
ANNOTATION EVIDENCE:
1020 11.11 1.46 0.00 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/1 17 151 0 + AluSx SINE/Alu 1 137 175
1020 11.11 1.46 0.00 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/1 17 151 (0) AluSx#SINE/Alu 1 137 (175) m_b4s356i49
ST-E00130:540 17 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 66
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 67 AGCAGGCAGACCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 114
i i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 115 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTAG 151
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAG 137
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.10
Transitions / transversions = 14.00 (14/1)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 21 52 (99) + (TG)n Simple_repeat 1 32 (0) 1173
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 21 52 99 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 21 52 (99) (TG)n#Simple_repeat 1 32 (0) m_b4s252i31
ST-E00130:540 21 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 52
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 53 65 (86) + (TGTATG)n Simple_repeat 1 41 (0) 1174
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 21 65 86 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 21 65 (86) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i30
ST-E00130:540 21 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 65
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 604 4.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 80 151 (0) C AluSx SINE/Alu (21) 291 220 1175
ANNOTATION EVIDENCE:
604 4.17 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 80 151 0 C AluSx SINE/Alu 220 291 21
604 4.17 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1215:14874:59323/2 80 151 (0) C AluSx#SINE/Alu (21) 291 220 m_b4s357i14
ST-E00130:540 80 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 129
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 130 GCGCGATCTCGGCTCACTGCAA 151
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAA 220
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.01
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 1250 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1216:4381:54225/1 1 151 (0) + L1P1 LINE/L1 4965 5115 (1031) 1176
ANNOTATION EVIDENCE:
1250 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1216:4381:54225/1 1 151 0 + L1P1_orf2 LINE/L1 2856 3006 288
1250 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1216:4381:54225/1 1 151 (0) L1P1_orf2#LINE/L1 2856 3006 (288) m_b1s551i47
ST-E00130:540 1 CCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTAAACA 50
v v i i
L1P1_orf2#LIN 2856 CCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACG 2905
ST-E00130:540 51 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATT 100
?
L1P1_orf2#LIN 2906 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATT 2955
ST-E00130:540 101 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 150
L1P1_orf2#LIN 2956 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 3005
ST-E00130:540 151 G 151
L1P1_orf2#LIN 3006 G 3006
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1313 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1216:4381:54225/2 1 151 (0) C L1P1 LINE/L1 (795) 5351 5201 1177
ANNOTATION EVIDENCE:
1313 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1216:4381:54225/2 1 151 0 C L1P1_orf2 LINE/L1 3092 3242 52
1313 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1216:4381:54225/2 1 151 (0) C L1P1_orf2#LINE/L1 (52) 3242 3092 m_b1s551i142
ST-E00130:540 1 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGT 50
C L1P1_orf2#LIN 3242 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGT 3193
ST-E00130:540 51 TTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCC 100
C L1P1_orf2#LIN 3192 TTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCC 3143
ST-E00130:540 101 CTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGC 150
i
C L1P1_orf2#LIN 3142 CTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGC 3093
ST-E00130:540 151 C 151
C L1P1_orf2#LIN 3092 C 3092
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1277 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1217:19309:29841/1 1 151 (0) + L1P1 LINE/L1 4876 5026 (1120) 1178
ANNOTATION EVIDENCE:
1277 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1217:19309:29841/1 1 151 0 + L1P1_orf2 LINE/L1 2767 2917 377
1277 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1217:19309:29841/1 1 151 (0) L1P1_orf2#LINE/L1 2767 2917 (377) m_b1s551i5
ST-E00130:540 1 AACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAA 50
L1P1_orf2#LIN 2767 AACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAA 2816
ST-E00130:540 51 CTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTG 100
v
L1P1_orf2#LIN 2817 CTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTT 2866
ST-E00130:540 101 ATAGAAAAATCAATTCAAGATGGATTAAAGCCTTAAACATTAGACCTAAA 150
v i v i
L1P1_orf2#LIN 2867 ATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAA 2916
ST-E00130:540 151 A 151
L1P1_orf2#LIN 2917 A 2917
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.77
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1281 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1217:19309:29841/2 1 151 (0) C L1P1 LINE/L1 (889) 5257 5107 1179
ANNOTATION EVIDENCE:
1281 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1217:19309:29841/2 1 151 0 C L1P1_orf2 LINE/L1 2998 3148 146
1281 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1217:19309:29841/2 1 151 (0) C L1P1_orf2#LINE/L1 (146) 3148 2998 m_b1s551i107
ST-E00130:540 1 TTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTA 50
i
C L1P1_orf2#LIN 3148 TTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTA 3099
ST-E00130:540 51 GGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTT 100
C L1P1_orf2#LIN 3098 GGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTT 3049
ST-E00130:540 101 TAGTTTAATTAGATCCCATTTGTCAATTCTGTCTTTTGTTGCCATTGCTT 150
i v
C L1P1_orf2#LIN 3048 TAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTT 2999
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 2998 T 2998
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1064 13.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1217:29680:3577/1 1 151 (0) + AluSx SINE/Alu 93 243 (69) 1180
ANNOTATION EVIDENCE:
1064 13.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1217:29680:3577/1 1 151 0 + AluSx SINE/Alu 93 243 69
1064 13.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1217:29680:3577/1 1 151 (0) AluSx#SINE/Alu 93 243 (69) m_b6s356i13
ST-E00130:540 1 GCCAACATGGTGAAACTCCATCTCTACGAAAAATAAAAAAATTAGCTGGG 50
i i v v i
AluSx#SINE/Al 93 GCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGG 142
ST-E00130:540 51 CATGGTGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGGATGAGGCAGGA 100
i iv i v
AluSx#SINE/Al 143 CGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
ST-E00130:540 101 GAATTGCTTGAACCGAGGAGGTAGAGGCTGAAGTGAACCGAGATCACACC 150
i vi ii i v i i i
AluSx#SINE/Al 193 GAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCC 242
ST-E00130:540 151 A 151
AluSx#SINE/Al 243 A 243
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.60
Transitions / transversions = 2.33 (14/6)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1305 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1218:6411:73141/1 1 151 (0) C L1P1 LINE/L1 (588) 5567 5417 1181
ANNOTATION EVIDENCE:
1305 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1218:6411:73141/1 1 151 0 C L1PA3_3end LINE/L1 164 314 588
1305 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1218:6411:73141/1 1 151 (0) C L1PA3_3end#LINE/L1 (588) 314 164 m_b1s551i247
ST-E00130:540 1 AATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTAT 50
vi
C L1PA3_3end#LI 314 AATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTAT 265
ST-E00130:540 51 TTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTG 100
i
C L1PA3_3end#LI 264 TTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTG 215
ST-E00130:540 101 CCATTCTAACTGGTGTGAGATGGTATCTCATTGTGTTTTTGATTTGCATT 150
v
C L1PA3_3end#LI 214 CCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATT 165
ST-E00130:540 151 T 151
C L1PA3_3end#LI 164 T 164
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1268 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1218:6411:73141/2 1 151 (0) + L1P1 LINE/L1 5234 5384 (762) 1182
ANNOTATION EVIDENCE:
1268 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1218:6411:73141/2 1 151 0 + L1P1_orf2 LINE/L1 3125 3275 19
1268 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1218:6411:73141/2 1 151 (0) L1P1_orf2#LINE/L1 3125 3275 (19) m_b1s551i154
ST-E00130:540 1 CCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAA 50
L1P1_orf2#LIN 3125 CCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAA 3174
ST-E00130:540 51 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGA 100
L1P1_orf2#LIN 3175 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGA 3224
ST-E00130:540 101 CATGAACAGACACTTCTCAAAAGAAGACATTTATGCATCCAAAAAACACA 150
v
L1P1_orf2#LIN 3225 CATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACA 3274
ST-E00130:540 151 T 151
L1P1_orf2#LIN 3275 T 3275
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1219:12926:6864/1 14 45 (106) + (CA)n Simple_repeat 1 32 (0) 1183
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1219:12926:6864/1 14 45 106 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1219:12926:6864/1 14 45 (106) (CA)n#Simple_repeat 1 32 (0) m_b4s252i29
ST-E00130:540 14 CATACATGCACACACATACACACACACACACA 45
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1315 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1220:28016:42604/1 1 151 (0) + L1P1 LINE/L1 5352 5502 (653) 1184
ANNOTATION EVIDENCE:
1315 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:28016:42604/1 1 151 0 + L1PA2_3end LINE/L1 99 249 653
1315 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:28016:42604/1 1 151 (0) L1PA2_3end#LINE/L1 99 249 (653) m_b1s551i222
ST-E00130:540 1 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 50
L1PA2_3end#LI 99 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 148
ST-E00130:540 51 CACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTC 100
L1PA2_3end#LI 149 CACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTC 198
ST-E00130:540 101 ACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTG 150
i
L1PA2_3end#LI 199 ACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTG 248
ST-E00130:540 151 G 151
L1PA2_3end#LI 249 G 249
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1352 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1220:28016:42604/2 1 151 (0) C L1P1 LINE/L1 (412) 5743 5593 1185
ANNOTATION EVIDENCE:
1352 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:28016:42604/2 1 151 0 C L1PA2_3end LINE/L1 340 490 412
1352 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:28016:42604/2 1 151 (0) C L1PA2_3end#LINE/L1 (412) 490 340 m_b1s551i301
ST-E00130:540 1 TGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATA 50
i
C L1PA2_3end#LI 490 TGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATA 441
ST-E00130:540 51 CGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATAT 100
i
C L1PA2_3end#LI 440 CGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATAT 391
ST-E00130:540 101 ACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCC 150
i
C L1PA2_3end#LI 390 ACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCC 341
ST-E00130:540 151 T 151
C L1PA2_3end#LI 340 T 340
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1300 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1220:8420:15373/1 1 151 (0) + L1P1 LINE/L1 5185 5335 (811) 1186
ANNOTATION EVIDENCE:
1300 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:8420:15373/1 1 151 0 + L1P1_orf2 LINE/L1 3076 3226 68
1300 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:8420:15373/1 1 151 (0) L1P1_orf2#LINE/L1 3076 3226 (68) m_b1s551i136
ST-E00130:540 1 ACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAAC 50
i
L1P1_orf2#LIN 3076 ACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAAC 3125
ST-E00130:540 51 CTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAC 100
L1P1_orf2#LIN 3126 CTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAC 3175
ST-E00130:540 101 AAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGAC 150
L1P1_orf2#LIN 3176 AAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGAC 3225
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3226 A 3226
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1337 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1220:8420:15373/2 1 151 (0) C L1P1 LINE/L1 (565) 5590 5440 1187
ANNOTATION EVIDENCE:
1337 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:8420:15373/2 1 151 0 C L1PA3_3end LINE/L1 187 337 565
1337 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1220:8420:15373/2 1 151 (0) C L1PA3_3end#LINE/L1 (565) 337 187 m_b1s551i259
ST-E00130:540 1 GGAATCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCAC 50
i
C L1PA3_3end#LI 337 GGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCAC 288
ST-E00130:540 51 CAACAGTGTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCACCTGTT 100
vi
C L1PA3_3end#LI 287 CAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTT 238
ST-E00130:540 101 GTTTCCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATC 150
i
C L1PA3_3end#LI 237 GTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATC 188
ST-E00130:540 151 T 151
C L1PA3_3end#LI 187 T 187
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1367 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1221:25570:33797/1 1 151 (0) C L1P1 LINE/L1 (460) 5695 5545 1188
ANNOTATION EVIDENCE:
1367 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1221:25570:33797/1 1 151 0 C L1PA3_3end LINE/L1 292 442 460
1367 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1221:25570:33797/1 1 151 (0) C L1PA3_3end#LINE/L1 (460) 442 292 m_b1s551i286
ST-E00130:540 1 TACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTAT 50
i
C L1PA3_3end#LI 442 TACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTAT 393
ST-E00130:540 51 ATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATC 100
i
C L1PA3_3end#LI 392 ATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATC 343
ST-E00130:540 101 CCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGT 150
i
C L1PA3_3end#LI 342 CCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGT 293
ST-E00130:540 151 C 151
C L1PA3_3end#LI 292 C 292
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1341 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1221:25570:33797/2 1 151 (0) + L1P1 LINE/L1 5394 5544 (611) 1189
ANNOTATION EVIDENCE:
1341 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1221:25570:33797/2 1 151 0 + L1PA2_3end LINE/L1 141 291 611
1341 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1221:25570:33797/2 1 151 (0) L1PA2_3end#LINE/L1 141 291 (611) m_b1s551i238
ST-E00130:540 1 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 50
L1PA2_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190
ST-E00130:540 51 ACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAAC 100
i
L1PA2_3end#LI 191 ACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAAC 240
ST-E00130:540 101 AGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTG 150
iv
L1PA2_3end#LI 241 AGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTG 290
ST-E00130:540 151 G 151
L1PA2_3end#LI 291 G 291
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 183 28.8 6.4 0.0 ST-E00130:540:HVYVWCCXX:1:1222:22394:22458/2 2 74 (77) + MIRb SINE/MIR 142 219 (49) 1190
ANNOTATION EVIDENCE:
183 28.77 6.41 0.00 ST-E00130:540:HVYVWCCXX:1:1222:22394:22458/2 2 74 77 + MIRb SINE/MIR 142 219 49
183 28.77 6.41 0.00 ST-E00130:540:HVYVWCCXX:1:1222:22394:22458/2 2 74 (77) MIRb#SINE/MIR 142 219 (49) m_b4s601i0
ST-E00130:540 2 GTAGAGTGAAGATA-TATCACTTACCTGGCCAGATAACTGTGAGGATTA- 49
i i ii - vi i v vi i vii -
MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191
ST-E00130:540 50 --GAGAAAATAAACGTAAAA-GTCTAGC 74
-- v iv i i- ii
MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.47
Transitions / transversions = 2.50 (15/6)
Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.25 (5 / 4)
+ 183 28.8 6.4 0.0 ST-E00130:540:HVYVWCCXX:1:1222:22698:21790/2 2 74 (77) + MIRb SINE/MIR 142 219 (49) 1191
ANNOTATION EVIDENCE:
183 28.77 6.41 0.00 ST-E00130:540:HVYVWCCXX:1:1222:22698:21790/2 2 74 77 + MIRb SINE/MIR 142 219 49
183 28.77 6.41 0.00 ST-E00130:540:HVYVWCCXX:1:1222:22698:21790/2 2 74 (77) MIRb#SINE/MIR 142 219 (49) m_b4s601i1
ST-E00130:540 2 GTAGAGTGAAGATA-TATCACTTACCTGGCCAGATAACTGTGAGGATTA- 49
i i ii - vi i v vi i vii -
MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191
ST-E00130:540 50 --GAGAAAATAAACGTAAAA-GTCTAGC 74
-- v iv i i- ii
MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.47
Transitions / transversions = 2.50 (15/6)
Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.25 (5 / 4)
+ 1274 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1222:26149:63314/2 1 151 (0) C L1P3 LINE/L1 (3030) 3116 2966 1192
ANNOTATION EVIDENCE:
1274 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1222:26149:63314/2 1 151 0 C L1P3_orf2 LINE/L1 857 1007 2287
1274 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1222:26149:63314/2 1 151 (0) C L1P3_orf2#LINE/L1 (2287) 1007 857 m_b6s551i276
ST-E00130:540 1 CTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTG 50
C L1P3_orf2#LIN 1007 CTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTG 958
ST-E00130:540 51 TGATGTTAGGGTGTTGATTTTAGATCTTTCCCACTTTGTCCTGTGGGCAT 100
i i v ?
C L1P3_orf2#LIN 957 TGATGTTAGGGTGTCGATTTTAGATCTTTCCCGCTTTCTCNTGTGGGCAT 908
ST-E00130:540 101 TTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGA 150
C L1P3_orf2#LIN 907 TTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGA 858
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 857 T 857
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 856 13.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1223:10510:72789/2 1 120 (31) C AluSx SINE/Alu (192) 120 1 1193
ANNOTATION EVIDENCE:
856 13.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1223:10510:72789/2 1 120 31 C AluSx SINE/Alu 1 120 192
856 13.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1223:10510:72789/2 1 120 (31) C AluSx#SINE/Alu (192) 120 1 m_b2s357i39
ST-E00130:540 1 AATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGA 50
i ii i i
C AluSx#SINE/Al 120 AGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGA 71
ST-E00130:540 51 CCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGATTACAGAT 100
i i v v v i ii
C AluSx#SINE/Al 70 CCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
ST-E00130:540 101 GTGAGCCACTGTGCCCAGCC 120
i i i
C AluSx#SINE/Al 20 GTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.63
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0)
+ 231 23.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:1223:31507:34061/1 13 64 (87) + L1MC4 LINE/L1 7901 7952 (90) 1194
ANNOTATION EVIDENCE:
231 23.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1223:31507:34061/1 13 64 87 + L1MC4_3end LINE/L1 2648 2699 90
231 23.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:1223:31507:34061/1 13 64 (87) L1MC4_3end#LINE/L1 2648 2699 (90) m_b3s551i0
ST-E00130:540 13 AGTGTGTGTGTGGAGAGAGGGAATGATTAAGCAAATATGGTAAAACGTTA 62
i i i i v ? ? i v i i i
L1MC4_3end#LI 2648 AATATGTATATGCANANAGAGAATGATAAAGCAAATGTGGCAAAATGTTA 2697
ST-E00130:540 63 AC 64
L1MC4_3end#LI 2698 AC 2699
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.40
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 247 27.2 4.2 12.3 ST-E00130:540:HVYVWCCXX:1:1224:10064:25042/1 3 132 (19) C L1MC4 LINE/L1 (1462) 6580 6462 1195
ANNOTATION EVIDENCE:
247 27.20 4.21 12.31 ST-E00130:540:HVYVWCCXX:1:1224:10064:25042/1 3 132 19 C L1MC4_3end LINE/L1 1209 1327 1462
247 27.20 4.21 12.31 ST-E00130:540:HVYVWCCXX:1:1224:10064:25042/1 3 132 (19) C L1MC4_3end#LINE/L1 (1462) 1327 1209 m_b3s551i160
ST-E00130:540 3 TCCAAGCCAACATCACACAGTTTAT-----CTTTTTTTCTGTCCAAATTT 47
v i vi i ----- i iiii v v
C L1MC4_3end#LI 1327 TCCAATCCAACACCACAGGGTTCATTCTAGCCTTCCCCCTTTCCATATTT 1278
ST-E00130:540 48 ATAAATTGCTTTACTAGCAGTTAAAAAAAAACACCCCAAAACCTGACTAT 97
i v iv iv iii v --------------i i -i
C L1MC4_3end#LI 1277 GTAACTCCCTTCTCCGACAGTGA--------------GAAACCTGGCT-C 1243
ST-E00130:540 98 CCACTCAACCTGAATGCATTTACTTATTTGCTCAA 132
- i v ?v ii
C L1MC4_3end#LI 1242 CCA-TTATCCNCAATATATTTACTTATTTGCTCAA 1209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.52
Transitions / transversions = 2.00 (20/10)
Gap_init rate = 0.13 (17 / 129), avg. gap size = 1.24 (21 / 17)
+ 250 24.6 6.2 3.9 ST-E00130:540:HVYVWCCXX:1:2101:2463:16867/1 25 151 (0) C L1ME4c LINE/L1 (297) 5786 5657 1196
ANNOTATION EVIDENCE:
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:1:2101:2463:16867/1 25 151 0 C L1ME4c_3end LINE/L1 404 533 297
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:1:2101:2463:16867/1 25 151 (0) C L1ME4c_3end#LINE/L1 (297) 533 404 m_b2s551i27
ST-E00130:540 25 TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTT 72
i - -iii ii v i v
C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484
ST-E00130:540 73 TCTATTTTC--CTACAATAAACATTATTGCAATGATCATT----TGTCTA 116
i v i-- iv i viii v i---- iv
C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434
ST-E00130:540 117 AGGGTTTTTTTTTCTCATATTTTAAATTATTTCTT 151
vi v ii ----- i i
C L1ME4c_3end#L 433 TAGCTTTTTCCTTC-----TTTTGAATTATTTCCT 404
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 643 17.3 2.1 2.1 ST-E00130:540:HVYVWCCXX:1:2101:26555:70768/2 1 142 (9) C AluSx SINE/Alu (98) 214 73 1197
ANNOTATION EVIDENCE:
643 17.26 2.11 2.11 ST-E00130:540:HVYVWCCXX:1:2101:26555:70768/2 1 142 9 C AluSx SINE/Alu 73 214 98
643 17.26 2.11 2.11 ST-E00130:540:HVYVWCCXX:1:2101:26555:70768/2 1 142 (9) C AluSx#SINE/Alu (98) 214 73 m_b4s357i35
ST-E00130:540 1 GCCTCCCAGGTTCAAGCGATTCGCCTGCCGCAGCCTCGTGAGCAGCTGGG 50
i v v vi i
C AluSx#SINE/Al 214 GCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGG 165
ST-E00130:540 51 ATTATAGGCGC-CGTCCACCACCCCTGGCGAAGTTTGGTGTTGGGAGGAG 99
i - - v i v v v i vvv v
C AluSx#SINE/Al 164 ATTACAGGCGCGCG-CCACCACGCCCGGCTAATTTTTGTATTTTTAGTAG 116
ST-E00130:540 100 ATAGTGAGTTTCACCATATTGGCCAGGC--GTTTCGCAAACTTCT 142
v vv i i -- i -- i
C AluSx#SINE/Al 115 AGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCG--AACTCCT 73
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 17.14
Transitions / transversions = 0.71 (10/14)
Gap_init rate = 0.04 (5 / 141), avg. gap size = 1.20 (6 / 5)
+ 1152 6.0 1.3 0.0 ST-E00130:540:HVYVWCCXX:1:2103:12713:42218/1 1 150 (1) C L1P3 LINE/L1 (2402) 3744 3593 1198
ANNOTATION EVIDENCE:
1152 6.00 1.31 0.00 ST-E00130:540:HVYVWCCXX:1:2103:12713:42218/1 1 150 1 C L1P3_orf2 LINE/L1 1484 1635 1659
1152 6.00 1.31 0.00 ST-E00130:540:HVYVWCCXX:1:2103:12713:42218/1 1 150 (1) C L1P3_orf2#LINE/L1 (1659) 1635 1484 m_b6s551i77
ST-E00130:540 1 TTTATCGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAAT 50
i i v v
C L1P3_orf2#LIN 1635 TTTATTGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAAT 1586
ST-E00130:540 51 TTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTG 98
i-- v
C L1P3_orf2#LIN 1585 TTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTG 1536
ST-E00130:540 99 GCATCATAAAATGAGTTAGGGAAGAGGCCCTCTTTTTCTATTGTTTGGAA 148
v i v
C L1P3_orf2#LIN 1535 GCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAA 1486
ST-E00130:540 149 TA 150
C L1P3_orf2#LIN 1485 TA 1484
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.60
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 1207 3.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:1:2103:12713:42218/2 1 150 (1) + L1P3 LINE/L1 3407 3558 (2588) 1199
ANNOTATION EVIDENCE:
1207 3.33 1.31 0.00 ST-E00130:540:HVYVWCCXX:1:2103:12713:42218/2 1 150 1 + L1P3_orf2 LINE/L1 1298 1449 1845
1207 3.33 1.31 0.00 ST-E00130:540:HVYVWCCXX:1:2103:12713:42218/2 1 150 (1) L1P3_orf2#LINE/L1 1298 1449 (1845) m_b6s551i134
ST-E00130:540 1 TAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTG 48
i v -- v
L1P3_orf2#LIN 1298 TGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTG 1347
ST-E00130:540 49 AATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACC 98
L1P3_orf2#LIN 1348 AATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACC 1397
ST-E00130:540 99 AACCAAAAAAAGCCCAGGACCAGAGGGATTCACAGCCGAATTCTACCAGG 148
v i
L1P3_orf2#LIN 1398 AACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGA 1447
ST-E00130:540 149 GG 150
L1P3_orf2#LIN 1448 GG 1449
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.41
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 329 27.2 14.0 0.0 ST-E00130:540:HVYVWCCXX:1:2103:23399:32637/1 5 151 (0) C MIR SINE/MIR (0) 262 92 1200
ANNOTATION EVIDENCE:
329 27.21 14.04 0.00 ST-E00130:540:HVYVWCCXX:1:2103:23399:32637/1 5 151 0 C MIR SINE/MIR 92 262 0
329 27.21 14.04 0.00 ST-E00130:540:HVYVWCCXX:1:2103:23399:32637/1 5 151 (0) C MIR#SINE/MIR (0) 262 92 m_b6s601i34
ST-E00130:540 5 AAAAATAGCTAACACTTGTTGAGCATATACGGTGTGCCTGGCA------- 47
v i i iiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 48 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 82
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 83 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 130
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
ST-E00130:540 131 TGAGGTAAAGTAACTTGCTTA 151
v v ii
C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCA 92
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.64
Transitions / transversions = 1.50 (24/16)
Gap_init rate = 0.03 (5 / 146), avg. gap size = 4.80 (24 / 5)
+ 19 4.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2103:23399:32637/2 1 23 (128) + (A)n Simple_repeat 1 23 (0) 1201
ANNOTATION EVIDENCE:
19 4.55 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2103:23399:32637/2 1 23 128 + (A)n Simple_repeat 1 23 0
19 4.55 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2103:23399:32637/2 1 23 (128) (A)n#Simple_repeat 1 23 (0) m_b6s252i9
ST-E00130:540 1 AAAAAAAAAAAAAAAAAAAAGAA 23
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 840 11.3 1.7 0.0 ST-E00130:540:HVYVWCCXX:1:2103:4543:18291/1 1 115 (36) C AluSx SINE/Alu (195) 117 1 1202
ANNOTATION EVIDENCE:
840 11.30 1.71 0.00 ST-E00130:540:HVYVWCCXX:1:2103:4543:18291/1 1 115 36 C AluSx SINE/Alu 1 117 195
840 11.30 1.71 0.00 ST-E00130:540:HVYVWCCXX:1:2103:4543:18291/1 1 115 (36) C AluSx#SINE/Alu (195) 117 1 m_b4s357i45
ST-E00130:540 1 AGAGATGGAGTTTCACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCT 50
i i i v i
C AluSx#SINE/Al 117 AGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCT 68
ST-E00130:540 51 T--GTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTG 98
i-- i i i i i
C AluSx#SINE/Al 67 CAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTG 18
ST-E00130:540 99 AGCCACTGCACCCGGCC 115
i i
C AluSx#SINE/Al 17 AGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.27
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 114), avg. gap size = 2.00 (2 / 1)
+ 953 4.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2105:15747:6231/1 36 150 (1) C AluSx SINE/Alu (21) 291 177 1203
ANNOTATION EVIDENCE:
953 4.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:15747:6231/1 36 150 1 C AluSx SINE/Alu 177 291 21
953 4.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:15747:6231/1 36 150 (1) C AluSx#SINE/Alu (21) 291 177 m_b4s357i22
ST-E00130:540 36 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 85
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 86 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCT 135
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
ST-E00130:540 136 CCTGCCTCAGCCTCC 150
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCC 177
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.86
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.0 (0 / 0)
+ 600 12.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2105:15747:6231/2 67 151 (0) + AluY SINE/Alu 1 85 (226) 1204
ANNOTATION EVIDENCE:
600 12.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:15747:6231/2 67 151 0 + AluY SINE/Alu 1 85 226
600 12.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:15747:6231/2 67 151 (0) AluY#SINE/Alu 1 85 (226) m_b4s357i59
ST-E00130:540 67 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 116
i i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 117 AGCAGGCAGATCACAAGGTCAGGAGTTTGAGAACA 151
i i i i v i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCA 85
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.61
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0)
+ 255 28.2 4.5 0.0 ST-E00130:540:HVYVWCCXX:1:2105:22810:42060/1 64 148 (3) + MIRb SINE/MIR 122 210 (58) 1205
ANNOTATION EVIDENCE:
255 28.24 4.50 0.00 ST-E00130:540:HVYVWCCXX:1:2105:22810:42060/1 64 148 3 + MIRb SINE/MIR 122 210 58
255 28.24 4.50 0.00 ST-E00130:540:HVYVWCCXX:1:2105:22810:42060/1 64 148 (3) MIRb#SINE/MIR 122 210 (58) m_b4s601i23
ST-E00130:540 64 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 112
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
ST-E00130:540 113 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAA 148
vi i vii --- v iv i
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAA 210
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.65
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 84), avg. gap size = 2.00 (4 / 2)
+ 458 17.7 5.9 0.0 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/1 1 96 (55) + L1MC4 LINE/L1 7548 7649 (393) 1206
ANNOTATION EVIDENCE:
458 17.71 5.88 0.00 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/1 1 96 55 + L1MC4_3end LINE/L1 2295 2396 393
458 17.71 5.88 0.00 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/1 1 96 (55) L1MC4_3end#LINE/L1 2295 2396 (393) m_b3s551i72
ST-E00130:540 1 CCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA------A 44
v v i v ? v i i i ------i
L1MC4_3end#LI 2295 CCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTGAG 2344
ST-E00130:540 45 GAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGCAA 94
i v vvv v
L1MC4_3end#LI 2345 GAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGCAA 2394
ST-E00130:540 95 TG 96
i
L1MC4_3end#LI 2395 CG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.88
Transitions / transversions = 0.78 (7/9)
Gap_init rate = 0.01 (1 / 95), avg. gap size = 6.00 (6 / 1)
+ 278 10.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/1 101 139 (12) + L1MC4 LINE/L1 7762 7800 (242) 1206
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/1 101 139 12 + L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/1 101 139 (12) L1MC4_3end#LINE/L1 2509 2547 (242) m_b3s551i73
ST-E00130:540 101 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTA 139
i i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTA 2547
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 259 19.3 0.0 20.2 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/2 47 150 (1) C L1MC4 LINE/L1 (90) 7952 7870 1207
ANNOTATION EVIDENCE:
259 19.27 0.00 20.19 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/2 47 150 1 C L1MC4_3end LINE/L1 2617 2699 90
259 19.27 0.00 20.19 ST-E00130:540:HVYVWCCXX:1:2105:25124:38719/2 47 150 (1) C L1MC4_3end#LINE/L1 (90) 2699 2617 m_b3s551i4
ST-E00130:540 47 GTTAACGTTTTACCATATTTGCTTAATCATTCCCTCTCTCCACACACACA 96
i i i v i ? ? -----------
C L1MC4_3end#LI 2699 GTTAACATTTTGCCACATTTGCTTTATCATTCTCTNTNT----------- 2661
ST-E00130:540 97 CTCATACGCAGATACACACATCATTTTCTCTGAACCATTTTGAGATGAAA 146
------- -- i i iv i - vv i
C L1MC4_3end#LI 2660 -------GC--ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAG 2621
ST-E00130:540 147 TCGC 150
i
C L1MC4_3end#LI 2620 TTGC 2617
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.17
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.20 (21 / 103), avg. gap size = 1.00 (21 / 21)
+ 458 17.7 5.9 0.0 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/1 1 96 (55) + L1MC4 LINE/L1 7548 7649 (393) 1208
ANNOTATION EVIDENCE:
458 17.71 5.88 0.00 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/1 1 96 55 + L1MC4_3end LINE/L1 2295 2396 393
458 17.71 5.88 0.00 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/1 1 96 (55) L1MC4_3end#LINE/L1 2295 2396 (393) m_b3s551i74
ST-E00130:540 1 CCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA------A 44
v v i v ? v i i i ------i
L1MC4_3end#LI 2295 CCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTGAG 2344
ST-E00130:540 45 GAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGCAA 94
i v vvv v
L1MC4_3end#LI 2345 GAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGCAA 2394
ST-E00130:540 95 TG 96
i
L1MC4_3end#LI 2395 CG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.88
Transitions / transversions = 0.78 (7/9)
Gap_init rate = 0.01 (1 / 95), avg. gap size = 6.00 (6 / 1)
+ 278 10.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/1 101 139 (12) + L1MC4 LINE/L1 7762 7800 (242) 1208
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/1 101 139 12 + L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/1 101 139 (12) L1MC4_3end#LINE/L1 2509 2547 (242) m_b3s551i75
ST-E00130:540 101 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTA 139
i i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTA 2547
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 268 19.1 0.0 20.0 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/2 47 151 (0) C L1MC4 LINE/L1 (90) 7952 7869 1209
ANNOTATION EVIDENCE:
268 19.05 0.00 20.00 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/2 47 151 0 C L1MC4_3end LINE/L1 2616 2699 90
268 19.05 0.00 20.00 ST-E00130:540:HVYVWCCXX:1:2105:26707:38684/2 47 151 (0) C L1MC4_3end#LINE/L1 (90) 2699 2616 m_b3s551i5
ST-E00130:540 47 GTTAACGTTTTACCATATTTGCTTAATCATTCCCTCTCTCCACACACACA 96
i i i v i ? ? -----------
C L1MC4_3end#LI 2699 GTTAACATTTTGCCACATTTGCTTTATCATTCTCTNTNT----------- 2661
ST-E00130:540 97 CTCATACGCAGATACACACATCATTTTCTCTGAACCATTTTGAGATGAAA 146
------- -- i i iv i - vv i
C L1MC4_3end#LI 2660 -------GC--ATATACATATTTTTTTTTCTGAACCA-TTTGAGAGTAAG 2621
ST-E00130:540 147 TCGCA 151
i
C L1MC4_3end#LI 2620 TTGCA 2616
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.88
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.20 (21 / 104), avg. gap size = 1.00 (21 / 21)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2107:19116:68183/2 43 74 (77) + (CA)n Simple_repeat 1 32 (0) 1210
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2107:19116:68183/2 43 74 77 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2107:19116:68183/2 43 74 (77) (CA)n#Simple_repeat 1 32 (0) m_b4s252i28
ST-E00130:540 43 CATACATGCACACACATACACACACACACACA 74
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1312 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2109:30239:34465/1 1 151 (0) + L1P1 LINE/L1 5468 5618 (537) 1211
ANNOTATION EVIDENCE:
1312 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2109:30239:34465/1 1 151 0 + L1PA3_3end LINE/L1 215 365 537
1312 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2109:30239:34465/1 1 151 (0) L1PA3_3end#LINE/L1 215 365 (537) m_b1s551i266
ST-E00130:540 1 CAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAA 50
i
L1PA3_3end#LI 215 CAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAA 264
ST-E00130:540 51 ATAGGAATCCTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATT 100
iv
L1PA3_3end#LI 265 ATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATT 314
ST-E00130:540 101 GTGGAAGTCAGTGTGGTGATTCCTCAGGGATCTAGAACTGGAAATACCAT 150
i i
L1PA3_3end#LI 315 GTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCAT 364
ST-E00130:540 151 T 151
L1PA3_3end#LI 365 T 365
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1291 2.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:2109:30239:34465/2 1 151 (0) C L1PA2 LINE/L1 (307) 5848 5699 1212
ANNOTATION EVIDENCE:
1291 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:2109:30239:34465/2 1 151 0 C L1PA2_3end LINE/L1 446 595 307
1291 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:2109:30239:34465/2 1 151 (0) C L1PA2_3end#LINE/L1 (307) 595 446 m_b1s551i338
ST-E00130:540 1 ATGTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTA 50
-
C L1PA2_3end#LI 595 ATGTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTA 547
ST-E00130:540 51 TTCCATGGTGTATATGTGCCACAGCTTCTTAATCCAGTCTATCATTGTTG 100
vi
C L1PA2_3end#LI 546 TTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTG 497
ST-E00130:540 101 GACATTTGGGTTGGTCCCAAGTCTTTGCTATTGTGAATAATGCCACAATA 150
i i
C L1PA2_3end#LI 496 GACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATA 447
ST-E00130:540 151 A 151
C L1PA2_3end#LI 446 A 446
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 492 15.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2109:8349:51078/2 1 77 (74) C AluSx SINE/Alu (235) 77 1 1213
ANNOTATION EVIDENCE:
492 15.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2109:8349:51078/2 1 77 74 C AluSx SINE/Alu 1 77 235
492 15.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2109:8349:51078/2 1 77 (74) C AluSx#SINE/Alu (235) 77 1 m_b2s357i53
ST-E00130:540 1 CTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGAT 50
i i i v v v i
C AluSx#SINE/Al 77 CTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGAT 28
ST-E00130:540 51 TACAGATGTGAGCCACTGTGCCCAGCC 77
ii i i i
C AluSx#SINE/Al 27 TACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.13
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 982 13.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2112:15605:15479/2 2 139 (12) C AluSx SINE/Alu (174) 138 1 1214
ANNOTATION EVIDENCE:
982 13.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2112:15605:15479/2 2 139 12 C AluSx SINE/Alu 1 138 174
982 13.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2112:15605:15479/2 2 139 (12) C AluSx#SINE/Alu (174) 138 1 m_b2s357i32
ST-E00130:540 2 GCTAATTTTTGTATTTTAAATAGAGACAAGGTGTCACCATGTTGGCCAGG 51
v i ii v
C AluSx#SINE/Al 138 GCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGG 89
ST-E00130:540 52 CTGGTTTCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAA 101
i i i i v v
C AluSx#SINE/Al 88 CTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA 39
ST-E00130:540 102 ATTGCTGAGATTACAGATGTGAGCCACTGTGCCCAGCC 139
v i ii i i i
C AluSx#SINE/Al 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.04
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 137), avg. gap size = 0.0 (0 / 0)
+ 262 27.1 5.9 0.7 ST-E00130:540:HVYVWCCXX:1:2114:29031:35397/2 1 145 (6) + L1ME4c LINE/L1 5705 5857 (226) 1215
ANNOTATION EVIDENCE:
262 27.09 5.89 0.69 ST-E00130:540:HVYVWCCXX:1:2114:29031:35397/2 1 145 6 + L1ME4c_3end LINE/L1 452 604 226
262 27.09 5.89 0.69 ST-E00130:540:HVYVWCCXX:1:2114:29031:35397/2 1 145 (6) L1ME4c_3end#LINE/L1 452 604 (226) m_b2s551i10
ST-E00130:540 1 TTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCTAAATTTCTG 48
iiiv i vi --i v i v i v ii
L1ME4c_3end#L 452 TTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 501
ST-E00130:540 49 ACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT--GACAGAAAA 92
iii- - i -- i? i-- ii v
L1ME4c_3end#L 502 ACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATA 551
ST-E00130:540 93 ATGGTGAAGCCATTAAAAAGTATGACTATCAAGAAAA-GCAACTACCTGG 141
- vi v vv i i v vv - i i v v
L1ME4c_3end#L 552 -TTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGG 600
ST-E00130:540 142 AAAA 145
L1ME4c_3end#L 601 AAAA 604
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.49
Transitions / transversions = 1.53 (23/15)
Gap_init rate = 0.05 (7 / 144), avg. gap size = 1.43 (10 / 7)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 22 53 (98) + (TG)n Simple_repeat 1 32 (0) 1216
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 22 53 98 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 22 53 (98) (TG)n#Simple_repeat 1 32 (0) m_b4s252i27
ST-E00130:540 22 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 53
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 54 66 (85) + (TGTATG)n Simple_repeat 1 41 (0) 1217
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 22 66 85 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 22 66 (85) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i26
ST-E00130:540 22 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 66
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 570 5.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 81 151 (0) C AluSx SINE/Alu (21) 291 221 1218
ANNOTATION EVIDENCE:
570 5.63 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 81 151 0 C AluSx SINE/Alu 221 291 21
570 5.63 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/1 81 151 (0) C AluSx#SINE/Alu (21) 291 221 m_b4s357i12
ST-E00130:540 81 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 130
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 131 GCGCGATCTCGGCTCAATGCA 151
v
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCA 221
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.52
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 1063 11.7 1.4 0.0 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/2 7 151 (0) + AluSx SINE/Alu 1 147 (165) 1219
ANNOTATION EVIDENCE:
1063 11.72 1.36 0.00 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/2 7 151 0 + AluSx SINE/Alu 1 147 165
1063 11.72 1.36 0.00 ST-E00130:540:HVYVWCCXX:1:2116:6076:18450/2 7 151 (0) AluSx#SINE/Alu 1 147 (165) m_b4s356i47
ST-E00130:540 7 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 56
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 57 TGCAGGCAGATCAC--AAGGTCATGAGTTTGAGAACAGCCTGGCCAATAT 104
v i i --i v i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 105 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCAGGGGTGG 151
i i i i v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGG 147
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.42
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.01 (1 / 144), avg. gap size = 2.00 (2 / 1)
+ 1044 12.8 0.0 1.3 ST-E00130:540:HVYVWCCXX:1:2120:32268:67445/1 1 151 (0) + AluSx SINE/Alu 40 188 (124) 1220
ANNOTATION EVIDENCE:
1044 12.75 0.00 1.32 ST-E00130:540:HVYVWCCXX:1:2120:32268:67445/1 1 151 0 + AluSx SINE/Alu 40 188 124
1044 12.75 0.00 1.32 ST-E00130:540:HVYVWCCXX:1:2120:32268:67445/1 1 151 (0) AluSx#SINE/Alu 40 188 (124) m_b5s356i20
ST-E00130:540 1 TGGGAGGCCAAGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGC 50
i i i i i i
AluSx#SINE/Al 40 TGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGC 89
ST-E00130:540 51 CTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAG 100
i v i --
AluSx#SINE/Al 90 CTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAG 137
ST-E00130:540 101 CCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGG 150
i i v i v v vi i i
AluSx#SINE/Al 138 CCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGG 187
ST-E00130:540 151 C 151
AluSx#SINE/Al 188 C 188
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.72
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 940 13.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2121:3041:59288/1 1 131 (20) C AluSx SINE/Alu (181) 131 1 1221
ANNOTATION EVIDENCE:
940 12.98 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2121:3041:59288/1 1 131 20 C AluSx SINE/Alu 1 131 181
940 12.98 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2121:3041:59288/1 1 131 (20) C AluSx#SINE/Alu (181) 131 1 m_b2s357i35
ST-E00130:540 1 TTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTT 50
v i ii i
C AluSx#SINE/Al 131 TTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCT 82
ST-E00130:540 51 CGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTG 100
i i i v v v
C AluSx#SINE/Al 81 CGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
ST-E00130:540 101 AGATTACAGATGTGAGCCACTGTGCCCAGCC 131
i ii i i i
C AluSx#SINE/Al 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.70
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 552 10.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2123:32319:27626/1 77 151 (0) + AluY SINE/Alu 1 75 (236) 1222
ANNOTATION EVIDENCE:
552 10.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2123:32319:27626/1 77 151 0 + AluY SINE/Alu 1 75 236
552 10.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2123:32319:27626/1 77 151 (0) AluY#SINE/Alu 1 75 (236) m_b2s357i64
ST-E00130:540 77 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 126
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 127 GGCGGGCTGATCATGAGGTCAGGAG 151
v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAG 75
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.84
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 670 8.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2123:32319:27626/2 57 147 (4) C AluSx SINE/Alu (14) 298 208 1223
ANNOTATION EVIDENCE:
670 8.79 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2123:32319:27626/2 57 147 4 C AluSx SINE/Alu 208 298 14
670 8.79 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2123:32319:27626/2 57 147 (4) C AluSx#SINE/Alu (14) 298 208 m_b2s357i101
ST-E00130:540 57 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 106
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
ST-E00130:540 107 TGCAGTGGCATGATGTCGGCTCACTGCACCCTCCACCTCCC 147
ii v v i
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCC 208
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.07
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0)
+ 376 4.5 0.0 8.3 ST-E00130:540:HVYVWCCXX:1:2124:21004:48986/1 1 72 (79) C L1PA2 LINE/L1 (100) 6055 5990 1224
ANNOTATION EVIDENCE:
376 4.55 0.00 8.33 ST-E00130:540:HVYVWCCXX:1:2124:21004:48986/1 1 72 79 C L1PA2_3end LINE/L1 737 802 100
376 4.55 0.00 8.33 ST-E00130:540:HVYVWCCXX:1:2124:21004:48986/1 1 72 (79) C L1PA2_3end#LINE/L1 (100) 802 737 m_b1s551i415
ST-E00130:540 1 CTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCGCCGCC 50
v -
C L1PA2_3end#LI 802 CTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCC-CC 754
ST-E00130:540 51 CACTCGCGCCTCCCACCCCGCC 72
- ---- i i
C L1PA2_3end#LI 753 C-CT----CCCCCCACCCCACC 737
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.71
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6)
+ 1295 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:2124:21004:48986/2 1 151 (0) + L1PA2 LINE/L1 5809 5958 (197) 1225
ANNOTATION EVIDENCE:
1295 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:2124:21004:48986/2 1 151 0 + L1PA2_3end LINE/L1 556 705 197
1295 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:2124:21004:48986/2 1 151 (0) L1PA2_3end#LINE/L1 556 705 (197) m_b1s551i379
ST-E00130:540 1 GCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAAT 50
-
L1PA2_3end#LI 556 GCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAAT 604
ST-E00130:540 51 TGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGAAAAAACCAAACAC 100
i v
L1PA2_3end#LI 605 TGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACAC 654
ST-E00130:540 101 CGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACA 150
i
L1PA2_3end#LI 655 CGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACA 704
ST-E00130:540 151 C 151
L1PA2_3end#LI 705 C 705
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1253 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2124:4178:55913/1 1 151 (0) C L1P3 LINE/L1 (3130) 3016 2866 1226
ANNOTATION EVIDENCE:
1253 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2124:4178:55913/1 1 151 0 C L1P3_orf2 LINE/L1 757 907 2387
1253 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2124:4178:55913/1 1 151 (0) C L1P3_orf2#LINE/L1 (2387) 907 757 m_b7s551i41
ST-E00130:540 1 TTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGA 50
C L1P3_orf2#LIN 907 TTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGA 858
ST-E00130:540 51 TTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTTAT 100
i i ?i
C L1P3_orf2#LIN 857 TTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTTAT 808
ST-E00130:540 101 TTCTGCCTTCATTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTTGT 150
v i i
C L1P3_orf2#LIN 807 TTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGT 758
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 757 T 757
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1220 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2201:2148:45048/1 1 151 (0) + L1P3 LINE/L1 2840 2990 (3156) 1227
ANNOTATION EVIDENCE:
1220 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2201:2148:45048/1 1 151 0 + L1P3_orf2 LINE/L1 731 881 2413
1220 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2201:2148:45048/1 1 151 (0) L1P3_orf2#LINE/L1 731 881 (2413) m_b7s551i47
ST-E00130:540 1 AAAACCACACAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTAC 50
i
L1P3_orf2#LIN 731 AAAACCGCACAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTAC 780
ST-E00130:540 51 TAGGTAAATAATGAAATGAAGGCAGAAATAAGTAAGTTCTTTGAAACCAA 100
i i v i?
L1P3_orf2#LIN 781 TGGGTAAATAACGAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAA 830
ST-E00130:540 101 TAAGAACAAAGACACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAG 150
i i
L1P3_orf2#LIN 831 TGAGAACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAG 880
ST-E00130:540 151 T 151
L1P3_orf2#LIN 881 T 881
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1058 7.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:1:2201:2148:45048/2 1 151 (0) C L1P3 LINE/L1 (2695) 3451 3299 1228
ANNOTATION EVIDENCE:
1058 7.28 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:2201:2148:45048/2 1 151 0 C L1P3_orf2 LINE/L1 1190 1342 1952
1058 7.28 1.30 0.00 ST-E00130:540:HVYVWCCXX:1:2201:2148:45048/2 1 151 (0) C L1P3_orf2#LINE/L1 (1952) 1342 1190 m_b6s551i163
ST-E00130:540 1 ATTCGACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAAT 48
v -- v i
C L1P3_orf2#LIN 1342 ATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAAT 1293
ST-E00130:540 49 TTATCACTTTCTTCTGGATTTTCTAGTTTATTTGCATAGAGGTATTTATA 98
vv i i i
C L1P3_orf2#LIN 1292 TTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATA 1243
ST-E00130:540 99 GTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCT 148
iv i
C L1P3_orf2#LIN 1242 GTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCC 1193
ST-E00130:540 149 CTT 151
C L1P3_orf2#LIN 1192 CTT 1190
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.02
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1175 9.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/1 1 151 (0) + AluSx SINE/Alu 79 229 (83) 1229
ANNOTATION EVIDENCE:
1175 9.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/1 1 151 0 + AluSx SINE/Alu 79 229 83
1175 9.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/1 1 151 (0) AluSx#SINE/Alu 79 229 (83) m_b4s356i25
ST-E00130:540 1 TTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACAC 50
i v i i i i
AluSx#SINE/Al 79 TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC 128
ST-E00130:540 51 AAAAATTAGCCAGGGGGGGTGGCAGGCGCCTATAATCCCAGCTACTCAGG 100
i v v iv i i
AluSx#SINE/Al 129 AAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGG 178
ST-E00130:540 101 AGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGA 150
i i
AluSx#SINE/Al 179 AGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGA 228
ST-E00130:540 151 G 151
AluSx#SINE/Al 229 G 229
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.67
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/2 86 117 (34) + (TG)n Simple_repeat 1 32 (0) 1230
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/2 86 117 34 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/2 86 117 (34) (TG)n#Simple_repeat 1 32 (0) m_b4s252i25
ST-E00130:540 86 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 117
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/2 118 130 (21) + (TGTATG)n Simple_repeat 1 41 (0) 1231
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/2 86 130 21 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:2203:30411:19575/2 86 130 (21) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i24
ST-E00130:540 86 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 130
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 1208 9.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/1 1 151 (0) + AluSx SINE/Alu 79 229 (83) 1232
ANNOTATION EVIDENCE:
1208 9.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/1 1 151 0 + AluSx SINE/Alu 79 229 83
1208 9.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/1 1 151 (0) AluSx#SINE/Alu 79 229 (83) m_b4s356i26
ST-E00130:540 1 TTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACAC 50
i v i i i i
AluSx#SINE/Al 79 TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC 128
ST-E00130:540 51 AAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGG 100
i v iv i i
AluSx#SINE/Al 129 AAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGG 178
ST-E00130:540 101 AGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGA 150
i i
AluSx#SINE/Al 179 AGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGA 228
ST-E00130:540 151 G 151
AluSx#SINE/Al 229 G 229
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.95
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/2 86 117 (34) + (TG)n Simple_repeat 1 32 (0) 1233
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/2 86 117 34 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/2 86 117 (34) (TG)n#Simple_repeat 1 32 (0) m_b4s252i23
ST-E00130:540 86 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 117
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/2 118 130 (21) + (TGTATG)n Simple_repeat 1 41 (0) 1234
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/2 86 130 21 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:1:2203:30705:19241/2 86 130 (21) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i22
ST-E00130:540 86 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 130
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 202 28.0 16.9 0.0 ST-E00130:540:HVYVWCCXX:1:2204:12642:65722/1 33 150 (1) C MIR SINE/MIR (0) 262 121 1235
ANNOTATION EVIDENCE:
202 27.97 16.90 0.00 ST-E00130:540:HVYVWCCXX:1:2204:12642:65722/1 33 150 1 C MIR SINE/MIR 121 262 0
202 27.97 16.90 0.00 ST-E00130:540:HVYVWCCXX:1:2204:12642:65722/1 33 150 (1) C MIR#SINE/MIR (0) 262 121 m_b6s601i20
ST-E00130:540 33 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 75
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 76 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 110
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 111 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTG 150
v i v vi ii v i i --
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTG 121
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.74
Transitions / transversions = 1.75 (21/12)
Gap_init rate = 0.04 (5 / 117), avg. gap size = 4.80 (24 / 5)
+ 27 11.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2204:12642:65722/2 24 62 (89) + (A)n Simple_repeat 1 39 (0) 1236
ANNOTATION EVIDENCE:
27 11.06 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2204:12642:65722/2 24 62 89 + (A)n Simple_repeat 1 39 0
27 11.06 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2204:12642:65722/2 24 62 (89) (A)n#Simple_repeat 1 39 (0) m_b6s252i8
ST-E00130:540 24 AAAAAAAAAAAAAAAAAAAAAAAAAAAGAATGAAAATAA 62
i vi v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 1071 10.7 0.7 0.0 ST-E00130:540:HVYVWCCXX:1:2204:15442:50287/1 12 151 (0) + AluY SINE/Alu 1 141 (170) 1237
ANNOTATION EVIDENCE:
1071 10.71 0.70 0.00 ST-E00130:540:HVYVWCCXX:1:2204:15442:50287/1 12 151 0 + AluY SINE/Alu 1 141 170
1071 10.71 0.70 0.00 ST-E00130:540:HVYVWCCXX:1:2204:15442:50287/1 12 151 (0) AluY#SINE/Alu 1 141 (170) m_b2s356i48
ST-E00130:540 12 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 61
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 62 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 111
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
ST-E00130:540 112 TGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGG 151
i i - vi
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGG 141
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.13
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.01 (1 / 139), avg. gap size = 1.00 (1 / 1)
+ 1037 13.4 0.0 1.3 ST-E00130:540:HVYVWCCXX:1:2207:5497:55702/1 1 151 (0) C AluSx SINE/Alu (133) 179 31 1238
ANNOTATION EVIDENCE:
1037 13.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:1:2207:5497:55702/1 1 151 0 C AluSx SINE/Alu 31 179 133
1037 13.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:1:2207:5497:55702/1 1 151 (0) C AluSx#SINE/Alu (133) 179 31 m_b5s356i22
ST-E00130:540 1 TCCTGAGCAGCTATGATTACAGGCTCCCACCACAATGCCTGGCTAATTTT 50
i i iv v v i v i i --
C AluSx#SINE/Al 179 TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAA--TT 132
ST-E00130:540 51 TTTGTATTTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCC 100
i v i i
C AluSx#SINE/Al 131 TTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCT 82
ST-E00130:540 101 CAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTG 150
i i i i i i
C AluSx#SINE/Al 81 CGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
ST-E00130:540 151 G 151
C AluSx#SINE/Al 31 G 31
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.48
Transitions / transversions = 3.00 (15/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 252 16.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2207:5497:55702/2 115 151 (0) C SVA_A Retroposon/SVA (951) 436 400 1239
ANNOTATION EVIDENCE:
252 16.22 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2207:5497:55702/2 115 151 0 C SVA_A Retroposon/SVA 400 436 951
252 16.22 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2207:5497:55702/2 115 151 (0) C SVA_A#Retroposon/SVA (951) 436 400 m_b5s502i5
ST-E00130:540 115 CTGTAATCCCAACACTTTGGGAGGCCAAGGTGGGCAG 151
i i i ii i
C SVA_A#Retropo 436 CTGCAATCCTAGCACTTTGGGAGGCCAAGGCAGGCGG 400
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.13
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 1163 6.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2208:6867:31353/2 1 144 (7) + AluSx SINE/Alu 148 291 (21) 1240
ANNOTATION EVIDENCE:
1163 6.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2208:6867:31353/2 1 144 7 + AluSx SINE/Alu 148 291 21
1163 6.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2208:6867:31353/2 1 144 (7) AluSx#SINE/Alu 148 291 (21) m_b4s357i30
ST-E00130:540 1 TGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATC 50
iv i i
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATC 197
ST-E00130:540 51 GCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGC 100
i i
AluSx#SINE/Al 198 GCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGC 247
ST-E00130:540 101 ACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 144
i i i
AluSx#SINE/Al 248 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.87
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 143), avg. gap size = 0.0 (0 / 0)
+ 250 26.4 5.9 1.4 ST-E00130:540:HVYVWCCXX:1:2209:1499:61608/1 2 147 (4) C L1ME4c LINE/L1 (217) 5866 5714 1241
ANNOTATION EVIDENCE:
250 26.39 5.88 1.37 ST-E00130:540:HVYVWCCXX:1:2209:1499:61608/1 2 147 4 C L1ME4c_3end LINE/L1 461 613 217
250 26.39 5.88 1.37 ST-E00130:540:HVYVWCCXX:1:2209:1499:61608/1 2 147 (4) C L1ME4c_3end#LINE/L1 (217) 613 461 m_b2s551i8
ST-E00130:540 2 TTATAAGTATTTTTCCAGGTAGTTGC-TTTTCTTGATAGTCATACTTTTT 50
i ii - v v i i - vv v i i vv
C L1ME4c_3end#L 613 TCATAAACA-TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTT 565
ST-E00130:540 51 AATGGCTTCACCATTTTTCTGTC--ATAAA--TACCATAATTTACTTGA- 95
v iv - v ii --i ?i -- i -
C L1ME4c_3end#L 564 AATGGCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAAC 516
ST-E00130:540 96 CATT-TTTTATTGTCAGAAATTTAGATTCTTTTCTATTTTC--CTACAAT 142
-iii ii v i v i v i-- iv
C L1ME4c_3end#L 515 CATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTAT 466
ST-E00130:540 143 AAACA 147
i
C L1ME4c_3end#L 465 AAATA 461
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.65
Transitions / transversions = 1.64 (23/14)
Gap_init rate = 0.06 (8 / 145), avg. gap size = 1.38 (11 / 8)
+ 632 5.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2209:6979:59182/1 1 77 (74) + AluSx SINE/Alu 215 291 (21) 1242
ANNOTATION EVIDENCE:
632 5.19 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2209:6979:59182/1 1 77 74 + AluSx SINE/Alu 215 291 21
632 5.19 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2209:6979:59182/1 1 77 (74) AluSx#SINE/Alu 215 291 (21) m_b4s357i15
ST-E00130:540 1 GAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCAAC 50
i i i
AluSx#SINE/Al 215 GGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGAC 264
ST-E00130:540 51 AGAGCGAGATTCCGTCTCAAAAAAAAA 77
i
AluSx#SINE/Al 265 AGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.20
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 18 18.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2209:6979:59182/1 105 136 (15) + (CA)n Simple_repeat 1 32 (0) 1243
ANNOTATION EVIDENCE:
18 18.13 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2209:6979:59182/1 105 136 15 + (CA)n Simple_repeat 1 32 0
18 18.13 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2209:6979:59182/1 105 136 (15) (CA)n#Simple_repeat 1 32 (0) m_b4s252i21
ST-E00130:540 105 CATACATGCACACACATACCCACACACACACA 136
i ii i v
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1335 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2210:13179:59376/1 1 151 (0) C L1P1 LINE/L1 (646) 5509 5359 1244
ANNOTATION EVIDENCE:
1335 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2210:13179:59376/1 1 151 0 C L1PA2_3end LINE/L1 106 256 646
1335 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2210:13179:59376/1 1 151 (0) C L1PA2_3end#LINE/L1 (646) 256 106 m_b1s551i227
ST-E00130:540 1 ATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTA 50
i
C L1PA2_3end#LI 256 ATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTA 207
ST-E00130:540 51 ACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGAT 100
C L1PA2_3end#LI 206 ACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGAT 157
ST-E00130:540 101 GGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGT 150
C L1PA2_3end#LI 156 GGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGT 107
ST-E00130:540 151 C 151
C L1PA2_3end#LI 106 C 106
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1269 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2210:13179:59376/2 1 151 (0) + L1P LINE/L1 5254 5404 (751) 1245
ANNOTATION EVIDENCE:
1269 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2210:13179:59376/2 1 151 0 + L1PA2_3end LINE/L1 1 151 751
1269 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2210:13179:59376/2 1 151 (0) L1PA2_3end#LINE/L1 1 151 (751) m_b1s551i163
ST-E00130:540 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
L1PA2_3end#LI 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
ST-E00130:540 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
L1PA2_3end#LI 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
ST-E00130:540 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 150
L1PA2_3end#LI 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 150
ST-E00130:540 151 C 151
L1PA2_3end#LI 151 C 151
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 316 26.7 3.2 0.0 ST-E00130:540:HVYVWCCXX:1:2215:2717:63050/2 62 151 (0) + MIRb SINE/MIR 67 159 (109) 1246
ANNOTATION EVIDENCE:
316 26.67 3.22 0.00 ST-E00130:540:HVYVWCCXX:1:2215:2717:63050/2 62 151 0 + MIRb SINE/MIR 67 159 109
316 26.67 3.22 0.00 ST-E00130:540:HVYVWCCXX:1:2215:2717:63050/2 62 151 (0) MIRb#SINE/MIR 67 159 (109) m_b6s601i73
ST-E00130:540 62 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 110
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
ST-E00130:540 111 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAA 151
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 159
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.98
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.50 (3 / 2)
+ 1283 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2217:14296:62927/1 1 151 (0) + L1P1 LINE/L1 5237 5387 (759) 1247
ANNOTATION EVIDENCE:
1283 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2217:14296:62927/1 1 151 0 + L1P1_orf2 LINE/L1 3128 3278 16
1283 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2217:14296:62927/1 1 151 (0) L1P1_orf2#LINE/L1 3128 3278 (16) m_b1s551i155
ST-E00130:540 1 ACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAA 50
L1P1_orf2#LIN 3128 ACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAA 3177
ST-E00130:540 51 ATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACAT 100
L1P1_orf2#LIN 3178 ATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACAT 3227
ST-E00130:540 101 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGA 150
L1P1_orf2#LIN 3228 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGA 3277
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3278 A 3278
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1358 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2217:14296:62927/2 1 151 (0) C L1P1 LINE/L1 (436) 5719 5569 1248
ANNOTATION EVIDENCE:
1358 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2217:14296:62927/2 1 151 0 C L1PA2_3end LINE/L1 316 466 436
1358 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2217:14296:62927/2 1 151 (0) C L1PA2_3end#LINE/L1 (436) 466 316 m_b1s551i294
ST-E00130:540 1 TTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCGG 50
i i
C L1PA2_3end#LI 466 TTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAG 417
ST-E00130:540 51 CATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTC 100
C L1PA2_3end#LI 416 CATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTC 367
ST-E00130:540 101 AAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCACCACACTGACTTCC 150
i i
C L1PA2_3end#LI 366 AAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCC 317
ST-E00130:540 151 A 151
C L1PA2_3end#LI 316 A 316
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2218:24525:18696/2 86 130 (21) C MIR SINE/MIR (0) 262 218 1249
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2218:24525:18696/2 86 130 21 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2218:24525:18696/2 86 130 (21) C MIR#SINE/MIR (0) 262 218 m_b6s601i5
ST-E00130:540 86 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 130
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 1352 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2219:10470:41673/1 1 151 (0) + L1P2 LINE/L1 5503 5653 (502) 1250
ANNOTATION EVIDENCE:
1352 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2219:10470:41673/1 1 151 0 + L1PA4_3end LINE/L1 250 400 502
1352 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2219:10470:41673/1 1 151 (0) L1PA4_3end#LINE/L1 250 400 (502) m_b1s551i277
ST-E00130:540 1 AGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTGGGACTGTAA 50
iv
L1PA4_3end#LI 250 AGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAA 299
ST-E00130:540 51 ACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGGGATCTAG 100
i
L1PA4_3end#LI 300 ACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAG 349
ST-E00130:540 101 AACTGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCA 150
i
L1PA4_3end#LI 350 AACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCA 399
ST-E00130:540 151 A 151
L1PA4_3end#LI 400 A 400
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1329 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2219:10470:41673/2 1 151 (0) C L1P1 LINE/L1 (363) 5792 5642 1251
ANNOTATION EVIDENCE:
1329 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2219:10470:41673/2 1 151 0 C L1PA2_3end LINE/L1 389 539 363
1329 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2219:10470:41673/2 1 151 (0) C L1PA2_3end#LINE/L1 (363) 539 389 m_b1s551i317
ST-E00130:540 1 GTGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTT 50
v
C L1PA2_3end#LI 539 GTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTT 490
ST-E00130:540 51 GGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATAC 100
i
C L1PA2_3end#LI 489 GGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATAC 440
ST-E00130:540 101 GTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATA 150
i
C L1PA2_3end#LI 439 GTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATA 390
ST-E00130:540 151 C 151
C L1PA2_3end#LI 389 C 389
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 18 4.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2220:30645:54823/2 1 22 (129) + (CA)n Simple_repeat 1 22 (0) 1252
ANNOTATION EVIDENCE:
18 4.77 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:30645:54823/2 1 22 129 + (CA)n Simple_repeat 1 22 0
18 4.77 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:30645:54823/2 1 22 (129) (CA)n#Simple_repeat 1 22 (0) m_b4s252i20
ST-E00130:540 1 CACACATACACACACACACACA 22
i
(CA)n#Simple_ 1 CACACACACACACACACACACA 22
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/1 56 148 (3) C MIRb SINE/MIR (49) 219 122 1253
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/1 56 148 3 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/1 56 148 (3) C MIRb#SINE/MIR (49) 219 122 m_b4s601i7
ST-E00130:540 56 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 101
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
ST-E00130:540 102 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 148
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 313 8.5 4.1 0.0 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/2 1 47 (104) + 7SLRNA srpRNA 261 309 (11) 1254
ANNOTATION EVIDENCE:
313 8.51 4.09 0.00 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/2 1 47 104 + 7SLRNA SINE/Alu 261 309 11
313 8.51 4.09 0.00 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/2 1 47 (104) 7SLRNA#SINE/Alu 261 309 (11) m_b4s502i2
ST-E00130:540 1 TGCACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTC--AAAAAAAAA 47
i v ii --
7SLRNA#SINE/A 261 TGCACTCCAGCCTGGGCAACATAGCGAGACCCCGTCTCTTAAAAAAAAA 309
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.15
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/2 75 106 (45) + (CA)n Simple_repeat 1 32 (0) 1255
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/2 75 106 45 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:5325:43835/2 75 106 (45) (CA)n#Simple_repeat 1 32 (0) m_b4s252i19
ST-E00130:540 75 CATACATGCACACACATACACACACACACACA 106
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1209 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2220:8552:62751/1 2 151 (0) C L1P3 LINE/L1 (3003) 3143 2994 1256
ANNOTATION EVIDENCE:
1209 2.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:8552:62751/1 2 151 0 C L1P3_orf2 LINE/L1 885 1034 2260
1209 2.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:8552:62751/1 2 151 (0) C L1P3_orf2#LINE/L1 (2260) 1034 885 m_b6s551i267
ST-E00130:540 2 GCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTG 51
C L1P3_orf2#LIN 1034 GCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTG 985
ST-E00130:540 52 CTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAG 101
i
C L1P3_orf2#LIN 984 CTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAG 935
ST-E00130:540 102 ATCTTTCCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTA 151
i v ?
C L1P3_orf2#LIN 934 ATCTTTCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTA 885
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.81
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1189 6.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2220:8552:62751/2 1 151 (0) + L1P3 LINE/L1 2818 2968 (3178) 1257
ANNOTATION EVIDENCE:
1189 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:8552:62751/2 1 151 0 + L1P3_orf2 LINE/L1 709 859 2435
1189 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:8552:62751/2 1 151 (0) L1P3_orf2#LINE/L1 709 859 (2435) m_b7s551i54
ST-E00130:540 1 CTGAGGATTAAGAAACTCACTCAAAACCACACAACTACATGGAAACTGAA 50
v i
L1P3_orf2#LIN 709 CTCAGGATTAAGAAACTCACTCAAAACCGCACAACTACATGGAAACTGAA 758
ST-E00130:540 51 CAACCTGCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAA 100
i i v
L1P3_orf2#LIN 759 CAACCTGCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAA 808
ST-E00130:540 101 TAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAAT 150
i? i i
L1P3_orf2#LIN 809 TAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAAT 858
ST-E00130:540 151 C 151
L1P3_orf2#LIN 859 C 859
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1002 11.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2220:9374:26308/2 5 137 (14) C AluSx SINE/Alu (179) 133 1 1258
ANNOTATION EVIDENCE:
1002 11.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:9374:26308/2 5 137 14 C AluSx SINE/Alu 1 133 179
1002 11.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2220:9374:26308/2 5 137 (14) C AluSx#SINE/Alu (179) 133 1 m_b5s357i46
ST-E00130:540 5 TTTTTGTATTTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGT 54
i v i
C AluSx#SINE/Al 133 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGT 84
ST-E00130:540 55 CCCAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGT 104
i i i i i i i
C AluSx#SINE/Al 83 CTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC 34
ST-E00130:540 105 TGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 137
i vi i i
C AluSx#SINE/Al 33 TGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.41
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
+ 1137 8.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2221:22678:2557/1 1 151 (0) + L1PA2 LINE/L1 5943 6093 (62) 1259
ANNOTATION EVIDENCE:
1137 7.95 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2221:22678:2557/1 1 151 0 + L1PA2_3end LINE/L1 690 840 62
1137 7.95 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2221:22678:2557/1 1 151 (0) L1PA2_3end#LINE/L1 690 840 (62) m_b1s551i395
ST-E00130:540 1 GAGGTCACATGGACACAGGAAGGGGAATATCACACTCTGTCGACTGTTGT 50
i vv v
L1PA2_3end#LI 690 GAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGT 739
ST-E00130:540 51 GGGGTGGGGAGAGGGGGGAGGGATAGCATCAGGGAATAAACCTAATGCTA 100
i ii ii v
L1PA2_3end#LI 740 GGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTA 789
ST-E00130:540 101 GATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCTCATGTATACATAT 150
i v
L1PA2_3end#LI 790 GATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATAT 839
ST-E00130:540 151 G 151
L1PA2_3end#LI 840 G 840
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.76
Transitions / transversions = 1.40 (7/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 32 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/1 48 77 (74) + (T)n Simple_repeat 1 30 (0) 1260
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/1 48 77 74 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/1 48 77 (74) (T)n#Simple_repeat 1 30 (0) c_b6s251i7
ST-E00130:540 48 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 77
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 690 7.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/2 1 92 (59) + L1P3 LINE/L1 3807 3898 (2248) 1261
ANNOTATION EVIDENCE:
690 7.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/2 1 92 59 + L1P3_orf2 LINE/L1 1698 1789 1505
690 7.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/2 1 92 (59) L1P3_orf2#LINE/L1 1698 1789 (1505) m_b6s551i17
ST-E00130:540 1 CATCCCTGGGACGCAAGGCTGATTCAGCATACACAAATCAATAAACATAA 50
i i i i i
L1P3_orf2#LIN 1698 CATCCCTGGGATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAA 1747
ST-E00130:540 51 TCCATCACATAAACAGAACGAATGACAAAAACTACATGATTA 92
v i
L1P3_orf2#LIN 1748 TCCATCACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.94
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0)
+ 419 10.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/2 95 151 (0) + AluSx SINE/Alu 14 70 (242) 1262
ANNOTATION EVIDENCE:
419 10.53 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/2 95 151 0 + AluSx SINE/Alu 14 70 242
419 10.53 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2223:30533:47597/2 95 151 (0) AluSx#SINE/Alu 14 70 (242) m_b6s357i24
ST-E00130:540 95 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAATGTGGGTGGATCA 144
i v i v i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 145 CCTGAGG 151
AluSx#SINE/Al 64 CCTGAGG 70
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 1261 2.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:1:2224:12631:63982/1 1 151 (0) + L1PA3 LINE/L1 5765 5914 (241) 1263
ANNOTATION EVIDENCE:
1261 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:2224:12631:63982/1 1 151 0 + L1PA3_3end LINE/L1 512 661 241
1261 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:1:2224:12631:63982/1 1 151 (0) L1PA3_3end#LINE/L1 512 661 (241) m_b1s551i355
ST-E00130:540 1 GGATTAAGAAACTGTGGCACATATACACCATGGAATACTATGCAGCCATA 50
v
L1PA3_3end#LI 512 GGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATA 561
ST-E00130:540 51 AAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAAA 100
-
L1PA3_3end#LI 562 AAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAA 610
ST-E00130:540 101 TCATCATTCTCAGTAAACTGTCGCAAGAAGAAAAAACCAAACACCGCATG 150
i v i
L1PA3_3end#LI 611 TCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATA 660
ST-E00130:540 151 T 151
L1PA3_3end#LI 661 T 661
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1236 3.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:1:2224:12631:63982/2 3 146 (5) C L1PA2 LINE/L1 (5) 6150 6007 1264
ANNOTATION EVIDENCE:
1236 3.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2224:12631:63982/2 3 146 5 C L1PA2_3end LINE/L1 754 897 5
1236 3.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:1:2224:12631:63982/2 3 146 (5) C L1PA2_3end#LINE/L1 (5) 897 754 m_b1s551i418
ST-E00130:540 3 TTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGG 52
i
C L1PA2_3end#LI 897 TTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGG 848
ST-E00130:540 53 TTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACTAAC 102
i
C L1PA2_3end#LI 847 TTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAAC 798
ST-E00130:540 103 TCGTCATCTAGCATTAGGTATATCTCCCAATGCTATACTACCCC 146
v iv
C L1PA2_3end#LI 797 TCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCC 754
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.90
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 143), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1102:26047:47773/1 85 129 (22) C MIR SINE/MIR (0) 262 218 1265
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1102:26047:47773/1 85 129 22 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1102:26047:47773/1 85 129 (22) C MIR#SINE/MIR (0) 262 218 m_b6s601i6
ST-E00130:540 85 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 129
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 1102 13.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1102:26758:72842/1 1 151 (0) C AluSx SINE/Alu (144) 168 18 1266
ANNOTATION EVIDENCE:
1102 13.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1102:26758:72842/1 1 151 0 C AluSx SINE/Alu 18 168 144
1102 13.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1102:26758:72842/1 1 151 (0) C AluSx#SINE/Alu (144) 168 18 m_b2s356i35
ST-E00130:540 1 TGGGATTACAGGTGCCCACCACCACACCCAGCTAATTTTTGTATTTTAAA 50
i v i i i v i
C AluSx#SINE/Al 168 TGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAG 119
ST-E00130:540 51 TAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGACC 100
ii i i
C AluSx#SINE/Al 118 TAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACC 69
ST-E00130:540 101 TCAGGTGATCCACCTGGCTCTGCCTCCCAGATTGCTGAGATTACAGATGT 150
i i v v i v i ii
C AluSx#SINE/Al 68 TCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 19
ST-E00130:540 151 G 151
C AluSx#SINE/Al 18 G 18
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.05
Transitions / transversions = 3.00 (15/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 429 16.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1102:26758:72842/2 85 151 (0) + AluSx SINE/Alu 1 67 (245) 1267
ANNOTATION EVIDENCE:
429 16.42 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1102:26758:72842/2 85 151 0 + AluSx SINE/Alu 1 67 245
429 16.42 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1102:26758:72842/2 85 151 (0) AluSx#SINE/Alu 1 67 (245) m_b2s357i57
ST-E00130:540 85 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 134
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 135 GCCAGGTGGATCACCTG 151
v i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTG 67
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.87
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 23 3.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1103:16254:26624/1 1 28 (123) + (A)n Simple_repeat 1 28 (0) 1268
ANNOTATION EVIDENCE:
23 3.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1103:16254:26624/1 1 28 123 + (A)n Simple_repeat 1 28 0
23 3.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1103:16254:26624/1 1 28 (123) (A)n#Simple_repeat 1 28 (0) m_b6s252i7
ST-E00130:540 1 AAAAAAAAAAAAAAAAAAAAAAAAAGAA 28
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 312 27.8 14.3 0.0 ST-E00130:540:HVYVWCCXX:2:1103:16254:26624/2 1 144 (7) C MIR SINE/MIR (3) 259 92 1269
ANNOTATION EVIDENCE:
312 27.78 14.29 0.00 ST-E00130:540:HVYVWCCXX:2:1103:16254:26624/2 1 144 7 C MIR SINE/MIR 92 259 3
312 27.78 14.29 0.00 ST-E00130:540:HVYVWCCXX:2:1103:16254:26624/2 1 144 (7) C MIR#SINE/MIR (3) 259 92 m_b6s601i35
ST-E00130:540 1 AATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA---------- 40
i i iiiv vi v ----------
C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210
ST-E00130:540 41 ---TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCACTTA 78
--- ii v ------i i i--- i vii i v vv
C MIR#SINE/MIR 209 CGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA 160
ST-E00130:540 79 GATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGA 126
i v vi ii v i i -- v i vi v
C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110
ST-E00130:540 127 GGTAAAGTAACTTGCTTA 144
v ii
C MIR#SINE/MIR 109 GGTTAAGTAACTTGCCCA 92
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.61
Transitions / transversions = 1.67 (25/15)
Gap_init rate = 0.03 (5 / 143), avg. gap size = 4.80 (24 / 5)
+ 599 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1104:16691:4878/1 77 151 (0) C L1PA2 LINE/L1 (2) 6153 6079 1270
ANNOTATION EVIDENCE:
599 2.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1104:16691:4878/1 77 151 0 C L1PA2_3end LINE/L1 826 900 2
599 2.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1104:16691:4878/1 77 151 (0) C L1PA2_3end#LINE/L1 (2) 900 826 m_b1s551i450
ST-E00130:540 77 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 126
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 127 AGGTTAGTTACATATGTATACATGT 151
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGT 826
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 1231 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1104:16691:4878/2 1 151 (0) + L1PA2 LINE/L1 5872 6022 (133) 1271
ANNOTATION EVIDENCE:
1231 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1104:16691:4878/2 1 151 0 + L1PA2_3end LINE/L1 619 769 133
1231 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1104:16691:4878/2 1 151 (0) L1PA2_3end#LINE/L1 619 769 (133) m_b1s551i386
ST-E00130:540 1 CTCAGTAAACTGTCGCAAGAAGAAAAAACCAAACACCGCATGTTCTCACT 50
i v i
L1PA2_3end#LI 619 CTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACT 668
ST-E00130:540 51 CATAGGTGGGAATTGAACAATGAGATCACATGGACACATGAAGGGGAATA 100
v
L1PA2_3end#LI 669 CATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATA 718
ST-E00130:540 101 TCACACTCTGTGGACTGTTGTGGGGTGGGGGGGGGGGGGAGGGATAGCAT 150
v v i
L1PA2_3end#LI 719 TCACACTCTGGGGACTGTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCAT 768
ST-E00130:540 151 T 151
L1PA2_3end#LI 769 T 769
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.79
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 471 17.9 6.8 14.6 ST-E00130:540:HVYVWCCXX:2:1104:24454:12033/2 8 151 (0) + L1MC4 LINE/L1 7811 7942 (100) 1272
ANNOTATION EVIDENCE:
471 17.89 6.82 14.58 ST-E00130:540:HVYVWCCXX:2:1104:24454:12033/2 8 151 0 + L1MC4_3end LINE/L1 2558 2689 100
471 17.89 6.82 14.58 ST-E00130:540:HVYVWCCXX:2:1104:24454:12033/2 8 151 (0) L1MC4_3end#LINE/L1 2558 2689 (100) m_b3s551i12
ST-E00130:540 8 TATCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGC 48
i i i --------- i
L1MC4_3end#LI 2558 TGTCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGC 2607
ST-E00130:540 49 ATCACGTGTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGT 98
? i v i i vv - i vi i i
L1MC4_3end#LI 2608 ATNATGTCTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTAT 2656
ST-E00130:540 99 ATCTGCGTATGAGTGTGTGTGTGGAGAGAGGGAATGATTAAGCAAATATG 148
-- ------------------ ? ? i v i
L1MC4_3end#LI 2657 AT--GC------------------ANANAGAGAATGATAAAGCAAATGTG 2686
ST-E00130:540 149 GTA 151
i
L1MC4_3end#LI 2687 GCA 2689
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.25
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.15 (22 / 143), avg. gap size = 1.36 (30 / 22)
+ 463 18.4 5.8 0.0 ST-E00130:540:HVYVWCCXX:2:1105:13575:11787/1 9 106 (45) + L1MC4 LINE/L1 7546 7649 (393) 1273
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:2:1105:13575:11787/1 9 106 45 + L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:2:1105:13575:11787/1 9 106 (45) L1MC4_3end#LINE/L1 2293 2396 (393) m_b3s551i82
ST-E00130:540 9 GACCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA----- 53
i v v i v ? v i i i -----
L1MC4_3end#LI 2293 GGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTG 2342
ST-E00130:540 54 -AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 102
-i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
ST-E00130:540 103 AATG 106
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 3.00 (6 / 2)
+ 278 10.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1105:13575:11787/1 111 149 (2) + L1MC4 LINE/L1 7762 7800 (242) 1273
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1105:13575:11787/1 111 149 2 + L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1105:13575:11787/1 111 149 (2) L1MC4_3end#LINE/L1 2509 2547 (242) m_b3s551i83
ST-E00130:540 111 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTA 149
i i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTA 2547
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 306 28.5 14.2 0.0 ST-E00130:540:HVYVWCCXX:2:1105:30533:29138/1 1 151 (0) + MIR SINE/MIR 80 255 (7) 1274
ANNOTATION EVIDENCE:
306 28.48 14.21 0.00 ST-E00130:540:HVYVWCCXX:2:1105:30533:29138/1 1 151 0 + MIR SINE/MIR 80 255 7
306 28.48 14.21 0.00 ST-E00130:540:HVYVWCCXX:2:1105:30533:29138/1 1 151 (0) MIR#SINE/MIR 80 255 (7) m_b6s601i37
ST-E00130:540 1 GCTCTGTGGCAT-AAGCAAGTTACTTTACCTCACTAAGTCACAGTTT--T 47
v i v -ii v v iv i v --
MIR#SINE/MIR 80 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCT 129
ST-E00130:540 48 CATTTATAAATTGAAGGAAATAATAGAATCTAAGTGACAGAAGTAT---A 94
i i v ii iv v i vv v i iiv i ---i
MIR#SINE/MIR 130 CATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTG 179
ST-E00130:540 95 AGAATTAAG------AATAAACATAAA-------------TGCCAGGCAC 125
i i------ v ii ------------- v
MIR#SINE/MIR 180 AGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCAC 229
ST-E00130:540 126 ACCGTATATACTCAACAAGTGTTAGC 151
iv viii i i
MIR#SINE/MIR 230 ATAGTAAGCGCTCAATAAATGTTAGC 255
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.70
Transitions / transversions = 1.53 (26/17)
Gap_init rate = 0.03 (5 / 150), avg. gap size = 5.00 (25 / 5)
+ 1329 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1105:4959:44116/1 1 151 (0) C L1P1 LINE/L1 (363) 5792 5642 1275
ANNOTATION EVIDENCE:
1329 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1105:4959:44116/1 1 151 0 C L1PA2_3end LINE/L1 389 539 363
1329 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1105:4959:44116/1 1 151 (0) C L1PA2_3end#LINE/L1 (363) 539 389 m_b1s551i318
ST-E00130:540 1 GTGTATATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTT 50
v
C L1PA2_3end#LI 539 GTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTT 490
ST-E00130:540 51 GGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATAC 100
i
C L1PA2_3end#LI 489 GGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATAC 440
ST-E00130:540 101 GTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATA 150
i
C L1PA2_3end#LI 439 GTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATA 390
ST-E00130:540 151 C 151
C L1PA2_3end#LI 389 C 389
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1312 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1105:4959:44116/2 1 151 (0) + L1P1 LINE/L1 5308 5458 (697) 1276
ANNOTATION EVIDENCE:
1312 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1105:4959:44116/2 1 151 0 + L1PA2_3end LINE/L1 55 205 697
1312 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1105:4959:44116/2 1 151 (0) L1PA2_3end#LINE/L1 55 205 (697) m_b1s551i195
ST-E00130:540 1 AACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGA 50
L1PA2_3end#LI 55 AACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGA 104
ST-E00130:540 51 AGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGG 100
L1PA2_3end#LI 105 AGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGG 154
ST-E00130:540 101 CCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCA 150
L1PA2_3end#LI 155 CCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCA 204
ST-E00130:540 151 G 151
L1PA2_3end#LI 205 G 205
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 313 14.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1106:6492:32215/2 9 62 (89) + L1MC4 LINE/L1 7596 7649 (393) 1277
ANNOTATION EVIDENCE:
313 14.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1106:6492:32215/2 9 62 89 + L1MC4_3end LINE/L1 2343 2396 393
313 14.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1106:6492:32215/2 9 62 (89) L1MC4_3end#LINE/L1 2343 2396 (393) m_b3s551i54
ST-E00130:540 9 AAGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 58
i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
ST-E00130:540 59 AATG 62
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.46
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 466 19.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1106:6492:32215/2 67 148 (3) + L1MC4 LINE/L1 7762 7843 (199) 1277
ANNOTATION EVIDENCE:
466 19.51 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1106:6492:32215/2 67 148 3 + L1MC4_3end LINE/L1 2509 2590 199
466 19.51 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1106:6492:32215/2 67 148 (3) L1MC4_3end#LINE/L1 2509 2590 (199) m_b3s551i55
ST-E00130:540 67 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 116
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
ST-E00130:540 117 ATCCTTGTTTTTAGGAAGTATACACTGGAGTA 148
i i i i i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACTGAAGTA 2590
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.02
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0)
+ 630 13.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1107:29366:27925/1 1 89 (62) C AluSx SINE/Alu (223) 89 1 1278
ANNOTATION EVIDENCE:
630 13.48 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1107:29366:27925/1 1 89 62 C AluSx SINE/Alu 1 89 223
630 13.48 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1107:29366:27925/1 1 89 (62) C AluSx#SINE/Alu (223) 89 1 m_b5s357i61
ST-E00130:540 1 GCTGGTCCCAAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCA 50
i i i i i i
C AluSx#SINE/Al 89 GCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCA 40
ST-E00130:540 51 AAGTGTTGGGATTACAGGTGTGAGCCAGTGCACCCAGCC 89
i i vi i i
C AluSx#SINE/Al 39 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.65
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 ST-E00130:540:HVYVWCCXX:2:1108:5416:33973/1 41 133 (18) C MIRb SINE/MIR (49) 219 122 1279
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:2:1108:5416:33973/1 41 133 18 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:2:1108:5416:33973/1 41 133 (18) C MIRb#SINE/MIR (49) 219 122 m_b4s601i11
ST-E00130:540 41 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 86
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
ST-E00130:540 87 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 133
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1175 8.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1108:5416:33973/2 6 151 (0) + AluSx SINE/Alu 68 213 (99) 1280
ANNOTATION EVIDENCE:
1175 8.90 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1108:5416:33973/2 6 151 0 + AluSx SINE/Alu 68 213 99
1175 8.90 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1108:5416:33973/2 6 151 (0) AluSx#SINE/Alu 68 213 (99) m_b4s356i30
ST-E00130:540 6 AGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCT 55
i v i i i
AluSx#SINE/Al 68 AGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCT 117
ST-E00130:540 56 ACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCC 105
i i v iv i
AluSx#SINE/Al 118 ACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCC 167
ST-E00130:540 106 AGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGG 151
i i
AluSx#SINE/Al 168 AGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGG 213
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.41
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0)
+ 1088 12.2 0.0 1.3 ST-E00130:540:HVYVWCCXX:2:1110:26342:63261/1 2 151 (0) C AluSx SINE/Alu (160) 152 5 1281
ANNOTATION EVIDENCE:
1088 12.16 0.00 1.33 ST-E00130:540:HVYVWCCXX:2:1110:26342:63261/1 2 151 0 C AluSx SINE/Alu 5 152 160
1088 12.16 0.00 1.33 ST-E00130:540:HVYVWCCXX:2:1110:26342:63261/1 2 151 (0) C AluSx#SINE/Alu (160) 152 5 m_b5s356i28
ST-E00130:540 2 CACCACAATGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGATGGGGTTT 51
i v i i -- i
C AluSx#SINE/Al 152 CGCCACCACGCCCGGCTAA--TTTTTGTATTTTTAGTAGAGACGGGGTTT 105
ST-E00130:540 52 CAACACGTTGGCCAGGCTGGTCCCAAACTCCTGACCTCAAGTGATCTGCC 101
v i i i i i
C AluSx#SINE/Al 104 CACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCC 55
ST-E00130:540 102 CACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTGTGAGCCAGTGCACCC 151
i i i i vi i
C AluSx#SINE/Al 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 5
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.71
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 1030 9.6 0.7 0.0 ST-E00130:540:HVYVWCCXX:2:1110:28950:2592/1 2 136 (15) C AluY SINE/Alu (175) 136 1 1282
ANNOTATION EVIDENCE:
1030 9.63 0.73 0.00 ST-E00130:540:HVYVWCCXX:2:1110:28950:2592/1 2 136 15 C AluY SINE/Alu 1 136 175
1030 9.63 0.73 0.00 ST-E00130:540:HVYVWCCXX:2:1110:28950:2592/1 2 136 (15) C AluY#SINE/Alu (175) 136 1 m_b2s357i78
ST-E00130:540 2 CTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGG 50
- i i ii
C AluY#SINE/Alu 136 CTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGG 87
ST-E00130:540 51 ATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCCTTGGCCTCCCAAAG 100
i i v i
C AluY#SINE/Alu 86 ATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 37
ST-E00130:540 101 TGCTGAGATTACAAGCGTGAGCCACCATGCCTGGCC 136
i i ii i
C AluY#SINE/Alu 36 TGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.46
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1)
+ 262 29.0 5.1 0.0 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/1 24 116 (35) C MIRb SINE/MIR (49) 219 122 1283
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/1 24 116 35 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/1 24 116 (35) C MIRb#SINE/MIR (49) 219 122 m_b4s601i17
ST-E00130:540 24 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 69
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
ST-E00130:540 70 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 116
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 589 4.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/2 1 71 (80) + AluSx SINE/Alu 221 291 (21) 1284
ANNOTATION EVIDENCE:
589 4.23 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/2 1 71 80 + AluSx SINE/Alu 221 291 21
589 4.23 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/2 1 71 (80) AluSx#SINE/Alu 221 291 (21) m_b4s357i13
ST-E00130:540 1 TGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCAACAGAGCG 50
i i
AluSx#SINE/Al 221 TGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCG 270
ST-E00130:540 51 AGATTCCGTCTCAAAAAAAAA 71
i
AluSx#SINE/Al 271 AGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.05
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/2 99 130 (21) + (CA)n Simple_repeat 1 32 (0) 1285
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/2 99 130 21 + (CA)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1110:30107:47527/2 99 130 (21) (CA)n#Simple_repeat 1 32 (0) m_b4s252i18
ST-E00130:540 99 CATACATGCACACACATACACACACACACACA 130
i ii i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 493 14.3 0.0 2.3 ST-E00130:540:HVYVWCCXX:2:1111:5203:57055/2 55 140 (11) C AluY SINE/Alu (8) 303 220 1286
ANNOTATION EVIDENCE:
493 14.28 0.00 2.33 ST-E00130:540:HVYVWCCXX:2:1111:5203:57055/2 55 140 11 C AluY SINE/Alu 220 303 8
493 14.28 0.00 2.33 ST-E00130:540:HVYVWCCXX:2:1111:5203:57055/2 55 140 (11) C AluY#SINE/Alu (8) 303 220 m_b2s357i6
ST-E00130:540 55 TTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTTCGGCAAACCCC 104
i i ii v i-- v
C AluY#SINE/Alu 303 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCA 256
ST-E00130:540 105 GGCTGGGGTGCAGTGGCAGTATCTCGACTCACTGCA 140
i ivv i
C AluY#SINE/Alu 255 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA 220
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.77
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2)
+ 261 26.2 7.4 0.8 ST-E00130:540:HVYVWCCXX:2:1112:5345:9941/1 6 150 (1) + L1ME4c LINE/L1 5672 5827 (297) 1287
ANNOTATION EVIDENCE:
249 26.62 7.95 0.71 ST-E00130:540:HVYVWCCXX:2:1112:5345:9941/1 6 145 6 + L1ME4c_3end LINE/L1 419 569 261
249 26.62 7.95 0.71 ST-E00130:540:HVYVWCCXX:2:1112:5345:9941/1 6 145 (6) L1ME4c_3end#LINE/L1 419 569 (261) m_b2s551i23
ST-E00130:540 6 AGAAAAAAAAACCCTTAGACA----AATGATCATTGCAATAATGTTTATT 51
ii v iv vi ----i v iiiv i v
L1ME4c_3end#L 419 AGAAGGAAAAAGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTATA 468
ST-E00130:540 52 GTAG--GAAAATAGAAAAGAATCTAAATTTCTGACAATAAAA-AATG-TC 97
i --i v i v i v ii iii- - i
L1ME4c_3end#L 469 ATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTT 518
ST-E00130:540 98 AAGTAAATTATGGTA--TTTAT--GACAGAAAAATGGTGAAGCCATTAAA 143
-- i? i-- ii v - vi v
L1ME4c_3end#L 519 AAGTAAATTATGGTACATCNACTCGATGGAATA-TTATGCAGCCATTAAA 567
ST-E00130:540 144 AA 145
L1ME4c_3end#L 568 AA 569
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.04
Transitions / transversions = 2.00 (24/12)
Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.86 (13 / 7)
261 26.19 7.35 0.79 ST-E00130:540:HVYVWCCXX:2:1112:5345:9941/1 24 150 1 + L1ME4a_3end LINE/L1 439 574 297
261 26.19 7.35 0.79 ST-E00130:540:HVYVWCCXX:2:1112:5345:9941/1 24 150 (1) L1ME4a_3end#LINE/L1 439 574 (297) m_b2s551i24
ST-E00130:540 24 ACAA--ATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGA 69
-- v i ii v i vi --i v i v
L1ME4a_3end#L 439 ACAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACA 488
ST-E00130:540 70 ATCTAAATTTCTGACAATAAAAAAT--GTCAAGTAAATTATGGTA--TTT 115
i v ii iiii ?-- i i -- ii
L1ME4a_3end#L 489 ACCTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCC 538
ST-E00130:540 116 ATGACA--GAAAAATGGTGAAGCCATTAAAAAGTATG 150
- i-- i v vi v v?
L1ME4a_3end#L 539 AT-ACGATGGAATATTATGCAGCCATTAAAAATNATG 574
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.14
Transitions / transversions = 2.10 (21/10)
Gap_init rate = 0.05 (6 / 126), avg. gap size = 1.83 (11 / 6)
+ 797 5.7 8.5 7.3 ST-E00130:540:HVYVWCCXX:2:1114:14387:50779/1 1 151 (0) C L1P3 LINE/L1 (2867) 3279 3127 1288
ANNOTATION EVIDENCE:
797 5.72 8.50 7.28 ST-E00130:540:HVYVWCCXX:2:1114:14387:50779/1 1 151 0 C L1P3_orf2 LINE/L1 1018 1170 2124
797 5.72 8.50 7.28 ST-E00130:540:HVYVWCCXX:2:1114:14387:50779/1 1 151 (0) C L1P3_orf2#LINE/L1 (2124) 1170 1018 m_b6s551i218
ST-E00130:540 1 TATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----T 38
-------- v ----
C L1P3_orf2#LIN 1170 TATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTAT 1121
ST-E00130:540 39 CTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTT 88
i i v -
C L1P3_orf2#LIN 1120 CTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTT 1072
ST-E00130:540 89 TTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCT 137
i i---------- -i v
C L1P3_orf2#LIN 1071 TTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCT 1032
ST-E00130:540 138 CTGATCTTAGTTAT 151
C L1P3_orf2#LIN 1031 CTGATCTTAGTTAT 1018
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1257 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1114:14387:50779/2 1 151 (0) + L1P3 LINE/L1 2852 3002 (3144) 1289
ANNOTATION EVIDENCE:
1257 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1114:14387:50779/2 1 151 0 + L1P3_orf2 LINE/L1 743 893 2401
1257 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1114:14387:50779/2 1 151 (0) L1P3_orf2#LINE/L1 743 893 (2401) m_b7s551i44
ST-E00130:540 1 CTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTAGGTAAATAAT 50
i i
L1P3_orf2#LIN 743 CTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTAAATAAC 792
ST-E00130:540 51 GAAATGAAGGCAGAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGA 100
v i? i
L1P3_orf2#LIN 793 GAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGA 842
ST-E00130:540 101 CACAATGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGA 150
i
L1P3_orf2#LIN 843 CACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGA 892
ST-E00130:540 151 A 151
L1P3_orf2#LIN 893 A 893
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 615 15.4 0.0 6.0 ST-E00130:540:HVYVWCCXX:2:1115:28676:36610/1 35 151 (0) C AluSx SINE/Alu (8) 304 195 1290
ANNOTATION EVIDENCE:
615 15.45 0.00 5.98 ST-E00130:540:HVYVWCCXX:2:1115:28676:36610/1 35 151 0 C AluSx SINE/Alu 195 304 8
615 15.45 0.00 5.98 ST-E00130:540:HVYVWCCXX:2:1115:28676:36610/1 35 151 (0) C AluSx#SINE/Alu (8) 304 195 m_b5s357i13
ST-E00130:540 35 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 84
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 85 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 134
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
ST-E00130:540 135 TAGTAGGTTCAAGCAAT 151
vvii i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGAT 195
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.26
Transitions / transversions = 1.12 (9/8)
Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7)
+ 244 11.8 5.6 3.8 ST-E00130:540:HVYVWCCXX:2:1116:20506:16270/1 98 150 (1) C 7SLRNA srpRNA (0) 320 267 1291
ANNOTATION EVIDENCE:
244 11.76 5.56 3.77 ST-E00130:540:HVYVWCCXX:2:1116:20506:16270/1 98 150 1 C 7SLRNA SINE/Alu 267 320 0
244 11.76 5.56 3.77 ST-E00130:540:HVYVWCCXX:2:1116:20506:16270/1 98 150 (1) C 7SLRNA#SINE/Alu (0) 320 267 m_b1s502i0
ST-E00130:540 98 TTTTTTTTTTTTTTTTTTTT---AGACAGAGTCTCGCTTCGTCAAACCCA 144
--- i i vi ii--
C 7SLRNA#SINE/A 320 TTTTTTTTTTTTTTTTTTTTAAGAGACGGGGTCTCGCTATGTTG--CCCA 273
ST-E00130:540 145 GGCTGG 150
C 7SLRNA#SINE/A 272 GGCTGG 267
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.95
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.67 (5 / 3)
+ 254 25.4 6.2 3.9 ST-E00130:540:HVYVWCCXX:2:1122:21034:66970/2 19 145 (6) C L1ME4c LINE/L1 (297) 5786 5657 1292
ANNOTATION EVIDENCE:
254 25.41 6.15 3.94 ST-E00130:540:HVYVWCCXX:2:1122:21034:66970/2 19 145 6 C L1ME4c_3end LINE/L1 404 533 297
254 25.41 6.15 3.94 ST-E00130:540:HVYVWCCXX:2:1122:21034:66970/2 19 145 (6) C L1ME4c_3end#LINE/L1 (297) 533 404 m_b2s551i30
ST-E00130:540 19 TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTT 66
i - -iii ii v i v
C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484
ST-E00130:540 67 TCTATTTTC--CTACAATAAACATTATTGCAATGATCATT----TGTCTA 110
i v i-- iv i viii v i---- iv
C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434
ST-E00130:540 111 CGGGTTTTTTTTTCTCATATGTTAAATTATTTCTT 145
ii v ii i----- i i
C L1ME4c_3end#L 433 TAGCTTTTTCCTTCTT-----TTGAATTATTTCCT 404
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.29
Transitions / transversions = 2.88 (23/8)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 806 16.7 0.0 4.6 ST-E00130:540:HVYVWCCXX:2:1122:8572:34236/2 1 151 (0) + AluSx SINE/Alu 133 276 (36) 1293
ANNOTATION EVIDENCE:
806 16.66 0.00 4.64 ST-E00130:540:HVYVWCCXX:2:1122:8572:34236/2 1 151 0 + AluSx SINE/Alu 133 276 36
806 16.66 0.00 4.64 ST-E00130:540:HVYVWCCXX:2:1122:8572:34236/2 1 151 (0) AluSx#SINE/Alu 133 276 (36) m_b5s356i1
ST-E00130:540 1 ATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGC 50
i i v i v v vi i i
AluSx#SINE/Al 133 ATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGC 182
ST-E00130:540 51 TGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAG 100
v i iivv v
AluSx#SINE/Al 183 TGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG 232
ST-E00130:540 101 ATATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGGGAGACT 150
v v i ------- i ii v
AluSx#SINE/Al 233 AGATCGCGCCACTGCACTCCAGCCTG-------GGCGACAGAGCGAGACT 275
ST-E00130:540 151 C 151
AluSx#SINE/Al 276 C 276
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 12.60
Transitions / transversions = 1.18 (13/11)
Gap_init rate = 0.05 (7 / 150), avg. gap size = 1.00 (7 / 7)
+ 856 13.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1122:8958:61943/2 1 120 (31) C AluSx SINE/Alu (192) 120 1 1294
ANNOTATION EVIDENCE:
856 13.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1122:8958:61943/2 1 120 31 C AluSx SINE/Alu 1 120 192
856 13.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1122:8958:61943/2 1 120 (31) C AluSx#SINE/Alu (192) 120 1 m_b2s357i40
ST-E00130:540 1 AATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGA 50
i ii i i
C AluSx#SINE/Al 120 AGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGA 71
ST-E00130:540 51 CCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGATTACAGAT 100
i i v v v i ii
C AluSx#SINE/Al 70 CCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
ST-E00130:540 101 GTGAGCCACTGTGCCCAGCC 120
i i i
C AluSx#SINE/Al 20 GTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.63
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0)
+ 1288 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1123:18223:39809/1 1 151 (0) + L1P LINE/L1 5264 5414 (741) 1295
ANNOTATION EVIDENCE:
1288 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1123:18223:39809/1 1 151 0 + L1PA2_3end LINE/L1 11 161 741
1288 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1123:18223:39809/1 1 151 (0) L1PA2_3end#LINE/L1 11 161 (741) m_b1s551i169
ST-E00130:540 1 GAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCC 50
L1PA2_3end#LI 11 GAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCC 60
ST-E00130:540 51 ATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACAT 100
L1PA2_3end#LI 61 ATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACAT 110
ST-E00130:540 101 TTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCA 150
L1PA2_3end#LI 111 TTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCA 160
ST-E00130:540 151 G 151
L1PA2_3end#LI 161 G 161
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1325 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1123:18223:39809/2 1 151 (0) C L1P1 LINE/L1 (335) 5820 5670 1296
ANNOTATION EVIDENCE:
1325 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1123:18223:39809/2 1 151 0 C L1PA2_3end LINE/L1 417 567 335
1325 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1123:18223:39809/2 1 151 (0) C L1PA2_3end#LINE/L1 (335) 567 417 m_b1s551i324
ST-E00130:540 1 ATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGTTTCT 50
v
C L1PA2_3end#LI 567 ATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCT 518
ST-E00130:540 51 TAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCT 100
C L1PA2_3end#LI 517 TAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCT 468
ST-E00130:540 101 ATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCG 150
i i
C L1PA2_3end#LI 467 ATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCA 418
ST-E00130:540 151 G 151
C L1PA2_3end#LI 417 G 417
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 233 25.0 6.1 3.9 ST-E00130:540:HVYVWCCXX:2:1123:21694:8482/2 19 147 (4) C L1ME4c LINE/L1 (297) 5786 5655 1297
ANNOTATION EVIDENCE:
233 25.00 6.06 3.88 ST-E00130:540:HVYVWCCXX:2:1123:21694:8482/2 19 147 4 C L1ME4c_3end LINE/L1 402 533 297
233 25.00 6.06 3.88 ST-E00130:540:HVYVWCCXX:2:1123:21694:8482/2 19 147 (4) C L1ME4c_3end#LINE/L1 (297) 533 402 m_b2s551i31
ST-E00130:540 19 TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTT 66
i - -iii ii v i v
C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484
ST-E00130:540 67 TCTATTTTC--CTACAATAAACATTATTGCAATGATCATT----TGTCTA 110
i v i-- iv i viii v i---- iv
C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434
ST-E00130:540 111 AGGGTTTTTTTTTCTCATATTTTAAATTTTTTCTTTA 147
vi v ii ----- i v i
C L1ME4c_3end#L 433 TAGCTTTTTCCTTC-----TTTTGAATTATTTCCTTA 402
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.21
Transitions / transversions = 2.10 (21/10)
Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.44 (13 / 9)
+ 1322 0.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:1124:3518:23724/1 1 151 (0) + L1PA3 LINE/L1 5720 5869 (286) 1298
ANNOTATION EVIDENCE:
1322 0.66 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:1124:3518:23724/1 1 151 0 + L1PA3_3end LINE/L1 467 616 286
1322 0.66 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:1124:3518:23724/1 1 151 (0) L1PA3_3end#LINE/L1 467 616 (286) m_b1s551i344
ST-E00130:540 1 TAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATT 50
L1PA3_3end#LI 467 TAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATT 516
ST-E00130:540 51 AAGAAACTGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAA 100
v
L1PA3_3end#LI 517 AAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAA 566
ST-E00130:540 101 TGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAAATCATC 150
-
L1PA3_3end#LI 567 TGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAATCATC 615
ST-E00130:540 151 A 151
L1PA3_3end#LI 616 A 616
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1065 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1124:3518:23724/2 1 122 (29) C L1PA2 LINE/L1 (18) 6137 6016 1299
ANNOTATION EVIDENCE:
1065 3.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1124:3518:23724/2 1 122 29 C L1PA2_3end LINE/L1 763 884 18
1065 3.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1124:3518:23724/2 1 122 (29) C L1PA2_3end#LINE/L1 (18) 884 763 m_b1s551i422
ST-E00130:540 1 ACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATG 50
C L1PA2_3end#LI 884 ACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATG 835
ST-E00130:540 51 TATACATGTGCCATGCTGGTGTGCTGCACCCACTAACGCGTCATCTAGCA 100
i v
C L1PA2_3end#LI 834 TATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCA 785
ST-E00130:540 101 GTAGGTATGTCTCCCAATGCTA 122
v i
C L1PA2_3end#LI 784 TTAGGTATATCTCCCAATGCTA 763
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.59
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 549 15.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1202:11028:46015/1 68 151 (0) + AluSx SINE/Alu 1 84 (228) 1300
ANNOTATION EVIDENCE:
549 15.48 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:11028:46015/1 68 151 0 + AluSx SINE/Alu 1 84 228
549 15.48 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:11028:46015/1 68 151 (0) AluSx#SINE/Alu 1 84 (228) m_b2s357i52
ST-E00130:540 68 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 117
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 118 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAA 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA 84
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.70
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0)
+ 1110 12.1 0.0 1.3 ST-E00130:540:HVYVWCCXX:2:1202:11028:46015/2 1 151 (0) C AluSx SINE/Alu (22) 290 142 1301
ANNOTATION EVIDENCE:
1110 12.08 0.00 1.32 ST-E00130:540:HVYVWCCXX:2:1202:11028:46015/2 1 151 0 C AluSx SINE/Alu 142 290 22
1110 12.08 0.00 1.32 ST-E00130:540:HVYVWCCXX:2:1202:11028:46015/2 1 151 (0) C AluSx#SINE/Alu (22) 290 142 m_b2s356i1
ST-E00130:540 1 TTTTTTTTGAGACAGAGTCTCGCTTCGTCAAACCCAGGCTGGAGTGCAGT 50
i ii i--
C AluSx#SINE/Al 290 TTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCAGGCTGGAGTGCAGT 243
ST-E00130:540 51 GGCATGATCTCAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAGTGATTC 100
ii i i i i i i
C AluSx#SINE/Al 242 GGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTC 193
ST-E00130:540 101 TCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCACA 150
i i i v i i
C AluSx#SINE/Al 192 TCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACG 143
ST-E00130:540 151 C 151
C AluSx#SINE/Al 142 C 142
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.05
Transitions / transversions = 17.00 (17/1)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1158 12.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/1 1 151 (0) + AluSx SINE/Alu 104 254 (58) 1302
ANNOTATION EVIDENCE:
1158 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/1 1 151 0 + AluSx SINE/Alu 104 254 58
1158 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/1 1 151 (0) AluSx#SINE/Alu 104 254 (58) m_b2s356i13
ST-E00130:540 1 GAAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGG 50
ii i v i i i v
AluSx#SINE/Al 104 GAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGC 153
ST-E00130:540 51 GCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGA 100
i i i i
AluSx#SINE/Al 154 GCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGA 203
ST-E00130:540 101 ACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCA 150
i i i i i ii
AluSx#SINE/Al 204 ACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 253
ST-E00130:540 151 G 151
AluSx#SINE/Al 254 G 254
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 243 24.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/2 4 57 (94) C L1M5 LINE/L1 (379) 5794 5741 1303
ANNOTATION EVIDENCE:
243 24.07 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/2 4 57 94 C L1ME3A_3end LINE/L1 488 541 379
243 24.07 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/2 4 57 (94) C L1ME3A_3end#LINE/L1 (379) 541 488 m_b1s551i527
ST-E00130:540 4 TTATGTAGACATATTACAGGTTATATATCCATTTTACTATTGTTGGACAT 53
i ii i ii iv v i i v
C L1ME3A_3end#L 541 TTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGATGGACAT 492
ST-E00130:540 54 TTAG 57
i
C L1ME3A_3end#L 491 TTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.69
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 22 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/2 119 142 (9) + (T)n Simple_repeat 1 24 (0) 1304
ANNOTATION EVIDENCE:
22 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/2 119 142 9 + (T)n Simple_repeat 1 24 0
22 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:14651:59640/2 119 142 (9) (T)n#Simple_repeat 1 24 (0) m_b1s252i7
ST-E00130:540 119 TTTTTTTTTTTTTTTTTTTTTTTT 142
(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)
+ 349 4.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 1 48 (103) + L1PA2 LINE/L1 6106 6153 (2) 1305
ANNOTATION EVIDENCE:
349 4.17 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 1 48 103 + L1PA2_3end LINE/L1 853 900 2
349 4.17 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 1 48 (103) L1PA2_3end#LINE/L1 853 900 (2) m_b1s551i478
ST-E00130:540 1 ACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 48
i v
L1PA2_3end#LI 853 ACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.29
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 247 27.6 0.0 0.3 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 42 130 (21) C L1M5 LINE/L1 (293) 5831 5741 1306 *
ANNOTATION EVIDENCE:
228 30.68 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 42 130 21 C L1ME4a_3end LINE/L1 491 578 293
228 30.68 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 42 130 (21) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i479
ST-E00130:540 42 AAAATAATAATTTTTAAAGTTTGCAGATTATTTTGTTATGTAGACATATT 91
i- ? v vi v v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 92 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 130
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.43
Transitions / transversions = 2.12 (17/8)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
247 26.23 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 70 130 21 C L1ME3A_3end LINE/L1 488 548 372
247 26.23 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/1 70 130 (21) C L1ME3A_3end#LINE/L1 (372) 548 488 m_b1s551i480
ST-E00130:540 70 TATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTACTATTGT 119
iii i ii i ii iv v i i v
C L1ME3A_3end#L 548 TATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGA 499
ST-E00130:540 120 TGGACATTTAG 130
i
C L1ME3A_3end#L 498 TGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.85
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 1158 12.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/2 1 151 (0) + AluSx SINE/Alu 104 254 (58) 1307
ANNOTATION EVIDENCE:
1158 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/2 1 151 0 + AluSx SINE/Alu 104 254 58
1158 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1202:3356:20172/2 1 151 (0) AluSx#SINE/Alu 104 254 (58) m_b2s356i14
ST-E00130:540 1 GAAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGG 50
ii i v i i i v
AluSx#SINE/Al 104 GAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGC 153
ST-E00130:540 51 GCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGA 100
i i i i
AluSx#SINE/Al 154 GCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGA 203
ST-E00130:540 101 ACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCA 150
i i i i i ii
AluSx#SINE/Al 204 ACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 253
ST-E00130:540 151 G 151
AluSx#SINE/Al 254 G 254
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 551 16.8 19.4 0.0 ST-E00130:540:HVYVWCCXX:2:1204:7324:56616/2 10 146 (5) C L1MC4 LINE/L1 (412) 7630 7461 1308
ANNOTATION EVIDENCE:
551 16.79 19.41 0.00 ST-E00130:540:HVYVWCCXX:2:1204:7324:56616/2 10 146 5 C L1MC4_3end LINE/L1 2208 2377 412
551 16.79 19.41 0.00 ST-E00130:540:HVYVWCCXX:2:1204:7324:56616/2 10 146 (5) C L1MC4_3end#LINE/L1 (412) 2377 2208 m_b3s551i104
ST-E00130:540 10 GTCTGTTTAGTCTCCTTCAATCTGGAACAGTTCT------TTTTTTTATT 53
v i i------ i i i
C L1MC4_3end#LI 2377 GTCTCTTTAGTCTCCTTTAATCTGGAACAGTTCCTCAGTCTTTCTTTGTC 2328
ST-E00130:540 54 TATCATGACCTTCATATATTTGAATAGTACAG------------------ 85
v ? v i v v ------------------
C L1MC4_3end#LI 2327 TTTCATGACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAA 2278
ST-E00130:540 86 -GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----T 129
- iiv i i i i -----
C L1MC4_3end#LI 2277 TGTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGT 2228
ST-E00130:540 130 TATAC---TTTGACGAGAAT 146
i --- i ii
C L1MC4_3end#LI 2227 TATGCATTTTTGGCAGGAAT 2208
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.69
Transitions / transversions = 2.67 (16/6)
Gap_init rate = 0.04 (5 / 136), avg. gap size = 6.60 (33 / 5)
+ 1344 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1205:13545:34377/1 1 151 (0) + L1P3 LINE/L1 3437 3587 (2559) 1309
ANNOTATION EVIDENCE:
1344 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1205:13545:34377/1 1 151 0 + L1P3_orf2 LINE/L1 1328 1478 1816
1344 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1205:13545:34377/1 1 151 (0) L1P3_orf2#LINE/L1 1328 1478 (1816) m_b6s551i127
ST-E00130:540 1 AGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAG 50
L1P3_orf2#LIN 1328 AGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAG 1377
ST-E00130:540 51 GCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAGAGGGATT 100
v
L1P3_orf2#LIN 1378 GCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAGACGGATT 1427
ST-E00130:540 101 CACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTACCATTCCTTC 150
i
L1P3_orf2#LIN 1428 CACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTACCATTCCTTC 1477
ST-E00130:540 151 T 151
L1P3_orf2#LIN 1478 T 1478
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1100 7.3 1.9 0.0 ST-E00130:540:HVYVWCCXX:2:1205:13545:34377/2 1 151 (0) C L1P3 LINE/L1 (2262) 3884 3731 1310
ANNOTATION EVIDENCE:
1100 7.28 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:1205:13545:34377/2 1 151 0 C L1P3_orf2 LINE/L1 1622 1775 1519
1100 7.28 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:1205:13545:34377/2 1 151 (0) C L1P3_orf2#LINE/L1 (1519) 1775 1622 m_b6s551i42
ST-E00130:540 1 TTGTCATTCGTTCTGTTTATGTGATGGATTATGTTTATTGATTTGTGTAT 50
v i i
C L1P3_orf2#LIN 1775 TTGTCATTGGTTCTGTTTATGTGATGGATTACGTTTATTGATTTGCGTAT 1726
ST-E00130:540 51 GCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGGTGGA 100
i i i i v
C L1P3_orf2#LIN 1725 GTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGGTGGA 1676
ST-E00130:540 101 TAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATCGAGG 147
v --- i i
C L1P3_orf2#LIN 1675 TAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGG 1626
ST-E00130:540 148 ATTT 151
C L1P3_orf2#LIN 1625 ATTT 1622
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.08
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1132 10.6 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:1205:7354:8991/2 1 151 (0) C AluSx SINE/Alu (111) 201 49 1311
ANNOTATION EVIDENCE:
1132 10.60 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:1205:7354:8991/2 1 151 0 C AluSx SINE/Alu 49 201 111
1132 10.60 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:1205:7354:8991/2 1 151 (0) C AluSx#SINE/Alu (111) 201 49 m_b4s356i32
ST-E00130:540 1 AAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCT 50
i i vi
C AluSx#SINE/Al 201 AAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGC 152
ST-E00130:540 51 GCCACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAGATGGAGTTTCAC 100
v i i i i
C AluSx#SINE/Al 151 GCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 102
ST-E00130:540 101 CATATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGC 148
i v i i-- i i
C AluSx#SINE/Al 101 CATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGC 52
ST-E00130:540 149 TTC 151
i
C AluSx#SINE/Al 51 CTC 49
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.76
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 860 12.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1206:24464:21649/2 1 119 (32) C AluSx SINE/Alu (193) 119 1 1312
ANNOTATION EVIDENCE:
860 12.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1206:24464:21649/2 1 119 32 C AluSx SINE/Alu 1 119 193
860 12.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1206:24464:21649/2 1 119 (32) C AluSx#SINE/Alu (193) 119 1 m_b5s357i51
ST-E00130:540 1 GTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCCCAAACTCCTGAC 50
i v i i i
C AluSx#SINE/Al 119 GTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGAC 70
ST-E00130:540 51 CTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGGTG 100
i i i i i i
C AluSx#SINE/Al 69 CTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCG 20
ST-E00130:540 101 TGAGCCAGTGCACCCAGCC 119
vi i i
C AluSx#SINE/Al 19 TGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.08
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1207:11089:21473/2 107 151 (0) C MIR SINE/MIR (0) 262 218 1313
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1207:11089:21473/2 107 151 0 C MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1207:11089:21473/2 107 151 (0) C MIR#SINE/MIR (0) 262 218 m_b6s601i0
ST-E00130:540 107 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCATT 151
v i i iiiv vi v i
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACT 218
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 1328 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1207:16427:68096/1 1 151 (0) C L1P1 LINE/L1 (681) 5474 5324 1314
ANNOTATION EVIDENCE:
1328 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1207:16427:68096/1 1 151 0 C L1PA2_3end LINE/L1 71 221 681
1328 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1207:16427:68096/1 1 151 (0) C L1PA2_3end#LINE/L1 (681) 221 71 m_b1s551i205
ST-E00130:540 1 ATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGAT 50
i
C L1PA2_3end#LI 221 ATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGAT 172
ST-E00130:540 51 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTT 100
C L1PA2_3end#LI 171 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTT 122
ST-E00130:540 101 TGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCC 150
C L1PA2_3end#LI 121 TGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCC 72
ST-E00130:540 151 C 151
C L1PA2_3end#LI 71 C 71
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1281 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1207:16427:68096/2 1 151 (0) + L1P1 LINE/L1 5070 5220 (926) 1315
ANNOTATION EVIDENCE:
1281 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1207:16427:68096/2 1 151 0 + L1P1_orf2 LINE/L1 2961 3111 183
1281 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1207:16427:68096/2 1 151 (0) L1P1_orf2#LINE/L1 2961 3111 (183) m_b1s551i91
ST-E00130:540 1 CATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAA 50
L1P1_orf2#LIN 2961 CATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAA 3010
ST-E00130:540 51 CAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGC 100
v i
L1P1_orf2#LIN 3011 CAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGC 3060
ST-E00130:540 101 ACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGA 150
i
L1P1_orf2#LIN 3061 ACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGA 3110
ST-E00130:540 151 G 151
L1P1_orf2#LIN 3111 G 3111
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 622 15.8 0.0 5.8 ST-E00130:540:HVYVWCCXX:2:1208:15118:30386/1 31 151 (0) C AluSx SINE/Alu (8) 304 191 1316
ANNOTATION EVIDENCE:
622 15.79 0.00 5.79 ST-E00130:540:HVYVWCCXX:2:1208:15118:30386/1 31 151 0 C AluSx SINE/Alu 191 304 8
622 15.79 0.00 5.79 ST-E00130:540:HVYVWCCXX:2:1208:15118:30386/1 31 151 (0) C AluSx#SINE/Alu (8) 304 191 m_b5s357i17
ST-E00130:540 31 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 80
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 81 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 130
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
ST-E00130:540 131 TAGTAGGTTCAAGCAATTGTC 151
vvii i v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTC 191
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.86
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7)
+ 564 12.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1208:15118:30386/2 74 151 (0) + AluSx SINE/Alu 1 78 (234) 1317
ANNOTATION EVIDENCE:
564 12.82 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1208:15118:30386/2 74 151 0 + AluSx SINE/Alu 1 78 234
564 12.82 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1208:15118:30386/2 74 151 (0) AluSx#SINE/Alu 1 78 (234) m_b5s357i63
ST-E00130:540 74 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 123
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 124 GGTGGGCAGATCACTTGAGGTCAGGAGT 151
i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGT 78
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 349 4.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 1 48 (103) + L1PA2 LINE/L1 6106 6153 (2) 1318
ANNOTATION EVIDENCE:
349 4.17 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 1 48 103 + L1PA2_3end LINE/L1 853 900 2
349 4.17 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 1 48 (103) L1PA2_3end#LINE/L1 853 900 (2) m_b1s551i481
ST-E00130:540 1 ACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 48
i v
L1PA2_3end#LI 853 ACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.29
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 42 130 (21) C L1M5 LINE/L1 (293) 5831 5741 1319 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 42 130 21 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 42 130 (21) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i482
ST-E00130:540 42 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 91
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 92 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 130
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 63 130 21 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/1 63 130 (21) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i483
ST-E00130:540 63 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 112
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 113 CTATTGTTGGACATTTAG 130
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1162 12.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/2 1 151 (0) + AluSx SINE/Alu 106 256 (56) 1320
ANNOTATION EVIDENCE:
1162 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/2 1 151 0 + AluSx SINE/Alu 106 256 56
1162 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:14468:41778/2 1 151 (0) AluSx#SINE/Alu 106 256 (56) m_b2s356i11
ST-E00130:540 1 AACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGC 50
ii i v i i i v
AluSx#SINE/Al 106 AACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGC 155
ST-E00130:540 51 ACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAAC 100
i i i i
AluSx#SINE/Al 156 GCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAAC 205
ST-E00130:540 101 TCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGC 150
i i i i i ii
AluSx#SINE/Al 206 CCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGC 255
ST-E00130:540 151 C 151
AluSx#SINE/Al 256 C 256
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 797 16.8 0.0 4.7 ST-E00130:540:HVYVWCCXX:2:1210:16234:59710/2 1 150 (1) + AluSx SINE/Alu 135 277 (35) 1321
ANNOTATION EVIDENCE:
797 16.78 0.00 4.67 ST-E00130:540:HVYVWCCXX:2:1210:16234:59710/2 1 150 1 + AluSx SINE/Alu 135 277 35
797 16.78 0.00 4.67 ST-E00130:540:HVYVWCCXX:2:1210:16234:59710/2 1 150 (1) AluSx#SINE/Alu 135 277 (35) m_b5s357i32
ST-E00130:540 1 TAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTG 50
i i v i v v vi i i
AluSx#SINE/Al 135 TAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTG 184
ST-E00130:540 51 AGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGAT 100
v i iivv v v
AluSx#SINE/Al 185 AGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAG 234
ST-E00130:540 101 ATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGACTCC 150
v i ------- i ii i
AluSx#SINE/Al 235 ATCGCGCCACTGCACTCCAGCCTG-------GGCGACAGAGCGAGACTCC 277
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.95
Transitions / transversions = 1.40 (14/10)
Gap_init rate = 0.05 (7 / 149), avg. gap size = 1.00 (7 / 7)
+ 1312 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1210:4401:70820/1 1 149 (2) + L1P1 LINE/L1 5125 5273 (873) 1322
ANNOTATION EVIDENCE:
1312 1.34 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:4401:70820/1 1 149 2 + L1P1_orf2 LINE/L1 3016 3164 130
1312 1.34 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:4401:70820/1 1 149 (2) L1P1_orf2#LINE/L1 3016 3164 (130) m_b1s551i112
ST-E00130:540 1 GCCAGAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 50
i
L1P1_orf2#LIN 3016 GCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 3065
ST-E00130:540 51 AAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAA 100
i
L1P1_orf2#LIN 3066 AAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAA 3115
ST-E00130:540 101 TTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAA 149
L1P1_orf2#LIN 3116 TTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAA 3164
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1266 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1210:4401:70820/2 1 151 (0) C L1P1 LINE/L1 (631) 5524 5374 1323
ANNOTATION EVIDENCE:
1266 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:4401:70820/2 1 151 0 C L1PA2_3end LINE/L1 121 271 631
1266 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1210:4401:70820/2 1 151 (0) C L1PA2_3end#LINE/L1 (631) 271 121 m_b1s551i230
ST-E00130:540 1 TTCCTATTTCTCCACATCCTCTCCAGCACCTGTGGTTTCCTGACTTTTTA 50
v
C L1PA2_3end#LI 271 TTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTA 222
ST-E00130:540 51 ATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGAT 100
i
C L1PA2_3end#LI 221 ATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGAT 172
ST-E00130:540 101 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATTTGTTTTT 150
v
C L1PA2_3end#LI 171 TTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTT 122
ST-E00130:540 151 T 151
C L1PA2_3end#LI 121 T 121
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1270 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1211:5528:57477/1 1 151 (0) C L1P1 LINE/L1 (718) 5437 5287 1324
ANNOTATION EVIDENCE:
1270 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1211:5528:57477/1 1 151 0 C L1PA2_3end LINE/L1 34 184 718
1270 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1211:5528:57477/1 1 151 (0) C L1PA2_3end#LINE/L1 (718) 184 34 m_b1s551i182
ST-E00130:540 1 TTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTT 50
C L1PA2_3end#LI 184 TTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTT 135
ST-E00130:540 51 TTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTT 100
C L1PA2_3end#LI 134 TTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTT 85
ST-E00130:540 101 CATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAA 150
C L1PA2_3end#LI 84 CATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAA 35
ST-E00130:540 151 T 151
C L1PA2_3end#LI 34 T 34
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1231 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1211:5528:57477/2 2 151 (0) + L1P1 LINE/L1 4980 5129 (1017) 1325
ANNOTATION EVIDENCE:
1231 2.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1211:5528:57477/2 2 151 0 + L1P1_orf2 LINE/L1 2871 3020 274
1231 2.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1211:5528:57477/2 2 151 (0) L1P1_orf2#LINE/L1 2871 3020 (274) m_b1s551i55
ST-E00130:540 2 AAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCA 51
i i
L1P1_orf2#LIN 2871 AAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCA 2920
ST-E00130:540 52 TAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATG 101
?
L1P1_orf2#LIN 2921 TAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATG 2970
ST-E00130:540 102 GGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAA 151
v
L1P1_orf2#LIN 2971 GGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAA 3020
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.42
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1313 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1211:7212:47105/1 1 151 (0) + L1P3 LINE/L1 3497 3647 (2499) 1326
ANNOTATION EVIDENCE:
1313 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1211:7212:47105/1 1 151 0 + L1P3_orf2 LINE/L1 1388 1538 1756
1313 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1211:7212:47105/1 1 151 (0) L1P3_orf2#LINE/L1 1388 1538 (1756) m_b6s551i104
ST-E00130:540 1 ATAGCCTACCAACCAAAAAAAGCCCAGGACCAGAGGGATTCACAGCCGAA 50
v
L1P3_orf2#LIN 1388 ATAGCCTACCAACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGAA 1437
ST-E00130:540 51 TTCTACCAGGGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATT 100
i
L1P3_orf2#LIN 1438 TTCTACCAGAGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATT 1487
ST-E00130:540 101 CCAAACAATAGAAAAAGAGGGACTCTTCCCTAACTCATTTTATGATGCCA 150
i v
L1P3_orf2#LIN 1488 CCAAACAATAGAAAAAGAGGGACTCCTCCCTAACTCATTTTATGAGGCCA 1537
ST-E00130:540 151 G 151
L1P3_orf2#LIN 1538 G 1538
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1128 8.0 1.9 0.0 ST-E00130:540:HVYVWCCXX:2:1211:7212:47105/2 1 151 (0) C L1P3 LINE/L1 (2309) 3837 3684 1327
ANNOTATION EVIDENCE:
1128 7.95 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:1211:7212:47105/2 1 151 0 C L1P3_orf2 LINE/L1 1575 1728 1566
1128 7.95 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:1211:7212:47105/2 1 151 (0) C L1P3_orf2#LINE/L1 (1566) 1728 1575 m_b6s551i56
ST-E00130:540 1 TATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGGT 50
i i i i v
C L1P3_orf2#LIN 1728 TATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGGT 1679
ST-E00130:540 51 GGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATCG 97
v --- i i
C L1P3_orf2#LIN 1678 GGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTG 1629
ST-E00130:540 98 AGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCTTT 147
i v v
C L1P3_orf2#LIN 1628 AGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCTTT 1579
ST-E00130:540 148 TTCT 151
i
C L1P3_orf2#LIN 1578 TTTT 1575
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.45
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1135 3.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1213:12723:65582/1 20 151 (0) C L1PA2 LINE/L1 (2) 6153 6022 1328
ANNOTATION EVIDENCE:
1135 3.03 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1213:12723:65582/1 20 151 0 C L1PA2_3end LINE/L1 769 900 2
1135 3.03 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1213:12723:65582/1 20 151 (0) C L1PA2_3end#LINE/L1 (2) 900 769 m_b1s551i428
ST-E00130:540 20 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 69
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 70 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 119
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
ST-E00130:540 120 AACTCGTCATCTAGCATTAGGTATAGCTCCCA 151
v
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCTCCCA 769
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.39
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 1295 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:1213:12723:65582/2 1 151 (0) + L1PA3 LINE/L1 5783 5932 (223) 1329
ANNOTATION EVIDENCE:
1295 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:1213:12723:65582/2 1 151 0 + L1PA3_3end LINE/L1 530 679 223
1295 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:1213:12723:65582/2 1 151 (0) L1PA3_3end#LINE/L1 530 679 (223) m_b1s551i359
ST-E00130:540 1 ACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATG 50
L1PA3_3end#LI 530 ACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATG 579
ST-E00130:540 51 TCCTTTGTTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAAC 100
-
L1PA3_3end#LI 580 TCCTTTGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAAC 628
ST-E00130:540 101 TGTCGCAAGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGG 150
i v i
L1PA3_3end#LI 629 TATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGG 678
ST-E00130:540 151 A 151
L1PA3_3end#LI 679 A 679
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1003 14.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1214:32491:65757/2 3 151 (0) C AluSx SINE/Alu (75) 237 89 1330
ANNOTATION EVIDENCE:
1003 14.77 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1214:32491:65757/2 3 151 0 C AluSx SINE/Alu 89 237 75
1003 14.77 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1214:32491:65757/2 3 151 (0) C AluSx#SINE/Alu (75) 237 89 m_b2s356i21
ST-E00130:540 3 GATCTCAGCTAACTGCAACCTCTGCCTCCTGCGTTCAAGTGATTCCCCTG 52
i v i i v i i
C AluSx#SINE/Al 237 GATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTG 188
ST-E00130:540 53 CCTCAGCTTCCTGAGTGGCTGGGATTACAGGTGCCCCCCACCACACCCAG 102
i i i i v v i i
C AluSx#SINE/Al 187 CCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGG 138
ST-E00130:540 103 CTCAATTTTGTATTTTGAATAGAGACAAGGTCTCACCATGTTGGCCAGG 151
v v v i ii i
C AluSx#SINE/Al 137 CTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGG 89
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.98
Transitions / transversions = 2.14 (15/7)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1325 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1215:15503:50041/1 1 151 (0) + L1P3 LINE/L1 3464 3614 (2532) 1331
ANNOTATION EVIDENCE:
1325 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1215:15503:50041/1 1 151 0 + L1P3_orf2 LINE/L1 1355 1505 1789
1325 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1215:15503:50041/1 1 151 (0) L1P3_orf2#LINE/L1 1355 1505 (1789) m_b6s551i117
ST-E00130:540 1 CAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAA 50
L1P3_orf2#LIN 1355 CAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAA 1404
ST-E00130:540 51 AAAAGCCCAGGACCAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAA 100
v i
L1P3_orf2#LIN 1405 AAAAGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGAGGTACAA 1454
ST-E00130:540 101 AGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAG 150
L1P3_orf2#LIN 1455 AGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAATAGAAAAAG 1504
ST-E00130:540 151 A 151
L1P3_orf2#LIN 1505 A 1505
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1096 7.3 1.9 0.0 ST-E00130:540:HVYVWCCXX:2:1215:15503:50041/2 1 151 (0) C L1P3 LINE/L1 (2258) 3888 3735 1332
ANNOTATION EVIDENCE:
1096 7.28 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:1215:15503:50041/2 1 151 0 C L1P3_orf2 LINE/L1 1626 1779 1515
1096 7.28 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:1215:15503:50041/2 1 151 (0) C L1P3_orf2#LINE/L1 (1515) 1779 1626 m_b6s551i41
ST-E00130:540 1 GTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTTATTGATTTGT 50
v i i
C L1P3_orf2#LIN 1779 GTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTTATTGATTTGC 1730
ST-E00130:540 51 GTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGG 100
i i i i v
C L1P3_orf2#LIN 1729 GTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGG 1680
ST-E00130:540 101 TGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATC 147
v --- i i
C L1P3_orf2#LIN 1679 TGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATT 1630
ST-E00130:540 148 GAGG 151
C L1P3_orf2#LIN 1629 GAGG 1626
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.08
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 278 10.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1216:22587:29050/2 10 48 (103) C L1MC4 LINE/L1 (242) 7800 7762 1333
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1216:22587:29050/2 10 48 103 C L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1216:22587:29050/2 10 48 (103) C L1MC4_3end#LINE/L1 (242) 2547 2509 m_b3s551i78
ST-E00130:540 10 TAGCCACAGTATAATCATCAAAATCAGGAAGTTAACATT 48
i i i i
C L1MC4_3end#LI 2547 TAACCACAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 463 18.4 5.8 0.0 ST-E00130:540:HVYVWCCXX:2:1216:22587:29050/2 53 150 (1) C L1MC4 LINE/L1 (393) 7649 7546 1333
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:2:1216:22587:29050/2 53 150 1 C L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:2:1216:22587:29050/2 53 150 (1) C L1MC4_3end#LINE/L1 (393) 2396 2293 m_b3s551i79
ST-E00130:540 53 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 102
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 103 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 146
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
ST-E00130:540 147 GGTC 150
i
C L1MC4_3end#LI 2296 GGCC 2293
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 6.00 (6 / 1)
+ 1180 4.0 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:1216:30776:64720/1 1 151 (0) C L1P3 LINE/L1 (2610) 3536 3384 1334
ANNOTATION EVIDENCE:
1180 3.97 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:1216:30776:64720/1 1 151 0 C L1P3_orf2 LINE/L1 1275 1427 1867
1180 3.97 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:1216:30776:64720/1 1 151 (0) C L1P3_orf2#LINE/L1 (1867) 1427 1275 m_b6s551i137
ST-E00130:540 1 AATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGC 50
v
C L1P3_orf2#LIN 1427 AATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAATTACTGC 1378
ST-E00130:540 51 CTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCT 100
C L1P3_orf2#LIN 1377 CTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGATTCGACTTCTTCCT 1328
ST-E00130:540 101 GCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAATTTATCACTTTCTTCT 148
v -- v i vv
C L1P3_orf2#LIN 1327 GGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCT 1278
ST-E00130:540 149 AGA 151
C L1P3_orf2#LIN 1277 AGA 1275
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.09
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 903 5.0 3.5 7.3 ST-E00130:540:HVYVWCCXX:2:1216:30776:64720/2 1 151 (0) + L1P3 LINE/L1 3098 3242 (2904) 1335
ANNOTATION EVIDENCE:
903 5.00 3.45 7.28 ST-E00130:540:HVYVWCCXX:2:1216:30776:64720/2 1 151 0 + L1P3_orf2 LINE/L1 989 1133 2161
903 5.00 3.45 7.28 ST-E00130:540:HVYVWCCXX:2:1216:30776:64720/2 1 151 (0) L1P3_orf2#LINE/L1 989 1133 (2161) m_b6s551i230
ST-E00130:540 1 CAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCTGAG 50
v i
L1P3_orf2#LIN 989 CAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCAGAA 1038
ST-E00130:540 51 -TGAAGGAGATAGAGACACACACACACAAAAAAAACCTTTCAAAAAAATC 99
- ----------i i -
L1P3_orf2#LIN 1039 CTGAAGGAGATAGAGACAC----------GAAAAACCCTTCAAAAAA-TC 1077
ST-E00130:540 100 AATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAACAGA----CC 145
v i i ----
L1P3_orf2#LIN 1078 AATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAATAGATAGACC 1127
ST-E00130:540 146 GCTAGC 151
L1P3_orf2#LIN 1128 GCTAGC 1133
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.51
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 1069 4.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1218:22130:7198/1 30 151 (0) C AluSx SINE/Alu (21) 291 170 1336
ANNOTATION EVIDENCE:
1069 4.92 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1218:22130:7198/1 30 151 0 C AluSx SINE/Alu 170 291 21
1069 4.92 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1218:22130:7198/1 30 151 (0) C AluSx#SINE/Alu (21) 291 170 m_b4s356i0
ST-E00130:540 30 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 79
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 80 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCT 129
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
ST-E00130:540 130 CCTGCCTCAGCCTCCTGAGTAG 151
i
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAG 170
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 950 10.6 1.6 0.0 ST-E00130:540:HVYVWCCXX:2:1218:22130:7198/2 29 151 (0) + AluSx SINE/Alu 1 125 (187) 1337
ANNOTATION EVIDENCE:
950 10.57 1.60 0.00 ST-E00130:540:HVYVWCCXX:2:1218:22130:7198/2 29 151 0 + AluSx SINE/Alu 1 125 187
950 10.57 1.60 0.00 ST-E00130:540:HVYVWCCXX:2:1218:22130:7198/2 29 151 (0) AluSx#SINE/Alu 1 125 (187) m_b4s356i55
ST-E00130:540 29 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 78
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 79 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 126
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 127 GGTGAAACTCCATCTCTACTAAAAA 151
i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAA 125
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.92
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)
+ 886 14.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1218:31385:64298/1 26 151 (0) + AluY SINE/Alu 1 126 (185) 1338
ANNOTATION EVIDENCE:
886 14.29 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1218:31385:64298/1 26 151 0 + AluY SINE/Alu 1 126 185
886 14.29 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1218:31385:64298/1 26 151 (0) AluY#SINE/Alu 1 126 (185) m_b2s356i45
ST-E00130:540 26 GGCCAGGCATGGTGGCTCACGCATGTTATCTCAGCACTTTGGGCGGCCAA 75
i ii v v i v i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 76 GGAGGGCTGATTATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTAG 125
v v i i i iii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
ST-E00130:540 126 TGAAACCCCATCTCTACTAAAAACAC 151
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATAC 126
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.04
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 125), avg. gap size = 0.0 (0 / 0)
+ 11 21.2 0.0 2.9 ST-E00130:540:HVYVWCCXX:2:1218:31385:64298/2 34 68 (83) + (ATGTGA)n Simple_repeat 1 34 (0) 1339
ANNOTATION EVIDENCE:
11 21.16 0.00 2.94 ST-E00130:540:HVYVWCCXX:2:1218:31385:64298/2 34 68 83 + (ATGTGA)n Simple_repeat 1 34 0
11 21.16 0.00 2.94 ST-E00130:540:HVYVWCCXX:2:1218:31385:64298/2 34 68 (83) (ATGTGA)n#Simple_repeat 1 34 (0) m_b2s252i4
ST-E00130:540 34 ATGTGAATGTGGATGTTGACTACAAATTTGAATGT 68
i - v iii v
(ATGTGA)n#Sim 1 ATGTGAATGTGAATG-TGAATGTGAATGTGAATGT 34
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1)
+ 20 14.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/1 29 60 (91) + (TG)n Simple_repeat 1 32 (0) 1340
ANNOTATION EVIDENCE:
20 13.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/1 29 60 91 + (TG)n Simple_repeat 1 32 0
20 13.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/1 29 60 (91) (TG)n#Simple_repeat 1 32 (0) m_b4s252i17
ST-E00130:540 29 TGTGTGTGTGTGTGTATGTGTGTGCATGTCTG 60
i ii v
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 515 4.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/1 88 151 (0) C AluSx SINE/Alu (21) 291 228 1341
ANNOTATION EVIDENCE:
515 4.69 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/1 88 151 0 C AluSx SINE/Alu 228 291 21
515 4.69 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/1 88 151 (0) C AluSx#SINE/Alu (21) 291 228 m_b4s357i9
ST-E00130:540 88 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 137
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 138 GCGCGATCTCGGCT 151
C AluSx#SINE/Al 241 GCGCGATCTCGGCT 228
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 1090 11.6 1.4 0.0 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/2 6 151 (0) + AluSx SINE/Alu 1 148 (164) 1342
ANNOTATION EVIDENCE:
1090 11.64 1.35 0.00 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/2 6 151 0 + AluSx SINE/Alu 1 148 164
1090 11.64 1.35 0.00 ST-E00130:540:HVYVWCCXX:2:1219:27225:35608/2 6 151 (0) AluSx#SINE/Alu 1 148 (164) m_b4s356i46
ST-E00130:540 6 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 55
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 56 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 103
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 104 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCAGGGGTGAT 151
i i i i v i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGT 148
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.42
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 2.00 (2 / 1)
+ 1350 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1220:19684:52678/1 1 151 (0) C L1PA2 LINE/L1 (325) 5830 5680 1343
ANNOTATION EVIDENCE:
1350 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19684:52678/1 1 151 0 C L1PA2_3end LINE/L1 427 577 325
1350 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19684:52678/1 1 151 (0) C L1PA2_3end#LINE/L1 (325) 577 427 m_b1s551i331
ST-E00130:540 1 TGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC 50
C L1PA2_3end#LI 577 TGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC 528
ST-E00130:540 51 CACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCA 100
v
C L1PA2_3end#LI 527 CACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCA 478
ST-E00130:540 101 AGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGT 150
i
C L1PA2_3end#LI 477 AGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGT 428
ST-E00130:540 151 C 151
C L1PA2_3end#LI 427 C 427
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.73
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1339 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1220:19684:52678/2 5 151 (0) + L1P1 LINE/L1 5527 5673 (482) 1344
ANNOTATION EVIDENCE:
1339 2.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19684:52678/2 5 151 0 + L1PA3_3end LINE/L1 274 420 482
1339 2.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19684:52678/2 5 151 (0) L1PA3_3end#LINE/L1 274 420 (482) m_b1s551i281
ST-E00130:540 5 CTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTC 54
L1PA3_3end#LI 274 CTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTC 323
ST-E00130:540 55 AGTGTGGTGATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAG 104
i i
L1PA3_3end#LI 324 AGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAG 373
ST-E00130:540 105 CCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCGC 151
i
L1PA3_3end#LI 374 CCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGC 420
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.45
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 1350 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1220:19938:52906/1 1 151 (0) C L1PA2 LINE/L1 (325) 5830 5680 1345
ANNOTATION EVIDENCE:
1350 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19938:52906/1 1 151 0 C L1PA2_3end LINE/L1 427 577 325
1350 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19938:52906/1 1 151 (0) C L1PA2_3end#LINE/L1 (325) 577 427 m_b1s551i332
ST-E00130:540 1 TGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC 50
C L1PA2_3end#LI 577 TGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC 528
ST-E00130:540 51 CACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCA 100
v
C L1PA2_3end#LI 527 CACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCA 478
ST-E00130:540 101 AGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGT 150
i
C L1PA2_3end#LI 477 AGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGT 428
ST-E00130:540 151 C 151
C L1PA2_3end#LI 427 C 427
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.73
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1339 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1220:19938:52906/2 5 151 (0) + L1P1 LINE/L1 5527 5673 (482) 1346
ANNOTATION EVIDENCE:
1339 2.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19938:52906/2 5 151 0 + L1PA3_3end LINE/L1 274 420 482
1339 2.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1220:19938:52906/2 5 151 (0) L1PA3_3end#LINE/L1 274 420 (482) m_b1s551i282
ST-E00130:540 5 CTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTC 54
L1PA3_3end#LI 274 CTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTC 323
ST-E00130:540 55 AGTGTGGTGATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAG 104
i i
L1PA3_3end#LI 324 AGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAG 373
ST-E00130:540 105 CCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCGC 151
i
L1PA3_3end#LI 374 CCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGC 420
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.45
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 1036 9.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:1220:5416:62171/1 1 151 (0) C L1P3 LINE/L1 (2420) 3726 3574 1347
ANNOTATION EVIDENCE:
1036 9.27 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:1220:5416:62171/1 1 151 0 C L1P3_orf2 LINE/L1 1465 1617 1677
1036 9.27 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:1220:5416:62171/1 1 151 (0) C L1P3_orf2#LINE/L1 (1677) 1617 1465 m_b6s551i83
ST-E00130:540 1 ATCGATGTTCATCACGGATAATGGCCTGAAAGTTTCTTTTTC--TTGTGT 48
v v v i--
C L1P3_orf2#LIN 1617 ATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGT 1568
ST-E00130:540 49 CTCTGCCAGGGTTTGGAATCAGGATGGTGCTGGCATCATAAAATGAGTTA 98
v v i v
C L1P3_orf2#LIN 1567 CTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTA 1518
ST-E00130:540 99 GGGAAGAGTCCCTCTTTTGCTATTGTTGGGAATGGTTTCTGAGGGAATGG 148
i v v i v i
C L1P3_orf2#LIN 1517 GGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGG 1468
ST-E00130:540 149 TAC 151
C L1P3_orf2#LIN 1467 TAC 1465
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.90
Transitions / transversions = 0.56 (5/9)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1008 8.7 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:1220:5416:62171/2 2 151 (0) + L1P3 LINE/L1 3303 3454 (2692) 1348
ANNOTATION EVIDENCE:
1008 8.67 1.31 0.00 ST-E00130:540:HVYVWCCXX:2:1220:5416:62171/2 2 151 0 + L1P3_orf2 LINE/L1 1194 1345 1949
1008 8.67 1.31 0.00 ST-E00130:540:HVYVWCCXX:2:1220:5416:62171/2 2 151 (0) L1P3_orf2#LINE/L1 1194 1345 (1949) m_b6s551i162
ST-E00130:540 2 GGATAATACCACTGATCCCACAGAAATACAAACTACCAGCAGAGAATACT 51
vi v
L1P3_orf2#LIN 1194 GGATATCACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACT 1243
ST-E00130:540 52 ATAAATACCTCGATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAAA 101
i v i vv
L1P3_orf2#LIN 1244 ATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAA 1293
ST-E00130:540 102 TTCCGAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAGGTCGAATC 149
vi v -- v i
L1P3_orf2#LIN 1294 TTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAATC 1343
ST-E00130:540 150 CC 151
L1P3_orf2#LIN 1344 CC 1345
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.53
Transitions / transversions = 0.62 (5/8)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 1257 4.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1221:31020:55227/2 1 151 (0) C L1P1 LINE/L1 (1105) 5041 4891 1349
ANNOTATION EVIDENCE:
1257 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1221:31020:55227/2 1 151 0 C L1P1_orf2 LINE/L1 2782 2932 362
1257 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1221:31020:55227/2 1 151 (0) C L1P1_orf2#LINE/L1 (362) 2932 2782 m_b1s551i13
ST-E00130:540 1 CTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTT 50
i
C L1P1_orf2#LIN 2932 CTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTT 2883
ST-E00130:540 51 GAATTGATTTTTCTATCAGGGGTAAGGAAGGGATCCAGTTTCAGCTTTCT 100
i v v v
C L1P1_orf2#LIN 2882 GAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCT 2833
ST-E00130:540 101 ACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTGAATAGGGAATCCT 150
i
C L1P1_orf2#LIN 2832 ACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCT 2783
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 2782 T 2782
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.46
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 654 17.7 6.8 0.8 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/1 2 126 (25) C L1MC4 LINE/L1 (148) 7894 7762 1350
ANNOTATION EVIDENCE:
654 17.74 6.77 0.80 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/1 2 126 25 C L1MC4_3end LINE/L1 2509 2641 148
654 17.74 6.77 0.80 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/1 2 126 (25) C L1MC4_3end#LINE/L1 (148) 2641 2509 m_b3s551i28
ST-E00130:540 2 TCTGAACCATTTTGAGATGAAATCGCACACGTGATGCTCCTT-------- 43
- vv i i v i ? i --------
C L1MC4_3end#LI 2641 TCTGAACCA-TTTGAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTA 2593
ST-E00130:540 44 -ATACTTCAGTGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCC 92
- i i i iv ii iiv i
C L1MC4_3end#LI 2592 AATACTTCAGTGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACC 2543
ST-E00130:540 93 ACAGTATAATCATCAAAATCAGGAAGTTAACATT 126
i i i
C L1MC4_3end#LI 2542 ACAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.01
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.02 (3 / 124), avg. gap size = 3.33 (10 / 3)
+ 286 21.2 11.2 0.0 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/2 76 150 (1) + L1MC4 LINE/L1 7416 7520 (522) 1351
ANNOTATION EVIDENCE:
283 21.33 13.79 0.00 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/2 76 150 1 + L1MC4a_3end LINE/L1 2163 2249 380
283 21.33 13.79 0.00 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/2 76 150 (1) L1MC4a_3end#LINE/L1 2163 2249 (380) m_b3s551i143
ST-E00130:540 76 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 116
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
ST-E00130:540 117 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGA 150
--- i i i i i
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAA 2249
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.34
Transitions / transversions = 15.00 (15/1)
Gap_init rate = 0.05 (4 / 74), avg. gap size = 3.00 (12 / 4)
286 21.21 10.81 0.00 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/2 85 150 1 + L1MC4_3end LINE/L1 2194 2267 522
286 21.21 10.81 0.00 ST-E00130:540:HVYVWCCXX:2:1222:16336:39352/2 85 150 (1) L1MC4_3end#LINE/L1 2194 2267 (522) m_b3s551i144
ST-E00130:540 85 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 126
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
ST-E00130:540 127 AAGGAAACATCAGACAAACTCAGA 150
i i i
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAA 2267
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.60
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 4.00 (8 / 2)
+ 1182 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1222:27671:20665/1 1 151 (0) C L1P3 LINE/L1 (3191) 2955 2805 1352
ANNOTATION EVIDENCE:
1182 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1222:27671:20665/1 1 151 0 C L1P3_orf2 LINE/L1 696 846 2448
1182 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1222:27671:20665/1 1 151 (0) C L1P3_orf2#LINE/L1 (2448) 846 696 m_b7s551i59
ST-E00130:540 1 TGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTTATTTCTGCCTTCA 50
i ?i v
C L1P3_orf2#LIN 846 TGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTTATTTCTGCCTTAA 797
ST-E00130:540 51 TTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCAT 100
i i
C L1P3_orf2#LIN 796 TTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCAT 747
ST-E00130:540 101 GTAGTTGTGTGGTTTTGAGTGAGTTTCTTAATCCTCAGTTCTAATTTGAT 150
i v
C L1P3_orf2#LIN 746 GTAGTTGTGCGGTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAATTTGAT 697
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 696 T 696
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.56
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 501 14.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1223:28239:24673/1 1 71 (80) C AluSx SINE/Alu (241) 71 1 1353
ANNOTATION EVIDENCE:
501 14.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1223:28239:24673/1 1 71 80 C AluSx SINE/Alu 1 71 241
501 14.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1223:28239:24673/1 1 71 (80) C AluSx#SINE/Alu (241) 71 1 m_b5s357i68
ST-E00130:540 1 ACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAGG 50
i i i i i
C AluSx#SINE/Al 71 ACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGG 22
ST-E00130:540 51 TGTGAGCCAGTGCACCCAGCC 71
i vi i i
C AluSx#SINE/Al 21 CGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.44
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 1326 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1224:20009:8482/1 1 151 (0) + L1P1 LINE/L1 5413 5563 (592) 1354
ANNOTATION EVIDENCE:
1326 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1224:20009:8482/1 1 151 0 + L1PA3_3end LINE/L1 160 310 592
1326 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1224:20009:8482/1 1 151 (0) L1PA3_3end#LINE/L1 160 310 (592) m_b1s551i245
ST-E00130:540 1 AGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAG 50
L1PA3_3end#LI 160 AGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAG 209
ST-E00130:540 51 AATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTG 100
i
L1PA3_3end#LI 210 AATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTG 259
ST-E00130:540 101 GAGAAATAGGAATCCTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAA 150
iv
L1PA3_3end#LI 260 GAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAA 309
ST-E00130:540 151 C 151
L1PA3_3end#LI 310 C 310
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1360 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:1224:20009:8482/2 1 151 (0) C L1P1 LINE/L1 (381) 5774 5624 1355
ANNOTATION EVIDENCE:
1360 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1224:20009:8482/2 1 151 0 C L1PA2_3end LINE/L1 371 521 381
1360 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:1224:20009:8482/2 1 151 (0) C L1PA2_3end#LINE/L1 (381) 521 371 m_b1s551i307
ST-E00130:540 1 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 50
C L1PA2_3end#LI 521 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 472
ST-E00130:540 51 TGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTAT 100
i
C L1PA2_3end#LI 471 TGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTAT 422
ST-E00130:540 101 AGCGGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCT 150
i
C L1PA2_3end#LI 421 AGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCT 372
ST-E00130:540 151 G 151
C L1PA2_3end#LI 371 G 371
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.73
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1126 11.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/1 1 151 (0) + AluSx SINE/Alu 16 168 (144) 1356
ANNOTATION EVIDENCE:
1126 11.26 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/1 1 151 0 + AluSx SINE/Alu 16 168 144
1126 11.26 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/1 1 151 (0) AluSx#SINE/Alu 16 168 (144) m_b4s356i41
ST-E00130:540 1 CTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAAGCAGGCAGATCAC- 49
i i i i i -
AluSx#SINE/Al 16 CTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACC 65
ST-E00130:540 50 -AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCT 98
-i i v i i i
AluSx#SINE/Al 66 TGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCT 115
ST-E00130:540 99 CTACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATC 148
i i v iv i
AluSx#SINE/Al 116 CTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATC 165
ST-E00130:540 149 CCA 151
AluSx#SINE/Al 166 CCA 168
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.84
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 34 65 (86) + (TG)n Simple_repeat 1 32 (0) 1357
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 34 65 86 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 34 65 (86) (TG)n#Simple_repeat 1 32 (0) m_b4s252i16
ST-E00130:540 34 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 65
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 66 78 (73) + (TGTATG)n Simple_repeat 1 41 (0) 1358
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 34 78 73 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 34 78 (73) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i15
ST-E00130:540 34 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 78
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 475 5.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 93 151 (0) C AluSx SINE/Alu (21) 291 233 1359
ANNOTATION EVIDENCE:
475 5.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 93 151 0 C AluSx SINE/Alu 233 291 21
475 5.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2101:10460:45628/2 93 151 (0) C AluSx#SINE/Alu (21) 291 233 m_b4s357i4
ST-E00130:540 93 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 142
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 143 GCGCGATCT 151
C AluSx#SINE/Al 241 GCGCGATCT 233
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.69
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 1372 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2102:1742:45751/1 1 151 (0) C L1P1 LINE/L1 (465) 5690 5540 1360
ANNOTATION EVIDENCE:
1372 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2102:1742:45751/1 1 151 0 C L1PA3_3end LINE/L1 287 437 465
1372 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2102:1742:45751/1 1 151 (0) C L1PA3_3end#LINE/L1 (465) 437 287 m_b1s551i285
ST-E00130:540 1 GTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACC 50
i
C L1PA3_3end#LI 437 GTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACC 388
ST-E00130:540 51 CAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGA 100
i
C L1PA3_3end#LI 387 CAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGA 338
ST-E00130:540 101 GGAATCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCAC 150
i
C L1PA3_3end#LI 337 GGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCAC 288
ST-E00130:540 151 C 151
C L1PA3_3end#LI 287 C 287
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1227 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2102:1742:45751/2 1 151 (0) + L1P1 LINE/L1 5241 5391 (755) 1361
ANNOTATION EVIDENCE:
1227 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2102:1742:45751/2 1 151 0 + L1P1_orf2 LINE/L1 3132 3282 12
1227 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2102:1742:45751/2 1 151 (0) L1P1_orf2#LINE/L1 3132 3282 (12) m_b1s551i159
ST-E00130:540 1 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 50
L1P1_orf2#LIN 3132 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 3181
ST-E00130:540 51 ACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAAC 100
L1P1_orf2#LIN 3182 ACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAAC 3231
ST-E00130:540 101 AGACACTACTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAA 150
v
L1P1_orf2#LIN 3232 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAA 3281
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3282 A 3282
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 938 4.3 0.7 7.3 ST-E00130:540:HVYVWCCXX:2:2104:15848:46103/2 1 151 (0) C L1P3 LINE/L1 (2925) 3221 3081 1362
ANNOTATION EVIDENCE:
938 4.28 0.71 7.28 ST-E00130:540:HVYVWCCXX:2:2104:15848:46103/2 1 151 0 C L1P3_orf2 LINE/L1 972 1112 2182
938 4.28 0.71 7.28 ST-E00130:540:HVYVWCCXX:2:2104:15848:46103/2 1 151 (0) C L1P3_orf2#LINE/L1 (2182) 1112 972 m_b6s551i243
ST-E00130:540 1 TTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGG 50
i v - i
C L1P3_orf2#LIN 1112 TTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGG 1064
ST-E00130:540 51 TTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTT 99
i---------- -i v
C L1P3_orf2#LIN 1063 TTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT 1024
ST-E00130:540 100 AGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCT 149
C L1P3_orf2#LIN 1023 AGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCT 974
ST-E00130:540 150 CT 151
C L1P3_orf2#LIN 973 CT 972
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 382 20.9 20.4 0.0 ST-E00130:540:HVYVWCCXX:2:2105:10094:10117/1 1 105 (46) C L1MC4 LINE/L1 (464) 7578 7447 1363
ANNOTATION EVIDENCE:
382 20.95 20.45 0.00 ST-E00130:540:HVYVWCCXX:2:2105:10094:10117/1 1 105 46 C L1MC4_3end LINE/L1 2194 2325 464
382 20.95 20.45 0.00 ST-E00130:540:HVYVWCCXX:2:2105:10094:10117/1 1 105 (46) C L1MC4_3end#LINE/L1 (464) 2325 2194 m_b3s551i113
ST-E00130:540 1 TCATGACCTTCATATATTTGAATAGTACAG-------------------G 31
? v i v v -------------------
C L1MC4_3end#LI 2325 TCATGACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATG 2276
ST-E00130:540 32 TCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTA 76
iiv i i i i -----
C L1MC4_3end#LI 2275 TCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTA 2226
ST-E00130:540 77 TAC---TTTGACGAGAATGTTGCAAAAGTAAT 105
i --- i ii iiii i i
C L1MC4_3end#LI 2225 TGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.74
Transitions / transversions = 4.25 (17/4)
Gap_init rate = 0.03 (3 / 104), avg. gap size = 9.00 (27 / 3)
+ 1296 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/1 1 151 (0) + L1PA2 LINE/L1 5818 5967 (188) 1364
ANNOTATION EVIDENCE:
1296 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/1 1 151 0 + L1PA2_3end LINE/L1 565 714 188
1296 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/1 1 151 (0) L1PA2_3end#LINE/L1 565 714 (188) m_b1s551i381
ST-E00130:540 1 AATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAAATCA 50
-
L1PA2_3end#LI 565 AATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAATCA 613
ST-E00130:540 51 TCATTCTCAGTAAACTGTCGCAAGAAGAAAAAACCAAACACCGCATGTTC 100
i v i
L1PA2_3end#LI 614 TCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTC 663
ST-E00130:540 101 TCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGG 150
L1PA2_3end#LI 664 TCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGG 713
ST-E00130:540 151 G 151
L1PA2_3end#LI 714 G 714
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/2 59 147 (4) + L1M5 LINE/L1 5741 5831 (293) 1365
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/2 59 147 4 + L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/2 59 147 (4) L1ME4a_3end#LINE/L1 491 578 (293) m_b1s551i512
ST-E00130:540 59 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 108
vii ? v v vi i ii ii i i
L1ME4a_3end#L 491 CTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCAT 540
ST-E00130:540 109 ATAACAAAATAATATGCAAACTTTAAAAATTATTATTTT 147
ii iii v iv v ? -i
L1ME4a_3end#L 541 ACGATGGAATATTATGCAGCCATTAAAAATNAT-GTTTT 578
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/2 59 126 25 + L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2105:21805:29138/2 59 126 (25) L1ME3A_3end#LINE/L1 488 555 (365) m_b1s551i513
ST-E00130:540 59 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 108
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
ST-E00130:540 109 ATAACAAAATAATATGCA 126
i iii v i
L1ME3A_3end#L 538 ACAATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 562 6.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2105:30218:11681/2 1 72 (79) + AluSx SINE/Alu 227 298 (14) 1366
ANNOTATION EVIDENCE:
562 6.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2105:30218:11681/2 1 72 79 + AluSx SINE/Alu 227 298 14
562 6.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2105:30218:11681/2 1 72 (79) AluSx#SINE/Alu 227 298 (14) m_b2s357i109
ST-E00130:540 1 GAGCCGAGATCATGCCACTGCATTCCAGCCTGGGCGACAGAGCGAGACTC 50
ii i
AluSx#SINE/Al 227 GAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTC 276
ST-E00130:540 51 CGTCTCAAAAAAAGAAATAAAA 72
i v
AluSx#SINE/Al 277 CGTCTCAAAAAAAAAAAAAAAA 298
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.60
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2106:16538:21632/1 24 45 (106) + (A)n Simple_repeat 1 22 (0) 1367
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2106:16538:21632/1 24 45 106 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2106:16538:21632/1 24 45 (106) (A)n#Simple_repeat 1 22 (0) m_b1s252i6
ST-E00130:540 24 AAAAAAAAAAAAAAAAAAAAAA 45
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1131 7.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2106:16538:21632/2 1 151 (0) + L1PA2 LINE/L1 5946 6096 (59) 1368
ANNOTATION EVIDENCE:
1131 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2106:16538:21632/2 1 151 0 + L1PA2_3end LINE/L1 693 843 59
1131 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2106:16538:21632/2 1 151 (0) L1PA2_3end#LINE/L1 693 843 (59) m_b1s551i397
ST-E00130:540 1 ATCACATGGACACAGGAAGGGGAATATCACACTCAGTGGACTGTTGCGGG 50
v v v i
L1PA2_3end#LI 693 ATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGG 742
ST-E00130:540 51 GTGGGGGGAGGGTGTAGGTATGGCATTGGGAGATATACCTAATGCTAGCT 100
v v v i v
L1PA2_3end#LI 743 GTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGAT 792
ST-E00130:540 101 GACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATACATAGGTA 150
i v
L1PA2_3end#LI 793 GACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTA 842
ST-E00130:540 151 A 151
L1PA2_3end#LI 843 A 843
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.01
Transitions / transversions = 0.38 (3/8)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1263 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2108:15290:29982/1 1 151 (0) + L1P3 LINE/L1 2864 3014 (3132) 1369
ANNOTATION EVIDENCE:
1263 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2108:15290:29982/1 1 151 0 + L1P3_orf2 LINE/L1 755 905 2389
1263 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2108:15290:29982/1 1 151 (0) L1P3_orf2#LINE/L1 755 905 (2389) m_b7s551i42
ST-E00130:540 1 TGAACAACCTGCTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCA 50
i i v
L1P3_orf2#LIN 755 TGAACAACCTGCTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCA 804
ST-E00130:540 51 GAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCA 100
i? i i
L1P3_orf2#LIN 805 GAAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCA 854
ST-E00130:540 101 GAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCAC 150
L1P3_orf2#LIN 855 GAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCAC 904
ST-E00130:540 151 T 151
L1P3_orf2#LIN 905 T 905
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 771 6.4 8.5 7.3 ST-E00130:540:HVYVWCCXX:2:2108:15290:29982/2 1 151 (0) C L1P3 LINE/L1 (2868) 3278 3126 1370
ANNOTATION EVIDENCE:
771 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:2:2108:15290:29982/2 1 151 0 C L1P3_orf2 LINE/L1 1017 1169 2125
771 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:2:2108:15290:29982/2 1 151 (0) C L1P3_orf2#LINE/L1 (2125) 1169 1017 m_b6s551i219
ST-E00130:540 1 ATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----TC 38
-------- v ----
C L1P3_orf2#LIN 1169 ATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATC 1120
ST-E00130:540 39 TGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTT 88
i i v -
C L1P3_orf2#LIN 1119 TATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTT 1071
ST-E00130:540 89 TGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTC 137
i i---------- -i v
C L1P3_orf2#LIN 1070 TGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCTC 1031
ST-E00130:540 138 TGATCTTAGTTCTT 151
v
C L1P3_orf2#LIN 1030 TGATCTTAGTTATT 1017
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1089 6.6 3.2 0.0 ST-E00130:540:HVYVWCCXX:2:2109:30685:17729/1 1 151 (0) C L1P3 LINE/L1 (2342) 3804 3649 1371
ANNOTATION EVIDENCE:
1089 6.62 3.20 0.00 ST-E00130:540:HVYVWCCXX:2:2109:30685:17729/1 1 151 0 C L1P3_orf2 LINE/L1 1540 1695 1599
1089 6.62 3.20 0.00 ST-E00130:540:HVYVWCCXX:2:2109:30685:17729/1 1 151 (0) C L1P3_orf2#LINE/L1 (1599) 1695 1540 m_b6s551i61
ST-E00130:540 1 GCTGACTTGATAGTGGTGGATAAGCGTTTTGATGG---GCTGGATTCAGT 47
i v v v--- i
C L1P3_orf2#LIN 1695 GCCGACTTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGT 1646
ST-E00130:540 48 TTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCATCAGGGATAAT 97
i i v
C L1P3_orf2#LIN 1645 TTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATCAGGGATATT 1596
ST-E00130:540 98 GGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAG 145
i-- v
C L1P3_orf2#LIN 1595 GGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAG 1546
ST-E00130:540 146 GATGAT 151
C L1P3_orf2#LIN 1545 GATGAT 1540
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 1211 4.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2109:30685:17729/2 1 151 (0) + L1P3 LINE/L1 3430 3580 (2566) 1372
ANNOTATION EVIDENCE:
1211 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2109:30685:17729/2 1 151 0 + L1P3_orf2 LINE/L1 1321 1471 1823
1211 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2109:30685:17729/2 1 151 (0) L1P3_orf2#LINE/L1 1321 1471 (1823) m_b6s551i129
ST-E00130:540 1 CTAAAGCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTGCGGA 50
v v v
L1P3_orf2#LIN 1321 CTAAACCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGA 1370
ST-E00130:540 51 AATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAG 100
L1P3_orf2#LIN 1371 AATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAG 1420
ST-E00130:540 101 AGGGATTCACAGCCGAATTCTACCAGGGGGACAAAGAGGAGCTGGTACCA 150
v i v
L1P3_orf2#LIN 1421 ACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTACCA 1470
ST-E00130:540 151 T 151
L1P3_orf2#LIN 1471 T 1471
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.09
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1177 6.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2110:13494:35660/2 1 151 (0) C L1P3 LINE/L1 (3188) 2958 2808 1373
ANNOTATION EVIDENCE:
1177 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2110:13494:35660/2 1 151 0 C L1P3_orf2 LINE/L1 699 849 2445
1177 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2110:13494:35660/2 1 151 (0) C L1P3_orf2#LINE/L1 (2445) 849 699 m_b7s551i57
ST-E00130:540 1 CATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTTATTTCTGCCT 50
i i ?i
C L1P3_orf2#LIN 849 CGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTTATTTCTGCCT 800
ST-E00130:540 51 TCATTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTC 100
v i i
C L1P3_orf2#LIN 799 TAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTC 750
ST-E00130:540 101 CATGTAGTTGTGTGGTTTTGAGTGAGTTTCTTAATCCTCAGTTCTAATTT 150
i v
C L1P3_orf2#LIN 749 CATGTAGTTGTGCGGTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAATTT 700
ST-E00130:540 151 G 151
C L1P3_orf2#LIN 699 G 699
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1253 3.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:2110:6735:69027/1 1 151 (0) C L1P3 LINE/L1 (2451) 3695 3543 1374
ANNOTATION EVIDENCE:
1253 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:2110:6735:69027/1 1 151 0 C L1P3_orf2 LINE/L1 1434 1586 1708
1253 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:2110:6735:69027/1 1 151 (0) C L1P3_orf2#LINE/L1 (1708) 1586 1434 m_b6s551i96
ST-E00130:540 1 TTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCT 48
i-- v
C L1P3_orf2#LIN 1586 TTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCT 1537
ST-E00130:540 49 GGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGA 98
v i
C L1P3_orf2#LIN 1536 GGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGA 1487
ST-E00130:540 99 ATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAAT 148
i
C L1P3_orf2#LIN 1486 ATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAAT 1437
ST-E00130:540 149 TCG 151
C L1P3_orf2#LIN 1436 TCG 1434
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1065 6.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2110:6735:69027/2 1 150 (1) + L1P3 LINE/L1 3272 3421 (2725) 1375
ANNOTATION EVIDENCE:
1065 6.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2110:6735:69027/2 1 150 1 + L1P3_orf2 LINE/L1 1163 1312 1982
1065 6.67 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2110:6735:69027/2 1 150 (1) L1P3_orf2#LINE/L1 1163 1312 (1982) m_b6s551i174
ST-E00130:540 1 ATCAAATAGACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCC 50
v i vi
L1P3_orf2#LIN 1163 ATCAAATAGACACAATAAAAAATGATAAAGGGGATATCACCACTGATCCC 1212
ST-E00130:540 51 ACAGAAATACAAACTACCATCAGAGAATACTATAAATACCTCTATGCAAA 100
i i
L1P3_orf2#LIN 1213 ACAGAAATACAAACTACCATCAGAGAATACTATAAACACCTCTACGCAAA 1262
ST-E00130:540 101 TAAACTAGAAAATCTAGAAGAAAGTGATAAATTCCTAGACACATACAACC 150
vv i v
L1P3_orf2#LIN 1263 TAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTGGACACATACACCC 1312
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.33
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1301 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2111:14854:60167/1 1 151 (0) C L1P1 LINE/L1 (836) 5310 5160 1376
ANNOTATION EVIDENCE:
1301 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:14854:60167/1 1 151 0 C L1P1_orf2 LINE/L1 3051 3201 93
1301 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:14854:60167/1 1 151 (0) C L1P1_orf2#LINE/L1 (93) 3201 3051 m_b1s551i128
ST-E00130:540 1 GTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGG 50
C L1P1_orf2#LIN 3201 GTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGG 3152
ST-E00130:540 51 ATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTT 100
i
C L1P1_orf2#LIN 3151 ATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCT 3102
ST-E00130:540 101 GTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCT 150
C L1P1_orf2#LIN 3101 GTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCT 3052
ST-E00130:540 151 C 151
C L1P1_orf2#LIN 3051 C 3051
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1259 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2111:14854:60167/2 1 151 (0) + L1P1 LINE/L1 4987 5137 (1009) 1377
ANNOTATION EVIDENCE:
1259 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:14854:60167/2 1 151 0 + L1P1_orf2 LINE/L1 2878 3028 266
1259 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:14854:60167/2 1 151 (0) L1P1_orf2#LINE/L1 2878 3028 (266) m_b1s551i58
ST-E00130:540 1 AATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAAC 50
i
L1P1_orf2#LIN 2878 AATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAAC 2927
ST-E00130:540 51 CCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGG 100
?
L1P1_orf2#LIN 2928 CCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGG 2977
ST-E00130:540 101 ACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGAC 150
v i
L1P1_orf2#LIN 2978 ACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAC 3027
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3028 A 3028
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1126 8.0 0.7 0.7 ST-E00130:540:HVYVWCCXX:2:2111:16518:31090/1 1 151 (0) + AluY SINE/Alu 85 235 (76) 1378
ANNOTATION EVIDENCE:
1126 8.00 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2111:16518:31090/1 1 151 0 + AluY SINE/Alu 85 235 76
1126 8.00 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2111:16518:31090/1 1 151 (0) AluY#SINE/Alu 85 235 (76) m_b2s356i66
ST-E00130:540 1 ATCCTGGCTAACGTGGTGAAACCCCGTCTCTACTAAAAACACAAAAA-TT 49
ii i -
AluY#SINE/Alu 85 ATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATT 134
ST-E00130:540 50 AGATGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGA 99
vi
AluY#SINE/Alu 135 AGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGA 184
ST-E00130:540 100 AGCAGGAGAACGGCATGAACCTGGGGGGGGGGAGGTTGCAGTGAGCCGAG 149
i i i i i v - v
AluY#SINE/Alu 185 GGCAGGAGAATGGCGTGAACCCGGGAGGCGG-AGCTTGCAGTGAGCCGAG 233
ST-E00130:540 150 AT 151
AluY#SINE/Alu 234 AT 235
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.85
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 243 24.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/1 3 56 (95) C L1M5 LINE/L1 (379) 5794 5741 1379
ANNOTATION EVIDENCE:
243 24.07 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/1 3 56 95 C L1ME3A_3end LINE/L1 488 541 379
243 24.07 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/1 3 56 (95) C L1ME3A_3end#LINE/L1 (379) 541 488 m_b1s551i528
ST-E00130:540 3 TTATGTAGACATATTACAGGTTATATATCCATTTTACTATTGTTGGACAT 52
i ii i ii iv v i i v
C L1ME3A_3end#L 541 TTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGATGGACAT 492
ST-E00130:540 53 TTAG 56
i
C L1ME3A_3end#L 491 TTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.69
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 16 9.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/1 118 139 (12) + (T)n Simple_repeat 1 22 (0) 1380
ANNOTATION EVIDENCE:
16 9.78 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/1 118 139 12 + (T)n Simple_repeat 1 22 0
16 9.78 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/1 118 139 (12) (T)n#Simple_repeat 1 22 (0) m_b1s252i5
ST-E00130:540 118 TTTTTTGTTTTGTTTTTTTTTT 139
v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 595 14.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/2 63 151 (0) + AluSx SINE/Alu 1 89 (223) 1381
ANNOTATION EVIDENCE:
595 14.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/2 63 151 0 + AluSx SINE/Alu 1 89 223
595 14.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2111:30350:51535/2 63 151 (0) AluSx#SINE/Alu 1 89 (223) m_b2s357i51
ST-E00130:540 63 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 112
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 113 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGC 151
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGC 89
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.12
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
+ 486 17.5 6.7 14.3 ST-E00130:540:HVYVWCCXX:2:2115:32248:25323/1 1 147 (4) + L1MC4 LINE/L1 7818 7952 (90) 1382
ANNOTATION EVIDENCE:
486 17.47 6.66 14.29 ST-E00130:540:HVYVWCCXX:2:2115:32248:25323/1 1 147 4 + L1MC4_3end LINE/L1 2565 2699 90
486 17.47 6.66 14.29 ST-E00130:540:HVYVWCCXX:2:2115:32248:25323/1 1 147 (4) L1MC4_3end#LINE/L1 2565 2699 (90) m_b3s551i10
ST-E00130:540 1 GTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCATCACGT 41
i i --------- i ? i
L1MC4_3end#LI 2565 GTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCATNATGT 2614
ST-E00130:540 42 GTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTATCTGCG 91
v i i vv - i vi i i -- -
L1MC4_3end#LI 2615 CTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT--GC- 2660
ST-E00130:540 92 TATGAGTGTGTGTGTGGAGAGAGGGAATGATTAAGCAAATATGGTAAAAC 141
----------------- ? ? i v i i i
L1MC4_3end#LI 2661 -----------------ANANAGAGAATGATAAAGCAAATGTGGCAAAAT 2693
ST-E00130:540 142 GTTAAC 147
L1MC4_3end#LI 2694 GTTAAC 2699
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.74
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.15 (22 / 146), avg. gap size = 1.36 (30 / 22)
+ 1122 9.3 0.7 0.7 ST-E00130:540:HVYVWCCXX:2:2117:31548:34096/1 1 151 (0) + AluY SINE/Alu 94 244 (67) 1383
ANNOTATION EVIDENCE:
1122 9.33 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2117:31548:34096/1 1 151 0 + AluY SINE/Alu 94 244 67
1122 9.33 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2117:31548:34096/1 1 151 (0) AluY#SINE/Alu 94 244 (67) m_b2s356i68
ST-E00130:540 1 AACGTGGTGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCG 49
ii i i - vi
AluY#SINE/Alu 94 AACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCG 143
ST-E00130:540 50 TGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGA 99
i
AluY#SINE/Alu 144 TGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGA 193
ST-E00130:540 100 ACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCA 149
i i i - i v ii
AluY#SINE/Alu 194 ATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCA 242
ST-E00130:540 150 CT 151
AluY#SINE/Alu 243 CT 244
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.70
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 285 26.1 5.6 0.7 ST-E00130:540:HVYVWCCXX:2:2117:31548:34096/2 1 135 (16) + L1ME4c LINE/L1 5696 5837 (246) 1384
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 ST-E00130:540:HVYVWCCXX:2:2117:31548:34096/2 1 135 16 + L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 ST-E00130:540:HVYVWCCXX:2:2117:31548:34096/2 1 135 (16) L1ME4c_3end#LINE/L1 443 584 (246) m_b2s551i11
ST-E00130:540 1 AAATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCT 48
i v iiiv i vi --i v i v i
L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492
ST-E00130:540 49 AAATTTCTGACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT-- 92
v ii iii- - i -- i? i--
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
ST-E00130:540 93 GACAGAAAAATGGTGAAGCCATTAAAAAGTATGACTATCAAGA 135
ii v - vi v vv i i v
L1ME4c_3end#L 543 GATGGAATA-TTATGCAGCCATTAAAAATGATAATTATGAAGA 584
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 1122 9.3 0.7 0.7 ST-E00130:540:HVYVWCCXX:2:2117:31619:32988/1 1 151 (0) + AluY SINE/Alu 94 244 (67) 1385
ANNOTATION EVIDENCE:
1122 9.33 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2117:31619:32988/1 1 151 0 + AluY SINE/Alu 94 244 67
1122 9.33 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2117:31619:32988/1 1 151 (0) AluY#SINE/Alu 94 244 (67) m_b2s356i69
ST-E00130:540 1 AACGTGGTGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCG 49
ii i i - vi
AluY#SINE/Alu 94 AACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCG 143
ST-E00130:540 50 TGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGA 99
i
AluY#SINE/Alu 144 TGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGA 193
ST-E00130:540 100 ACGGCATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCA 149
i i i - i v ii
AluY#SINE/Alu 194 ATGGCGTGAACCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCA 242
ST-E00130:540 150 CT 151
AluY#SINE/Alu 243 CT 244
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.70
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 285 26.1 5.6 0.7 ST-E00130:540:HVYVWCCXX:2:2117:31619:32988/2 1 135 (16) + L1ME4c LINE/L1 5696 5837 (246) 1386
ANNOTATION EVIDENCE:
285 26.12 5.64 0.74 ST-E00130:540:HVYVWCCXX:2:2117:31619:32988/2 1 135 16 + L1ME4c_3end LINE/L1 443 584 246
285 26.12 5.64 0.74 ST-E00130:540:HVYVWCCXX:2:2117:31619:32988/2 1 135 (16) L1ME4c_3end#LINE/L1 443 584 (246) m_b2s551i12
ST-E00130:540 1 AAATGATCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCT 48
i v iiiv i vi --i v i v i
L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492
ST-E00130:540 49 AAATTTCTGACAATAAAA-AATG-TCAAGTAAATTATGGTA--TTTAT-- 92
v ii iii- - i -- i? i--
L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542
ST-E00130:540 93 GACAGAAAAATGGTGAAGCCATTAAAAAGTATGACTATCAAGA 135
ii v - vi v vv i i v
L1ME4c_3end#L 543 GATGGAATA-TTATGCAGCCATTAAAAATGATAATTATGAAGA 584
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.02
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6)
+ 1246 4.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2117:5325:39088/1 1 151 (0) + L1P1 LINE/L1 4961 5111 (1035) 1387
ANNOTATION EVIDENCE:
1246 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2117:5325:39088/1 1 151 0 + L1P1_orf2 LINE/L1 2852 3002 292
1246 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2117:5325:39088/1 1 151 (0) L1P1_orf2#LINE/L1 2852 3002 (292) m_b1s551i42
ST-E00130:540 1 CCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGATTAAAGACTTA 50
v v i
L1P1_orf2#LIN 2852 CCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTA 2901
ST-E00130:540 51 AACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTAC 100
i ?
L1P1_orf2#LIN 2902 AACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTAC 2951
ST-E00130:540 101 CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACTAAAAG 150
i
L1P1_orf2#LIN 2952 CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAG 3001
ST-E00130:540 151 C 151
L1P1_orf2#LIN 3002 C 3002
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.79
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1177 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2117:5325:39088/2 1 151 (0) C L1P LINE/L1 (738) 5417 5267 1388
ANNOTATION EVIDENCE:
1177 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2117:5325:39088/2 1 151 0 C L1PA2_3end LINE/L1 14 164 738
1177 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2117:5325:39088/2 1 151 (0) C L1PA2_3end#LINE/L1 (738) 164 14 m_b1s551i172
ST-E00130:540 1 TCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGC 50
C L1PA2_3end#LI 164 TCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGC 115
ST-E00130:540 51 ATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTT 100
C L1PA2_3end#LI 114 ATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTT 65
ST-E00130:540 101 TGATGGGGTTGTTGGTTTTTTTCTTGTCAATTTGGTTGAGGTCATTGTGG 150
v v v v i
C L1PA2_3end#LI 64 TGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAG 15
ST-E00130:540 151 A 151
C L1PA2_3end#LI 14 A 14
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 198 28.7 16.4 0.0 ST-E00130:540:HVYVWCCXX:2:2118:14215:32830/1 26 147 (4) C MIR SINE/MIR (0) 262 117 1389
ANNOTATION EVIDENCE:
198 28.69 16.44 0.00 ST-E00130:540:HVYVWCCXX:2:2118:14215:32830/1 26 147 4 C MIR SINE/MIR 117 262 0
198 28.69 16.44 0.00 ST-E00130:540:HVYVWCCXX:2:2118:14215:32830/1 26 147 (4) C MIR#SINE/MIR (0) 262 117 m_b6s601i22
ST-E00130:540 26 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 68
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 69 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 103
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 104 TTAGCTTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGAC 147
v v v vi ii v i i -- v i
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 117
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.74
Transitions / transversions = 1.50 (21/14)
Gap_init rate = 0.04 (5 / 121), avg. gap size = 4.80 (24 / 5)
+ 689 14.3 0.0 0.8 ST-E00130:540:HVYVWCCXX:2:2118:14215:32830/2 1 120 (31) + AluSx SINE/Alu 194 312 (0) 1390
ANNOTATION EVIDENCE:
689 14.29 0.00 0.83 ST-E00130:540:HVYVWCCXX:2:2118:14215:32830/2 1 120 31 + AluSx SINE/Alu 194 312 0
689 14.29 0.00 0.83 ST-E00130:540:HVYVWCCXX:2:2118:14215:32830/2 1 120 (31) AluSx#SINE/Alu 194 312 (0) m_b6s357i5
ST-E00130:540 1 AATTGCTTGAACCGAGGAGGTAGAGGCTGAAGTGAACCGAGATCACACCA 50
i vi ii i v i i i
AluSx#SINE/Al 194 AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCA 243
ST-E00130:540 51 TTGCCCTCCAGCCTGGGAGAGATGAGCGAAACTCCATCTCAAAAAAAAAA 100
i v v v - i i
AluSx#SINE/Al 244 CTGCACTCCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAA 292
ST-E00130:540 101 AAAAAAAAAAAAAAAAAGAA 120
i
AluSx#SINE/Al 293 AAAAAAAAAAAAAAAAAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.39
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.01 (1 / 119), avg. gap size = 1.00 (1 / 1)
+ 1143 8.0 0.7 0.7 ST-E00130:540:HVYVWCCXX:2:2118:15940:55790/1 1 151 (0) + AluY SINE/Alu 118 268 (43) 1391
ANNOTATION EVIDENCE:
1143 8.00 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2118:15940:55790/1 1 151 0 + AluY SINE/Alu 118 268 43
1143 8.00 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2118:15940:55790/1 1 151 (0) AluY#SINE/Alu 118 268 (43) m_b2s356i76
ST-E00130:540 1 TAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGGCGCCTGTAGTCCCA 49
i - vi
AluY#SINE/Alu 118 TAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCA 167
ST-E00130:540 50 GCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAACCTGGGGAGGTGGA 99
i i i i - i
AluY#SINE/Alu 168 GCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGG-AGGCGGA 216
ST-E00130:540 100 GGTTGCAGTGAGCCGAGATCATGCCACTGCATTCCAGCCTGGGCGACAGA 149
v ii i
AluY#SINE/Alu 217 GCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGA 266
ST-E00130:540 150 GC 151
AluY#SINE/Alu 267 GC 268
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1299 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2118:16914:46472/1 1 151 (0) + L1P1 LINE/L1 5152 5302 (844) 1392
ANNOTATION EVIDENCE:
1299 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:16914:46472/1 1 151 0 + L1P1_orf2 LINE/L1 3043 3193 101
1299 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:16914:46472/1 1 151 (0) L1P1_orf2#LINE/L1 3043 3193 (101) m_b1s551i124
ST-E00130:540 1 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 50
L1P1_orf2#LIN 3043 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 3092
ST-E00130:540 51 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 100
i
L1P1_orf2#LIN 3093 GCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 3142
ST-E00130:540 101 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 150
L1P1_orf2#LIN 3143 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 3192
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3193 A 3193
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1338 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2118:16914:46472/2 1 151 (0) C L1P1 LINE/L1 (640) 5515 5365 1393
ANNOTATION EVIDENCE:
1338 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:16914:46472/2 1 151 0 C L1PA2_3end LINE/L1 112 262 640
1338 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:16914:46472/2 1 151 (0) C L1PA2_3end#LINE/L1 (640) 262 112 m_b1s551i229
ST-E00130:540 1 CTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCC 50
i
C L1PA2_3end#LI 262 CTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCC 213
ST-E00130:540 51 ATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTC 100
C L1PA2_3end#LI 212 ATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTC 163
ST-E00130:540 101 TCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCAT 150
C L1PA2_3end#LI 162 TCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCAT 113
ST-E00130:540 151 A 151
C L1PA2_3end#LI 112 A 112
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1318 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2118:6015:68060/1 1 151 (0) C L1P1 LINE/L1 (669) 5486 5336 1394
ANNOTATION EVIDENCE:
1318 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:6015:68060/1 1 151 0 C L1PA2_3end LINE/L1 83 233 669
1318 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:6015:68060/1 1 151 (0) C L1PA2_3end#LINE/L1 (669) 233 83 m_b1s551i213
ST-E00130:540 1 CCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAGATGGTATCTCAT 50
i
C L1PA2_3end#LI 233 CCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCAT 184
ST-E00130:540 51 TGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTT 100
C L1PA2_3end#LI 183 TGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTT 134
ST-E00130:540 101 TCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTC 150
C L1PA2_3end#LI 133 TCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTC 84
ST-E00130:540 151 A 151
C L1PA2_3end#LI 83 A 83
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1266 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2118:6015:68060/2 1 151 (0) + L1P1 LINE/L1 5169 5319 (827) 1395
ANNOTATION EVIDENCE:
1266 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:6015:68060/2 1 151 0 + L1P1_orf2 LINE/L1 3060 3210 84
1266 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2118:6015:68060/2 1 151 (0) L1P1_orf2#LINE/L1 3060 3210 (84) m_b1s551i130
ST-E00130:540 1 CACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGG 50
i
L1P1_orf2#LIN 3060 CACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGG 3109
ST-E00130:540 51 AGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATC 100
L1P1_orf2#LIN 3110 AGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATC 3159
ST-E00130:540 101 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 150
L1P1_orf2#LIN 3160 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 3209
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3210 A 3210
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 433 8.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/1 1 56 (95) C AluSx SINE/Alu (243) 69 14 1396
ANNOTATION EVIDENCE:
433 8.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/1 1 56 95 C AluSx SINE/Alu 14 69 243
433 8.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/1 1 56 (95) C AluSx#SINE/Alu (243) 69 14 m_b6s357i26
ST-E00130:540 1 CTCAGGTGATCCACCCACCTTGTCCTCCCAAAGTGCTGAGATTACAGGCG 50
i i i v i
C AluSx#SINE/Al 69 CTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCG 20
ST-E00130:540 51 TGAGCC 56
C AluSx#SINE/Al 19 TGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.23
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 702 7.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/1 59 151 (0) C L1P3 LINE/L1 (2248) 3898 3806 1397
ANNOTATION EVIDENCE:
702 7.53 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/1 59 151 0 C L1P3_orf2 LINE/L1 1697 1789 1505
702 7.53 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/1 59 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1697 m_b6s551i19
ST-E00130:540 59 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 108
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
ST-E00130:540 109 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGA 151
i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGA 1697
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.87
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0)
+ 1101 6.0 3.2 0.0 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/2 1 151 (0) + L1P3 LINE/L1 3643 3798 (2348) 1398
ANNOTATION EVIDENCE:
1101 5.96 3.20 0.00 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/2 1 151 0 + L1P3_orf2 LINE/L1 1534 1689 1605
1101 5.96 3.20 0.00 ST-E00130:540:HVYVWCCXX:2:2119:10125:3102/2 1 151 (0) L1P3_orf2#LINE/L1 1534 1689 (1605) m_b6s551i62
ST-E00130:540 1 GCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAA--GAAAAAGA 48
v --i
L1P3_orf2#LIN 1534 GCCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAAAAAAAGA 1583
ST-E00130:540 49 AAATTTCAGGCCATTATCCGTGATGAACATCGATGTGAAAATCCTCGATA 98
v v i i
L1P3_orf2#LIN 1584 AAATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATCCTCAATA 1633
ST-E00130:540 99 AAATACTGGCAAACTGAATCCAGCA---CATCAAAACGCTTATCCACCAC 145
i --- v
L1P3_orf2#LIN 1634 AAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCAC 1683
ST-E00130:540 146 TATCAA 151
v
L1P3_orf2#LIN 1684 GATCAA 1689
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 409 10.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/1 1 56 (95) C AluSx SINE/Alu (243) 69 14 1399
ANNOTATION EVIDENCE:
409 10.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/1 1 56 95 C AluSx SINE/Alu 14 69 243
409 10.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/1 1 56 (95) C AluSx#SINE/Alu (243) 69 14 m_b6s357i27
ST-E00130:540 1 CTCAGGTGATCCACCCACCTTGTCCTCCCAAAGTGCTGAGATTACAGGCG 50
i i i v i
C AluSx#SINE/Al 69 CTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCG 20
ST-E00130:540 51 CGAGCC 56
i
C AluSx#SINE/Al 19 TGAGCC 14
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 6.18
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 681 8.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/1 59 151 (0) C L1P3 LINE/L1 (2248) 3898 3806 1400
ANNOTATION EVIDENCE:
681 8.60 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/1 59 151 0 C L1P3_orf2 LINE/L1 1697 1789 1505
681 8.60 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/1 59 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1697 m_b6s551i20
ST-E00130:540 59 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 108
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
ST-E00130:540 109 ATTGATTGGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGA 151
v i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGA 1697
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.03
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0)
+ 1101 6.0 3.2 0.0 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/2 1 151 (0) + L1P3 LINE/L1 3643 3798 (2348) 1401
ANNOTATION EVIDENCE:
1101 5.96 3.20 0.00 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/2 1 151 0 + L1P3_orf2 LINE/L1 1534 1689 1605
1101 5.96 3.20 0.00 ST-E00130:540:HVYVWCCXX:2:2119:9973:2381/2 1 151 (0) L1P3_orf2#LINE/L1 1534 1689 (1605) m_b6s551i63
ST-E00130:540 1 GCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAA--GAAAAAGA 48
v --i
L1P3_orf2#LIN 1534 GCCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAAAAAAAGA 1583
ST-E00130:540 49 AAATTTCAGGCCATTATCCGTGATGAACATCGATGTGAAAATCCTCGATA 98
v v i i
L1P3_orf2#LIN 1584 AAATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATCCTCAATA 1633
ST-E00130:540 99 AAATACTGGCAAACTGAATCCAGCA---CATCAAAACGCTTATCCACCAC 145
i --- v
L1P3_orf2#LIN 1634 AAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCAC 1683
ST-E00130:540 146 TATCAA 151
v
L1P3_orf2#LIN 1684 GATCAA 1689
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 261 26.2 7.4 0.8 ST-E00130:540:HVYVWCCXX:2:2120:30442:16990/1 2 146 (5) C L1ME4c LINE/L1 (297) 5827 5672 1402
ANNOTATION EVIDENCE:
261 26.19 7.35 0.79 ST-E00130:540:HVYVWCCXX:2:2120:30442:16990/1 2 128 23 C L1ME4a_3end LINE/L1 439 574 297
261 26.19 7.35 0.79 ST-E00130:540:HVYVWCCXX:2:2120:30442:16990/1 2 128 (23) C L1ME4a_3end#LINE/L1 (297) 574 439 m_b2s551i21
ST-E00130:540 2 CATACTTTTTAATGGCTTCACCATTTTTC--TGTCATAAA--TACCATAA 47
?v v iv v i --i - ii --
C L1ME4a_3end#L 574 CATNATTTTTAATGGCTGCATAATATTCCATCGT-ATGGATGTACCATAA 526
ST-E00130:540 48 TTTACTTGAC--ATTTTTTATTGTCAGAAATTTAGATTCTTTTCTATTTT 95
i i --? iiii ii v i v i v
C L1ME4a_3end#L 525 TTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476
ST-E00130:540 96 C--CTACAATAAACATTATTGCAATGATCAT--TTGT 128
i-- iv i v ii i v --
C L1ME4a_3end#L 475 TCGCTATTATAAATAATGCTGCGATGAACATCCTTGT 439
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.14
Transitions / transversions = 2.10 (21/10)
Gap_init rate = 0.05 (6 / 126), avg. gap size = 1.83 (11 / 6)
249 26.62 7.95 0.71 ST-E00130:540:HVYVWCCXX:2:2120:30442:16990/1 7 146 5 C L1ME4c_3end LINE/L1 419 569 261
249 26.62 7.95 0.71 ST-E00130:540:HVYVWCCXX:2:2120:30442:16990/1 7 146 (5) C L1ME4c_3end#LINE/L1 (261) 569 419 m_b2s551i22
ST-E00130:540 7 TTTTTAATGGCTTCACCATTTTTCTGTC--ATAAA--TACCATAATTTAC 52
v iv - v ii --i ?i --
C L1ME4c_3end#L 569 TTTTTAATGGCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTAC 521
ST-E00130:540 53 TTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTTTCTATTTTC--CT 98
i - -iii ii v i v i v i--
C L1ME4c_3end#L 520 TTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCT 471
ST-E00130:540 99 ACAATAAACATTATTGCAATGATCATT----TGTCTAAGGGTTTTTTTTT 144
iv i viii v i---- iv vi v ii
C L1ME4c_3end#L 470 ATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTT 421
ST-E00130:540 145 CT 146
C L1ME4c_3end#L 420 CT 419
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.04
Transitions / transversions = 2.00 (24/12)
Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.86 (13 / 7)
+ 327 22.6 12.5 0.0 ST-E00130:540:HVYVWCCXX:2:2121:6370:36293/2 3 86 (65) C L1MC4 LINE/L1 (513) 7529 7416 1403
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 ST-E00130:540:HVYVWCCXX:2:2121:6370:36293/2 3 86 65 C L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 ST-E00130:540:HVYVWCCXX:2:2121:6370:36293/2 3 86 (65) C L1MC4a_3end#LINE/L1 (371) 2258 2163 m_b3s551i135
ST-E00130:540 3 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 47
iiv i i i i i -----
C L1MC4a_3end#L 2258 GTCCCTCAATTTGGGTTTGTCTGATGTTTTCTCATGATTAGATTGAGGTT 2209
ST-E00130:540 48 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT----TCCTCTTCT 86
i --- i i iiii i i ---- v i
C L1MC4a_3end#L 2208 ATGCATTTTTGGCAAGAATACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 4.00 (12 / 3)
327 22.67 9.64 0.00 ST-E00130:540:HVYVWCCXX:2:2121:6370:36293/2 3 77 74 C L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 ST-E00130:540:HVYVWCCXX:2:2121:6370:36293/2 3 77 (74) C L1MC4_3end#LINE/L1 (513) 2276 2194 m_b3s551i136
ST-E00130:540 3 GTCCCTTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TT 47
iiv i i i i -----
C L1MC4_3end#LI 2276 GTCCCTCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTT 2227
ST-E00130:540 48 ATAC---TTTGACGAGAATGTTGCAAAAGTAAT 77
i --- i ii iiii i i
C L1MC4_3end#LI 2226 ATGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 574 19.6 7.4 0.0 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/1 1 112 (39) C L1MC4 LINE/L1 (160) 7882 7762 1404
ANNOTATION EVIDENCE:
574 19.64 7.44 0.00 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/1 1 112 39 C L1MC4_3end LINE/L1 2509 2629 160
574 19.64 7.44 0.00 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/1 1 112 (39) C L1MC4_3end#LINE/L1 (160) 2629 2509 m_b3s551i34
ST-E00130:540 1 GAGATGAAATCGCACACGTGATGCTCCTT---------ATACTTCAGTGT 41
vv i i v i ? i ---------
C L1MC4_3end#LI 2629 GAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAATACTTCAGTGT 2580
ST-E00130:540 42 ATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCAT 91
i i i iv ii iiv i i i
C L1MC4_3end#LI 2579 GTATTTCCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTAT 2530
ST-E00130:540 92 CAAAATCAGGAAGTTAACATT 112
i
C L1MC4_3end#LI 2529 CAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.63
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 9.00 (9 / 1)
+ 463 18.4 5.8 0.0 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/2 14 111 (40) + L1MC4 LINE/L1 7546 7649 (393) 1405
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/2 14 111 40 + L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/2 14 111 (40) L1MC4_3end#LINE/L1 2293 2396 (393) m_b3s551i84
ST-E00130:540 14 GACCTGTACTATTCAAATATATGAAGGTCATGATAAATAAAAAAA----- 58
i v v i v ? v i i i -----
L1MC4_3end#LI 2293 GGCCTGTACTCTTCAAAAATGTCAANGTCATGAAAGACAAAGAAAGACTG 2342
ST-E00130:540 59 -AGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 107
-i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
ST-E00130:540 108 AATG 111
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 3.00 (6 / 2)
+ 265 8.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/2 116 151 (0) + L1MC4 LINE/L1 7762 7797 (245) 1405
ANNOTATION EVIDENCE:
265 8.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/2 116 151 0 + L1MC4_3end LINE/L1 2509 2544 245
265 8.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2122:4300:22581/2 116 151 (0) L1MC4_3end#LINE/L1 2509 2544 (245) m_b3s551i85
ST-E00130:540 116 AATGTTAACTTCCTGATTTTGATGATTATACTGTGG 151
i i i
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGG 2544
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.12
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 543 17.6 0.0 1.8 ST-E00130:540:HVYVWCCXX:2:2122:8998:64615/1 42 151 (0) C AluSx SINE/Alu (8) 304 197 1406
ANNOTATION EVIDENCE:
543 17.59 0.00 1.82 ST-E00130:540:HVYVWCCXX:2:2122:8998:64615/1 42 151 0 C AluSx SINE/Alu 197 304 8
543 17.59 0.00 1.82 ST-E00130:540:HVYVWCCXX:2:2122:8998:64615/1 42 151 (0) C AluSx#SINE/Alu (8) 304 197 m_b2s357i10
ST-E00130:540 42 TTTTTTTTTTTTTTTTTTTTTTTAGACAGAGTCTCGCTTCGTCAAACCCC 91
v i ii i-- v
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG--CCCA 257
ST-E00130:540 92 GGCTGGCGTGCAGTGGCCTGATTTCAGCTCCCTGCAATCTCTTCCCCCTG 141
v vi i i v i iv i i
C AluSx#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCG 207
ST-E00130:540 142 TGTTCAAGTG 151
v i
C AluSx#SINE/Al 206 GGTTCAAGCG 197
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 12.81
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2)
+ 714 12.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2122:8998:64615/2 50 151 (0) + AluSx SINE/Alu 1 102 (210) 1407
ANNOTATION EVIDENCE:
714 12.75 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2122:8998:64615/2 50 151 0 + AluSx SINE/Alu 1 102 210
714 12.75 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2122:8998:64615/2 50 151 (0) AluSx#SINE/Alu 1 102 (210) m_b2s357i44
ST-E00130:540 50 GGCTGGGCACAGTGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 99
i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 100 GCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACAT 149
v i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 150 GG 151
AluSx#SINE/Al 101 GG 102
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.89
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.0 (0 / 0)
+ 1036 10.7 0.7 0.0 ST-E00130:540:HVYVWCCXX:2:2123:7364:44345/2 1 140 (11) C AluY SINE/Alu (170) 141 1 1408
ANNOTATION EVIDENCE:
1036 10.71 0.70 0.00 ST-E00130:540:HVYVWCCXX:2:2123:7364:44345/2 1 140 11 C AluY SINE/Alu 1 141 170
1036 10.71 0.70 0.00 ST-E00130:540:HVYVWCCXX:2:2123:7364:44345/2 1 140 (11) C AluY#SINE/Alu (170) 141 1 m_b2s357i81
ST-E00130:540 1 CCCATCTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAG 49
iv - i i ii
C AluY#SINE/Alu 141 CCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAG 92
ST-E00130:540 50 CCAGGATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCCTTGGCCTCC 99
i i v i
C AluY#SINE/Alu 91 CCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCC 42
ST-E00130:540 100 CAAAGTGCTGAGATTACAAGCGTGAGCCACCATGCCTGGCC 140
i i ii i
C AluY#SINE/Alu 41 CAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.13
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.01 (1 / 139), avg. gap size = 1.00 (1 / 1)
+ 653 20.0 6.2 0.7 ST-E00130:540:HVYVWCCXX:2:2124:25631:54576/2 1 136 (15) + L1MC4 LINE/L1 7768 7911 (131) 1409
ANNOTATION EVIDENCE:
653 20.00 6.25 0.74 ST-E00130:540:HVYVWCCXX:2:2124:25631:54576/2 1 136 15 + L1MC4_3end LINE/L1 2515 2658 131
653 20.00 6.25 0.74 ST-E00130:540:HVYVWCCXX:2:2124:25631:54576/2 1 136 (15) L1MC4_3end#LINE/L1 2515 2658 (131) m_b3s551i23
ST-E00130:540 1 AACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGTATCCTT 50
i i i i vii ii vi i
L1MC4_3end#LI 2515 AATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAATGTCCTT 2564
ST-E00130:540 51 GTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCATCACGT 91
i i --------- i ? i
L1MC4_3end#LI 2565 GTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCATNATGT 2614
ST-E00130:540 92 GTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTAT 136
v i i vv - i vi i i
L1MC4_3end#LI 2615 CTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.37
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 135), avg. gap size = 5.00 (10 / 2)
+ 1083 8.6 1.9 0.0 ST-E00130:540:HVYVWCCXX:2:2203:30797:68658/1 1 151 (0) C L1P3 LINE/L1 (2266) 3880 3727 1410
ANNOTATION EVIDENCE:
1083 8.61 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:2203:30797:68658/1 1 151 0 C L1P3_orf2 LINE/L1 1618 1771 1523
1083 8.61 1.95 0.00 ST-E00130:540:HVYVWCCXX:2:2203:30797:68658/1 1 151 (0) C L1P3_orf2#LINE/L1 (1523) 1771 1618 m_b6s551i43
ST-E00130:540 1 CATTCGTTCTGTTTATGTGATGGATTATGTTTCTTGATTTGTGTATGCTG 50
v i v i i
C L1P3_orf2#LIN 1771 CATTGGTTCTGTTTATGTGATGGATTACGTTTATTGATTTGCGTATGTTG 1722
ST-E00130:540 51 AATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGGTGGATAAG 100
i i i v
C L1P3_orf2#LIN 1721 AACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGGTGGATAAG 1672
ST-E00130:540 101 CGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATCGAGGATTT 147
v --- i i
C L1P3_orf2#LIN 1671 CTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGGATTT 1622
ST-E00130:540 148 TCAC 151
i
C L1P3_orf2#LIN 1621 TCGC 1618
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.86
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1292 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2203:30797:68658/2 1 151 (0) + L1P3 LINE/L1 3455 3605 (2541) 1411
ANNOTATION EVIDENCE:
1292 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2203:30797:68658/2 1 151 0 + L1P3_orf2 LINE/L1 1346 1496 1798
1292 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2203:30797:68658/2 1 151 (0) L1P3_orf2#LINE/L1 1346 1496 (1798) m_b6s551i120
ST-E00130:540 1 TGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTA 50
L1P3_orf2#LIN 1346 TGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGCCTA 1395
ST-E00130:540 51 CCAACCAAAAAAAGCACAGGACCAGAGGGATTCACAGCCGAATTCTACCA 100
v v
L1P3_orf2#LIN 1396 CCAACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCA 1445
ST-E00130:540 101 GGGGTACAACGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAA 150
i v
L1P3_orf2#LIN 1446 GAGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAAACAA 1495
ST-E00130:540 151 T 151
L1P3_orf2#LIN 1496 T 1496
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 856 13.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2204:11688:22968/2 3 122 (29) C AluSx SINE/Alu (192) 120 1 1412
ANNOTATION EVIDENCE:
856 13.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2204:11688:22968/2 3 122 29 C AluSx SINE/Alu 1 120 192
856 13.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2204:11688:22968/2 3 122 (29) C AluSx#SINE/Alu (192) 120 1 m_b2s357i38
ST-E00130:540 3 AATAGAGACAAGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCCGA 52
i ii i i
C AluSx#SINE/Al 120 AGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGA 71
ST-E00130:540 53 CCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTGCTGAGATTACAGAT 102
i i v v v i ii
C AluSx#SINE/Al 70 CCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
ST-E00130:540 103 GTGAGCCACTGTGCCCAGCC 122
i i i
C AluSx#SINE/Al 20 GTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.63
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0)
+ 1167 6.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2206:24596:65160/2 3 151 (0) C L1P3 LINE/L1 (3118) 3028 2880 1413
ANNOTATION EVIDENCE:
1167 6.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2206:24596:65160/2 3 151 0 C L1P3_orf2 LINE/L1 771 919 2375
1167 6.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2206:24596:65160/2 3 151 (0) C L1P3_orf2#LINE/L1 (2375) 919 771 m_b7s551i32
ST-E00130:540 3 TCCTGTGGGCATTTAGTGCTATAAGTTTCCCTCTAAACACTGCTTTAGCT 52
? i
C L1P3_orf2#LIN 919 TCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCT 870
ST-E00130:540 53 GTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGGTTTCAAA 102
i i
C L1P3_orf2#LIN 869 GTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGGTTTCAAA 820
ST-E00130:540 103 GAACTTACTTATTTCTGCCTTCATTTCATTATTTACCTAGTATTCATTC 151
?i v i i v
C L1P3_orf2#LIN 819 GAACTTNTTTATTTCTGCCTTAATTTCGTTATTTACCCAGTAGTCATTC 771
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.36
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1286 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2207:11627:53522/1 1 151 (0) C L1P1 LINE/L1 (1116) 5030 4880 1414
ANNOTATION EVIDENCE:
1286 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2207:11627:53522/1 1 151 0 C L1P1_orf2 LINE/L1 2771 2921 373
1286 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2207:11627:53522/1 1 151 (0) C L1P1_orf2#LINE/L1 (373) 2921 2771 m_b1s551i9
ST-E00130:540 1 ATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTT 50
i i
C L1P1_orf2#LIN 2921 ATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTT 2872
ST-E00130:540 51 TCTATCAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTA 100
v v
C L1P1_orf2#LIN 2871 TGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTA 2822
ST-E00130:540 101 GCCAGTTTTCCCAGCACCATGTATTAAATAGGGAATCCTTTCCCCATTGC 150
v
C L1P1_orf2#LIN 2821 GCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGC 2772
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 2771 T 2771
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.77
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1139 9.4 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2207:9151:65441/2 2 151 (0) + AluSx SINE/Alu 100 248 (64) 1415
ANNOTATION EVIDENCE:
1139 9.39 0.00 0.67 ST-E00130:540:HVYVWCCXX:2:2207:9151:65441/2 2 151 0 + AluSx SINE/Alu 100 248 64
1139 9.39 0.00 0.67 ST-E00130:540:HVYVWCCXX:2:2207:9151:65441/2 2 151 (0) AluSx#SINE/Alu 100 248 (64) m_b2s356i71
ST-E00130:540 2 TGGTGAAACCCCATCTCTACTAAAAACACAAAAATTAGATGGGCGTGGTG 51
i i vi
AluSx#SINE/Al 100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTG 149
ST-E00130:540 52 GCGTGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGC 101
i i i iv
AluSx#SINE/Al 150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199
ST-E00130:540 102 ATGAACCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCA 151
v i - i ii
AluSx#SINE/Al 200 TTGAACCCGGG-AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.37
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 330 27.1 3.5 0.0 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/1 24 145 (6) C MIRb SINE/MIR (75) 187 60 1416
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/1 24 145 6 C MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/1 24 145 (6) C MIR#SINE/MIR (75) 187 60 m_b6s601i49
ST-E00130:540 24 TTAATTCTT---ATACTTCTGTCACTTAGATTCTATTATTTCCTTCAATT 70
i i--- i vii i v vv i v vi ii v
C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTT 138
ST-E00130:540 71 TATAAATGA--AAACTGTGACTTAGTGAGGTAAAGTAACTTGCTT-ATGC 117
i i -- v i vi v v ii- v i
C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88
ST-E00130:540 118 CACAGAGCTAACAAGTGGTTGACTCGAG 145
v ii iv vi i
C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAGCCGGG 60
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/1 54 145 6 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/1 54 145 (6) C MIRb#SINE/MIR (107) 161 67 m_b6s601i50
ST-E00130:540 54 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 101
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
ST-E00130:540 102 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 145
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 16 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/2 1 20 (131) + (A)n Simple_repeat 1 20 (0) 1417
ANNOTATION EVIDENCE:
16 5.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/2 1 20 131 + (A)n Simple_repeat 1 20 0
16 5.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2208:22830:50428/2 1 20 (131) (A)n#Simple_repeat 1 20 (0) m_b6s252i6
ST-E00130:540 1 AAAAAAAAAAAAAAAAAGAA 20
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 1293 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2209:11261:46349/1 1 151 (0) + L1P1 LINE/L1 5180 5330 (816) 1418
ANNOTATION EVIDENCE:
1293 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2209:11261:46349/1 1 151 0 + L1P1_orf2 LINE/L1 3071 3221 73
1293 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2209:11261:46349/1 1 151 (0) L1P1_orf2#LINE/L1 3071 3221 (73) m_b1s551i134
ST-E00130:540 1 AAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTC 50
i
L1P1_orf2#LIN 3071 AAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTC 3120
ST-E00130:540 51 GCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACT 100
L1P1_orf2#LIN 3121 GCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACT 3170
ST-E00130:540 101 CAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGA 150
L1P1_orf2#LIN 3171 CAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGA 3220
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3221 A 3221
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1329 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2209:11261:46349/2 1 151 (0) C L1P1 LINE/L1 (690) 5465 5315 1419
ANNOTATION EVIDENCE:
1329 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2209:11261:46349/2 1 151 0 C L1PA2_3end LINE/L1 62 212 690
1329 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2209:11261:46349/2 1 151 (0) C L1PA2_3end#LINE/L1 (690) 212 62 m_b1s551i201
ST-E00130:540 1 ATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTC 50
C L1PA2_3end#LI 212 ATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTC 163
ST-E00130:540 51 TCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCAT 100
C L1PA2_3end#LI 162 TCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCAT 113
ST-E00130:540 101 AAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTG 150
C L1PA2_3end#LI 112 AAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTG 63
ST-E00130:540 151 A 151
C L1PA2_3end#LI 62 A 62
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 909 13.2 0.0 2.2 ST-E00130:540:HVYVWCCXX:2:2209:13108:6337/2 13 151 (0) + AluY SINE/Alu 1 136 (175) 1420
ANNOTATION EVIDENCE:
909 13.24 0.00 2.16 ST-E00130:540:HVYVWCCXX:2:2209:13108:6337/2 13 151 0 + AluY SINE/Alu 1 136 175
909 13.24 0.00 2.16 ST-E00130:540:HVYVWCCXX:2:2209:13108:6337/2 13 151 (0) AluY#SINE/Alu 1 136 (175) m_b5s356i30
ST-E00130:540 13 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 62
i i iv i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 63 GGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACGT 112
i i -- v i i v i ii
AluY#SINE/Alu 51 GGCGGGCGGATCAC--GAGGTCAGGAGATCGAGACCATCCTGGCTAACAC 98
ST-E00130:540 113 GTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAG 151
v i -
AluY#SINE/Alu 99 GGTGAAACCCCGTCTCTACTAAAAATACAAAAAA-TTAG 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.95
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.00 (3 / 3)
+ 1149 8.7 0.7 0.7 ST-E00130:540:HVYVWCCXX:2:2209:17076:57477/1 1 151 (0) + AluY SINE/Alu 104 254 (57) 1421
ANNOTATION EVIDENCE:
1149 8.67 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2209:17076:57477/1 1 151 0 + AluY SINE/Alu 104 254 57
1149 8.67 0.66 0.66 ST-E00130:540:HVYVWCCXX:2:2209:17076:57477/1 1 151 (0) AluY#SINE/Alu 104 254 (57) m_b2s356i73
ST-E00130:540 1 AACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGGCGGG 49
i i - vi
AluY#SINE/Alu 104 AACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGG 153
ST-E00130:540 50 CGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCATGAA 99
i i i
AluY#SINE/Alu 154 CGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAA 203
ST-E00130:540 100 CCTGGGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCATTCCA 149
i - i v ii i
AluY#SINE/Alu 204 CCCGGG-AGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 252
ST-E00130:540 150 GC 151
AluY#SINE/Alu 253 GC 254
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 485 7.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2209:17076:57477/2 89 151 (0) C AluSx SINE/Alu (14) 298 236 1422
ANNOTATION EVIDENCE:
485 7.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2209:17076:57477/2 89 151 0 C AluSx SINE/Alu 236 298 14
485 7.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2209:17076:57477/2 89 151 (0) C AluSx#SINE/Alu (14) 298 236 m_b2s357i113
ST-E00130:540 89 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 138
v i i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
ST-E00130:540 139 TGCAGTGGCATGA 151
ii
C AluSx#SINE/Al 248 TGCAGTGGCGCGA 236
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.29
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 1092 9.6 0.0 1.4 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/1 1 148 (3) + AluSx SINE/Alu 159 304 (8) 1423
ANNOTATION EVIDENCE:
1092 9.59 0.00 1.35 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/1 1 148 3 + AluSx SINE/Alu 159 304 8
1092 9.59 0.00 1.35 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/1 1 148 (3) AluSx#SINE/Alu 159 304 (8) m_b2s357i15
ST-E00130:540 1 TGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCA 50
i i i i i
AluSx#SINE/Al 159 TGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCG 208
ST-E00130:540 51 GGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTG 100
i i i ii
AluSx#SINE/Al 209 GGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258
ST-E00130:540 101 GGTTTGACGAAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA 148
--i ii i
AluSx#SINE/Al 259 GG--CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.21
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 400 3.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 1 52 (99) + L1PA2 LINE/L1 6102 6153 (2) 1424
ANNOTATION EVIDENCE:
400 3.85 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 1 52 99 + L1PA2_3end LINE/L1 849 900 2
400 3.85 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 1 52 (99) L1PA2_3end#LINE/L1 849 900 (2) m_b1s551i472
ST-E00130:540 1 CTGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAAT 50
i v
L1PA2_3end#LI 849 CTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAA 898
ST-E00130:540 51 AA 52
L1PA2_3end#LI 899 AA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.95
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 46 134 (17) C L1M5 LINE/L1 (293) 5831 5741 1425 *
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 46 134 17 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 46 134 (17) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i473
ST-E00130:540 46 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 95
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 96 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 134
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 67 134 17 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:11617:34061/2 67 134 (17) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i474
ST-E00130:540 67 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 116
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 117 CTATTGTTGGACATTTAG 134
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1317 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2211:13819:66250/1 1 151 (0) C L1P1 LINE/L1 (369) 5786 5636 1426
ANNOTATION EVIDENCE:
1317 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:13819:66250/1 1 151 0 C L1PA2_3end LINE/L1 383 533 369
1317 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:13819:66250/1 1 151 (0) C L1PA2_3end#LINE/L1 (369) 533 383 m_b1s551i314
ST-E00130:540 1 ATGTGCCACAGTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTG 50
v
C L1PA2_3end#LI 533 ATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTG 484
ST-E00130:540 51 GTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGC 100
i
C L1PA2_3end#LI 483 GTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGC 434
ST-E00130:540 101 ATGTGGCTTTATAGCGGCATGATTTATAGTCCTTTGGGTATATACCCAGT 150
v i
C L1PA2_3end#LI 433 ATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGT 384
ST-E00130:540 151 A 151
C L1PA2_3end#LI 383 A 383
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1341 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2211:13819:66250/2 1 151 (0) + L1P1 LINE/L1 5394 5544 (611) 1427
ANNOTATION EVIDENCE:
1341 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:13819:66250/2 1 151 0 + L1PA2_3end LINE/L1 141 291 611
1341 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:13819:66250/2 1 151 (0) L1PA2_3end#LINE/L1 141 291 (611) m_b1s551i239
ST-E00130:540 1 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 50
L1PA2_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190
ST-E00130:540 51 ACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAAC 100
i
L1PA2_3end#LI 191 ACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAAC 240
ST-E00130:540 101 AGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTG 150
iv
L1PA2_3end#LI 241 AGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTG 290
ST-E00130:540 151 G 151
L1PA2_3end#LI 291 G 291
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 36 67 (84) + (TG)n Simple_repeat 1 32 (0) 1428
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 36 67 84 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 36 67 (84) (TG)n#Simple_repeat 1 32 (0) m_b4s252i14
ST-E00130:540 36 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 67
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 68 80 (71) + (TGTATG)n Simple_repeat 1 41 (0) 1429
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 36 80 71 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 36 80 (71) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i13
ST-E00130:540 36 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 80
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 457 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 95 151 (0) C AluSx SINE/Alu (21) 291 235 1430
ANNOTATION EVIDENCE:
457 5.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 95 151 0 C AluSx SINE/Alu 235 291 21
457 5.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/1 95 151 (0) C AluSx#SINE/Alu (21) 291 235 m_b4s357i3
ST-E00130:540 95 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 144
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 145 GCGCGAT 151
C AluSx#SINE/Al 241 GCGCGAT 235
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.83
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 913 10.9 1.6 0.0 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/2 33 151 (0) + AluSx SINE/Alu 1 121 (191) 1431
ANNOTATION EVIDENCE:
913 10.92 1.65 0.00 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/2 33 151 0 + AluSx SINE/Alu 1 121 191
913 10.92 1.65 0.00 ST-E00130:540:HVYVWCCXX:2:2211:17137:31951/2 33 151 (0) AluSx#SINE/Alu 1 121 (191) m_b4s356i60
ST-E00130:540 33 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 82
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 83 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 130
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 131 GGTGAAACTCCATCTCTACTA 151
i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTA 121
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.09
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 2.00 (2 / 1)
+ 218 29.2 15.6 0.0 ST-E00130:540:HVYVWCCXX:2:2212:20628:47175/2 20 149 (2) C MIR SINE/MIR (0) 262 109 1432
ANNOTATION EVIDENCE:
218 29.23 15.58 0.00 ST-E00130:540:HVYVWCCXX:2:2212:20628:47175/2 20 149 2 C MIR SINE/MIR 109 262 0
218 29.23 15.58 0.00 ST-E00130:540:HVYVWCCXX:2:2212:20628:47175/2 20 149 (2) C MIR#SINE/MIR (0) 262 109 m_b6s601i24
ST-E00130:540 20 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 62
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 63 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 97
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 98 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 145
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
ST-E00130:540 146 TGAG 149
v
C MIR#SINE/MIR 112 AGAG 109
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.80
Transitions / transversions = 1.53 (23/15)
Gap_init rate = 0.04 (5 / 129), avg. gap size = 4.80 (24 / 5)
+ 920 16.1 0.0 1.3 ST-E00130:540:HVYVWCCXX:2:2212:22901:25095/2 1 151 (0) + AluJb SINE/Alu 41 189 (123) 1433
ANNOTATION EVIDENCE:
920 16.10 0.00 1.32 ST-E00130:540:HVYVWCCXX:2:2212:22901:25095/2 1 151 0 + AluJb SINE/Alu 41 189 123
920 16.10 0.00 1.32 ST-E00130:540:HVYVWCCXX:2:2212:22901:25095/2 1 151 (0) AluJb#SINE/Alu 41 189 (123) m_b5s356i21
ST-E00130:540 1 GGGAGGCCAAGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCC 50
i i ?i i vi i i
AluJb#SINE/Al 41 GGGAGGCCGAGGCGGGNGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCC 90
ST-E00130:540 51 TGGCCAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGC 100
v i vi i v --
AluJb#SINE/Al 91 TGGGCAACATGGCGAAACCCCGTCTCTACAAAAAATACAAAAA--TTAGC 138
ST-E00130:540 101 CAGGCATTGTGGTGGGAGCCTGTAGTCACAGCTACTCTGGAGGCTGAGGT 150
i i v i v v v v i
AluJb#SINE/Al 139 CGGGCGTGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGC 188
ST-E00130:540 151 G 151
AluJb#SINE/Al 189 G 189
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 10.11
Transitions / transversions = 1.56 (14/9)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 546 10.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2212:28696:36223/1 78 151 (0) + AluY SINE/Alu 1 74 (237) 1434
ANNOTATION EVIDENCE:
546 10.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2212:28696:36223/1 78 151 0 + AluY SINE/Alu 1 74 237
546 10.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2212:28696:36223/1 78 151 (0) AluY#SINE/Alu 1 74 (237) m_b2s357i62
ST-E00130:540 78 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 127
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 128 GGCGGGCTGATCATGAGGTCAGGA 151
v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGA 74
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.91
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 16 21.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2212:9120:71787/2 114 145 (6) + A-rich Low_complexity 1 32 (0) 1435
ANNOTATION EVIDENCE:
16 21.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2212:9120:71787/2 114 145 6 + (A)n Simple_repeat 1 32 0
16 21.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2212:9120:71787/2 114 145 (6) (A)n#Simple_repeat 1 32 (0) m_b2s252i3
ST-E00130:540 114 AAAAATAAAAAAAAAATAAAGAATATAAGAAA 145
v v i v v i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 34 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/1 7 38 (113) + (T)n Simple_repeat 1 32 (0) 1436
ANNOTATION EVIDENCE:
34 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/1 7 38 113 + (T)n Simple_repeat 1 32 0
34 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/1 7 38 (113) (T)n#Simple_repeat 1 32 (0) c_b6s251i6
ST-E00130:540 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 614 9.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/2 1 86 (65) + L1P3 LINE/L1 3813 3898 (2248) 1437
ANNOTATION EVIDENCE:
614 9.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/2 1 86 65 + L1P3_orf2 LINE/L1 1704 1789 1505
614 9.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/2 1 86 (65) L1P3_orf2#LINE/L1 1704 1789 (1505) m_b6s551i16
ST-E00130:540 1 TGGGACGCAAGGCTGATTCAGCATACACAAATCAATAAACATAATCCCTC 50
i i i i i v
L1P3_orf2#LIN 1704 TGGGATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAATCCATC 1753
ST-E00130:540 51 ACATAAACAGAACGAATGACAAAAACTACATGATTA 86
v i
L1P3_orf2#LIN 1754 ACATAAACAGAACCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.64
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)
+ 481 7.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/2 89 151 (0) + AluSx SINE/Alu 14 76 (236) 1438
ANNOTATION EVIDENCE:
481 7.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/2 89 151 0 + AluSx SINE/Alu 14 76 236
481 7.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:20983:46947/2 89 151 (0) AluSx#SINE/Alu 14 76 (236) m_b6s357i23
ST-E00130:540 89 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACCAGGTGGGTGGATCA 138
i v v i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 139 CCTGAGGTCAGGA 151
AluSx#SINE/Al 64 CCTGAGGTCAGGA 76
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 1234 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2213:28016:25341/1 1 151 (0) C L1P3 LINE/L1 (3009) 3137 2987 1439
ANNOTATION EVIDENCE:
1234 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:28016:25341/1 1 151 0 C L1P3_orf2 LINE/L1 878 1028 2266
1234 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:28016:25341/1 1 151 (0) C L1P3_orf2#LINE/L1 (2266) 1028 878 m_b6s551i269
ST-E00130:540 1 ATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTG 50
C L1P3_orf2#LIN 1028 ATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTG 979
ST-E00130:540 51 CTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTTT 100
i
C L1P3_orf2#LIN 978 CTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTT 929
ST-E00130:540 101 CCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACT 150
i v ?
C L1P3_orf2#LIN 928 CCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACT 879
ST-E00130:540 151 G 151
C L1P3_orf2#LIN 878 G 878
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 327 22.6 12.5 0.0 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/1 61 144 (7) + L1MC4 LINE/L1 7416 7529 (513) 1440
ANNOTATION EVIDENCE:
317 22.62 12.50 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/1 61 144 7 + L1MC4a_3end LINE/L1 2163 2258 371
317 22.62 12.50 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/1 61 144 (7) L1MC4a_3end#LINE/L1 2163 2258 (371) m_b3s551i133
ST-E00130:540 61 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 101
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
ST-E00130:540 102 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGGAC 144
--- i i i i i vii
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAATTGAGGGAC 2258
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.05 (4 / 83), avg. gap size = 3.00 (12 / 4)
327 22.67 9.64 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/1 70 144 7 + L1MC4_3end LINE/L1 2194 2276 513
327 22.67 9.64 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/1 70 144 (7) L1MC4_3end#LINE/L1 2194 2276 (513) m_b3s551i134
ST-E00130:540 70 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 111
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
ST-E00130:540 112 AAGGAAACATCAGACAAACTCAGAGCAAGGGAC 144
i i i vii
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGGAC 2276
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.00 (8 / 2)
+ 504 16.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/2 2 84 (67) C L1MC4 LINE/L1 (198) 7844 7762 1441
ANNOTATION EVIDENCE:
504 16.87 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/2 2 84 67 C L1MC4_3end LINE/L1 2509 2591 198
504 16.87 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/2 2 84 (67) C L1MC4_3end#LINE/L1 (198) 2591 2509 m_b3s551i58
ST-E00130:540 2 ATACTTCAGTGTATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCA 51
i i i iv ii iiv i
C L1MC4_3end#LI 2591 ATACTTCAGTGTGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCA 2542
ST-E00130:540 52 CAGTATAATCATCAAAATCAGGAAGTTAACATT 84
i i i
C L1MC4_3end#LI 2541 CAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.02
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 313 14.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/2 89 142 (9) C L1MC4 LINE/L1 (393) 7649 7596 1441
ANNOTATION EVIDENCE:
313 14.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/2 89 142 9 C L1MC4_3end LINE/L1 2343 2396 393
313 14.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2213:8826:24866/2 89 142 (9) C L1MC4_3end#LINE/L1 (393) 2396 2343 m_b3s551i59
ST-E00130:540 89 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 138
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 139 TCTT 142
i
C L1MC4_3end#LI 2346 TCCT 2343
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.46
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 1274 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2214:29021:50920/1 1 151 (0) C L1P1 LINE/L1 (909) 5237 5087 1442
ANNOTATION EVIDENCE:
1274 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2214:29021:50920/1 1 151 0 C L1P1_orf2 LINE/L1 2978 3128 166
1274 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2214:29021:50920/1 1 151 (0) C L1P1_orf2#LINE/L1 (166) 3128 2978 m_b1s551i94
ST-E00130:540 1 TAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGAT 50
i
C L1P1_orf2#LIN 3128 TAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGAT 3079
ST-E00130:540 51 GGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATT 100
C L1P1_orf2#LIN 3078 GGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATT 3029
ST-E00130:540 101 TGTCAATTCTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAG 150
i v
C L1P1_orf2#LIN 3028 TGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAG 2979
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 2978 T 2978
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 632 15.7 0.0 5.7 ST-E00130:540:HVYVWCCXX:2:2216:13058:67076/1 30 151 (0) C AluSx SINE/Alu (8) 304 190 1443
ANNOTATION EVIDENCE:
632 15.65 0.00 5.74 ST-E00130:540:HVYVWCCXX:2:2216:13058:67076/1 30 151 0 C AluSx SINE/Alu 190 304 8
632 15.65 0.00 5.74 ST-E00130:540:HVYVWCCXX:2:2216:13058:67076/1 30 151 (0) C AluSx#SINE/Alu (8) 304 190 m_b5s357i19
ST-E00130:540 30 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 79
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 80 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 129
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
ST-E00130:540 130 TAGTAGGTTCAAGCAATTGTCC 151
vvii i v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCC 190
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.75
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.00 (7 / 7)
+ 236 10.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2216:13058:67076/2 119 148 (3) C SVA_A Retroposon/SVA (951) 436 407 1444
ANNOTATION EVIDENCE:
236 10.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2216:13058:67076/2 119 148 3 C SVA_A Retroposon/SVA 407 436 951
236 10.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2216:13058:67076/2 119 148 (3) C SVA_A#Retroposon/SVA (951) 436 407 m_b5s502i7
ST-E00130:540 119 CTGTAATCCCAACACTTTGGGAGGCCAAGG 148
i i i
C SVA_A#Retropo 436 CTGCAATCCTAGCACTTTGGGAGGCCAAGG 407
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.16
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1292 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2217:20151:25569/1 1 151 (0) + L1PA3 LINE/L1 5796 5945 (210) 1445
ANNOTATION EVIDENCE:
1292 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2217:20151:25569/1 1 151 0 + L1PA3_3end LINE/L1 543 692 210
1292 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2217:20151:25569/1 1 151 (0) L1PA3_3end#LINE/L1 543 692 (210) m_b1s551i371
ST-E00130:540 1 GGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGG 50
-
L1PA3_3end#LI 543 GGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGG 591
ST-E00130:540 51 ACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCGCAAGAAGA 100
i v
L1PA3_3end#LI 592 ACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACA 641
ST-E00130:540 101 AAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAATTGAACAATGA 150
i
L1PA3_3end#LI 642 AAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGA 691
ST-E00130:540 151 G 151
L1PA3_3end#LI 692 G 692
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1155 2.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2217:20151:25569/2 20 151 (0) C L1PA2 LINE/L1 (2) 6153 6022 1446
ANNOTATION EVIDENCE:
1155 2.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2217:20151:25569/2 20 151 0 C L1PA2_3end LINE/L1 769 900 2
1155 2.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2217:20151:25569/2 20 151 (0) C L1PA2_3end#LINE/L1 (2) 900 769 m_b1s551i429
ST-E00130:540 20 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 69
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 70 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 119
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
ST-E00130:540 120 AACTCGTCATCTAGCATTAGGTATATCTCCCA 151
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCTCCCA 769
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.61
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 844 3.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2217:2514:73176/1 53 151 (0) C L1PA2 LINE/L1 (2) 6153 6055 1447
ANNOTATION EVIDENCE:
844 3.03 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2217:2514:73176/1 53 151 0 C L1PA2_3end LINE/L1 802 900 2
844 3.03 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2217:2514:73176/1 53 151 (0) C L1PA2_3end#LINE/L1 (2) 900 802 m_b1s551i445
ST-E00130:540 53 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 102
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 103 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCAC 151
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCAC 802
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.15
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0)
+ 1190 5.3 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2217:2514:73176/2 1 151 (0) + L1PA3 LINE/L1 5788 5937 (218) 1448
ANNOTATION EVIDENCE:
1190 5.34 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2217:2514:73176/2 1 151 0 + L1PA3_3end LINE/L1 535 684 218
1190 5.34 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2217:2514:73176/2 1 151 (0) L1PA3_3end#LINE/L1 535 684 (218) m_b1s551i362
ST-E00130:540 1 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTT 50
L1PA3_3end#LI 535 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTT 584
ST-E00130:540 51 TGTTAGGGACATGGACTAAATTAGAAATCATCATTCTCAGTACACTGTCG 100
- iv i v i
L1PA3_3end#LI 585 TGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCG 633
ST-E00130:540 101 CAAGAAGAAAAAAACAAACACCGCATGTTCTCACTCATAGGTGGGAATTG 150
v v i
L1PA3_3end#LI 634 CAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTG 683
ST-E00130:540 151 A 151
L1PA3_3end#LI 684 A 684
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.54
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1208 4.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2217:30269:33850/1 1 150 (1) C L1PA2 LINE/L1 (175) 5980 5832 1449
ANNOTATION EVIDENCE:
1208 4.70 0.00 0.67 ST-E00130:540:HVYVWCCXX:2:2217:30269:33850/1 1 150 1 C L1PA2_3end LINE/L1 579 727 175
1208 4.70 0.00 0.67 ST-E00130:540:HVYVWCCXX:2:2217:30269:33850/1 1 150 (1) C L1PA2_3end#LINE/L1 (175) 727 579 m_b1s551i384
ST-E00130:540 1 AGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTC 50
C L1PA2_3end#LI 727 AGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTC 678
ST-E00130:540 51 CCACCTATGAGTGAGAACATGCGGTGTTTGGCTTTTTCTTCTTGCGACAG 100
i i v i
C L1PA2_3end#LI 677 CCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAG 628
ST-E00130:540 101 TTTACTGCGAATGATGATTTCCAATTTCATCCATGTCCCTAACAACGAAC 150
v - v i
C L1PA2_3end#LI 627 TTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCT-ACAAAGGAC 579
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 808 15.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2217:30269:33850/2 1 150 (1) + L1P1 LINE/L1 5457 5606 (549) 1450
ANNOTATION EVIDENCE:
808 15.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2217:30269:33850/2 1 150 1 + L1PA3_3end LINE/L1 204 353 549
808 15.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2217:30269:33850/2 1 150 (1) L1PA3_3end#LINE/L1 204 353 (549) m_b1s551i263
ST-E00130:540 1 AGTAAGAATGGCAGTCAGTAAAAAGTCGGGAAACAACAGGGGCTGGAGCG 50
v i v i v v
L1PA3_3end#LI 204 AGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAG 253
ST-E00130:540 51 GATGGGGAGAGATAGGAAATCTGTTACAGTGTTGGTGGGACTATAAAATA 100
v i vv v v i v
L1PA3_3end#LI 254 GATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTA 303
ST-E00130:540 101 GTTCAACCACAAGGGAAGTCAGTGTGGGGAATCCACAGGTAGCTAGAACT 150
iviv v v v v v
L1PA3_3end#LI 304 GTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACT 353
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.17
Transitions / transversions = 0.35 (6/17)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 955 3.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2218:2341:12754/1 1 110 (41) C L1PA2 LINE/L1 (36) 6119 6010 1451
ANNOTATION EVIDENCE:
955 3.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2218:2341:12754/1 1 110 41 C L1PA2_3end LINE/L1 757 866 36
955 3.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2218:2341:12754/1 1 110 (41) C L1PA2_3end#LINE/L1 (36) 866 757 m_b1s551i419
ST-E00130:540 1 CATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTG 50
C L1PA2_3end#LI 866 CATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTG 817
ST-E00130:540 51 GTGTGCTGCACCCACTAACTCGTCATCTAGCATTAGGGATATCTCCCAAT 100
i v
C L1PA2_3end#LI 816 GTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAAT 767
ST-E00130:540 101 GCTATTGCTC 110
iv
C L1PA2_3end#LI 766 GCTATCCCTC 757
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0)
+ 1283 2.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2218:2341:12754/2 1 151 (0) + L1PA3 LINE/L1 5788 5937 (218) 1452
ANNOTATION EVIDENCE:
1283 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2218:2341:12754/2 1 151 0 + L1PA3_3end LINE/L1 535 684 218
1283 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:2:2218:2341:12754/2 1 151 (0) L1PA3_3end#LINE/L1 535 684 (218) m_b1s551i363
ST-E00130:540 1 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTT 50
L1PA3_3end#LI 535 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTT 584
ST-E00130:540 51 TGTTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTGTCG 100
- i
L1PA3_3end#LI 585 TGT-AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCG 633
ST-E00130:540 101 CAAGAAGAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGGATTG 150
v i i
L1PA3_3end#LI 634 CAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTG 683
ST-E00130:540 151 A 151
L1PA3_3end#LI 684 A 684
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.73
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 630 11.2 2.2 0.0 ST-E00130:540:HVYVWCCXX:2:2219:21278:31283/2 1 89 (62) C AluSx SINE/Alu (221) 91 1 1453
ANNOTATION EVIDENCE:
630 11.24 2.20 0.00 ST-E00130:540:HVYVWCCXX:2:2219:21278:31283/2 1 89 62 C AluSx SINE/Alu 1 91 221
630 11.24 2.20 0.00 ST-E00130:540:HVYVWCCXX:2:2219:21278:31283/2 1 89 (62) C AluSx#SINE/Alu (221) 91 1 m_b4s357i57
ST-E00130:540 1 AGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCTTCAGCCTCC 48
v i i-- i i i i
C AluSx#SINE/Al 91 AGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCC 42
ST-E00130:540 49 CAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCC 89
i i i
C AluSx#SINE/Al 41 CAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.30
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 2.00 (2 / 1)
+ 830 9.0 0.0 0.9 ST-E00130:540:HVYVWCCXX:2:2221:11373:44222/1 40 151 (0) C AluY SINE/Alu (14) 297 187 1454
ANNOTATION EVIDENCE:
830 9.01 0.00 0.89 ST-E00130:540:HVYVWCCXX:2:2221:11373:44222/1 40 151 0 C AluY SINE/Alu 187 297 14
830 9.01 0.00 0.89 ST-E00130:540:HVYVWCCXX:2:2221:11373:44222/1 40 151 (0) C AluY#SINE/Alu (14) 297 187 m_b2s356i96
ST-E00130:540 40 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 89
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
ST-E00130:540 90 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 139
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
ST-E00130:540 140 GCCGTTCTCCTG 151
i
C AluY#SINE/Alu 198 GCCATTCTCCTG 187
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.15
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 1.00 (1 / 1)
+ 441 11.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2221:11373:44222/2 91 151 (0) + AluSx SINE/Alu 1 61 (251) 1455
ANNOTATION EVIDENCE:
441 11.48 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2221:11373:44222/2 91 151 0 + AluSx SINE/Alu 1 61 251
441 11.48 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2221:11373:44222/2 91 151 (0) AluSx#SINE/Alu 1 61 (251) m_b2s357i58
ST-E00130:540 91 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 140
i ii i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 141 GGCGGGCTGAT 151
v
AluSx#SINE/Al 51 GGCGGGCGGAT 61
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.83
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 889 10.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:2:2221:15564:24690/1 40 151 (0) + AluY SINE/Alu 1 112 (199) 1456
ANNOTATION EVIDENCE:
889 10.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2221:15564:24690/1 40 151 0 + AluY SINE/Alu 1 112 199
889 10.71 0.00 0.00 ST-E00130:540:HVYVWCCXX:2:2221:15564:24690/1 40 151 (0) AluY#SINE/Alu 1 112 (199) m_b2s356i42
ST-E00130:540 40 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 89
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 90 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTGG 139
v i i ii
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
ST-E00130:540 140 TGAAACCCCATC 151
i
AluY#SINE/Alu 101 TGAAACCCCGTC 112
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
+ 1053 8.8 0.0 0.7 ST-E00130:540:HVYVWCCXX:2:2221:15564:24690/2 1 149 (2) C AluY SINE/Alu (33) 278 131 1457
ANNOTATION EVIDENCE:
1053 8.78 0.00 0.67 ST-E00130:540:HVYVWCCXX:2:2221:15564:24690/2 1 149 2 C AluY SINE/Alu 131 278 33
1053 8.78 0.00 0.67 ST-E00130:540:HVYVWCCXX:2:2221:15564:24690/2 1 149 (2) C AluY#SINE/Alu (33) 278 131 m_b2s357i91
ST-E00130:540 1 ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATCTCGG 50
i ii
C AluY#SINE/Alu 278 ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGG 229
ST-E00130:540 51 CTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGGTCTCCTGCTTCAGC 100
v i - i i iv i
C AluY#SINE/Alu 228 CTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAGC 180
ST-E00130:540 101 CTCCCGAGGAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAATT 149
v iv
C AluY#SINE/Alu 179 CTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATT 131
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.32
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 256 33.6 6.5 2.7 ST-E00130:540:HVYVWCCXX:2:2222:10135:14969/1 1 147 (4) + MIRb SINE/MIR 40 192 (76) 1458
ANNOTATION EVIDENCE:
256 33.56 6.53 2.72 ST-E00130:540:HVYVWCCXX:2:2222:10135:14969/1 1 147 4 + MIRb SINE/MIR 40 192 76
256 33.56 6.53 2.72 ST-E00130:540:HVYVWCCXX:2:2222:10135:14969/1 1 147 (4) MIRb#SINE/MIR 40 192 (76) m_b4s601i30
ST-E00130:540 1 TGAAGTCAAACAGA---AAATTCAAATCCCAGTACCACAGCCT--TAACT 45
i i ---iii i i iv ii vi i -- i
MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89
ST-E00130:540 46 TT----TCTGGTAAAAAACTTGCCTTATGTCATCTAGGGCCTTCGTACCC 91
v ----i -- iiiv v i i v iv - - i iv vi
MIRb#SINE/MIR 90 GTGTGACCT--TGGGCAAGTTACTTAACCTC-TCT-GAGCCTCAGTTTCC 135
ST-E00130:540 92 TCATCAGTAGAGTGAAGATA-TATCACTTACCTGGCCAGATAACTGTGAG 140
v i i ii - vi i v vi i vii
MIRb#SINE/MIR 136 TCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAG 185
ST-E00130:540 141 GATTAGA 147
i
MIRb#SINE/MIR 186 GATTAAA 192
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 45.18
Transitions / transversions = 2.43 (34/14)
Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.75 (14 / 8)
+ 1261 3.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:2:2224:21217:25657/1 1 151 (0) C L1P3 LINE/L1 (2447) 3699 3547 1459
ANNOTATION EVIDENCE:
1261 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:2224:21217:25657/1 1 151 0 C L1P3_orf2 LINE/L1 1438 1590 1704
1261 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:2:2224:21217:25657/1 1 151 (0) C L1P3_orf2#LINE/L1 (1704) 1590 1438 m_b6s551i95
ST-E00130:540 1 GAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAGGATGA 48
i-- v
C L1P3_orf2#LIN 1590 GAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGA 1541
ST-E00130:540 49 TGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTT 98
v i
C L1P3_orf2#LIN 1540 TGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTT 1491
ST-E00130:540 99 TGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTA 148
i
C L1P3_orf2#LIN 1490 TGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTA 1441
ST-E00130:540 149 GAA 151
C L1P3_orf2#LIN 1440 GAA 1438
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 961 6.0 7.4 0.0 ST-E00130:540:HVYVWCCXX:2:2224:21217:25657/2 1 151 (0) + L1P3 LINE/L1 3219 3381 (2765) 1460
ANNOTATION EVIDENCE:
961 5.96 7.36 0.00 ST-E00130:540:HVYVWCCXX:2:2224:21217:25657/2 1 151 0 + L1P3_orf2 LINE/L1 1110 1272 2022
961 5.96 7.36 0.00 ST-E00130:540:HVYVWCCXX:2:2224:21217:25657/2 1 151 (0) L1P3_orf2#LINE/L1 1110 1272 (2022) m_b6s551i186
ST-E00130:540 1 TAACAAAACAGA----CCGCTAGCAAGACTAATAAAGA--------GAGA 38
i ---- v --------
L1P3_orf2#LIN 1110 TAACAAAATAGATAGACCGCTAGCCAGACTAATAAAGAAGAAAAGAGAGA 1159
ST-E00130:540 39 AGAATCAAATAGACTCAATAAAAAATGATAAAGAGGAAAATACCACTGAT 88
v i v vi
L1P3_orf2#LIN 1160 AGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATCACCACTGAT 1209
ST-E00130:540 89 CCCACAGAAATACAAACTACCATCAGAGAATACTATAAATACCTCTATGC 138
i i
L1P3_orf2#LIN 1210 CCCACAGAAATACAAACTACCATCAGAGAATACTATAAACACCTCTACGC 1259
ST-E00130:540 139 AAATAAACTAGAA 151
L1P3_orf2#LIN 1260 AAATAAACTAGAA 1272
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.57
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 205 26.8 1.8 0.0 ST-E00130:540:HVYVWCCXX:2:2224:26697:5475/1 96 151 (0) + MIRb SINE/MIR 67 123 (145) 1461
ANNOTATION EVIDENCE:
205 26.79 1.76 0.00 ST-E00130:540:HVYVWCCXX:2:2224:26697:5475/1 96 151 0 + MIRb SINE/MIR 67 123 145
205 26.79 1.76 0.00 ST-E00130:540:HVYVWCCXX:2:2224:26697:5475/1 96 151 (0) MIRb#SINE/MIR 67 123 (145) m_b6s601i81
ST-E00130:540 96 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 144
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
ST-E00130:540 145 TCACTAA 151
v i
MIRb#SINE/MIR 117 TCTCTGA 123
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.01
Transitions / transversions = 1.50 (9/6)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1)
+ 262 26.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/1 1 67 (84) C L1M5 LINE/L1 (366) 5807 5741 1462
ANNOTATION EVIDENCE:
262 26.87 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/1 1 67 84 C L1ME3A_3end LINE/L1 488 554 366
262 26.87 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/1 1 67 (84) C L1ME3A_3end#LINE/L1 (366) 554 488 m_b1s551i521
ST-E00130:540 1 GCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTAC 50
i v iii i ii i ii iv v i
C L1ME3A_3end#L 554 GTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTAC 505
ST-E00130:540 51 TATTGTTGGACATTTAG 67
i v i
C L1ME3A_3end#L 504 TGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.65
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/1 129 150 (1) + (T)n Simple_repeat 1 22 (0) 1463
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/1 129 150 1 + (T)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/1 129 150 (1) (T)n#Simple_repeat 1 22 (0) m_b1s252i4
ST-E00130:540 129 TTTTTTTTTTTTTTTTTTTTTT 150
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 1217 9.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/2 1 151 (0) + AluSx SINE/Alu 55 205 (107) 1464
ANNOTATION EVIDENCE:
1217 9.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/2 1 151 0 + AluSx SINE/Alu 55 205 107
1217 9.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:23987:49162/2 1 151 (0) AluSx#SINE/Alu 55 205 (107) c_b2s352i1
ST-E00130:540 1 GGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAACATGGTG 50
i i i
AluSx#SINE/Al 55 GGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTG 104
ST-E00130:540 51 AAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGG 100
ii i v i i i v
AluSx#SINE/Al 105 AAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCG 154
ST-E00130:540 101 CACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAA 150
i i i i
AluSx#SINE/Al 155 CGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAA 204
ST-E00130:540 151 C 151
AluSx#SINE/Al 205 C 205
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.39
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 693 19.3 6.0 0.7 ST-E00130:540:HVYVWCCXX:3:1105:9759:58831/1 1 141 (10) + L1MC4 LINE/L1 7763 7911 (131) 1465
ANNOTATION EVIDENCE:
693 19.29 6.04 0.71 ST-E00130:540:HVYVWCCXX:3:1105:9759:58831/1 1 141 10 + L1MC4_3end LINE/L1 2510 2658 131
693 19.29 6.04 0.71 ST-E00130:540:HVYVWCCXX:3:1105:9759:58831/1 1 141 (10) L1MC4_3end#LINE/L1 2510 2658 (131) m_b3s551i26
ST-E00130:540 1 ATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGTA 50
i i i i vii ii vi i
L1MC4_3end#LI 2510 ATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAATG 2559
ST-E00130:540 51 TCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCAT 91
i i --------- i
L1MC4_3end#LI 2560 TCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCAT 2609
ST-E00130:540 92 CACGTGTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTAT 141
? i v i i vv - i vi i i
L1MC4_3end#LI 2610 NATGTCTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.35
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 5.00 (10 / 2)
+ 247 16.2 0.0 22.1 ST-E00130:540:HVYVWCCXX:3:1105:9759:58831/2 57 151 (0) C L1MC4 LINE/L1 (90) 7952 7879 1466
ANNOTATION EVIDENCE:
247 16.22 0.00 22.11 ST-E00130:540:HVYVWCCXX:3:1105:9759:58831/2 57 151 0 C L1MC4_3end LINE/L1 2626 2699 90
247 16.22 0.00 22.11 ST-E00130:540:HVYVWCCXX:3:1105:9759:58831/2 57 151 (0) C L1MC4_3end#LINE/L1 (90) 2699 2626 m_b3s551i3
ST-E00130:540 57 GTTAACGTTTTACCATATTTGCTTAATCATTCCCTCTCTCCACACACACA 106
i i i v i ? ? -----------
C L1MC4_3end#LI 2699 GTTAACATTTTGCCACATTTGCTTTATCATTCTCTNTNT----------- 2661
ST-E00130:540 107 CTCATACGCAGATACACACATCATTTTCTCTGAACCATTTTGAGA 151
------- -- i i iv i -
C L1MC4_3end#LI 2660 -------GC--ATATACATATTTTTTTTTCTGAACCA-TTTGAGA 2626
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.81
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.22 (21 / 94), avg. gap size = 1.00 (21 / 21)
+ 693 19.3 6.0 0.7 ST-E00130:540:HVYVWCCXX:3:1105:9800:59218/1 1 141 (10) + L1MC4 LINE/L1 7763 7911 (131) 1467
ANNOTATION EVIDENCE:
693 19.29 6.04 0.71 ST-E00130:540:HVYVWCCXX:3:1105:9800:59218/1 1 141 10 + L1MC4_3end LINE/L1 2510 2658 131
693 19.29 6.04 0.71 ST-E00130:540:HVYVWCCXX:3:1105:9800:59218/1 1 141 (10) L1MC4_3end#LINE/L1 2510 2658 (131) m_b3s551i27
ST-E00130:540 1 ATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGTA 50
i i i i vii ii vi i
L1MC4_3end#LI 2510 ATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAATG 2559
ST-E00130:540 51 TCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCAT 91
i i --------- i
L1MC4_3end#LI 2560 TCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCAT 2609
ST-E00130:540 92 CACGTGTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTAT 141
? i v i i vv - i vi i i
L1MC4_3end#LI 2610 NATGTCTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.35
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 5.00 (10 / 2)
+ 16 19.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1105:9800:59218/2 97 126 (25) + (CA)n Simple_repeat 1 30 (0) 1468
ANNOTATION EVIDENCE:
16 19.09 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:9800:59218/2 97 126 25 + (CA)n Simple_repeat 1 30 0
16 19.09 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1105:9800:59218/2 97 126 (25) (CA)n#Simple_repeat 1 30 (0) m_b3s252i1
ST-E00130:540 97 CACACACACACTCATACGCAGATACACACA 126
v i i v i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACA 30
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1281 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1106:15189:23653/1 1 151 (0) + L1P1 LINE/L1 4900 5050 (1096) 1469
ANNOTATION EVIDENCE:
1281 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1106:15189:23653/1 1 151 0 + L1P1_orf2 LINE/L1 2791 2941 353
1281 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1106:15189:23653/1 1 151 (0) L1P1_orf2#LINE/L1 2791 2941 (353) m_b1s551i18
ST-E00130:540 1 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 50
L1P1_orf2#LIN 2791 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2840
ST-E00130:540 51 GAAACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAAGATGGA 100
v v i
L1P1_orf2#LIN 2841 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2890
ST-E00130:540 101 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 150
i
L1P1_orf2#LIN 2891 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2940
ST-E00130:540 151 C 151
L1P1_orf2#LIN 2941 C 2941
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1321 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1106:15189:23653/2 1 151 (0) C L1P1 LINE/L1 (849) 5297 5147 1470
ANNOTATION EVIDENCE:
1321 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1106:15189:23653/2 1 151 0 C L1P1_orf2 LINE/L1 3038 3188 106
1321 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1106:15189:23653/2 1 151 (0) C L1P1_orf2#LINE/L1 (106) 3188 3038 m_b1s551i122
ST-E00130:540 1 TTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTT 50
C L1P1_orf2#LIN 3188 TTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTT 3139
ST-E00130:540 51 GTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGT 100
i
C L1P1_orf2#LIN 3138 GTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGT 3089
ST-E00130:540 101 TCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATT 150
C L1P1_orf2#LIN 3088 TCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATT 3039
ST-E00130:540 151 A 151
C L1P1_orf2#LIN 3038 A 3038
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 780 6.4 8.5 7.3 ST-E00130:540:HVYVWCCXX:3:1109:13697:33199/1 1 151 (0) C L1P3 LINE/L1 (2858) 3288 3136 1471
ANNOTATION EVIDENCE:
780 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:3:1109:13697:33199/1 1 151 0 C L1P3_orf2 LINE/L1 1027 1179 2115
780 6.43 8.50 7.28 ST-E00130:540:HVYVWCCXX:3:1109:13697:33199/1 1 151 (0) C L1P3_orf2#LINE/L1 (2115) 1179 1027 m_b6s551i212
ST-E00130:540 1 TATTGAGTCTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTA 42
v -------- v
C L1P3_orf2#LIN 1179 TATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTA 1130
ST-E00130:540 43 GCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAA 88
---- i i v
C L1P3_orf2#LIN 1129 GCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCA 1080
ST-E00130:540 89 TTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTC 138
- i i----------
C L1P3_orf2#LIN 1079 TTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTC 1041
ST-E00130:540 139 A-CTCAGCTCTGAT 151
-i v
C L1P3_orf2#LIN 1040 AGTTCTGCTCTGAT 1027
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.03
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.71 (24 / 14)
+ 1268 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1109:13697:33199/2 1 151 (0) + L1P3 LINE/L1 2958 3108 (3038) 1472
ANNOTATION EVIDENCE:
1268 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:13697:33199/2 1 151 0 + L1P3_orf2 LINE/L1 849 999 2295
1268 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:13697:33199/2 1 151 (0) L1P3_orf2#LINE/L1 849 999 (2295) m_b7s551i2
ST-E00130:540 1 GTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTA 50
L1P3_orf2#LIN 849 GTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTA 898
ST-E00130:540 51 TAGCACTAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACC 100
? v i i
L1P3_orf2#LIN 899 TAGCACTAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACC 948
ST-E00130:540 101 CTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAA 150
L1P3_orf2#LIN 949 CTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAA 998
ST-E00130:540 151 A 151
L1P3_orf2#LIN 999 A 999
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1034 10.4 1.5 0.0 ST-E00130:540:HVYVWCCXX:3:1109:17888:72701/1 18 151 (0) + AluSx SINE/Alu 1 136 (176) 1473
ANNOTATION EVIDENCE:
1034 10.45 1.47 0.00 ST-E00130:540:HVYVWCCXX:3:1109:17888:72701/1 18 151 0 + AluSx SINE/Alu 1 136 176
1034 10.45 1.47 0.00 ST-E00130:540:HVYVWCCXX:3:1109:17888:72701/1 18 151 (0) AluSx#SINE/Alu 1 136 (176) m_b4s356i50
ST-E00130:540 18 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 67
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 68 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 115
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 116 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTA 151
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTA 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.31
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 2.00 (2 / 1)
+ 1161 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1109:17888:72701/2 21 151 (0) C AluSx SINE/Alu (21) 291 161 1474
ANNOTATION EVIDENCE:
1161 4.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:17888:72701/2 21 151 0 C AluSx SINE/Alu 161 291 21
1161 4.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:17888:72701/2 21 151 (0) C AluSx#SINE/Alu (21) 291 161 m_b4s356i1
ST-E00130:540 21 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 70
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 71 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCT 120
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
ST-E00130:540 121 CCTGCCTCAGCCTCCTGAGTAGCTGGGATTA 151
i
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.58
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 181 29.5 16.4 0.0 ST-E00130:540:HVYVWCCXX:3:1109:25175:54981/1 38 149 (2) C MIR SINE/MIR (0) 262 129 1475
ANNOTATION EVIDENCE:
181 29.46 16.42 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:54981/1 38 149 2 C MIR SINE/MIR 129 262 0
181 29.46 16.42 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:54981/1 38 149 (2) C MIR#SINE/MIR (0) 262 129 m_b6s601i17
ST-E00130:540 38 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 80
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 81 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 115
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 116 TTAGATTCTATTATTTCCTTCAATTTATAAATGA 149
v i v vi ii v i i
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGA 129
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 37.24
Transitions / transversions = 1.75 (21/12)
Gap_init rate = 0.04 (4 / 111), avg. gap size = 5.50 (22 / 4)
+ 30 29.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1109:25175:54981/2 1 86 (65) + GA-rich Low_complexity 1 86 (0) 1476
ANNOTATION EVIDENCE:
30 29.75 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:54981/2 1 86 65 + (AA)n Simple_repeat 1 86 0
30 29.75 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:54981/2 1 86 (65) (AA)n#Simple_repeat 1 86 (0) m_b6s252i5
ST-E00130:540 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAATTAATATATGTTTAT 50
vi vv v v vivvv v
(AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
ST-E00130:540 51 TCCAGGAATAAAAAAAAAAAAAACCAAATAAAAAAA 86
vvv ii v vv v
(AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 86
Matrix = Unknown
Transitions / transversions = 0.24 (4/17)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)
+ 181 29.5 16.4 0.0 ST-E00130:540:HVYVWCCXX:3:1109:25175:55016/1 38 149 (2) C MIR SINE/MIR (0) 262 129 1477
ANNOTATION EVIDENCE:
181 29.46 16.42 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:55016/1 38 149 2 C MIR SINE/MIR 129 262 0
181 29.46 16.42 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:55016/1 38 149 (2) C MIR#SINE/MIR (0) 262 129 m_b6s601i18
ST-E00130:540 38 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 80
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 81 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 115
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 116 TTAGATTCTATTATTTCCTTCAATTTATAAATGA 149
v i v vi ii v i i
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGA 129
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 37.24
Transitions / transversions = 1.75 (21/12)
Gap_init rate = 0.04 (4 / 111), avg. gap size = 5.50 (22 / 4)
+ 25 3.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1109:25175:55016/2 1 30 (121) + (A)n Simple_repeat 1 30 (0) 1478
ANNOTATION EVIDENCE:
25 3.45 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:55016/2 1 30 121 + (A)n Simple_repeat 1 30 0
25 3.45 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:25175:55016/2 1 30 (121) (A)n#Simple_repeat 1 30 (0) m_b6s252i4
ST-E00130:540 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 30
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1303 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1109:3285:12666/1 1 150 (1) C L1P1 LINE/L1 (331) 5824 5675 1479
ANNOTATION EVIDENCE:
1303 2.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:3285:12666/1 1 150 1 C L1PA2_3end LINE/L1 422 571 331
1303 2.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:3285:12666/1 1 150 (1) C L1PA2_3end#LINE/L1 (331) 571 422 m_b1s551i329
ST-E00130:540 1 CATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGT 50
v
C L1PA2_3end#LI 571 CATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATT 522
ST-E00130:540 51 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 100
C L1PA2_3end#LI 521 TTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTT 472
ST-E00130:540 101 TGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTGTTTAT 150
i v
C L1PA2_3end#LI 471 TGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTAT 422
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1317 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1109:3285:12666/2 1 151 (0) + L1P1 LINE/L1 5446 5596 (559) 1480
ANNOTATION EVIDENCE:
1317 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:3285:12666/2 1 151 0 + L1PA3_3end LINE/L1 193 343 559
1317 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1109:3285:12666/2 1 151 (0) L1PA3_3end#LINE/L1 193 343 (559) m_b1s551i261
ST-E00130:540 1 CATCTCACACCAGTTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAG 50
i
L1PA3_3end#LI 193 CATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAG 242
ST-E00130:540 51 GTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTGCACTGTTGGTGGG 100
iv i
L1PA3_3end#LI 243 GTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGG 292
ST-E00130:540 101 ACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCAGG 150
i
L1PA3_3end#LI 293 ACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGG 342
ST-E00130:540 151 G 151
L1PA3_3end#LI 343 G 343
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1034 10.4 1.5 0.0 ST-E00130:540:HVYVWCCXX:3:1110:18051:1327/1 18 151 (0) + AluSx SINE/Alu 1 136 (176) 1481
ANNOTATION EVIDENCE:
1034 10.45 1.47 0.00 ST-E00130:540:HVYVWCCXX:3:1110:18051:1327/1 18 151 0 + AluSx SINE/Alu 1 136 176
1034 10.45 1.47 0.00 ST-E00130:540:HVYVWCCXX:3:1110:18051:1327/1 18 151 (0) AluSx#SINE/Alu 1 136 (176) m_b4s356i51
ST-E00130:540 18 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 67
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 68 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 115
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 116 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTA 151
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTA 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.31
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 2.00 (2 / 1)
+ 1133 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1110:18051:1327/2 21 151 (0) C AluSx SINE/Alu (21) 291 161 1482
ANNOTATION EVIDENCE:
1133 5.34 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1110:18051:1327/2 21 151 0 C AluSx SINE/Alu 161 291 21
1133 5.34 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1110:18051:1327/2 21 151 (0) C AluSx#SINE/Alu (21) 291 161 m_b4s356i2
ST-E00130:540 21 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 70
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 71 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATGCT 120
i i v
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
ST-E00130:540 121 CCTGCCTCAGCCTCCTGAGTAGCTGGGATTA 151
i
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.37
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 1122 10.3 0.0 1.4 ST-E00130:540:HVYVWCCXX:3:1111:29579:11769/1 4 151 (0) + AluSx SINE/Alu 154 299 (13) 1483
ANNOTATION EVIDENCE:
1122 10.28 0.00 1.35 ST-E00130:540:HVYVWCCXX:3:1111:29579:11769/1 4 151 0 + AluSx SINE/Alu 154 299 13
1122 10.28 0.00 1.35 ST-E00130:540:HVYVWCCXX:3:1111:29579:11769/1 4 151 (0) AluSx#SINE/Alu 154 299 (13) m_b2s356i0
ST-E00130:540 4 GCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGA 53
i i i i
AluSx#SINE/Al 154 GCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGA 203
ST-E00130:540 54 ACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCA 103
i i i i i ii
AluSx#SINE/Al 204 ACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA 253
ST-E00130:540 104 GCCTGGGTTTGACGAAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAA 151
--i ii i
AluSx#SINE/Al 254 GCCTGGG--CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 299
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.29
Transitions / transversions = 1.00 (15/0)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 930 2.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1111:29579:11769/2 1 108 (43) + L1PA2 LINE/L1 6046 6153 (2) 1484
ANNOTATION EVIDENCE:
930 2.78 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1111:29579:11769/2 1 108 43 + L1PA2_3end LINE/L1 793 900 2
930 2.78 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1111:29579:11769/2 1 108 (43) L1PA2_3end#LINE/L1 793 900 (2) m_b1s551i439
ST-E00130:540 1 GACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATACATATGTA 50
i
L1PA2_3end#LI 793 GACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTA 842
ST-E00130:540 51 ACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAA 100
i
L1PA2_3end#LI 843 ACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAA 892
ST-E00130:540 101 AAAAATAA 108
v
L1PA2_3end#LI 893 AAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.97
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0)
+ 31 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1112:9069:20120/1 59 87 (64) + (T)n Simple_repeat 1 29 (0) 1485
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9069:20120/1 59 87 64 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9069:20120/1 59 87 (64) (T)n#Simple_repeat 1 29 (0) c_b6s251i5
ST-E00130:540 59 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 87
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 1181 5.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:1112:9069:20120/2 1 151 (0) + L1P3 LINE/L1 3586 3738 (2408) 1486
ANNOTATION EVIDENCE:
1181 5.30 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9069:20120/2 1 151 0 + L1P3_orf2 LINE/L1 1477 1629 1665
1181 5.30 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9069:20120/2 1 151 (0) L1P3_orf2#LINE/L1 1477 1629 (1665) m_b6s551i79
ST-E00130:540 1 CTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCCTAACTCATT 50
i
L1P3_orf2#LIN 1477 CTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCCTAACTCATT 1526
ST-E00130:540 51 TTATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAA--G 98
v v --i
L1P3_orf2#LIN 1527 TTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAA 1576
ST-E00130:540 99 AAAAAGAAAATTTCAGGCCATTATCCGTGATGAACATCGAGGTGAAAATC 148
v v v i
L1P3_orf2#LIN 1577 AAAAAGAAAATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATC 1626
ST-E00130:540 149 CTC 151
L1P3_orf2#LIN 1627 CTC 1629
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.86
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 30 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1112:9120:20278/1 59 86 (65) + (T)n Simple_repeat 1 28 (0) 1487
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9120:20278/1 59 86 65 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9120:20278/1 59 86 (65) (T)n#Simple_repeat 1 28 (0) c_b6s251i4
ST-E00130:540 59 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 86
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 1205 4.6 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:1112:9120:20278/2 1 151 (0) + L1P3 LINE/L1 3586 3738 (2408) 1488
ANNOTATION EVIDENCE:
1205 4.64 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9120:20278/2 1 151 0 + L1P3_orf2 LINE/L1 1477 1629 1665
1205 4.64 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1112:9120:20278/2 1 151 (0) L1P3_orf2#LINE/L1 1477 1629 (1665) m_b6s551i80
ST-E00130:540 1 CTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCCTAACTCATT 50
i
L1P3_orf2#LIN 1477 CTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCCTAACTCATT 1526
ST-E00130:540 51 TTATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGAGACACAA--G 98
v v --i
L1P3_orf2#LIN 1527 TTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAA 1576
ST-E00130:540 99 AAAAAGAAAATTTCAGGCCATTATCCGTGATGAACATCGATGTGAAAATC 148
v v i
L1P3_orf2#LIN 1577 AAAAAGAAAATTTCAGGCCAATATCCCTGATGAACATCGATGCGAAAATC 1626
ST-E00130:540 149 CTC 151
L1P3_orf2#LIN 1627 CTC 1629
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.15
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1071 12.8 0.0 1.3 ST-E00130:540:HVYVWCCXX:3:1114:12439:33516/2 1 151 (0) C AluSx SINE/Alu (39) 273 125 1489
ANNOTATION EVIDENCE:
1071 12.75 0.00 1.32 ST-E00130:540:HVYVWCCXX:3:1114:12439:33516/2 1 151 0 C AluSx SINE/Alu 125 273 39
1071 12.75 0.00 1.32 ST-E00130:540:HVYVWCCXX:3:1114:12439:33516/2 1 151 (0) C AluSx#SINE/Alu (39) 273 125 m_b2s356i5
ST-E00130:540 1 TCTCGCTTCGTCAAACCCAGGCTGGAGTGCAGTGGCATGATCTCAGCTCA 50
ii i-- ii i
C AluSx#SINE/Al 273 TCTCGCTCTGTCG--CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCA 226
ST-E00130:540 51 CTGCAATCTCTGCCTCCTGAGTTCAAGTGATTCTCCTGCCTCAGCTTCCT 100
i i i i i i i
C AluSx#SINE/Al 225 CTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCC 176
ST-E00130:540 101 GAGTAGCTGGGATTACAGGTGCCCACCACCACACCCAGCTCATTTTTGTA 150
i v i i i v
C AluSx#SINE/Al 175 GAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTA 126
ST-E00130:540 151 T 151
C AluSx#SINE/Al 125 T 125
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.76
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1176 7.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1115:13677:34395/2 1 151 (0) + L1PA3 LINE/L1 5949 6099 (56) 1490
ANNOTATION EVIDENCE:
1176 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1115:13677:34395/2 1 151 0 + L1PA3_3end LINE/L1 696 846 56
1176 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1115:13677:34395/2 1 151 (0) L1PA3_3end#LINE/L1 696 846 (56) m_b1s551i400
ST-E00130:540 1 ACATGGACACAGGAAGGGGAATATCACACTCTGTCGACTGTTGTGGGGTG 50
i vv
L1PA3_3end#LI 696 ACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGGTG 745
ST-E00130:540 51 GGGAGAGGGGGGAGGGATAGCATCAGGGAATAAACCTAATGCTAGATGAC 100
i ii ii v
L1PA3_3end#LI 746 GGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGAC 795
ST-E00130:540 101 GAGTTAGTGGGTGCAGCACACCAGCATGGCTCATGTATACATATGTAACT 150
i v
L1PA3_3end#LI 796 GAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACT 845
ST-E00130:540 151 A 151
L1PA3_3end#LI 846 A 846
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.04
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 864 17.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1115:27651:66443/2 1 145 (6) + AluSx SINE/Alu 99 243 (69) 1491
ANNOTATION EVIDENCE:
864 17.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1115:27651:66443/2 1 145 6 + AluSx SINE/Alu 99 243 69
864 17.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1115:27651:66443/2 1 145 (6) AluSx#SINE/Alu 99 243 (69) m_b6s357i10
ST-E00130:540 1 ATGGTGAAACTCCATCTCTACGAACAATAAAAAAATTAGCTGGGCATGGT 50
i i v v v i i
AluSx#SINE/Al 99 ATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGT 148
ST-E00130:540 51 GGCAGGCGCCTGTAATCCCAGCTACTCAGGAGAATGATACAGGAGAATTG 100
iv i iv vi i
AluSx#SINE/Al 149 GGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG 198
ST-E00130:540 101 CTTGAACCGAGGAGGTAGACGCTGAAGTGAACCGATATCACACCA 145
vi ii v i v i v i i
AluSx#SINE/Al 199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCA 243
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 12.68
Transitions / transversions = 1.60 (16/10)
Gap_init rate = 0.00 (0 / 144), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1115:28097:58708/1 44 88 (63) + MIR SINE/MIR 218 262 (0) 1492
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1115:28097:58708/1 44 88 63 + MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1115:28097:58708/1 44 88 (63) MIR#SINE/MIR 218 262 (0) m_b6s601i11
ST-E00130:540 44 AATGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTATTTTT 88
i v iv viii i i v
MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 1289 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:3:1118:12834:17324/1 1 151 (0) C L1PA2 LINE/L1 (208) 5947 5798 1493
ANNOTATION EVIDENCE:
1289 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:3:1118:12834:17324/1 1 151 0 C L1PA2_3end LINE/L1 545 694 208
1289 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:3:1118:12834:17324/1 1 151 (0) C L1PA2_3end#LINE/L1 (208) 694 545 m_b1s551i373
ST-E00130:540 1 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTT 50
i
C L1PA2_3end#LI 694 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTT 645
ST-E00130:540 51 TTTTCTTCTTGCGACAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 100
v i
C L1PA2_3end#LI 644 TTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 595
ST-E00130:540 101 TGTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 150
-
C L1PA2_3end#LI 594 TGTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 546
ST-E00130:540 151 T 151
C L1PA2_3end#LI 545 T 545
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1336 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1118:12834:17324/2 1 151 (0) + L1P1 LINE/L1 5628 5778 (377) 1494
ANNOTATION EVIDENCE:
1336 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:12834:17324/2 1 151 0 + L1PA2_3end LINE/L1 375 525 377
1336 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:12834:17324/2 1 151 (0) L1PA2_3end#LINE/L1 375 525 (377) m_b1s551i308
ST-E00130:540 1 CATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCGCTATA 50
i
L1PA2_3end#LI 375 CATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATA 424
ST-E00130:540 51 AAGACACATGCACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAG 100
i
L1PA2_3end#LI 425 AAGACACATGCACACGTATGTTTATTGCGGCATTATTCACAATAGCAAAG 474
ST-E00130:540 101 ACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAACT 150
v
L1PA2_3end#LI 475 ACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAAT 524
ST-E00130:540 151 G 151
L1PA2_3end#LI 525 G 525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1305 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1118:21684:37541/1 1 151 (0) + L1PA2 LINE/L1 5946 6096 (59) 1495
ANNOTATION EVIDENCE:
1305 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21684:37541/1 1 151 0 + L1PA2_3end LINE/L1 693 843 59
1305 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21684:37541/1 1 151 (0) L1PA2_3end#LINE/L1 693 843 (59) m_b1s551i398
ST-E00130:540 1 ATCACATGGACACAGGAAGGGGAATATCACACTCTGTGGACTGTTGTGGG 50
v v
L1PA2_3end#LI 693 ATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGG 742
ST-E00130:540 51 GTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGAT 100
L1PA2_3end#LI 743 GTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGAT 792
ST-E00130:540 101 GACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATACATATGTA 150
i
L1PA2_3end#LI 793 GACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTA 842
ST-E00130:540 151 A 151
L1PA2_3end#LI 843 A 843
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1118:21684:37541/2 24 45 (106) + (A)n Simple_repeat 1 22 (0) 1496
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21684:37541/2 24 45 106 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21684:37541/2 24 45 (106) (A)n#Simple_repeat 1 22 (0) m_b1s252i3
ST-E00130:540 24 AAAAAAAAAAAAAAAAAAAAAA 45
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/1 16 104 (47) C L1M5 LINE/L1 (293) 5831 5741 1497
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/1 16 104 47 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/1 16 104 (47) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i504
ST-E00130:540 16 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 65
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 66 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 104
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/1 37 104 47 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/1 37 104 (47) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i505
ST-E00130:540 37 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 86
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 87 CTATTGTTGGACATTTAG 104
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1112 11.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/2 1 147 (4) + AluSx SINE/Alu 114 260 (52) 1498
ANNOTATION EVIDENCE:
1112 11.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/2 1 147 4 + AluSx SINE/Alu 114 260 52
1112 11.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1118:21704:24743/2 1 147 (4) AluSx#SINE/Alu 114 260 (52) m_b2s357i22
ST-E00130:540 1 CTCTATTTAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAA 50
i v i i i v i
AluSx#SINE/Al 114 CTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAA 163
ST-E00130:540 51 TCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGG 100
i i i i i
AluSx#SINE/Al 164 TCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGG 213
ST-E00130:540 101 CAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGG 147
i i i ii
AluSx#SINE/Al 214 CGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.02
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 1103 7.3 2.0 0.0 ST-E00130:540:HVYVWCCXX:3:1118:30239:9431/1 2 151 (0) C L1P3 LINE/L1 (2248) 3898 3746 1499
ANNOTATION EVIDENCE:
1103 7.33 1.96 0.00 ST-E00130:540:HVYVWCCXX:3:1118:30239:9431/1 2 151 0 C L1P3_orf2 LINE/L1 1637 1789 1505
1103 7.33 1.96 0.00 ST-E00130:540:HVYVWCCXX:3:1118:30239:9431/1 2 151 (0) C L1P3_orf2#LINE/L1 (1505) 1789 1637 m_b6s551i37
ST-E00130:540 2 TAATCATGTAGTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTT 51
i v i
C L1P3_orf2#LIN 1789 TAATCATGTGGTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTT 1740
ST-E00130:540 52 ATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGAC 101
i i i i i
C L1P3_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGAC 1690
ST-E00130:540 102 TTGATAGTGGTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCA 148
v v --- i
C L1P3_orf2#LIN 1689 TTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCA 1640
ST-E00130:540 149 GTA 151
C L1P3_orf2#LIN 1639 GTA 1637
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.12
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 3.00 (3 / 1)
+ 1097 6.6 3.2 0.0 ST-E00130:540:HVYVWCCXX:3:1118:30239:9431/2 1 151 (0) + L1P3 LINE/L1 3652 3807 (2339) 1500
ANNOTATION EVIDENCE:
1097 6.62 3.20 0.00 ST-E00130:540:HVYVWCCXX:3:1118:30239:9431/2 1 151 0 + L1P3_orf2 LINE/L1 1543 1698 1596
1097 6.62 3.20 0.00 ST-E00130:540:HVYVWCCXX:3:1118:30239:9431/2 1 151 (0) L1P3_orf2#LINE/L1 1543 1698 (1596) m_b6s551i60
ST-E00130:540 1 ATCCTGATTCCAAAACCTGGCAGAGACACAA--GAAAAAGAAAATTTCAG 48
v --i
L1P3_orf2#LIN 1543 ATCCTGATACCAAAACCTGGCAGAGACACAACAAAAAAAGAAAATTTCAG 1592
ST-E00130:540 49 GCCATTATCCGTGATGAACATCGATGTGAAAATCCTCGATAAAATACTGG 98
v v i i
L1P3_orf2#LIN 1593 GCCAATATCCCTGATGAACATCGATGCGAAAATCCTCAATAAAATACTGG 1642
ST-E00130:540 99 CAAACTGAATCCAGCA---CATCAAAACGCTTATCCACCACTATCAAGTC 145
i --- v v
L1P3_orf2#LIN 1643 CAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCACGATCAAGTC 1692
ST-E00130:540 146 AGCTTC 151
i
L1P3_orf2#LIN 1693 GGCTTC 1698
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.00
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 1041 7.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:1119:25449:3805/1 1 151 (0) C L1P3 LINE/L1 (2696) 3450 3298 1501
ANNOTATION EVIDENCE:
1041 7.28 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1119:25449:3805/1 1 151 0 C L1P3_orf2 LINE/L1 1189 1341 1953
1041 7.28 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1119:25449:3805/1 1 151 (0) C L1P3_orf2#LINE/L1 (1953) 1341 1189 m_b6s551i164
ST-E00130:540 1 TTCGACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGTCTAGGAATT 48
v -- v i
C L1P3_orf2#LIN 1341 TTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATT 1292
ST-E00130:540 49 TATCACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTATTTATAG 98
vv i i
C L1P3_orf2#LIN 1291 TATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAG 1242
ST-E00130:540 99 TATTCTCTTATGGTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTC 148
v iv i
C L1P3_orf2#LIN 1241 TATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCC 1192
ST-E00130:540 149 TTT 151
C L1P3_orf2#LIN 1191 TTT 1189
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.01
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1225 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1119:25449:3805/2 1 151 (0) + L1P3 LINE/L1 2984 3134 (3012) 1502
ANNOTATION EVIDENCE:
1225 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1119:25449:3805/2 1 151 0 + L1P3_orf2 LINE/L1 875 1025 2269
1225 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1119:25449:3805/2 1 151 (0) L1P3_orf2#LINE/L1 875 1025 (2269) m_b6s551i270
ST-E00130:540 1 AAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAAG 50
? v
L1P3_orf2#LIN 875 AAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAAG 924
ST-E00130:540 51 TGGGAAAGATCTAAAATCAACACCCTAACATCACAATTAAAAGAACTAGA 100
i i
L1P3_orf2#LIN 925 CGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTAGA 974
ST-E00130:540 101 GAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTA 150
L1P3_orf2#LIN 975 GAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTA 1024
ST-E00130:540 151 A 151
L1P3_orf2#LIN 1025 A 1025
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 250 24.6 6.2 3.9 ST-E00130:540:HVYVWCCXX:3:1121:1783:7392/1 4 130 (21) + L1ME4c LINE/L1 5657 5786 (297) 1503
ANNOTATION EVIDENCE:
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:3:1121:1783:7392/1 4 130 21 + L1ME4c_3end LINE/L1 404 533 297
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:3:1121:1783:7392/1 4 130 (21) L1ME4c_3end#LINE/L1 404 533 (297) m_b2s551i29
ST-E00130:540 4 AAGAAATAATTTAAAATATGAGAAAAAAAAACCCTTAGACA----AATGA 49
i i ----- ii v iv vi ----i v
L1ME4c_3end#L 404 AGGAAATAATTCAAAA-----GAAGGAAAAAGCTATATGCACGAAGATGT 448
ST-E00130:540 50 TCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCTAAATTT 97
iiiv i vi --i v i v i v
L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498
ST-E00130:540 98 CTGACAATAAAA-AATG-TCAAGTAAATTATGGTA 130
ii iii- - i
L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTA 533
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 1341 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1122:30776:8323/1 1 151 (0) C L1P1 LINE/L1 (855) 5291 5141 1504
ANNOTATION EVIDENCE:
1341 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1122:30776:8323/1 1 151 0 C L1P1_orf2 LINE/L1 3032 3182 112
1341 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1122:30776:8323/1 1 151 (0) C L1P1_orf2#LINE/L1 (112) 3182 3032 m_b1s551i116
ST-E00130:540 1 TAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGA 50
C L1P1_orf2#LIN 3182 TAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGA 3133
ST-E00130:540 51 TGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTC 100
i
C L1P1_orf2#LIN 3132 TGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTC 3083
ST-E00130:540 101 TGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCC 150
C L1P1_orf2#LIN 3082 TGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCC 3033
ST-E00130:540 151 C 151
C L1P1_orf2#LIN 3032 C 3032
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1256 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1122:30776:8323/2 1 151 (0) + L1P1 LINE/L1 4902 5052 (1094) 1505
ANNOTATION EVIDENCE:
1256 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1122:30776:8323/2 1 151 0 + L1P1_orf2 LINE/L1 2793 2943 351
1256 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1122:30776:8323/2 1 151 (0) L1P1_orf2#LINE/L1 2793 2943 (351) m_b1s551i19
ST-E00130:540 1 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 50
L1P1_orf2#LIN 2793 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2842
ST-E00130:540 51 AACTGGATCCCTTCCTTACACCTGCTAGAAAAATCAATTCAAGATGGATT 100
vv v i
L1P1_orf2#LIN 2843 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 2892
ST-E00130:540 101 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 150
i
L1P1_orf2#LIN 2893 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 2942
ST-E00130:540 151 A 151
L1P1_orf2#LIN 2943 A 2943
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.77
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 231 23.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1203:18568:21280/2 32 83 (68) + L1MC4 LINE/L1 7901 7952 (90) 1506
ANNOTATION EVIDENCE:
231 23.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1203:18568:21280/2 32 83 68 + L1MC4_3end LINE/L1 2648 2699 90
231 23.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1203:18568:21280/2 32 83 (68) L1MC4_3end#LINE/L1 2648 2699 (90) m_b3s551i2
ST-E00130:540 32 AGTGTGTGTGTGGAGAGAGGGAATGATTAAGCAAATATGGTAAAACGTTA 81
i i i i v ? ? i v i i i
L1MC4_3end#LI 2648 AATATGTATATGCANANAGAGAATGATAAAGCAAATGTGGCAAAATGTTA 2697
ST-E00130:540 82 AC 83
L1MC4_3end#LI 2698 AC 2699
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.40
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 1332 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1203:2169:56932/1 1 151 (0) + L1P3 LINE/L1 3481 3631 (2515) 1507
ANNOTATION EVIDENCE:
1332 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1203:2169:56932/1 1 151 0 + L1P3_orf2 LINE/L1 1372 1522 1772
1332 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1203:2169:56932/1 1 151 (0) L1P3_orf2#LINE/L1 1372 1522 (1772) m_b6s551i110
ST-E00130:540 1 ATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAGA 50
L1P3_orf2#LIN 1372 ATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAGA 1421
ST-E00130:540 51 GGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTACCAT 100
v i
L1P3_orf2#LIN 1422 CGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTACCAT 1471
ST-E00130:540 101 TCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCCTAAC 150
i
L1P3_orf2#LIN 1472 TCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCCTAAC 1521
ST-E00130:540 151 T 151
L1P3_orf2#LIN 1522 T 1522
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1111 8.6 1.9 0.0 ST-E00130:540:HVYVWCCXX:3:1203:2169:56932/2 1 151 (0) C L1P3 LINE/L1 (2302) 3844 3691 1508
ANNOTATION EVIDENCE:
1111 8.61 1.95 0.00 ST-E00130:540:HVYVWCCXX:3:1203:2169:56932/2 1 151 0 C L1P3_orf2 LINE/L1 1582 1735 1559
1111 8.61 1.95 0.00 ST-E00130:540:HVYVWCCXX:3:1203:2169:56932/2 1 151 (0) C L1P3_orf2#LINE/L1 (1559) 1735 1582 m_b6s551i51
ST-E00130:540 1 ATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGA 50
i i i i i
C L1P3_orf2#LIN 1735 ATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGA 1686
ST-E00130:540 51 TAGTGGTGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTAT 97
v v --- i
C L1P3_orf2#LIN 1685 TCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTAT 1636
ST-E00130:540 98 TTTATCGAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAAT 147
i i v v
C L1P3_orf2#LIN 1635 TTTATTGAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAAT 1586
ST-E00130:540 148 GTTC 151
v
C L1P3_orf2#LIN 1585 TTTC 1582
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.51
Transitions / transversions = 1.60 (8/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
+ 1214 9.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1203:26788:53487/1 1 151 (0) C AluSx SINE/Alu (142) 170 20 1509
ANNOTATION EVIDENCE:
1214 9.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1203:26788:53487/1 1 151 0 C AluSx SINE/Alu 20 170 142
1214 9.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1203:26788:53487/1 1 151 (0) C AluSx#SINE/Alu (142) 170 20 m_b6s356i18
ST-E00130:540 1 GCTGGGATTACAGGCGCCTGCCACCATGCCCAGCTAATTTTTTTATTTTT 50
vi i i v
C AluSx#SINE/Al 170 GCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTT 121
ST-E00130:540 51 CGTAGAGATGGAGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGA 100
v i i i
C AluSx#SINE/Al 120 AGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGA 71
ST-E00130:540 101 CCTCAGGTGATCCACCCACCTTGTCCTCCCAAAGTGCTGAGATTACAGGC 150
i i i v i
C AluSx#SINE/Al 70 CCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
ST-E00130:540 151 G 151
C AluSx#SINE/Al 20 G 20
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.65
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1082 7.3 2.0 0.0 ST-E00130:540:HVYVWCCXX:3:1203:26788:53487/2 2 151 (0) + L1P3 LINE/L1 3740 3892 (2254) 1510
ANNOTATION EVIDENCE:
1082 7.33 1.96 0.00 ST-E00130:540:HVYVWCCXX:3:1203:26788:53487/2 2 151 0 + L1P3_orf2 LINE/L1 1631 1783 1511
1082 7.33 1.96 0.00 ST-E00130:540:HVYVWCCXX:3:1203:26788:53487/2 2 151 (0) L1P3_orf2#LINE/L1 1631 1783 (1511) m_b6s551i39
ST-E00130:540 2 ATAAAATACTGGCAAACTGAATCCAGCA---CATCAAAACGCTTATCCAC 48
i --- v
L1P3_orf2#LIN 1631 ATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCAC 1680
ST-E00130:540 49 CACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCATACA 98
v i i i i i
L1P3_orf2#LIN 1681 CACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACATACG 1730
ST-E00130:540 99 CAAATCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAAACT 148
i v i
L1P3_orf2#LIN 1731 CAAATCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAACC 1780
ST-E00130:540 149 ACA 151
L1P3_orf2#LIN 1781 ACA 1783
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.12
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 3.00 (3 / 1)
+ 250 24.6 6.2 3.9 ST-E00130:540:HVYVWCCXX:3:1206:15777:58884/2 15 141 (10) + L1ME4c LINE/L1 5657 5786 (297) 1511
ANNOTATION EVIDENCE:
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:3:1206:15777:58884/2 15 141 10 + L1ME4c_3end LINE/L1 404 533 297
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:3:1206:15777:58884/2 15 141 (10) L1ME4c_3end#LINE/L1 404 533 (297) m_b2s551i33
ST-E00130:540 15 AAGAAATAATTTAAAATATGAGAAAAAAAAACCCTTAGACA----AATGA 60
i i ----- ii v iv vi ----i v
L1ME4c_3end#L 404 AGGAAATAATTCAAAA-----GAAGGAAAAAGCTATATGCACGAAGATGT 448
ST-E00130:540 61 TCATTGCAATAATGTTTATTGTAG--GAAAATAGAAAAGAATCTAAATTT 108
iiiv i vi --i v i v i v
L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498
ST-E00130:540 109 CTGACAATAAAA-AATG-TCAAGTAAATTATGGTA 141
ii iii- - i
L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTA 533
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 1295 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1206:25408:30175/1 1 151 (0) + L1P1 LINE/L1 4894 5044 (1102) 1512
ANNOTATION EVIDENCE:
1295 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1206:25408:30175/1 1 151 0 + L1P1_orf2 LINE/L1 2785 2935 359
1295 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1206:25408:30175/1 1 151 (0) L1P1_orf2#LINE/L1 2785 2935 (359) m_b1s551i14
ST-E00130:540 1 GATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAG 50
L1P1_orf2#LIN 2785 GATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAG 2834
ST-E00130:540 51 AAAGCTGAAACTGGATCCCTTCCTTACACCTGATAGAAAAATCAATTCAA 100
v v i
L1P1_orf2#LIN 2835 AAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAA 2884
ST-E00130:540 101 GATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAA 150
i
L1P1_orf2#LIN 2885 GATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAA 2934
ST-E00130:540 151 G 151
L1P1_orf2#LIN 2935 G 2935
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1329 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1206:25408:30175/2 1 151 (0) C L1P1 LINE/L1 (859) 5287 5137 1513
ANNOTATION EVIDENCE:
1329 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1206:25408:30175/2 1 151 0 C L1P1_orf2 LINE/L1 3028 3178 116
1329 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1206:25408:30175/2 1 151 (0) C L1P1_orf2#LINE/L1 (116) 3178 3028 m_b1s551i114
ST-E00130:540 1 TTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAG 50
C L1P1_orf2#LIN 3178 TTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAG 3129
ST-E00130:540 51 TAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGAT 100
i
C L1P1_orf2#LIN 3128 TAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGAT 3079
ST-E00130:540 101 GGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATT 150
C L1P1_orf2#LIN 3078 GGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATT 3029
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 3028 T 3028
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 826 7.9 7.9 0.7 ST-E00130:540:HVYVWCCXX:3:1206:6857:20120/1 11 151 (0) + L1P1 LINE/L1 3163 3314 (2832) 1514
ANNOTATION EVIDENCE:
826 7.86 7.89 0.71 ST-E00130:540:HVYVWCCXX:3:1206:6857:20120/1 11 151 0 + L1P1_orf2 LINE/L1 1054 1205 2089
826 7.86 7.89 0.71 ST-E00130:540:HVYVWCCXX:3:1206:6857:20120/1 11 151 (0) L1P1_orf2#LINE/L1 1054 1205 (2089) m_b6s551i207
ST-E00130:540 11 ACAAAAAAAACCTTTCAAAAAAATCAATTAATCCAGGAGCTGATTTTTTG 60
v i - v i
L1P1_orf2#LIN 1054 ACACAAAAAACCCTTCAAAAAA-TCAATGAATCCAGGAGCTGGTTTTTTG 1102
ST-E00130:540 61 AAAAGATTAACAAAA----CAGACCGCTAGCAAGACTAATAAAGA----- 101
i i ----i -----
L1P1_orf2#LIN 1103 AAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAGAAA 1152
ST-E00130:540 102 ---GAGAAGAATCAAATAGACTCAATAAAAAATGATAAAGAGGATAATAC 148
--- v i vi
L1P1_orf2#LIN 1153 AGAGAGAAGAATCAAATAGACGCAATAAAAAATGATAAAGGGGATATCAC 1202
ST-E00130:540 149 CAC 151
L1P1_orf2#LIN 1203 CAC 1205
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.35
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 3.25 (13 / 4)
+ 1288 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1206:6857:20120/2 1 151 (0) C L1P3 LINE/L1 (2526) 3620 3470 1515
ANNOTATION EVIDENCE:
1288 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1206:6857:20120/2 1 151 0 C L1P3_orf2 LINE/L1 1361 1511 1783
1288 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1206:6857:20120/2 1 151 (0) C L1P3_orf2#LINE/L1 (1783) 1511 1361 m_b6s551i113
ST-E00130:540 1 AGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAG 50
C L1P3_orf2#LIN 1511 AGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCAGAAGGAATGGTACCAG 1462
ST-E00130:540 51 CTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTGAATCCCTCTGGTCCTG 100
i v
C L1P3_orf2#LIN 1461 CTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTG 1412
ST-E00130:540 101 GGCTTTTTGTGGTTGGTAGGCTCTTAATTACTGCCTCAATTTCAGAACTT 150
v v
C L1P3_orf2#LIN 1411 GGCTTTTTTTGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAACTT 1362
ST-E00130:540 151 G 151
C L1P3_orf2#LIN 1361 G 1361
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 317 26.3 5.0 10.1 ST-E00130:540:HVYVWCCXX:3:1207:29437:59306/1 2 149 (2) C L1MC4 LINE/L1 (1441) 6601 6462 1516
ANNOTATION EVIDENCE:
317 26.32 5.00 10.14 ST-E00130:540:HVYVWCCXX:3:1207:29437:59306/1 2 149 2 C L1MC4_3end LINE/L1 1209 1348 1441
317 26.32 5.00 10.14 ST-E00130:540:HVYVWCCXX:3:1207:29437:59306/1 2 149 (2) C L1MC4_3end#LINE/L1 (1441) 1348 1209 m_b3s551i156
ST-E00130:540 2 GTTGATA--GATATCTTCAAATCCAAGCCAACATCACACAGTTTAT---- 45
v -- i i v v i vi i ----
C L1MC4_3end#LI 1348 GTTCATACCGATACCTCCAATTCCAATCCAACACCACAGGGTTCATTCTA 1299
ST-E00130:540 46 -CTTTTTTTCTGTCCAAATTTATAAATTGCTTTACTAGCAGTTAAAAAAA 94
- i iiii v v i v iv iv iii v ------
C L1MC4_3end#LI 1298 GCCTTCCCCCTTTCCATATTTGTAACTCCCTTCTCCGACAGTGA------ 1255
ST-E00130:540 95 ACACCCCAAAACCTGACTATCCACTCAACCTGAATGCATTTACTTATTTG 144
-------i i -i - i v ?v ii
C L1MC4_3end#LI 1254 -------GAAACCTGGCT-CCCA-TTATCCNCAATATATTTACTTATTTG 1214
ST-E00130:540 145 CTCAA 149
C L1MC4_3end#LI 1213 CTCAA 1209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.32
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.12 (18 / 147), avg. gap size = 1.22 (22 / 18)
+ 1187 7.3 0.7 0.0 ST-E00130:540:HVYVWCCXX:3:1207:7304:34641/2 1 150 (1) C AluY SINE/Alu (137) 174 24 1517
ANNOTATION EVIDENCE:
1187 7.33 0.67 0.00 ST-E00130:540:HVYVWCCXX:3:1207:7304:34641/2 1 150 1 C AluY SINE/Alu 24 174 137
1187 7.33 0.67 0.00 ST-E00130:540:HVYVWCCXX:3:1207:7304:34641/2 1 150 (1) C AluY#SINE/Alu (137) 174 24 m_b2s357i84
ST-E00130:540 1 GAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA-TTTTTGT 49
iv -
C AluY#SINE/Alu 174 GAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGT 125
ST-E00130:540 50 GTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGATC 99
i i ii i
C AluY#SINE/Alu 124 ATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATC 75
ST-E00130:540 100 TCCTGACCTCATGATCAGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTAC 149
i v i i
C AluY#SINE/Alu 74 TCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTAC 25
ST-E00130:540 150 A 150
C AluY#SINE/Alu 24 A 24
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.84
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 801 5.1 8.1 7.4 ST-E00130:540:HVYVWCCXX:3:1208:27316:52643/1 1 148 (3) C L1P3 LINE/L1 (2849) 3297 3149 1518
ANNOTATION EVIDENCE:
801 5.11 8.06 7.43 ST-E00130:540:HVYVWCCXX:3:1208:27316:52643/1 1 148 3 C L1P3_orf2 LINE/L1 1040 1188 2106
801 5.11 8.06 7.43 ST-E00130:540:HVYVWCCXX:3:1208:27316:52643/1 1 148 (3) C L1P3_orf2#LINE/L1 (2106) 1188 1040 m_b6s551i209
ST-E00130:540 1 ATCATTTTTTATTGAGTCTATTTGATTCTTCTC--------TCTTTATTA 42
v --------
C L1P3_orf2#LIN 1188 ATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTA 1139
ST-E00130:540 43 GTCTTGCTAGCGG----TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTC 88
v ---- i i
C L1P3_orf2#LIN 1138 GTCTGGCTAGCGGTCTATCTATTTTGTTAATCTTTTCAAAAAACCAGCTC 1089
ST-E00130:540 89 CTGGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCT 138
v - i i----------
C L1P3_orf2#LIN 1088 CTGGATTCATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCT 1050
ST-E00130:540 139 ATCTCCTTCA 148
C L1P3_orf2#LIN 1049 ATCTCCTTCA 1040
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.60
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.09 (13 / 147), avg. gap size = 1.77 (23 / 13)
+ 1236 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1208:27316:52643/2 1 151 (0) + L1P3 LINE/L1 2915 3065 (3081) 1519
ANNOTATION EVIDENCE:
1236 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1208:27316:52643/2 1 151 0 + L1P3_orf2 LINE/L1 806 956 2338
1236 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1208:27316:52643/2 1 151 (0) L1P3_orf2#LINE/L1 806 956 (2338) m_b7s551i22
ST-E00130:540 1 AAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAG 50
i? i i
L1P3_orf2#LIN 806 AAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAG 855
ST-E00130:540 51 AATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACT 100
L1P3_orf2#LIN 856 AATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACT 905
ST-E00130:540 101 AAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACAT 150
? v i i
L1P3_orf2#LIN 906 AAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACAT 955
ST-E00130:540 151 C 151
L1P3_orf2#LIN 956 C 956
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.25
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1106 11.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:1208:8197:53451/1 2 151 (0) + AluSx SINE/Alu 22 173 (139) 1520
ANNOTATION EVIDENCE:
1106 11.33 1.31 0.00 ST-E00130:540:HVYVWCCXX:3:1208:8197:53451/1 2 151 0 + AluSx SINE/Alu 22 173 139
1106 11.33 1.31 0.00 ST-E00130:540:HVYVWCCXX:3:1208:8197:53451/1 2 151 (0) AluSx#SINE/Alu 22 173 (139) m_b4s356i39
ST-E00130:540 2 CCTGTAATCCCAGCACTTTGGGAGGCTGAAGCAGGCAGATCAC--AAGGT 49
i i i i --i
AluSx#SINE/Al 22 CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGT 71
ST-E00130:540 50 CAGGAGTTTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCTACTA 99
i v i i i
AluSx#SINE/Al 72 CAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTA 121
ST-E00130:540 100 AAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATCATCCCAGCT 149
i i v iv i v
AluSx#SINE/Al 122 AAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCT 171
ST-E00130:540 150 AC 151
AluSx#SINE/Al 172 AC 173
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.54
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 1228 8.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1208:8197:53451/2 1 151 (0) C AluSx SINE/Alu (73) 239 89 1521
ANNOTATION EVIDENCE:
1228 8.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1208:8197:53451/2 1 151 0 C AluSx SINE/Alu 89 239 73
1228 8.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1208:8197:53451/2 1 151 (0) C AluSx#SINE/Alu (73) 239 89 m_b4s356i23
ST-E00130:540 1 GCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCTCC 50
i i
C AluSx#SINE/Al 239 GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCC 190
ST-E00130:540 51 TGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCT 100
i i vi v i
C AluSx#SINE/Al 189 TGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCC 140
ST-E00130:540 101 GGCTAATTTTTGTGTTTTTAGTAGAGATGGAGTTTCACCGTATTGGCCAG 150
i i i i i
C AluSx#SINE/Al 139 GGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAG 90
ST-E00130:540 151 G 151
C AluSx#SINE/Al 89 G 89
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.90
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 232 27.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/1 4 62 (89) C L1M5 LINE/L1 (374) 5799 5741 1522
ANNOTATION EVIDENCE:
232 27.12 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/1 4 62 89 C L1ME3A_3end LINE/L1 488 546 374
232 27.12 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/1 4 62 (89) C L1ME3A_3end#LINE/L1 (374) 546 488 m_b1s551i525
ST-E00130:540 4 TTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTACTATTGTTG 53
iii i ii i ii iv v i i v
C L1ME3A_3end#L 546 TTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGATG 497
ST-E00130:540 54 GACATTTAG 62
i
C L1ME3A_3end#L 496 GACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.50
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 21 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/1 124 146 (5) + (T)n Simple_repeat 1 23 (0) 1523
ANNOTATION EVIDENCE:
21 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/1 124 146 5 + (T)n Simple_repeat 1 23 0
21 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/1 124 146 (5) (T)n#Simple_repeat 1 23 (0) m_b1s252i2
ST-E00130:540 124 TTTTTTTTTTTTTTTTTTTTTTT 146
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 1165 10.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/2 3 151 (0) + AluSx SINE/Alu 49 197 (115) 1524
ANNOTATION EVIDENCE:
1165 10.74 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/2 3 151 0 + AluSx SINE/Alu 49 197 115
1165 10.74 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1209:14154:16129/2 3 151 (0) AluSx#SINE/Alu 49 197 (115) m_b2s356i28
ST-E00130:540 3 GAGCCAGGTGGATCACCTGAGGTCGGGAGTTCGAAACCAGCCTGGCCAAC 52
v i i i i
AluSx#SINE/Al 49 GAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAAC 98
ST-E00130:540 53 ATGGTGAAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGT 102
ii i v i i
AluSx#SINE/Al 99 ATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGT 148
ST-E00130:540 103 GGTGGGCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATC 151
i v i i i
AluSx#SINE/Al 149 GGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATC 197
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.18
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 910 11.6 1.6 0.0 ST-E00130:540:HVYVWCCXX:3:1211:32238:13211/1 31 151 (0) + AluSx SINE/Alu 1 123 (189) 1525
ANNOTATION EVIDENCE:
910 11.57 1.62 0.00 ST-E00130:540:HVYVWCCXX:3:1211:32238:13211/1 31 151 0 + AluSx SINE/Alu 1 123 189
910 11.57 1.62 0.00 ST-E00130:540:HVYVWCCXX:3:1211:32238:13211/1 31 151 (0) AluSx#SINE/Alu 1 123 (189) m_b4s356i58
ST-E00130:540 31 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 80
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 81 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 128
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 129 GGTGAAGCTCCATCTCTACTAAA 151
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAA 123
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.91
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.01 (1 / 120), avg. gap size = 2.00 (2 / 1)
+ 1156 7.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1211:32238:13211/2 9 151 (0) C AluSx SINE/Alu (21) 291 149 1526
ANNOTATION EVIDENCE:
1156 7.69 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1211:32238:13211/2 9 151 0 C AluSx SINE/Alu 149 291 21
1156 7.69 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1211:32238:13211/2 9 151 (0) C AluSx#SINE/Alu (21) 291 149 m_b4s356i4
ST-E00130:540 9 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 58
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 59 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCT 108
i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
ST-E00130:540 109 CCTGCCTCAGGCTCCTGAGTAGCTGGGATTGTAGGCGCCTGCC 151
v i ii vi
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCC 149
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.40
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 142), avg. gap size = 0.0 (0 / 0)
+ 1315 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1212:24038:28189/1 3 151 (0) C L1P3 LINE/L1 (2505) 3641 3493 1527
ANNOTATION EVIDENCE:
1315 2.01 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1212:24038:28189/1 3 151 0 C L1P3_orf2 LINE/L1 1384 1532 1762
1315 2.01 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1212:24038:28189/1 3 151 (0) C L1P3_orf2#LINE/L1 (1762) 1532 1384 m_b6s551i106
ST-E00130:540 3 TCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAG 52
i
C L1P3_orf2#LIN 1532 TCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAG 1483
ST-E00130:540 53 TTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGG 102
i
C L1P3_orf2#LIN 1482 TTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGG 1433
ST-E00130:540 103 CTGTGAATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAAT 151
v
C L1P3_orf2#LIN 1432 CTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGCTATTAAT 1384
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.04
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1071 6.6 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:1212:24038:28189/2 1 151 (0) + L1P3 LINE/L1 3298 3450 (2696) 1528
ANNOTATION EVIDENCE:
1071 6.62 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1212:24038:28189/2 1 151 0 + L1P3_orf2 LINE/L1 1189 1341 1953
1071 6.62 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:1212:24038:28189/2 1 151 (0) L1P3_orf2#LINE/L1 1189 1341 (1953) m_b6s551i165
ST-E00130:540 1 AAAGAGGATAATACCACTGATCCCACAGAAATACAAACTACCATCAGAGA 50
i vi
L1P3_orf2#LIN 1189 AAAGGGGATATCACCACTGATCCCACAGAAATACAAACTACCATCAGAGA 1238
ST-E00130:540 51 ATACTATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTG 100
i i vv
L1P3_orf2#LIN 1239 ATACTATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGG 1288
ST-E00130:540 101 ATAAATTCCTAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTC 148
i v -- v
L1P3_orf2#LIN 1289 ATAAATTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTC 1338
ST-E00130:540 149 GAA 151
L1P3_orf2#LIN 1339 GAA 1341
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.29
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 226 27.5 5.9 0.0 ST-E00130:540:HVYVWCCXX:3:1213:20699:73317/2 1 80 (71) + MIRb SINE/MIR 135 219 (49) 1529
ANNOTATION EVIDENCE:
226 27.50 5.88 0.00 ST-E00130:540:HVYVWCCXX:3:1213:20699:73317/2 1 80 71 + MIRb SINE/MIR 135 219 49
226 27.50 5.88 0.00 ST-E00130:540:HVYVWCCXX:3:1213:20699:73317/2 1 80 (71) MIRb#SINE/MIR 135 219 (49) m_b4s601i3
ST-E00130:540 1 CTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGCCAGATAACTGTGA 49
v i i ii - vi i v vi i vii
MIRb#SINE/MIR 135 CTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGA 184
ST-E00130:540 50 GGATTA---GAGAAAATAAACGTAAAA-GTCTAGC 80
--- v iv i i- ii
MIRb#SINE/MIR 185 GGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 35.85
Transitions / transversions = 2.14 (15/7)
Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.67 (5 / 3)
+ 811 9.2 0.0 0.9 ST-E00130:540:HVYVWCCXX:3:1214:17533:23495/1 42 151 (0) C AluY SINE/Alu (14) 297 189 1530
ANNOTATION EVIDENCE:
811 9.17 0.00 0.91 ST-E00130:540:HVYVWCCXX:3:1214:17533:23495/1 42 151 0 C AluY SINE/Alu 189 297 14
811 9.17 0.00 0.91 ST-E00130:540:HVYVWCCXX:3:1214:17533:23495/1 42 151 (0) C AluY#SINE/Alu (14) 297 189 m_b2s356i97
ST-E00130:540 42 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 91
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
ST-E00130:540 92 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 141
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
ST-E00130:540 142 GCCGTTCTCC 151
i
C AluY#SINE/Alu 198 GCCATTCTCC 189
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.24
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.01 (1 / 109), avg. gap size = 1.00 (1 / 1)
+ 687 20.9 0.0 0.7 ST-E00130:540:HVYVWCCXX:3:1214:17533:23495/2 1 149 (2) + AluY SINE/Alu 131 278 (33) 1531
ANNOTATION EVIDENCE:
687 20.95 0.00 0.67 ST-E00130:540:HVYVWCCXX:3:1214:17533:23495/2 1 149 2 + AluY SINE/Alu 131 278 33
687 20.95 0.00 0.67 ST-E00130:540:HVYVWCCXX:3:1214:17533:23495/2 1 149 (2) AluY#SINE/Alu 131 278 (33) m_b2s357i95
ST-E00130:540 1 AATTAGCCGGTCGTGGTAGTGGTCACGTGTAGTCCGAGCTCCTCGGGAGG 50
v i i v i v v v
AluY#SINE/Alu 131 AATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGG 180
ST-E00130:540 51 CTGAAGCAGGAGTTCGTCATGAACCTGGTGGTGTGGAGGTTTCAGTTAGC 100
i vvi v i i - iv i v v v
AluY#SINE/Alu 181 CTGAGGCAGGAGAATGGCGTGAACCCGG-GAGGCGGAGCTTGCAGTGAGC 229
ST-E00130:540 101 TGAGGTCATGCCAACGCTTTCCAGCCTGGGCGACGGATCGAGACTCCGT 149
i i ii vi vi i v
AluY#SINE/Alu 230 CGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT 278
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 18.10
Transitions / transversions = 1.07 (16/15)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)
+ 1220 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1214:21745:54629/1 1 150 (1) C L1P1 LINE/L1 (784) 5362 5213 1532
ANNOTATION EVIDENCE:
1220 2.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1214:21745:54629/1 1 150 1 C L1P1_orf2 LINE/L1 3104 3253 41
1220 2.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1214:21745:54629/1 1 150 (1) C L1P1_orf2#LINE/L1 (41) 3253 3104 m_b1s551i146
ST-E00130:540 1 TGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATG 50
C L1P1_orf2#LIN 3253 TGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATG 3204
ST-E00130:540 51 GGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCT 100
C L1P1_orf2#LIN 3203 GGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCT 3154
ST-E00130:540 101 GGATATTAGCCCTTTGTCAGTTGAGTAGGTTGCGAAGATTTTCTCCCGTT 150
v i i
C L1P1_orf2#LIN 3153 GGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATT 3104
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1258 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1214:21745:54629/2 1 151 (0) + L1P1 LINE/L1 5012 5162 (984) 1533
ANNOTATION EVIDENCE:
1258 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1214:21745:54629/2 1 151 0 + L1P1_orf2 LINE/L1 2903 3053 241
1258 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1214:21745:54629/2 1 151 (0) L1P1_orf2#LINE/L1 2903 3053 (241) m_b1s551i69
ST-E00130:540 1 ACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACC 50
i ?
L1P1_orf2#LIN 2903 ACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACC 2952
ST-E00130:540 51 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 100
L1P1_orf2#LIN 2953 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 3002
ST-E00130:540 101 AATGGCAACAAAAGACAGAATTGACAAATGGGATCTAATTAAACTAAAGA 150
v i
L1P1_orf2#LIN 3003 AATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGA 3052
ST-E00130:540 151 G 151
L1P1_orf2#LIN 3053 G 3053
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1304 1.3 0.0 0.7 ST-E00130:540:HVYVWCCXX:3:1215:28422:59376/1 1 151 (0) + L1PA3 LINE/L1 5715 5864 (291) 1534
ANNOTATION EVIDENCE:
1304 1.33 0.00 0.66 ST-E00130:540:HVYVWCCXX:3:1215:28422:59376/1 1 151 0 + L1PA3_3end LINE/L1 462 611 291
1304 1.33 0.00 0.66 ST-E00130:540:HVYVWCCXX:3:1215:28422:59376/1 1 151 (0) L1PA3_3end#LINE/L1 462 611 (291) m_b1s551i343
ST-E00130:540 1 CACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACT 50
L1PA3_3end#LI 462 CACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACT 511
ST-E00130:540 51 GGATTAAGAAACTGTGGCACATATACACCATGGAATACTATGCAGCCATA 100
v
L1PA3_3end#LI 512 GGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATA 561
ST-E00130:540 101 AAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAATTGGAGA 150
- i
L1PA3_3end#LI 562 AAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAATTGGAAA 610
ST-E00130:540 151 T 151
L1PA3_3end#LI 611 T 611
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 806 5.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1215:28422:59376/2 52 151 (0) C L1PA2 LINE/L1 (2) 6153 6054 1535
ANNOTATION EVIDENCE:
806 5.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1215:28422:59376/2 52 151 0 C L1PA2_3end LINE/L1 801 900 2
806 5.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1215:28422:59376/2 52 151 (0) C L1PA2_3end#LINE/L1 (2) 900 801 m_b1s551i442
ST-E00130:540 52 TTATTTTTTTTATTACGCTTTAAGTTTTAGGGTACATGTGCACATTGTGC 101
v ii
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 102 AGGTTAGTTACATATGTATACATGTGCCCTGCTGGTGTGCTGCACCCACT 151
v i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.22
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0)
+ 286 21.2 11.2 0.0 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/1 73 147 (4) + L1MC4 LINE/L1 7416 7520 (522) 1536
ANNOTATION EVIDENCE:
283 21.33 13.79 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/1 73 147 4 + L1MC4a_3end LINE/L1 2163 2249 380
283 21.33 13.79 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/1 73 147 (4) L1MC4a_3end#LINE/L1 2163 2249 (380) m_b3s551i141
ST-E00130:540 73 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 113
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
ST-E00130:540 114 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGA 147
--- i i i i i
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAA 2249
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.34
Transitions / transversions = 15.00 (15/1)
Gap_init rate = 0.05 (4 / 74), avg. gap size = 3.00 (12 / 4)
286 21.21 10.81 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/1 82 147 4 + L1MC4_3end LINE/L1 2194 2267 522
286 21.21 10.81 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/1 82 147 (4) L1MC4_3end#LINE/L1 2194 2267 (522) m_b3s551i142
ST-E00130:540 82 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 123
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
ST-E00130:540 124 AAGGAAACATCAGACAAACTCAGA 147
i i i
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAA 2267
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.60
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 4.00 (8 / 2)
+ 237 9.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/2 1 33 (118) C L1MC4 LINE/L1 (248) 7794 7762 1537
ANNOTATION EVIDENCE:
237 9.09 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/2 1 33 118 C L1MC4_3end LINE/L1 2509 2541 248
237 9.09 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/2 1 33 (118) C L1MC4_3end#LINE/L1 (248) 2541 2509 m_b3s551i90
ST-E00130:540 1 CAGTATAATCATCAAAATCAGGAAGTTAACATT 33
i i i
C L1MC4_3end#LI 2541 CAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.03
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 463 18.4 5.8 0.0 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/2 38 135 (16) C L1MC4 LINE/L1 (393) 7649 7546 1537
ANNOTATION EVIDENCE:
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/2 38 135 16 C L1MC4_3end LINE/L1 2293 2396 393
463 18.37 5.77 0.00 ST-E00130:540:HVYVWCCXX:3:1217:11393:56422/2 38 135 (16) C L1MC4_3end#LINE/L1 (393) 2396 2293 m_b3s551i91
ST-E00130:540 38 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 87
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 88 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 131
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
ST-E00130:540 132 GGTC 135
i
C L1MC4_3end#LI 2296 GGCC 2293
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 6.00 (6 / 1)
+ 16 19.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/1 113 142 (9) + (CA)n Simple_repeat 1 30 (0) 1538
ANNOTATION EVIDENCE:
16 19.09 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/1 113 142 9 + (CA)n Simple_repeat 1 30 0
16 19.09 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/1 113 142 (9) (CA)n#Simple_repeat 1 30 (0) m_b3s252i0
ST-E00130:540 113 CACACACACACTCATACGCAGATACACACA 142
v i i v i
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACA 30
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 313 14.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/2 2 55 (96) + L1MC4 LINE/L1 7596 7649 (393) 1539
ANNOTATION EVIDENCE:
313 14.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/2 2 55 96 + L1MC4_3end LINE/L1 2343 2396 393
313 14.81 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/2 2 55 (96) L1MC4_3end#LINE/L1 2343 2396 (393) m_b3s551i50
ST-E00130:540 2 AAGAACTGTTCCAGATTGAAGGAGACTAAACAGACTACACACCTAAATGC 51
i i v vvv v
L1MC4_3end#LI 2343 AGGAACTGTTCCAGATTAAAGGAGACTAAAGAGACATGACAACTAAATGC 2392
ST-E00130:540 52 AATG 55
i
L1MC4_3end#LI 2393 AACG 2396
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.46
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 508 16.3 8.9 0.0 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/2 60 151 (0) + L1MC4 LINE/L1 7762 7862 (180) 1539
ANNOTATION EVIDENCE:
508 16.30 8.91 0.00 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/2 60 151 0 + L1MC4_3end LINE/L1 2509 2609 180
508 16.30 8.91 0.00 ST-E00130:540:HVYVWCCXX:3:1217:30787:44697/2 60 151 (0) L1MC4_3end#LINE/L1 2509 2609 (180) m_b3s551i51
ST-E00130:540 60 AATGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGT 109
i i i i vii ii vi
L1MC4_3end#LI 2509 AATGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAAT 2558
ST-E00130:540 110 ATCCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCA 150
i i i --------- i
L1MC4_3end#LI 2559 GTCCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCA 2608
ST-E00130:540 151 T 151
L1MC4_3end#LI 2609 T 2609
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.26
Transitions / transversions = 6.50 (13/2)
Gap_init rate = 0.01 (1 / 91), avg. gap size = 9.00 (9 / 1)
+ 727 9.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1217:4239:55420/1 58 151 (0) + AluY SINE/Alu 1 94 (217) 1540
ANNOTATION EVIDENCE:
727 9.57 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:4239:55420/1 58 151 0 + AluY SINE/Alu 1 94 217
727 9.57 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1217:4239:55420/1 58 151 (0) AluY#SINE/Alu 1 94 (217) m_b2s357i69
ST-E00130:540 58 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 107
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 108 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTA 151
v i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTA 94
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.95
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0)
+ 1142 7.6 0.0 0.7 ST-E00130:540:HVYVWCCXX:3:1217:4239:55420/2 7 151 (0) C AluY SINE/Alu (14) 297 154 1541
ANNOTATION EVIDENCE:
1142 7.64 0.00 0.69 ST-E00130:540:HVYVWCCXX:3:1217:4239:55420/2 7 151 0 C AluY SINE/Alu 154 297 14
1142 7.64 0.00 0.69 ST-E00130:540:HVYVWCCXX:3:1217:4239:55420/2 7 151 (0) C AluY#SINE/Alu (14) 297 154 m_b2s356i90
ST-E00130:540 7 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 56
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
ST-E00130:540 57 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 106
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
ST-E00130:540 107 GCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCG 151
i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCG 154
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.68
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 144), avg. gap size = 1.00 (1 / 1)
+ 1242 4.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:1219:5680:66461/1 1 151 (0) C L1P3 LINE/L1 (3061) 3085 2935 1542
ANNOTATION EVIDENCE:
1242 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1219:5680:66461/1 1 151 0 C L1P3_orf2 LINE/L1 826 976 2318
1242 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:1219:5680:66461/1 1 151 (0) C L1P3_orf2#LINE/L1 (2318) 976 826 m_b7s551i15
ST-E00130:540 1 TCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGATCTTTCC 50
i
C L1P3_orf2#LIN 976 TCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTTCC 927
ST-E00130:540 51 CACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGC 100
i v ?
C L1P3_orf2#LIN 926 CGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAAACACTGC 877
ST-E00130:540 101 TTTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTCTTATTGG 150
i i
C L1P3_orf2#LIN 876 TTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTCATTGG 827
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 826 T 826
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 904 5.0 0.7 7.3 ST-E00130:540:HVYVWCCXX:3:1220:10531:1133/2 2 151 (0) C L1P3 LINE/L1 (2918) 3228 3089 1543
ANNOTATION EVIDENCE:
904 5.04 0.72 7.33 ST-E00130:540:HVYVWCCXX:3:1220:10531:1133/2 2 151 0 C L1P3_orf2 LINE/L1 980 1119 2175
904 5.04 0.72 7.33 ST-E00130:540:HVYVWCCXX:3:1220:10531:1133/2 2 151 (0) C L1P3_orf2#LINE/L1 (2175) 1119 980 m_b6s551i239
ST-E00130:540 2 TGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTT 51
i i v -
C L1P3_orf2#LIN 1119 TATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTT 1071
ST-E00130:540 52 TGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTC 100
i i---------- -i v
C L1P3_orf2#LIN 1070 TGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTGCTC 1031
ST-E00130:540 101 TGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCT 150
C L1P3_orf2#LIN 1030 TGATCTTAGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCT 981
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 980 T 980
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.54
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.00 (12 / 12)
+ 275 28.0 5.1 0.0 ST-E00130:540:HVYVWCCXX:3:1221:20446:51781/2 39 131 (20) + MIRb SINE/MIR 122 219 (49) 1544
ANNOTATION EVIDENCE:
275 27.96 5.11 0.00 ST-E00130:540:HVYVWCCXX:3:1221:20446:51781/2 39 131 20 + MIRb SINE/MIR 122 219 49
275 27.96 5.11 0.00 ST-E00130:540:HVYVWCCXX:3:1221:20446:51781/2 39 131 (20) MIRb#SINE/MIR 122 219 (49) m_b4s601i18
ST-E00130:540 39 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 87
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
ST-E00130:540 88 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAA-CGTCTAGC 131
vi i vii --- v iv i - ii
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.41
Transitions / transversions = 1.89 (17/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 1066 8.8 0.7 0.7 ST-E00130:540:HVYVWCCXX:3:1221:31588:7620/1 1 149 (2) C AluY SINE/Alu (64) 247 99 1545
ANNOTATION EVIDENCE:
1066 8.78 0.67 0.67 ST-E00130:540:HVYVWCCXX:3:1221:31588:7620/1 1 149 2 C AluY SINE/Alu 99 247 64
1066 8.78 0.67 0.67 ST-E00130:540:HVYVWCCXX:3:1221:31588:7620/1 1 149 (2) C AluY#SINE/Alu (64) 247 99 m_b2s357i87
ST-E00130:540 1 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 50
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
ST-E00130:540 51 GCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGTCGCCCGC 100
i i v
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGC 149
ST-E00130:540 101 CACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACC 149
iv - i i
C AluY#SINE/Alu 148 CACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 99
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.68
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 1.00 (2 / 2)
+ 15 18.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/1 45 76 (75) + (TGTG)n Simple_repeat 1 32 (0) 1546
ANNOTATION EVIDENCE:
15 18.13 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/1 45 76 75 + (TGTG)n Simple_repeat 1 32 0
15 18.13 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/1 45 76 (75) (TGTG)n#Simple_repeat 1 32 (0) m_b4s252i12
ST-E00130:540 45 TGTGTGTGTGTGTGTATGTGGGTGCATGTATG 76
i v ii i
(TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 321 8.3 4.0 0.0 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/1 104 151 (0) C 7SLRNA srpRNA (11) 309 260 1547
ANNOTATION EVIDENCE:
321 8.33 4.00 0.00 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/1 104 151 0 C 7SLRNA SINE/Alu 260 309 11
321 8.33 4.00 0.00 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/1 104 151 (0) C 7SLRNA#SINE/Alu (11) 309 260 m_b4s502i4
ST-E00130:540 104 TTTTTTTTT--GAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAG 151
-- ii v i
C 7SLRNA#SINE/A 309 TTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGGAGTGCAG 260
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.95
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1)
+ 1216 8.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/2 1 151 (0) + AluSx SINE/Alu 90 240 (72) 1548
ANNOTATION EVIDENCE:
1216 8.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/2 1 151 0 + AluSx SINE/Alu 90 240 72
1216 8.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2101:14844:14406/2 1 151 (0) AluSx#SINE/Alu 90 240 (72) m_b4s356i22
ST-E00130:540 1 CTGGCCAATATGGTGAAACTCCATCTCTACGAAAAACACAAAAATTAGCC 50
i i i v i
AluSx#SINE/Al 90 CTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCC 139
ST-E00130:540 51 AGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCA 100
i v iv i i
AluSx#SINE/Al 140 GGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCA 189
ST-E00130:540 101 GGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGC 150
i i
AluSx#SINE/Al 190 GGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGC 239
ST-E00130:540 151 G 151
AluSx#SINE/Al 240 G 240
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.88
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1323 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2104:16183:24954/1 1 151 (0) + L1P1 LINE/L1 5144 5294 (852) 1549
ANNOTATION EVIDENCE:
1323 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:16183:24954/1 1 151 0 + L1P1_orf2 LINE/L1 3035 3185 109
1323 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:16183:24954/1 1 151 (0) L1P1_orf2#LINE/L1 3035 3185 (109) m_b1s551i119
ST-E00130:540 1 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 50
L1P1_orf2#LIN 3035 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 3084
ST-E00130:540 51 GTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATC 100
i
L1P1_orf2#LIN 3085 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATC 3134
ST-E00130:540 101 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 150
L1P1_orf2#LIN 3135 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 3184
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3185 A 3185
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1337 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2104:16183:24954/2 1 151 (0) C L1P1 LINE/L1 (587) 5568 5418 1550
ANNOTATION EVIDENCE:
1337 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:16183:24954/2 1 151 0 C L1PA3_3end LINE/L1 165 315 587
1337 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:16183:24954/2 1 151 (0) C L1PA3_3end#LINE/L1 (587) 315 165 m_b1s551i248
ST-E00130:540 1 CAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGGATTCCTA 50
vi
C L1PA3_3end#LI 315 CAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTA 266
ST-E00130:540 51 TTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACT 100
i
C L1PA3_3end#LI 265 TTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATT 216
ST-E00130:540 101 GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCAT 150
C L1PA3_3end#LI 215 GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCAT 166
ST-E00130:540 151 T 151
C L1PA3_3end#LI 165 T 165
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1077 2.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/1 1 124 (27) + L1PA2 LINE/L1 6030 6153 (2) 1551
ANNOTATION EVIDENCE:
1077 2.42 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/1 1 124 27 + L1PA2_3end LINE/L1 777 900 2
1077 2.42 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/1 1 124 (27) L1PA2_3end#LINE/L1 777 900 (2) m_b1s551i433
ST-E00130:540 1 ATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCA 50
i
L1PA2_3end#LI 777 ATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCA 826
ST-E00130:540 51 CATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAA 100
L1PA2_3end#LI 827 CATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAA 876
ST-E00130:540 101 CTTAAAGTGTAATAAAAAAAATAA 124
i v
L1PA2_3end#LI 877 CTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.71
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/2 3 24 (127) + (A)n Simple_repeat 1 22 (0) 1552
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/2 3 24 127 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/2 3 24 (127) (A)n#Simple_repeat 1 22 (0) m_b1s252i1
ST-E00130:540 3 AAAAAAAAAAAAAAAAAAAAAA 24
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 255 25.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/2 86 151 (0) + L1M5 LINE/L1 5741 5806 (367) 1553
ANNOTATION EVIDENCE:
255 25.76 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/2 86 151 0 + L1ME3A_3end LINE/L1 488 553 367
255 25.76 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2104:4584:50111/2 86 151 (0) L1ME3A_3end#LINE/L1 488 553 (367) m_b1s551i522
ST-E00130:540 86 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 135
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
ST-E00130:540 136 ATAACAAAATAATATA 151
i iii v
L1ME3A_3end#L 538 ACAATGGAATACTATA 553
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.54
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 1092 11.9 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:2106:11992:7708/2 1 151 (0) C AluSx SINE/Alu (122) 190 38 1554
ANNOTATION EVIDENCE:
1092 11.92 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:2106:11992:7708/2 1 151 0 C AluSx SINE/Alu 38 190 122
1092 11.92 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:2106:11992:7708/2 1 151 (0) C AluSx#SINE/Alu (122) 190 38 m_b4s356i34
ST-E00130:540 1 CTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCC 50
i i vi v
C AluSx#SINE/Al 190 CTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC 141
ST-E00130:540 51 TGGCTAATTTTTGTGGTTTTAGTAGAGATGGAGTTTCACCATATTGGCCA 100
i iv i i i
C AluSx#SINE/Al 140 CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCA 91
ST-E00130:540 101 GGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCTTCAGCCTCCC 148
v i i-- i i i i
C AluSx#SINE/Al 90 GGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCC 41
ST-E00130:540 149 AAA 151
C AluSx#SINE/Al 40 AAA 38
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.56
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1195 8.0 0.7 0.0 ST-E00130:540:HVYVWCCXX:3:2106:29589:23460/1 2 151 (0) + AluY SINE/Alu 50 200 (111) 1555
ANNOTATION EVIDENCE:
1195 8.00 0.67 0.00 ST-E00130:540:HVYVWCCXX:3:2106:29589:23460/1 2 151 0 + AluY SINE/Alu 50 200 111
1195 8.00 0.67 0.00 ST-E00130:540:HVYVWCCXX:3:2106:29589:23460/1 2 151 (0) AluY#SINE/Alu 50 200 (111) m_b2s356i61
ST-E00130:540 2 AGGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACGTG 51
v i i ii
AluY#SINE/Alu 50 AGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACG 99
ST-E00130:540 52 GTGAAACCCCATCTCTACTAAAAACACAAAAA-TTAGATGGGCGTGGTGG 100
i i - vi
AluY#SINE/Alu 100 GTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGG 149
ST-E00130:540 101 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAAGCAGGAGAACGGCA 150
i i i
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
ST-E00130:540 151 T 151
AluY#SINE/Alu 200 T 200
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 282 13.7 3.8 0.0 ST-E00130:540:HVYVWCCXX:3:2106:29589:23460/2 101 151 (0) C 7SLRNA srpRNA (4) 316 264 1556
ANNOTATION EVIDENCE:
282 13.73 3.77 0.00 ST-E00130:540:HVYVWCCXX:3:2106:29589:23460/2 101 151 0 C 7SLRNA SINE/Alu 264 316 4
282 13.73 3.77 0.00 ST-E00130:540:HVYVWCCXX:3:2106:29589:23460/2 101 151 (0) C 7SLRNA#SINE/Alu (4) 316 264 m_b2s502i2
ST-E00130:540 101 TTTTATTTCTTTTTTT--GAGACGGAGGCTCGCTCTGTCGCCCAGGCTGG 148
v i -- i v v i
C 7SLRNA#SINE/A 316 TTTTTTTTTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGG 267
ST-E00130:540 149 AAT 151
i
C 7SLRNA#SINE/A 266 AGT 264
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.28
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 2.00 (2 / 1)
+ 1253 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2107:2189:64456/1 1 151 (0) C L1P3 LINE/L1 (3054) 3092 2942 1557
ANNOTATION EVIDENCE:
1253 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2107:2189:64456/1 1 151 0 C L1P3_orf2 LINE/L1 833 983 2311
1253 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2107:2189:64456/1 1 151 (0) C L1P3_orf2#LINE/L1 (2311) 983 833 m_b7s551i11
ST-E00130:540 1 TCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTTGATTTTAGA 50
i
C L1P3_orf2#LIN 983 TCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGA 934
ST-E00130:540 51 TCTTTCCCACTTTGTCCTGTGGGCATTTAGTGCTATAAATTTCCCTCTAA 100
i v ?
C L1P3_orf2#LIN 933 TCTTTCCCGCTTTCTCNTGTGGGCATTTAGTGCTATAAATTTCCCTCTAA 884
ST-E00130:540 101 ACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACATTGTGTCTTTGTTC 150
i
C L1P3_orf2#LIN 883 ACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTC 834
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 833 T 833
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1311 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2110:10460:67006/1 1 151 (0) + L1P1 LINE/L1 5328 5478 (677) 1558
ANNOTATION EVIDENCE:
1311 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2110:10460:67006/1 1 151 0 + L1PA2_3end LINE/L1 75 225 677
1311 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2110:10460:67006/1 1 151 (0) L1PA2_3end#LINE/L1 75 225 (677) m_b1s551i209
ST-E00130:540 1 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 50
L1PA2_3end#LI 75 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 124
ST-E00130:540 51 AACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATC 100
L1PA2_3end#LI 125 AACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATC 174
ST-E00130:540 101 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAA 150
i
L1PA2_3end#LI 175 AAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAA 224
ST-E00130:540 151 A 151
L1PA2_3end#LI 225 A 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1330 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2110:10460:67006/2 1 151 (0) C L1P1 LINE/L1 (337) 5818 5668 1559
ANNOTATION EVIDENCE:
1330 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2110:10460:67006/2 1 151 0 C L1PA2_3end LINE/L1 415 565 337
1330 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2110:10460:67006/2 1 151 (0) C L1PA2_3end#LINE/L1 (337) 565 415 m_b1s551i322
ST-E00130:540 1 TTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACAGTTTCTTA 50
v
C L1PA2_3end#LI 565 TTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTA 516
ST-E00130:540 51 ATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTAT 100
C L1PA2_3end#LI 515 ATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTAT 466
ST-E00130:540 101 TGTGAATAATGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCGGC 150
i i
C L1PA2_3end#LI 465 TGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGC 416
ST-E00130:540 151 A 151
C L1PA2_3end#LI 415 A 415
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 310 23.2 12.8 0.0 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/1 70 151 (0) + L1MC4 LINE/L1 7416 7527 (515) 1560
ANNOTATION EVIDENCE:
299 23.17 12.76 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/1 70 151 0 + L1MC4a_3end LINE/L1 2163 2256 373
299 23.17 12.76 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/1 70 151 (0) L1MC4a_3end#LINE/L1 2163 2256 (373) m_b3s551i137
ST-E00130:540 70 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 110
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
ST-E00130:540 111 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGG 151
--- i i i i i vii
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAATTGAGGG 2256
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.15
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.05 (4 / 81), avg. gap size = 3.00 (12 / 4)
310 23.29 9.88 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/1 79 151 0 + L1MC4_3end LINE/L1 2194 2274 515
310 23.29 9.88 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/1 79 151 (0) L1MC4_3end#LINE/L1 2194 2274 (515) m_b3s551i138
ST-E00130:540 79 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 120
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
ST-E00130:540 121 AAGGAAACATCAGACAAACTCAGAGCAAGGG 151
i i i vii
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGG 2274
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.77
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 4.00 (8 / 2)
+ 583 19.5 7.4 0.0 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/2 1 113 (38) C L1MC4 LINE/L1 (159) 7883 7762 1561
ANNOTATION EVIDENCE:
583 19.47 7.37 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/2 1 113 38 C L1MC4_3end LINE/L1 2509 2630 159
583 19.47 7.37 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6279:14582/2 1 113 (38) C L1MC4_3end#LINE/L1 (159) 2630 2509 m_b3s551i32
ST-E00130:540 1 TGAGATGAAATCGCACACGTGATGCTCCTT---------ATACTTCAGTG 41
vv i i v i ? i ---------
C L1MC4_3end#LI 2630 TGAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAATACTTCAGTG 2581
ST-E00130:540 42 TATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCA 91
i i i iv ii iiv i i i
C L1MC4_3end#LI 2580 TGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTA 2531
ST-E00130:540 92 TCAAAATCAGGAAGTTAACATT 113
i
C L1MC4_3end#LI 2530 TCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.39
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.01 (1 / 112), avg. gap size = 9.00 (9 / 1)
+ 310 23.2 12.8 0.0 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/1 70 151 (0) + L1MC4 LINE/L1 7416 7527 (515) 1562
ANNOTATION EVIDENCE:
299 23.17 12.76 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/1 70 151 0 + L1MC4a_3end LINE/L1 2163 2256 373
299 23.17 12.76 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/1 70 151 (0) L1MC4a_3end#LINE/L1 2163 2256 (373) m_b3s551i139
ST-E00130:540 70 AGAAGAGGA----ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-- 110
i v ---- i i iiii i i --- i --
L1MC4a_3end#L 2163 AGAAGGGCACAACATCACTTCTGTGGTATTCTTGCCAAAAATGCATAACC 2212
ST-E00130:540 111 ---ATTTAATCATAAGGAAACATCAGACAAACTCAGAGCAAGGG 151
--- i i i i i vii
L1MC4a_3end#L 2213 TCAATCTAATCATGAGAAAACATCAGACAAACCCAAATTGAGGG 2256
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.15
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.05 (4 / 81), avg. gap size = 3.00 (12 / 4)
310 23.29 9.88 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/1 79 151 0 + L1MC4_3end LINE/L1 2194 2274 515
310 23.29 9.88 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/1 79 151 (0) L1MC4_3end#LINE/L1 2194 2274 (515) m_b3s551i140
ST-E00130:540 79 ATTACTTTTGCAACATTCTCGTCAAA---GTATAA-----ATTTAATCAT 120
i i iiii ii i --- i ----- i
L1MC4_3end#LI 2194 ATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCTGAATCTAATCAT 2243
ST-E00130:540 121 AAGGAAACATCAGACAAACTCAGAGCAAGGG 151
i i i vii
L1MC4_3end#LI 2244 GAGGAAACATCAGACAAACCCAAATTGAGGG 2274
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.77
Transitions / transversions = 16.00 (16/1)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 4.00 (8 / 2)
+ 583 19.5 7.4 0.0 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/2 1 113 (38) C L1MC4 LINE/L1 (159) 7883 7762 1563
ANNOTATION EVIDENCE:
583 19.47 7.37 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/2 1 113 38 C L1MC4_3end LINE/L1 2509 2630 159
583 19.47 7.37 0.00 ST-E00130:540:HVYVWCCXX:3:2110:6431:14635/2 1 113 (38) C L1MC4_3end#LINE/L1 (159) 2630 2509 m_b3s551i33
ST-E00130:540 1 TGAGATGAAATCGCACACGTGATGCTCCTT---------ATACTTCAGTG 41
vv i i v i ? i ---------
C L1MC4_3end#LI 2630 TGAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAATACTTCAGTG 2581
ST-E00130:540 42 TATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCA 91
i i i iv ii iiv i i i
C L1MC4_3end#LI 2580 TGTATTTCCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTA 2531
ST-E00130:540 92 TCAAAATCAGGAAGTTAACATT 113
i
C L1MC4_3end#LI 2530 TCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.39
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.01 (1 / 112), avg. gap size = 9.00 (9 / 1)
+ 854 16.8 0.0 1.3 ST-E00130:540:HVYVWCCXX:3:2112:20963:38684/2 1 151 (0) + AluSx SINE/Alu 105 253 (59) 1564
ANNOTATION EVIDENCE:
854 16.78 0.00 1.32 ST-E00130:540:HVYVWCCXX:3:2112:20963:38684/2 1 151 0 + AluSx SINE/Alu 105 253 59
854 16.78 0.00 1.32 ST-E00130:540:HVYVWCCXX:3:2112:20963:38684/2 1 151 (0) AluSx#SINE/Alu 105 253 (59) m_b5s356i6
ST-E00130:540 1 AAACCCCATCTCTACTAACAATACAAAAAAATTAGCCAGGCATTGTGGTG 50
i v -- i i v i
AluSx#SINE/Al 105 AAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCGTGGTGGCG 152
ST-E00130:540 51 GGAGCCTGTAATCATAGCTGCTCAGGAGGCTGCGGCAGGCCAATTGCTTG 100
v v vi i i v vv i
AluSx#SINE/Al 153 CGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTG 202
ST-E00130:540 101 AACCTACTAGGCGGAGGGTGCAGTGAGCAGATATAGCACCACTGCACTCC 150
iivv v v v v i
AluSx#SINE/Al 203 AACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC 252
ST-E00130:540 151 A 151
AluSx#SINE/Al 253 A 253
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 12.96
Transitions / transversions = 0.79 (11/14)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 273 27.6 3.9 10.9 ST-E00130:540:HVYVWCCXX:3:2112:30695:25271/1 14 151 (0) + L1MC4 LINE/L1 6462 6589 (1453) 1565
ANNOTATION EVIDENCE:
273 27.65 3.90 10.87 ST-E00130:540:HVYVWCCXX:3:2112:30695:25271/1 14 151 0 + L1MC4_3end LINE/L1 1209 1336 1453
273 27.65 3.90 10.87 ST-E00130:540:HVYVWCCXX:3:2112:30695:25271/1 14 151 (0) L1MC4_3end#LINE/L1 1209 1336 (1453) m_b3s551i159
ST-E00130:540 14 TTGAGCAAATAAGTAAATGCATTCAGGTTGAGTGGATAGTCAGGTTTTGG 63
ii v? v i - i- i i--
L1MC4_3end#LI 1209 TTGAGCAAATAAGTAAATATATTGNGGATAA-TGGG-AGCCAGGTTTC-- 1254
ST-E00130:540 64 GGTGTTTTTTTTAACTGCTAGTAAAGCAATTTATAAATTTGGACAGAAAA 113
----------- v iii vi vi v i v v iiii
L1MC4_3end#LI 1255 -----------TCACTGTCGGAGAAGGGAGTTACAAATATGGAAAGGGGG 1293
ST-E00130:540 114 AAAG-----ATAAACTGTGTGATGTTGGCTTGGATTTGAAGAT 151
i ----- i iv i v v i i
L1MC4_3end#LI 1294 AAGGCTAGAATGAACCCTGTGGTGTTGGATTGGAATTGGAGGT 1336
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.47
Transitions / transversions = 2.00 (22/11)
Gap_init rate = 0.12 (16 / 137), avg. gap size = 1.25 (20 / 16)
+ 574 19.6 7.4 0.0 ST-E00130:540:HVYVWCCXX:3:2112:30695:25271/2 1 112 (39) C L1MC4 LINE/L1 (160) 7882 7762 1566
ANNOTATION EVIDENCE:
574 19.64 7.44 0.00 ST-E00130:540:HVYVWCCXX:3:2112:30695:25271/2 1 112 39 C L1MC4_3end LINE/L1 2509 2629 160
574 19.64 7.44 0.00 ST-E00130:540:HVYVWCCXX:3:2112:30695:25271/2 1 112 (39) C L1MC4_3end#LINE/L1 (160) 2629 2509 m_b3s551i35
ST-E00130:540 1 GAGATGAAATCGCACACGTGATGCTCCTT---------ATACTTCAGTGT 41
vv i i v i ? i ---------
C L1MC4_3end#LI 2629 GAGAGTAAGTTGCAGACATNATGCCCCTTTACCCCTAAATACTTCAGTGT 2580
ST-E00130:540 42 ATATTTCCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCAT 91
i i i iv ii iiv i i i
C L1MC4_3end#LI 2579 GTATTTCCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTAT 2530
ST-E00130:540 92 CAAAATCAGGAAGTTAACATT 112
i
C L1MC4_3end#LI 2529 CAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.63
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 9.00 (9 / 1)
+ 1152 11.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2112:4452:3858/1 1 151 (0) C AluSx SINE/Alu (118) 194 44 1567
ANNOTATION EVIDENCE:
1152 11.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2112:4452:3858/1 1 151 0 C AluSx SINE/Alu 44 194 118
1152 11.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2112:4452:3858/1 1 151 (0) C AluSx#SINE/Alu (118) 194 44 m_b2s356i30
ST-E00130:540 1 TCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCA 50
i i i v i
C AluSx#SINE/Al 194 TCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCA 145
ST-E00130:540 51 CACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTG 100
i i v i ii
C AluSx#SINE/Al 144 CGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTG 95
ST-E00130:540 101 GCCAGGCTGGTTTCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGCC 150
i i i i v v
C AluSx#SINE/Al 94 GCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCC 45
ST-E00130:540 151 T 151
C AluSx#SINE/Al 44 T 44
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.81
Transitions / transversions = 3.25 (13/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 ST-E00130:540:HVYVWCCXX:3:2113:20456:43466/1 26 118 (33) + MIRb SINE/MIR 122 219 (49) 1568
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:3:2113:20456:43466/1 26 118 33 + MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:3:2113:20456:43466/1 26 118 (33) MIRb#SINE/MIR 122 219 (49) m_b4s601i15
ST-E00130:540 26 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 74
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
ST-E00130:540 75 CAGATAACTGTGAGGATTA---GAGAAAATAAACGTAAAA-GTCTAGC 118
vi i vii --- v iv i i- ii
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGC 219
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 267 26.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2114:4584:50779/1 9 76 (75) C L1M5 LINE/L1 (365) 5808 5741 1569
ANNOTATION EVIDENCE:
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2114:4584:50779/1 9 76 75 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2114:4584:50779/1 9 76 (75) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i517
ST-E00130:540 9 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 58
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 59 CTATTGTTGGACATTTAG 76
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1065 12.2 0.0 1.3 ST-E00130:540:HVYVWCCXX:3:2114:4584:50779/2 2 151 (0) + AluSx SINE/Alu 122 269 (43) 1570
ANNOTATION EVIDENCE:
1065 12.16 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2114:4584:50779/2 2 151 0 + AluSx SINE/Alu 122 269 43
1065 12.16 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2114:4584:50779/2 2 151 (0) AluSx#SINE/Alu 122 269 (43) m_b2s357i17
ST-E00130:540 2 AAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCT 51
i i i v i
AluSx#SINE/Al 122 AAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCT 171
ST-E00130:540 52 ACTCAGGAAGCTGAGGCAGGAGAATCACTTGAACTCAGGAGGCAGAGATT 101
i i i i i i i
AluSx#SINE/Al 172 ACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT 221
ST-E00130:540 102 GCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTTTGACGAAGC 151
i ii --i ii
AluSx#SINE/Al 222 GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG--CGACAGAGC 269
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.09
Transitions / transversions = 17.00 (17/1)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 1232 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2117:25530:31406/1 1 151 (0) C L1P1 LINE/L1 (1047) 5099 4949 1571
ANNOTATION EVIDENCE:
1232 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2117:25530:31406/1 1 151 0 C L1P1_orf2 LINE/L1 2840 2990 304
1232 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2117:25530:31406/1 1 151 (0) C L1P1_orf2#LINE/L1 (304) 2990 2840 m_b1s551i37
ST-E00130:540 1 TTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCAGAG 50
? vv
C L1P1_orf2#LIN 2990 TTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAG 2941
ST-E00130:540 51 GTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAA 100
i
C L1P1_orf2#LIN 2940 GTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAA 2891
ST-E00130:540 101 TCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTTC 150
i v v
C L1P1_orf2#LIN 2890 TCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTC 2841
ST-E00130:540 151 A 151
C L1P1_orf2#LIN 2840 A 2840
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.48
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1289 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2118:14905:6812/2 1 151 (0) C L1P1 LINE/L1 (962) 5184 5034 1572
ANNOTATION EVIDENCE:
1289 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:14905:6812/2 1 151 0 C L1P1_orf2 LINE/L1 2925 3075 219
1289 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:14905:6812/2 1 151 (0) C L1P1_orf2#LINE/L1 (219) 3075 2925 m_b1s551i81
ST-E00130:540 1 AGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGT 50
C L1P1_orf2#LIN 3075 AGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGT 3026
ST-E00130:540 51 CAATTCTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCC 100
i v
C L1P1_orf2#LIN 3025 CAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCC 2976
ST-E00130:540 101 TTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGT 150
?
C L1P1_orf2#LIN 2975 TTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGT 2926
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 2925 T 2925
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1155 12.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/1 1 151 (0) + AluSx SINE/Alu 99 249 (63) 1573
ANNOTATION EVIDENCE:
1155 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/1 1 151 0 + AluSx SINE/Alu 99 249 63
1155 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/1 1 151 (0) AluSx#SINE/Alu 99 249 (63) m_b2s356i15
ST-E00130:540 1 ATGGTGAAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGT 50
ii i v i i
AluSx#SINE/Al 99 ATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGT 148
ST-E00130:540 51 GGTGGGCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCA 100
i v i i i i
AluSx#SINE/Al 149 GGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG 198
ST-E00130:540 101 CTTGAACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCA 150
i i i i i ii
AluSx#SINE/Al 199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248
ST-E00130:540 151 C 151
AluSx#SINE/Al 249 C 249
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/2 20 108 (43) C L1M5 LINE/L1 (293) 5831 5741 1574
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/2 20 108 43 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/2 20 108 (43) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i492
ST-E00130:540 20 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 69
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 70 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 108
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/2 41 108 43 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2828:4526/2 41 108 (43) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i493
ST-E00130:540 41 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 90
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 91 CTATTGTTGGACATTTAG 108
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1155 12.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/1 1 151 (0) + AluSx SINE/Alu 99 249 (63) 1575
ANNOTATION EVIDENCE:
1155 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/1 1 151 0 + AluSx SINE/Alu 99 249 63
1155 12.58 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/1 1 151 (0) AluSx#SINE/Alu 99 249 (63) m_b2s356i16
ST-E00130:540 1 ATGGTGAAACCTTGTCTCTATTTAAAATACAAAAATTAGCTGGGTGTGGT 50
ii i v i i
AluSx#SINE/Al 99 ATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGT 148
ST-E00130:540 51 GGTGGGCACCTGTAATCCCAGCTACTCAGGAAGCTGAGGCAGGAGAATCA 100
i v i i i i
AluSx#SINE/Al 149 GGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG 198
ST-E00130:540 101 CTTGAACTCAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCA 150
i i i i i ii
AluSx#SINE/Al 199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248
ST-E00130:540 151 C 151
AluSx#SINE/Al 249 C 249
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.68
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/2 20 108 (43) C L1M5 LINE/L1 (293) 5831 5741 1576
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/2 20 108 43 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/2 20 108 (43) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i494
ST-E00130:540 20 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 69
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 70 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 108
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/2 41 108 43 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:2879:4509/2 41 108 (43) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i495
ST-E00130:540 41 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 90
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 91 CTATTGTTGGACATTTAG 108
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1325 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2118:30157:14670/1 1 151 (0) C L1P1 LINE/L1 (850) 5296 5146 1577
ANNOTATION EVIDENCE:
1325 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:30157:14670/1 1 151 0 C L1P1_orf2 LINE/L1 3037 3187 107
1325 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:30157:14670/1 1 151 (0) C L1P1_orf2#LINE/L1 (107) 3187 3037 m_b1s551i120
ST-E00130:540 1 TCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTG 50
C L1P1_orf2#LIN 3187 TCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTG 3138
ST-E00130:540 51 TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTTGCCTGTT 100
i
C L1P1_orf2#LIN 3137 TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTT 3088
ST-E00130:540 101 CACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTA 150
C L1P1_orf2#LIN 3087 CACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTA 3038
ST-E00130:540 151 G 151
C L1P1_orf2#LIN 3037 G 3037
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1301 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2118:30157:14670/2 1 151 (0) + L1P1 LINE/L1 5047 5197 (949) 1578
ANNOTATION EVIDENCE:
1301 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:30157:14670/2 1 151 0 + L1P1_orf2 LINE/L1 2938 3088 206
1301 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2118:30157:14670/2 1 151 (0) L1P1_orf2#LINE/L1 2938 3088 (206) m_b1s551i85
ST-E00130:540 1 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 50
?
L1P1_orf2#LIN 2938 AACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 2987
ST-E00130:540 51 TAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATC 100
v i
L1P1_orf2#LIN 2988 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3037
ST-E00130:540 101 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 150
L1P1_orf2#LIN 3038 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3087
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3088 A 3088
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1088 7.3 2.0 0.0 ST-E00130:540:HVYVWCCXX:3:2120:17797:13123/1 2 151 (0) C L1P3 LINE/L1 (2258) 3888 3736 1579
ANNOTATION EVIDENCE:
1088 7.33 1.96 0.00 ST-E00130:540:HVYVWCCXX:3:2120:17797:13123/1 2 151 0 C L1P3_orf2 LINE/L1 1627 1779 1515
1088 7.33 1.96 0.00 ST-E00130:540:HVYVWCCXX:3:2120:17797:13123/1 2 151 (0) C L1P3_orf2#LINE/L1 (1515) 1779 1627 m_b6s551i40
ST-E00130:540 2 GTTTTTGTCATTCGTTCTGTTTATGTGATGGATTATGTTTATTGATTTGT 51
v i i
C L1P3_orf2#LIN 1779 GTTTTTGTCATTGGTTCTGTTTATGTGATGGATTACGTTTATTGATTTGC 1730
ST-E00130:540 52 GTATGCTGAATCAGCCTTGCGTCCCAGGGATGAAGCTGACTTGATAGTGG 101
i i i i v
C L1P3_orf2#LIN 1729 GTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCGACTTGATCGTGG 1680
ST-E00130:540 102 TGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATC 148
v --- i i
C L1P3_orf2#LIN 1679 TGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATT 1630
ST-E00130:540 149 GAG 151
C L1P3_orf2#LIN 1629 GAG 1627
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.12
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 3.00 (3 / 1)
+ 1014 5.4 5.1 0.0 ST-E00130:540:HVYVWCCXX:3:2120:17797:13123/2 3 151 (0) + L1P3 LINE/L1 3244 3400 (2746) 1580
ANNOTATION EVIDENCE:
1014 5.37 5.10 0.00 ST-E00130:540:HVYVWCCXX:3:2120:17797:13123/2 3 151 0 + L1P3_orf2 LINE/L1 1135 1291 2003
1014 5.37 5.10 0.00 ST-E00130:540:HVYVWCCXX:3:2120:17797:13123/2 3 151 (0) L1P3_orf2#LINE/L1 1135 1291 (2003) m_b6s551i179
ST-E00130:540 3 AGACTAATAAAGA--------GAGAAGAATCAAATAGACTCAATAAAAAA 44
-------- v
L1P3_orf2#LIN 1135 AGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGACACAATAAAAAA 1184
ST-E00130:540 45 TGATAAAGAGGATAATACCACTGATCCCACAGAAATACAAACTACCATCA 94
i vi
L1P3_orf2#LIN 1185 TGATAAAGGGGATATCACCACTGATCCCACAGAAATACAAACTACCATCA 1234
ST-E00130:540 95 GAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAAGAA 144
i i
L1P3_orf2#LIN 1235 GAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAA 1284
ST-E00130:540 145 AGTGATA 151
vv
L1P3_orf2#LIN 1285 ATGGATA 1291
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 8.00 (8 / 1)
+ 687 2.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/1 1 83 (68) + L1PA2 LINE/L1 6071 6153 (2) 1581
ANNOTATION EVIDENCE:
687 2.41 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/1 1 83 68 + L1PA2_3end LINE/L1 818 900 2
687 2.41 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/1 1 83 (68) L1PA2_3end#LINE/L1 818 900 (2) m_b1s551i447
ST-E00130:540 1 AGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGT 50
L1PA2_3end#LI 818 AGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGT 867
ST-E00130:540 51 ACCCTAAAACTTAAAGTGTAATAAAAAAAATAA 83
i v
L1PA2_3end#LI 868 ACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.45
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/2 13 34 (117) + (A)n Simple_repeat 1 22 (0) 1582
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/2 13 34 117 + (A)n Simple_repeat 1 22 0
20 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/2 13 34 (117) (A)n#Simple_repeat 1 22 (0) m_b1s252i0
ST-E00130:540 13 AAAAAAAAAAAAAAAAAAAAAA 34
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 243 24.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/2 96 149 (2) + L1M5 LINE/L1 5741 5794 (379) 1583
ANNOTATION EVIDENCE:
243 24.07 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/2 96 149 2 + L1ME3A_3end LINE/L1 488 541 379
243 24.07 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2121:5639:8974/2 96 149 (2) L1ME3A_3end#LINE/L1 488 541 (379) m_b1s551i529
ST-E00130:540 96 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATATGTCTAC 145
i v i i v vi ii i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
ST-E00130:540 146 ATAA 149
i
L1ME3A_3end#L 538 ACAA 541
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.69
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 1233 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2122:25317:19047/2 1 151 (0) C L1P1 LINE/L1 (1023) 5123 4973 1584
ANNOTATION EVIDENCE:
1233 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2122:25317:19047/2 1 151 0 C L1P1_orf2 LINE/L1 2864 3014 280
1233 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2122:25317:19047/2 1 151 (0) C L1P1_orf2#LINE/L1 (280) 3014 2864 m_b1s551i49
ST-E00130:540 1 TTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCC 50
C L1P1_orf2#LIN 3014 TTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCC 2965
ST-E00130:540 51 TATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTT 100
?
C L1P1_orf2#LIN 2964 TATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTT 2915
ST-E00130:540 101 TAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTCTATCA 150
i i v v
C L1P1_orf2#LIN 2914 TAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAA 2865
ST-E00130:540 151 G 151
C L1P1_orf2#LIN 2864 G 2864
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 425 14.6 0.0 7.9 ST-E00130:540:HVYVWCCXX:3:2122:6573:39809/1 63 151 (0) C AluSx SINE/Alu (8) 304 223 1585
ANNOTATION EVIDENCE:
425 14.63 0.00 7.87 ST-E00130:540:HVYVWCCXX:3:2122:6573:39809/1 63 151 0 C AluSx SINE/Alu 223 304 8
425 14.63 0.00 7.87 ST-E00130:540:HVYVWCCXX:3:2122:6573:39809/1 63 151 (0) C AluSx#SINE/Alu (8) 304 223 m_b5s357i1
ST-E00130:540 63 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 112
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 113 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTG 151
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTG 223
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.02
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.00 (7 / 7)
+ 978 13.5 0.0 1.3 ST-E00130:540:HVYVWCCXX:3:2122:6573:39809/2 1 150 (1) + AluSx SINE/Alu 45 192 (120) 1586
ANNOTATION EVIDENCE:
978 13.51 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2122:6573:39809/2 1 150 1 + AluSx SINE/Alu 45 192 120
978 13.51 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2122:6573:39809/2 1 150 (1) AluSx#SINE/Alu 45 192 (120) m_b5s357i43
ST-E00130:540 1 GGCCAAGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGC 50
i i i i i i
AluSx#SINE/Al 45 GGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGC 94
ST-E00130:540 51 CAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGG 100
i v i -- i
AluSx#SINE/Al 95 CAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGG 142
ST-E00130:540 101 CATTGTGGTGGGAGCCTGTAATCATAGCTGCTAAGGAGGCTGAGGCAGGA 150
i v i v v vi i vi
AluSx#SINE/Al 143 CGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.52
Transitions / transversions = 2.33 (14/6)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 425 14.6 0.0 7.9 ST-E00130:540:HVYVWCCXX:3:2122:7557:39264/1 63 151 (0) C AluSx SINE/Alu (8) 304 223 1587
ANNOTATION EVIDENCE:
425 14.63 0.00 7.87 ST-E00130:540:HVYVWCCXX:3:2122:7557:39264/1 63 151 0 C AluSx SINE/Alu 223 304 8
425 14.63 0.00 7.87 ST-E00130:540:HVYVWCCXX:3:2122:7557:39264/1 63 151 (0) C AluSx#SINE/Alu (8) 304 223 m_b5s357i2
ST-E00130:540 63 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 112
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 113 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTG 151
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTG 223
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.02
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.00 (7 / 7)
+ 978 13.5 0.0 1.3 ST-E00130:540:HVYVWCCXX:3:2122:7557:39264/2 1 150 (1) + AluSx SINE/Alu 45 192 (120) 1588
ANNOTATION EVIDENCE:
978 13.51 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2122:7557:39264/2 1 150 1 + AluSx SINE/Alu 45 192 120
978 13.51 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2122:7557:39264/2 1 150 (1) AluSx#SINE/Alu 45 192 (120) m_b5s357i44
ST-E00130:540 1 GGCCAAGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGC 50
i i i i i i
AluSx#SINE/Al 45 GGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGC 94
ST-E00130:540 51 CAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGG 100
i v i -- i
AluSx#SINE/Al 95 CAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGG 142
ST-E00130:540 101 CATTGTGGTGGGAGCCTGTAATCATAGCTGCTAAGGAGGCTGAGGCAGGA 150
i v i v v vi i vi
AluSx#SINE/Al 143 CGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.52
Transitions / transversions = 2.33 (14/6)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 425 14.6 0.0 7.9 ST-E00130:540:HVYVWCCXX:3:2122:8217:38965/1 63 151 (0) C AluSx SINE/Alu (8) 304 223 1589
ANNOTATION EVIDENCE:
425 14.63 0.00 7.87 ST-E00130:540:HVYVWCCXX:3:2122:8217:38965/1 63 151 0 C AluSx SINE/Alu 223 304 8
425 14.63 0.00 7.87 ST-E00130:540:HVYVWCCXX:3:2122:8217:38965/1 63 151 (0) C AluSx#SINE/Alu (8) 304 223 m_b5s357i3
ST-E00130:540 63 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 112
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 113 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTG 151
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTG 223
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.02
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.00 (7 / 7)
+ 978 13.5 0.0 1.3 ST-E00130:540:HVYVWCCXX:3:2122:8217:38965/2 1 150 (1) + AluSx SINE/Alu 45 192 (120) 1590
ANNOTATION EVIDENCE:
978 13.51 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2122:8217:38965/2 1 150 1 + AluSx SINE/Alu 45 192 120
978 13.51 0.00 1.33 ST-E00130:540:HVYVWCCXX:3:2122:8217:38965/2 1 150 (1) AluSx#SINE/Alu 45 192 (120) m_b5s357i45
ST-E00130:540 1 GGCCAAGGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGC 50
i i i i i i
AluSx#SINE/Al 45 GGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGC 94
ST-E00130:540 51 CAACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGG 100
i v i -- i
AluSx#SINE/Al 95 CAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGG 142
ST-E00130:540 101 CATTGTGGTGGGAGCCTGTAATCATAGCTGCTAAGGAGGCTGAGGCAGGA 150
i v i v v vi i vi
AluSx#SINE/Al 143 CGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.52
Transitions / transversions = 2.33 (14/6)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 928 3.6 0.7 7.3 ST-E00130:540:HVYVWCCXX:3:2122:9648:32900/2 1 151 (0) + L1P3 LINE/L1 3058 3198 (2948) 1591
ANNOTATION EVIDENCE:
928 3.57 0.71 7.28 ST-E00130:540:HVYVWCCXX:3:2122:9648:32900/2 1 151 0 + L1P3_orf2 LINE/L1 949 1089 2205
928 3.57 0.71 7.28 ST-E00130:540:HVYVWCCXX:3:2122:9648:32900/2 1 151 (0) L1P3_orf2#LINE/L1 949 1089 (2205) m_b6s551i251
ST-E00130:540 1 CTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAA 50
L1P3_orf2#LIN 949 CTAACATCACAATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAA 998
ST-E00130:540 51 AGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGA 99
v i-
L1P3_orf2#LIN 999 AGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGA 1048
ST-E00130:540 100 TAGAGACACACACACACAAAAAAAACCTTTCAAAAAAATCAATTAATCCA 149
----------i i - v
L1P3_orf2#LIN 1049 TAGAGACAC----------GAAAAACCCTTCAAAAAA-TCAATGAATCCA 1087
ST-E00130:540 150 GG 151
L1P3_orf2#LIN 1088 GG 1089
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.99
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 957 5.7 0.8 0.0 ST-E00130:540:HVYVWCCXX:3:2123:9140:27029/2 30 151 (0) C L1PA2 LINE/L1 (2) 6153 6031 1592
ANNOTATION EVIDENCE:
957 5.74 0.81 0.00 ST-E00130:540:HVYVWCCXX:3:2123:9140:27029/2 30 151 0 C L1PA2_3end LINE/L1 778 900 2
957 5.74 0.81 0.00 ST-E00130:540:HVYVWCCXX:3:2123:9140:27029/2 30 151 (0) C L1PA2_3end#LINE/L1 (2) 900 778 m_b1s551i436
ST-E00130:540 30 TTATTTTTTGTATTACACTGTAAGTTTTAGGGTACATGTGCACATTGTGC 79
v v i v
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 80 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 129
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
ST-E00130:540 130 AACTCATCATTTA-CATTAGGTA 151
i i -
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTA 778
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.39
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.01 (1 / 121), avg. gap size = 1.00 (1 / 1)
+ 584 14.3 0.0 6.2 ST-E00130:540:HVYVWCCXX:3:2123:9516:21561/2 1 112 (39) + AluSx SINE/Alu 200 304 (8) 1593
ANNOTATION EVIDENCE:
584 14.28 0.00 6.25 ST-E00130:540:HVYVWCCXX:3:2123:9516:21561/2 1 112 39 + AluSx SINE/Alu 200 304 8
584 14.28 0.00 6.25 ST-E00130:540:HVYVWCCXX:3:2123:9516:21561/2 1 112 (39) AluSx#SINE/Alu 200 304 (8) m_b5s357i10
ST-E00130:540 1 TTGAATGAGGGAGGCGGAGGTTGCAGTGAGCAGATATAGCACCACTGCAC 50
ivv v v v i
AluSx#SINE/Al 200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249
ST-E00130:540 51 TCCAGCCTGCAGCCTGGGTGATGGAGTGAGACTCCATCTCAAAAAAACAC 100
------- i ii i i v v
AluSx#SINE/Al 250 TCCAGCCTG-------GGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA 292
ST-E00130:540 101 AAAAACAAAAAA 112
v
AluSx#SINE/Al 293 AAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.73
Transitions / transversions = 0.88 (7/8)
Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7)
+ 267 27.2 0.0 0.3 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/1 19 107 (44) C L1M5 LINE/L1 (293) 5831 5741 1594
ANNOTATION EVIDENCE:
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/1 19 107 44 C L1ME4a_3end LINE/L1 491 578 293
244 29.54 0.00 1.12 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/1 19 107 (44) C L1ME4a_3end#LINE/L1 (293) 578 491 m_b1s551i500
ST-E00130:540 19 AAAATAATAATTTTTAAAGTTTGCATATTATTTTGTTATGTAGACATATT 68
i- ? v vi v iii ii i i ii ii
C L1ME4a_3end#L 578 AAAAC-ATNATTTTTAATGGCTGCATAATATTCCATCGTATGGATGTACC 530
ST-E00130:540 69 ACAGGTTATATATCCATTTTACTATTGTTGGACATTTAG 107
i iv v v ? iiv
C L1ME4a_3end#L 529 ATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAG 491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.65
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/1 40 107 44 C L1ME3A_3end LINE/L1 488 555 365
267 26.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/1 40 107 (44) C L1ME3A_3end#LINE/L1 (365) 555 488 m_b1s551i501
ST-E00130:540 40 TGCATATTATTTTGTTATGTAGACATATTACAGGTTATATATCCATTTTA 89
i v iii i ii i ii iv v i
C L1ME3A_3end#L 555 TGTATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTA 506
ST-E00130:540 90 CTATTGTTGGACATTTAG 107
i v i
C L1ME3A_3end#L 505 CTGTTGATGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1122 12.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/2 2 151 (0) + AluSx SINE/Alu 32 181 (131) 1595
ANNOTATION EVIDENCE:
1122 12.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/2 2 151 0 + AluSx SINE/Alu 32 181 131
1122 12.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2124:20476:66039/2 2 151 (0) AluSx#SINE/Alu 32 181 (131) m_b2s356i31
ST-E00130:540 2 CAGCAATTTGGGAGGCAGAGCCAGGTGGATCACCTGAGGTCGGGAGTTCG 51
v v v i i i
AluSx#SINE/Al 32 CAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCG 81
ST-E00130:540 52 AAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTAAAATACAAA 101
i ii i v
AluSx#SINE/Al 82 AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAA 131
ST-E00130:540 102 AATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTACTCAGGAAG 151
i i i v i i i
AluSx#SINE/Al 132 AATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGG 181
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.59
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0)
+ 1244 4.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2204:18051:50516/2 1 151 (0) C L1P1 LINE/L1 (1052) 5094 4944 1596
ANNOTATION EVIDENCE:
1244 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2204:18051:50516/2 1 151 0 C L1P1_orf2 LINE/L1 2835 2985 309
1244 3.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2204:18051:50516/2 1 151 (0) C L1P1_orf2#LINE/L1 (309) 2985 2835 m_b1s551i34
ST-E00130:540 1 CATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTAGGTTTT 50
?
C L1P1_orf2#LIN 2985 CATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTT 2936
ST-E00130:540 51 CTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCAT 100
i
C L1P1_orf2#LIN 2935 CTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCAT 2886
ST-E00130:540 101 CTTGAATTGATTTTTCTATCAGGTGTAAGGATGGGATCCAGTTTCAGCTT 150
i v v v
C L1P1_orf2#LIN 2885 CTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTT 2836
ST-E00130:540 151 T 151
C L1P1_orf2#LIN 2835 T 2835
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1261 2.0 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:2205:12540:41005/1 1 151 (0) + L1P3 LINE/L1 3422 3574 (2572) 1597
ANNOTATION EVIDENCE:
1261 1.99 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:2205:12540:41005/1 1 151 0 + L1P3_orf2 LINE/L1 1313 1465 1829
1261 1.99 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:2205:12540:41005/1 1 151 (0) L1P3_orf2#LINE/L1 1313 1465 (1829) m_b6s551i131
ST-E00130:540 1 TCCCAA--CTAAAGCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACA 48
-- v
L1P3_orf2#LIN 1313 TCCCAAGACTAAACCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACA 1362
ST-E00130:540 49 AGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCC 98
L1P3_orf2#LIN 1363 AGTTCTGAAATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCC 1412
ST-E00130:540 99 AGGACCAGAGGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAGGAGC 148
v i
L1P3_orf2#LIN 1413 AGGACCAGACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGC 1462
ST-E00130:540 149 TGG 151
L1P3_orf2#LIN 1463 TGG 1465
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1022 7.5 3.3 0.0 ST-E00130:540:HVYVWCCXX:3:2205:12540:41005/2 1 146 (5) C L1P3 LINE/L1 (2333) 3813 3663 1598
ANNOTATION EVIDENCE:
1022 7.53 3.31 0.00 ST-E00130:540:HVYVWCCXX:3:2205:12540:41005/2 1 146 5 C L1P3_orf2 LINE/L1 1554 1704 1590
1022 7.53 3.31 0.00 ST-E00130:540:HVYVWCCXX:3:2205:12540:41005/2 1 146 (5) C L1P3_orf2#LINE/L1 (1590) 1704 1554 m_b6s551i58
ST-E00130:540 1 AGGGATGAAGCTGACTTGATAGTGGTGGATAAGCGTTTTGATG---TGCT 47
i v v ---
C L1P3_orf2#LIN 1704 AGGGATGAAGCCGACTTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCT 1655
ST-E00130:540 48 GGATTCAGGTTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCATC 97
i v i i
C L1P3_orf2#LIN 1654 GGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATC 1605
ST-E00130:540 98 ACGGATAATGGCCTGAAATTTTCTTTTTC--TTGTTTCTCTGCCAGGTTT 145
v v i-- v
C L1P3_orf2#LIN 1604 AGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTT 1555
ST-E00130:540 146 T 146
C L1P3_orf2#LIN 1554 T 1554
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.91
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.01 (2 / 145), avg. gap size = 2.50 (5 / 2)
+ 250 30.8 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:2205:4219:52186/1 69 146 (5) + MIRb SINE/MIR 122 200 (68) 1599
ANNOTATION EVIDENCE:
250 30.77 1.26 0.00 ST-E00130:540:HVYVWCCXX:3:2205:4219:52186/1 69 146 5 + MIRb SINE/MIR 122 200 68
250 30.77 1.26 0.00 ST-E00130:540:HVYVWCCXX:3:2205:4219:52186/1 69 146 (5) MIRb#SINE/MIR 122 200 (68) m_b4s601i25
ST-E00130:540 69 GGGCCTTCGTACCCTCATCAGTAGAGTGAAGATA-TATCACTTACCTGGC 117
i iv vi v i i ii - vi i v
MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC 171
ST-E00130:540 118 CAGATAACTGTGAGGATTAGAGAAAATAA 146
vi i vii i vi i
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAA 200
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 41.70
Transitions / transversions = 2.00 (16/8)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1)
+ 1160 8.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2208:14905:53399/1 1 151 (0) C AluSx SINE/Alu (37) 275 125 1600
ANNOTATION EVIDENCE:
1160 7.95 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2208:14905:53399/1 1 151 0 C AluSx SINE/Alu 125 275 37
1160 7.95 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2208:14905:53399/1 1 151 (0) C AluSx#SINE/Alu (37) 275 125 m_b4s357i34
ST-E00130:540 1 AATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGGCTCA 50
i i i
C AluSx#SINE/Al 275 AGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCA 226
ST-E00130:540 51 CTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCT 100
i i i
C AluSx#SINE/Al 225 CTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCC 176
ST-E00130:540 101 GAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTG 150
i vi v i i
C AluSx#SINE/Al 175 GAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTA 126
ST-E00130:540 151 T 151
C AluSx#SINE/Al 125 T 125
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.17
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 596 12.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2208:14905:53399/2 69 150 (1) + AluY SINE/Alu 1 82 (229) 1601
ANNOTATION EVIDENCE:
596 12.20 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2208:14905:53399/2 69 150 1 + AluY SINE/Alu 1 82 229
596 12.20 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2208:14905:53399/2 69 150 (1) AluY#SINE/Alu 1 82 (229) m_b4s357i60
ST-E00130:540 69 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 118
i i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 119 AGCAGGCAGATCACAAGGTCAGGAGTTTGAGA 150
i i i i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGA 82
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.50
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0)
+ 1143 8.0 0.7 0.7 ST-E00130:540:HVYVWCCXX:3:2208:22627:38086/1 1 151 (0) C AluY SINE/Alu (43) 268 118 1602
ANNOTATION EVIDENCE:
1143 8.00 0.66 0.66 ST-E00130:540:HVYVWCCXX:3:2208:22627:38086/1 1 151 0 C AluY SINE/Alu 118 268 43
1143 8.00 0.66 0.66 ST-E00130:540:HVYVWCCXX:3:2208:22627:38086/1 1 151 (0) C AluY#SINE/Alu (43) 268 118 m_b2s356i77
ST-E00130:540 1 GCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATCTCGGCTCACTGCAA 50
i ii
C AluY#SINE/Alu 268 GCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAA 219
ST-E00130:540 51 CCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCCTCCCGAGTA 100
v i - i i i i
C AluY#SINE/Alu 218 GCTCCGCCT-CCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTA 170
ST-E00130:540 101 GCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTT 149
iv - i
C AluY#SINE/Alu 169 GCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTT 120
ST-E00130:540 150 TA 151
C AluY#SINE/Alu 119 TA 118
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.56
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1207 8.0 0.7 0.0 ST-E00130:540:HVYVWCCXX:3:2208:27285:58356/1 1 150 (1) C AluY SINE/Alu (102) 209 59 1603
ANNOTATION EVIDENCE:
1207 8.00 0.67 0.00 ST-E00130:540:HVYVWCCXX:3:2208:27285:58356/1 1 150 1 C AluY SINE/Alu 59 209 102
1207 8.00 0.67 0.00 ST-E00130:540:HVYVWCCXX:3:2208:27285:58356/1 1 150 (1) C AluY#SINE/Alu (102) 209 59 c_b2s352i5
ST-E00130:540 1 CCCAGGTTCATGCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTA 50
i i i i
C AluY#SINE/Alu 209 CCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTA 160
ST-E00130:540 51 CAGGCGCCCGCCACCACGCCCATCTAA-TTTTTGTGTTTTTAGTAGAGAT 99
iv - i i
C AluY#SINE/Alu 159 CAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGAC 110
ST-E00130:540 100 GGGGTTTCACCACGTTAGCCAGGATGGTCTTGATCTCCTGACCTCATGAT 149
ii i i
C AluY#SINE/Alu 109 GGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGAT 60
ST-E00130:540 150 C 150
C AluY#SINE/Alu 59 C 59
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.93
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)
+ 229 7.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2208:27285:58356/2 125 151 (0) C SVA_F Retroposon/SVA (955) 420 394 1604
ANNOTATION EVIDENCE:
229 7.41 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2208:27285:58356/2 125 151 0 C SVA_F Retroposon/SVA 394 420 955
229 7.41 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2208:27285:58356/2 125 151 (0) C SVA_F#Retroposon/SVA (955) 420 394 m_b2s502i1
ST-E00130:540 125 TGTAATCTCAGCACTTTGGGAGGCCAA 151
i i
C SVA_F#Retropo 420 TGCAATCTCGGCACTTTGGGAGGCCAA 394
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.25
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 1267 6.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2209:21450:32390/1 1 151 (0) + AluSx SINE/Alu 113 263 (49) 1605
ANNOTATION EVIDENCE:
1267 6.62 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2209:21450:32390/1 1 151 0 + AluSx SINE/Alu 113 263 49
1267 6.62 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2209:21450:32390/1 1 151 (0) AluSx#SINE/Alu 113 263 (49) m_b4s356i16
ST-E00130:540 1 TCTCTACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATA 50
i i v iv i
AluSx#SINE/Al 113 TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTA 162
ST-E00130:540 51 ATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAG 100
i i
AluSx#SINE/Al 163 ATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAG 212
ST-E00130:540 101 GCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCG 150
i i
AluSx#SINE/Al 213 GCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCG 262
ST-E00130:540 151 A 151
AluSx#SINE/Al 263 A 263
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.38
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 262 29.0 5.1 0.0 ST-E00130:540:HVYVWCCXX:3:2209:21450:32390/2 44 136 (15) C MIRb SINE/MIR (49) 219 122 1606
ANNOTATION EVIDENCE:
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:3:2209:21450:32390/2 44 136 15 C MIRb SINE/MIR 122 219 49
262 29.03 5.11 0.00 ST-E00130:540:HVYVWCCXX:3:2209:21450:32390/2 44 136 (15) C MIRb#SINE/MIR (49) 219 122 m_b4s601i10
ST-E00130:540 44 GCTAGAC-TTTTACGTTTATTTTCTC---TAATCCTCACAGTTATCTGGC 89
ii -i i vi v --- iiv i iv
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
ST-E00130:540 90 CAGGTAAGTGATA-TATCTTCACTCTACTGATGAGGGTACGAAGGCCC 136
v i iv - ii i i v iv vi i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 2.00 (18/9)
Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3)
+ 18 17.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2211:24393:38333/2 63 94 (57) + (T)n Simple_repeat 1 32 (0) 1607
ANNOTATION EVIDENCE:
18 17.57 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2211:24393:38333/2 63 94 57 + (T)n Simple_repeat 1 32 0
18 17.57 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2211:24393:38333/2 63 94 (57) (T)n#Simple_repeat 1 32 (0) m_b2s252i2
ST-E00130:540 63 TTTTTTTTTTTTCTATTTTTAAATTTTTTTTT 94
i v vvv
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 978 8.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2212:32217:4632/1 31 151 (0) + AluSx SINE/Alu 14 134 (178) 1608
ANNOTATION EVIDENCE:
978 8.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2212:32217:4632/1 31 151 0 + AluSx SINE/Alu 14 134 178
978 8.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2212:32217:4632/1 31 151 (0) AluSx#SINE/Alu 14 134 (178) m_b6s356i20
ST-E00130:540 31 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGAGGGTGGATCA 80
i v i v i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 81 CCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCAT 130
i i i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGT 113
ST-E00130:540 131 CTCTACGAAAAATAAAAAAAT 151
v v
AluSx#SINE/Al 114 CTCTACTAAAAATACAAAAAT 134
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.49
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0)
+ 22 10.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2212:32217:4632/2 41 71 (80) + (T)n Simple_repeat 1 31 (0) 1609
ANNOTATION EVIDENCE:
22 10.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2212:32217:4632/2 41 71 80 + (T)n Simple_repeat 1 31 0
22 10.47 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2212:32217:4632/2 41 71 (80) (T)n#Simple_repeat 1 31 (0) m_b6s252i2
ST-E00130:540 41 TTTTTGTGTTTTTTATTTTTTTTTTTTTTTT 71
v v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 1178 6.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2214:4726:67937/1 1 151 (0) C L1P3 LINE/L1 (3187) 2959 2809 1610
ANNOTATION EVIDENCE:
1178 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2214:4726:67937/1 1 151 0 C L1P3_orf2 LINE/L1 700 850 2444
1178 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2214:4726:67937/1 1 151 (0) C L1P3_orf2#LINE/L1 (2444) 850 700 m_b7s551i56
ST-E00130:540 1 ACATTGTGTCTTTGTTCTTATTGGTTTCAAAGAACTTACTTATTTCTGCC 50
i i ?i
C L1P3_orf2#LIN 850 ACGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACTTNTTTATTTCTGCC 801
ST-E00130:540 51 TTCATTTCATTATTTACCTAGTAGTCATTCAGGAGCAGGTTGTTCAGTTT 100
v i i
C L1P3_orf2#LIN 800 TTAATTTCGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTT 751
ST-E00130:540 101 CCATGTAGTTGTGTGGTTTTGAGTGAGTTTCTTAATCCTCAGTTCTAATT 150
i v
C L1P3_orf2#LIN 750 CCATGTAGTTGTGCGGTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAATT 701
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 700 T 700
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1090 9.4 0.7 0.7 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/1 2 151 (0) C AluY SINE/Alu (75) 236 87 1611
ANNOTATION EVIDENCE:
1090 9.39 0.67 0.67 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/1 2 151 0 C AluY SINE/Alu 87 236 75
1090 9.39 0.67 0.67 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/1 2 151 (0) C AluY#SINE/Alu (75) 236 87 m_b2s356i67
ST-E00130:540 2 GATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCATGCCGATCTCCT 51
v i - i i iv
C AluY#SINE/Alu 236 GATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCACGCCATTCTCCT 188
ST-E00130:540 52 GCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGGCACCACGCCCA 101
i v i
C AluY#SINE/Alu 187 GCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCG 138
ST-E00130:540 102 TCTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAG 150
v - i i ii
C AluY#SINE/Alu 137 GCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAG 88
ST-E00130:540 151 G 151
C AluY#SINE/Alu 87 G 87
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.02
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2)
+ 12 25.4 0.0 6.1 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/2 22 73 (78) + (TATTT)n Simple_repeat 1 49 (0) 1612
ANNOTATION EVIDENCE:
12 25.38 0.00 6.12 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/2 22 73 78 + (TATTT)n Simple_repeat 1 49 0
12 25.38 0.00 6.12 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/2 22 73 (78) (TATTT)n#Simple_repeat 1 49 (0) m_b2s252i1
ST-E00130:540 22 TACTTTATTTTTTTTTTAATTTTACTTGAATGTATTGGTTTCATATTTTA 71
i - v - i v v v -v v iv
(TATTT)n#Simp 1 TATTTTA-TTTTATTTT-ATTTTATTTTATTTTATT-TTATTTTATTTTA 47
ST-E00130:540 72 TT 73
(TATTT)n#Simp 48 TT 49
Matrix = Unknown
Transitions / transversions = 0.43 (3/7)
Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3)
+ 234 22.6 5.4 1.9 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/2 98 151 (0) C SVA_D Retroposon/SVA (1171) 215 160 1613
ANNOTATION EVIDENCE:
234 22.64 5.36 1.85 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/2 98 151 0 C SVA_D Retroposon/SVA 160 215 1171
234 22.64 5.36 1.85 ST-E00130:540:HVYVWCCXX:3:2217:19766:35907/2 98 151 (0) C SVA_D#Retroposon/SVA (1171) 215 160 m_b2s502i0
ST-E00130:540 98 CTATTAAAGAAAT---AAAACGAGGCCAGGCATGGTGGCTCACGCTTGTA 144
i ii i --- v - i i i v i i i
C SVA_D#Retropo 215 CCACCAAAAAAATACGAAAACCA-GTCAGGCGTGGCGGCGCGCGCCTGCA 167
ST-E00130:540 145 ATCGCAG 151
C SVA_D#Retropo 166 ATCGCAG 160
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.75
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.04 (2 / 53), avg. gap size = 2.00 (4 / 2)
+ 1273 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2218:2138:64580/1 1 151 (0) + L1P1 LINE/L1 5297 5447 (708) 1614
ANNOTATION EVIDENCE:
1273 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2218:2138:64580/1 1 151 0 + L1PA2_3end LINE/L1 44 194 708
1273 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2218:2138:64580/1 1 151 (0) L1PA2_3end#LINE/L1 44 194 (708) m_b1s551i189
ST-E00130:540 1 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 50
L1PA2_3end#LI 44 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 93
ST-E00130:540 51 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 100
L1PA2_3end#LI 94 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 143
ST-E00130:540 101 ATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACC 150
L1PA2_3end#LI 144 ATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACC 193
ST-E00130:540 151 A 151
L1PA2_3end#LI 194 A 194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1297 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2218:2138:64580/2 1 149 (2) C L1P1 LINE/L1 (609) 5546 5398 1615
ANNOTATION EVIDENCE:
1297 2.68 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2218:2138:64580/2 1 149 2 C L1PA2_3end LINE/L1 145 293 609
1297 2.68 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2218:2138:64580/2 1 149 (2) C L1PA2_3end#LINE/L1 (609) 293 145 m_b1s551i240
ST-E00130:540 1 TCCCACCAACAGTGTAAAAGGATTCCTATTTCTCCACATCCTCTCCAGCA 50
vi
C L1PA2_3end#LI 293 TCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCA 244
ST-E00130:540 51 CCTGTTGTGTCCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAGAT 100
v i
C L1PA2_3end#LI 243 CCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGAT 194
ST-E00130:540 101 GGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGA 149
C L1PA2_3end#LI 193 GGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGA 145
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.74
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 871 5.7 3.5 7.3 ST-E00130:540:HVYVWCCXX:3:2219:21298:58427/1 1 151 (0) + L1P3 LINE/L1 3110 3254 (2892) 1616
ANNOTATION EVIDENCE:
871 5.72 3.45 7.28 ST-E00130:540:HVYVWCCXX:3:2219:21298:58427/1 1 151 0 + L1P3_orf2 LINE/L1 1001 1145 2149
871 5.72 3.45 7.28 ST-E00130:540:HVYVWCCXX:3:2219:21298:58427/1 1 151 (0) L1P3_orf2#LINE/L1 1001 1145 (2149) m_b6s551i226
ST-E00130:540 1 CTAGCAGAAGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATA 49
v i-
L1P3_orf2#LIN 1001 CTAGCAGAAGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATA 1050
ST-E00130:540 50 GAGACACACACACACAAAAAAAACCTTTCAAAAAAATCAATTAATCCAGG 99
----------i i - v
L1P3_orf2#LIN 1051 GAGACAC----------GAAAAACCCTTCAAAAAA-TCAATGAATCCAGG 1089
ST-E00130:540 100 AGCTGATTTTTTGAAAAGATTAACAAAACAGA----CCGCTAGCAAGACT 145
i i ---- v
L1P3_orf2#LIN 1090 AGCTGGTTTTTTGAAAAGATTAACAAAATAGATAGACCGCTAGCCAGACT 1139
ST-E00130:540 146 AATAAA 151
L1P3_orf2#LIN 1140 AATAAA 1145
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.23 (16 / 13)
+ 1033 7.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:2219:21298:58427/2 1 151 (0) C L1P3 LINE/L1 (2708) 3438 3286 1617
ANNOTATION EVIDENCE:
1033 7.28 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:2219:21298:58427/2 1 151 0 C L1P3_orf2 LINE/L1 1177 1329 1965
1033 7.28 1.30 0.00 ST-E00130:540:HVYVWCCXX:3:2219:21298:58427/2 1 151 (0) C L1P3_orf2#LINE/L1 (1965) 1329 1177 m_b6s551i167
ST-E00130:540 1 CTGCTTTAG--TTGGGAGGTTGTAAGTGTCTAGGAATTTATCACTTTCTT 48
v -- v v i vv
C L1P3_orf2#LIN 1329 CTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTT 1280
ST-E00130:540 49 CTAGATTTTCTAGTTTATTTGCATAGAGGTATTTATAGTATTCTCTGATG 98
i i
C L1P3_orf2#LIN 1279 CTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTATAGTATTCTCTGATG 1230
ST-E00130:540 99 GTAGTTTGTATTTCTGTGGGATCAGTGGTATTATCCTCTTTATCATTTTT 148
iv i
C L1P3_orf2#LIN 1229 GTAGTTTGTATTTCTGTGGGATCAGTGGTGATATCCCCTTTATCATTTTT 1180
ST-E00130:540 149 TAT 151
C L1P3_orf2#LIN 1179 TAT 1177
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.01
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 779 13.7 0.0 5.1 ST-E00130:540:HVYVWCCXX:3:2220:5741:22546/2 1 138 (13) + AluSx SINE/Alu 174 304 (8) 1618
ANNOTATION EVIDENCE:
779 13.74 0.00 5.07 ST-E00130:540:HVYVWCCXX:3:2220:5741:22546/2 1 138 13 + AluSx SINE/Alu 174 304 8
779 13.74 0.00 5.07 ST-E00130:540:HVYVWCCXX:3:2220:5741:22546/2 1 138 (13) AluSx#SINE/Alu 174 304 (8) m_b5s357i27
ST-E00130:540 1 TCAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGC 50
i v i iivv
AluSx#SINE/Al 174 TCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGC 223
ST-E00130:540 51 AGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGG 100
v v v i ------- i ii
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG-------GGCGACAG 266
ST-E00130:540 101 AGTGAGACTCCGTCTCAAAAAAACACAAAAACAAAAAA 138
i v v v
AluSx#SINE/Al 267 AGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 10.21
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.00 (7 / 7)
+ 1200 8.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2222:10176:13176/1 1 147 (4) + AluSx SINE/Alu 60 206 (106) 1619
ANNOTATION EVIDENCE:
1200 8.16 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10176:13176/1 1 147 4 + AluSx SINE/Alu 60 206 106
1200 8.16 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10176:13176/1 1 147 (4) AluSx#SINE/Alu 60 206 (106) c_b6s352i0
ST-E00130:540 1 ATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACT 50
i i
AluSx#SINE/Al 60 ATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACC 109
ST-E00130:540 51 CCATCTCTACGAAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCT 100
i v v i i iv
AluSx#SINE/Al 110 CCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT 159
ST-E00130:540 101 GTAATCCCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACC 147
i v i
AluSx#SINE/Al 160 GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC 206
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.98
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 15 5.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2222:10176:13176/2 133 151 (0) + (T)n Simple_repeat 1 19 (0) 1620
ANNOTATION EVIDENCE:
15 5.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10176:13176/2 133 151 0 + (T)n Simple_repeat 1 19 0
15 5.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10176:13176/2 133 151 (0) (T)n#Simple_repeat 1 19 (0) m_b6s252i1
ST-E00130:540 133 TTCTTTTTTTTTTTTTTTT 151
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 1200 8.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2222:10277:12859/1 1 147 (4) + AluSx SINE/Alu 60 206 (106) 1621
ANNOTATION EVIDENCE:
1200 8.16 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10277:12859/1 1 147 4 + AluSx SINE/Alu 60 206 106
1200 8.16 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10277:12859/1 1 147 (4) AluSx#SINE/Alu 60 206 (106) c_b6s352i1
ST-E00130:540 1 ATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACT 50
i i
AluSx#SINE/Al 60 ATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACC 109
ST-E00130:540 51 CCATCTCTACGAAAAATAAAAAAATTAGCTGGGCATGGTGGCAGGCGCCT 100
i v v i i iv
AluSx#SINE/Al 110 CCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT 159
ST-E00130:540 101 GTAATCCCAGCTACTCAGGAGGATGAGGCAGGAGAATTGCTTGAACC 147
i v i
AluSx#SINE/Al 160 GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC 206
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.98
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 15 5.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:3:2222:10277:12859/2 133 151 (0) + (T)n Simple_repeat 1 19 (0) 1622
ANNOTATION EVIDENCE:
15 5.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10277:12859/2 133 151 0 + (T)n Simple_repeat 1 19 0
15 5.56 0.00 0.00 ST-E00130:540:HVYVWCCXX:3:2222:10277:12859/2 133 151 (0) (T)n#Simple_repeat 1 19 (0) m_b6s252i0
ST-E00130:540 133 TTCTTTTTTTTTTTTTTTT 151
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 1018 12.8 1.3 0.0 ST-E00130:540:HVYVWCCXX:3:2224:2615:32531/2 1 149 (2) C AluSx SINE/Alu (149) 163 13 1623
ANNOTATION EVIDENCE:
1018 12.75 1.32 0.00 ST-E00130:540:HVYVWCCXX:3:2224:2615:32531/2 1 149 2 C AluSx SINE/Alu 13 163 149
1018 12.75 1.32 0.00 ST-E00130:540:HVYVWCCXX:3:2224:2615:32531/2 1 149 (2) C AluSx#SINE/Alu (149) 163 13 m_b4s357i37
ST-E00130:540 1 TTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTGTTTTTAGTAGAG 50
i vi v i i
C AluSx#SINE/Al 163 TTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAG 114
ST-E00130:540 51 ATGGAGTTTCACCCTATTGGCCAGGCTGTTCTCAAACTCCTGACCTT--G 98
i i v i v i i--
C AluSx#SINE/Al 113 ACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGG 64
ST-E00130:540 99 TGATCTGCCTGCTTCAGCCTCCCCAAGTGCTGGGATTACAGGTGTGAGCC 148
i i i i v i
C AluSx#SINE/Al 63 TGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
ST-E00130:540 149 A 149
C AluSx#SINE/Al 13 A 13
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.40
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 314 27.1 14.3 0.0 ST-E00130:540:HVYVWCCXX:3:2224:6938:65195/1 8 151 (0) C MIR SINE/MIR (0) 262 95 1624
ANNOTATION EVIDENCE:
314 27.08 14.29 0.00 ST-E00130:540:HVYVWCCXX:3:2224:6938:65195/1 8 151 0 C MIR SINE/MIR 95 262 0
314 27.08 14.29 0.00 ST-E00130:540:HVYVWCCXX:3:2224:6938:65195/1 8 151 (0) C MIR#SINE/MIR (0) 262 95 m_b6s601i30
ST-E00130:540 8 AAAAATAGCTAACACTTGTTGAGTATATACGGTGTGCCTGGCA------- 50
v i i iiiv vi v -------
C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213
ST-E00130:540 51 ------TTTATGTTTATT------CTTAATTCTT---ATACTTCTGTCAC 85
------ ii v ------i i i--- i vii i v v
C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163
ST-E00130:540 86 TTAGATTCTATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAG 133
v i v vi ii v i i -- v i vi
C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113
ST-E00130:540 134 TGAGGTAAAGTAACTTGC 151
v v
C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGC 95
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.23
Transitions / transversions = 1.44 (23/16)
Gap_init rate = 0.03 (5 / 143), avg. gap size = 4.80 (24 / 5)
+ 569 19.3 18.5 0.0 ST-E00130:540:HVYVWCCXX:3:2224:8308:71647/1 1 145 (6) C L1MC4 LINE/L1 (418) 7624 7447 1625
ANNOTATION EVIDENCE:
569 19.31 18.54 0.00 ST-E00130:540:HVYVWCCXX:3:2224:8308:71647/1 1 145 6 C L1MC4_3end LINE/L1 2194 2371 418
569 19.31 18.54 0.00 ST-E00130:540:HVYVWCCXX:3:2224:8308:71647/1 1 145 (6) C L1MC4_3end#LINE/L1 (418) 2371 2194 m_b3s551i107
ST-E00130:540 1 TTAGTCTCCTTCAATCTGGAACAGTTCT------TTTTTTTATTTATCAT 44
i i------ i i i v
C L1MC4_3end#LI 2371 TTAGTCTCCTTTAATCTGGAACAGTTCCTCAGTCTTTCTTTGTCTTTCAT 2322
ST-E00130:540 45 GACCTTCATATATTTGAATAGTACAG-------------------GTCCC 75
? v i v v -------------------
C L1MC4_3end#LI 2321 GACNTTGACATTTTTGAAGAGTACAGGCCAGTTATTTTGTAGAATGTCCC 2272
ST-E00130:540 76 TTGCTCTGAGTTTGTCTGATGTTTCCTTATGATTAAAT-----TTATAC- 119
iiv i i i i ----- i -
C L1MC4_3end#LI 2271 TCAATTTGGGTTTGTCTGATGTTTCCTCATGATTAGATTCAGGTTATGCA 2222
ST-E00130:540 120 --TTTGACGAGAATGTTGCAAAAGTAAT 145
-- i ii iiii i i
C L1MC4_3end#LI 2221 TTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.60
Transitions / transversions = 4.40 (22/5)
Gap_init rate = 0.03 (5 / 144), avg. gap size = 6.60 (33 / 5)
+ 237 27.7 4.3 11.8 ST-E00130:540:HVYVWCCXX:4:1101:10206:6618/1 1 127 (24) C L1MC4 LINE/L1 (1464) 6578 6462 1626
ANNOTATION EVIDENCE:
237 27.68 4.28 11.81 ST-E00130:540:HVYVWCCXX:4:1101:10206:6618/1 1 127 24 C L1MC4_3end LINE/L1 1209 1325 1464
237 27.68 4.28 11.81 ST-E00130:540:HVYVWCCXX:4:1101:10206:6618/1 1 127 (24) C L1MC4_3end#LINE/L1 (1464) 1325 1209 m_b3s551i162
ST-E00130:540 1 CAAGCCAACATCACACAGTTTAT-----CTTTTTTTCTGTCCAAATTTAT 45
v i vi i ----- i iiii v v i
C L1MC4_3end#LI 1325 CAATCCAACACCACAGGGTTCATTCTAGCCTTCCCCCTTTCCATATTTGT 1276
ST-E00130:540 46 AAATTGCTTTACTAGCAGTTAAAAAAAACACCCCAAAACCTGACTATCCA 95
v iv iv iii v -------------i i -i
C L1MC4_3end#LI 1275 AACTCCCTTCTCCGACAGTGA-------------GAAACCTGGCT-CCCA 1240
ST-E00130:540 96 CTCAACCTGAATGCATTTACTTATTTGCTCAA 127
- i v ?v ii
C L1MC4_3end#LI 1239 -TTATCCNCAATATATTTACTTATTTGCTCAA 1209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.29
Transitions / transversions = 2.00 (20/10)
Gap_init rate = 0.13 (16 / 126), avg. gap size = 1.25 (20 / 16)
+ 692 10.2 0.0 2.0 ST-E00130:540:HVYVWCCXX:4:1101:26250:25060/1 2 101 (50) + AluSx SINE/Alu 207 304 (8) 1627
ANNOTATION EVIDENCE:
692 10.20 0.00 2.00 ST-E00130:540:HVYVWCCXX:4:1101:26250:25060/1 2 101 50 + AluSx SINE/Alu 207 304 8
692 10.20 0.00 2.00 ST-E00130:540:HVYVWCCXX:4:1101:26250:25060/1 2 101 (50) AluSx#SINE/Alu 207 304 (8) m_b2s357i7
ST-E00130:540 2 CAGGAGGCAGAGATTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCC 51
i i i i ii
AluSx#SINE/Al 207 CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCC 256
ST-E00130:540 52 TGGGTTTGACGAAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA 101
--i ii i
AluSx#SINE/Al 257 TGGG--CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.93
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.00 (2 / 2)
+ 1031 2.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1101:26250:25060/2 1 119 (32) + L1PA2 LINE/L1 6035 6153 (2) 1628
ANNOTATION EVIDENCE:
1031 2.52 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1101:26250:25060/2 1 119 32 + L1PA2_3end LINE/L1 782 900 2
1031 2.52 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1101:26250:25060/2 1 119 (32) L1PA2_3end#LINE/L1 782 900 (2) m_b1s551i437
ST-E00130:540 1 TAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGT 50
i
L1PA2_3end#LI 782 TAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGT 831
ST-E00130:540 51 ATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAA 100
L1PA2_3end#LI 832 ATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAA 881
ST-E00130:540 101 AGTGTAATAAAAAAAATAA 119
i v
L1PA2_3end#LI 882 AGTATAATAAAAAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.79
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 880 15.8 0.0 1.4 ST-E00130:540:HVYVWCCXX:4:1101:29102:72192/1 4 151 (0) C AluSx SINE/Alu (79) 233 88 1629
ANNOTATION EVIDENCE:
880 15.75 0.00 1.35 ST-E00130:540:HVYVWCCXX:4:1101:29102:72192/1 4 151 0 C AluSx SINE/Alu 88 233 79
880 15.75 0.00 1.35 ST-E00130:540:HVYVWCCXX:4:1101:29102:72192/1 4 151 (0) C AluSx#SINE/Alu (79) 233 88 m_b5s356i12
ST-E00130:540 4 TCTGCTCACTGCAACCTCCGCCTAGTAGGTTCAAGCAATGGTCCTGCCTC 53
v vvii i vv
C AluSx#SINE/Al 233 TCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTC 184
ST-E00130:540 54 AGCCTCCTGAGCGGCTATGATTACAGGCTCCCACCACAATGCCTGGCTAA 103
i ii iv v v i v i i
C AluSx#SINE/Al 183 AGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAA 134
ST-E00130:540 104 TTTTTTTGTCTTTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGC 151
-- v i v i
C AluSx#SINE/Al 133 --TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGC 88
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 12.33
Transitions / transversions = 1.09 (12/11)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 918 10.6 1.6 0.0 ST-E00130:540:HVYVWCCXX:4:1103:20354:13404/2 2 124 (27) C AluSx SINE/Alu (187) 125 1 1630
ANNOTATION EVIDENCE:
918 10.57 1.60 0.00 ST-E00130:540:HVYVWCCXX:4:1103:20354:13404/2 2 124 27 C AluSx SINE/Alu 1 125 187
918 10.57 1.60 0.00 ST-E00130:540:HVYVWCCXX:4:1103:20354:13404/2 2 124 (27) C AluSx#SINE/Alu (187) 125 1 m_b4s357i42
ST-E00130:540 2 TTTTTAGTAGAGATGGAGTTTCACCATATTGGCCAGGCTGTTCTCAAACT 51
i i i v i
C AluSx#SINE/Al 125 TTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACT 76
ST-E00130:540 52 CCTGACCTT--GTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTA 99
i-- i i i i
C AluSx#SINE/Al 75 CCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA 26
ST-E00130:540 100 CAGGTGTGAGCCACTGCACCCGGCC 124
i i i
C AluSx#SINE/Al 25 CAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.92
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)
+ 1030 9.6 0.7 0.0 ST-E00130:540:HVYVWCCXX:4:1104:21501:6108/2 5 139 (12) C AluY SINE/Alu (175) 136 1 1631
ANNOTATION EVIDENCE:
1030 9.63 0.73 0.00 ST-E00130:540:HVYVWCCXX:4:1104:21501:6108/2 5 139 12 C AluY SINE/Alu 1 136 175
1030 9.63 0.73 0.00 ST-E00130:540:HVYVWCCXX:4:1104:21501:6108/2 5 139 (12) C AluY#SINE/Alu (175) 136 1 m_b2s357i80
ST-E00130:540 5 CTAA-TTTTTGTGTTTTTAGTAGAGATGGGGTTTCACCACGTTAGCCAGG 53
- i i ii
C AluY#SINE/Alu 136 CTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGG 87
ST-E00130:540 54 ATGGTCTTGATCTCCTGACCTCATGATCAGCCCGCCTTGGCCTCCCAAAG 103
i i v i
C AluY#SINE/Alu 86 ATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 37
ST-E00130:540 104 TGCTGAGATTACAAGCGTGAGCCACCATGCCTGGCC 139
i i ii i
C AluY#SINE/Alu 36 TGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.46
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1)
+ 600 17.7 15.1 0.0 ST-E00130:540:HVYVWCCXX:4:1105:16417:13545/1 9 149 (2) C L1MC4 LINE/L1 (393) 7649 7484 1632
ANNOTATION EVIDENCE:
600 17.73 15.06 0.00 ST-E00130:540:HVYVWCCXX:4:1105:16417:13545/1 9 149 2 C L1MC4_3end LINE/L1 2231 2396 393
600 17.73 15.06 0.00 ST-E00130:540:HVYVWCCXX:4:1105:16417:13545/1 9 149 (2) C L1MC4_3end#LINE/L1 (393) 2396 2231 m_b3s551i98
ST-E00130:540 9 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 58
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 59 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 102
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
ST-E00130:540 103 G-------------------GTCCCTTGCTCTGAGTTTGTCTGATGTTTC 133
------------------- iiv i i
C L1MC4_3end#LI 2296 GGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTTC 2247
ST-E00130:540 134 CTTATGATTAAATTTA 149
i i i
C L1MC4_3end#LI 2246 CTCATGATTAGATTCA 2231
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.81
Transitions / transversions = 1.40 (14/10)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 12.50 (25 / 2)
+ 977 15.4 0.0 1.3 ST-E00130:540:HVYVWCCXX:4:1105:26920:33357/1 1 151 (0) C AluSx SINE/Alu (27) 285 137 1633
ANNOTATION EVIDENCE:
977 15.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:1105:26920:33357/1 1 151 0 C AluSx SINE/Alu 137 285 27
977 15.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:1105:26920:33357/1 1 151 (0) C AluSx#SINE/Alu (27) 285 137 m_b2s356i3
ST-E00130:540 1 TTTGAGACAGAGTCTCGCTTCGTCAAACCCAGGCTGGAGAACAGTGGCAT 50
i ii i-- vi ii
C AluSx#SINE/Al 285 TTTGAGACGGAGTCTCGCTCTGTCG--CCCAGGCTGGAGTGCAGTGGCGC 238
ST-E00130:540 51 GATCTCAGCTCACTGCAATCTCTGCCTCCTGAGTTCAAGTGATTCTCCTG 100
i i i i i i
C AluSx#SINE/Al 237 GATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTG 188
ST-E00130:540 101 CCGCAGCTTCCTGAGTAGCTGGGATTACAGTTGCCCACCACCACACCCCG 150
v i i vi v i i v
C AluSx#SINE/Al 187 CCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGG 138
ST-E00130:540 151 C 151
C AluSx#SINE/Al 137 C 137
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.71
Transitions / transversions = 3.60 (18/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 444 16.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1105:26920:33357/2 81 151 (0) + AluSx SINE/Alu 1 71 (241) 1634
ANNOTATION EVIDENCE:
444 16.90 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1105:26920:33357/2 81 151 0 + AluSx SINE/Alu 1 71 241
444 16.90 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1105:26920:33357/2 81 151 (0) AluSx#SINE/Alu 1 71 (241) m_b2s357i55
ST-E00130:540 81 GGCTGGGCACAGCGGCTCACATCTGTAATCTCAGCAATTTGGGAGGCAGA 130
i i i i ii i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 131 GCCAGGTGGATCACCTGAGGT 151
v i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGT 71
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.96
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 1121 11.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:1105:5264:34975/1 1 151 (0) + AluSx SINE/Alu 36 188 (124) 1635
ANNOTATION EVIDENCE:
1121 11.26 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1105:5264:34975/1 1 151 0 + AluSx SINE/Alu 36 188 124
1121 11.26 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1105:5264:34975/1 1 151 (0) AluSx#SINE/Alu 36 188 (124) m_b4s356i36
ST-E00130:540 1 ACTTTGGGAGGCTGAAGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAA 48
i i i i --i i v
AluSx#SINE/Al 36 ACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGAC 85
ST-E00130:540 49 CAGCCTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAAAATT 98
i i i i
AluSx#SINE/Al 86 CAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATT 135
ST-E00130:540 99 AGCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGA 148
i v iv i i
AluSx#SINE/Al 136 AGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA 185
ST-E00130:540 149 GGC 151
AluSx#SINE/Al 186 GGC 188
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.84
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 204 34.1 7.9 3.0 ST-E00130:540:HVYVWCCXX:4:1105:5264:34975/2 3 135 (16) C MIRb SINE/MIR (113) 155 16 1636
ANNOTATION EVIDENCE:
204 34.11 7.86 3.01 ST-E00130:540:HVYVWCCXX:4:1105:5264:34975/2 3 135 16 C MIRb SINE/MIR 16 155 113
204 34.11 7.86 3.01 ST-E00130:540:HVYVWCCXX:4:1105:5264:34975/2 3 135 (16) C MIRb#SINE/MIR (113) 155 16 m_b4s601i35
ST-E00130:540 3 TATCTTCACTCTACTGATGAGGGTACGAAGGCCCTAGATGACATAAGGCA 52
ii i i v iv vi i - - vi v i i
C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGAGGCTC-AGA-GAGGTTAAGTA 108
ST-E00130:540 53 AGTTTTTTACCAGA----AAAGTTA--AGGCTGTGGTACTGGGATTTGAA 96
v viii -- i---- v i -- i iv ii vi i i
C MIRb#SINE/MIR 107 ACTTGCCCA--AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60
ST-E00130:540 97 TTT---TCTGTTTGACTTCAAAGCC--TTTTGTTTTTACTATAC 135
iii--- i i -- vi v ii ii
C MIRb#SINE/MIR 59 CCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCAC 16
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 46.34
Transitions / transversions = 2.67 (32/12)
Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.88 (15 / 8)
+ 19 4.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1107:6603:17184/1 126 149 (2) + (TG)n Simple_repeat 1 24 (0) 1637
ANNOTATION EVIDENCE:
19 4.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1107:6603:17184/1 126 149 2 + (TG)n Simple_repeat 1 24 0
19 4.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1107:6603:17184/1 126 149 (2) (TG)n#Simple_repeat 1 24 (0) m_b4s252i10
ST-E00130:540 126 TGTGTGTGTGTGTGTATGTGTGTG 149
i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 972 5.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1107:6603:17184/2 2 119 (32) + AluSx SINE/Alu 174 291 (21) 1638
ANNOTATION EVIDENCE:
972 5.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1107:6603:17184/2 2 119 32 + AluSx SINE/Alu 174 291 21
972 5.08 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1107:6603:17184/2 2 119 (32) AluSx#SINE/Alu 174 291 (21) m_b4s357i23
ST-E00130:540 2 TCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGC 51
i i i
AluSx#SINE/Al 174 TCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGC 223
ST-E00130:540 52 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCCGGGCAACAGAGCGAGA 101
i i
AluSx#SINE/Al 224 AGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGA 273
ST-E00130:540 102 TTCCGTCTCAAAAAAAAA 119
i
AluSx#SINE/Al 274 CTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.88
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0)
+ 1253 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1108:20446:67322/2 1 151 (0) C L1P3 LINE/L1 (3032) 3114 2964 1639
ANNOTATION EVIDENCE:
1253 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1108:20446:67322/2 1 151 0 C L1P3_orf2 LINE/L1 855 1005 2289
1253 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1108:20446:67322/2 1 151 (0) C L1P3_orf2#LINE/L1 (2289) 1005 855 m_b7s551i0
ST-E00130:540 1 GCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTG 50
C L1P3_orf2#LIN 1005 GCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTG 956
ST-E00130:540 51 ATGTTAGGGTGTTGATTTTAGATCTTTCCCACTTTGTCCTGTGGGCATTT 100
i i v ?
C L1P3_orf2#LIN 955 ATGTTAGGGTGTCGATTTTAGATCTTTCCCGCTTTCTCNTGTGGGCATTT 906
ST-E00130:540 101 AGTGCTGTAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATT 150
i
C L1P3_orf2#LIN 905 AGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATT 856
ST-E00130:540 151 C 151
C L1P3_orf2#LIN 855 C 855
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 235 28.8 15.4 0.0 ST-E00130:540:HVYVWCCXX:4:1110:21856:31301/1 3 134 (17) + MIR SINE/MIR 107 262 (0) 1640
ANNOTATION EVIDENCE:
235 28.79 15.38 0.00 ST-E00130:540:HVYVWCCXX:4:1110:21856:31301/1 3 134 17 + MIR SINE/MIR 107 262 0
235 28.79 15.38 0.00 ST-E00130:540:HVYVWCCXX:4:1110:21856:31301/1 3 134 (17) MIR#SINE/MIR 107 262 (0) m_b6s601i26
ST-E00130:540 3 ACCTCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATAGA 50
v iv i v -- i i v ii iv v
MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156
ST-E00130:540 51 ATCTAAGTGACAGAAGTAT---AAGAATTAAG------AATAAACATAAA 91
i vv v i iiv i ---i i i------ v ii
MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206
ST-E00130:540 92 -------------TGCCAGGCACACCGTATATACTCAACAAGTGTTAGCT 128
------------- v iv viii i i
MIR#SINE/MIR 207 GCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCT 256
ST-E00130:540 129 ATTTTT 134
v
MIR#SINE/MIR 257 ATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.06
Transitions / transversions = 1.53 (23/15)
Gap_init rate = 0.03 (4 / 131), avg. gap size = 6.00 (24 / 4)
+ 1346 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1110:9770:33604/1 1 151 (0) + L1P3 LINE/L1 3450 3600 (2546) 1641
ANNOTATION EVIDENCE:
1346 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1110:9770:33604/1 1 151 0 + L1P3_orf2 LINE/L1 1341 1491 1803
1346 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1110:9770:33604/1 1 151 (0) L1P3_orf2#LINE/L1 1341 1491 (1803) m_b6s551i122
ST-E00130:540 1 ATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATA 50
L1P3_orf2#LIN 1341 ATCCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATA 1390
ST-E00130:540 51 GCCTACCAACCAAAAAAAGCCCAGGACCAGAGGGATTCACAGCCGAATTC 100
v
L1P3_orf2#LIN 1391 GCCTACCAACCAAAAAAAGCCCAGGACCAGACGGATTCACAGCCGAATTC 1440
ST-E00130:540 101 TACCAGGGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCA 150
i
L1P3_orf2#LIN 1441 TACCAGAGGTACAAAGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCA 1490
ST-E00130:540 151 A 151
L1P3_orf2#LIN 1491 A 1491
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1113 8.1 2.0 0.0 ST-E00130:540:HVYVWCCXX:4:1110:9770:33604/2 1 149 (2) C L1P3 LINE/L1 (2288) 3858 3707 1642
ANNOTATION EVIDENCE:
1113 8.05 1.97 0.00 ST-E00130:540:HVYVWCCXX:4:1110:9770:33604/2 1 149 2 C L1P3_orf2 LINE/L1 1598 1749 1545
1113 8.05 1.97 0.00 ST-E00130:540:HVYVWCCXX:4:1110:9770:33604/2 1 149 (2) C L1P3_orf2#LINE/L1 (1545) 1749 1598 m_b6s551i49
ST-E00130:540 1 GATTATGTTTATTGATTTGTGTATGCTGAATCAGCCTTGCGTCCCAGGGA 50
i i i i i
C L1P3_orf2#LIN 1749 GATTACGTTTATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGA 1700
ST-E00130:540 51 TGAAGCTGACTTGATAGTGGTGGATAAGCGTTTTGATG---TGCTGGATT 97
i v v ---
C L1P3_orf2#LIN 1699 TGAAGCCGACTTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATT 1650
ST-E00130:540 98 CAGTTTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCATCACGGA 147
i i i v
C L1P3_orf2#LIN 1649 CGGTTTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATCAGGGA 1600
ST-E00130:540 148 TA 149
C L1P3_orf2#LIN 1599 TA 1598
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.23
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 3.00 (3 / 1)
+ 1038 13.4 0.0 1.3 ST-E00130:540:HVYVWCCXX:4:1111:7395:73194/1 1 151 (0) C AluSx SINE/Alu (134) 178 30 1643
ANNOTATION EVIDENCE:
1038 13.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:1111:7395:73194/1 1 151 0 C AluSx SINE/Alu 30 178 134
1038 13.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:1111:7395:73194/1 1 151 (0) C AluSx#SINE/Alu (134) 178 30 m_b5s356i23
ST-E00130:540 1 CCTGAGCAGCTATGATTACAGGCTCCCACCACAATGCCTGGCTAATTTTT 50
i i iv v v i v i i --
C AluSx#SINE/Al 178 CCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAA--TTT 131
ST-E00130:540 51 TTGTATTTTTAGTAGAGATGGGGTTTCAACACGTTGGCCAGGCTGGTCCC 100
i v i i
C AluSx#SINE/Al 130 TTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTC 81
ST-E00130:540 101 AAACTCCTGACCTCAAGTGATCTGCCCACCTTGGCCTCCCAAAGTGTTGG 150
i i i i i i
C AluSx#SINE/Al 80 GAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGG 31
ST-E00130:540 151 G 151
C AluSx#SINE/Al 30 G 30
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.48
Transitions / transversions = 3.00 (15/5)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 984 14.1 0.0 1.3 ST-E00130:540:HVYVWCCXX:4:1112:13961:50322/2 1 151 (0) + AluSx SINE/Alu 77 225 (87) 1644
ANNOTATION EVIDENCE:
984 14.10 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:1112:13961:50322/2 1 151 0 + AluSx SINE/Alu 77 225 87
984 14.10 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:1112:13961:50322/2 1 151 (0) AluSx#SINE/Alu 77 225 (87) m_b5s356i15
ST-E00130:540 1 GTTTGGGACCAGCCTGGCCAACGTGTTGAAACCCCATCTCTACTAAAAAT 50
i i i v i
AluSx#SINE/Al 77 GTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT 126
ST-E00130:540 51 ACAAAAAAATTAGCCAGGCATTGTGGTGGGAGCCTGTAATCATAGCTGCT 100
-- i i v i v v vi i
AluSx#SINE/Al 127 ACAAAAA--TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACT 174
ST-E00130:540 101 CAGGAGGCTGAGGCAGGACAATTGCTTGAACCTACTAGGCGGAGGTTGCA 150
i v i iivv
AluSx#SINE/Al 175 CGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCA 224
ST-E00130:540 151 G 151
AluSx#SINE/Al 225 G 225
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 9.81
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 1104 9.3 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:1113:9577:9431/1 1 151 (0) C AluSx SINE/Alu (39) 273 124 1645
ANNOTATION EVIDENCE:
1104 9.33 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1113:9577:9431/1 1 151 0 C AluSx SINE/Alu 124 273 39
1104 9.33 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1113:9577:9431/1 1 151 (0) C AluSx#SINE/Alu (39) 273 124 m_b2s356i79
ST-E00130:540 1 TCTCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCATGATCTCGGCTCACT 50
i ii
C AluSx#SINE/Al 273 TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACT 224
ST-E00130:540 51 GCAACCTCCACCTCCCCAGGTTCATGCCGTTCTCCTGCTTCAGCCTCCCG 100
i - i v vi i
C AluSx#SINE/Al 223 GCAACCTCCGCCT-CCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCG 175
ST-E00130:540 101 AGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCATCTAATTTTTGTGT 150
i v iv i
C AluSx#SINE/Al 174 AGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTAT 125
ST-E00130:540 151 T 151
C AluSx#SINE/Al 124 T 124
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.64
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 747 9.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1113:9577:9431/2 53 148 (3) + AluY SINE/Alu 1 96 (215) 1646
ANNOTATION EVIDENCE:
747 9.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1113:9577:9431/2 53 148 3 + AluY SINE/Alu 1 96 215
747 9.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1113:9577:9431/2 53 148 (3) AluY#SINE/Alu 1 96 (215) m_b2s357i72
ST-E00130:540 53 GGCCAGGCATGGTGGCTCACGCTTGTAATCTCAGCACTTTGGGAGGCCAA 102
i ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 103 GGCGGGCTGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAAC 148
v i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAAC 96
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.86
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 309 2.8 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1118:23287:54559/1 1 36 (0) C L1P1 LINE/L1 (485) 5670 5635 1647
ANNOTATION EVIDENCE:
309 2.78 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:23287:54559/1 1 36 0 C L1PA3_3end LINE/L1 382 417 485
309 2.78 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:23287:54559/1 1 36 (0) C L1PA3_3end#LINE/L1 (485) 417 382 m_b1s551i312
ST-E00130:540 1 GCATGATTTATAGTCCTTTGGGTATATCCCCAGTAA 36
v
C L1PA3_3end#LI 417 GCATGATTTATAGTCCTTTGGGTATATACCCAGTAA 382
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.84
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 355 4.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1118:23287:54559/2 1 44 (0) + L1P1 LINE/L1 5636 5679 (476) 1648
ANNOTATION EVIDENCE:
355 4.55 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:23287:54559/2 1 44 0 + L1PA3_3end LINE/L1 383 426 476
355 4.55 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:23287:54559/2 1 44 (0) L1PA3_3end#LINE/L1 383 426 (476) m_b1s551i313
ST-E00130:540 1 TACTGGGTATATACCCAAAGGACTATAAATCATGCCGCAATAAA 44
i v
L1PA3_3end#LI 383 TACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAA 426
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.69
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 637 11.5 0.0 0.9 ST-E00130:540:HVYVWCCXX:4:1118:24424:64158/1 2 106 (45) + AluSx SINE/Alu 209 312 (0) 1649
ANNOTATION EVIDENCE:
637 11.54 0.00 0.95 ST-E00130:540:HVYVWCCXX:4:1118:24424:64158/1 2 106 45 + AluSx SINE/Alu 209 312 0
637 11.54 0.00 0.95 ST-E00130:540:HVYVWCCXX:4:1118:24424:64158/1 2 106 (45) AluSx#SINE/Alu 209 312 (0) m_b6s357i3
ST-E00130:540 2 GGAGGTAGAGGCTGAAGTGAACCGAGATCACACCATTGCACTCCAGCCTG 51
ii i v i i i i
AluSx#SINE/Al 209 GGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258
ST-E00130:540 52 GGAGACATGAGCGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAA 101
v - i i
AluSx#SINE/Al 259 GGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAA 307
ST-E00130:540 102 AAGAA 106
i
AluSx#SINE/Al 308 AAAAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.54
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.01 (1 / 104), avg. gap size = 1.00 (1 / 1)
+ 261 26.5 1.4 0.0 ST-E00130:540:HVYVWCCXX:4:1118:24424:64158/2 4 71 (80) C MIRb SINE/MIR (133) 135 67 1650
ANNOTATION EVIDENCE:
261 26.47 1.45 0.00 ST-E00130:540:HVYVWCCXX:4:1118:24424:64158/2 4 71 80 C MIRb SINE/MIR 67 135 133
261 26.47 1.45 0.00 ST-E00130:540:HVYVWCCXX:4:1118:24424:64158/2 4 71 (80) C MIRb#SINE/MIR (133) 135 67 m_b6s601i76
ST-E00130:540 4 GAAAACTGTGACTTAGTGAGGTAAAGTAACTTGCTTA-TGCCACAGAGCT 52
i v i i v v ii -v i v
C MIRb#SINE/MIR 135 GGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 86
ST-E00130:540 53 AACAAGTGGTTGACTCGAG 71
ii iv vi i
C MIRb#SINE/MIR 85 AGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.56
Transitions / transversions = 1.57 (11/7)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)
+ 1346 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1118:28118:11207/1 1 151 (0) C L1P3 LINE/L1 (2547) 3599 3449 1651
ANNOTATION EVIDENCE:
1346 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:28118:11207/1 1 151 0 C L1P3_orf2 LINE/L1 1340 1490 1804
1346 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:28118:11207/1 1 151 (0) C L1P3_orf2#LINE/L1 (1804) 1490 1340 m_b6s551i123
ST-E00130:540 1 TGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTA 50
i
C L1P3_orf2#LIN 1490 TGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTA 1441
ST-E00130:540 51 GAATTCGGCTGTGAATCCCTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGC 100
v
C L1P3_orf2#LIN 1440 GAATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGGTTGGTAGGC 1391
ST-E00130:540 101 TATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGAT 150
C L1P3_orf2#LIN 1390 TATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAGGGAT 1341
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 1340 T 1340
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1160 3.4 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:1118:28118:11207/2 1 149 (2) + L1P3 LINE/L1 3380 3530 (2616) 1652
ANNOTATION EVIDENCE:
1160 3.36 1.32 0.00 ST-E00130:540:HVYVWCCXX:4:1118:28118:11207/2 1 149 2 + L1P3_orf2 LINE/L1 1271 1421 1873
1160 3.36 1.32 0.00 ST-E00130:540:HVYVWCCXX:4:1118:28118:11207/2 1 149 (2) L1P3_orf2#LINE/L1 1271 1421 (1873) m_b6s551i138
ST-E00130:540 1 AAAATCTAGAAGAAAGTGATAAATTCCTAGACACATACAACCTCCCAA-- 48
vv i v --
L1P3_orf2#LIN 1271 AAAATCTAGAAGAAATGGATAAATTCCTGGACACATACACCCTCCCAAGA 1320
ST-E00130:540 49 CTAAAGCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGA 98
v
L1P3_orf2#LIN 1321 CTAAACCAGGAAGAAGTCGAATCCCTGAATAGACCAATAACAAGTTCTGA 1370
ST-E00130:540 99 AATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAG 148
L1P3_orf2#LIN 1371 AATTGAGGCAGTAATTAATAGCCTACCAACCAAAAAAAGCCCAGGACCAG 1420
ST-E00130:540 149 A 149
L1P3_orf2#LIN 1421 A 1421
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.43
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 2.00 (2 / 1)
+ 1235 7.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1118:29751:47017/1 1 151 (0) C AluSx SINE/Alu (43) 269 119 1653
ANNOTATION EVIDENCE:
1235 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:29751:47017/1 1 151 0 C AluSx SINE/Alu 119 269 43
1235 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:29751:47017/1 1 151 (0) C AluSx#SINE/Alu (43) 269 119 m_b4s356i12
ST-E00130:540 1 GCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAA 50
i i
C AluSx#SINE/Al 269 GCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAA 220
ST-E00130:540 51 CCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAG 100
i i i
C AluSx#SINE/Al 219 CCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAG 170
ST-E00130:540 101 CTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTGTTTTTA 150
i vi v i i
C AluSx#SINE/Al 169 CTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA 120
ST-E00130:540 151 G 151
C AluSx#SINE/Al 119 G 119
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1235 7.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1118:29975:46982/1 1 151 (0) C AluSx SINE/Alu (43) 269 119 1654
ANNOTATION EVIDENCE:
1235 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:29975:46982/1 1 151 0 C AluSx SINE/Alu 119 269 43
1235 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1118:29975:46982/1 1 151 (0) C AluSx#SINE/Alu (43) 269 119 m_b4s356i13
ST-E00130:540 1 GCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAA 50
i i
C AluSx#SINE/Al 269 GCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAA 220
ST-E00130:540 51 CCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAG 100
i i i
C AluSx#SINE/Al 219 CCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAG 170
ST-E00130:540 101 CTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTTTTGTGTTTTTA 150
i vi v i i
C AluSx#SINE/Al 169 CTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA 120
ST-E00130:540 151 G 151
C AluSx#SINE/Al 119 G 119
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 250 24.6 6.2 3.9 ST-E00130:540:HVYVWCCXX:4:1120:11870:14353/1 3 129 (22) C L1ME4c LINE/L1 (297) 5786 5657 1655
ANNOTATION EVIDENCE:
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:4:1120:11870:14353/1 3 129 22 C L1ME4c_3end LINE/L1 404 533 297
250 24.59 6.15 3.94 ST-E00130:540:HVYVWCCXX:4:1120:11870:14353/1 3 129 (22) C L1ME4c_3end#LINE/L1 (297) 533 404 m_b2s551i35
ST-E00130:540 3 TACCATAATTTACTTGA-CATT-TTTTATTGTCAGAAATTTAGATTCTTT 50
i - -iii ii v i v
C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484
ST-E00130:540 51 TCTATTTTC--CTACAATAAACATTATTGCAATGATCATT----TGTCTA 94
i v i-- iv i viii v i---- iv
C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434
ST-E00130:540 95 AGGGTTTTTTTTTCTCATATTTTAAATTATTTCTT 129
vi v ii ----- i i
C L1ME4c_3end#L 433 TAGCTTTTTCCTTC-----TTTTGAATTATTTCCT 404
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.67
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.44 (13 / 9)
+ 1329 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1120:21542:49883/1 1 151 (0) C L1P1 LINE/L1 (695) 5460 5310 1656
ANNOTATION EVIDENCE:
1329 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1120:21542:49883/1 1 151 0 C L1PA2_3end LINE/L1 57 207 695
1329 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1120:21542:49883/1 1 151 (0) C L1PA2_3end#LINE/L1 (695) 207 57 m_b1s551i197
ST-E00130:540 1 AACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGA 50
C L1PA2_3end#LI 207 AACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGA 158
ST-E00130:540 51 TGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATG 100
C L1PA2_3end#LI 157 TGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATG 108
ST-E00130:540 101 TCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGG 150
C L1PA2_3end#LI 107 TCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGG 58
ST-E00130:540 151 G 151
C L1PA2_3end#LI 57 G 57
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1226 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1120:21542:49883/2 2 150 (1) + L1P1 LINE/L1 4980 5128 (1018) 1657
ANNOTATION EVIDENCE:
1226 2.68 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1120:21542:49883/2 2 150 1 + L1P1_orf2 LINE/L1 2871 3019 275
1226 2.68 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1120:21542:49883/2 2 150 (1) L1P1_orf2#LINE/L1 2871 3019 (275) m_b1s551i56
ST-E00130:540 2 AAAAATCAATTCAAGATGGATTAAAGACTTAAACATTAGACCTAAAACCA 51
i i
L1P1_orf2#LIN 2871 AAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCA 2920
ST-E00130:540 52 TAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATG 101
?
L1P1_orf2#LIN 2921 TAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATG 2970
ST-E00130:540 102 GGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACA 150
v
L1P1_orf2#LIN 2971 GGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCA 3019
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1029 8.6 1.5 0.0 ST-E00130:540:HVYVWCCXX:4:1121:22333:63771/2 24 151 (0) + AluSx SINE/Alu 1 130 (182) 1658
ANNOTATION EVIDENCE:
1029 8.59 1.54 0.00 ST-E00130:540:HVYVWCCXX:4:1121:22333:63771/2 24 151 0 + AluSx SINE/Alu 1 130 182
1029 8.59 1.54 0.00 ST-E00130:540:HVYVWCCXX:4:1121:22333:63771/2 24 151 (0) AluSx#SINE/Alu 1 130 (182) m_b4s356i54
ST-E00130:540 24 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 73
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 74 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 121
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 122 GGTGAAACCCCGTCTCTACTAAAAATACAA 151
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAA 130
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.79
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 127), avg. gap size = 2.00 (2 / 1)
+ 1093 9.1 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:1121:22993:10767/2 8 151 (0) C AluSx SINE/Alu (14) 298 156 1659
ANNOTATION EVIDENCE:
1093 9.09 0.00 0.69 ST-E00130:540:HVYVWCCXX:4:1121:22993:10767/2 8 151 0 C AluSx SINE/Alu 156 298 14
1093 9.09 0.00 0.69 ST-E00130:540:HVYVWCCXX:4:1121:22993:10767/2 8 151 (0) C AluSx#SINE/Alu (14) 298 156 m_b2s356i91
ST-E00130:540 8 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGATGGAA 57
v i v i
C AluSx#SINE/Al 298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 249
ST-E00130:540 58 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 107
ii i - i v
C AluSx#SINE/Al 248 TGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT-CCCGGGTTCAA 200
ST-E00130:540 108 GCAGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGC 151
ii i i
C AluSx#SINE/Al 199 GCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGC 156
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.22
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 1.00 (1 / 1)
+ 1293 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1123:11485:43466/1 1 151 (0) C L1P1 LINE/L1 (767) 5379 5229 1660
ANNOTATION EVIDENCE:
1293 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1123:11485:43466/1 1 151 0 C L1P1_orf2 LINE/L1 3120 3270 24
1293 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1123:11485:43466/1 1 151 (0) C L1P1_orf2#LINE/L1 (24) 3270 3120 m_b1s551i150
ST-E00130:540 1 TTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 50
C L1P1_orf2#LIN 3270 TTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 3221
ST-E00130:540 51 TCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTG 100
C L1P1_orf2#LIN 3220 TCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTG 3171
ST-E00130:540 101 AGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGC 150
C L1P1_orf2#LIN 3170 AGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGC 3121
ST-E00130:540 151 G 151
C L1P1_orf2#LIN 3120 G 3120
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1251 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1123:11485:43466/2 1 151 (0) + L1P1 LINE/L1 4992 5142 (1004) 1661
ANNOTATION EVIDENCE:
1251 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1123:11485:43466/2 1 151 0 + L1P1_orf2 LINE/L1 2883 3033 261
1251 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1123:11485:43466/2 1 151 (0) L1P1_orf2#LINE/L1 2883 3033 (261) m_b1s551i62
ST-E00130:540 1 AAGATGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAG 50
i
L1P1_orf2#LIN 2883 AAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAG 2932
ST-E00130:540 51 AAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTC 100
?
L1P1_orf2#LIN 2933 AAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTC 2982
ST-E00130:540 101 ATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACACAATTGACAAATG 150
v v
L1P1_orf2#LIN 2983 ATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 3032
ST-E00130:540 151 G 151
L1P1_orf2#LIN 3033 G 3033
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1321 0.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:1124:9252:49302/1 1 151 (0) + L1PA2 LINE/L1 5709 5858 (297) 1662
ANNOTATION EVIDENCE:
1321 0.66 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1124:9252:49302/1 1 151 0 + L1PA2_3end LINE/L1 456 605 297
1321 0.66 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1124:9252:49302/1 1 151 (0) L1PA2_3end#LINE/L1 456 605 (297) m_b1s551i340
ST-E00130:540 1 ATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGA 50
L1PA2_3end#LI 456 ATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGA 505
ST-E00130:540 51 TAGACTGGATTAAGAAACTGTGGCACATATACACCATGGAATACTATGCA 100
v
L1PA2_3end#LI 506 TAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCA 555
ST-E00130:540 101 GCCATAAAAAATGATGAGTTCATGTCCTTTGTTAGGGACATGGATGAAAT 150
-
L1PA2_3end#LI 556 GCCATAAAAAATGATGAGTTCATGTCCTTTGT-AGGGACATGGATGAAAT 604
ST-E00130:540 151 T 151
L1PA2_3end#LI 605 T 605
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 259 27.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1201:26159:22264/1 78 145 (6) + L1M5 LINE/L1 5741 5808 (365) 1663
ANNOTATION EVIDENCE:
259 27.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1201:26159:22264/1 78 145 6 + L1ME3A_3end LINE/L1 488 555 365
259 27.94 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1201:26159:22264/1 78 145 (6) L1ME3A_3end#LINE/L1 488 555 (365) m_b1s551i519
ST-E00130:540 78 CTAAATGTCCAACAATAGTAAAATGGATATATAACCTGTAATGTGTCTAC 127
i v i i v vi ii i i ii
L1ME3A_3end#L 488 CCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCAC 537
ST-E00130:540 128 ATAACAAAATAATATGCA 145
i iii v i
L1ME3A_3end#L 538 ACAATGGAATACTATACA 555
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.79
Transitions / transversions = 3.75 (15/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1226 2.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1202:4432:59270/1 1 149 (2) C L1P1 LINE/L1 (1018) 5128 4980 1664
ANNOTATION EVIDENCE:
1226 2.68 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1202:4432:59270/1 1 149 2 C L1P1_orf2 LINE/L1 2871 3019 275
1226 2.68 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1202:4432:59270/1 1 149 (2) C L1P1_orf2#LINE/L1 (275) 3019 2871 m_b1s551i54
ST-E00130:540 1 TGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCC 50
v
C L1P1_orf2#LIN 3019 TGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCC 2970
ST-E00130:540 51 ATGCCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTAT 100
?
C L1P1_orf2#LIN 2969 ATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTAT 2920
ST-E00130:540 101 GGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTT 149
i i
C L1P1_orf2#LIN 2919 GGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTT 2871
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1184 6.0 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:1204:11129:65248/1 1 151 (0) C L1P3 LINE/L1 (2382) 3764 3612 1665
ANNOTATION EVIDENCE:
1184 5.96 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1204:11129:65248/1 1 151 0 C L1P3_orf2 LINE/L1 1503 1655 1639
1184 5.96 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1204:11129:65248/1 1 151 (0) C L1P3_orf2#LINE/L1 (1639) 1655 1503 m_b6s551i72
ST-E00130:540 1 TGGATTCAGTTTGCCAGTATTTTATCGAGGATTTTCACATCGATGTTCAT 50
i i i
C L1P3_orf2#LIN 1655 TGGATTCGGTTTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCAT 1606
ST-E00130:540 51 CACGGATAATGGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTT 98
v v i--
C L1P3_orf2#LIN 1605 CAGGGATATTGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTT 1556
ST-E00130:540 99 TTGGAATCAGGATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCC 148
v v i
C L1P3_orf2#LIN 1555 TTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCC 1506
ST-E00130:540 149 TCT 151
C L1P3_orf2#LIN 1505 TCT 1503
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.93
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1305 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1204:11129:65248/2 1 151 (0) + L1P3 LINE/L1 3528 3678 (2468) 1666
ANNOTATION EVIDENCE:
1305 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1204:11129:65248/2 1 151 0 + L1P3_orf2 LINE/L1 1419 1569 1725
1305 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1204:11129:65248/2 1 151 (0) L1P3_orf2#LINE/L1 1419 1569 (1725) m_b6s551i101
ST-E00130:540 1 AGAGGGATTCACAGCCGAATTCTACCAGGGGTACAAAGAGGAGCTGGTAC 50
v i
L1P3_orf2#LIN 1419 AGACGGATTCACAGCCGAATTCTACCAGAGGTACAAAGAGGAGCTGGTAC 1468
ST-E00130:540 51 CATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCTTCCCT 100
i
L1P3_orf2#LIN 1469 CATTCCTTCTGAAACTATTCCAAACAATAGAAAAAGAGGGACTCCTCCCT 1518
ST-E00130:540 101 AACTCATTTTATGATGCCAGCATCATCCTGATTCCAAAACCTGGCAGAGA 150
v v
L1P3_orf2#LIN 1519 AACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAGAGA 1568
ST-E00130:540 151 C 151
L1P3_orf2#LIN 1569 C 1569
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 198 24.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1204:18365:58831/2 54 98 (53) + MIR SINE/MIR 218 262 (0) 1667
ANNOTATION EVIDENCE:
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1204:18365:58831/2 54 98 53 + MIR SINE/MIR 218 262 0
198 24.44 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1204:18365:58831/2 54 98 (53) MIR#SINE/MIR 218 262 (0) m_b6s601i14
ST-E00130:540 54 AATGCCAGGCACACCGTATATACTCAACAAGTGTTAGCTATTTTT 98
i v iv viii i i v
MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 26.86
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 796 5.7 8.5 7.3 ST-E00130:540:HVYVWCCXX:4:1205:12642:49092/1 1 151 (0) C L1P3 LINE/L1 (2865) 3281 3129 1668
ANNOTATION EVIDENCE:
796 5.72 8.50 7.28 ST-E00130:540:HVYVWCCXX:4:1205:12642:49092/1 1 151 0 C L1P3_orf2 LINE/L1 1020 1172 2122
796 5.72 8.50 7.28 ST-E00130:540:HVYVWCCXX:4:1205:12642:49092/1 1 151 (0) C L1P3_orf2#LINE/L1 (2122) 1172 1020 m_b6s551i215
ST-E00130:540 1 TCTATTTGATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG--- 39
-------- v ---
C L1P3_orf2#LIN 1172 TCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCT 1123
ST-E00130:540 40 -TCTGTTTTGTTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTT 88
- i i v -
C L1P3_orf2#LIN 1122 ATCTATTTTGTTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TT 1074
ST-E00130:540 89 TTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAG 137
i i---------- -i v
C L1P3_orf2#LIN 1073 TTTTGAAGGGTTTTTC----------GTGTCTCTATCTCCTTCAGTTCTG 1034
ST-E00130:540 138 CTCTGATCTTAGTT 151
C L1P3_orf2#LIN 1033 CTCTGATCTTAGTT 1020
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.26
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.10 (15 / 150), avg. gap size = 1.60 (24 / 15)
+ 1237 5.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1205:12642:49092/2 1 151 (0) + L1P3 LINE/L1 2914 3064 (3082) 1669
ANNOTATION EVIDENCE:
1237 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1205:12642:49092/2 1 151 0 + L1P3_orf2 LINE/L1 805 955 2339
1237 5.30 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1205:12642:49092/2 1 151 (0) L1P3_orf2#LINE/L1 805 955 (2339) m_b7s551i23
ST-E00130:540 1 GAAATAAGTAAGTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCA 50
i? i i
L1P3_orf2#LIN 805 GAAATAAANAAGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCA 854
ST-E00130:540 51 GAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCAC 100
L1P3_orf2#LIN 855 GAATCTCTGGGACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCAC 904
ST-E00130:540 101 TAAATGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACA 150
? v i i
L1P3_orf2#LIN 905 TAAATGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACA 954
ST-E00130:540 151 T 151
L1P3_orf2#LIN 955 T 955
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.25
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1190 1.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1206:26839:50867/1 1 148 (3) C L1P1 LINE/L1 (755) 5391 5244 1670
ANNOTATION EVIDENCE:
1190 1.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1206:26839:50867/1 1 148 3 C L1P1_orf2 LINE/L1 3135 3282 12
1190 1.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1206:26839:50867/1 1 148 (3) C L1P1_orf2#LINE/L1 (12) 3282 3135 m_b1s551i161
ST-E00130:540 1 TTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTC 50
C L1P1_orf2#LIN 3282 TTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTC 3233
ST-E00130:540 51 TGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTG 100
i
C L1P1_orf2#LIN 3232 TGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTG 3183
ST-E00130:540 101 TAAATTTGTTTCAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCA 148
v
C L1P1_orf2#LIN 3182 TAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCA 3135
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.75
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0)
+ 1096 6.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1206:26839:50867/2 3 151 (0) + L1P1 LINE/L1 5002 5150 (996) 1671
ANNOTATION EVIDENCE:
1096 6.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1206:26839:50867/2 3 151 0 + L1P1_orf2 LINE/L1 2893 3041 253
1096 6.04 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1206:26839:50867/2 3 151 (0) L1P1_orf2#LINE/L1 2893 3041 (253) m_b1s551i66
ST-E00130:540 3 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAGCT 52
i v
L1P1_orf2#LIN 2893 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 2942
ST-E00130:540 53 AGGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 102
?
L1P1_orf2#LIN 2943 AGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 2992
ST-E00130:540 103 CACAAAAAGCAATGGCAACAAAAGACAGAATGGACAAATGGGAGCGAAT 151
v v i v v v
L1P1_orf2#LIN 2993 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3041
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.96
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.0 (0 / 0)
+ 1259 4.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1207:11870:57671/1 1 151 (0) + L1P3 LINE/L1 2875 3025 (3121) 1672
ANNOTATION EVIDENCE:
1259 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1207:11870:57671/1 1 151 0 + L1P3_orf2 LINE/L1 766 916 2378
1259 4.64 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1207:11870:57671/1 1 151 (0) L1P3_orf2#LINE/L1 766 916 (2378) m_b7s551i34
ST-E00130:540 1 CTCCTGAATGACTACTAGGTAAATAATGAAATGAAGGCAGAAATAAGTAA 50
i i v i?
L1P3_orf2#LIN 766 CTCCTGAATGACTACTGGGTAAATAACGAAATTAAGGCAGAAATAAANAA 815
ST-E00130:540 51 GTTCTTTGAAACCAATAAGAACAAAGACACAATGTACCAGAATCTCTGGG 100
i i
L1P3_orf2#LIN 816 GTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGGG 865
ST-E00130:540 101 ACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCAC 150
L1P3_orf2#LIN 866 ACACAGCTAAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCAC 915
ST-E00130:540 151 A 151
L1P3_orf2#LIN 916 A 916
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 891 4.3 0.7 7.3 ST-E00130:540:HVYVWCCXX:4:1207:11870:57671/2 1 151 (0) C L1P3 LINE/L1 (2951) 3195 3055 1673
ANNOTATION EVIDENCE:
891 4.28 0.71 7.28 ST-E00130:540:HVYVWCCXX:4:1207:11870:57671/2 1 151 0 C L1P3_orf2 LINE/L1 946 1086 2208
891 4.28 0.71 7.28 ST-E00130:540:HVYVWCCXX:4:1207:11870:57671/2 1 151 (0) C L1P3_orf2#LINE/L1 (2208) 1086 946 m_b6s551i252
ST-E00130:540 1 GGATTAATTGATTTTTTTGAAAGGTTTTTTTTGTGTGTGTGTGTCTCTAT 50
v - i i----------
C L1P3_orf2#LIN 1086 GGATTCATTGA-TTTTTTGAAGGGTTTTTC----------GTGTCTCTAT 1048
ST-E00130:540 51 CTCCTTCA-CTCAGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTT 99
-i v
C L1P3_orf2#LIN 1047 CTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGTCTTCTGCTAGCTT 998
ST-E00130:540 100 TTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTATTTGTGATGTTAGG 149
v
C L1P3_orf2#LIN 997 TTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGG 948
ST-E00130:540 150 GT 151
C L1P3_orf2#LIN 947 GT 946
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.73
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 938 4.3 0.7 7.3 ST-E00130:540:HVYVWCCXX:4:1207:6025:5106/2 1 151 (0) C L1P3 LINE/L1 (2932) 3214 3074 1674
ANNOTATION EVIDENCE:
938 4.28 0.71 7.28 ST-E00130:540:HVYVWCCXX:4:1207:6025:5106/2 1 151 0 C L1P3_orf2 LINE/L1 965 1105 2189
938 4.28 0.71 7.28 ST-E00130:540:HVYVWCCXX:4:1207:6025:5106/2 1 151 (0) C L1P3_orf2#LINE/L1 (2189) 1105 965 m_b6s551i246
ST-E00130:540 1 TTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGGTTTTTTT 50
i v - i i-
C L1P3_orf2#LIN 1105 TTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGGTTTTTC- 1058
ST-E00130:540 51 TGTGTGTGTGTGTCTCTATCTCCTTCA-CTCAGCTCTGATCTTAGTTATT 99
--------- -i v
C L1P3_orf2#LIN 1057 ---------GTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATT 1017
ST-E00130:540 100 TCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTC 149
C L1P3_orf2#LIN 1016 TCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTC 967
ST-E00130:540 150 TT 151
C L1P3_orf2#LIN 966 TT 965
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.00 (12 / 12)
+ 1300 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1211:6279:28927/1 1 151 (0) + L1PA2 LINE/L1 5938 6088 (67) 1675
ANNOTATION EVIDENCE:
1300 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1211:6279:28927/1 1 151 0 + L1PA2_3end LINE/L1 685 835 67
1300 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1211:6279:28927/1 1 151 (0) L1PA2_3end#LINE/L1 685 835 (67) m_b1s551i393
ST-E00130:540 1 ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGTGGACT 50
v
L1PA2_3end#LI 685 ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACT 734
ST-E00130:540 51 GTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAA 100
v
L1PA2_3end#LI 735 GTGGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAA 784
ST-E00130:540 101 TGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATA 150
i
L1PA2_3end#LI 785 TGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATA 834
ST-E00130:540 151 C 151
L1PA2_3end#LI 835 C 835
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 16 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1211:6279:28927/2 1 18 (133) + (A)n Simple_repeat 1 18 (0) 1676
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1211:6279:28927/2 1 18 133 + (A)n Simple_repeat 1 18 0
16 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1211:6279:28927/2 1 18 (133) (A)n#Simple_repeat 1 18 (0) m_b2s252i0
ST-E00130:540 1 AAAAAAAAAAAAAAAAAA 18
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0)
+ 1260 3.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:1211:7933:60167/1 1 151 (0) C L1P3 LINE/L1 (2442) 3704 3552 1677
ANNOTATION EVIDENCE:
1260 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7933:60167/1 1 151 0 C L1P3_orf2 LINE/L1 1443 1595 1699
1260 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7933:60167/1 1 151 (0) C L1P3_orf2#LINE/L1 (1699) 1595 1443 m_b6s551i92
ST-E00130:540 1 GGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAG 48
i-- v
C L1P3_orf2#LIN 1595 GGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAG 1546
ST-E00130:540 49 GATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTA 98
v i
C L1P3_orf2#LIN 1545 GATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTA 1496
ST-E00130:540 99 TTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCC 148
i
C L1P3_orf2#LIN 1495 TTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTC 1446
ST-E00130:540 149 TGG 151
C L1P3_orf2#LIN 1445 TGG 1443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1017 6.1 5.2 0.0 ST-E00130:540:HVYVWCCXX:4:1211:7933:60167/2 5 151 (0) + L1P1 LINE/L1 3230 3384 (2762) 1678
ANNOTATION EVIDENCE:
1017 6.12 5.16 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7933:60167/2 5 151 0 + L1P1_orf2 LINE/L1 1121 1275 2019
1017 6.12 5.16 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7933:60167/2 5 151 (0) L1P1_orf2#LINE/L1 1121 1275 (2019) m_b6s551i184
ST-E00130:540 5 ACAGACCGCTAGCAAGACTAATAAAGA--------GAGAAGAATCAAATA 46
i --------
L1P1_orf2#LIN 1121 ATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATA 1170
ST-E00130:540 47 GACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCCACAGAAAT 96
v i vi i
L1P1_orf2#LIN 1171 GACGCAATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAAT 1220
ST-E00130:540 97 ACAAACTACCATCAGAGAATACTATAAATACCTCTATGCAAATAAACTAG 146
i i i
L1P1_orf2#LIN 1221 ACAAACTACCATCAGAGAATACTACAAACACCTCTACGCAAATAAACTAG 1270
ST-E00130:540 147 AAAAT 151
L1P1_orf2#LIN 1271 AAAAT 1275
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.10
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.01 (1 / 146), avg. gap size = 8.00 (8 / 1)
+ 1260 3.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:1211:7943:60255/1 1 151 (0) C L1P3 LINE/L1 (2442) 3704 3552 1679
ANNOTATION EVIDENCE:
1260 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7943:60255/1 1 151 0 C L1P3_orf2 LINE/L1 1443 1595 1699
1260 3.31 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7943:60255/1 1 151 (0) C L1P3_orf2#LINE/L1 (1699) 1595 1443 m_b6s551i93
ST-E00130:540 1 GGCCTGAAATTTTCTTTTTC--TTGTGTCTCTGCCAGGTTTTGGAATCAG 48
i-- v
C L1P3_orf2#LIN 1595 GGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAG 1546
ST-E00130:540 49 GATGATGCTGGCATCATAAAATGAGTTAGGGAAGAGTCCCTCTTTTTCTA 98
v i
C L1P3_orf2#LIN 1545 GATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCTTTTTCTA 1496
ST-E00130:540 99 TTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCCC 148
i
C L1P3_orf2#LIN 1495 TTGTTTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCTTTGTACCTC 1446
ST-E00130:540 149 TGG 151
C L1P3_orf2#LIN 1445 TGG 1443
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1017 6.1 5.2 0.0 ST-E00130:540:HVYVWCCXX:4:1211:7943:60255/2 5 151 (0) + L1P1 LINE/L1 3230 3384 (2762) 1680
ANNOTATION EVIDENCE:
1017 6.12 5.16 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7943:60255/2 5 151 0 + L1P1_orf2 LINE/L1 1121 1275 2019
1017 6.12 5.16 0.00 ST-E00130:540:HVYVWCCXX:4:1211:7943:60255/2 5 151 (0) L1P1_orf2#LINE/L1 1121 1275 (2019) m_b6s551i185
ST-E00130:540 5 ACAGACCGCTAGCAAGACTAATAAAGA--------GAGAAGAATCAAATA 46
i --------
L1P1_orf2#LIN 1121 ATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATA 1170
ST-E00130:540 47 GACTCAATAAAAAATGATAAAGAGGATAATACCACTGATCCCACAGAAAT 96
v i vi i
L1P1_orf2#LIN 1171 GACGCAATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAAT 1220
ST-E00130:540 97 ACAAACTACCATCAGAGAATACTATAAATACCTCTATGCAAATAAACTAG 146
i i i
L1P1_orf2#LIN 1221 ACAAACTACCATCAGAGAATACTACAAACACCTCTACGCAAATAAACTAG 1270
ST-E00130:540 147 AAAAT 151
L1P1_orf2#LIN 1271 AAAAT 1275
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.10
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.01 (1 / 146), avg. gap size = 8.00 (8 / 1)
+ 513 8.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/1 1 74 (77) + L1P3 LINE/L1 3825 3898 (2248) 1681
ANNOTATION EVIDENCE:
513 8.11 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/1 1 74 77 + L1P3_orf2 LINE/L1 1716 1789 1505
513 8.11 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/1 1 74 (77) L1P3_orf2#LINE/L1 1716 1789 (1505) m_b6s551i12
ST-E00130:540 1 CTGATTCAGCATACACAAATCAATAAACATAATCCATCACATAAACAGAA 50
i i i i
L1P3_orf2#LIN 1716 CTGGTTCAACATACGCAAATCAATAAACGTAATCCATCACATAAACAGAA 1765
ST-E00130:540 51 CGAATGACAAAAACTACATGATTA 74
v i
L1P3_orf2#LIN 1766 CCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.95
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 595 8.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/1 77 151 (0) + AluSx SINE/Alu 14 88 (224) 1682
ANNOTATION EVIDENCE:
595 8.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/1 77 151 0 + AluSx SINE/Alu 14 88 224
595 8.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/1 77 151 (0) AluSx#SINE/Alu 14 88 (224) m_b6s357i19
ST-E00130:540 77 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 126
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 127 CCTGAGGTCAGGAGTTCAAGACCAG 151
i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAG 88
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.28
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 30 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/2 21 48 (103) + (T)n Simple_repeat 1 28 (0) 1683
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/2 21 48 103 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:28960:50322/2 21 48 (103) (T)n#Simple_repeat 1 28 (0) c_b6s251i3
ST-E00130:540 21 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 513 8.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/1 1 74 (77) + L1P3 LINE/L1 3825 3898 (2248) 1684
ANNOTATION EVIDENCE:
513 8.11 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/1 1 74 77 + L1P3_orf2 LINE/L1 1716 1789 1505
513 8.11 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/1 1 74 (77) L1P3_orf2#LINE/L1 1716 1789 (1505) m_b6s551i13
ST-E00130:540 1 CTGATTCAGCATACACAAATCAATAAACATAATCCATCACATAAACAGAA 50
i i i i
L1P3_orf2#LIN 1716 CTGGTTCAACATACGCAAATCAATAAACGTAATCCATCACATAAACAGAA 1765
ST-E00130:540 51 CGAATGACAAAAACTACATGATTA 74
v i
L1P3_orf2#LIN 1766 CCAATGACAAAAACCACATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.95
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 595 8.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/1 77 151 (0) + AluSx SINE/Alu 14 88 (224) 1685
ANNOTATION EVIDENCE:
595 8.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/1 77 151 0 + AluSx SINE/Alu 14 88 224
595 8.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/1 77 151 (0) AluSx#SINE/Alu 14 88 (224) m_b6s357i20
ST-E00130:540 77 GGCTCACGCCTGTAATCTCAGCACTTTGGGAGGACAAGGTGGGTGGATCA 126
i v i i i
AluSx#SINE/Al 14 GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCA 63
ST-E00130:540 127 CCTGAGGTCAGGAGTTCAAGACCAG 151
i
AluSx#SINE/Al 64 CCTGAGGTCAGGAGTTCGAGACCAG 88
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.28
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 28 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/2 21 47 (104) + (T)n Simple_repeat 1 27 (0) 1686
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/2 21 47 104 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1212:29356:50691/2 21 47 (104) (T)n#Simple_repeat 1 27 (0) c_b6s251i2
ST-E00130:540 21 TTTTTTTTTTTTTTTTTTTTTTTTTTT 47
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 240 21.1 12.7 0.0 ST-E00130:540:HVYVWCCXX:4:1212:32268:7427/1 1 66 (85) C L1MC4 LINE/L1 (531) 7511 7416 1687
ANNOTATION EVIDENCE:
238 21.21 15.38 0.00 ST-E00130:540:HVYVWCCXX:4:1212:32268:7427/1 1 66 85 C L1MC4a_3end LINE/L1 2163 2240 389
238 21.21 15.38 0.00 ST-E00130:540:HVYVWCCXX:4:1212:32268:7427/1 1 66 (85) C L1MC4a_3end#LINE/L1 (389) 2240 2163 m_b3s551i145
ST-E00130:540 1 GTCTGATGTTTCCTTATGATTAAAT-----TTATAC---TTTGACGAGAA 42
i i i ----- i --- i i
C L1MC4a_3end#L 2240 GTCTGATGTTTTCTCATGATTAGATTGAGGTTATGCATTTTTGGCAAGAA 2191
ST-E00130:540 43 TGTTGCAAAAGTAAT----TCCTCTTCT 66
iiii i i ---- v i
C L1MC4a_3end#L 2190 TACCACAGAAGTGATGTTGTGCCCTTCT 2163
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.07
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.05 (3 / 65), avg. gap size = 4.00 (12 / 3)
240 21.05 12.31 0.00 ST-E00130:540:HVYVWCCXX:4:1212:32268:7427/1 1 57 94 C L1MC4_3end LINE/L1 2194 2258 531
240 21.05 12.31 0.00 ST-E00130:540:HVYVWCCXX:4:1212:32268:7427/1 1 57 (94) C L1MC4_3end#LINE/L1 (531) 2258 2194 m_b3s551i146
ST-E00130:540 1 GTCTGATGTTTCCTTATGATTAAAT-----TTATAC---TTTGACGAGAA 42
i i ----- i --- i ii
C L1MC4_3end#LI 2258 GTCTGATGTTTCCTCATGATTAGATTCAGGTTATGCATTTTTGGCAGGAA 2209
ST-E00130:540 43 TGTTGCAAAAGTAAT 57
iiii i i
C L1MC4_3end#LI 2208 TACCACAGAAGTGAT 2194
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.33
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.04 (2 / 56), avg. gap size = 4.00 (8 / 2)
+ 432 25.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1213:19086:37647/2 3 103 (48) C AluSx SINE/Alu (211) 101 1 1688
ANNOTATION EVIDENCE:
432 25.74 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1213:19086:37647/2 3 103 48 C AluSx SINE/Alu 1 101 211
432 25.74 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1213:19086:37647/2 3 103 (48) C AluSx#SINE/Alu (211) 101 1 m_b5s357i65
ST-E00130:540 3 CAGGTGGGCCAGAATGGTATCAAAATCCTGACCTAAAATGATCTGCCAAC 52
v v iv v i v v ii i vi
C AluSx#SINE/Al 101 CATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGC 52
ST-E00130:540 53 CTTGGCATCCCGAAGTGTTGGTATTAAAGATGTGAGCGAGGGCACCCAGC 102
i v i i v v ii v vv i i
C AluSx#SINE/Al 51 CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
ST-E00130:540 103 C 103
C AluSx#SINE/Al 1 C 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 22.59
Transitions / transversions = 1.00 (13/13)
Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0)
+ 806 8.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/1 1 108 (43) + L1P3 LINE/L1 3791 3898 (2248) 1689
ANNOTATION EVIDENCE:
806 8.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/1 1 108 43 + L1P3_orf2 LINE/L1 1682 1789 1505
806 8.33 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/1 1 108 (43) L1P3_orf2#LINE/L1 1682 1789 (1505) m_b6s551i22
ST-E00130:540 1 ACTATCAAGTCAGCTTCATCCCTGGGACGCAAGGCTGATTCAGCATACAC 50
v i i i i i
L1P3_orf2#LIN 1682 ACGATCAAGTCGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACATACGC 1731
ST-E00130:540 51 AAATCAATAAACATAATCCATCACATAAACAGAACGAATGACAAAAACTA 100
i v i
L1P3_orf2#LIN 1732 AAATCAATAAACGTAATCCATCACATAAACAGAACCAATGACAAAAACCA 1781
ST-E00130:540 101 CATGATTA 108
L1P3_orf2#LIN 1782 CATGATTA 1789
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.11
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0)
+ 230 10.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/1 120 149 (2) C SVA_F Retroposon/SVA (954) 421 392 1690
ANNOTATION EVIDENCE:
230 10.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/1 120 149 2 C SVA_F Retroposon/SVA 392 421 954
230 10.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/1 120 149 (2) C SVA_F#Retroposon/SVA (954) 421 392 m_b6s502i2
ST-E00130:540 120 CTGTAATCTCAGCACTTTGGGAGGACAAGG 149
i i v
C SVA_F#Retropo 421 CTGCAATCTCGGCACTTTGGGAGGCCAAGG 392
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.36
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 35 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/2 5 37 (114) + (T)n Simple_repeat 1 33 (0) 1691
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/2 5 37 114 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1215:20933:41550/2 5 37 (114) (T)n#Simple_repeat 1 33 (0) c_b6s251i1
ST-E00130:540 5 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 1367 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1217:26514:2733/1 1 151 (0) C L1P1 LINE/L1 (460) 5695 5545 1692
ANNOTATION EVIDENCE:
1367 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1217:26514:2733/1 1 151 0 C L1PA3_3end LINE/L1 292 442 460
1367 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1217:26514:2733/1 1 151 (0) C L1PA3_3end#LINE/L1 (460) 442 292 m_b1s551i287
ST-E00130:540 1 TACGTGTGCATGTGTCTTTATAGCGGCATGATTTATAGTCCTTTGGGTAT 50
i
C L1PA3_3end#LI 442 TACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTAT 393
ST-E00130:540 51 ATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATC 100
i
C L1PA3_3end#LI 392 ATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATC 343
ST-E00130:540 101 CCTGAGGAATCACCACACTGACTTCCACAATGGTTGAACTAGTTTACAGT 150
i
C L1PA3_3end#LI 342 CCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGT 293
ST-E00130:540 151 C 151
C L1PA3_3end#LI 292 C 292
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1344 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1217:26514:2733/2 1 151 (0) + L1P2 LINE/L1 5494 5644 (511) 1693
ANNOTATION EVIDENCE:
1344 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1217:26514:2733/2 1 151 0 + L1PA4_3end LINE/L1 241 391 511
1344 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1217:26514:2733/2 1 151 (0) L1PA4_3end#LINE/L1 241 391 (511) m_b1s551i272
ST-E00130:540 1 AGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTTACACTGTTGGTG 50
iv
L1PA4_3end#LI 241 AGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTG 290
ST-E00130:540 51 GGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGTGATTCCTCA 100
i
L1PA4_3end#LI 291 GGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCA 340
ST-E00130:540 101 GGGATCTAGAACTGGAAATACCATTTGACCCAGCCATCCCATTACTGGGT 150
i
L1PA4_3end#LI 341 GGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGT 390
ST-E00130:540 151 A 151
L1PA4_3end#LI 391 A 391
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.09
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 909 13.2 0.0 2.2 ST-E00130:540:HVYVWCCXX:4:1219:30685:18608/1 13 151 (0) + AluY SINE/Alu 1 136 (175) 1694
ANNOTATION EVIDENCE:
909 13.24 0.00 2.16 ST-E00130:540:HVYVWCCXX:4:1219:30685:18608/1 13 151 0 + AluY SINE/Alu 1 136 175
909 13.24 0.00 2.16 ST-E00130:540:HVYVWCCXX:4:1219:30685:18608/1 13 151 (0) AluY#SINE/Alu 1 136 (175) m_b5s356i31
ST-E00130:540 13 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 62
i i iv i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 63 GGTGGGCAGATCACTTGAGGTCAGGAGTTTGGGACCAGCCTGGCCAACGT 112
i i -- v i i v i ii
AluY#SINE/Alu 51 GGCGGGCGGATCAC--GAGGTCAGGAGATCGAGACCATCCTGGCTAACAC 98
ST-E00130:540 113 GTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAG 151
v i -
AluY#SINE/Alu 99 GGTGAAACCCCGTCTCTACTAAAAATACAAAAAA-TTAG 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.95
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.00 (3 / 3)
+ 1336 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1220:15493:62997/1 1 151 (0) + L1P1 LINE/L1 5628 5778 (377) 1695
ANNOTATION EVIDENCE:
1336 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1220:15493:62997/1 1 151 0 + L1PA2_3end LINE/L1 375 525 377
1336 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1220:15493:62997/1 1 151 (0) L1PA2_3end#LINE/L1 375 525 (377) m_b1s551i309
ST-E00130:540 1 CATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCGCTATA 50
i
L1PA2_3end#LI 375 CATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATA 424
ST-E00130:540 51 AAGACACATGCACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAG 100
i
L1PA2_3end#LI 425 AAGACACATGCACACGTATGTTTATTGCGGCATTATTCACAATAGCAAAG 474
ST-E00130:540 101 ACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAACT 150
v
L1PA2_3end#LI 475 ACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAAT 524
ST-E00130:540 151 G 151
L1PA2_3end#LI 525 G 525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1259 2.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:1220:15493:62997/2 1 151 (0) C L1PA2 LINE/L1 (208) 5947 5798 1696
ANNOTATION EVIDENCE:
1259 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1220:15493:62997/2 1 151 0 C L1PA2_3end LINE/L1 545 694 208
1259 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1220:15493:62997/2 1 151 (0) C L1PA2_3end#LINE/L1 (208) 694 545 m_b1s551i374
ST-E00130:540 1 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTT 50
i
C L1PA2_3end#LI 694 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTT 645
ST-E00130:540 51 TTTTCTTCTTGCGACAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 100
v i
C L1PA2_3end#LI 644 TTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 595
ST-E00130:540 101 TGTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATATTAT 150
- v
C L1PA2_3end#LI 594 TGTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 546
ST-E00130:540 151 T 151
C L1PA2_3end#LI 545 T 545
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1336 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1220:15879:62435/1 1 151 (0) + L1P1 LINE/L1 5628 5778 (377) 1697
ANNOTATION EVIDENCE:
1336 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1220:15879:62435/1 1 151 0 + L1PA2_3end LINE/L1 375 525 377
1336 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1220:15879:62435/1 1 151 (0) L1PA2_3end#LINE/L1 375 525 (377) m_b1s551i310
ST-E00130:540 1 CATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCGCTATA 50
i
L1PA2_3end#LI 375 CATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATA 424
ST-E00130:540 51 AAGACACATGCACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAG 100
i
L1PA2_3end#LI 425 AAGACACATGCACACGTATGTTTATTGCGGCATTATTCACAATAGCAAAG 474
ST-E00130:540 101 ACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAACT 150
v
L1PA2_3end#LI 475 ACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAAT 524
ST-E00130:540 151 G 151
L1PA2_3end#LI 525 G 525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1289 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:1220:15879:62435/2 1 151 (0) C L1PA2 LINE/L1 (208) 5947 5798 1698
ANNOTATION EVIDENCE:
1289 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1220:15879:62435/2 1 151 0 C L1PA2_3end LINE/L1 545 694 208
1289 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:1220:15879:62435/2 1 151 (0) C L1PA2_3end#LINE/L1 (208) 694 545 m_b1s551i375
ST-E00130:540 1 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTT 50
i
C L1PA2_3end#LI 694 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTT 645
ST-E00130:540 51 TTTTCTTCTTGCGACAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 100
v i
C L1PA2_3end#LI 644 TTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 595
ST-E00130:540 101 TGTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 150
-
C L1PA2_3end#LI 594 TGTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 546
ST-E00130:540 151 T 151
C L1PA2_3end#LI 545 T 545
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1183 9.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1223:16285:35608/1 1 151 (0) + AluSx SINE/Alu 48 198 (114) 1699
ANNOTATION EVIDENCE:
1183 9.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1223:16285:35608/1 1 151 0 + AluSx SINE/Alu 48 198 114
1183 9.93 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1223:16285:35608/1 1 151 (0) AluSx#SINE/Alu 48 198 (114) m_b6s356i15
ST-E00130:540 1 CAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAA 50
i i i i
AluSx#SINE/Al 48 CGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAA 97
ST-E00130:540 51 CATGGTGAAACTCCATCTCTACGAAAAATAAAAAAATTAGCTGGGCATGG 100
i i v v i i
AluSx#SINE/Al 98 CATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGG 147
ST-E00130:540 101 TGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGGATGAGGCAGGAGAATT 150
iv i v i
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATC 197
ST-E00130:540 151 G 151
AluSx#SINE/Al 198 G 198
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.08
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 32 0.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1223:16285:35608/2 50 79 (72) + (T)n Simple_repeat 1 30 (0) 1700
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1223:16285:35608/2 50 79 72 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1223:16285:35608/2 50 79 (72) (T)n#Simple_repeat 1 30 (0) c_b6s251i0
ST-E00130:540 50 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 79
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1274 2.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1223:20699:12806/1 1 151 (0) C L1P3 LINE/L1 (3030) 3116 2966 1701
ANNOTATION EVIDENCE:
1274 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1223:20699:12806/1 1 151 0 C L1P3_orf2 LINE/L1 857 1007 2287
1274 2.65 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1223:20699:12806/1 1 151 (0) C L1P3_orf2#LINE/L1 (2287) 1007 857 m_b6s551i277
ST-E00130:540 1 CTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTG 50
C L1P3_orf2#LIN 1007 CTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTG 958
ST-E00130:540 51 TGATGTTAGGGTGTTGATTTTAGATCTTTCCCACTTTGTCCTGTGGGCAT 100
i i v ?
C L1P3_orf2#LIN 957 TGATGTTAGGGTGTCGATTTTAGATCTTTCCCGCTTTCTCNTGTGGGCAT 908
ST-E00130:540 101 TTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGA 150
C L1P3_orf2#LIN 907 TTAGTGCTATAAATTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGA 858
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 857 T 857
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.80
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1132 7.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:1224:32146:37665/1 14 151 (0) C AluSx SINE/Alu (21) 291 154 1702
ANNOTATION EVIDENCE:
1132 7.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1224:32146:37665/1 14 151 0 C AluSx SINE/Alu 154 291 21
1132 7.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:1224:32146:37665/1 14 151 (0) C AluSx#SINE/Alu (21) 291 154 m_b4s356i3
ST-E00130:540 14 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 63
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 64 GCGCGATCTCGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGGTTCT 113
i i i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
ST-E00130:540 114 CCTGCCTCAGCCTCCTGAGTAGCTGGGATTATGTGCGC 151
i iiv
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC 154
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.55
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 137), avg. gap size = 0.0 (0 / 0)
+ 662 13.3 2.0 0.0 ST-E00130:540:HVYVWCCXX:4:1224:32146:37665/2 54 151 (0) + AluSx SINE/Alu 1 100 (212) 1703
ANNOTATION EVIDENCE:
662 13.27 2.00 0.00 ST-E00130:540:HVYVWCCXX:4:1224:32146:37665/2 54 151 0 + AluSx SINE/Alu 1 100 212
662 13.27 2.00 0.00 ST-E00130:540:HVYVWCCXX:4:1224:32146:37665/2 54 151 (0) AluSx#SINE/Alu 1 100 (212) m_b4s357i54
ST-E00130:540 54 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGTAGGCTGA 103
i i i v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 104 AGCAGGCATATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 151
i i iv --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.19
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 2.00 (2 / 1)
+ 1243 7.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2102:18487:53276/1 1 151 (0) C AluSx SINE/Alu (32) 280 130 1704
ANNOTATION EVIDENCE:
1243 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2102:18487:53276/1 1 151 0 C AluSx SINE/Alu 130 280 32
1243 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2102:18487:53276/1 1 151 (0) C AluSx#SINE/Alu (32) 280 130 m_b4s356i8
ST-E00130:540 1 GACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCGCGATCTCG 50
i i i
C AluSx#SINE/Al 280 GACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCG 231
ST-E00130:540 51 GCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGC 100
i i
C AluSx#SINE/Al 230 GCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGC 181
ST-E00130:540 101 CTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGGCTAATTT 150
i i vi v i
C AluSx#SINE/Al 180 CTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTT 131
ST-E00130:540 151 T 151
C AluSx#SINE/Al 130 T 130
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.45
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 636 11.1 2.2 0.0 ST-E00130:540:HVYVWCCXX:4:2102:18487:53276/2 62 151 (0) + AluSx SINE/Alu 1 92 (220) 1705
ANNOTATION EVIDENCE:
636 11.11 2.17 0.00 ST-E00130:540:HVYVWCCXX:4:2102:18487:53276/2 62 151 0 + AluSx SINE/Alu 1 92 220
636 11.11 2.17 0.00 ST-E00130:540:HVYVWCCXX:4:2102:18487:53276/2 62 151 (0) AluSx#SINE/Alu 1 92 (220) m_b4s357i56
ST-E00130:540 62 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 111
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 112 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTG 151
i i i --i i v
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTG 92
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.25
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.01 (1 / 89), avg. gap size = 2.00 (2 / 1)
+ 881 5.8 0.7 7.3 ST-E00130:540:HVYVWCCXX:4:2102:25672:9396/1 1 150 (1) C L1P3 LINE/L1 (2925) 3221 3082 1706
ANNOTATION EVIDENCE:
881 5.75 0.72 7.33 ST-E00130:540:HVYVWCCXX:4:2102:25672:9396/1 1 150 1 C L1P3_orf2 LINE/L1 973 1112 2182
881 5.75 0.72 7.33 ST-E00130:540:HVYVWCCXX:4:2102:25672:9396/1 1 150 (1) C L1P3_orf2#LINE/L1 (2182) 1112 973 m_b6s551i244
ST-E00130:540 1 TTAATCTTTTCAAAAAATCAGCTCCTGGATTAATTGATTTTTTTGAAAGG 50
i v - i
C L1P3_orf2#LIN 1112 TTAATCTTTTCAAAAAACCAGCTCCTGGATTCATTGA-TTTTTTGAAGGG 1064
ST-E00130:540 51 TTTTTTTTGTGTGTTTGTGTCTCTATCTCCTTCACTTA-GCTCTGATCTT 99
---------- i v v-
C L1P3_orf2#LIN 1063 TTT----------TTCGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT 1024
ST-E00130:540 100 AGTTATTTCTTGTCTTCTGCTGGCTTTTGAATTTGTTTGCTGTTGCTTCT 149
i v
C L1P3_orf2#LIN 1023 AGTTATTTCTTGTCTTCTGCTAGCTTTTGAATTTGTTTGCTCTTGCTTCT 974
ST-E00130:540 150 C 150
C L1P3_orf2#LIN 973 C 973
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.29
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.00 (12 / 12)
+ 1186 7.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2102:25672:9396/2 1 151 (0) + L1P3 LINE/L1 2844 2994 (3152) 1707
ANNOTATION EVIDENCE:
1186 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2102:25672:9396/2 1 151 0 + L1P3_orf2 LINE/L1 735 885 2409
1186 7.28 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2102:25672:9396/2 1 151 (0) L1P3_orf2#LINE/L1 735 885 (2409) m_b7s551i46
ST-E00130:540 1 CCACACAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTAGG 50
i i
L1P3_orf2#LIN 735 CCGCACAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGG 784
ST-E00130:540 51 TAAATAATGAAATGAAGACAGCAATAAGTAAGTTCTTTGAAACCAATAAG 100
i v i v i? i
L1P3_orf2#LIN 785 TAAATAACGAAATTAAGGCAGAAATAAANAAGTTCTTTGAAACCAATGAG 834
ST-E00130:540 101 AACAAAGACACAATGTACCAGAATCTCTGGGTCACAGCTAAAGCAGTGTT 150
i v
L1P3_orf2#LIN 835 AACAAAGACACAACGTACCAGAATCTCTGGGACACAGCTAAAGCAGTGTT 884
ST-E00130:540 151 T 151
L1P3_orf2#LIN 885 T 885
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.04
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1195 3.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2104:27255:1415/1 2 151 (0) C L1P3 LINE/L1 (2585) 3561 3410 1708
ANNOTATION EVIDENCE:
1195 3.33 1.31 0.00 ST-E00130:540:HVYVWCCXX:4:2104:27255:1415/1 2 151 0 C L1P3_orf2 LINE/L1 1301 1452 1842
1195 3.33 1.31 0.00 ST-E00130:540:HVYVWCCXX:4:2104:27255:1415/1 2 151 (0) C L1P3_orf2#LINE/L1 (1842) 1452 1301 m_b6s551i133
ST-E00130:540 2 GTACCCCTGGTAGAATTCGGCTGTGAATCCCTCTGGTCCTGGGCTTTTTT 51
i v
C L1P3_orf2#LIN 1452 GTACCTCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTTT 1403
ST-E00130:540 52 TGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGT 101
C L1P3_orf2#LIN 1402 TGGTTGGTAGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATTGGT 1353
ST-E00130:540 102 CTATTCAGGGATTCGACTTCTTCCTGCTTTAG--TTGGGAGGTGGTATGT 149
v -- vv
C L1P3_orf2#LIN 1352 CTATTCAGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGT 1303
ST-E00130:540 150 GT 151
C L1P3_orf2#LIN 1302 GT 1301
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.41
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 1159 4.7 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2104:27255:1415/2 2 151 (0) + L1P3 LINE/L1 3352 3503 (2643) 1709
ANNOTATION EVIDENCE:
1159 4.67 1.31 0.00 ST-E00130:540:HVYVWCCXX:4:2104:27255:1415/2 2 151 0 + L1P3_orf2 LINE/L1 1243 1394 1900
1159 4.67 1.31 0.00 ST-E00130:540:HVYVWCCXX:4:2104:27255:1415/2 2 151 (0) L1P3_orf2#LINE/L1 1243 1394 (1900) m_b6s551i145
ST-E00130:540 2 TATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAAGAAAGTGATAA 51
i i vv
L1P3_orf2#LIN 1243 TATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAA 1292
ST-E00130:540 52 ATTCCTAGACACATACAACCTCCCAA--CTAAAGCAGGAAGAAGTCGAAT 99
i v -- v
L1P3_orf2#LIN 1293 ATTCCTGGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTCGAAT 1342
ST-E00130:540 100 CCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGC 149
L1P3_orf2#LIN 1343 CCCTGAATAGACCAATAACAAGTTCTGAAATTGAGGCAGTAATTAATAGC 1392
ST-E00130:540 150 CT 151
L1P3_orf2#LIN 1393 CT 1394
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.18
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 2.00 (2 / 1)
+ 250 30.8 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2105:12905:23354/1 3 80 (71) C MIRb SINE/MIR (68) 200 122 1710
ANNOTATION EVIDENCE:
250 30.77 1.26 0.00 ST-E00130:540:HVYVWCCXX:4:2105:12905:23354/1 3 80 71 C MIRb SINE/MIR 122 200 68
250 30.77 1.26 0.00 ST-E00130:540:HVYVWCCXX:4:2105:12905:23354/1 3 80 (71) C MIRb#SINE/MIR (68) 200 122 m_b4s601i28
ST-E00130:540 3 TTATTTTCTCTAATCCTCACAGTTATCTGGCCAGGTAAGTGATA-TATCT 51
i iv i iiv i iv v i iv - i
C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCC 151
ST-E00130:540 52 TCACTCTACTGATGAGGGTACGAAGGCCC 80
i i i v iv vi i
C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTC 122
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 41.70
Transitions / transversions = 2.00 (16/8)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1)
+ 1163 6.2 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2105:12905:23354/2 1 144 (7) + AluSx SINE/Alu 148 291 (21) 1711
ANNOTATION EVIDENCE:
1163 6.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2105:12905:23354/2 1 144 7 + AluSx SINE/Alu 148 291 21
1163 6.25 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2105:12905:23354/2 1 144 (7) AluSx#SINE/Alu 148 291 (21) m_b4s357i31
ST-E00130:540 1 TGGCAGGCGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATC 50
iv i i
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATC 197
ST-E00130:540 51 GCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCGCGCCACTGC 100
i i
AluSx#SINE/Al 198 GCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGC 247
ST-E00130:540 101 ACTCCAGCCCGGGCAACAGAGCGAGATTCCGTCTCAAAAAAAAA 144
i i i
AluSx#SINE/Al 248 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.87
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 143), avg. gap size = 0.0 (0 / 0)
+ 1131 7.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:2106:4909:31230/1 8 151 (0) C AluY SINE/Alu (14) 297 155 1712
ANNOTATION EVIDENCE:
1131 7.69 0.00 0.69 ST-E00130:540:HVYVWCCXX:4:2106:4909:31230/1 8 151 0 C AluY SINE/Alu 155 297 14
1131 7.69 0.00 0.69 ST-E00130:540:HVYVWCCXX:4:2106:4909:31230/1 8 151 (0) C AluY#SINE/Alu (14) 297 155 m_b2s356i92
ST-E00130:540 8 TTTTATTTCTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAA 57
v i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG 248
ST-E00130:540 58 TGCAGTGGCATGATCTCGGCTCACTGCAACCTCCACCTCCCCAGGTTCAT 107
ii v i - i i
C AluY#SINE/Alu 247 TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCT-CCCGGGTTCAC 199
ST-E00130:540 108 GCCGTTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGC 151
i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 155
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.71
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 1.00 (1 / 1)
+ 1274 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2108:4148:63068/1 1 151 (0) C L1P1 LINE/L1 (1046) 5100 4950 1713
ANNOTATION EVIDENCE:
1274 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2108:4148:63068/1 1 151 0 C L1P1_orf2 LINE/L1 2841 2991 303
1274 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2108:4148:63068/1 1 151 (0) C L1P1_orf2#LINE/L1 (303) 2991 2841 m_b1s551i38
ST-E00130:540 1 TTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTA 50
?
C L1P1_orf2#LIN 2991 TTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTA 2942
ST-E00130:540 51 GGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTA 100
i
C L1P1_orf2#LIN 2941 GGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTA 2892
ST-E00130:540 101 ATCCATCTTGAATTGATTTTTCTATCAGGTGTAAGGAAGGGATCCAGTTT 150
i v v
C L1P1_orf2#LIN 2891 ATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTT 2842
ST-E00130:540 151 C 151
C L1P1_orf2#LIN 2841 C 2841
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/1 86 117 (34) + (TG)n Simple_repeat 1 32 (0) 1714
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/1 86 117 34 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/1 86 117 (34) (TG)n#Simple_repeat 1 32 (0) m_b4s252i9
ST-E00130:540 86 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 117
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/1 118 130 (21) + (TGTATG)n Simple_repeat 1 41 (0) 1715
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/1 86 130 21 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/1 86 130 (21) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i8
ST-E00130:540 86 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 130
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 1208 9.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/2 1 151 (0) + AluSx SINE/Alu 79 229 (83) 1716
ANNOTATION EVIDENCE:
1208 9.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/2 1 151 0 + AluSx SINE/Alu 79 229 83
1208 9.27 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2109:11383:32672/2 1 151 (0) AluSx#SINE/Alu 79 229 (83) m_b4s356i27
ST-E00130:540 1 TTGAGAACAGCCTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACAC 50
i v i i i i
AluSx#SINE/Al 79 TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC 128
ST-E00130:540 51 AAAAATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGG 100
i v iv i i
AluSx#SINE/Al 129 AAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGG 178
ST-E00130:540 101 AGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGA 150
i i
AluSx#SINE/Al 179 AGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGA 228
ST-E00130:540 151 G 151
AluSx#SINE/Al 229 G 229
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.95
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 774 10.4 1.9 0.0 ST-E00130:540:HVYVWCCXX:4:2112:22069:12402/1 45 150 (1) + AluSx SINE/Alu 1 108 (204) 1717
ANNOTATION EVIDENCE:
774 10.38 1.85 0.00 ST-E00130:540:HVYVWCCXX:4:2112:22069:12402/1 45 150 1 + AluSx SINE/Alu 1 108 204
774 10.38 1.85 0.00 ST-E00130:540:HVYVWCCXX:4:2112:22069:12402/1 45 150 (1) AluSx#SINE/Alu 1 108 (204) m_b4s357i47
ST-E00130:540 45 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 94
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 95 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 142
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 143 GGTGAAAC 150
AluSx#SINE/Al 101 GGTGAAAC 108
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.60
Transitions / transversions = 10.00 (10/1)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 2.00 (2 / 1)
+ 19 4.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2112:22069:12402/2 128 151 (0) + (TG)n Simple_repeat 1 24 (0) 1718
ANNOTATION EVIDENCE:
19 4.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2112:22069:12402/2 128 151 0 + (TG)n Simple_repeat 1 24 0
19 4.35 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2112:22069:12402/2 128 151 (0) (TG)n#Simple_repeat 1 24 (0) m_b4s252i7
ST-E00130:540 128 TGTGTGTGTGTGTGTATGTGTGTG 151
i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 1292 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2113:16833:44749/1 1 151 (0) C L1P3 LINE/L1 (2460) 3686 3536 1719
ANNOTATION EVIDENCE:
1292 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2113:16833:44749/1 1 151 0 C L1P3_orf2 LINE/L1 1427 1577 1717
1292 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2113:16833:44749/1 1 151 (0) C L1P3_orf2#LINE/L1 (1717) 1577 1427 m_b6s551i98
ST-E00130:540 1 TTTCTTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATCATA 50
v v v
C L1P3_orf2#LIN 1577 TTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCATA 1528
ST-E00130:540 51 AAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 100
i
C L1P3_orf2#LIN 1527 AAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 1478
ST-E00130:540 101 GAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTG 150
i
C L1P3_orf2#LIN 1477 GAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTG 1428
ST-E00130:540 151 A 151
C L1P3_orf2#LIN 1427 A 1427
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1008 4.8 5.2 0.0 ST-E00130:540:HVYVWCCXX:4:2113:16833:44749/2 1 146 (5) + L1P3 LINE/L1 3241 3394 (2752) 1720
ANNOTATION EVIDENCE:
1008 4.79 5.20 0.00 ST-E00130:540:HVYVWCCXX:4:2113:16833:44749/2 1 146 5 + L1P3_orf2 LINE/L1 1132 1285 2009
1008 4.79 5.20 0.00 ST-E00130:540:HVYVWCCXX:4:2113:16833:44749/2 1 146 (5) L1P3_orf2#LINE/L1 1132 1285 (2009) m_b6s551i180
ST-E00130:540 1 GCAAGACTAATAAAGA--------GAGAAGAATCAAATAGACTCAATAAA 42
v -------- v
L1P3_orf2#LIN 1132 GCCAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGACACAATAAA 1181
ST-E00130:540 43 AAATGATAAAGAGGATAATACCACTGATCCCACAGAAATACAAACTACCA 92
i vi
L1P3_orf2#LIN 1182 AAATGATAAAGGGGATATCACCACTGATCCCACAGAAATACAAACTACCA 1231
ST-E00130:540 93 TCAGAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAA 142
i i
L1P3_orf2#LIN 1232 TCAGAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAA 1281
ST-E00130:540 143 GAAA 146
L1P3_orf2#LIN 1282 GAAA 1285
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.30
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 8.00 (8 / 1)
+ 1292 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2113:17218:43835/1 1 151 (0) C L1P3 LINE/L1 (2460) 3686 3536 1721
ANNOTATION EVIDENCE:
1292 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2113:17218:43835/1 1 151 0 C L1P3_orf2 LINE/L1 1427 1577 1717
1292 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2113:17218:43835/1 1 151 (0) C L1P3_orf2#LINE/L1 (1717) 1577 1427 m_b6s551i99
ST-E00130:540 1 TTTCTTGTGTCTCTGCCAGGTTTTGGAATCAGGATGATGCTGGCATCATA 50
v v v
C L1P3_orf2#LIN 1577 TTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCATA 1528
ST-E00130:540 51 AAATGAGTTAGGGAAGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 100
i
C L1P3_orf2#LIN 1527 AAATGAGTTAGGGAGGAGTCCCTCTTTTTCTATTGTTTGGAATAGTTTCA 1478
ST-E00130:540 101 GAAGGAATGGTACCAGCTCCTCTTTGTACCCCTGGTAGAATTCGGCTGTG 150
i
C L1P3_orf2#LIN 1477 GAAGGAATGGTACCAGCTCCTCTTTGTACCTCTGGTAGAATTCGGCTGTG 1428
ST-E00130:540 151 A 151
C L1P3_orf2#LIN 1427 A 1427
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1008 4.8 5.2 0.0 ST-E00130:540:HVYVWCCXX:4:2113:17218:43835/2 1 146 (5) + L1P3 LINE/L1 3241 3394 (2752) 1722
ANNOTATION EVIDENCE:
1008 4.79 5.20 0.00 ST-E00130:540:HVYVWCCXX:4:2113:17218:43835/2 1 146 5 + L1P3_orf2 LINE/L1 1132 1285 2009
1008 4.79 5.20 0.00 ST-E00130:540:HVYVWCCXX:4:2113:17218:43835/2 1 146 (5) L1P3_orf2#LINE/L1 1132 1285 (2009) m_b6s551i181
ST-E00130:540 1 GCAAGACTAATAAAGA--------GAGAAGAATCAAATAGACTCAATAAA 42
v -------- v
L1P3_orf2#LIN 1132 GCCAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGACACAATAAA 1181
ST-E00130:540 43 AAATGATAAAGAGGATAATACCACTGATCCCACAGAAATACAAACTACCA 92
i vi
L1P3_orf2#LIN 1182 AAATGATAAAGGGGATATCACCACTGATCCCACAGAAATACAAACTACCA 1231
ST-E00130:540 93 TCAGAGAATACTATAAATACCTCTATGCAAATAAACTAGAAAATCTAGAA 142
i i
L1P3_orf2#LIN 1232 TCAGAGAATACTATAAACACCTCTACGCAAATAAACTAGAAAATCTAGAA 1281
ST-E00130:540 143 GAAA 146
L1P3_orf2#LIN 1282 GAAA 1285
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.30
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 8.00 (8 / 1)
+ 1031 5.3 7.4 0.0 ST-E00130:540:HVYVWCCXX:4:2113:24880:30703/1 1 151 (0) + L1P3 LINE/L1 3205 3367 (2779) 1723
ANNOTATION EVIDENCE:
1031 5.30 7.36 0.00 ST-E00130:540:HVYVWCCXX:4:2113:24880:30703/1 1 151 0 + L1P3_orf2 LINE/L1 1096 1258 2036
1031 5.30 7.36 0.00 ST-E00130:540:HVYVWCCXX:4:2113:24880:30703/1 1 151 (0) L1P3_orf2#LINE/L1 1096 1258 (2036) m_b6s551i192
ST-E00130:540 1 TTTTTTGAAAAGATTAACAAAACAGA----CCGCTAGCAAGACTAATAAA 46
i ---- v
L1P3_orf2#LIN 1096 TTTTTTGAAAAGATTAACAAAATAGATAGACCGCTAGCCAGACTAATAAA 1145
ST-E00130:540 47 GA--------GAGAAGAATCAAATAGACTCAATAAAAAATGATAAAGAGG 88
-------- v i
L1P3_orf2#LIN 1146 GAAGAAAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGG 1195
ST-E00130:540 89 ATAATACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTAT 138
vi
L1P3_orf2#LIN 1196 ATATCACCACTGATCCCACAGAAATACAAACTACCATCAGAGAATACTAT 1245
ST-E00130:540 139 AAATACCTCTATG 151
i i
L1P3_orf2#LIN 1246 AAACACCTCTACG 1258
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 1044 8.0 3.2 0.0 ST-E00130:540:HVYVWCCXX:4:2113:24880:30703/2 1 151 (0) C L1P3 LINE/L1 (2358) 3788 3633 1724
ANNOTATION EVIDENCE:
1044 7.95 3.20 0.00 ST-E00130:540:HVYVWCCXX:4:2113:24880:30703/2 1 151 0 C L1P3_orf2 LINE/L1 1524 1679 1615
1044 7.95 3.20 0.00 ST-E00130:540:HVYVWCCXX:4:2113:24880:30703/2 1 151 (0) C L1P3_orf2#LINE/L1 (1615) 1679 1524 m_b6s551i68
ST-E00130:540 1 TGGATAAGCGTTTTGATG---TGCTGGATTCAGTTTGCCAGTATTTTATC 47
v --- i i
C L1P3_orf2#LIN 1679 TGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATT 1630
ST-E00130:540 48 GAGGATTTTCACATCGATGTTCATCACGGATAATGGCCTGAAATTTTCTT 97
i v v
C L1P3_orf2#LIN 1629 GAGGATTTTCGCATCGATGTTCATCAGGGATATTGGCCTGAAATTTTCTT 1580
ST-E00130:540 98 TTTC--TTGTGTCTCTTCCAGGTTTTGGAATCAGGATGATGCTGTCATCA 145
i-- v v v v
C L1P3_orf2#LIN 1579 TTTTTGTTGTGTCTCTGCCAGGTTTTGGTATCAGGATGATGCTGGCCTCA 1530
ST-E00130:540 146 TAAAGT 151
i
C L1P3_orf2#LIN 1529 TAAAAT 1524
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.08
Transitions / transversions = 0.71 (5/7)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 2.50 (5 / 2)
+ 330 26.1 3.2 0.0 ST-E00130:540:HVYVWCCXX:4:2113:4797:35080/1 50 141 (10) + MIRb SINE/MIR 67 161 (107) 1725
ANNOTATION EVIDENCE:
330 26.09 3.16 0.00 ST-E00130:540:HVYVWCCXX:4:2113:4797:35080/1 50 141 10 + MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 ST-E00130:540:HVYVWCCXX:4:2113:4797:35080/1 50 141 (10) MIRb#SINE/MIR 67 161 (107) m_b6s601i70
ST-E00130:540 50 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 98
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
ST-E00130:540 99 TCACTAAGTCACAGTTT--TCATTTATAAATTGAAGGAAATAATA 141
v i i v -- i i v ii iv
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 249 26.1 1.5 0.0 ST-E00130:540:HVYVWCCXX:4:2117:10186:56932/1 87 151 (0) + MIRb SINE/MIR 67 132 (136) 1726
ANNOTATION EVIDENCE:
249 26.15 1.52 0.00 ST-E00130:540:HVYVWCCXX:4:2117:10186:56932/1 87 151 0 + MIRb SINE/MIR 67 132 136
249 26.15 1.52 0.00 ST-E00130:540:HVYVWCCXX:4:2117:10186:56932/1 87 151 (0) MIRb#SINE/MIR 67 132 (136) m_b6s601i78
ST-E00130:540 87 CTCGAGTCAACCACTTGTTAGCTCTGTGGCA-TAAGCAAGTTACTTTACC 135
i iv vi ii v i v- ii v
MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116
ST-E00130:540 136 TCACTAAGTCACAGTT 151
v i i v
MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTT 132
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 32.90
Transitions / transversions = 1.43 (10/7)
Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1)
+ 521 13.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2119:17584:6671/1 79 151 (0) + AluSx SINE/Alu 1 73 (239) 1727
ANNOTATION EVIDENCE:
521 13.70 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2119:17584:6671/1 79 151 0 + AluSx SINE/Alu 1 73 239
521 13.70 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2119:17584:6671/1 79 151 (0) AluSx#SINE/Alu 1 73 (239) m_b5s357i66
ST-E00130:540 79 GGCTGGGTGCACTGGCTCACACCTGTAATCCCAACACTTTGGGAGGCCAA 128
i i iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 129 GGTGGGCAGATCACTTGAGGTCA 151
i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCA 73
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.28
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0)
+ 684 15.4 0.0 5.4 ST-E00130:540:HVYVWCCXX:4:2119:17584:6671/2 22 151 (0) C AluSx SINE/Alu (8) 304 182 1728
ANNOTATION EVIDENCE:
684 15.45 0.00 5.38 ST-E00130:540:HVYVWCCXX:4:2119:17584:6671/2 22 151 0 C AluSx SINE/Alu 182 304 8
684 15.45 0.00 5.38 ST-E00130:540:HVYVWCCXX:4:2119:17584:6671/2 22 151 (0) C AluSx#SINE/Alu (8) 304 182 m_b5s357i24
ST-E00130:540 22 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 71
v v v i i ii i ----
C AluSx#SINE/Al 304 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---- 259
ST-E00130:540 72 CTGCAGGCTGGAGTGCAGTGGTGCTATATCTGCTCACTGCAACCTCCGCC 121
--- i v v v
C AluSx#SINE/Al 258 ---CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
ST-E00130:540 122 TAGTAGGTTCAAGCAGTTGTCCTGCCTCAG 151
vvii ii v
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAG 182
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.87
Transitions / transversions = 1.11 (10/9)
Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.00 (7 / 7)
+ 893 10.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:11789:11470/1 1 116 (35) C AluY SINE/Alu (195) 116 1 1729
ANNOTATION EVIDENCE:
893 10.34 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:11789:11470/1 1 116 35 C AluY SINE/Alu 1 116 195
893 10.34 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:11789:11470/1 1 116 (35) C AluY#SINE/Alu (195) 116 1 m_b2s357i75
ST-E00130:540 1 TAGAGATGGGGTTTCACCACGTTAGCCAGGATGGTCTTGATCTCCTGACC 50
i ii i
C AluY#SINE/Alu 116 TAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACC 67
ST-E00130:540 51 TCATGATCAGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTACAAGCGTGA 100
i v i i i
C AluY#SINE/Alu 66 TCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA 17
ST-E00130:540 101 GCCACCATGCCTGGCC 116
ii i
C AluY#SINE/Alu 16 GCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.29
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0)
+ 1314 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:26240:23108/1 1 151 (0) C L1P1 LINE/L1 (658) 5497 5347 1730
ANNOTATION EVIDENCE:
1314 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:26240:23108/1 1 151 0 C L1PA2_3end LINE/L1 94 244 658
1314 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:26240:23108/1 1 151 (0) C L1PA2_3end#LINE/L1 (658) 244 94 m_b1s551i218
ST-E00130:540 1 ACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAGA 50
i
C L1PA2_3end#LI 244 ACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGA 195
ST-E00130:540 51 TGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGA 100
C L1PA2_3end#LI 194 TGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGA 145
ST-E00130:540 101 TGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGA 150
C L1PA2_3end#LI 144 TGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGA 95
ST-E00130:540 151 A 151
C L1PA2_3end#LI 94 A 94
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1218 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:26240:23108/2 1 151 (0) + L1P1 LINE/L1 5097 5247 (899) 1731
ANNOTATION EVIDENCE:
1218 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:26240:23108/2 1 151 0 + L1P1_orf2 LINE/L1 2988 3138 156
1218 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:26240:23108/2 1 151 (0) L1P1_orf2#LINE/L1 2988 3138 (156) m_b1s551i97
ST-E00130:540 1 TAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATC 50
v i
L1P1_orf2#LIN 2988 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3037
ST-E00130:540 51 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 100
L1P1_orf2#LIN 3038 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3087
ST-E00130:540 101 AACAGGCAACCTACAAAAGGGGAGAAAATGTTCGCAACCTACTCATCTGA 150
i v v
L1P1_orf2#LIN 3088 AACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 3137
ST-E00130:540 151 C 151
L1P1_orf2#LIN 3138 C 3138
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.39
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1314 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:27407:24075/1 1 151 (0) C L1P1 LINE/L1 (658) 5497 5347 1732
ANNOTATION EVIDENCE:
1314 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:27407:24075/1 1 151 0 C L1PA2_3end LINE/L1 94 244 658
1314 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:27407:24075/1 1 151 (0) C L1PA2_3end#LINE/L1 (658) 244 94 m_b1s551i219
ST-E00130:540 1 ACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAACTGGTGTGAGA 50
i
C L1PA2_3end#LI 244 ACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGA 195
ST-E00130:540 51 TGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGA 100
C L1PA2_3end#LI 194 TGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGA 145
ST-E00130:540 101 TGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGA 150
C L1PA2_3end#LI 144 TGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGA 95
ST-E00130:540 151 A 151
C L1PA2_3end#LI 94 A 94
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1272 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:27407:24075/2 1 151 (0) + L1P1 LINE/L1 5097 5247 (899) 1733
ANNOTATION EVIDENCE:
1272 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:27407:24075/2 1 151 0 + L1P1_orf2 LINE/L1 2988 3138 156
1272 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:27407:24075/2 1 151 (0) L1P1_orf2#LINE/L1 2988 3138 (156) m_b1s551i98
ST-E00130:540 1 TAAAACACCAAAAGCAATGGCAACAAAAGACAGAATTGACAAATGGGATC 50
v i
L1P1_orf2#LIN 2988 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3037
ST-E00130:540 51 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 100
L1P1_orf2#LIN 3038 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3087
ST-E00130:540 101 AACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 150
i
L1P1_orf2#LIN 3088 AACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 3137
ST-E00130:540 151 C 151
L1P1_orf2#LIN 3138 C 3138
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 943 13.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:29437:55016/2 1 134 (17) C AluSx SINE/Alu (178) 134 1 1734
ANNOTATION EVIDENCE:
943 13.43 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:29437:55016/2 1 134 17 C AluSx SINE/Alu 1 134 178
943 13.43 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:29437:55016/2 1 134 (17) C AluSx#SINE/Alu (178) 134 1 m_b2s357i33
ST-E00130:540 1 ATTTTTGTATTTTAAATAGAGACAAGGTTTCACCATGTTGGCCATGCTGG 50
v i ii v
C AluSx#SINE/Al 134 ATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGG 85
ST-E00130:540 51 TTTCGAACTCCCGACCTCAGGTGATCCACCTGGCTCTGCCTCCCAAATTG 100
i i i i v v v
C AluSx#SINE/Al 84 TCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 35
ST-E00130:540 101 CTGAGATTACAGATGTGAGCCACTGTGCCCAGCC 134
i ii i i i
C AluSx#SINE/Al 34 CTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.32
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 133), avg. gap size = 0.0 (0 / 0)
+ 1363 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2120:6441:54383/1 1 151 (0) + L1P1 LINE/L1 5623 5773 (382) 1735
ANNOTATION EVIDENCE:
1363 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:6441:54383/1 1 151 0 + L1PA2_3end LINE/L1 370 520 382
1363 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2120:6441:54383/1 1 151 (0) L1PA2_3end#LINE/L1 370 520 (382) m_b1s551i305
ST-E00130:540 1 CCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCCG 50
i
L1PA2_3end#LI 370 CCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTG 419
ST-E00130:540 51 CTATAAAGACACATGCACACGTATGTTTATTGTGGCATTATTCACAATAG 100
i
L1PA2_3end#LI 420 CTATAAAGACACATGCACACGTATGTTTATTGCGGCATTATTCACAATAG 469
ST-E00130:540 101 CAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAG 150
L1PA2_3end#LI 470 CAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAG 519
ST-E00130:540 151 A 151
L1PA2_3end#LI 520 A 520
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.73
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1289 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:2120:6441:54383/2 1 151 (0) C L1PA2 LINE/L1 (208) 5947 5798 1736
ANNOTATION EVIDENCE:
1289 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2120:6441:54383/2 1 151 0 C L1PA2_3end LINE/L1 545 694 208
1289 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2120:6441:54383/2 1 151 (0) C L1PA2_3end#LINE/L1 (208) 694 545 m_b1s551i376
ST-E00130:540 1 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTT 50
i
C L1PA2_3end#LI 694 ATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTT 645
ST-E00130:540 51 TTTTCTTCTTGCGACAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 100
v i
C L1PA2_3end#LI 644 TTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCA 595
ST-E00130:540 101 TGTCCCTAACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 150
-
C L1PA2_3end#LI 594 TGTCCCT-ACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTAT 546
ST-E00130:540 151 T 151
C L1PA2_3end#LI 545 T 545
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 491 17.7 16.8 0.0 ST-E00130:540:HVYVWCCXX:4:2120:6624:53926/2 28 151 (0) C L1MC4 LINE/L1 (393) 7649 7501 1737
ANNOTATION EVIDENCE:
491 17.74 16.78 0.00 ST-E00130:540:HVYVWCCXX:4:2120:6624:53926/2 28 151 0 C L1MC4_3end LINE/L1 2248 2396 393
491 17.74 16.78 0.00 ST-E00130:540:HVYVWCCXX:4:2120:6624:53926/2 28 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2248 m_b3s551i93
ST-E00130:540 28 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 77
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 78 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTACA 121
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTACA 2297
ST-E00130:540 122 G-------------------GTCCCTTGCTCTGAGTTTGTCTGATGTTT 151
------------------- iiv i i
C L1MC4_3end#LI 2296 GGCCAGTTATTTTGTAGAATGTCCCTCAATTTGGGTTTGTCTGATGTTT 2248
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.52
Transitions / transversions = 1.10 (11/10)
Gap_init rate = 0.02 (2 / 123), avg. gap size = 12.50 (25 / 2)
+ 1278 2.0 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:2121:9485:14160/1 1 151 (0) + L1PA3 LINE/L1 5730 5879 (276) 1738
ANNOTATION EVIDENCE:
1278 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2121:9485:14160/1 1 151 0 + L1PA3_3end LINE/L1 477 626 276
1278 2.00 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2121:9485:14160/1 1 151 (0) L1PA3_3end#LINE/L1 477 626 (276) m_b1s551i349
ST-E00130:540 1 TTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAACTGT 50
v
L1PA3_3end#LI 477 TTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGT 526
ST-E00130:540 51 GGCACATATACACCATGGAATACTATTCAGCCATAAAAAATGATGAGTTC 100
v
L1PA3_3end#LI 527 GGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTC 576
ST-E00130:540 101 ATGTCCTTTCTTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTA 150
-v
L1PA3_3end#LI 577 ATGTCCTTT-GTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTA 625
ST-E00130:540 151 A 151
L1PA3_3end#LI 626 A 626
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 938 6.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2121:9485:14160/2 1 116 (35) C L1PA2 LINE/L1 (32) 6123 6008 1739
ANNOTATION EVIDENCE:
938 6.90 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2121:9485:14160/2 1 116 35 C L1PA2_3end LINE/L1 755 870 32
938 6.90 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2121:9485:14160/2 1 116 (35) C L1PA2_3end#LINE/L1 (32) 870 755 m_b1s551i423
ST-E00130:540 1 GGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCAT 50
C L1PA2_3end#LI 870 GGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCAT 821
ST-E00130:540 51 GCTGGGGTGCTGCACCCACTAACTCGTCGTCTAGCATGAGGTATATCTCC 100
v i i v
C L1PA2_3end#LI 820 GCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCC 771
ST-E00130:540 101 CAATGCTACCTCGCTC 116
i i v i
C L1PA2_3end#LI 770 CAATGCTATCCCTCCC 755
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.40
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0)
+ 317 24.6 4.0 0.0 ST-E00130:540:HVYVWCCXX:4:2122:20131:24585/1 35 146 (5) C MIRb SINE/MIR (75) 187 70 1740
ANNOTATION EVIDENCE:
307 28.57 5.09 0.00 ST-E00130:540:HVYVWCCXX:4:2122:20131:24585/1 35 146 5 C MIR SINE/MIR 70 187 75
307 28.57 5.09 0.00 ST-E00130:540:HVYVWCCXX:4:2122:20131:24585/1 35 146 (5) C MIR#SINE/MIR (75) 187 70 m_b6s601i40
ST-E00130:540 35 TTAATTCTT---ATACTTCTGTCACTTAGATTCTATTATTTCCTTCAATT 81
i i--- i vii i v vv i v vi ii v
C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTT 138
ST-E00130:540 82 TATAAATGA--AAACTGTGACTTAGTGAGGTAAAGTAACTTGCTT-ATGC 128
i i -- v i vi v v ii- v i
C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88
ST-E00130:540 129 CACAGAGCTAACAAGTGG 146
v ii
C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGG 70
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 36.99
Transitions / transversions = 1.46 (19/13)
Gap_init rate = 0.03 (3 / 111), avg. gap size = 2.00 (6 / 3)
317 23.17 3.53 0.00 ST-E00130:540:HVYVWCCXX:4:2122:20131:24585/1 65 146 5 C MIRb SINE/MIR 77 161 107
317 23.17 3.53 0.00 ST-E00130:540:HVYVWCCXX:4:2122:20131:24585/1 65 146 (5) C MIRb#SINE/MIR (107) 161 77 m_b6s601i41
ST-E00130:540 65 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 112
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
ST-E00130:540 113 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGG 146
ii -v i v ii
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG 77
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 28.42
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2)
+ 1154 11.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2124:8146:41515/1 1 151 (0) + AluSx SINE/Alu 23 173 (139) 1741
ANNOTATION EVIDENCE:
1154 11.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2124:8146:41515/1 1 151 0 + AluSx SINE/Alu 23 173 139
1154 11.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2124:8146:41515/1 1 151 (0) AluSx#SINE/Alu 23 173 (139) m_b2s356i34
ST-E00130:540 1 CTGTAATCTCAGCAATTTGGGAGGCAGAGCCAGGTGGATCACCTGAGGTC 50
i v v v i i
AluSx#SINE/Al 23 CTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTC 72
ST-E00130:540 51 GGGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCTTGTCTCTATTTA 100
i i ii i v
AluSx#SINE/Al 73 AGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAA 122
ST-E00130:540 101 AAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATCCCAGCTA 150
i i i v i
AluSx#SINE/Al 123 AAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTA 172
ST-E00130:540 151 C 151
AluSx#SINE/Al 173 C 173
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.46
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 861 3.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2124:8146:41515/2 1 101 (50) + L1PA2 LINE/L1 6053 6153 (2) 1742
ANNOTATION EVIDENCE:
861 2.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2124:8146:41515/2 1 101 50 + L1PA2_3end LINE/L1 800 900 2
861 2.97 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2124:8146:41515/2 1 101 (50) L1PA2_3end#LINE/L1 800 900 (2) m_b1s551i441
ST-E00130:540 1 TAGTGGGTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAACC 50
i
L1PA2_3end#LI 800 TAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACC 849
ST-E00130:540 51 TGCACAATGTGCACATGTACCCTAAAACTTAAAGTGTAATAAAAAAAATA 100
i v
L1PA2_3end#LI 850 TGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAA 899
ST-E00130:540 101 A 101
L1PA2_3end#LI 900 A 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.11
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0)
+ 426 10.5 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2124:9932:29244/1 1 57 (94) C AluSx SINE/Alu (255) 57 1 1743
ANNOTATION EVIDENCE:
426 10.53 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2124:9932:29244/1 1 57 94 C AluSx SINE/Alu 1 57 255
426 10.53 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2124:9932:29244/1 1 57 (94) C AluSx#SINE/Alu (255) 57 1 m_b4s357i64
ST-E00130:540 1 GCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCA 50
i i i i i i
C AluSx#SINE/Al 57 GCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCG 8
ST-E00130:540 51 CCCGGCC 57
C AluSx#SINE/Al 7 CCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.70
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 1220 8.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2202:17472:58409/1 1 151 (0) + AluSx SINE/Alu 82 232 (80) 1744
ANNOTATION EVIDENCE:
1220 8.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2202:17472:58409/1 1 151 0 + AluSx SINE/Alu 82 232 80
1220 8.61 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2202:17472:58409/1 1 151 (0) AluSx#SINE/Alu 82 232 (80) m_b4s356i24
ST-E00130:540 1 AGAACAGCCTGGCCAATATGGTGAAACTCCATCTCTACTAAAAACACAAA 50
v i i i i
AluSx#SINE/Al 82 AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAA 131
ST-E00130:540 51 AATTAGCCAGGGGTGGTGGCAGGCGCCTATAATCCCAGCTACTCAGGAGG 100
i v iv i i
AluSx#SINE/Al 132 AATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGG 181
ST-E00130:540 101 CTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCC 150
i i
AluSx#SINE/Al 182 CTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCC 231
ST-E00130:540 151 G 151
AluSx#SINE/Al 232 G 232
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.88
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2202:17472:58409/2 114 145 (6) + (TG)n Simple_repeat 1 32 (0) 1745
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2202:17472:58409/2 114 145 6 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2202:17472:58409/2 114 145 (6) (TG)n#Simple_repeat 1 32 (0) m_b4s252i6
ST-E00130:540 114 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 145
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1271 2.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:2202:31061:22985/1 1 151 (0) C L1PA3 LINE/L1 (271) 5884 5735 1746
ANNOTATION EVIDENCE:
1271 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2202:31061:22985/1 1 151 0 C L1PA3_3end LINE/L1 482 631 271
1271 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2202:31061:22985/1 1 151 (0) C L1PA3_3end#LINE/L1 (271) 631 482 m_b1s551i351
ST-E00130:540 1 ACAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCTAACAAA 50
i -
C L1PA3_3end#LI 631 ATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCT-ACAAA 583
ST-E00130:540 51 GGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATA 100
C L1PA3_3end#LI 582 GGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATA 533
ST-E00130:540 101 TGTGCCACAGTTTCTTAATACAGTCTATCATTGTTAGACATTTGGGTTGG 150
v v i
C L1PA3_3end#LI 532 TGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGG 483
ST-E00130:540 151 T 151
C L1PA3_3end#LI 482 T 482
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1348 2.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2202:31061:22985/2 1 151 (0) + L1P1 LINE/L1 5432 5582 (573) 1747
ANNOTATION EVIDENCE:
1348 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2202:31061:22985/2 1 151 0 + L1PA3_3end LINE/L1 179 329 573
1348 1.99 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2202:31061:22985/2 1 151 (0) L1PA3_3end#LINE/L1 179 329 (573) m_b1s551i253
ST-E00130:540 1 CCACAATGAGATACCATCTCACACCAGTTAGAATGGCAGTCATTAAAAAG 50
i
L1PA3_3end#LI 179 CCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAG 228
ST-E00130:540 51 TCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAATCCTTTT 100
iv
L1PA3_3end#LI 229 TCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTT 278
ST-E00130:540 101 ACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGT 150
L1PA3_3end#LI 279 ACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGT 328
ST-E00130:540 151 G 151
L1PA3_3end#LI 329 G 329
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.02
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 921 15.4 0.0 1.3 ST-E00130:540:HVYVWCCXX:4:2203:22232:10609/1 1 151 (0) + AluSx SINE/Alu 97 245 (67) 1748
ANNOTATION EVIDENCE:
921 15.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:2203:22232:10609/1 1 151 0 + AluSx SINE/Alu 97 245 67
921 15.43 0.00 1.32 ST-E00130:540:HVYVWCCXX:4:2203:22232:10609/1 1 151 (0) AluSx#SINE/Alu 97 245 (67) m_b5s356i10
ST-E00130:540 1 ACGTGTTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCA 50
i v i -- i i
AluSx#SINE/Al 97 ACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCG 144
ST-E00130:540 51 TTGTGGTGGGAGCCTGTAATCATAGCTGCTCAGGAGGCTGAGGCAGGACA 100
v i v v vi i i v
AluSx#SINE/Al 145 TGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGA 194
ST-E00130:540 101 ATTGCTTGAACCTACTAGGCGGAGGTTGCAGTGAGCAGATATAGCACCAC 150
i iivv v v v i
AluSx#SINE/Al 195 ATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCAC 244
ST-E00130:540 151 T 151
AluSx#SINE/Al 245 T 245
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 11.36
Transitions / transversions = 1.09 (12/11)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 1.00 (2 / 2)
+ 244 19.1 0.0 11.7 ST-E00130:540:HVYVWCCXX:4:2203:22232:10609/2 70 146 (5) C 7SLRNA srpRNA (0) 320 253 1749
ANNOTATION EVIDENCE:
244 19.11 0.00 11.69 ST-E00130:540:HVYVWCCXX:4:2203:22232:10609/2 70 146 5 C 7SLRNA SINE/Alu 253 320 0
244 19.11 0.00 11.69 ST-E00130:540:HVYVWCCXX:4:2203:22232:10609/2 70 146 (5) C 7SLRNA#SINE/Alu (0) 320 253 m_b5s502i3
ST-E00130:540 70 TTTTTTGTTTTTGTGTTTTTTTGAGATGGAGTCTCACTCCATCACCCAGG 119
v v v vv i i i vii ii ----
C 7SLRNA#SINE/A 320 TTTTTTTTTTTTTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCC---- 275
ST-E00130:540 120 CTGCAGGCTGGAGTGCAGTGGTGCTAT 146
--- --
C 7SLRNA#SINE/A 274 ---CAGGCTGGAGTGCAGTG--GCTAT 253
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.65
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.12 (9 / 76), avg. gap size = 1.00 (9 / 9)
+ 244 19.1 0.0 11.7 ST-E00130:540:HVYVWCCXX:4:2205:22617:42429/2 7 83 (68) + 7SLRNA srpRNA 253 320 (0) 1750
ANNOTATION EVIDENCE:
244 19.11 0.00 11.69 ST-E00130:540:HVYVWCCXX:4:2205:22617:42429/2 7 83 68 + 7SLRNA SINE/Alu 253 320 0
244 19.11 0.00 11.69 ST-E00130:540:HVYVWCCXX:4:2205:22617:42429/2 7 83 (68) 7SLRNA#SINE/Alu 253 320 (0) m_b5s502i4
ST-E00130:540 7 ATAGCACCACTGCACTCCAGCCTGCAGCCTGGGTGATGGAGTGAGACTCC 56
-- ------- ii iiv i i
7SLRNA#SINE/A 253 ATAGC--CACTGCACTCCAGCCTG-------GGCAACATAGCGAGACCCC 293
ST-E00130:540 57 ATCTCAAAAAAACACAAAAACAAAAAA 83
i vv v v v
7SLRNA#SINE/A 294 GTCTCTTAAAAAAAAAAAAAAAAAAAA 320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.65
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.12 (9 / 76), avg. gap size = 1.00 (9 / 9)
+ 1256 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2205:30594:21825/1 1 151 (0) C L1P1 LINE/L1 (757) 5389 5239 1751
ANNOTATION EVIDENCE:
1256 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2205:30594:21825/1 1 151 0 C L1P1_orf2 LINE/L1 3130 3280 14
1256 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2205:30594:21825/1 1 151 (0) C L1P1_orf2#LINE/L1 (14) 3280 3130 m_b1s551i158
ST-E00130:540 1 TTTTCATGTGTTTTTTGGTTGCATAAATGTCTTCTTTTGAGAAGTGTCTG 50
i
C L1P1_orf2#LIN 3280 TTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTG 3231
ST-E00130:540 51 TTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTA 100
C L1P1_orf2#LIN 3230 TTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTA 3181
ST-E00130:540 101 AATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATG 150
C L1P1_orf2#LIN 3180 AATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATG 3131
ST-E00130:540 151 A 151
C L1P1_orf2#LIN 3130 A 3130
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1080 11.9 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2206:28077:25482/1 1 151 (0) C AluSx SINE/Alu (127) 185 33 1752
ANNOTATION EVIDENCE:
1080 11.92 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:2206:28077:25482/1 1 151 0 C AluSx SINE/Alu 33 185 127
1080 11.92 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:2206:28077:25482/1 1 151 (0) C AluSx#SINE/Alu (127) 185 33 m_b4s356i37
ST-E00130:540 1 TCAGCCTCCTGAGTAGCTGGGATTATAGGCGCCTGCCACCACCCCTGGCT 50
i i vi v i
C AluSx#SINE/Al 185 TCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCT 136
ST-E00130:540 51 GATTTTTGTGTTTTTAGTAGAGATGGAGTTTCACCATATTGGCCAGGCTG 100
i i i i i
C AluSx#SINE/Al 135 AATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG 86
ST-E00130:540 101 TTCTCAAACTCCTGACCTT--GTGATCTGCCTGCTTCCGCCTCCCAAAGT 148
v i i-- i i i v
C AluSx#SINE/Al 85 GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGT 36
ST-E00130:540 149 GCT 151
C AluSx#SINE/Al 35 GCT 33
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 8.24
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1111 4.7 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2206:5132:48142/1 1 148 (3) C L1P3 LINE/L1 (2687) 3459 3310 1753
ANNOTATION EVIDENCE:
1111 4.73 1.33 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5132:48142/1 1 148 3 C L1P3_orf2 LINE/L1 1201 1350 1944
1111 4.73 1.33 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5132:48142/1 1 148 (3) C L1P3_orf2#LINE/L1 (1944) 1350 1201 m_b6s551i159
ST-E00130:540 1 ATTCAGGGATTCGACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGT 48
v -- v
C L1P3_orf2#LIN 1350 ATTCAGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGT 1301
ST-E00130:540 49 CTAGGAATTTATCACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGG 98
i vv i
C L1P3_orf2#LIN 1300 CCAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGG 1251
ST-E00130:540 99 TATTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGT 148
i
C L1P3_orf2#LIN 1250 TGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGT 1201
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.24
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 2.00 (2 / 1)
+ 1095 4.7 0.7 0.0 ST-E00130:540:HVYVWCCXX:4:2206:5132:48142/2 1 148 (3) + L1P3 LINE/L1 3018 3166 (2980) 1754
ANNOTATION EVIDENCE:
1095 4.73 0.68 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5132:48142/2 1 148 3 + L1P3_orf2 LINE/L1 909 1057 2237
1095 4.73 0.68 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5132:48142/2 1 148 (3) L1P3_orf2#LINE/L1 909 1057 (2237) m_b6s551i260
ST-E00130:540 1 TGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACATCAC 50
? v i i
L1P3_orf2#LIN 909 TGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACATCAC 958
ST-E00130:540 51 AATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGA 100
L1P3_orf2#LIN 959 AATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGA 1008
ST-E00130:540 101 AGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAAATAGAGACAC 148
v i- i
L1P3_orf2#LIN 1009 AGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGACAC 1057
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.92
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 1.00 (1 / 1)
+ 1111 4.7 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2206:5436:46806/1 1 148 (3) C L1P3 LINE/L1 (2687) 3459 3310 1755
ANNOTATION EVIDENCE:
1111 4.73 1.33 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5436:46806/1 1 148 3 C L1P3_orf2 LINE/L1 1201 1350 1944
1111 4.73 1.33 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5436:46806/1 1 148 (3) C L1P3_orf2#LINE/L1 (1944) 1350 1201 m_b6s551i160
ST-E00130:540 1 ATTCAGGGATTCGACTTCTTCCTGCTTTAG--TTGGGAGGTTGTATGTGT 48
v -- v
C L1P3_orf2#LIN 1350 ATTCAGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGT 1301
ST-E00130:540 49 CTAGGAATTTATCACTTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGG 98
i vv i
C L1P3_orf2#LIN 1300 CCAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGG 1251
ST-E00130:540 99 TATTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGT 148
i
C L1P3_orf2#LIN 1250 TGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCAGTGGT 1201
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.24
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 2.00 (2 / 1)
+ 1114 4.0 0.7 0.0 ST-E00130:540:HVYVWCCXX:4:2206:5436:46806/2 1 148 (3) + L1P3 LINE/L1 3018 3166 (2980) 1756
ANNOTATION EVIDENCE:
1114 4.05 0.68 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5436:46806/2 1 148 3 + L1P3_orf2 LINE/L1 909 1057 2237
1114 4.05 0.68 0.00 ST-E00130:540:HVYVWCCXX:4:2206:5436:46806/2 1 148 (3) L1P3_orf2#LINE/L1 909 1057 (2237) m_b6s551i261
ST-E00130:540 1 TGCCCACAGGACAAAGTGGGAAAGATCTAAAATCAACACCCTAACATCAC 50
? v i i
L1P3_orf2#LIN 909 TGCCCACANGAGAAAGCGGGAAAGATCTAAAATCGACACCCTAACATCAC 958
ST-E00130:540 51 AATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGA 100
L1P3_orf2#LIN 959 AATTAAAAGAACTAGAGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGA 1008
ST-E00130:540 101 AGACAAGAAATAACTAAGATCAGAGCTGAG-TGAAGGAGATAGAGACAC 148
v i-
L1P3_orf2#LIN 1009 AGACAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAGATAGAGACAC 1057
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.21
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 1.00 (1 / 1)
+ 883 5.1 0.7 7.5 ST-E00130:540:HVYVWCCXX:4:2207:11799:71190/1 1 147 (4) + L1P3 LINE/L1 3094 3230 (2916) 1757
ANNOTATION EVIDENCE:
883 5.14 0.73 7.48 ST-E00130:540:HVYVWCCXX:4:2207:11799:71190/1 1 147 4 + L1P3_orf2 LINE/L1 985 1121 2173
883 5.14 0.73 7.48 ST-E00130:540:HVYVWCCXX:4:2207:11799:71190/1 1 147 (4) L1P3_orf2#LINE/L1 985 1121 (2173) m_b6s551i236
ST-E00130:540 1 CAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGC 50
L1P3_orf2#LIN 985 CAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACTAAGATCAGAGC 1034
ST-E00130:540 51 TGAG-TGAAGGAGATAGAGACACACACACACAAAAAAAACCTTTCAAAAA 99
v i- ----------i i
L1P3_orf2#LIN 1035 AGAACTGAAGGAGATAGAGACAC----------GAAAAACCCTTCAAAAA 1074
ST-E00130:540 100 AATCAATTAATCCAGGAGCTGATTTTTTGAAAAGATTAACAAAACAGA 147
- v i i
L1P3_orf2#LIN 1075 A-TCAATGAATCCAGGAGCTGGTTTTTTGAAAAGATTAACAAAATAGA 1121
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.64
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.08 (12 / 146), avg. gap size = 1.00 (12 / 12)
+ 999 5.3 7.4 0.0 ST-E00130:540:HVYVWCCXX:4:2207:11799:71190/2 1 151 (0) C L1P3 LINE/L1 (2773) 3373 3211 1758
ANNOTATION EVIDENCE:
999 5.30 7.36 0.00 ST-E00130:540:HVYVWCCXX:4:2207:11799:71190/2 1 151 0 C L1P3_orf2 LINE/L1 1102 1264 2030
999 5.30 7.36 0.00 ST-E00130:540:HVYVWCCXX:4:2207:11799:71190/2 1 151 (0) C L1P3_orf2#LINE/L1 (2030) 1264 1102 m_b6s551i190
ST-E00130:540 1 TATTTGCATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTTCT 50
i i
C L1P3_orf2#LIN 1264 TATTTGCGTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCT 1215
ST-E00130:540 51 GTGGGATCAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCTATTTG 100
iv i v
C L1P3_orf2#LIN 1214 GTGGGATCAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTG 1165
ST-E00130:540 101 ATTCTTCTC--------TCTTTATTAGTCTTGCTAGCGG----TCTGTTT 138
-------- v ---- i
C L1P3_orf2#LIN 1164 ATTCTTCTCTCTTTTCTTCTTTATTAGTCTGGCTAGCGGTCTATCTATTT 1115
ST-E00130:540 139 TGTTAATCTTTTC 151
C L1P3_orf2#LIN 1114 TGTTAATCTTTTC 1102
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 6.00 (12 / 2)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 27 58 (93) + (TG)n Simple_repeat 1 32 (0) 1759
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 27 58 93 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 27 58 (93) (TG)n#Simple_repeat 1 32 (0) m_b4s252i5
ST-E00130:540 27 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 58
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 59 71 (80) + (TGTATG)n Simple_repeat 1 41 (0) 1760
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 27 71 80 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 27 71 (80) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i4
ST-E00130:540 27 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 71
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 512 6.1 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 86 151 (0) C AluSx SINE/Alu (21) 291 226 1761
ANNOTATION EVIDENCE:
512 6.06 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 86 151 0 C AluSx SINE/Alu 226 291 21
512 6.06 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2207:5873:4561/1 86 151 (0) C AluSx#SINE/Alu (21) 291 226 m_b4s357i10
ST-E00130:540 86 TTTTTTTTTGAGACGGAATCTCGCTGTGTTGCCCGGGCTGGAGTGCAGTG 135
i v i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 136 GCGCGATCTCGGCTCA 151
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCA 226
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 1208 3.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2208:21643:33393/1 1 151 (0) + L1P3 LINE/L1 2983 3133 (3013) 1762
ANNOTATION EVIDENCE:
1208 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2208:21643:33393/1 1 151 0 + L1P3_orf2 LINE/L1 874 1024 2270
1208 3.31 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2208:21643:33393/1 1 151 (0) L1P3_orf2#LINE/L1 874 1024 (2270) m_b6s551i272
ST-E00130:540 1 AAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACAGGACAAA 50
? v
L1P3_orf2#LIN 874 AAAGCAGTGTTTAGAGGGAAATTTATAGCACTAAATGCCCACANGAGAAA 923
ST-E00130:540 51 GTGGGAAAGATCTAAAATCAACACCCTAACATCACAATTATAAGAACTAG 100
i i v
L1P3_orf2#LIN 924 GCGGGAAAGATCTAAAATCGACACCCTAACATCACAATTAAAAGAACTAG 973
ST-E00130:540 101 AGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACT 150
L1P3_orf2#LIN 974 AGAAGCAAGAGCAAACAAATTCAAAAGCTAGCAGAAGACAAGAAATAACT 1023
ST-E00130:540 151 A 151
L1P3_orf2#LIN 1024 A 1024
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1094 6.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2208:21643:33393/2 1 151 (0) C L1P3 LINE/L1 (2730) 3416 3266 1763
ANNOTATION EVIDENCE:
1094 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2208:21643:33393/2 1 151 0 C L1P3_orf2 LINE/L1 1157 1307 1987
1094 5.96 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2208:21643:33393/2 1 151 (0) C L1P3_orf2#LINE/L1 (1987) 1307 1157 m_b6s551i175
ST-E00130:540 1 TATGTGTCTAGGAATTTATCACTTTCTTCTAGATTTTCTAGTTTATTTGC 50
i vv
C L1P3_orf2#LIN 1307 TATGTGTCCAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGC 1258
ST-E00130:540 51 ATAGAGGTATTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGAT 100
i i
C L1P3_orf2#LIN 1257 GTAGAGGTGTTTATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGAT 1208
ST-E00130:540 101 CAGTGGTATTATCCTCTTTATCATTTTTTATTGAGTCTATTTGATTCTTC 150
iv i v
C L1P3_orf2#LIN 1207 CAGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTC 1158
ST-E00130:540 151 T 151
C L1P3_orf2#LIN 1157 T 1157
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.57
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1165 6.6 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2208:32157:14652/1 1 151 (0) + L1PA2 LINE/L1 5943 6093 (62) 1764
ANNOTATION EVIDENCE:
1165 6.62 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2208:32157:14652/1 1 151 0 + L1PA2_3end LINE/L1 690 840 62
1165 6.62 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2208:32157:14652/1 1 151 (0) L1PA2_3end#LINE/L1 690 840 (62) m_b1s551i396
ST-E00130:540 1 GAGGTCACATGGACACAGGAAGGGGAATATCACACTCTGTGGACTGTTGT 50
i v v
L1PA2_3end#LI 690 GAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGT 739
ST-E00130:540 51 GGGGTGGGGAGAGGGGGGAGGGATAGCATCAGGGGATAAACCTAATGCTA 100
i ii i v
L1PA2_3end#LI 740 GGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTA 789
ST-E00130:540 101 GATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCTCATGTATACATAT 150
i v
L1PA2_3end#LI 790 GATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATAT 839
ST-E00130:540 151 G 151
L1PA2_3end#LI 840 G 840
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.30
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 636 11.1 2.2 0.0 ST-E00130:540:HVYVWCCXX:4:2209:25885:41761/2 1 90 (61) C AluSx SINE/Alu (220) 92 1 1765
ANNOTATION EVIDENCE:
636 11.11 2.17 0.00 ST-E00130:540:HVYVWCCXX:4:2209:25885:41761/2 1 90 61 C AluSx SINE/Alu 1 92 220
636 11.11 2.17 0.00 ST-E00130:540:HVYVWCCXX:4:2209:25885:41761/2 1 90 (61) C AluSx#SINE/Alu (220) 92 1 m_b4s357i55
ST-E00130:540 1 CAGGCTGTTCTCAAACTCCTGACCTT--GTGATCTGCCTGCTTCAGCCTC 48
v i i-- i i i i
C AluSx#SINE/Al 92 CAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTC 43
ST-E00130:540 49 CCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCC 90
i i i
C AluSx#SINE/Al 42 CCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.25
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.01 (1 / 89), avg. gap size = 2.00 (2 / 1)
+ 544 12.8 0.0 6.9 ST-E00130:540:HVYVWCCXX:4:2211:30665:72895/2 2 102 (49) + AluSx SINE/Alu 211 304 (8) 1766
ANNOTATION EVIDENCE:
544 12.76 0.00 6.93 ST-E00130:540:HVYVWCCXX:4:2211:30665:72895/2 2 102 49 + AluSx SINE/Alu 211 304 8
544 12.76 0.00 6.93 ST-E00130:540:HVYVWCCXX:4:2211:30665:72895/2 2 102 (49) AluSx#SINE/Alu 211 304 (8) m_b5s357i9
ST-E00130:540 2 AGGCGGAGGTTGCAGTGAGCAGATATAGCACCACTGCACTCCAGCCTGCA 51
v v v i --
AluSx#SINE/Al 211 AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG-- 258
ST-E00130:540 52 GCCTGGGTGATGGAGTGAGACTCCATCTCAAAAAAACACAAAAACAAAAA 101
----- i ii i i v v v
AluSx#SINE/Al 259 -----GGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAA 303
ST-E00130:540 102 A 102
AluSx#SINE/Al 304 A 304
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.52
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7)
+ 1168 9.3 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2213:22577:21755/1 1 151 (0) + AluSx SINE/Alu 56 208 (104) 1767
ANNOTATION EVIDENCE:
1168 9.27 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:2213:22577:21755/1 1 151 0 + AluSx SINE/Alu 56 208 104
1168 9.27 1.30 0.00 ST-E00130:540:HVYVWCCXX:4:2213:22577:21755/1 1 151 (0) AluSx#SINE/Alu 56 208 (104) m_b4s356i31
ST-E00130:540 1 GCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATATGGTGA 48
i --i i v i
AluSx#SINE/Al 56 GCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGA 105
ST-E00130:540 49 AACTCCATCTCTACTAAAAACACAAAAATTAGCCAGGGGTGGTGGCAGGC 98
i i i i v iv
AluSx#SINE/Al 106 AACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGC 155
ST-E00130:540 99 GCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAAC 148
i i
AluSx#SINE/Al 156 GCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAAC 205
ST-E00130:540 149 CCG 151
AluSx#SINE/Al 206 CCG 208
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.95
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 2.00 (2 / 1)
+ 1167 4.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2216:14204:71137/1 7 147 (4) C L1PA2 LINE/L1 (2) 6153 6013 1768
ANNOTATION EVIDENCE:
1167 4.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2216:14204:71137/1 7 147 4 C L1PA2_3end LINE/L1 760 900 2
1167 4.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2216:14204:71137/1 7 147 (4) C L1PA2_3end#LINE/L1 (2) 900 760 m_b1s551i424
ST-E00130:540 7 TTATTTTTTTTATTACACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 56
v i
C L1PA2_3end#LI 900 TTTTTTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGC 851
ST-E00130:540 57 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACT 106
i
C L1PA2_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
ST-E00130:540 107 CACTCGTCATCTAGCATTAGGTATATCTCCCACTGCTAGCC 147
v v v
C L1PA2_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCC 760
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.71
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 140), avg. gap size = 0.0 (0 / 0)
+ 1281 2.7 0.0 0.7 ST-E00130:540:HVYVWCCXX:4:2216:14204:71137/2 1 151 (0) + L1PA3 LINE/L1 5742 5891 (264) 1769
ANNOTATION EVIDENCE:
1281 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2216:14204:71137/2 1 151 0 + L1PA3_3end LINE/L1 489 638 264
1281 2.67 0.00 0.66 ST-E00130:540:HVYVWCCXX:4:2216:14204:71137/2 1 151 (0) L1PA3_3end#LINE/L1 489 638 (264) m_b1s551i353
ST-E00130:540 1 CAAATGTCCAACAGTGATAGACTGGATTAAGAAACTGTGGCACATATACA 50
i v
L1PA3_3end#LI 489 CAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACA 538
ST-E00130:540 51 CCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTT 100
-
L1PA3_3end#LI 539 CCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGT- 587
ST-E00130:540 101 AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAGACTGTCGCAAG 150
i i
L1PA3_3end#LI 588 AGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAG 637
ST-E00130:540 151 A 151
L1PA3_3end#LI 638 A 638
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.73
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1)
+ 1315 1.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2218:18111:26185/1 1 151 (0) C L1P1 LINE/L1 (647) 5508 5358 1770
ANNOTATION EVIDENCE:
1315 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2218:18111:26185/1 1 151 0 C L1PA2_3end LINE/L1 105 255 647
1315 1.32 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2218:18111:26185/1 1 151 (0) C L1PA2_3end#LINE/L1 (647) 255 105 m_b1s551i225
ST-E00130:540 1 TCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGACTGCCATTCTAA 50
i
C L1PA2_3end#LI 255 TCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAA 206
ST-E00130:540 51 CTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATG 100
C L1PA2_3end#LI 205 CTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATG 156
ST-E00130:540 101 GCCAGTGATGATGAGCACTTTTTCATGTGTTTTTTGGCTGCATAAATGTC 150
i
C L1PA2_3end#LI 155 GCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTC 106
ST-E00130:540 151 T 151
C L1PA2_3end#LI 105 T 105
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 1331 0.7 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2218:18111:26185/2 1 151 (0) + L1P1 LINE/L1 5143 5293 (853) 1771
ANNOTATION EVIDENCE:
1331 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2218:18111:26185/2 1 151 0 + L1P1_orf2 LINE/L1 3034 3184 110
1331 0.66 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2218:18111:26185/2 1 151 (0) L1P1_orf2#LINE/L1 3034 3184 (110) m_b1s551i118
ST-E00130:540 1 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 50
L1P1_orf2#LIN 3034 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 3083
ST-E00130:540 51 AGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCAT 100
i
L1P1_orf2#LIN 3084 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCAT 3133
ST-E00130:540 101 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC 150
L1P1_orf2#LIN 3134 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC 3183
ST-E00130:540 151 A 151
L1P1_orf2#LIN 3184 A 3184
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 685 19.4 6.1 0.7 ST-E00130:540:HVYVWCCXX:4:2218:4696:6776/1 1 140 (11) + L1MC4 LINE/L1 7764 7911 (131) 1772
ANNOTATION EVIDENCE:
685 19.43 6.08 0.71 ST-E00130:540:HVYVWCCXX:4:2218:4696:6776/1 1 140 11 + L1MC4_3end LINE/L1 2511 2658 131
685 19.43 6.08 0.71 ST-E00130:540:HVYVWCCXX:4:2218:4696:6776/1 1 140 (11) L1MC4_3end#LINE/L1 2511 2658 (131) m_b3s551i25
ST-E00130:540 1 TGTTAACTTCCTGATTTTGATGATTATACTGTGGCTAAACAGAAGTGTAT 50
i i i i vii ii vi i
L1MC4_3end#LI 2511 TGTTAATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGAATGT 2560
ST-E00130:540 51 CCTTGTTTTTAGGAAATATACACTGAAGTAT---------AAGGAGCATC 91
i i --------- i ?
L1MC4_3end#LI 2561 CCTTGTTCTTAGGAAATACACACTGAAGTATTTAGGGGTAAAGGGGCATN 2610
ST-E00130:540 92 ACGTGTGCGATTTCATCTCAAAATGGTTCAGAGAAAATGATGTGTGTAT 140
i v i i vv - i vi i i
L1MC4_3end#LI 2611 ATGTCTGCAACTTACTCTCAAA-TGGTTCAGAAAAAAAAATATGTATAT 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.55
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.01 (2 / 139), avg. gap size = 5.00 (10 / 2)
+ 278 10.3 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2219:18152:61239/1 16 54 (97) C L1MC4 LINE/L1 (242) 7800 7762 1773
ANNOTATION EVIDENCE:
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2219:18152:61239/1 16 54 97 C L1MC4_3end LINE/L1 2509 2547 242
278 10.26 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2219:18152:61239/1 16 54 (97) C L1MC4_3end#LINE/L1 (242) 2547 2509 m_b3s551i70
ST-E00130:540 16 TAGCCACAGTATAATCATCAAAATCAGGAAGTTAACATT 54
i i i i
C L1MC4_3end#LI 2547 TAACCACAGTACAATTATCAAAATCAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.48
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 423 18.3 6.1 0.0 ST-E00130:540:HVYVWCCXX:4:2219:18152:61239/1 59 151 (0) C L1MC4 LINE/L1 (393) 7649 7551 1773
ANNOTATION EVIDENCE:
423 18.28 6.06 0.00 ST-E00130:540:HVYVWCCXX:4:2219:18152:61239/1 59 151 0 C L1MC4_3end LINE/L1 2298 2396 393
423 18.28 6.06 0.00 ST-E00130:540:HVYVWCCXX:4:2219:18152:61239/1 59 151 (0) C L1MC4_3end#LINE/L1 (393) 2396 2298 m_b3s551i71
ST-E00130:540 59 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 108
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 109 TCT------TTTTTTTATTTATCATGACCTTCATATATTTGAATAGTAC 151
i------ i i i v ? v i v v
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACATTTTTGAAGAGTAC 2298
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.54
Transitions / transversions = 0.78 (7/9)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 6.00 (6 / 1)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 32 63 (88) + (TG)n Simple_repeat 1 32 (0) 1774
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 32 63 88 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 32 63 (88) (TG)n#Simple_repeat 1 32 (0) m_b4s252i3
ST-E00130:540 32 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 63
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 64 76 (75) + (TGTATG)n Simple_repeat 1 41 (0) 1775
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 32 76 75 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 32 76 (75) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i2
ST-E00130:540 32 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 76
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 491 4.9 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 91 151 (0) C AluSx SINE/Alu (21) 291 231 1776
ANNOTATION EVIDENCE:
491 4.92 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 91 151 0 C AluSx SINE/Alu 231 291 21
491 4.92 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/1 91 151 (0) C AluSx#SINE/Alu (21) 291 231 m_b4s357i7
ST-E00130:540 91 TTTTTTTTTGAGACGGAATCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTG 140
i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
ST-E00130:540 141 GCGCGATCTCG 151
C AluSx#SINE/Al 241 GCGCGATCTCG 231
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.57
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 1115 10.9 1.3 0.0 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/2 5 151 (0) + AluSx SINE/Alu 1 149 (163) 1777
ANNOTATION EVIDENCE:
1115 10.88 1.34 0.00 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/2 5 151 0 + AluSx SINE/Alu 1 149 163
1115 10.88 1.34 0.00 ST-E00130:540:HVYVWCCXX:4:2220:11789:62698/2 5 151 (0) AluSx#SINE/Alu 1 149 (163) m_b4s356i45
ST-E00130:540 5 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 54
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 55 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 102
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 103 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCAGGGGTGGTG 151
i i i i v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTG 149
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.62
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 146), avg. gap size = 2.00 (2 / 1)
+ 20 14.4 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 52 83 (68) + (TG)n Simple_repeat 1 32 (0) 1778
ANNOTATION EVIDENCE:
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 52 83 68 + (TG)n Simple_repeat 1 32 0
20 14.38 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 52 83 (68) (TG)n#Simple_repeat 1 32 (0) m_b4s252i1
ST-E00130:540 52 TGTGTGTGTGTGTGTATGTGTGTGCATGTATG 83
i ii i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 13 14.9 0.0 9.8 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 84 96 (55) + (TGTATG)n Simple_repeat 1 41 (0) 1779
ANNOTATION EVIDENCE:
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 52 96 55 + (TGTATG)n Simple_repeat 1 41 0
13 14.87 0.00 9.76 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 52 96 (55) (TGTATG)n#Simple_repeat 1 41 (0) m_b4s252i0
ST-E00130:540 52 TGTGTGTGTGTGTGTATGTGTGTGCATGTATGAATTTATGTTTAT 96
i i i -- -- v v
(TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATG--TGTATG--TGTATGTGTAT 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4)
+ 249 9.8 4.7 0.0 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 111 151 (0) C 7SLRNA srpRNA (11) 309 267 1780
ANNOTATION EVIDENCE:
249 9.76 4.65 0.00 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 111 151 0 C 7SLRNA SINE/Alu 267 309 11
249 9.76 4.65 0.00 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/1 111 151 (0) C 7SLRNA#SINE/Alu (11) 309 267 m_b4s502i0
ST-E00130:540 111 TTTTTTTTT--GAGACGGAATCTCGCTCTGTTGCCCGGGCTGG 151
-- ii v i
C 7SLRNA#SINE/A 309 TTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGG 267
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.61
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 2.00 (2 / 1)
+ 1094 11.0 1.4 0.0 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/2 7 151 (0) + AluSx SINE/Alu 1 147 (165) 1781
ANNOTATION EVIDENCE:
1094 11.03 1.36 0.00 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/2 7 151 0 + AluSx SINE/Alu 1 147 165
1094 11.03 1.36 0.00 ST-E00130:540:HVYVWCCXX:4:2220:26575:55262/2 7 151 (0) AluSx#SINE/Alu 1 147 (165) m_b4s356i48
ST-E00130:540 7 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 56
i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
ST-E00130:540 57 AGCAGGCAGATCAC--AAGGTCAGGAGTTTGAGAACAGCCTGGCCAATAT 104
i i i --i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
ST-E00130:540 105 GGTGAAACTCCATCTCTACTAAAAACACAAAAATTAGCCAGGGGTGG 151
i i i i v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGG 147
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.70
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.01 (1 / 144), avg. gap size = 2.00 (2 / 1)
+ 330 27.1 3.5 0.0 ST-E00130:540:HVYVWCCXX:4:2220:27143:43554/2 16 137 (14) C MIRb SINE/MIR (75) 187 60 1782
ANNOTATION EVIDENCE:
321 30.33 4.69 0.00 ST-E00130:540:HVYVWCCXX:4:2220:27143:43554/2 16 137 14 C MIR SINE/MIR 60 187 75
321 30.33 4.69 0.00 ST-E00130:540:HVYVWCCXX:4:2220:27143:43554/2 16 137 (14) C MIR#SINE/MIR (75) 187 60 m_b6s601i53
ST-E00130:540 16 TTAATTCTT---ATACTTCTGTCACTTAGATTCTATTATTTCCTTCAATT 62
i i--- i vii i v vv i v vi ii v
C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTT 138
ST-E00130:540 63 TATAAATGA--AAACTGTGACTTAGTGAGGTAAAGTAACTTGCTT-ATGC 109
i i -- v i vi v v ii- v i
C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88
ST-E00130:540 110 CACAGAGCTAACAAGTGGTTGACTCGAG 137
v ii iv vi i
C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAGCCGGG 60
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 40.10
Transitions / transversions = 1.47 (22/15)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3)
330 26.09 3.16 0.00 ST-E00130:540:HVYVWCCXX:4:2220:27143:43554/2 46 137 14 C MIRb SINE/MIR 67 161 107
330 26.09 3.16 0.00 ST-E00130:540:HVYVWCCXX:4:2220:27143:43554/2 46 137 (14) C MIRb#SINE/MIR (107) 161 67 m_b6s601i54
ST-E00130:540 46 TATTATTTCCTTCAATTTATAAATGA--AAACTGTGACTTAGTGAGGTAA 93
vi ii v i i -- v i i v v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
ST-E00130:540 94 AGTAACTTGCTTA-TGCCACAGAGCTAACAAGTGGTTGACTCGAG 137
ii -v i v ii iv vi i
C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 33.02
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 251 27.8 5.3 10.6 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/1 1 141 (10) + L1MC4 LINE/L1 6469 6601 (1441) 1783
ANNOTATION EVIDENCE:
251 27.78 5.26 10.64 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/1 1 141 10 + L1MC4_3end LINE/L1 1216 1348 1441
251 27.78 5.26 10.64 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/1 1 141 (10) L1MC4_3end#LINE/L1 1216 1348 (1441) m_b3s551i154
ST-E00130:540 1 AATAAGTAAATGCATTCAGGTTGAGTGGATAGTCAGGTTTTGGGGTGTTT 50
ii v? v i - i- i i---------
L1MC4_3end#LI 1216 AATAAGTAAATATATTGNGGATAA-TGGG-AGCCAGGTTTC--------- 1254
ST-E00130:540 51 TTTTTAACTGCTAGTAAAGCAATTTATAAATTTGGACAGAAAAAAAG--- 97
---- v iii vi vi v i v v iiii i ---
L1MC4_3end#LI 1255 ----TCACTGTCGGAGAAGGGAGTTACAAATATGGAAAGGGGGAAGGCTA 1300
ST-E00130:540 98 --ATAAACTGTGTGATGTTGGCTTGGATTTGAAGATATC--TATCAAC 141
-- i iv i v v i i -- v
L1MC4_3end#LI 1301 GAATGAACCCTGTGGTGTTGGATTGGAATTGGAGGTATCGGTATGAAC 1348
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.61
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.12 (17 / 140), avg. gap size = 1.29 (22 / 17)
+ 355 20.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/2 1 65 (86) C L1MC4 LINE/L1 (216) 7826 7762 1784
ANNOTATION EVIDENCE:
355 20.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/2 1 65 86 C L1MC4_3end LINE/L1 2509 2573 216
355 20.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/2 1 65 (86) C L1MC4_3end#LINE/L1 (216) 2573 2509 m_b3s551i66
ST-E00130:540 1 CCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAAAT 50
i i iv ii iiv i i i
C L1MC4_3end#LI 2573 CCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTATCAAAAT 2524
ST-E00130:540 51 CAGGAAGTTAACATT 65
i
C L1MC4_3end#LI 2523 CAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 353 18.8 7.0 0.0 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/2 70 149 (2) C L1MC4 LINE/L1 (393) 7649 7564 1784
ANNOTATION EVIDENCE:
353 18.75 6.98 0.00 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/2 70 149 2 C L1MC4_3end LINE/L1 2311 2396 393
353 18.75 6.98 0.00 ST-E00130:540:HVYVWCCXX:4:2224:24890:3717/2 70 149 (2) C L1MC4_3end#LINE/L1 (393) 2396 2311 m_b3s551i67
ST-E00130:540 70 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 119
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 120 TCT------TTTTTTTATTTATCATGACCTTCATAT 149
i------ i i i v ? v i
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACAT 2311
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 6.00 (6 / 1)
+ 251 27.8 5.3 10.6 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/1 1 141 (10) + L1MC4 LINE/L1 6469 6601 (1441) 1785
ANNOTATION EVIDENCE:
251 27.78 5.26 10.64 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/1 1 141 10 + L1MC4_3end LINE/L1 1216 1348 1441
251 27.78 5.26 10.64 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/1 1 141 (10) L1MC4_3end#LINE/L1 1216 1348 (1441) m_b3s551i155
ST-E00130:540 1 AATAAGTAAATGCATTCAGGTTGAGTGGATAGTCAGGTTTTGGGGTGTTT 50
ii v? v i - i- i i---------
L1MC4_3end#LI 1216 AATAAGTAAATATATTGNGGATAA-TGGG-AGCCAGGTTTC--------- 1254
ST-E00130:540 51 TTTTTAACTGCTAGTAAAGCAATTTATAAATTTGGACAGAAAAAAAG--- 97
---- v iii vi vi v i v v iiii i ---
L1MC4_3end#LI 1255 ----TCACTGTCGGAGAAGGGAGTTACAAATATGGAAAGGGGGAAGGCTA 1300
ST-E00130:540 98 --ATAAACTGTGTGATGTTGGCTTGGATTTGAAGATATC--TATCAAC 141
-- i iv i v v i i -- v
L1MC4_3end#LI 1301 GAATGAACCCTGTGGTGTTGGATTGGAATTGGAGGTATCGGTATGAAC 1348
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.61
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.12 (17 / 140), avg. gap size = 1.29 (22 / 17)
+ 355 20.0 0.0 0.0 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/2 1 65 (86) C L1MC4 LINE/L1 (216) 7826 7762 1786
ANNOTATION EVIDENCE:
355 20.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/2 1 65 86 C L1MC4_3end LINE/L1 2509 2573 216
355 20.00 0.00 0.00 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/2 1 65 (86) C L1MC4_3end#LINE/L1 (216) 2573 2509 m_b3s551i68
ST-E00130:540 1 CCTAAAAACAAGGATACACTTCTGTTTAGCCACAGTATAATCATCAAAAT 50
i i iv ii iiv i i i
C L1MC4_3end#LI 2573 CCTAAGAACAAGGACATTCTCTTACATAACCACAGTACAATTATCAAAAT 2524
ST-E00130:540 51 CAGGAAGTTAACATT 65
i
C L1MC4_3end#LI 2523 CAGGAAATTAACATT 2509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.63
Transitions / transversions = 5.50 (11/2)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 353 18.8 7.0 0.0 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/2 70 149 (2) C L1MC4 LINE/L1 (393) 7649 7564 1786
ANNOTATION EVIDENCE:
353 18.75 6.98 0.00 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/2 70 149 2 C L1MC4_3end LINE/L1 2311 2396 393
353 18.75 6.98 0.00 ST-E00130:540:HVYVWCCXX:4:2224:25591:2926/2 70 149 (2) C L1MC4_3end#LINE/L1 (393) 2396 2311 m_b3s551i69
ST-E00130:540 70 CATTGCATTTAGGTGTGTAGTCTGTTTAGTCTCCTTCAATCTGGAACAGT 119
i v vvv v i
C L1MC4_3end#LI 2396 CGTTGCATTTAGTTGTCATGTCTCTTTAGTCTCCTTTAATCTGGAACAGT 2347
ST-E00130:540 120 TCT------TTTTTTTATTTATCATGACCTTCATAT 149
i------ i i i v ? v i
C L1MC4_3end#LI 2346 TCCTCAGTCTTTCTTTGTCTTTCATGACNTTGACAT 2311
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.80
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 6.00 (6 / 1)