+ 2494 3.7 0.0 2.4 X_118043443_118043786_INS 3 344 (0) C AluY SINE/Alu (0) 311 3 122
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_118043443_118043786_INS 18 57 287 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_118043443_118043786_INS 18 57 (287) (T)n#Simple_repeat 1 40 (0) c_b2s251i147
X_118043443_1 18 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 57
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2494 3.72 0.00 2.36 X_118043443_118043786_INS 3 17 327 C AluY SINE/Alu 283 297 14
2494 3.72 0.00 2.36 X_118043443_118043786_INS 3 17 (327) C AluY#SINE/Alu (14) 297 283 c_b2s352i33
X_118043443_1 3 TTTTATTTCTTTCTC 17
v i i i
C AluY#SINE/Alu 297 TTTTTTTTTTTTTTT 283
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 14), avg. gap size = 0.0 (0 / 0)
2494 3.72 0.00 2.36 X_118043443_118043786_INS 58 344 0 C AluY SINE/Alu 3 282 29
2494 3.72 0.00 2.36 X_118043443_118043786_INS 58 344 (0) C AluY#SINE/Alu (29) 282 3 c_b2s352i33
X_118043443_1 58 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 107
----- -- v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 240
X_118043443_1 108 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 157
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_118043443_1 158 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 207
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_118043443_1 208 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 257
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_118043443_1 258 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 307
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_118043443_1 308 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 344
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.87
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 286), avg. gap size = 1.00 (7 / 7)
+ 40 25.2 0.0 0.0 X_118073509_118073597_INS 1 86 (3) + (TA)n Simple_repeat 1 86 (0) 123
ANNOTATION EVIDENCE:
40 25.16 0.00 0.00 X_118073509_118073597_INS 1 86 3 + (TA)n Simple_repeat 1 86 0
40 25.16 0.00 0.00 X_118073509_118073597_INS 1 86 (3) (TA)n#Simple_repeat 1 86 (0) m_b2s252i73
X_118073509_1 1 TATATACACATATATACATATATATACACACACATATATATACACATATA 50
i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_118073509_1 51 TACACACACATATATACACATATATACACATATATA 86
i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATA 86
Matrix = Unknown
Transitions / transversions = 1.00 (17/0)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)
+ 2643 2.6 0.0 2.3 X_118203384_118203707_INS 15 324 (0) + AluY SINE/Alu 1 303 (8) 124
ANNOTATION EVIDENCE:
2643 2.64 0.00 2.31 X_118203384_118203707_INS 15 324 0 + AluY SINE/Alu 1 303 8
2643 2.64 0.00 2.31 X_118203384_118203707_INS 15 324 (0) AluY#SINE/Alu 1 303 (8) c_b2s352i34
X_118203384_1 15 GGCCGGGCGCGTTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
v
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_118203384_1 65 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 114
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_118203384_1 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_118203384_1 165 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 214
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_118203384_1 215 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 264
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_118203384_1 265 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 314
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_118203384_1 315 AAAAAAAAAA 324
AluY#SINE/Alu 294 AAAAAAAAAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.77
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 1.00 (7 / 7)
+ 1960 2.6 0.0 3.1 X_118380060_118380305_INS 11 246 (0) C AluY SINE/Alu (2) 309 81 125
ANNOTATION EVIDENCE:
1960 2.62 0.00 3.06 X_118380060_118380305_INS 11 246 0 C AluY SINE/Alu 81 309 2
1960 2.62 0.00 3.06 X_118380060_118380305_INS 11 246 (0) C AluY#SINE/Alu (2) 309 81 m_b2s356i3
X_118380060_1 11 TTTCTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG 60
i
C AluY#SINE/Alu 309 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG 260
X_118380060_1 61 CCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGC 110
i ----- -- i
C AluY#SINE/Alu 259 CCCAGGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGC 217
X_118380060_1 111 TCTGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCT 160
i
C AluY#SINE/Alu 216 TCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCT 167
X_118380060_1 161 GGGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAG 210
i
C AluY#SINE/Alu 166 GGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAG 117
X_118380060_1 211 TAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTC 246
v
C AluY#SINE/Alu 116 TAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTC 81
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.86
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.03 (7 / 235), avg. gap size = 1.00 (7 / 7)
+ 31 11.6 0.0 0.0 X_118645813_118645863_INS 4 50 (1) + (AT)n Simple_repeat 1 47 (0) 126
ANNOTATION EVIDENCE:
31 11.60 0.00 0.00 X_118645813_118645863_INS 4 50 1 + (AT)n Simple_repeat 1 47 0
31 11.60 0.00 0.00 X_118645813_118645863_INS 4 50 (1) (AT)n#Simple_repeat 1 47 (0) m_b2s252i72
X_118645813_1 4 ATATATATATATAAATATATATAAAAATATATATATTTCTATATATA 50
v v v v v
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 2563 2.1 0.0 0.0 X_118781932_118782252_INS 1 309 (12) C AluY SINE/Alu (0) 311 1 127
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_118781932_118782252_INS 1 28 293 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_118781932_118782252_INS 1 28 (293) (T)n#Simple_repeat 1 28 (0) c_b2s251i146
X_118781932_1 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
(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)
2563 2.14 0.00 0.00 X_118781932_118782252_INS 29 309 12 C AluY SINE/Alu 1 281 30
2563 2.14 0.00 0.00 X_118781932_118782252_INS 29 309 (12) C AluY#SINE/Alu (30) 281 1 c_b2s352i35
X_118781932_1 29 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 78
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_118781932_1 79 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 128
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_118781932_1 129 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 178
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_118781932_1 179 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCTGGGATGGT 228
v ii
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_118781932_1 229 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 278
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_118781932_1 279 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 309
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.84
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 0.0 X_11885333_11885752_INS 12 51 (369) + (T)n Simple_repeat 1 40 (0) 128
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_11885333_11885752_INS 12 51 369 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_11885333_11885752_INS 12 51 (369) (T)n#Simple_repeat 1 40 (0) c_b1s251i172
X_11885333_11 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 15 4.0 3.7 0.0 X_11885333_11885752_INS 52 70 (350) + (ATT)n Simple_repeat 3 21 (0) 129
ANNOTATION EVIDENCE:
15 3.96 3.70 0.00 X_11885333_11885752_INS 52 70 350 + (ATT)n Simple_repeat 9 27 1
15 3.96 3.70 0.00 X_11885333_11885752_INS 52 70 (350) (ATT)n#Simple_repeat 9 27 (1) m_b1s252i126
X_11885333_11 52 ATTATTATTATTATTATTA 70
(ATT)n#Simple 9 ATTATTATTATTATTATTA 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 3195 0.6 0.0 0.0 X_11885333_11885752_INS 71 420 (0) C L1HS LINE/L1 (1) 6154 5805 130
ANNOTATION EVIDENCE:
3195 0.57 0.00 0.00 X_11885333_11885752_INS 71 420 0 C L1HS_3end LINE/L1 552 901 1
3195 0.57 0.00 0.00 X_11885333_11885752_INS 71 420 (0) C L1HS_3end#LINE/L1 (1) 901 552 m_b1s551i1
X_11885333_11 71 TTATTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTG 120
v
C L1HS_3end#LIN 901 TTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTG 852
X_11885333_11 121 CAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCAC 170
C L1HS_3end#LIN 851 CAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCAC 802
X_11885333_11 171 TAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCC 220
i
C L1HS_3end#LIN 801 TAACGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCC 752
X_11885333_11 221 TCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGT 270
C L1HS_3end#LIN 751 TCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGT 702
X_11885333_11 271 CCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTG 320
C L1HS_3end#LIN 701 CCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTG 652
X_11885333_11 321 TTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATT 370
C L1HS_3end#LIN 651 TTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATT 602
X_11885333_11 371 TCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCA 420
C L1HS_3end#LIN 601 TCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCA 552
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.31
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 349), avg. gap size = 0.0 (0 / 0)
+ 16 19.8 4.1 2.0 X_118979891_118979950_INS 10 58 (2) + (ATGT)n Simple_repeat 1 50 (0) 131
ANNOTATION EVIDENCE:
16 19.82 4.08 2.00 X_118979891_118979950_INS 10 58 2 + (ATGT)n Simple_repeat 1 50 0
16 19.82 4.08 2.00 X_118979891_118979950_INS 10 58 (2) (ATGT)n#Simple_repeat 1 50 (0) m_b2s252i71
X_118979891_1 10 ATGTATATATGTATACAT-TATGTATACATTTCAT-AATGTATATATGTA 57
i ii - ii v - -v i
(ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGT-ATGTATGTATGTATGTA 49
X_118979891_1 58 T 58
(ATGT)n#Simpl 50 T 50
Matrix = Unknown
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3)
+ 41 19.4 3.5 0.0 X_119084212_119084300_INS 1 87 (2) + (TA)n Simple_repeat 1 90 (0) 132
ANNOTATION EVIDENCE:
41 19.42 3.45 0.00 X_119084212_119084300_INS 1 87 2 + (TA)n Simple_repeat 1 90 0
41 19.42 3.45 0.00 X_119084212_119084300_INS 1 87 (2) (TA)n#Simple_repeat 1 90 (0) m_b2s252i70
X_119084212_1 1 TATATATGTATACATATAT-TGTATATGTGTGTATATATATACACA-ATA 48
i i - i i i i i i -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_119084212_1 49 TATGTATACATATAT-TGTATATGTGTGTATATATATATA 87
i i - i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATA 90
Matrix = Unknown
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.00 (3 / 3)
+ 55 14.5 6.6 0.8 X_119246348_119246469_INS 1 121 (1) + (AT)n Simple_repeat 1 128 (0) 133
ANNOTATION EVIDENCE:
55 14.49 6.61 0.78 X_119246348_119246469_INS 1 121 1 + (AT)n Simple_repeat 1 128 0
55 14.49 6.61 0.78 X_119246348_119246469_INS 1 121 (1) (AT)n#Simple_repeat 1 128 (0) m_b2s252i69
X_119246348_1 1 ATATGTATGATATATATACATATATGTAT-TATATATA-ATACACATATA 48
i - i i - - i i
(AT)n#Simple_ 1 ATATATAT-ATATATATATATATATATATATATATATATATATATATATA 49
X_119246348_1 49 T-TATATATA-ATACACATATATGTAT-TATATATA-ATACACATATATG 94
- - i i i - - i i i
(AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATATATATATATA 99
X_119246348_1 95 TGT-TATATATA-ATACACATATATGTAT 121
i - - i i i
(AT)n#Simple_ 100 TATATATATATATATATATATATATATAT 128
Matrix = Unknown
Transitions / transversions = 1.00 (15/0)
Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.00 (9 / 9)
+ 44 7.7 0.0 0.0 X_119488902_119488966_INS 1 56 (9) + (AT)n Simple_repeat 1 56 (0) 134
ANNOTATION EVIDENCE:
44 7.71 0.00 0.00 X_119488902_119488966_INS 1 56 9 + (AT)n Simple_repeat 1 56 0
44 7.71 0.00 0.00 X_119488902_119488966_INS 1 56 (9) (AT)n#Simple_repeat 1 56 (0) c_b2s251i145
X_119488902_1 1 ATATATATATATATGTATGTATATATATATATATATATATATGTATGTAT 50
i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_119488902_1 51 ATATAT 56
(AT)n#Simple_ 51 ATATAT 56
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 36 5.0 9.3 2.2 X_119508651_119508741_INS 2 87 (4) + (TA)n Simple_repeat 1 92 (0) 135
ANNOTATION EVIDENCE:
36 5.04 9.30 2.17 X_119508651_119508741_INS 2 87 4 + (TA)n Simple_repeat 1 92 0
36 5.04 9.30 2.17 X_119508651_119508741_INS 2 87 (4) (TA)n#Simple_repeat 1 92 (0) c_b2s251i144
X_119508651_1 2 TATATATA-ATATA-ATATATATATACCCT-TATATATA-ATATATATAT 47
- - -iv - -
(TA)n#Simple_ 1 TATATATATATATATATATATATATA-TATATATATATATATATATATAT 49
X_119508651_1 48 -TATAT-TATATATA-AGGGTATATATATATATAT-TATATATA 87
- - - -vi -
(TA)n#Simple_ 50 ATATATATATATATATA-TATATATATATATATATATATATATA 92
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.12 (10 / 85), avg. gap size = 1.00 (10 / 10)
+ 2737 2.0 0.0 0.0 X_119527842_119528150_INS 12 309 (0) C AluY SINE/Alu (13) 298 1 136
ANNOTATION EVIDENCE:
2737 2.01 0.00 0.00 X_119527842_119528150_INS 12 309 0 C AluY SINE/Alu 1 298 13
2737 2.01 0.00 0.00 X_119527842_119528150_INS 12 309 (0) C AluY#SINE/Alu (13) 298 1 c_b2s352i36
X_119527842_1 12 TTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA 61
C AluY#SINE/Alu 298 TTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA 249
X_119527842_1 62 GTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCAC 111
v
C AluY#SINE/Alu 248 GTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCAC 199
X_119527842_1 112 GCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCCGC 161
i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGC 149
X_119527842_1 162 CACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 211
i
C AluY#SINE/Alu 148 CACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 99
X_119527842_1 212 ATTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTC 261
i v i
C AluY#SINE/Alu 98 GTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTC 49
X_119527842_1 262 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 309
C AluY#SINE/Alu 48 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.42
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 297), avg. gap size = 0.0 (0 / 0)
+ 55 1.9 0.0 0.0 X_11953382_11953444_INS 10 63 (0) + (T)n Simple_repeat 1 54 (0) 137
ANNOTATION EVIDENCE:
55 1.88 0.00 0.00 X_11953382_11953444_INS 10 63 0 + (T)n Simple_repeat 1 54 0
55 1.88 0.00 0.00 X_11953382_11953444_INS 10 63 (0) (T)n#Simple_repeat 1 54 (0) c_b1s251i171
X_11953382_11 10 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTT 59
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_11953382_11 60 TTTT 63
(T)n#Simple_r 51 TTTT 54
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 2187 2.5 0.0 1.6 X_119553925_119554228_INS 1 291 (13) C AluY SINE/Alu (0) 311 37 138
ANNOTATION EVIDENCE:
46 0.00 0.00 0.00 X_119553925_119554228_INS 1 42 262 + (T)n Simple_repeat 1 42 0
46 0.00 0.00 0.00 X_119553925_119554228_INS 1 42 (262) (T)n#Simple_repeat 1 42 (0) c_b2s251i143
X_119553925_1 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
2187 2.45 0.00 1.63 X_119553925_119554228_INS 43 291 13 C AluY SINE/Alu 37 281 30
2187 2.45 0.00 1.63 X_119553925_119554228_INS 43 291 (13) C AluY#SINE/Alu (30) 281 37 c_b2s352i37
X_119553925_1 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCT 92
i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_119553925_1 93 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCATGCCATTCTCCTGCCTCA 142
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_119553925_1 143 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 192
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_119553925_1 193 TTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGA 242
---- v i
C AluY#SINE/Alu 131 T----TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGA 86
X_119553925_1 243 TGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 291
C AluY#SINE/Alu 85 TGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 37
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.02 (4 / 248), avg. gap size = 1.00 (4 / 4)
+ 67 0.0 2.8 1.4 X_119765982_119766052_INS 1 71 (0) + (ATAAA)n Simple_repeat 1 72 (0) 139
ANNOTATION EVIDENCE:
67 0.00 2.82 1.39 X_119765982_119766052_INS 1 71 0 + (ATAAA)n Simple_repeat 1 72 0
67 0.00 2.82 1.39 X_119765982_119766052_INS 1 71 (0) (ATAAA)n#Simple_repeat 1 72 (0) c_b2s251i142
X_119765982_1 1 ATAAAATTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAA 50
-
(ATAAA)n#Simp 1 ATAAAA-TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAA 49
X_119765982_1 51 AATAAAAT--AATAAAATAAAAT 71
--
(ATAAA)n#Simp 50 AATAAAATAAAATAAAATAAAAT 72
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.50 (3 / 2)
+ 58 0.0 0.0 0.0 X_119821821_119821873_INS 2 53 (0) + (TTTC)n Simple_repeat 1 52 (0) 140
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_119821821_119821873_INS 2 53 0 + (TTTC)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_119821821_119821873_INS 2 53 (0) (TTTC)n#Simple_repeat 1 52 (0) c_b2s251i141
X_119821821_1 2 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 51
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_119821821_1 52 TC 53
(TTTC)n#Simpl 51 TC 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 1836 0.5 0.0 0.0 X_119892830_119893050_INS 20 221 (0) C L1HS LINE/L1 (0) 6155 5954 141
ANNOTATION EVIDENCE:
1836 0.50 0.00 0.00 X_119892830_119893050_INS 20 221 0 C L1HS_3end LINE/L1 701 902 0
1836 0.50 0.00 0.00 X_119892830_119893050_INS 20 221 (0) C L1HS_3end#LINE/L1 (0) 902 701 m_b2s551i8
X_119892830_1 20 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 69
C L1HS_3end#LIN 902 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 853
X_119892830_1 70 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 119
C L1HS_3end#LIN 852 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 803
X_119892830_1 120 CTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 169
i
C L1HS_3end#LIN 802 CTAACGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 753
X_119892830_1 170 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTG 219
C L1HS_3end#LIN 752 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTG 703
X_119892830_1 220 TC 221
C L1HS_3end#LIN 702 TC 701
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.05
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 201), avg. gap size = 0.0 (0 / 0)
+ 54 0.0 0.0 1.9 X_119918831_119918884_INS 2 54 (0) + (AAAG)n Simple_repeat 1 52 (0) 142
ANNOTATION EVIDENCE:
54 0.00 0.00 1.92 X_119918831_119918884_INS 2 54 0 + (AAAG)n Simple_repeat 1 52 0
54 0.00 0.00 1.92 X_119918831_119918884_INS 2 54 (0) (AAAG)n#Simple_repeat 1 52 (0) c_b2s251i140
X_119918831_1 2 AAAGAAAGAAAGAAAGAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 51
-
(AAAG)n#Simpl 1 AAAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 49
X_119918831_1 52 AAG 54
(AAAG)n#Simpl 50 AAG 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1)
+ 31 0.0 0.0 0.0 X_119938929_119939001_INS 11 37 (36) + (TG)n Simple_repeat 1 27 (0) 143
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_119938929_119939001_INS 11 37 36 + (TG)n Simple_repeat 1 27 0
31 0.00 0.00 0.00 X_119938929_119939001_INS 11 37 (36) (TG)n#Simple_repeat 1 27 (0) c_b2s251i138
X_119938929_1 11 TGTGTGTGTGTGTGTGTGTGTGTGTGT 37
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 40 0.0 0.0 0.0 X_119938929_119939001_INS 40 73 (0) + (TA)n Simple_repeat 1 34 (0) 144
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 X_119938929_119939001_INS 40 73 0 + (TA)n Simple_repeat 1 34 0
40 0.00 0.00 0.00 X_119938929_119939001_INS 40 73 (0) (TA)n#Simple_repeat 1 34 (0) c_b2s251i139
X_119938929_1 40 TATATATATATATATATATATATATATATATATA 73
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATA 34
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 2673 2.0 0.7 0.3 X_12033313_12033630_INS 18 318 (0) + AluY SINE/Alu 1 302 (9) 145
ANNOTATION EVIDENCE:
2673 2.00 0.66 0.33 X_12033313_12033630_INS 18 318 0 + AluY SINE/Alu 1 302 9
2673 2.00 0.66 0.33 X_12033313_12033630_INS 18 318 (0) AluY#SINE/Alu 1 302 (9) c_b1s352i2
X_12033313_12 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_12033313_12 68 GGCGGGCGGATCACGAGGTCAGGAGATCAAGACCATCCTGGCTAACACGG 117
i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_12033313_12 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGAGGTGGC 167
v
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_12033313_12 168 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 217
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_12033313_12 218 GAACCCCAGGGGGCGGAGCCTGCAGTGAGCCGAGATTGCGCCACTGCACT 267
- i i i i
AluY#SINE/Alu 201 GAA-CCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_12033313_12 268 CCAGCCTGGGCGAC--AGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 315
--
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_12033313_12 316 AAA 318
AluY#SINE/Alu 300 AAA 302
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.11
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.01 (2 / 300), avg. gap size = 1.50 (3 / 2)
+ 45 6.1 0.0 0.0 X_120904560_120904612_INS 1 52 (1) + (TA)n Simple_repeat 1 52 (0) 146
ANNOTATION EVIDENCE:
45 6.13 0.00 0.00 X_120904560_120904612_INS 1 52 1 + (TA)n Simple_repeat 1 52 0
45 6.13 0.00 0.00 X_120904560_120904612_INS 1 52 (1) (TA)n#Simple_repeat 1 52 (0) c_b2s251i137
X_120904560_1 1 TATATATACATATATATATATATACATATATATATATATATACATATATA 50
i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_120904560_1 51 TA 52
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2569 2.1 0.0 0.0 X_120912381_120912702_INS 18 322 (0) C AluY SINE/Alu (0) 311 5 147
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_120912381_120912702_INS 18 44 278 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 X_120912381_120912702_INS 18 44 (278) (T)n#Simple_repeat 1 27 (0) c_b2s251i136
X_120912381_1 18 TTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(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)
2569 2.12 0.00 0.00 X_120912381_120912702_INS 45 322 0 C AluY SINE/Alu 5 282 29
2569 2.12 0.00 0.00 X_120912381_120912702_INS 45 322 (0) C AluY#SINE/Alu (29) 282 5 c_b2s352i38
X_120912381_1 45 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 94
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_120912381_1 95 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 144
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_120912381_1 145 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 194
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_120912381_1 195 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 244
v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_120912381_1 245 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 294
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_120912381_1 295 GGATTACAGGCGTGAGCCACCGCGCCCG 322
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCG 5
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.83
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 277), avg. gap size = 0.0 (0 / 0)
+ 50 6.3 0.0 2.9 X_121264573_121264643_INS 2 71 (0) + (TA)n Simple_repeat 1 68 (0) 148
ANNOTATION EVIDENCE:
50 6.35 0.00 2.94 X_121264573_121264643_INS 2 71 0 + (TA)n Simple_repeat 1 68 0
50 6.35 0.00 2.94 X_121264573_121264643_INS 2 71 (0) (TA)n#Simple_repeat 1 68 (0) c_b2s251i135
X_121264573_1 2 TATATATATATATATATATATATATATTTGCTATATATATATATATATAT 51
v -v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATAT-ATATATATATATATATATAT 49
X_121264573_1 52 ATATATTTGCTATATATATA 71
v -v
(TA)n#Simple_ 50 ATATATAT-ATATATATATA 68
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2)
+ 46 2.0 3.9 0.0 X_121270382_121270435_INS 1 51 (3) + (TA)n Simple_repeat 1 53 (0) 149
ANNOTATION EVIDENCE:
46 1.99 3.92 0.00 X_121270382_121270435_INS 1 51 3 + (TA)n Simple_repeat 1 53 0
46 1.99 3.92 0.00 X_121270382_121270435_INS 1 51 (3) (TA)n#Simple_repeat 1 53 (0) c_b2s251i134
X_121270382_1 1 TATATATATATATATATATATATATATATATATATAAAT-TAT-TATATA 48
v - -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_121270382_1 49 TAT 51
(TA)n#Simple_ 51 TAT 53
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2)
+ 2768 1.7 0.0 0.0 X_12146387_12146697_INS 14 311 (0) C AluY SINE/Alu (11) 300 3 150
ANNOTATION EVIDENCE:
2768 1.68 0.00 0.00 X_12146387_12146697_INS 14 311 0 C AluY SINE/Alu 3 300 11
2768 1.68 0.00 0.00 X_12146387_12146697_INS 14 311 (0) C AluY#SINE/Alu (11) 300 3 c_b1s352i3
X_12146387_12 14 TTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTG 63
C AluY#SINE/Alu 300 TTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTG 251
X_12146387_12 64 GAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTC 113
i
C AluY#SINE/Alu 250 GAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTC 201
X_12146387_12 114 ACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCC 163
i
C AluY#SINE/Alu 200 ACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCC 151
X_12146387_12 164 GCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCA 213
i
C AluY#SINE/Alu 150 GCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCA 101
X_12146387_12 214 CCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 263
v i
C AluY#SINE/Alu 100 CCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 51
X_12146387_12 264 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 311
C AluY#SINE/Alu 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.08
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 297), avg. gap size = 0.0 (0 / 0)
+ 2387 3.9 0.0 3.1 X_121569311_121569641_INS 17 331 (0) C AluY SINE/Alu (0) 311 2 151
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_121569311_121569641_INS 17 41 290 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_121569311_121569641_INS 17 41 (290) (T)n#Simple_repeat 1 25 (0) c_b2s251i133
X_121569311_1 17 TTTTTTTTTTTTTTTTTTTTTTTTT 41
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2387 3.85 0.00 3.15 X_121569311_121569641_INS 42 331 0 C AluY SINE/Alu 2 282 29
2387 3.85 0.00 3.15 X_121569311_121569641_INS 42 331 (0) C AluY#SINE/Alu (29) 282 2 c_b2s352i39
X_121569311_1 42 GAGACGGAGTCTCGCTCTGTCGCCCAGGCGGGACTGCGGACTGCAGCGGC 91
-------i v i
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGC-------TGGAGTGCAGTGGC 240
X_121569311_1 92 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 141
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_121569311_1 142 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 191
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_121569311_1 192 GGCTAATTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGC 241
-- v
C AluY#SINE/Alu 139 GGCTAATTTTTT--GTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGC 92
X_121569311_1 242 CAGGATGATCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCC 291
i i i
C AluY#SINE/Alu 91 CAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCC 42
X_121569311_1 292 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 331
C AluY#SINE/Alu 41 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.98
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.03 (9 / 289), avg. gap size = 1.00 (9 / 9)
+ 2568 1.8 0.0 0.0 X_121609557_121609867_INS 7 311 (0) C AluY SINE/Alu (0) 311 2 152
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_121609557_121609867_INS 7 31 280 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_121609557_121609867_INS 7 31 (280) (T)n#Simple_repeat 1 25 (0) c_b2s251i132
X_121609557_1 7 TTTTTTTTTTTTTTTTTTTTTTTTT 31
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2568 1.79 0.00 0.00 X_121609557_121609867_INS 32 311 0 C AluY SINE/Alu 2 281 30
2568 1.79 0.00 0.00 X_121609557_121609867_INS 32 311 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i40
X_121609557_1 32 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 81
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_121609557_1 82 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 131
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_121609557_1 132 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 181
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_121609557_1 182 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 231
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_121609557_1 232 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 281
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_121609557_1 282 GGATTACAGGCGTGAGCCACCGCGCCCGGC 311
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 53 7.7 0.0 0.0 X_121759772_121760056_INS 3 72 (213) + (T)n Simple_repeat 1 70 (0) 153
ANNOTATION EVIDENCE:
53 7.71 0.00 0.00 X_121759772_121760056_INS 3 72 213 + (T)n Simple_repeat 1 70 0
53 7.71 0.00 0.00 X_121759772_121760056_INS 3 72 (213) (T)n#Simple_repeat 1 70 (0) c_b2s251i131
X_121759772_1 3 TTTTTTTTTTTCTTTTTTTCTTTTTCTTTTCTTTTTTTTTTCTTTTTTTT 52
i i i i i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_121759772_1 53 TTTTTTTTTTTTTTTTTTTT 72
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTT 70
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 1921 2.8 0.0 0.0 X_121759772_121760056_INS 73 285 (0) C AluY SINE/Alu (30) 281 69 154
ANNOTATION EVIDENCE:
1921 2.82 0.00 0.00 X_121759772_121760056_INS 73 285 0 C AluY SINE/Alu 69 281 30
1921 2.82 0.00 0.00 X_121759772_121760056_INS 73 285 (0) C AluY#SINE/Alu (30) 281 69 c_b2s352i41
X_121759772_1 73 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 122
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_121759772_1 123 CGGCTCGCTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 172
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_121759772_1 173 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 222
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_121759772_1 223 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 272
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_121759772_1 273 CTCGATCTCCTGA 285
C AluY#SINE/Alu 81 CTCGATCTCCTGA 69
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.44
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 212), avg. gap size = 0.0 (0 / 0)
+ 764 1.1 0.0 0.0 X_121889832_121889936_INS 16 105 (0) + AluY SINE/Alu 213 302 (9) 155
ANNOTATION EVIDENCE:
764 1.11 0.00 0.00 X_121889832_121889936_INS 16 105 0 + AluY SINE/Alu 213 302 9
764 1.11 0.00 0.00 X_121889832_121889936_INS 16 105 (0) AluY#SINE/Alu 213 302 (9) m_b2s357i4
X_121889832_1 16 CGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGA 65
v
AluY#SINE/Alu 213 CGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGA 262
X_121889832_1 66 CAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAA 105
AluY#SINE/Alu 263 CAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAA 302
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 1.12
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0)
+ 58 0.0 0.0 0.0 X_12211871_12211923_INS 2 53 (0) + (AGAA)n Simple_repeat 1 52 (0) 156
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_12211871_12211923_INS 2 53 0 + (AGAA)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_12211871_12211923_INS 2 53 (0) (AGAA)n#Simple_repeat 1 52 (0) c_b1s251i170
X_12211871_12 2 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 51
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50
X_12211871_12 52 AA 53
(AGAA)n#Simpl 51 AA 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 29 0.0 0.0 0.0 X_122394268_122394349_INS 1 35 (47) + (AAAG)n Simple_repeat 1 35 (0) 157
ANNOTATION EVIDENCE:
29 0.00 0.00 0.00 X_122394268_122394349_INS 1 35 1 + (AAAG)n Simple_repeat 1 35 0
29 0.00 0.00 0.00 X_122394268_122394349_INS 1 35 (1) (AAAG)n#Simple_repeat 1 35 (0) m_b2s252i68
X_122394268_1 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 35
(AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 35
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
+ 52 0.0 0.0 0.0 X_122394268_122394349_INS 36 82 (0) + (GAAG)n Simple_repeat 1 47 (0) 158
ANNOTATION EVIDENCE:
52 0.00 0.00 0.00 X_122394268_122394349_INS 36 82 0 + (GAAG)n Simple_repeat 1 47 0
52 0.00 0.00 0.00 X_122394268_122394349_INS 36 82 (0) (GAAG)n#Simple_repeat 1 47 (0) c_b2s251i130
X_122394268_1 36 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 82
(GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 2451 2.8 0.0 2.5 X_12240328_12240657_INS 16 330 (0) C AluY SINE/Alu (0) 311 2 159
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_12240328_12240657_INS 16 42 288 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 X_12240328_12240657_INS 16 42 (288) (T)n#Simple_repeat 1 27 (0) c_b1s251i169
X_12240328_12 16 TTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(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)
2451 2.81 0.00 2.46 X_12240328_12240657_INS 43 330 0 C AluY SINE/Alu 2 282 29
2451 2.81 0.00 2.46 X_12240328_12240657_INS 43 330 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i4
X_12240328_12 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 92
----- -- v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 240
X_12240328_12 93 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 142
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_12240328_12 143 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 192
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_12240328_12 193 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 242
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_12240328_12 243 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 292
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_12240328_12 293 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 330
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 2543 2.1 0.0 0.0 X_122504190_122504525_INS 7 336 (0) C AluY SINE/Alu (0) 311 2 160
ANNOTATION EVIDENCE:
50 2.04 0.00 0.00 X_122504190_122504525_INS 7 56 280 + (T)n Simple_repeat 1 50 0
50 2.04 0.00 0.00 X_122504190_122504525_INS 7 56 (280) (T)n#Simple_repeat 1 50 (0) c_b2s251i129
X_122504190_1 7 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 56
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
2543 2.14 0.00 0.00 X_122504190_122504525_INS 57 336 0 C AluY SINE/Alu 2 281 30
2543 2.14 0.00 0.00 X_122504190_122504525_INS 57 336 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i42
X_122504190_1 57 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGACCT 106
v i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_122504190_1 107 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 156
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_122504190_1 157 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 206
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_122504190_1 207 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 256
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_122504190_1 257 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 306
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_122504190_1 307 GGATTACAGGCGTGAGCCACCGCGCCCGGC 336
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.85
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 58 0.0 0.0 0.0 X_122597427_122597479_INS 1 52 (1) + (AAGG)n Simple_repeat 1 52 (0) 161
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_122597427_122597479_INS 1 52 1 + (AAGG)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_122597427_122597479_INS 1 52 (1) (AAGG)n#Simple_repeat 1 52 (0) c_b2s251i128
X_122597427_1 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50
(AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50
X_122597427_1 51 GG 52
(AAGG)n#Simpl 51 GG 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2506 2.1 0.0 2.5 X_122672363_122672704_INS 14 341 (1) C AluY SINE/Alu (0) 311 2 162
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_122672363_122672704_INS 14 53 289 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_122672363_122672704_INS 14 53 (289) (T)n#Simple_repeat 1 40 (0) c_b2s251i127
X_122672363_1 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 53
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2506 2.10 0.00 2.45 X_122672363_122672704_INS 54 341 1 C AluY SINE/Alu 2 282 29
2506 2.10 0.00 2.45 X_122672363_122672704_INS 54 341 (1) C AluY#SINE/Alu (29) 282 2 c_b2s352i43
X_122672363_1 54 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGACTGCGGACTGCAGTGGC 103
----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_122672363_1 104 GCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 153
i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_122672363_1 154 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 203
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_122672363_1 204 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 253
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_122672363_1 254 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 303
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_122672363_1 304 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 341
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.17
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 2329 1.6 0.0 0.0 X_122777202_122777495_INS 5 292 (2) C AluY SINE/Alu (0) 311 29 163
ANNOTATION EVIDENCE:
38 0.00 0.00 0.00 X_122777202_122777495_INS 5 39 255 + (T)n Simple_repeat 1 35 0
38 0.00 0.00 0.00 X_122777202_122777495_INS 5 39 (255) (T)n#Simple_repeat 1 35 (0) c_b2s251i126
X_122777202_1 5 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
2329 1.58 0.00 0.00 X_122777202_122777495_INS 40 292 2 C AluY SINE/Alu 29 281 30
2329 1.58 0.00 0.00 X_122777202_122777495_INS 40 292 (2) C AluY#SINE/Alu (30) 281 29 c_b2s352i44
X_122777202_1 40 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 89
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_122777202_1 90 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 139
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_122777202_1 140 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 189
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_122777202_1 190 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 239
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_122777202_1 240 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 289
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_122777202_1 290 GGA 292
C AluY#SINE/Alu 31 GGA 29
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.60
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 252), avg. gap size = 0.0 (0 / 0)
+ 2725 2.3 0.0 0.0 X_122872712_122873027_INS 18 316 (0) + AluY SINE/Alu 2 300 (11) 164
ANNOTATION EVIDENCE:
2725 2.34 0.00 0.00 X_122872712_122873027_INS 18 316 0 + AluY SINE/Alu 2 300 11
2725 2.34 0.00 0.00 X_122872712_122873027_INS 18 316 (0) AluY#SINE/Alu 2 300 (11) c_b2s352i45
X_122872712_1 18 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 67
AluY#SINE/Alu 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
X_122872712_1 68 GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGT 117
i v
AluY#SINE/Alu 52 GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGT 101
X_122872712_1 118 GAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCG 167
i
AluY#SINE/Alu 102 GAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCG 151
X_122872712_1 168 GGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTG 217
i i
AluY#SINE/Alu 152 GGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTG 201
X_122872712_1 218 AACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCGCTGCACTCC 267
v i
AluY#SINE/Alu 202 AACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC 251
X_122872712_1 268 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 252 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.76
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 2796 1.9 0.0 0.0 X_122881173_122881493_INS 15 321 (0) + AluY SINE/Alu 1 307 (4) 165
ANNOTATION EVIDENCE:
2796 1.95 0.00 0.00 X_122881173_122881493_INS 15 321 0 + AluY SINE/Alu 1 307 4
2796 1.95 0.00 0.00 X_122881173_122881493_INS 15 321 (0) AluY#SINE/Alu 1 307 (4) c_b2s352i46
X_122881173_1 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_122881173_1 65 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 114
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_122881173_1 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_122881173_1 165 GGGCGCCTGTGGTCCGAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 214
i v
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_122881173_1 215 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 264
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_122881173_1 265 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAATAAAATA 314
v v
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_122881173_1 315 AAATAAA 321
v
AluY#SINE/Alu 301 AAAAAAA 307
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.98
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 306), avg. gap size = 0.0 (0 / 0)
+ 66 0.0 3.0 0.0 X_122923934_122923999_INS 1 66 (0) + (GAAA)n Simple_repeat 1 68 (0) 166
ANNOTATION EVIDENCE:
66 0.00 3.03 0.00 X_122923934_122923999_INS 1 66 0 + (GAAA)n Simple_repeat 1 68 0
66 0.00 3.03 0.00 X_122923934_122923999_INS 1 66 (0) (GAAA)n#Simple_repeat 1 68 (0) c_b2s251i125
X_122923934_1 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AA-AAAGA 48
- -
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
X_122923934_1 49 AAGAAAGAAAGAAAGAAA 66
(GAAA)n#Simpl 51 AAGAAAGAAAGAAAGAAA 68
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2)
+ 95 0.0 3.2 0.0 X_123055702_123055798_INS 4 97 (0) + (TTTAT)n Simple_repeat 1 97 (0) 167
ANNOTATION EVIDENCE:
95 0.00 3.19 0.00 X_123055702_123055798_INS 4 97 0 + (TTTAT)n Simple_repeat 1 97 0
95 0.00 3.19 0.00 X_123055702_123055798_INS 4 97 (0) (TTTAT)n#Simple_repeat 1 97 (0) c_b2s251i124
X_123055702_1 4 TTTA-TTTATTTTATTTTATTTTATTTTATTTTA--TTATTTTATTTTAT 50
- --
(TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT 50
X_123055702_1 51 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 97
(TTTAT)n#Simp 51 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 97
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.50 (3 / 2)
+ 388 3.6 5.5 0.0 X_123243910_123243967_INS 1 55 (3) C L1P1 LINE/L1 (5676) 479 422 168
ANNOTATION EVIDENCE:
388 3.64 5.45 0.00 X_123243910_123243967_INS 1 55 3 C L1P1_5end LINE/L1 422 479 1780
388 3.64 5.45 0.00 X_123243910_123243967_INS 1 55 (3) C L1P1_5end#LINE/L1 (1780) 479 422 m_b2s551i9
X_123243910_1 1 TCTGTTTACCTACTCAAG---GGGCAATGGCGGGCACCCCTCCCCCAGCC 47
i ? --- i
C L1P1_5end#LIN 479 TTTGTTTACCTANTCAAGCCTGGGCAATGGCGGGCGCCCCTCCCCCAGCC 430
X_123243910_1 48 TCGCTGCC 55
C L1P1_5end#LIN 429 TCGCTGCC 422
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.08
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 3.00 (3 / 1)
+ 38 0.0 3.8 1.9 X_123268171_123268223_INS 1 53 (0) + (GAAA)n Simple_repeat 1 54 (0) 169
ANNOTATION EVIDENCE:
38 0.00 3.77 1.85 X_123268171_123268223_INS 1 53 0 + (GAAA)n Simple_repeat 1 54 0
38 0.00 3.77 1.85 X_123268171_123268223_INS 1 53 (0) (GAAA)n#Simple_repeat 1 54 (0) m_b2s252i67
X_123268171_1 1 GAAAGAAAGAAAGAAAG-AA-AAAGAAAGAAAGAAAGGAAAGAAAGAAAG 48
- - -
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA-GAAAGAAAGAAAG 49
X_123268171_1 49 AAAGA 53
(GAAA)n#Simpl 50 AAAGA 54
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3)
+ 19 14.8 0.0 2.5 X_123311506_123311569_INS 24 64 (0) + (CCTCCT)n Simple_repeat 1 40 (0) 170
ANNOTATION EVIDENCE:
19 14.75 0.00 2.50 X_123311506_123311569_INS 24 64 0 + (CCTCCT)n Simple_repeat 1 40 0
19 14.75 0.00 2.50 X_123311506_123311569_INS 24 64 (0) (CCTCCT)n#Simple_repeat 1 40 (0) m_b2s252i66
X_123311506_1 24 CCTCCTTCTCTTTCTCCTCCTCTTCCTCCTCTTCCTCTCTC 64
i i i i i -
(CCTCCT)n#Sim 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTC 40
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1)
+ 47 0.0 0.0 0.0 X_123360415_123360469_INS 1 43 (12) + (TTTCC)n Simple_repeat 1 43 (0) 171
ANNOTATION EVIDENCE:
47 0.00 0.00 0.00 X_123360415_123360469_INS 1 43 12 + (TTTCC)n Simple_repeat 1 43 0
47 0.00 0.00 0.00 X_123360415_123360469_INS 1 43 (12) (TTTCC)n#Simple_repeat 1 43 (0) c_b2s251i123
X_123360415_1 1 TTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTT 43
(TTTCC)n#Simp 1 TTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTT 43
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 2532 2.1 0.0 0.3 X_123928186_123928513_INS 17 328 (0) C AluY SINE/Alu (0) 311 4 172
ANNOTATION EVIDENCE:
34 0.00 0.00 0.00 X_123928186_123928513_INS 17 48 280 + (T)n Simple_repeat 1 32 0
34 0.00 0.00 0.00 X_123928186_123928513_INS 17 48 (280) (T)n#Simple_repeat 1 32 (0) c_b2s251i122
X_123928186_1 17 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
(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)
2532 2.12 0.00 0.35 X_123928186_123928513_INS 49 328 0 C AluY SINE/Alu 4 282 29
2532 2.12 0.00 0.35 X_123928186_123928513_INS 49 328 (0) C AluY#SINE/Alu (29) 282 4 c_b2s352i47
X_123928186_1 49 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 98
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_123928186_1 99 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 148
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_123928186_1 149 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 198
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_123928186_1 199 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 248
- v i
C AluY#SINE/Alu 132 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 84
X_123928186_1 249 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 298
C AluY#SINE/Alu 83 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 34
X_123928186_1 299 GGGATTACAGGCGTGAGCCACCGCGCCCGG 328
C AluY#SINE/Alu 33 GGGATTACAGGCGTGAGCCACCGCGCCCGG 4
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.83
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (1 / 279), avg. gap size = 1.00 (1 / 1)
+ 77 0.0 0.0 2.7 X_12400649_12400731_INS 7 83 (0) + (AGCAT)n Simple_repeat 1 75 (0) 173
ANNOTATION EVIDENCE:
77 0.00 0.00 2.67 X_12400649_12400731_INS 7 83 0 + (AGCAT)n Simple_repeat 1 75 0
77 0.00 0.00 2.67 X_12400649_12400731_INS 7 83 (0) (AGCAT)n#Simple_repeat 1 75 (0) c_b1s251i168
X_12400649_12 7 AGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCAT 56
(AGCAT)n#Simp 1 AGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCAT 50
X_12400649_12 57 AGCATAGCATAGCATAGAGCATAGCAT 83
--
(AGCAT)n#Simp 51 AGCATAGCATAGCAT--AGCATAGCAT 75
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2)
+ 37 2.6 0.0 0.0 X_124173666_124173769_INS 5 43 (61) + (T)n Simple_repeat 1 39 (0) 174
ANNOTATION EVIDENCE:
37 2.63 0.00 0.00 X_124173666_124173769_INS 5 43 61 + (T)n Simple_repeat 1 39 0
37 2.63 0.00 0.00 X_124173666_124173769_INS 5 43 (61) (T)n#Simple_repeat 1 39 (0) c_b2s251i121
X_124173666_1 5 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 878 14.4 0.7 0.0 X_124313925_124314070_INS 1 146 (0) C AluSx SINE/Alu (29) 283 137 175
ANNOTATION EVIDENCE:
878 14.38 0.68 0.00 X_124313925_124314070_INS 1 146 0 C AluSx SINE/Alu 137 283 29
878 14.38 0.68 0.00 X_124313925_124314070_INS 1 146 (0) C AluSx#SINE/Alu (29) 283 137 m_b2s357i5
X_124313925_1 1 TGAGATGGAGTCCTGCTCGGTCTCCCTGGCTGGAGTGCAGTGGTGCAATC 50
i ii v v v i i
C AluSx#SINE/Al 283 TGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATC 234
X_124313925_1 51 TTGGCTCACTGCAACCTCCGCCTCCTGCCTCCCAG-GTTTCTCCTGCCTC 99
i i vv i v - v
C AluSx#SINE/Al 233 TCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTC 184
X_124313925_1 100 AGCCTCCTGAGTAGCTGTGATTACAGGTGCACACCACCACGCCTGGC 146
i v i i i i
C AluSx#SINE/Al 183 AGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGC 137
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.02
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 1.00 (1 / 1)
+ 358 2.2 2.2 0.0 X_124390094_124390144_INS 1 46 (5) + LTR12C LTR/ERV1 796 842 (737) 176
ANNOTATION EVIDENCE:
358 2.17 2.17 0.00 X_124390094_124390144_INS 1 46 5 + LTR12C LTR/ERV1 796 842 737
358 2.17 2.17 0.00 X_124390094_124390144_INS 1 46 (5) LTR12C#LTR/ERV1 796 842 (737) m_b2s502i3
X_124390094_1 1 ACTCTGT-ATCTAGCTACTCTGGTGGGGCCTTGGAGAACCTTTGTGT 46
- ? i
LTR12C#LTR/ER 796 ACTCTGTNATCTAGCTACTCTGGTGGGGNCTTGGAGAACCTTTATGT 842
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.27
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1)
+ 69 4.3 0.0 0.0 X_124485120_124485192_INS 1 72 (1) + (GA)n Simple_repeat 1 72 (0) 177
ANNOTATION EVIDENCE:
69 4.30 0.00 0.00 X_124485120_124485192_INS 1 72 1 + (GA)n Simple_repeat 1 72 0
69 4.30 0.00 0.00 X_124485120_124485192_INS 1 72 (1) (GA)n#Simple_repeat 1 72 (0) c_b2s251i120
X_124485120_1 1 GAGAGAGAGAGAGAGAGAGAGACAGAGAGAGAGAGAGACAGAGAGAGAGA 50
v v
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50
X_124485120_1 51 GACAGAGAGAGAGAGAGAGAGA 72
v
(GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGA 72
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 46 14.2 0.0 0.0 X_12497542_12497621_INS 4 76 (4) + (AT)n Simple_repeat 1 73 (0) 178
ANNOTATION EVIDENCE:
46 14.16 0.00 0.00 X_12497542_12497621_INS 4 76 4 + (AT)n Simple_repeat 1 73 0
46 14.16 0.00 0.00 X_12497542_12497621_INS 4 76 (4) (AT)n#Simple_repeat 1 73 (0) m_b1s252i125
X_12497542_12 4 ATATATATACATATATACGTATATATATATATACACATATATATACATAT 53
i ii i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_12497542_12 54 ATACACATATATATACATATATA 76
i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATA 73
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0)
+ 2589 3.1 0.0 0.0 X_125159693_125160021_INS 9 329 (0) C AluY SINE/Alu (0) 311 2 179
ANNOTATION EVIDENCE:
38 2.56 0.00 0.00 X_125159693_125160021_INS 9 48 281 + (T)n Simple_repeat 1 40 0
38 2.56 0.00 0.00 X_125159693_125160021_INS 9 48 (281) (T)n#Simple_repeat 1 40 (0) c_b2s251i119
X_125159693_1 9 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2589 3.10 0.00 0.00 X_125159693_125160021_INS 49 329 0 C AluY SINE/Alu 2 282 29
2589 3.10 0.00 0.00 X_125159693_125160021_INS 49 329 (0) C AluY#SINE/Alu (29) 282 2 c_b2s352i48
X_125159693_1 49 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 98
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_125159693_1 99 CAGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 148
i
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_125159693_1 149 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 198
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_125159693_1 199 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 248
v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_125159693_1 249 CTCGATCTCCTGACCTCATGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 298
i
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_125159693_1 299 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 329
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.22
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 67 3.2 7.4 0.0 X_125169824_125169922_INS 2 96 (3) + (TA)n Simple_repeat 1 102 (0) 180
ANNOTATION EVIDENCE:
67 3.24 7.37 0.00 X_125169824_125169922_INS 2 96 3 + (TA)n Simple_repeat 1 102 0
67 3.24 7.37 0.00 X_125169824_125169922_INS 2 96 (3) (TA)n#Simple_repeat 1 102 (0) c_b2s251i118
X_125169824_1 2 TATATATATAT-TTTATATATAT-TATATATATAT-TATATATATAT-TT 47
- v - - - v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_125169824_1 48 TATATATATA-ATATATATATATAT-TATATATATAT-TTTATATATATA 94
- - - v
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_125169824_1 95 TA 96
(TA)n#Simple_ 101 TA 102
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.07 (7 / 94), avg. gap size = 1.00 (7 / 7)
+ 42 2.0 4.0 0.0 X_125471754_125471804_INS 2 51 (0) + (GATA)n Simple_repeat 1 52 (0) 181
ANNOTATION EVIDENCE:
42 2.03 4.00 0.00 X_125471754_125471804_INS 2 51 0 + (GATA)n Simple_repeat 1 52 0
42 2.03 4.00 0.00 X_125471754_125471804_INS 2 51 (0) (GATA)n#Simple_repeat 1 52 (0) c_b2s251i117
X_125471754_1 2 GATAGATAGATAGATAGATAGATAGATAGATAG--AGATAGATATATAGA 49
-- v
(GATA)n#Simpl 1 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 50
X_125471754_1 50 TA 51
(GATA)n#Simpl 51 TA 52
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.02 (1 / 49), avg. gap size = 2.00 (2 / 1)
+ 2404 1.8 0.7 2.5 X_125560556_125560889_INS 16 334 (0) C AluY SINE/Alu (0) 311 1 182
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_125560556_125560889_INS 16 48 286 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_125560556_125560889_INS 16 48 (286) (T)n#Simple_repeat 1 33 (0) c_b2s251i116
X_125560556_1 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
(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)
2404 1.79 0.70 2.49 X_125560556_125560889_INS 49 334 0 C AluY SINE/Alu 1 281 30
2404 1.79 0.70 2.49 X_125560556_125560889_INS 49 334 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i49
X_125560556_1 49 GAGACGGAGTCTCGCT--GTCGCCCAGGCTGGAGTGCAGTGGCGCAATCT 96
-- i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_125560556_1 97 CGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTC 146
i i i -
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGG-TTCACGCCATTCTCCTGCCTC 183
X_125560556_1 147 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAA 196
v
C AluY#SINE/Alu 182 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAA 133
X_125560556_1 197 TTTTTTGTATTTTTTTTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 246
------
C AluY#SINE/Alu 132 TTTTTTGTATTTTT------AGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_125560556_1 247 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 296
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_125560556_1 297 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 334
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.16
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.03 (8 / 285), avg. gap size = 1.12 (9 / 8)
+ 2827 1.6 0.0 0.0 X_125735147_125735465_INS 15 319 (0) + AluY SINE/Alu 1 305 (6) 183
ANNOTATION EVIDENCE:
2827 1.64 0.00 0.00 X_125735147_125735465_INS 15 319 0 + AluY SINE/Alu 1 305 6
2827 1.64 0.00 0.00 X_125735147_125735465_INS 15 319 (0) AluY#SINE/Alu 1 305 (6) c_b2s352i50
X_125735147_1 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_125735147_1 65 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAAAACGG 114
v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_125735147_1 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_125735147_1 165 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 214
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_125735147_1 215 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCACTC 264
i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_125735147_1 265 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAACAAAAAAAAAAAAAAAA 314
v
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_125735147_1 315 AAAAA 319
AluY#SINE/Alu 301 AAAAA 305
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.06
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 304), avg. gap size = 0.0 (0 / 0)
+ 38 6.3 2.0 0.0 X_125865683_125865764_INS 30 79 (3) + (TA)n Simple_repeat 1 51 (0) 184
ANNOTATION EVIDENCE:
38 6.29 2.00 0.00 X_125865683_125865764_INS 30 79 3 + (TA)n Simple_repeat 1 51 0
38 6.29 2.00 0.00 X_125865683_125865764_INS 30 79 (3) (TA)n#Simple_repeat 1 51 (0) c_b2s251i115
X_125865683_1 30 TATATTTATATATATATATAT-TATATATATATATATATAAATATAAATA 78
v - v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_125865683_1 79 T 79
(TA)n#Simple_ 51 T 51
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1)
+ 31 15.4 0.0 0.0 X_125874082_125874136_INS 1 52 (3) + (TA)n Simple_repeat 1 52 (0) 185
ANNOTATION EVIDENCE:
31 15.36 0.00 0.00 X_125874082_125874136_INS 1 52 3 + (TA)n Simple_repeat 1 52 0
31 15.36 0.00 0.00 X_125874082_125874136_INS 1 52 (3) (TA)n#Simple_repeat 1 52 (0) m_b2s252i65
X_125874082_1 1 TATATATATACACATATATATAAACATATATATATATACACACATATATA 50
i i v i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_125874082_1 51 TA 52
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 73 11.2 6.3 1.8 X_125913508_125913667_INS 1 159 (1) + (TATATAA)n Simple_repeat 1 166 (0) 186
ANNOTATION EVIDENCE:
73 11.23 6.29 1.81 X_125913508_125913667_INS 1 159 1 + (TATATAA)n Simple_repeat 1 166 0
73 11.23 6.29 1.81 X_125913508_125913667_INS 1 159 (1) (TATATAA)n#Simple_repeat 1 166 (0) m_b2s252i63
X_125913508_1 1 TATATATAATATAGTATATACTATATTATATAT-A-ATATAGTATATACT 48
vv i v v - - i v
(TATATAA)n#Si 1 TATATAATATATAATATATAATATATAATATATAATATATAATATATAAT 50
X_125913508_1 49 ATATTATATAT-A-ATATAGTATATACTATATTATATAT-A-ATATAATA 94
v - - i v v - -
(TATATAA)n#Si 51 ATATAATATATAATATATAATATATAATATATAATATATAATATATAATA 100
X_125913508_1 95 TATACTCATATTATATAT-A-ATATAACATATACTCATATGATATAT-A- 140
v - v - - i v - i - -
(TATATAA)n#Si 101 TATAAT-ATATAATATATAATATATAATATATAAT-ATATAATATATAAT 148
X_125913508_1 141 ATATAATATATACATATAT 159
-
(TATATAA)n#Si 149 ATATAATATATA-ATATAT 166
Matrix = Unknown
Transitions / transversions = 0.45 (5/11)
Gap_init rate = 0.08 (13 / 158), avg. gap size = 1.00 (13 / 13)
+ 58 0.0 0.0 1.8 X_125922752_125922808_INS 1 57 (0) + (TTTC)n Simple_repeat 1 56 (0) 187
ANNOTATION EVIDENCE:
58 0.00 0.00 1.79 X_125922752_125922808_INS 1 57 0 + (TTTC)n Simple_repeat 1 56 0
58 0.00 0.00 1.79 X_125922752_125922808_INS 1 57 (0) (TTTC)n#Simple_repeat 1 56 (0) c_b2s251i114
X_125922752_1 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCT 50
-
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT-CT 49
X_125922752_1 51 TTCTTTC 57
(TTTC)n#Simpl 50 TTCTTTC 56
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1)
+ 2706 2.0 0.0 0.0 X_125960607_125960919_INS 18 313 (0) + AluY SINE/Alu 1 296 (15) 188
ANNOTATION EVIDENCE:
2706 2.03 0.00 0.00 X_125960607_125960919_INS 18 313 0 + AluY SINE/Alu 1 296 15
2706 2.03 0.00 0.00 X_125960607_125960919_INS 18 313 (0) AluY#SINE/Alu 1 296 (15) c_b2s352i51
X_125960607_1 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_125960607_1 68 GGCGGGCGGATCACGAGGTCAGGAGATCGAGGCCATCCCGGCTAAAACGG 117
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_125960607_1 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_125960607_1 168 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 217
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_125960607_1 218 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 267
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_125960607_1 268 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 313
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 296
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.74
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 295), avg. gap size = 0.0 (0 / 0)
+ 2077 0.8 9.5 0.0 X_126290676_126290958_INS 17 283 (0) C AluY SINE/Alu (0) 311 22 189
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_126290676_126290958_INS 17 45 238 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_126290676_126290958_INS 17 45 (238) (T)n#Simple_repeat 1 29 (0) c_b2s251i113
X_126290676_1 17 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(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)
2077 0.83 9.50 0.00 X_126290676_126290958_INS 46 283 0 C AluY SINE/Alu 22 282 29
2077 0.83 9.50 0.00 X_126290676_126290958_INS 46 283 (0) C AluY#SINE/Alu (29) 282 22 c_b2s352i52
X_126290676_1 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 95
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_126290676_1 96 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 145
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_126290676_1 146 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 195
i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_126290676_1 196 TTTTTGTATTTTTAGTAGAGACGG-----------------------GGT 222
-----------------------
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_126290676_1 223 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 272
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_126290676_1 273 GGATTACAGGC 283
C AluY#SINE/Alu 32 GGATTACAGGC 22
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.84
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (1 / 237), avg. gap size = 23.00 (23 / 1)
+ 42 30.7 0.0 0.0 X_126311092_126311206_INS 2 110 (5) + (TA)n Simple_repeat 1 109 (0) 190
ANNOTATION EVIDENCE:
42 30.69 0.00 0.00 X_126311092_126311206_INS 2 110 5 + (TA)n Simple_repeat 1 109 0
42 30.69 0.00 0.00 X_126311092_126311206_INS 2 110 (5) (TA)n#Simple_repeat 1 109 (0) m_b2s252i62
X_126311092_1 2 TATATATACACGTATATACACATATATATGTATATATACACGTATATATA 51
i ii i i i i ii
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_126311092_1 52 CACACGTGTATATATACGTATATATACACGTGTGTATATATACGTGTATA 101
i i ii i ii i ii i i ii i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_126311092_1 102 TATACATAT 110
i
(TA)n#Simple_ 101 TATATATAT 109
Matrix = Unknown
Transitions / transversions = 1.00 (25/0)
Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0)
+ 2393 2.9 0.0 2.5 X_12643113_12643406_INS 12 294 (0) + AluY SINE/Alu 30 305 (6) 191
ANNOTATION EVIDENCE:
2393 2.90 0.00 2.54 X_12643113_12643406_INS 12 294 0 + AluY SINE/Alu 30 305 6
2393 2.90 0.00 2.54 X_12643113_12643406_INS 12 294 (0) AluY#SINE/Alu 30 305 (6) c_b1s352i5
X_12643113_12 12 CCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCG 61
i i
AluY#SINE/Alu 30 CCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCG 79
X_12643113_12 62 AGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAA 111
v
AluY#SINE/Alu 80 AGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAA 129
X_12643113_12 112 AAATTAGCCGGGCGCGGTGGCAGGCGCCTGTAGTCCCAGCTACTCGGGAG 161
i i
AluY#SINE/Alu 130 AAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAG 179
X_12643113_12 162 GCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGC 211
i
AluY#SINE/Alu 180 GCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGC 229
X_12643113_12 212 CGAGATTGCGCCACTGCAGTCCGCAGTCCGGCCTGGGCGACAGAGCGAGA 261
i -- ----- i
AluY#SINE/Alu 230 CGAGATCGCGCCACTGCA--C-----TCCAGCCTGGGCGACAGAGCGAGA 272
X_12643113_12 262 CTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAA 294
AluY#SINE/Alu 273 CTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAA 305
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.62
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.02 (7 / 282), avg. gap size = 1.00 (7 / 7)
+ 2751 2.2 0.0 2.6 X_126583421_126583751_INS 13 331 (0) + AluY SINE/Alu 1 311 (0) 192
ANNOTATION EVIDENCE:
2751 2.25 0.00 2.57 X_126583421_126583751_INS 13 331 0 + AluY SINE/Alu 1 311 0
2751 2.25 0.00 2.57 X_126583421_126583751_INS 13 331 (0) AluY#SINE/Alu 1 311 (0) c_b2s352i53
X_126583421_1 13 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGA 62
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_126583421_1 63 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 112
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_126583421_1 113 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAAAAAATTAGCCGGGC 162
--------
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA--------AATTAGCCGGGC 142
X_126583421_1 163 GTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAG 212
i i
AluY#SINE/Alu 143 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAG 192
X_126583421_1 213 AATGGCGTGAACCCGGGAGGCGGAGCATGCAGTGAGCCGAGATTGCGCCA 262
v i
AluY#SINE/Alu 193 AATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCA 242
X_126583421_1 263 CTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 312
AluY#SINE/Alu 243 CTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
X_126583421_1 313 AAAAAAAAAAAAAAAAAAA 331
AluY#SINE/Alu 293 AAAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (8 / 318), avg. gap size = 1.00 (8 / 8)
+ 2851 0.7 0.0 1.3 X_126662653_126662986_INS 18 329 (5) + AluY SINE/Alu 1 308 (3) 193
ANNOTATION EVIDENCE:
2851 0.65 0.00 1.30 X_126662653_126662986_INS 18 329 5 + AluY SINE/Alu 1 308 3
2851 0.65 0.00 1.30 X_126662653_126662986_INS 18 329 (5) AluY#SINE/Alu 1 308 (3) c_b2s352i54
X_126662653_1 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_126662653_1 68 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 117
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_126662653_1 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAATTAGCCGGGCGTGG 167
----
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA----AATTAGCCGGGCGTGG 146
X_126662653_1 168 TAGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATG 217
i
AluY#SINE/Alu 147 TGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATG 196
X_126662653_1 218 GCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGC 267
AluY#SINE/Alu 197 GCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGC 246
X_126662653_1 268 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 247 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 296
X_126662653_1 318 AAAAATAAAAAA 329
v
AluY#SINE/Alu 297 AAAAAAAAAAAA 308
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.65
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.01 (4 / 311), avg. gap size = 1.00 (4 / 4)
+ 16 21.0 5.3 1.7 X_126665600_126665670_INS 1 57 (14) + (GTAT)n Simple_repeat 1 59 (0) 194
ANNOTATION EVIDENCE:
16 21.04 5.26 1.69 X_126665600_126665670_INS 1 57 14 + (GTAT)n Simple_repeat 1 59 0
16 21.04 5.26 1.69 X_126665600_126665670_INS 1 57 (14) (GTAT)n#Simple_repeat 1 59 (0) m_b2s252i61
X_126665600_1 1 GTATGTAAATATGTAT-TATATAGTCCATGTAT-AATATATGTAAATATG 48
vi - i - vi -v i vi
(GTAT)n#Simpl 1 GTATGTATGTATGTATGTATGTA-TGTATGTATGTATGTATGTATGTATG 49
X_126665600_1 49 TAT-TATATA 57
- i
(GTAT)n#Simpl 50 TATGTATGTA 59
Matrix = Unknown
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4)
+ 47 5.9 0.0 0.0 X_126849274_126849328_INS 1 54 (1) + (AT)n Simple_repeat 1 54 (0) 195
ANNOTATION EVIDENCE:
47 5.89 0.00 0.00 X_126849274_126849328_INS 1 54 1 + (AT)n Simple_repeat 1 54 0
47 5.89 0.00 0.00 X_126849274_126849328_INS 1 54 (1) (AT)n#Simple_repeat 1 54 (0) c_b2s251i112
X_126849274_1 1 ATATATACATATATATATATATGTATATATATATATATACATATATATAT 50
i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_126849274_1 51 ATAT 54
(AT)n#Simple_ 51 ATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 27 21.2 0.0 0.0 X_126883471_126883523_INS 1 52 (1) + (TA)n Simple_repeat 1 52 (0) 196
ANNOTATION EVIDENCE:
27 21.24 0.00 0.00 X_126883471_126883523_INS 1 52 1 + (TA)n Simple_repeat 1 52 0
27 21.24 0.00 0.00 X_126883471_126883523_INS 1 52 (1) (TA)n#Simple_repeat 1 52 (0) m_b2s252i60
X_126883471_1 1 TACATATACACATATATACGTATATATATACACATATATACGTATATATA 50
i i i ii i i ii
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_126883471_1 51 TA 52
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2575 3.4 0.0 2.3 X_126928088_126928400_INS 8 313 (0) C AluY SINE/Alu (11) 300 2 197
ANNOTATION EVIDENCE:
2575 3.35 0.00 2.34 X_126928088_126928400_INS 8 313 0 C AluY SINE/Alu 2 300 11
2575 3.35 0.00 2.34 X_126928088_126928400_INS 8 313 (0) C AluY#SINE/Alu (11) 300 2 c_b2s352i55
X_126928088_1 8 TTTCTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCCG 57
i i i
C AluY#SINE/Alu 300 TTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTG 251
X_126928088_1 58 GACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCC 107
----- -- i i
C AluY#SINE/Alu 250 GA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCC 208
X_126928088_1 108 CGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCCAGTAGCTGGGACTACA 157
v
C AluY#SINE/Alu 207 CGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACA 158
X_126928088_1 158 GGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGG 207
i
C AluY#SINE/Alu 157 GGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGG 108
X_126928088_1 208 GGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCC 257
i
C AluY#SINE/Alu 107 GGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCC 58
X_126928088_1 258 ACCCGCCTCGGCCTCCCAAAGTGCTGGGACTACAGGCGTGAGCCACCGCG 307
i i
C AluY#SINE/Alu 57 GCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCG 8
X_126928088_1 308 CCCGGC 313
C AluY#SINE/Alu 7 CCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.18
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.02 (7 / 305), avg. gap size = 1.00 (7 / 7)
+ 409 4.1 0.0 0.0 X_127132172_127132225_INS 4 52 (2) + L1M1 LINE/L1 5533 5581 (724) 198
ANNOTATION EVIDENCE:
409 4.08 0.00 0.00 X_127132172_127132225_INS 4 52 2 + L1MA3_3end LINE/L1 280 328 724
409 4.08 0.00 0.00 X_127132172_127132225_INS 4 52 (2) L1MA3_3end#LINE/L1 280 328 (724) m_b2s551i10
X_127132172_1 4 CACTGTTGGTGGGAATGTAATTTAGTACAACTACTATGGAGAACAGTTT 52
v i
L1MA3_3end#LI 280 CACTGTTGGTGGGAATGTAAATTAGTACAACCACTATGGAGAACAGTTT 328
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.20
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 2422 2.2 0.0 1.1 X_127169765_127170048_INS 8 284 (0) + AluY SINE/Alu 32 305 (6) 199
ANNOTATION EVIDENCE:
2422 2.19 0.00 1.09 X_127169765_127170048_INS 8 284 0 + AluY SINE/Alu 32 305 6
2422 2.19 0.00 1.09 X_127169765_127170048_INS 8 284 (0) AluY#SINE/Alu 32 305 (6) c_b2s352i56
X_127169765_1 8 CAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAG 57
AluY#SINE/Alu 32 CAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAG 81
X_127169765_1 58 ACCATCCCGGCTAAAAAATGGTGAAACCCCGTCTCTACTAAAAATACAAA 107
i v --i
AluY#SINE/Alu 82 ACCATCCTGGCTAACA--CGGTGAAACCCCGTCTCTACTAAAAATACAAA 129
X_127169765_1 108 AAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGA 157
- i i
AluY#SINE/Alu 130 A-AATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGA 178
X_127169765_1 158 GGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAG 207
AluY#SINE/Alu 179 GGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAG 228
X_127169765_1 208 CCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT 257
v
AluY#SINE/Alu 229 CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT 278
X_127169765_1 258 CTCAAAAAAAAAAAAAAAAAAAAAAAA 284
AluY#SINE/Alu 279 CTCAAAAAAAAAAAAAAAAAAAAAAAA 305
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.01 (3 / 276), avg. gap size = 1.00 (3 / 3)
+ 2807 1.3 0.0 0.0 X_127356137_127356451_INS 3 304 (11) + AluY SINE/Alu 1 302 (9) 200
ANNOTATION EVIDENCE:
2807 1.32 0.00 0.00 X_127356137_127356451_INS 3 304 11 + AluY SINE/Alu 1 302 9
2807 1.32 0.00 0.00 X_127356137_127356451_INS 3 304 (11) AluY#SINE/Alu 1 302 (9) c_b2s352i57
X_127356137_1 3 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 52
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_127356137_1 53 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATTCTGGCTAACACGG 102
i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_127356137_1 103 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 152
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_127356137_1 153 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGGAGGGCGT 202
i v
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_127356137_1 203 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 252
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_127356137_1 253 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 302
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_127356137_1 303 AA 304
AluY#SINE/Alu 301 AA 302
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 301), avg. gap size = 0.0 (0 / 0)
+ 385 12.5 0.0 0.0 X_127584713_127584768_INS 1 56 (0) C THE1C LTR/ERVL-MaLR (318) 57 2 201
ANNOTATION EVIDENCE:
385 12.50 0.00 0.00 X_127584713_127584768_INS 1 56 0 C THE1C LTR/ERVL-MaLR 2 57 318
385 12.50 0.00 0.00 X_127584713_127584768_INS 1 56 (0) C THE1C#LTR/ERVL-MaLR (318) 57 2 m_b2s502i4
X_127584713_1 1 TTATTGGAACTATAATTTAAGAAGAGATTTGGCTGGGGACACAGCCAAAC 50
v i i v v
C THE1C#LTR/ERV 57 TTATGGGAACTACAATTCAAGATGAGATTTGGGTGGGGACACAGCCAAAC 8
X_127584713_1 51 TGTATC 56
ii
C THE1C#LTR/ERV 7 CATATC 2
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.77
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 2801 2.2 0.0 0.0 X_127612672_127613004_INS 10 320 (13) + AluY SINE/Alu 1 311 (0) 202
ANNOTATION EVIDENCE:
2801 2.25 0.00 0.00 X_127612672_127613004_INS 10 320 13 + AluY SINE/Alu 1 311 0
2801 2.25 0.00 0.00 X_127612672_127613004_INS 10 320 (13) AluY#SINE/Alu 1 311 (0) c_b2s352i58
X_127612672_1 10 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 59
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_127612672_1 60 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCAACCCCGCTAAAACGG 109
v iv v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_127612672_1 110 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 159
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_127612672_1 160 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 209
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_127612672_1 210 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 259
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_127612672_1 260 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 309
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_127612672_1 310 AAAAAAAAAAA 320
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.99
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 28 15.9 5.7 0.0 X_127661242_127661317_INS 4 73 (3) + (TATAATA)n Simple_repeat 1 74 (0) 203
ANNOTATION EVIDENCE:
28 15.89 5.71 0.00 X_127661242_127661317_INS 4 73 3 + (TATAATA)n Simple_repeat 1 74 0
28 15.89 5.71 0.00 X_127661242_127661317_INS 4 73 (3) (TATAATA)n#Simple_repeat 1 74 (0) m_b2s252i59
X_127661242_1 4 TATATTATATAATATAGAGTATAT--TATAT-A-ATATAGTCTATATTAT 49
v v i -- - - i v v
(TATAATA)n#Si 1 TATAATATATAATATATAATATATAATATATAATATATAATATATAATAT 50
X_127661242_1 50 ATAATATAGTCTATATTATATATA 73
vvv v
(TATAATA)n#Si 51 ATAATATATAATATATAATATATA 74
Matrix = Unknown
Transitions / transversions = 0.25 (2/8)
Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.33 (4 / 3)
+ 36 29.4 0.0 0.0 X_127685820_127685912_INS 4 93 (0) + (TA)n Simple_repeat 1 90 (0) 204
ANNOTATION EVIDENCE:
36 29.39 0.00 0.00 X_127685820_127685912_INS 4 93 0 + (TA)n Simple_repeat 1 90 0
36 29.39 0.00 0.00 X_127685820_127685912_INS 4 93 (0) (TA)n#Simple_repeat 1 90 (0) m_b2s252i58
X_127685820_1 4 TATATATACACATATATGTGTATATATACATACACATGTGTATATATACA 53
i i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_127685820_1 54 TACACATATGTGTGTATATATATACACATATGTGTGTATA 93
i i i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATA 90
Matrix = Unknown
Transitions / transversions = 1.00 (20/0)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0)
+ 1103 0.8 0.0 0.0 X_127763536_127763673_INS 10 138 (0) C AluY SINE/Alu (4) 307 179 205
ANNOTATION EVIDENCE:
1103 0.78 0.00 0.00 X_127763536_127763673_INS 10 138 0 C AluY SINE/Alu 179 307 4
1103 0.78 0.00 0.00 X_127763536_127763673_INS 10 138 (0) C AluY#SINE/Alu (4) 307 179 m_b2s357i6
X_127763536_1 10 TCTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC 59
i
C AluY#SINE/Alu 307 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC 258
X_127763536_1 60 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCC 109
C AluY#SINE/Alu 257 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCC 208
X_127763536_1 110 CGGGTTCACGCCATTCTCCTGCCTCAGCC 138
C AluY#SINE/Alu 207 CGGGTTCACGCCATTCTCCTGCCTCAGCC 179
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 0.78
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 128), avg. gap size = 0.0 (0 / 0)
+ 54 6.6 0.0 0.0 X_127850131_127850195_INS 1 64 (1) + (TA)n Simple_repeat 1 64 (0) 206
ANNOTATION EVIDENCE:
54 6.57 0.00 0.00 X_127850131_127850195_INS 1 64 1 + (TA)n Simple_repeat 1 64 0
54 6.57 0.00 0.00 X_127850131_127850195_INS 1 64 (1) (TA)n#Simple_repeat 1 64 (0) c_b2s251i111
X_127850131_1 1 TATATATATATCTATATATATATATATAGATATATAGATATATATATATA 50
v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_127850131_1 51 TATATAGATATATA 64
v
(TA)n#Simple_ 51 TATATATATATATA 64
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 89 5.4 0.0 0.0 X_12785888_12785990_INS 2 99 (4) + (AT)n Simple_repeat 1 98 (0) 207
ANNOTATION EVIDENCE:
89 5.38 0.00 0.00 X_12785888_12785990_INS 2 99 4 + (AT)n Simple_repeat 1 98 0
89 5.38 0.00 0.00 X_12785888_12785990_INS 2 99 (4) (AT)n#Simple_repeat 1 98 (0) c_b1s251i167
X_12785888_12 2 ATATATATATATATATATATATATATATATATACATATATATATATATAC 51
i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_12785888_12 52 ATATATATGTATATATATATATACATATATATATATATACATATATAT 99
i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATAT 98
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0)
+ 33 2.2 0.0 8.0 X_12789708_12789766_INS 1 54 (5) + (TGCACAGCGG)n Simple_repeat 1 50 (0) 208
ANNOTATION EVIDENCE:
33 2.21 0.00 8.00 X_12789708_12789766_INS 1 54 5 + (TGCACAGCGG)n Simple_repeat 1 50 0
33 2.21 0.00 8.00 X_12789708_12789766_INS 1 54 (5) (TGCACAGCGG)n#Simple_repeat 1 50 (0) c_b1s251i166
X_12789708_12 1 TGCACAGCGGTGCACAGCGGAGGCGGCACAGCGGTGCACAGCGGTGCACA 50
--- -v
(TGCACAGCGG)n 1 TGCACAGCGGTGCACAGC---GG-TGCACAGCGGTGCACAGCGGTGCACA 46
X_12789708_12 51 GCGG 54
(TGCACAGCGG)n 47 GCGG 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4)
+ 19 29.8 0.0 0.0 X_128070922_128070976_INS 1 49 (6) + (AT)n Simple_repeat 1 49 (0) 209
ANNOTATION EVIDENCE:
19 29.80 0.00 0.00 X_128070922_128070976_INS 1 49 6 + (AT)n Simple_repeat 1 49 0
19 29.80 0.00 0.00 X_128070922_128070976_INS 1 49 (6) (AT)n#Simple_repeat 1 49 (0) m_b2s252i57
X_128070922_1 1 ATATGTGTGTATATGTGTGTATATGTGTGTATATATACATGTATATATA 49
i i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 105 41.3 0.0 0.0 X_128071029_128071476_INS 3 226 (222) + (TA)n Simple_repeat 1 224 (0) 210
ANNOTATION EVIDENCE:
105 41.26 0.00 0.00 X_128071029_128071476_INS 3 226 222 + (TA)n Simple_repeat 1 224 165
105 41.26 0.00 0.00 X_128071029_128071476_INS 3 226 (222) (TA)n#Simple_repeat 1 224 (165) m_b2s252i56
X_128071029_1 3 TATATGTGTGTATATATACATGTATATATACGTGTGTATATGTGTGTATA 52
i i i i i ii i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_128071029_1 53 TATGTGTGTATATGTGTGTATATATACACACATATATGTGTGTGTATATG 102
i i i i i i i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_128071029_1 103 TGTGTATATGTGTGTATATATACACACATGTATGTGTGTATATATGTGTG 152
i i i i i i i i i i i i i i i
(TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150
X_128071029_1 153 TGTATGTGTGTATATATACACACATGTATGTGTGTATATATGTGTGTGTA 202
i i i i i i i i i i i i i i i
(TA)n#Simple_ 151 TATATATATATATATATATATATATATATATATATATATATATATATATA 200
X_128071029_1 203 TATGTGTGTATATATACACACATG 226
i i i i i i i
(TA)n#Simple_ 201 TATATATATATATATATATATATA 224
Matrix = Unknown
Transitions / transversions = 1.00 (63/0)
Gap_init rate = 0.00 (0 / 223), avg. gap size = 0.0 (0 / 0)
+ 50 0.0 0.0 3.8 X_128071029_128071476_INS 227 281 (167) + (TATGTGTGTA)n Simple_repeat 1 53 (0) 211
ANNOTATION EVIDENCE:
50 0.00 0.00 3.77 X_128071029_128071476_INS 227 281 167 + (TATGTGTGTA)n Simple_repeat 1 53 0
50 0.00 0.00 3.77 X_128071029_128071476_INS 227 281 (167) (TATGTGTGTA)n#Simple_repeat 1 53 (0) c_b2s251i110
X_128071029_1 227 TATGTGTGTATATGTGTGTGTATATGTGTGTATATGTGTGTATATGTGTG 276
--
(TATGTGTGTA)n 1 TATGTGTGTATA--TGTGTGTATATGTGTGTATATGTGTGTATATGTGTG 48
X_128071029_1 277 TATAT 281
(TATGTGTGTA)n 49 TATAT 53
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2)
+ 105 41.3 0.0 0.0 X_128071029_128071476_INS 282 445 (3) + (TA)n Simple_repeat 1 164 (0) 212
ANNOTATION EVIDENCE:
105 41.26 0.00 0.00 X_128071029_128071476_INS 282 445 3 + (TA)n Simple_repeat 225 388 1
105 41.26 0.00 0.00 X_128071029_128071476_INS 282 445 (3) (TA)n#Simple_repeat 225 388 (1) m_b2s252i56
X_128071029_1 282 ATACACACATATATGTGTGTATATATGTGTGTATATATGTGTGTATATGT 331
i i i i i i i i i i i i i
(TA)n#Simple_ 225 ATATATATATATATATATATATATATATATATATATATATATATATATAT 274
X_128071029_1 332 GTGTGTATATATACACACATATGTGTGTATATATGTGTGTATATGTGTGT 381
i i i i i i i i i i i i i i i
(TA)n#Simple_ 275 ATATATATATATATATATATATATATATATATATATATATATATATATAT 324
X_128071029_1 382 GTATATACACACATATATGTGTATATATGTGCATGTGTATGTGTGTATAT 431
i i i i i i i ii i i i i i
(TA)n#Simple_ 325 ATATATATATATATATATATATATATATATATATATATATATATATATAT 374
X_128071029_1 432 ACACACACATATAT 445
i i i i
(TA)n#Simple_ 375 ATATATATATATAT 388
Matrix = Unknown
Transitions / transversions = 1.00 (46/0)
Gap_init rate = 0.00 (0 / 163), avg. gap size = 0.0 (0 / 0)
+ 17 15.8 10.5 0.0 X_128116154_128116212_INS 3 59 (0) + (CAAG)n Simple_repeat 1 63 (0) 213
ANNOTATION EVIDENCE:
17 15.80 10.53 0.00 X_128116154_128116212_INS 3 59 0 + (CAAG)n Simple_repeat 1 63 0
17 15.80 10.53 0.00 X_128116154_128116212_INS 3 59 (0) (CAAG)n#Simple_repeat 1 63 (0) m_b2s252i55
X_128116154_1 3 CAAGCAAG--AGAAAGCAATAAAGCAAG--AGAAAGCAATCAAGCAAG-- 46
-- v vv -- v v --
(CAAG)n#Simpl 1 CAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCA 50
X_128116154_1 47 AGAAAGAAATCAA 59
v v v
(CAAG)n#Simpl 51 AGCAAGCAAGCAA 63
Matrix = Unknown
Transitions / transversions = 0.00 (0/8)
Gap_init rate = 0.05 (3 / 56), avg. gap size = 2.00 (6 / 3)
+ 63 0.0 0.0 0.0 X_128428280_128428335_INS 1 56 (0) + (GAAA)n Simple_repeat 1 56 (0) 214
ANNOTATION EVIDENCE:
63 0.00 0.00 0.00 X_128428280_128428335_INS 1 56 0 + (GAAA)n Simple_repeat 1 56 0
63 0.00 0.00 0.00 X_128428280_128428335_INS 1 56 (0) (GAAA)n#Simple_repeat 1 56 (0) c_b2s251i109
X_128428280_1 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
X_128428280_1 51 AAGAAA 56
(GAAA)n#Simpl 51 AAGAAA 56
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 41 0.0 2.1 4.3 X_12851154_12851206_INS 2 49 (4) + (AT)n Simple_repeat 1 47 (0) 215
ANNOTATION EVIDENCE:
41 0.00 2.08 4.26 X_12851154_12851206_INS 2 49 4 + (AT)n Simple_repeat 1 47 0
41 0.00 2.08 4.26 X_12851154_12851206_INS 2 49 (4) (AT)n#Simple_repeat 1 47 (0) c_b1s251i165
X_12851154_12 2 ATATATATATATGAGT-TATATATATATATATATATATATATATATATA 49
- - -
(AT)n#Simple_ 1 ATATATATATAT-A-TATATATATATATATATATATATATATATATATA 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3)
+ 2604 3.5 0.0 2.9 X_128980209_128980532_INS 6 324 (0) C AluY SINE/Alu (0) 311 2 216
ANNOTATION EVIDENCE:
2604 3.55 0.00 2.90 X_128980209_128980532_INS 6 324 0 C AluY SINE/Alu 2 311 0
2604 3.55 0.00 2.90 X_128980209_128980532_INS 6 324 (0) C AluY#SINE/Alu (0) 311 2 c_b2s352i59
X_128980209_1 6 TTTTTCCTATTCTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 55
ii v i
C AluY#SINE/Alu 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 262
X_128980209_1 56 CGCCCAGGCCGGATTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAA 105
i ----- -- i
C AluY#SINE/Alu 261 CGCCCAGGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAA 219
X_128980209_1 106 GCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAG 155
i
C AluY#SINE/Alu 218 GCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAG 169
X_128980209_1 156 CTGGGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTTTGTATTT 205
i --
C AluY#SINE/Alu 168 CTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTT--GTATTT 121
X_128980209_1 206 TTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCT 255
v
C AluY#SINE/Alu 120 TTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCT 71
X_128980209_1 256 GACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 305
i i
C AluY#SINE/Alu 70 GACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC 21
X_128980209_1 306 GTGAGCCACCGCGCCCGGC 324
C AluY#SINE/Alu 20 GTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.74
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.03 (9 / 318), avg. gap size = 1.00 (9 / 9)
+ 2682 2.3 0.0 2.3 X_129064802_129065124_INS 13 323 (0) C AluY SINE/Alu (7) 304 1 217
ANNOTATION EVIDENCE:
2682 2.30 0.00 2.30 X_129064802_129065124_INS 13 323 0 C AluY SINE/Alu 1 304 7
2682 2.30 0.00 2.30 X_129064802_129065124_INS 13 323 (0) C AluY#SINE/Alu (7) 304 1 c_b2s352i60
X_129064802_1 13 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 62
C AluY#SINE/Alu 304 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 255
X_129064802_1 63 GCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGC 112
i ----- -- i
C AluY#SINE/Alu 254 GCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGC 212
X_129064802_1 113 TTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 162
i
C AluY#SINE/Alu 211 CTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 162
X_129064802_1 163 TACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAG 212
i
C AluY#SINE/Alu 161 TACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAG 112
X_129064802_1 213 ACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATG 262
v i
C AluY#SINE/Alu 111 ACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTG 62
X_129064802_1 263 ATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 312
i
C AluY#SINE/Alu 61 ATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 12
X_129064802_1 313 CGCGCCCGGCC 323
C AluY#SINE/Alu 11 CGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 310), avg. gap size = 1.00 (7 / 7)
+ 3776 0.5 0.0 0.0 X_12920353_12920789_INS 23 437 (0) C L1HS LINE/L1 (0) 6155 5741 218
ANNOTATION EVIDENCE:
3776 0.48 0.00 0.00 X_12920353_12920789_INS 23 437 0 C L1HS_3end LINE/L1 488 902 0
3776 0.48 0.00 0.00 X_12920353_12920789_INS 23 437 (0) C L1HS_3end#LINE/L1 (0) 902 488 m_b1s551i2
X_12920353_12 23 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 72
C L1HS_3end#LIN 902 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 853
X_12920353_12 73 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 122
C L1HS_3end#LIN 852 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 803
X_12920353_12 123 CTAATGTGTCATCTAGCATTAGGTATATCTCCCTATGCTATCCCTCCCCC 172
i v
C L1HS_3end#LIN 802 CTAACGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 753
X_12920353_12 173 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTG 222
C L1HS_3end#LIN 752 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTG 703
X_12920353_12 223 TCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGT 272
C L1HS_3end#LIN 702 TCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGT 653
X_12920353_12 273 GTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAAT 322
C L1HS_3end#LIN 652 GTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAAT 603
X_12920353_12 323 TTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGC 372
C L1HS_3end#LIN 602 TTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGC 553
X_12920353_12 373 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 422
C L1HS_3end#LIN 552 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 503
X_12920353_12 423 TTGTTGGACATTTGG 437
C L1HS_3end#LIN 502 TTGTTGGACATTTGG 488
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.27
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 414), avg. gap size = 0.0 (0 / 0)
+ 278 10.8 0.0 0.0 X_12942585_12942678_INS 58 94 (0) + LTR36 LTR/ERV1 1 37 (574) 219
ANNOTATION EVIDENCE:
278 10.81 0.00 0.00 X_12942585_12942678_INS 58 94 0 + LTR36 LTR/ERV1 1 37 574
278 10.81 0.00 0.00 X_12942585_12942678_INS 58 94 (0) LTR36#LTR/ERV1 1 37 (574) m_b1s502i0
X_12942585_12 58 TATAACTGAGTACCCCTCTTTTTCTAAGAGAAAGAGA 94
i i iv
LTR36#LTR/ERV 1 TGTAACCGAGTACCCCCATTTTTCTAAGAGAAAGAGA 37
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.96
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 56 0.0 0.0 0.0 X_130107347_130107447_INS 2 51 (50) + (T)n Simple_repeat 1 50 (0) 220
ANNOTATION EVIDENCE:
56 0.00 0.00 0.00 X_130107347_130107447_INS 2 51 50 + (T)n Simple_repeat 1 50 0
56 0.00 0.00 0.00 X_130107347_130107447_INS 2 51 (50) (T)n#Simple_repeat 1 50 (0) c_b2s251i108
X_130107347_1 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 24 5.6 2.7 0.0 X_130107347_130107447_INS 52 88 (13) + (ATT)n Simple_repeat 1 38 (0) 221
ANNOTATION EVIDENCE:
24 5.64 2.70 0.00 X_130107347_130107447_INS 52 88 13 + (ATT)n Simple_repeat 1 38 0
24 5.64 2.70 0.00 X_130107347_130107447_INS 52 88 (13) (ATT)n#Simple_repeat 1 38 (0) m_b2s252i54
X_130107347_1 52 ATTATTATTATTATTATTATTATT-TTTTTTTTATTAT 88
- v v
(ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTAT 38
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1)
+ 25 23.7 0.0 0.0 X_130123060_130123118_INS 2 54 (5) + (AT)n Simple_repeat 1 53 (0) 222
ANNOTATION EVIDENCE:
25 23.69 0.00 0.00 X_130123060_130123118_INS 2 54 5 + (AT)n Simple_repeat 1 53 0
25 23.69 0.00 0.00 X_130123060_130123118_INS 2 54 (5) (AT)n#Simple_repeat 1 53 (0) m_b2s252i53
X_130123060_1 2 ATATATGTACACATATACATATATACACATATATGTACACATATACATAT 51
i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_130123060_1 52 ATA 54
(AT)n#Simple_ 51 ATA 53
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 2847 0.7 0.0 0.0 X_130224831_130225147_INS 17 317 (0) + AluY SINE/Alu 1 301 (10) 223
ANNOTATION EVIDENCE:
2847 0.66 0.00 0.00 X_130224831_130225147_INS 17 317 0 + AluY SINE/Alu 1 301 10
2847 0.66 0.00 0.00 X_130224831_130225147_INS 17 317 (0) AluY#SINE/Alu 1 301 (10) c_b2s352i61
X_130224831_1 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_130224831_1 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 116
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_130224831_1 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_130224831_1 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_130224831_1 217 GAACCCGGGAGGCGGAGCTTGCATTGAGCCGAGATCGCGCCACTGCACTC 266
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_130224831_1 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_130224831_1 317 A 317
AluY#SINE/Alu 301 A 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 300), avg. gap size = 0.0 (0 / 0)
+ 410 11.9 0.0 0.0 X_130251501_130251589_INS 2 60 (29) C L1PA17 LINE/L1 (67) 6099 6041 224
ANNOTATION EVIDENCE:
410 11.86 0.00 0.00 X_130251501_130251589_INS 2 60 29 C L1PA17_3end LINE/L1 788 846 67
410 11.86 0.00 0.00 X_130251501_130251589_INS 2 60 (29) C L1PA17_3end#LINE/L1 (67) 846 788 m_b2s551i11
X_130251501_1 2 TGTGTGATGCTGAGGTTTGGGCTTCTAATAGTCCTGTCTCCCAAGTAGCG 51
i ? ii? i v i i
C L1PA17_3end#L 846 TGCGTGATGCTGAGGTTTGGGCTTCTANTGANCCCGTCACCCAAATAGTG 797
X_130251501_1 52 AACATAGTA 60
C L1PA17_3end#L 796 AACATAGTA 788
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.90
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 1520 3.7 0.0 3.7 X_130304410_130304645_INS 13 236 (0) C AluY SINE/Alu (0) 311 92 225
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_130304410_130304645_INS 13 39 197 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 X_130304410_130304645_INS 13 39 (197) (T)n#Simple_repeat 1 27 (0) c_b2s251i107
X_130304410_1 13 TTTTTTTTTTTTTTTTTTTTTTTTTTT 39
(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)
1520 3.69 0.00 3.68 X_130304410_130304645_INS 40 236 0 C AluY SINE/Alu 92 281 30
1520 3.69 0.00 3.68 X_130304410_130304645_INS 40 236 (0) C AluY#SINE/Alu (30) 281 92 m_b2s357i7
X_130304410_1 40 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACCGCAGTGGC 89
i v -------
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGC-------AGTGGC 239
X_130304410_1 90 GCAATCTCGGCTCACTGCAAGCTCTGCTTCCCGGGTTCACGCCATTCTCC 139
i i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_130304410_1 140 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 189
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_130304410_1 190 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAG 236
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAG 92
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.79
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.04 (7 / 196), avg. gap size = 1.00 (7 / 7)
+ 649 3.7 1.2 0.0 X_130601138_130601218_INS 1 81 (0) + L1PA5 LINE/L1 6009 6090 (64) 226
ANNOTATION EVIDENCE:
649 3.70 1.23 0.00 X_130601138_130601218_INS 1 81 0 + L1PA5_3end LINE/L1 756 837 64
649 3.70 1.23 0.00 X_130601138_130601218_INS 1 81 (0) L1PA5_3end#LINE/L1 756 837 (64) m_b2s551i12
X_130601138_1 1 GGAGGGATAGCATTAAGAGAAATACCTAA-GTAAATGACAAGTTAATGGG 49
i v - i
L1PA5_3end#LI 756 GGAGGGATAGCATTAGGAGATATACCTAATGTAAATGACGAGTTAATGGG 805
X_130601138_1 50 TGCAGCACACCAACATGGCACATGTATACATA 81
L1PA5_3end#LI 806 TGCAGCACACCAACATGGCACATGTATACATA 837
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.64
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1)
+ 2528 2.1 0.0 0.4 X_130921940_130922254_INS 9 315 (0) C AluY SINE/Alu (0) 311 1 227
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_130921940_130922254_INS 9 33 282 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_130921940_130922254_INS 9 33 (282) (T)n#Simple_repeat 1 25 (0) c_b2s251i106
X_130921940_1 9 TTTTTTTTTTTTTTTTTTTTTTTTT 33
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2528 2.14 0.00 0.36 X_130921940_130922254_INS 34 315 0 C AluY SINE/Alu 1 281 30
2528 2.14 0.00 0.36 X_130921940_130922254_INS 34 315 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i62
X_130921940_1 34 GAGACGGAGTCTCGCTTTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 83
i v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_130921940_1 84 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 133
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_130921940_1 134 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 183
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_130921940_1 184 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 233
- v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_130921940_1 234 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 283
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_130921940_1 284 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 315
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.84
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 281), avg. gap size = 1.00 (1 / 1)
+ 56 1.9 0.0 0.0 X_130929384_130929439_INS 2 56 (0) + (T)n Simple_repeat 1 55 (0) 228
ANNOTATION EVIDENCE:
56 1.85 0.00 0.00 X_130929384_130929439_INS 2 56 0 + (T)n Simple_repeat 1 55 0
56 1.85 0.00 0.00 X_130929384_130929439_INS 2 56 (0) (T)n#Simple_repeat 1 55 (0) c_b2s251i105
X_130929384_1 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTT 51
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_130929384_1 52 TTTTT 56
(T)n#Simple_r 51 TTTTT 55
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 2641 2.6 0.0 2.3 X_130984697_130985016_INS 11 320 (0) C AluY SINE/Alu (8) 303 1 229
ANNOTATION EVIDENCE:
2641 2.64 0.00 2.31 X_130984697_130985016_INS 11 320 0 C AluY SINE/Alu 1 303 8
2641 2.64 0.00 2.31 X_130984697_130985016_INS 11 320 (0) C AluY#SINE/Alu (8) 303 1 c_b2s352i63
X_130984697_1 11 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGG 60
C AluY#SINE/Alu 303 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGG 254
X_130984697_1 61 CCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCT 110
i ----- -- i i
C AluY#SINE/Alu 253 CTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCC 211
X_130984697_1 111 TCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCCAGTAGCTGGGACT 160
v
C AluY#SINE/Alu 210 TCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACT 161
X_130984697_1 161 ACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGA 210
i
C AluY#SINE/Alu 160 ACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGA 111
X_130984697_1 211 CGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGA 260
v i
C AluY#SINE/Alu 110 CGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGA 61
X_130984697_1 261 TCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 310
i
C AluY#SINE/Alu 60 TCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 11
X_130984697_1 311 GCGCCCGGCC 320
C AluY#SINE/Alu 10 GCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.77
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 1.00 (7 / 7)
+ 359 10.7 1.8 0.0 X_131393590_131393793_INS 12 67 (137) C MLT1B LTR/ERVL-MaLR (223) 167 111 230
ANNOTATION EVIDENCE:
359 10.71 1.79 0.00 X_131393590_131393793_INS 12 67 137 C MLT1B LTR/ERVL-MaLR 111 167 223
359 10.71 1.79 0.00 X_131393590_131393793_INS 12 67 (137) C MLT1B#LTR/ERVL-MaLR (223) 167 111 m_b2s502i5
X_131393590_1 12 TCTTATCAGGACAC-AATCATATTGGATTTGGGACCACCCTAATGACATT 60
v - i v v v i
C MLT1B#LTR/ERV 167 TCTTATAAGGACACCAGTCATATTGGATTAGGGCCCACCCTAATGACCTC 118
X_131393590_1 61 ATTTTAA 67
C MLT1B#LTR/ERV 117 ATTTTAA 111
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.56
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1)
+ 2819 1.9 0.0 0.3 X_13167636_13167964_INS 14 325 (4) + AluY SINE/Alu 1 311 (0) 231
ANNOTATION EVIDENCE:
2819 1.93 0.00 0.32 X_13167636_13167964_INS 14 325 4 + AluY SINE/Alu 1 311 0
2819 1.93 0.00 0.32 X_13167636_13167964_INS 14 325 (4) AluY#SINE/Alu 1 311 (0) c_b1s352i6
X_13167636_13 14 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 63
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_13167636_13 64 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 113
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_13167636_13 114 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTAGTGG 163
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_13167636_13 164 CGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCG 213
i
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_13167636_13 214 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACT 263
v
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_13167636_13 264 CCAGCCTGGGCGACAGAGTGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 313
i
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_13167636_13 314 AAAAAAAAAAAA 325
AluY#SINE/Alu 300 AAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 311), avg. gap size = 1.00 (1 / 1)
+ 35 0.0 0.0 5.1 X_132215364_132215429_INS 2 42 (24) + (TTTATT)n Simple_repeat 1 39 (0) 232
ANNOTATION EVIDENCE:
35 0.00 0.00 5.13 X_132215364_132215429_INS 2 42 24 + (TTTATT)n Simple_repeat 1 39 0
35 0.00 0.00 5.13 X_132215364_132215429_INS 2 42 (24) (TTTATT)n#Simple_repeat 1 39 (0) c_b2s251i104
X_132215364_1 2 TTTATTTTTATTTATTTATTTTTATTTTTATTTTTATTTTT 42
- -
(TTTATT)n#Sim 1 TTTATTTTTA-TT-TTTATTTTTATTTTTATTTTTATTTTT 39
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2)
+ 59 10.7 0.0 2.1 X_132386424_132386521_INS 1 97 (1) + (AGGGG)n Simple_repeat 1 95 (0) 233
ANNOTATION EVIDENCE:
59 10.73 0.00 2.11 X_132386424_132386521_INS 1 97 1 + (AGGGG)n Simple_repeat 1 95 0
59 10.73 0.00 2.11 X_132386424_132386521_INS 1 97 (1) (AGGGG)n#Simple_repeat 1 95 (0) m_b2s252i52
X_132386424_1 1 AGGAGAGGGGAGGGGAGGAGAGGGGAGGGGGGGAGGGGGGAGGGGAGAGA 50
i i i i i - -
(AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAG-G- 48
X_132386424_1 51 AGAGGAGAGGGGAGGGGAGGAGAGGGGAGGGGAGGAGAGGGGAGGGG 97
i i i i
(AGGGG)n#Simp 49 GGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGG 95
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2)
+ 30 8.3 0.0 0.0 X_132602710_132602762_INS 8 46 (7) + (TA)n Simple_repeat 1 39 (0) 234
ANNOTATION EVIDENCE:
30 8.35 0.00 0.00 X_132602710_132602762_INS 8 46 7 + (TA)n Simple_repeat 1 39 0
30 8.35 0.00 0.00 X_132602710_132602762_INS 8 46 (7) (TA)n#Simple_repeat 1 39 (0) c_b2s251i103
X_132602710_1 8 TATATATATATATATGTGTGTATATATATATATATATAT 46
i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT 39
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 17 5.0 0.0 0.0 X_132656878_132656978_INS 4 24 (77) + (G)n Simple_repeat 1 21 (0) 235
ANNOTATION EVIDENCE:
17 5.00 0.00 0.00 X_132656878_132656978_INS 4 24 77 + (G)n Simple_repeat 1 21 0
17 5.00 0.00 0.00 X_132656878_132656978_INS 4 24 (77) (G)n#Simple_repeat 1 21 (0) m_b2s252i50
X_132656878_1 4 GGGAGGGGGGGGGGGGGGGGG 24
i
(G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 60 5.6 0.0 0.0 X_132656878_132656978_INS 25 99 (2) + (A)n Simple_repeat 1 75 (0) 236
ANNOTATION EVIDENCE:
60 5.64 0.00 0.00 X_132656878_132656978_INS 25 99 2 + (A)n Simple_repeat 1 75 0
60 5.64 0.00 0.00 X_132656878_132656978_INS 25 99 (2) (A)n#Simple_repeat 1 75 (0) m_b2s252i51
X_132656878_1 25 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 74
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_132656878_1 75 AAAAAGAAAAAGAAAAAAAAGAAAA 99
i i i
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAA 75
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 420 14.7 0.0 0.0 X_132945124_132945194_INS 1 68 (3) + BLACKJACK DNA/hAT-Blackjack 2902 2969 (0) 237
ANNOTATION EVIDENCE:
420 14.71 0.00 0.00 X_132945124_132945194_INS 1 68 3 + BLACKJACK DNA/hAT-Blackjack 2902 2969 0
420 14.71 0.00 0.00 X_132945124_132945194_INS 1 68 (3) BLACKJACK#DNA/hAT-Blackjack 2902 2969 (0) m_b2s502i6
X_132945124_1 1 TATTTTTAGCACTTCCTTTCACTCTCAAAAGTATCCTTGTTTGGACAATA 50
i ii i iv i
BLACKJACK#DNA 2902 TATTTTTAGCGCCCCCTTTCACTCTCAAAAGTGTCCCGGTTTGGACGATA 2951
X_132945124_1 51 ATTTATATTGTCACTCTA 68
v v i
BLACKJACK#DNA 2952 AATTATATGGTCACCCTA 2969
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.66
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 2445 2.5 0.0 2.5 X_133004636_133004966_INS 15 331 (0) C AluY SINE/Alu (0) 311 1 238
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_133004636_133004966_INS 15 43 288 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_133004636_133004966_INS 15 43 (288) (T)n#Simple_repeat 1 29 (0) c_b2s251i102
X_133004636_1 15 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
(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)
2445 2.49 0.00 2.49 X_133004636_133004966_INS 44 331 0 C AluY SINE/Alu 1 281 30
2445 2.49 0.00 2.49 X_133004636_133004966_INS 44 331 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i64
X_133004636_1 44 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 93
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_133004636_1 94 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 143
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_133004636_1 144 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 193
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_133004636_1 194 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 243
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_133004636_1 244 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 293
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_133004636_1 294 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 331
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 2675 2.9 0.0 2.3 X_13320071_13320393_INS 9 323 (0) C AluY SINE/Alu (3) 308 1 239
ANNOTATION EVIDENCE:
2675 2.93 0.00 2.27 X_13320071_13320393_INS 9 323 0 C AluY SINE/Alu 1 308 3
2675 2.93 0.00 2.27 X_13320071_13320393_INS 9 323 (0) C AluY#SINE/Alu (3) 308 1 c_b1s352i7
X_13320071_13 9 TTTCTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 58
i
C AluY#SINE/Alu 308 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 259
X_13320071_13 59 CCAGGTCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCT 108
----- -- v i
C AluY#SINE/Alu 258 CCAGG-----CTG--GAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCT 216
X_13320071_13 109 CCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTG 158
i
C AluY#SINE/Alu 215 CCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTG 166
X_13320071_13 159 GGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGT 208
i
C AluY#SINE/Alu 165 GGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGT 116
X_13320071_13 209 AGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 258
v
C AluY#SINE/Alu 115 AGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 66
X_13320071_13 259 CATGATCCACCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAG 308
i i i
C AluY#SINE/Alu 65 CGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAG 16
X_13320071_13 309 CCACCGCGCCCGGCC 323
C AluY#SINE/Alu 15 CCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.78
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.02 (7 / 314), avg. gap size = 1.00 (7 / 7)
+ 2059 2.6 0.0 0.0 X_134015007_134015247_INS 14 241 (0) C AluY SINE/Alu (9) 302 75 240
ANNOTATION EVIDENCE:
2059 2.63 0.00 0.00 X_134015007_134015247_INS 14 241 0 C AluY SINE/Alu 75 302 9
2059 2.63 0.00 0.00 X_134015007_134015247_INS 14 241 (0) C AluY#SINE/Alu (9) 302 75 m_b2s356i4
X_134015007_1 14 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 63
C AluY#SINE/Alu 302 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 253
X_134015007_1 64 TGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 113
v
C AluY#SINE/Alu 252 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 203
X_134015007_1 114 TCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGC 163
i
C AluY#SINE/Alu 202 TCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGC 153
X_134015007_1 164 CCGCCACTACGCCCGGCTAATTTTTTGTATTTTCAGTAGAGACGGGGTTT 213
i i
C AluY#SINE/Alu 152 CCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTT 103
X_134015007_1 214 CACCGTTTTAGCCGGGATGGTCTCGATC 241
v i
C AluY#SINE/Alu 102 CACCGTGTTAGCCAGGATGGTCTCGATC 75
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.27
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 227), avg. gap size = 0.0 (0 / 0)
+ 47 4.2 0.0 0.0 X_134780305_134780357_INS 3 51 (2) + (TA)n Simple_repeat 1 49 (0) 241
ANNOTATION EVIDENCE:
47 4.20 0.00 0.00 X_134780305_134780357_INS 3 51 2 + (TA)n Simple_repeat 1 49 0
47 4.20 0.00 0.00 X_134780305_134780357_INS 3 51 (2) (TA)n#Simple_repeat 1 49 (0) c_b2s251i101
X_134780305_1 3 TATATATATATATATATATATCCATATATATATATATATATATATATAT 51
vi
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATAT 49
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 23 25.6 3.1 0.0 X_135029718_135029787_INS 6 70 (0) + (AT)n Simple_repeat 1 67 (0) 242
ANNOTATION EVIDENCE:
23 25.57 3.08 0.00 X_135029718_135029787_INS 6 70 0 + (AT)n Simple_repeat 1 67 0
23 25.57 3.08 0.00 X_135029718_135029787_INS 6 70 (0) (AT)n#Simple_repeat 1 67 (0) m_b2s252i49
X_135029718_1 6 ATATAGAAGTATGTATACTTATATAT-TATATAAATATAGAAGTACGTAT 54
v vi i iv - v v vi ii
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_135029718_1 55 ACTTATATAT-TATATA 70
iv -
(AT)n#Simple_ 51 ATATATATATATATATA 67
Matrix = Unknown
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2)
+ 2846 0.7 0.0 0.0 X_135152197_135152515_INS 1 302 (17) C AluY SINE/Alu (9) 302 1 243
ANNOTATION EVIDENCE:
2846 0.66 0.00 0.00 X_135152197_135152515_INS 1 302 17 C AluY SINE/Alu 1 302 9
2846 0.66 0.00 0.00 X_135152197_135152515_INS 1 302 (17) C AluY#SINE/Alu (9) 302 1 c_b2s352i65
X_135152197_1 1 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 50
C AluY#SINE/Alu 302 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 253
X_135152197_1 51 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 100
C AluY#SINE/Alu 252 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 203
X_135152197_1 101 TCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGC 150
C AluY#SINE/Alu 202 TCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGC 153
X_135152197_1 151 CCGCTACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTT 200
i
C AluY#SINE/Alu 152 CCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTT 103
X_135152197_1 201 CACCGTGTTAGCCACGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCG 250
v
C AluY#SINE/Alu 102 CACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCG 53
X_135152197_1 251 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 300
C AluY#SINE/Alu 52 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
X_135152197_1 301 CC 302
C AluY#SINE/Alu 2 CC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.67
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 301), avg. gap size = 0.0 (0 / 0)
+ 2575 1.8 0.0 0.0 X_135162416_135162727_INS 7 312 (0) C AluY SINE/Alu (0) 311 1 244
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_135162416_135162727_INS 7 31 281 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_135162416_135162727_INS 7 31 (281) (T)n#Simple_repeat 1 25 (0) c_b2s251i100
X_135162416_1 7 TTTTTTTTTTTTTTTTTTTTTTTTT 31
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2575 1.78 0.00 0.00 X_135162416_135162727_INS 32 312 0 C AluY SINE/Alu 1 281 30
2575 1.78 0.00 0.00 X_135162416_135162727_INS 32 312 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i66
X_135162416_1 32 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 81
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_135162416_1 82 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 131
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_135162416_1 132 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 181
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_135162416_1 182 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 231
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_135162416_1 232 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 281
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_135162416_1 282 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 312
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.47
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 33 15.0 0.0 0.0 X_135768876_135768930_INS 1 54 (1) + (TA)n Simple_repeat 1 54 (0) 245
ANNOTATION EVIDENCE:
33 15.01 0.00 0.00 X_135768876_135768930_INS 1 54 1 + (TA)n Simple_repeat 1 54 0
33 15.01 0.00 0.00 X_135768876_135768930_INS 1 54 (1) (TA)n#Simple_repeat 1 54 (0) m_b2s252i48
X_135768876_1 1 TATATACATGTGTATATATATATACACATATATATATATACACATATATA 50
i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_135768876_1 51 TATA 54
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 80 2.6 0.0 0.0 X_135895024_135895104_INS 2 81 (0) + (GAAGGGAG)n Simple_repeat 1 80 (0) 246
ANNOTATION EVIDENCE:
80 2.56 0.00 0.00 X_135895024_135895104_INS 2 81 0 + (GAAGGGAG)n Simple_repeat 1 80 0
80 2.56 0.00 0.00 X_135895024_135895104_INS 2 81 (0) (GAAGGGAG)n#Simple_repeat 1 80 (0) c_b2s251i99
X_135895024_1 2 GAAGGGAGGAAGGGAGGAAGGGAGGAAGAGAGGAAGGGAGGAAGGGAGGA 51
i
(GAAGGGAG)n#S 1 GAAGGGAGGAAGGGAGGAAGGGAGGAAGGGAGGAAGGGAGGAAGGGAGGA 50
X_135895024_1 52 AGGGAGGAAGGGAGGAAGAGAGGAAGGGAG 81
i
(GAAGGGAG)n#S 51 AGGGAGGAAGGGAGGAAGGGAGGAAGGGAG 80
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 2653 1.1 0.0 0.0 X_136013811_136014130_INS 13 320 (0) C AluY SINE/Alu (0) 311 3 247
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_136013811_136014130_INS 13 40 280 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_136013811_136014130_INS 13 40 (280) (T)n#Simple_repeat 1 28 (0) c_b2s251i98
X_136013811_1 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
(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)
2653 1.06 0.00 0.00 X_136013811_136014130_INS 41 320 0 C AluY SINE/Alu 3 282 29
2653 1.06 0.00 0.00 X_136013811_136014130_INS 41 320 (0) C AluY#SINE/Alu (29) 282 3 c_b2s352i67
X_136013811_1 41 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 90
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_136013811_1 91 CGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCA 140
i
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_136013811_1 141 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 190
i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_136013811_1 191 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 240
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_136013811_1 241 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 290
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_136013811_1 291 GGATTACAGGCGTGAGCCACCGCGCCCGGC 320
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGC 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.75
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 2796 2.6 0.0 0.0 X_136025695_136026019_INS 16 325 (0) C AluY SINE/Alu (1) 310 1 248
ANNOTATION EVIDENCE:
2796 2.58 0.00 0.00 X_136025695_136026019_INS 16 325 0 C AluY SINE/Alu 1 310 1
2796 2.58 0.00 0.00 X_136025695_136026019_INS 16 325 (0) C AluY#SINE/Alu (1) 310 1 c_b2s352i68
X_136025695_1 16 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTC 65
i
C AluY#SINE/Alu 310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTC 261
X_136025695_1 66 GCCCAGGCTTGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCC 115
v v
C AluY#SINE/Alu 260 GCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCC 211
X_136025695_1 116 TCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACT 165
i
C AluY#SINE/Alu 210 TCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACT 161
X_136025695_1 166 ACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGA 215
i
C AluY#SINE/Alu 160 ACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGA 111
X_136025695_1 216 CGGGGTTTCACCATTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGA 265
i v i
C AluY#SINE/Alu 110 CGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGA 61
X_136025695_1 266 TCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 315
C AluY#SINE/Alu 60 TCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 11
X_136025695_1 316 GCGCCCGGCC 325
C AluY#SINE/Alu 10 GCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.03
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.00 (0 / 309), avg. gap size = 0.0 (0 / 0)
+ 76 1.4 0.0 0.0 X_13618398_13618475_INS 7 78 (0) + (T)n Simple_repeat 1 72 (0) 249
ANNOTATION EVIDENCE:
76 1.40 0.00 0.00 X_13618398_13618475_INS 7 78 0 + (T)n Simple_repeat 1 72 0
76 1.40 0.00 0.00 X_13618398_13618475_INS 7 78 (0) (T)n#Simple_repeat 1 72 (0) c_b1s251i164
X_13618398_13 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 56
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_13618398_13 57 TTTTTGTTTTTTTTTTTTTTTT 78
v
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTT 72
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 1006 1.7 0.0 0.0 X_136209203_136209321_INS 1 117 (2) + L1P1 LINE/L1 4649 4765 (1381) 250
ANNOTATION EVIDENCE:
1006 1.71 0.00 0.00 X_136209203_136209321_INS 1 117 2 + L1P1_orf2 LINE/L1 2540 2656 638
1006 1.71 0.00 0.00 X_136209203_136209321_INS 1 117 (2) L1P1_orf2#LINE/L1 2540 2656 (638) m_b2s551i13
X_136209203_1 1 TCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAA 50
i
L1P1_orf2#LIN 2540 TCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAA 2589
X_136209203_1 51 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 100
i
L1P1_orf2#LIN 2590 AAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAA 2639
X_136209203_1 101 GGCTACAGTAACCAAAA 117
L1P1_orf2#LIN 2640 GGCTACAGTAACCAAAA 2656
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.17
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 116), avg. gap size = 0.0 (0 / 0)
+ 2816 1.6 0.0 1.0 X_136349837_136350177_INS 5 318 (23) + AluY SINE/Alu 1 311 (0) 251
ANNOTATION EVIDENCE:
2816 1.61 0.00 0.96 X_136349837_136350177_INS 5 318 23 + AluY SINE/Alu 1 311 0
2816 1.61 0.00 0.96 X_136349837_136350177_INS 5 318 (23) AluY#SINE/Alu 1 311 (0) c_b2s352i69
X_136349837_1 5 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 54
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_136349837_1 55 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 104
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_136349837_1 105 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAAATTAGCCGGGCGTAGT 154
--- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA---AATTAGCCGGGCGTGGT 147
X_136349837_1 155 GGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGG 204
i
AluY#SINE/Alu 148 GGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGG 197
X_136349837_1 205 CGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCA 254
v
AluY#SINE/Alu 198 CGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA 247
X_136349837_1 255 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 304
AluY#SINE/Alu 248 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
X_136349837_1 305 AAAAAAAAAAAAAA 318
AluY#SINE/Alu 298 AAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.33
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (3 / 313), avg. gap size = 1.00 (3 / 3)
+ 2796 1.6 0.0 0.0 X_136425300_136425620_INS 17 321 (0) + AluY SINE/Alu 1 305 (6) 252
ANNOTATION EVIDENCE:
2796 1.64 0.00 0.00 X_136425300_136425620_INS 17 321 0 + AluY SINE/Alu 1 305 6
2796 1.64 0.00 0.00 X_136425300_136425620_INS 17 321 (0) AluY#SINE/Alu 1 305 (6) c_b2s352i70
X_136425300_1 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_136425300_1 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 116
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_136425300_1 117 TGAAACCCCGCCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 166
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_136425300_1 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_136425300_1 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 266
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_136425300_1 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_136425300_1 317 AAAAA 321
AluY#SINE/Alu 301 AAAAA 305
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.66
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 304), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 0.0 X_136746431_136746491_INS 1 40 (21) + (TTCT)n Simple_repeat 1 40 (0) 253
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_136746431_136746491_INS 1 40 21 + (TTCT)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_136746431_136746491_INS 1 40 (21) (TTCT)n#Simple_repeat 1 40 (0) c_b2s251i97
X_136746431_1 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 40
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 19 0.0 0.0 0.0 X_136746431_136746491_INS 41 61 (0) + (CT)n Simple_repeat 1 21 (0) 254
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 X_136746431_136746491_INS 41 61 0 + (CT)n Simple_repeat 1 21 0
19 0.00 0.00 0.00 X_136746431_136746491_INS 41 61 (0) (CT)n#Simple_repeat 1 21 (0) m_b2s252i47
X_136746431_1 41 CTCTCTCTCTCTCTCTCTCTC 61
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTC 21
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 16 4.3 4.0 0.0 X_13693578_13693632_INS 2 20 (35) + (AG)n Simple_repeat 1 20 (0) 255
ANNOTATION EVIDENCE:
16 4.35 4.00 0.00 X_13693578_13693632_INS 2 20 35 + (AG)n Simple_repeat 1 20 6
16 4.35 4.00 0.00 X_13693578_13693632_INS 2 20 (35) (AG)n#Simple_repeat 1 20 (6) m_b1s252i124
X_13693578_13 2 AGAGAGAAAGAGAGAGAG-G 20
i -
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAG 20
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1)
+ 32 0.0 0.0 0.0 X_13693578_13693632_INS 21 50 (5) + (GAAA)n Simple_repeat 1 30 (0) 256
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 X_13693578_13693632_INS 21 50 5 + (GAAA)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 X_13693578_13693632_INS 21 50 (5) (GAAA)n#Simple_repeat 1 30 (0) c_b1s251i163
X_13693578_13 21 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 2373 3.8 0.0 0.0 X_136957285_136957585_INS 11 300 (1) C AluY SINE/Alu (0) 311 17 257
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_136957285_136957585_INS 11 35 266 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_136957285_136957585_INS 11 35 (266) (T)n#Simple_repeat 1 25 (0) c_b2s251i96
X_136957285_1 11 TTTTTTTTTTTTTTTTTTTTTTTTT 35
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2373 3.77 0.00 0.00 X_136957285_136957585_INS 36 300 1 C AluY SINE/Alu 17 281 30
2373 3.77 0.00 0.00 X_136957285_136957585_INS 36 300 (1) C AluY#SINE/Alu (30) 281 17 c_b2s352i71
X_136957285_1 36 GAGACGGAGTCTCGCTGTGTCTCCCAGGTTGGAGTGCGGTGGCGCAATCT 85
v v i i i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_136957285_1 86 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 135
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_136957285_1 136 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCAACACGCCCGGCTAAT 185
i v
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_136957285_1 186 TTTTTGTATTTTTAGTAGAAACGGGGTTTCACCGTGTTAGCCAAGATGGT 235
i i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_136957285_1 236 CTCGATCTCCTGACCTCGTGATCCGCCCGTCTCGGCCTCCCAAAGTGCTG 285
i
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_136957285_1 286 GGATTACAGGCGTGA 300
C AluY#SINE/Alu 31 GGATTACAGGCGTGA 17
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 3.17
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 264), avg. gap size = 0.0 (0 / 0)
+ 34 13.1 0.0 0.0 X_137234592_137234644_INS 2 53 (0) + (TA)n Simple_repeat 1 52 (0) 258
ANNOTATION EVIDENCE:
34 13.12 0.00 0.00 X_137234592_137234644_INS 2 53 0 + (TA)n Simple_repeat 1 52 0
34 13.12 0.00 0.00 X_137234592_137234644_INS 2 53 (0) (TA)n#Simple_repeat 1 52 (0) m_b2s252i46
X_137234592_1 2 TATATATATGTATATATGTATATATACGTATATATATATGTATATATATG 51
i i ii i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_137234592_1 52 TA 53
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 261 22.6 0.0 0.0 X_137279059_137279111_INS 1 53 (0) C L1M1 LINE/L1 (805) 5498 5446 259
ANNOTATION EVIDENCE:
261 22.64 0.00 0.00 X_137279059_137279111_INS 1 53 0 C L1MA4A_3end LINE/L1 193 245 805
261 22.64 0.00 0.00 X_137279059_137279111_INS 1 53 (0) C L1MA4A_3end#LINE/L1 (805) 245 193 m_b2s551i14
X_137279059_1 1 CAACTGTTGTTGTCTATTTCTTTGATAATAGCCATTCTGACGGGAGTAAG 50
v i v i i i i i i v i
C L1MA4A_3end#L 245 CATCTGTTATTTTTTGTCTTTTTAATAATAGCCATTCTAACTGGGGTAAG 196
X_137279059_1 51 GTG 53
i
C L1MA4A_3end#L 195 ATG 193
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.23
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 452 2.0 0.0 0.0 X_137352047_137352098_INS 2 52 (0) C LTR7 LTR/ERV1 (268) 182 132 260
ANNOTATION EVIDENCE:
452 1.96 0.00 0.00 X_137352047_137352098_INS 2 52 0 C LTR7 LTR/ERV1 132 182 268
452 1.96 0.00 0.00 X_137352047_137352098_INS 2 52 (0) C LTR7#LTR/ERV1 (268) 182 132 m_b2s502i7
X_137352047_1 2 AATGTCATCAGTTAAGGCAGGAACAGGCCATTTTCACTTCTTTTGTGGTG 51
i ?
C LTR7#LTR/ERV1 182 AATGTCATCAGTTAAGGCAGGGACNGGCCATTTTCACTTCTTTTGTGGTG 133
X_137352047_1 52 G 52
C LTR7#LTR/ERV1 132 G 132
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.04
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 68 1.3 0.0 0.0 X_13740327_13740406_INS 5 80 (0) + (A)n Simple_repeat 1 76 (0) 261
ANNOTATION EVIDENCE:
68 1.33 0.00 0.00 X_13740327_13740406_INS 5 80 0 + (A)n Simple_repeat 1 76 0
68 1.33 0.00 0.00 X_13740327_13740406_INS 5 80 (0) (A)n#Simple_repeat 1 76 (0) m_b1s252i123
X_13740327_13 5 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 54
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_13740327_13 55 AAAAAAAAAACAAAAAAAAAAAAAAA 80
v
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAA 76
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0)
+ 35 0.0 0.0 0.0 X_137423065_137423121_INS 1 33 (24) + (AAAG)n Simple_repeat 1 33 (0) 262
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_137423065_137423121_INS 1 33 24 + (AAAG)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_137423065_137423121_INS 1 33 (24) (AAAG)n#Simple_repeat 1 33 (0) c_b2s251i95
X_137423065_1 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 33
(AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 33
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 14 9.1 0.0 0.0 X_137423065_137423121_INS 34 57 (0) + (GAGG)n Simple_repeat 1 24 (0) 263
ANNOTATION EVIDENCE:
14 9.12 0.00 0.00 X_137423065_137423121_INS 34 57 0 + (GAGG)n Simple_repeat 1 24 0
14 9.12 0.00 0.00 X_137423065_137423121_INS 34 57 (0) (GAGG)n#Simple_repeat 1 24 (0) m_b2s252i45
X_137423065_1 34 GAGGAAGGAAGGGAGGGAGGGAGG 57
i i
(GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGG 24
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 36 11.8 0.0 0.0 X_138066901_138066958_INS 1 57 (1) + (GAG)n Simple_repeat 1 57 (0) 264
ANNOTATION EVIDENCE:
36 11.82 0.00 0.00 X_138066901_138066958_INS 1 57 1 + (GAG)n Simple_repeat 1 57 0
36 11.82 0.00 0.00 X_138066901_138066958_INS 1 57 (1) (GAG)n#Simple_repeat 1 57 (0) m_b2s252i44
X_138066901_1 1 GAGGAGGAGGAGAAGAAGAGGGAGGAGGGGGAGGAGGAGGGGGAGGAGGA 50
i i ii i i
(GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50
X_138066901_1 51 GGAGGAG 57
(GAG)n#Simple 51 GGAGGAG 57
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 30 0.0 0.0 0.0 X_138110746_138110838_INS 1 26 (67) + (TG)n Simple_repeat 1 26 (0) 265
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_138110746_138110838_INS 1 26 67 + (TG)n Simple_repeat 1 26 0
30 0.00 0.00 0.00 X_138110746_138110838_INS 1 26 (67) (TG)n#Simple_repeat 1 26 (0) c_b2s251i94
X_138110746_1 1 TGTGTGTGTGTGTGTGTGTGTGTGTG 26
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTG 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 31 22.8 0.0 0.0 X_138110746_138110838_INS 27 93 (0) + GA-rich Low_complexity 1 67 (0) 266
ANNOTATION EVIDENCE:
31 22.81 0.00 0.00 X_138110746_138110838_INS 27 93 0 + (AG)n Simple_repeat 1 67 0
31 22.81 0.00 0.00 X_138110746_138110838_INS 27 93 (0) (AG)n#Simple_repeat 1 67 (0) m_b2s252i43
X_138110746_1 27 AGAGAGAGAGAGAGAGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAG 76
v v v v v v v v
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50
X_138110746_1 77 AGTGTGTGTGAAAGAGA 93
v v v v i
(AG)n#Simple_ 51 AGAGAGAGAGAGAGAGA 67
Matrix = Unknown
Transitions / transversions = 0.08 (1/12)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 2361 3.6 0.0 2.5 X_138218419_138218723_INS 20 305 (0) C AluY SINE/Alu (3) 308 30 267
ANNOTATION EVIDENCE:
2361 3.59 0.00 2.51 X_138218419_138218723_INS 20 305 0 C AluY SINE/Alu 30 308 3
2361 3.59 0.00 2.51 X_138218419_138218723_INS 20 305 (0) C AluY#SINE/Alu (3) 308 30 c_b2s352i72
X_138218419_1 20 TTTTTTATTTTATTTTTTTATTTTTTTGAGACGGAGTCTCGCTCTGTCGC 69
v v v
C AluY#SINE/Alu 308 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 259
X_138218419_1 70 CCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCT 119
i ----- -- i
C AluY#SINE/Alu 258 CCAGGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCT 216
X_138218419_1 120 CCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTG 169
i
C AluY#SINE/Alu 215 CCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTG 166
X_138218419_1 170 GGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGT 219
i
C AluY#SINE/Alu 165 GGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGT 116
X_138218419_1 220 AGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 269
v
C AluY#SINE/Alu 115 AGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 66
X_138218419_1 270 CATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGG 305
i i
C AluY#SINE/Alu 65 CGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGG 30
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.66
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.02 (7 / 285), avg. gap size = 1.00 (7 / 7)
+ 54 0.0 0.0 0.0 X_138478774_138478826_INS 1 46 (7) + (TA)n Simple_repeat 1 46 (0) 268
ANNOTATION EVIDENCE:
54 0.00 0.00 0.00 X_138478774_138478826_INS 1 46 7 + (TA)n Simple_repeat 1 46 0
54 0.00 0.00 0.00 X_138478774_138478826_INS 1 46 (7) (TA)n#Simple_repeat 1 46 (0) c_b2s251i93
X_138478774_1 1 TATATATATATATATATATATATATATATATATATATATATATATA 46
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATA 46
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 2764 2.0 0.0 0.0 X_138479893_138480209_INS 15 317 (0) + AluY SINE/Alu 1 303 (8) 269
ANNOTATION EVIDENCE:
2764 1.98 0.00 0.00 X_138479893_138480209_INS 15 317 0 + AluY SINE/Alu 1 303 8
2764 1.98 0.00 0.00 X_138479893_138480209_INS 15 317 (0) AluY#SINE/Alu 1 303 (8) c_b2s352i73
X_138479893_1 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_138479893_1 65 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATGCCGGCTAAAACGG 114
v i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_138479893_1 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_138479893_1 165 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 214
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_138479893_1 215 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 264
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_138479893_1 265 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 314
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_138479893_1 315 AAA 317
AluY#SINE/Alu 301 AAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.70
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 23 25.5 0.0 0.0 X_138618398_138618448_INS 2 51 (0) + (TA)n Simple_repeat 1 50 (0) 270
ANNOTATION EVIDENCE:
23 25.54 0.00 0.00 X_138618398_138618448_INS 2 51 0 + (TA)n Simple_repeat 1 50 0
23 25.54 0.00 0.00 X_138618398_138618448_INS 2 51 (0) (TA)n#Simple_repeat 1 50 (0) m_b2s252i42
X_138618398_1 2 TATATATATGTACACACATATATGTATATATATGTACACACATATATGTA 51
i i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 416 12.8 0.0 0.0 X_138663346_138663480_INS 3 134 (1) C SAR Satellite (14) 132 1 271
ANNOTATION EVIDENCE:
384 14.29 0.00 0.00 X_138663346_138663480_INS 3 72 63 C SAR Satellite 1 70 14
384 14.29 0.00 0.00 X_138663346_138663480_INS 3 72 (63) C SAR#Satellite (14) 70 1 m_b2s502i8
X_138663346_1 3 AATACACCAGATATATATTCTATAGTGTACATAAAATATCAAAGTACCCA 52
i i i v v v v
C SAR#Satellite 70 AGTACACCAAATACATATTATATACTGTACATAAAATATCAAAGTACACC 21
X_138663346_1 53 AAGTATAAATTATATACTGT 72
i i v
C SAR#Satellite 20 AAATACATATTATATACTGT 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.91
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
416 11.39 0.00 0.00 X_138663346_138663480_INS 31 109 26 C SAR Satellite 6 84 0
416 11.39 0.00 0.00 X_138663346_138663480_INS 31 109 (26) C SAR#Satellite (0) 84 6 m_b2s502i9
X_138663346_1 31 ACATAAAATATCAAAGTACCCAAAGTATAAATTATATACTGTACATAAAA 80
v v i i v
C SAR#Satellite 84 ACATAAAATATCAAAGTACACCAAATACATATTATATACTGTACATAAAA 35
X_138663346_1 81 TATGAAATTACATCAAATATATATTATAT 109
v v i i
C SAR#Satellite 34 TATCAAAGTACACCAAATACATATTATAT 6
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.37
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0)
294 12.90 0.00 0.00 X_138663346_138663480_INS 73 134 1 C SAR Satellite 23 84 0
294 12.90 0.00 0.00 X_138663346_138663480_INS 73 134 (1) C SAR#Satellite (0) 84 23 m_b2s502i10
X_138663346_1 73 ACATAAAATATGAAATTACATCAAATATATATTATATTAGGTACATAAAA 122
v v i i vvv
C SAR#Satellite 84 ACATAAAATATCAAAGTACACCAAATACATATTATATACTGTACATAAAA 35
X_138663346_1 123 TATGAAAGTACA 134
v
C SAR#Satellite 34 TATCAAAGTACA 23
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.17
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 2668 2.0 0.0 2.3 X_138669113_138669431_INS 12 319 (0) C AluY SINE/Alu (10) 301 1 272
ANNOTATION EVIDENCE:
2668 2.00 0.00 2.33 X_138669113_138669431_INS 12 319 0 C AluY SINE/Alu 1 301 10
2668 2.00 0.00 2.33 X_138669113_138669431_INS 12 319 (0) C AluY#SINE/Alu (10) 301 1 c_b2s352i74
X_138669113_1 12 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCC 61
i
C AluY#SINE/Alu 301 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT 252
X_138669113_1 62 GGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTC 111
----- -- i
C AluY#SINE/Alu 251 GGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTC 209
X_138669113_1 112 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 161
C AluY#SINE/Alu 208 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 159
X_138669113_1 162 AGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACG 211
i
C AluY#SINE/Alu 158 AGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACG 109
X_138669113_1 212 GGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATC 261
v i
C AluY#SINE/Alu 108 GGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATC 59
X_138669113_1 262 CACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 311
i
C AluY#SINE/Alu 58 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
X_138669113_1 312 GCCCGGCC 319
C AluY#SINE/Alu 8 GCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.11
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.02 (7 / 307), avg. gap size = 1.00 (7 / 7)
+ 2695 2.3 0.3 0.0 X_138744466_138744778_INS 14 313 (0) C AluY SINE/Alu (9) 302 2 273
ANNOTATION EVIDENCE:
2695 2.33 0.33 0.00 X_138744466_138744778_INS 14 313 0 C AluY SINE/Alu 2 302 9
2695 2.33 0.33 0.00 X_138744466_138744778_INS 14 313 (0) C AluY#SINE/Alu (9) 302 2 c_b2s352i75
X_138744466_1 14 TTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTGTCGCCCAGGC 63
i i
C AluY#SINE/Alu 302 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 253
X_138744466_1 64 TGGAGTGCAGTGGCGCGATCTCGACTCACTGCAAGCTCCGCCTCCCGGGT 113
i
C AluY#SINE/Alu 252 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 203
X_138744466_1 114 TTACGCCATTCTCCTGCCTCAGCCTCCCGTGTAGCTGGGACTACAGGCGC 163
i v
C AluY#SINE/Alu 202 TCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGC 153
X_138744466_1 164 GCGCCACCATGCCCGGCTAAT-TTTTGTATTTTTAGTAGAGACGGGGTTT 212
v i -
C AluY#SINE/Alu 152 CCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTT 103
X_138744466_1 213 CACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCG 262
C AluY#SINE/Alu 102 CACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCG 53
X_138744466_1 263 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 312
C AluY#SINE/Alu 52 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
X_138744466_1 313 C 313
C AluY#SINE/Alu 2 C 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.07
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (1 / 299), avg. gap size = 1.00 (1 / 1)
+ 1034 0.8 0.0 0.0 X_138771802_138771930_INS 9 129 (0) C AluY SINE/Alu (6) 305 185 274
ANNOTATION EVIDENCE:
1034 0.83 0.00 0.00 X_138771802_138771930_INS 9 129 0 C AluY SINE/Alu 185 305 6
1034 0.83 0.00 0.00 X_138771802_138771930_INS 9 129 (0) C AluY#SINE/Alu (6) 305 185 m_b2s357i8
X_138771802_1 9 TCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 58
i
C AluY#SINE/Alu 305 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 256
X_138771802_1 59 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCG 108
C AluY#SINE/Alu 255 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCG 206
X_138771802_1 109 GGTTCACGCCATTCTCCTGCC 129
C AluY#SINE/Alu 205 GGTTCACGCCATTCTCCTGCC 185
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 0.83
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0)
+ 57 1.6 0.0 0.0 X_13883681_13883744_INS 1 64 (0) + (A)n Simple_repeat 1 64 (0) 275
ANNOTATION EVIDENCE:
57 1.58 0.00 0.00 X_13883681_13883744_INS 1 64 0 + (A)n Simple_repeat 1 64 0
57 1.58 0.00 0.00 X_13883681_13883744_INS 1 64 (0) (A)n#Simple_repeat 1 64 (0) m_b1s252i122
X_13883681_13 1 AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_13883681_13 51 AAAAAAAAAAAAAA 64
(A)n#Simple_r 51 AAAAAAAAAAAAAA 64
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 43 9.4 2.9 0.0 X_139124830_139124900_INS 2 71 (0) + (AAGA)n Simple_repeat 1 72 (0) 276
ANNOTATION EVIDENCE:
43 9.40 2.86 0.00 X_139124830_139124900_INS 2 71 0 + (AAGA)n Simple_repeat 1 72 0
43 9.40 2.86 0.00 X_139124830_139124900_INS 2 71 (0) (AAGA)n#Simple_repeat 1 72 (0) m_b2s252i41
X_139124830_1 2 AAGAAAGAAAG-AA-AAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAA 49
- - i i i i i
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
X_139124830_1 50 GGAAGAAAGAAAGAAAGAAAGA 71
i
(AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGA 72
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2)
+ 36 0.0 0.0 0.0 X_139146430_139146486_INS 8 38 (19) + (AT)n Simple_repeat 1 31 (0) 277
ANNOTATION EVIDENCE:
36 0.00 0.00 0.00 X_139146430_139146486_INS 8 38 19 + (AT)n Simple_repeat 1 31 0
36 0.00 0.00 0.00 X_139146430_139146486_INS 8 38 (19) (AT)n#Simple_repeat 1 31 (0) c_b2s251i92
X_139146430_1 8 ATATATATATATATATATATATATATATATA 38
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATA 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 2649 3.0 0.0 2.3 X_139377521_139377843_INS 15 323 (0) + AluY SINE/Alu 1 302 (9) 278
ANNOTATION EVIDENCE:
2649 2.98 0.00 2.32 X_139377521_139377843_INS 15 323 0 + AluY SINE/Alu 1 302 9
2649 2.98 0.00 2.32 X_139377521_139377843_INS 15 323 (0) AluY#SINE/Alu 1 302 (9) c_b2s352i76
X_139377521_1 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_139377521_1 65 GGCGGGTGGATCATGAGGTCAGGAGATTGAGACCATCCTGGCTAACAAGG 114
i i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_139377521_1 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_139377521_1 165 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 214
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_139377521_1 215 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 264
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_139377521_1 265 CGCAGTCTGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 314
-------i
AluY#SINE/Alu 251 C-------AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_139377521_1 315 AAAAAAAAA 323
AluY#SINE/Alu 294 AAAAAAAAA 302
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.81
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.02 (7 / 308), avg. gap size = 1.00 (7 / 7)
+ 211 29.6 1.4 0.0 X_139596667_139596737_INS 1 71 (0) C L2a LINE/L2 (0) 3426 3355 279
ANNOTATION EVIDENCE:
211 29.58 1.41 0.00 X_139596667_139596737_INS 1 71 0 C L2a_3end LINE/L2 446 517 0
211 29.58 1.41 0.00 X_139596667_139596737_INS 1 71 (0) C L2a_3end#LINE/L2 (0) 517 446 m_b2s601i0
X_139596667_1 1 ATTTATTAAT-AGACACATTTTTATTGAAGGTCTACTATAGGCCAGATAT 49
i v -vi v v iv i iv ii i
C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468
X_139596667_1 50 TCTTCAAGAACTTGGGGGTACA 71
v v ivvi i
C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACA 446
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.23
Transitions / transversions = 1.10 (11/10)
Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1)
+ 2499 0.4 0.0 0.0 X_139853431_139853708_INS 16 278 (0) + AluY SINE/Alu 39 301 (10) 280
ANNOTATION EVIDENCE:
2499 0.38 0.00 0.00 X_139853431_139853708_INS 16 278 0 + AluY SINE/Alu 39 301 10
2499 0.38 0.00 0.00 X_139853431_139853708_INS 16 278 (0) AluY#SINE/Alu 39 301 (10) c_b3s352i0
X_139853431_1 16 TTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCC 65
AluY#SINE/Alu 39 TTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCC 88
X_139853431_1 66 TGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC 115
AluY#SINE/Alu 89 TGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC 138
X_139853431_1 116 GGGCGTGGTAGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCA 165
i
AluY#SINE/Alu 139 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCA 188
X_139853431_1 166 GGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGC 215
AluY#SINE/Alu 189 GGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGC 238
X_139853431_1 216 GCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 265
AluY#SINE/Alu 239 GCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 288
X_139853431_1 266 AAAAAAAAAAAAA 278
AluY#SINE/Alu 289 AAAAAAAAAAAAA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.38
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 262), avg. gap size = 0.0 (0 / 0)
+ 42 24.3 2.0 0.0 X_139870919_139871024_INS 6 106 (0) + (AT)n Simple_repeat 1 103 (0) 281
ANNOTATION EVIDENCE:
42 24.34 1.98 0.00 X_139870919_139871024_INS 6 106 0 + (AT)n Simple_repeat 1 103 0
42 24.34 1.98 0.00 X_139870919_139871024_INS 6 106 (0) (AT)n#Simple_repeat 1 103 (0) m_b3s252i41
X_139870919_1 6 ATATATACACATATATGTGTATATATGTATAT-TCCATATATACACATAT 54
i i i i i - vi i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_139870919_1 55 ATGTGTATATATGTAGAT-TCCATATATACACATATATGTGTATATATGT 103
i i i v - vi i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_139870919_1 104 ATA 106
(AT)n#Simple_ 101 ATA 103
Matrix = Unknown
Transitions / transversions = 5.67 (17/3)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2)
+ 36 18.9 3.5 1.1 X_140749834_140749923_INS 5 90 (0) + (TA)n Simple_repeat 1 88 (0) 282
ANNOTATION EVIDENCE:
36 18.94 3.49 1.14 X_140749834_140749923_INS 5 90 0 + (TA)n Simple_repeat 1 88 0
36 18.94 3.49 1.14 X_140749834_140749923_INS 5 90 (0) (TA)n#Simple_repeat 1 88 (0) m_b3s252i40
X_140749834_1 5 TATAAATAAAGCT-TATATATAAATTTATATATATATATATATTTATTTA 53
v v vv - v v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_140749834_1 54 TAAATA-AAACTTATATATAAAGCAT-TATATATATATA 90
v - v iv v -i -
(TA)n#Simple_ 51 TATATATATATATATATATATA-TATATATATATATATA 88
Matrix = Unknown
Transitions / transversions = 0.17 (2/12)
Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4)
+ 49 3.8 0.0 0.0 X_14075607_14075661_INS 1 54 (1) + (TTTAT)n Simple_repeat 1 54 (0) 283
ANNOTATION EVIDENCE:
49 3.81 0.00 0.00 X_14075607_14075661_INS 1 54 1 + (TTTAT)n Simple_repeat 1 54 0
49 3.81 0.00 0.00 X_14075607_14075661_INS 1 54 (1) (TTTAT)n#Simple_repeat 1 54 (0) c_b1s251i162
X_14075607_14 1 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAGTTTAG 50
v v
(TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT 50
X_14075607_14 51 TTTA 54
(TTTAT)n#Simp 51 TTTA 54
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 38 7.0 0.0 0.0 X_140811327_140811383_INS 2 47 (10) + (AT)n Simple_repeat 1 46 (0) 284
ANNOTATION EVIDENCE:
38 6.99 0.00 0.00 X_140811327_140811383_INS 2 47 10 + (AT)n Simple_repeat 1 46 0
38 6.99 0.00 0.00 X_140811327_140811383_INS 2 47 (10) (AT)n#Simple_repeat 1 46 (0) c_b3s251i59
X_140811327_1 2 ATATATATATATATATATGTGTATACATATATATATATATATATAT 47
i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT 46
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 296 21.3 0.0 0.0 X_141145922_141146062_INS 15 75 (66) C HSAT4 Satellite/centr (40) 65 5 285
ANNOTATION EVIDENCE:
296 21.31 0.00 0.00 X_141145922_141146062_INS 15 75 66 C HSAT4 Satellite/centromeric 5 65 40
296 21.31 0.00 0.00 X_141145922_141146062_INS 15 75 (66) C HSAT4#Satellite/centromeric (40) 65 5 m_b3s502i0
X_141145922_1 15 AGAGACATCTGGTCCACCTTAGACATTGCAAGGGGACAGACACCTGGTCG 64
?i i v ii i vi v iv v ? ?
C HSAT4#Satelli 65 AGAGACNCCTGGCCGACCCCAGGCATTCTAATGATAGAGACNCCTGGNCG 16
X_141145922_1 65 ACCTCAGGCAT 75
i
C HSAT4#Satelli 15 ACCCCAGGCAT 5
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.21
Transitions / transversions = 1.60 (8/5)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 67 7.6 0.0 0.0 X_141207982_141208074_INS 10 93 (0) + (AT)n Simple_repeat 1 84 (0) 286
ANNOTATION EVIDENCE:
67 7.56 0.00 0.00 X_141207982_141208074_INS 10 93 0 + (AT)n Simple_repeat 1 84 0
67 7.56 0.00 0.00 X_141207982_141208074_INS 10 93 (0) (AT)n#Simple_repeat 1 84 (0) c_b3s251i58
X_141207982_1 10 ATATCTATATATATATATAGATATATATATATATCTATATATATATATAG 59
v v v v
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_141207982_1 60 ATATATATATATCTATATATATATAGATATATAT 93
v v
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATAT 84
Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0)
+ 2575 1.8 0.0 0.0 X_141387535_141387853_INS 11 319 (0) C AluY SINE/Alu (0) 311 1 287
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_141387535_141387853_INS 11 38 281 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_141387535_141387853_INS 11 38 (281) (T)n#Simple_repeat 1 28 (0) c_b3s251i57
X_141387535_1 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 38
(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)
2575 1.78 0.00 0.00 X_141387535_141387853_INS 39 319 0 C AluY SINE/Alu 1 281 30
2575 1.78 0.00 0.00 X_141387535_141387853_INS 39 319 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i1
X_141387535_1 39 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 88
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_141387535_1 89 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 138
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_141387535_1 139 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 188
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_141387535_1 189 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 238
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_141387535_1 239 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 288
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_141387535_1 289 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 319
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.47
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 67 0.0 3.0 0.0 X_141529336_141529402_INS 1 67 (0) + (TTTC)n Simple_repeat 1 69 (0) 288
ANNOTATION EVIDENCE:
67 0.00 2.99 0.00 X_141529336_141529402_INS 1 67 0 + (TTTC)n Simple_repeat 1 69 0
67 0.00 2.99 0.00 X_141529336_141529402_INS 1 67 (0) (TTTC)n#Simple_repeat 1 69 (0) c_b3s251i56
X_141529336_1 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_141529336_1 51 TCTTTC-TT-TTTCTTTCT 67
- -
(TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCT 69
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2)
+ 2230 3.7 0.0 3.7 X_141583591_141583894_INS 1 304 (0) C AluY SINE/Alu (0) 311 14 289
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_141583591_141583894_INS 1 26 278 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_141583591_141583894_INS 1 26 (278) (T)n#Simple_repeat 1 26 (0) c_b3s251i55
X_141583591_1 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2230 3.74 0.00 3.73 X_141583591_141583894_INS 27 304 0 C AluY SINE/Alu 14 281 30
2230 3.74 0.00 3.73 X_141583591_141583894_INS 27 304 (0) C AluY#SINE/Alu (30) 281 14 c_b3s352i2
X_141583591_1 27 GAGACGGAGTCTCGCTCTGTCACCCAGGCCGGACTGCGGACTGCAGTGGC 76
i i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_141583591_1 77 GCAATCTCGGCTCACTTGCAAGCTCCACTTCCCGGGTTCACGCCATTCTC 126
i - i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACT-GCAAGCTCCGCCTCCCGGGTTCACGCCATTCTC 190
X_141583591_1 127 CTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCCGCCACCGCGCC 176
i i
C AluY#SINE/Alu 189 CTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCC 140
X_141583591_1 177 CGGCTAATTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAG 226
-- v
C AluY#SINE/Alu 139 CGGCTAATTTTTT--GTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAG 92
X_141583591_1 227 CCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCC 276
i i
C AluY#SINE/Alu 91 CCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCC 42
X_141583591_1 277 CAAAGTGCTGGGATTACAGGCGTGAGCC 304
C AluY#SINE/Alu 41 CAAAGTGCTGGGATTACAGGCGTGAGCC 14
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.74
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.04 (10 / 277), avg. gap size = 1.00 (10 / 10)
+ 580 8.1 0.0 0.0 X_141730587_141730660_INS 1 74 (0) C L1PB LINE/L1 (1355) 4791 4718 290
ANNOTATION EVIDENCE:
580 8.11 0.00 0.00 X_141730587_141730660_INS 1 74 0 C L1PB_orf2 LINE/L1 2609 2682 612
580 8.11 0.00 0.00 X_141730587_141730660_INS 1 74 (0) C L1PB_orf2#LINE/L1 (612) 2682 2609 m_b3s551i0
X_141730587_1 1 CCTGTTTTTATACCAGTACCATGTTGTTTTGGTAACTATAGCCTTATAGT 50
i i i i
C L1PB_orf2#LIN 2682 CCTATTTTTATACCAGTACCATGCTGTTTTGGTGACTATGGCCTTATAGT 2633
X_141730587_1 51 GTAGTTTGAAGTCGGGTAATGCGA 74
i i
C L1PB_orf2#LIN 2632 ATAGTTTGAAGTCGGGTAATGTGA 2609
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.85
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 55 0.0 0.0 0.0 X_142060696_142060746_INS 2 51 (0) + (AAAAT)n Simple_repeat 1 50 (0) 291
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 X_142060696_142060746_INS 2 51 0 + (AAAAT)n Simple_repeat 1 50 0
55 0.00 0.00 0.00 X_142060696_142060746_INS 2 51 (0) (AAAAT)n#Simple_repeat 1 50 (0) c_b3s251i54
X_142060696_1 2 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAT 51
(AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 2553 2.5 0.0 0.0 X_142157168_142157484_INS 7 317 (0) C AluY SINE/Alu (0) 311 1 292
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 X_142157168_142157484_INS 7 36 281 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 X_142157168_142157484_INS 7 36 (281) (T)n#Simple_repeat 1 30 (0) c_b3s251i53
X_142157168_1 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
(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)
2553 2.49 0.00 0.00 X_142157168_142157484_INS 37 317 0 C AluY SINE/Alu 1 281 30
2553 2.49 0.00 0.00 X_142157168_142157484_INS 37 317 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i3
X_142157168_1 37 GAGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 86
i v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_142157168_1 87 CGGCTCACTGCAAGCTCCACCTCCCGGGTTCACGCCATTCTCCTGCCTCA 136
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_142157168_1 137 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 186
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_142157168_1 187 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 236
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_142157168_1 237 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 286
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_142157168_1 287 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 317
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2820 1.9 0.0 0.0 X_142499131_142499454_INS 18 324 (0) + AluY SINE/Alu 1 307 (4) 293
ANNOTATION EVIDENCE:
2820 1.95 0.00 0.00 X_142499131_142499454_INS 18 324 0 + AluY SINE/Alu 1 307 4
2820 1.95 0.00 0.00 X_142499131_142499454_INS 18 324 (0) AluY#SINE/Alu 1 307 (4) c_b3s352i4
X_142499131_1 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_142499131_1 68 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAATGG 117
i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_142499131_1 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_142499131_1 168 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 217
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_142499131_1 218 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 267
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_142499131_1 268 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_142499131_1 318 AAAAAAA 324
AluY#SINE/Alu 301 AAAAAAA 307
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.38
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 306), avg. gap size = 0.0 (0 / 0)
+ 553 0.0 0.0 0.0 X_142648892_142648993_INS 2 65 (37) C L1PA3 LINE/L1 (5) 6150 6087 294
ANNOTATION EVIDENCE:
553 0.00 0.00 0.00 X_142648892_142648993_INS 2 65 37 C L1PA3_3end LINE/L1 834 897 5
553 0.00 0.00 0.00 X_142648892_142648993_INS 2 65 (37) C L1PA3_3end#LINE/L1 (5) 897 834 m_b3s551i1
X_142648892_1 2 TTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGCAGG 51
C L1PA3_3end#LI 897 TTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGCAGG 848
X_142648892_1 52 TTAGTTACATATGT 65
C L1PA3_3end#LI 847 TTAGTTACATATGT 834
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 47 13.8 7.4 0.0 X_142751116_142751224_INS 2 109 (0) + (ATACAT)n Simple_repeat 1 116 (0) 295
ANNOTATION EVIDENCE:
47 13.77 7.41 0.00 X_142751116_142751224_INS 2 109 0 + (ATACAT)n Simple_repeat 1 116 0
47 13.77 7.41 0.00 X_142751116_142751224_INS 2 109 (0) (ATACAT)n#Simple_repeat 1 116 (0) m_b3s252i39
X_142751116_1 2 ATATATATACATAT--ATGTACATAT--ATGTACATATATATATACATAT 47
i -- i -- i i
(ATACAT)n#Sim 1 ATACATATACATATACATATACATATACATATACATATACATATACATAT 50
X_142751116_1 48 --ATATACATATACATATATATATACACAT--ATATATATATATATATGT 93
-- i i -- i i ii
(ATACAT)n#Sim 51 ACATATACATATACATATACATATACATATACATATACATATACATATAC 100
X_142751116_1 94 ATATGTATACACATAT 109
ii i
(ATACAT)n#Sim 101 ATATACATATACATAT 116
Matrix = Unknown
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.00 (8 / 4)
+ 49 2.2 0.0 0.0 X_142833451_142833503_INS 8 53 (0) + (TA)n Simple_repeat 1 46 (0) 296
ANNOTATION EVIDENCE:
49 2.22 0.00 0.00 X_142833451_142833503_INS 8 53 0 + (TA)n Simple_repeat 1 46 0
49 2.22 0.00 0.00 X_142833451_142833503_INS 8 53 (0) (TA)n#Simple_repeat 1 46 (0) c_b3s251i52
X_142833451_1 8 TATATATATATATATATATATATATATACATATATATATATATATA 53
i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATA 46
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 2471 2.9 0.0 1.8 X_142926112_142926429_INS 7 318 (0) C AluY SINE/Alu (0) 311 1 297
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_142926112_142926429_INS 7 32 286 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_142926112_142926429_INS 7 32 (286) (T)n#Simple_repeat 1 26 (0) c_b3s251i51
X_142926112_1 7 TTTTTTTTTTTTTTTTTTTTTTTTTT 32
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2471 2.85 0.00 1.78 X_142926112_142926429_INS 33 318 0 C AluY SINE/Alu 1 281 30
2471 2.85 0.00 1.78 X_142926112_142926429_INS 33 318 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i5
X_142926112_1 33 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 82
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_142926112_1 83 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 132
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_142926112_1 133 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 182
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_142926112_1 183 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTTTCTTAGCCGGG 232
----- v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCG-----TGTTAGCCAGG 87
X_142926112_1 233 ATGGTCTCGATCTCCTGACCTCATGATCCGCCCGCCTCGGCCTCCCAAAG 282
i
C AluY#SINE/Alu 86 ATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 37
X_142926112_1 283 TGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCC 318
i i
C AluY#SINE/Alu 36 TGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.58
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.02 (5 / 285), avg. gap size = 1.00 (5 / 5)
+ 373 19.1 0.0 0.0 X_142978225_142978293_INS 1 63 (6) C MSTA LTR/ERVL-MaLR (206) 222 160 298
ANNOTATION EVIDENCE:
373 19.05 0.00 0.00 X_142978225_142978293_INS 1 63 6 C MSTA LTR/ERVL-MaLR 160 222 206
373 19.05 0.00 0.00 X_142978225_142978293_INS 1 63 (6) C MSTA#LTR/ERVL-MaLR (206) 222 160 m_b3s502i1
X_142978225_1 1 AGAGACAGAGAATGAAAGGGGAAGTGCTACACACTTTCAAACAACCAGGT 50
?i v ii ii i i i i
C MSTA#LTR/ERVL 222 AGNAAGAGAGAGCGAGGGGGGAGGTGCCACACACTTTTAAACAACCAGAT 173
X_142978225_1 51 CTTGTGAGTACTC 63
i v
C MSTA#LTR/ERVL 172 CTCGTGAGAACTC 160
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.27
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 35 9.1 0.0 0.0 X_143000957_143001009_INS 5 52 (1) + (TA)n Simple_repeat 1 48 (0) 299
ANNOTATION EVIDENCE:
35 9.12 0.00 0.00 X_143000957_143001009_INS 5 52 1 + (TA)n Simple_repeat 1 48 0
35 9.12 0.00 0.00 X_143000957_143001009_INS 5 52 (1) (TA)n#Simple_repeat 1 48 (0) c_b3s251i50
X_143000957_1 5 TATATATACATATATATATGTATATATACATATATATATGTATATATA 52
i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 72 1.5 0.0 0.0 X_14311839_14311907_INS 1 68 (1) + (TTCT)n Simple_repeat 1 68 (0) 300
ANNOTATION EVIDENCE:
72 1.49 0.00 0.00 X_14311839_14311907_INS 1 68 1 + (TTCT)n Simple_repeat 1 68 0
72 1.49 0.00 0.00 X_14311839_14311907_INS 1 68 (1) (TTCT)n#Simple_repeat 1 68 (0) c_b1s251i161
X_14311839_14 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTCTTTCTTT 50
i
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50
X_14311839_14 51 CTTTCTTTCTTTCTTTCT 68
(TTCT)n#Simpl 51 CTTTCTTTCTTTCTTTCT 68
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 45 0.0 0.0 0.0 X_143424699_143424749_INS 1 49 (2) + (A)n Simple_repeat 1 49 (0) 301
ANNOTATION EVIDENCE:
45 0.00 0.00 0.00 X_143424699_143424749_INS 1 49 2 + (A)n Simple_repeat 1 49 0
45 0.00 0.00 0.00 X_143424699_143424749_INS 1 49 (2) (A)n#Simple_repeat 1 49 (0) m_b3s252i38
X_143424699_1 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 31 11.4 0.0 0.0 X_143456504_143456559_INS 1 49 (7) + (AT)n Simple_repeat 1 49 (0) 302
ANNOTATION EVIDENCE:
31 11.41 0.00 0.00 X_143456504_143456559_INS 1 49 7 + (AT)n Simple_repeat 1 49 0
31 11.41 0.00 0.00 X_143456504_143456559_INS 1 49 (7) (AT)n#Simple_repeat 1 49 (0) c_b3s251i49
X_143456504_1 1 ATATATATACACACATATATATATATACACATATATATATATATATATA 49
i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 327 5.9 7.8 0.0 X_143482081_143482131_INS 1 51 (0) + L1M1 LINE/L1 2615 2669 (4896) 303
ANNOTATION EVIDENCE:
327 5.88 7.84 0.00 X_143482081_143482131_INS 1 51 0 + L1M1_5end LINE/L1 2615 2669 1006
327 5.88 7.84 0.00 X_143482081_143482131_INS 1 51 (0) L1M1_5end#LINE/L1 2615 2669 (1006) m_b3s551i2
X_143482081_1 1 CAGTATCCT-GTACAAGA---TTATAGAACACCAAGCAGATTTAATCCAA 46
i v- --- i
L1M1_5end#LIN 2615 CAATATCCAAGTACAAGAAGGTTATAGAACACCAAGCAGATTTAACCCAA 2664
X_143482081_1 47 AGAAG 51
L1M1_5end#LIN 2665 AGAAG 2669
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.16
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.04 (2 / 50), avg. gap size = 2.00 (4 / 2)
+ 2806 1.6 0.0 0.0 X_143723336_143723653_INS 16 318 (0) + AluY SINE/Alu 1 303 (8) 304
ANNOTATION EVIDENCE:
2806 1.65 0.00 0.00 X_143723336_143723653_INS 16 318 0 + AluY SINE/Alu 1 303 8
2806 1.65 0.00 0.00 X_143723336_143723653_INS 16 318 (0) AluY#SINE/Alu 1 303 (8) c_b3s352i6
X_143723336_1 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_143723336_1 66 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAAAACGG 115
v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_143723336_1 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_143723336_1 166 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 215
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_143723336_1 216 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATCCCGCCACTGCACTC 265
i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_143723336_1 266 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 315
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_143723336_1 316 AAA 318
AluY#SINE/Alu 301 AAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.06
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 65 1.3 5.2 0.0 X_143729294_143729373_INS 1 77 (3) + (ATAGATAT)n Simple_repeat 1 81 (0) 305
ANNOTATION EVIDENCE:
65 1.31 5.19 0.00 X_143729294_143729373_INS 1 77 3 + (ATAGATAT)n Simple_repeat 1 81 0
65 1.31 5.19 0.00 X_143729294_143729373_INS 1 77 (3) (ATAGATAT)n#Simple_repeat 1 81 (0) c_b3s251i48
X_143729294_1 1 ATAGATAGATAG--ATATAGATATATAGATATATAGATATATAG--ATAT 46
v -- --
(ATAGATAT)n#S 1 ATAGATATATAGATATATAGATATATAGATATATAGATATATAGATATAT 50
X_143729294_1 47 AGATATATAGATATATAGATATATAGATATA 77
(ATAGATAT)n#S 51 AGATATATAGATATATAGATATATAGATATA 81
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.03 (2 / 76), avg. gap size = 2.00 (4 / 2)
+ 72 6.3 7.3 0.0 X_143750893_143751033_INS 6 141 (0) + (TATGTGCATA)n Simple_repeat 1 146 (0) 306
ANNOTATION EVIDENCE:
72 6.26 7.35 0.00 X_143750893_143751033_INS 6 141 0 + (TATGTGCATA)n Simple_repeat 1 146 0
72 6.26 7.35 0.00 X_143750893_143751033_INS 6 141 (0) (TATGTGCATA)n#Simple_repeat 1 146 (0) c_b3s251i47
X_143750893_1 6 TATGTGCATATATGT--ATATATGTACATGTGTGTGCATATATGT--ATA 51
-- i i i --
(TATGTGCATA)n 1 TATGTGCATATATGTGCATATATGTGCATATATGTGCATATATGTGCATA 50
X_143750893_1 52 TATGTACATGTATGTGCATATATGT--ATATATGTACATGTATGTGCATA 99
i i -- i i
(TATGTGCATA)n 51 TATGTGCATATATGTGCATATATGTGCATATATGTGCATATATGTGCATA 100
X_143750893_1 100 TATGT--ATATATGTGCATGTATGTGCATATATGT--ATATATGTG 141
-- i --
(TATGTGCATA)n 101 TATGTGCATATATGTGCATATATGTGCATATATGTGCATATATGTG 146
Matrix = Unknown
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.04 (5 / 135), avg. gap size = 2.00 (10 / 5)
+ 69 12.6 0.0 0.0 X_143793948_143794072_INS 4 120 (5) + (AT)n Simple_repeat 1 117 (0) 307
ANNOTATION EVIDENCE:
69 12.57 0.00 0.00 X_143793948_143794072_INS 4 120 5 + (AT)n Simple_repeat 1 117 0
69 12.57 0.00 0.00 X_143793948_143794072_INS 4 120 (5) (AT)n#Simple_repeat 1 117 (0) c_b3s251i46
X_143793948_1 4 ATATATATATATACACATATATATATACATATATATACACATATATATAC 53
i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_143793948_1 54 ATATATATATATACACATATATATACATATATATATACACACATATATAT 103
i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_143793948_1 104 ATATACATATATATATA 120
i
(AT)n#Simple_ 101 ATATATATATATATATA 117
Matrix = Unknown
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.00 (0 / 116), avg. gap size = 0.0 (0 / 0)
+ 2819 0.7 0.0 0.0 X_143806454_143806765_INS 16 312 (0) + AluY SINE/Alu 1 297 (14) 308
ANNOTATION EVIDENCE:
2819 0.67 0.00 0.00 X_143806454_143806765_INS 16 312 0 + AluY SINE/Alu 1 297 14
2819 0.67 0.00 0.00 X_143806454_143806765_INS 16 312 (0) AluY#SINE/Alu 1 297 (14) c_b3s352i7
X_143806454_1 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_143806454_1 66 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 115
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_143806454_1 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_143806454_1 166 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 215
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_143806454_1 216 GAACCTGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 265
i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_143806454_1 266 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 312
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.37
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 296), avg. gap size = 0.0 (0 / 0)
+ 2549 1.8 0.0 0.4 X_144060264_144060594_INS 11 331 (0) C AluY SINE/Alu (0) 311 2 309
ANNOTATION EVIDENCE:
38 2.56 0.00 0.00 X_144060264_144060594_INS 11 50 281 + (T)n Simple_repeat 1 40 0
38 2.56 0.00 0.00 X_144060264_144060594_INS 11 50 (281) (T)n#Simple_repeat 1 40 (0) c_b3s251i45
X_144060264_1 11 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2549 1.79 0.00 0.36 X_144060264_144060594_INS 51 331 0 C AluY SINE/Alu 2 281 30
2549 1.79 0.00 0.36 X_144060264_144060594_INS 51 331 (0) C AluY#SINE/Alu (30) 281 2 c_b3s352i8
X_144060264_1 51 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCT 100
i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_144060264_1 101 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 150
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_144060264_1 151 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 200
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_144060264_1 201 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 250
- v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_144060264_1 251 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 300
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_144060264_1 301 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 331
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.15
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 442 0.0 0.0 0.0 X_144188808_144188860_INS 1 53 (0) + L1HS LINE/L1 5856 5908 (247) 310
ANNOTATION EVIDENCE:
442 0.00 0.00 0.00 X_144188808_144188860_INS 1 53 0 + L1HS_3end LINE/L1 603 655 247
442 0.00 0.00 0.00 X_144188808_144188860_INS 1 53 (0) L1HS_3end#LINE/L1 603 655 (247) m_b3s551i3
X_144188808_1 1 ATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAAC 50
L1HS_3end#LIN 603 ATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAAC 652
X_144188808_1 51 ACC 53
L1HS_3end#LIN 653 ACC 655
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 18 6.3 5.9 0.0 X_14419498_14419595_INS 8 41 (57) + (TCATACG)n Simple_repeat 1 36 (0) 311
ANNOTATION EVIDENCE:
18 6.26 5.88 0.00 X_14419498_14419595_INS 8 41 57 + (TCATACG)n Simple_repeat 1 36 0
18 6.26 5.88 0.00 X_14419498_14419595_INS 8 41 (57) (TCATACG)n#Simple_repeat 1 36 (0) m_b1s252i121
X_14419498_14 8 TCATACGT-ATGCGTCATACGT-ATGCGTCATACGT 41
- i - i
(TCATACG)n#Si 1 TCATACGTCATACGTCATACGTCATACGTCATACGT 36
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2)
+ 2812 1.6 0.0 0.0 X_144443218_144443531_INS 10 314 (0) C AluY SINE/Alu (6) 305 1 312
ANNOTATION EVIDENCE:
2812 1.64 0.00 0.00 X_144443218_144443531_INS 10 314 0 C AluY SINE/Alu 1 305 6
2812 1.64 0.00 0.00 X_144443218_144443531_INS 10 314 (0) C AluY#SINE/Alu (6) 305 1 c_b3s352i9
X_144443218_1 10 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 59
C AluY#SINE/Alu 305 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 256
X_144443218_1 60 GGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCG 109
v
C AluY#SINE/Alu 255 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCG 206
X_144443218_1 110 GGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGG 159
i
C AluY#SINE/Alu 205 GGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 156
X_144443218_1 160 CGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGG 209
i
C AluY#SINE/Alu 155 CGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGG 106
X_144443218_1 210 TTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGC 259
v i
C AluY#SINE/Alu 105 TTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGC 56
X_144443218_1 260 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 309
C AluY#SINE/Alu 55 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 6
X_144443218_1 310 CGGCC 314
C AluY#SINE/Alu 5 CGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 304), avg. gap size = 0.0 (0 / 0)
+ 35 8.5 7.9 0.0 X_144576638_144576702_INS 2 64 (1) + (AT)n Simple_repeat 1 68 (0) 313
ANNOTATION EVIDENCE:
35 8.51 7.94 0.00 X_144576638_144576702_INS 2 64 1 + (AT)n Simple_repeat 1 68 0
35 8.51 7.94 0.00 X_144576638_144576702_INS 2 64 (1) (AT)n#Simple_repeat 1 68 (0) m_b3s252i37
X_144576638_1 2 ATATAT-TATATAT-TATATATACACATATAGA-ATATAT-TATATAT-T 46
- - i i v - - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_144576638_1 47 ATATATACACATATATAT 64
i i
(AT)n#Simple_ 51 ATATATATATATATATAT 68
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5)
+ 20 5.8 0.0 7.7 X_144596177_144596244_INS 25 66 (2) + (TAGTTAA)n Simple_repeat 1 39 (0) 314
ANNOTATION EVIDENCE:
20 5.78 0.00 7.69 X_144596177_144596244_INS 25 66 2 + (TAGTTAA)n Simple_repeat 1 39 0
20 5.78 0.00 7.69 X_144596177_144596244_INS 25 66 (2) (TAGTTAA)n#Simple_repeat 1 39 (0) m_b3s252i35
X_144596177_1 25 TAGTTAATAGTAAAATAGTTAATAGTAAAAATAGTTAATAGT 66
-v --v
(TAGTTAA)n#Si 1 TAGTTAATAGT-TAATAGTTAATAGT--TAATAGTTAATAGT 39
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3)
+ 36 0.0 0.0 0.0 X_144902642_144902699_INS 5 35 (23) + (CA)n Simple_repeat 1 31 (0) 315
ANNOTATION EVIDENCE:
36 0.00 0.00 0.00 X_144902642_144902699_INS 5 35 23 + (CA)n Simple_repeat 1 31 0
36 0.00 0.00 0.00 X_144902642_144902699_INS 5 35 (23) (CA)n#Simple_repeat 1 31 (0) c_b3s251i44
X_144902642_1 5 CACACACACACACACACACACACACACACAC 35
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACAC 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 18 0.0 0.0 0.0 X_144902642_144902699_INS 36 55 (3) + (TC)n Simple_repeat 1 20 (0) 316
ANNOTATION EVIDENCE:
18 0.00 0.00 0.00 X_144902642_144902699_INS 36 55 3 + (TC)n Simple_repeat 1 20 0
18 0.00 0.00 0.00 X_144902642_144902699_INS 36 55 (3) (TC)n#Simple_repeat 1 20 (0) m_b3s252i34
X_144902642_1 36 TCTCTCTCTCTCTCTCTCTC 55
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTC 20
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 34 12.7 0.0 0.0 X_144934749_144934826_INS 15 75 (3) + (TG)n Simple_repeat 1 61 (0) 317
ANNOTATION EVIDENCE:
34 12.65 0.00 0.00 X_144934749_144934826_INS 15 75 3 + (TG)n Simple_repeat 1 61 0
34 12.65 0.00 0.00 X_144934749_144934826_INS 15 75 (3) (TG)n#Simple_repeat 1 61 (0) c_b3s251i43
X_144934749_1 15 TGTGTGTATGTGCGTGTGTGTGTGTGCATGTGTGTGTCTGTGTGTGTGTC 64
i i ii v v
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50
X_144934749_1 65 TGCGTGTGTGT 75
i
(TG)n#Simple_ 51 TGTGTGTGTGT 61
Matrix = Unknown
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 4.2 X_144999534_144999586_INS 4 53 (0) + (TATATATCTA)n Simple_repeat 1 48 (0) 318
ANNOTATION EVIDENCE:
44 0.00 0.00 4.17 X_144999534_144999586_INS 4 53 0 + (TATATATCTA)n Simple_repeat 1 48 0
44 0.00 0.00 4.17 X_144999534_144999586_INS 4 53 (0) (TATATATCTA)n#Simple_repeat 1 48 (0) c_b3s251i42
X_144999534_1 4 TATATATCTATATATATCTATATATATCTATATATATATCTATATATATC 53
--
(TATATATCTA)n 1 TATATATCTATATATATCTATATATATC--TATATATATCTATATATATC 48
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2)
+ 28 0.0 12.5 1.6 X_145016971_145017028_INS 3 58 (0) + (ATTACAT)n Simple_repeat 1 62 (0) 319
ANNOTATION EVIDENCE:
28 0.00 12.50 1.61 X_145016971_145017028_INS 3 58 0 + (ATTACAT)n Simple_repeat 1 62 0
28 0.00 12.50 1.61 X_145016971_145017028_INS 3 58 (0) (ATTACAT)n#Simple_repeat 1 62 (0) c_b3s251i41
X_145016971_1 3 ATTACATATTACATATTA-A-ATTACATATTA-ATATGTA-AT-TTA-AT 46
- - - - - - -
(ATTACAT)n#Si 1 ATTACATATTACATATTACATATTACATATTACATAT-TACATATTACAT 49
X_145016971_1 47 -TTACATATTACA 58
-
(ATTACAT)n#Si 50 ATTACATATTACA 62
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.15 (8 / 55), avg. gap size = 1.00 (8 / 8)
+ 42 25.9 0.0 0.0 X_145124665_145124761_INS 4 97 (0) + (AT)n Simple_repeat 1 94 (0) 320
ANNOTATION EVIDENCE:
42 25.90 0.00 0.00 X_145124665_145124761_INS 4 97 0 + (AT)n Simple_repeat 1 94 0
42 25.90 0.00 0.00 X_145124665_145124761_INS 4 97 (0) (AT)n#Simple_repeat 1 94 (0) m_b3s252i33
X_145124665_1 4 ATATATATGTGTATATATATACACATATATGTGTGTATATATATACACAC 53
i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_145124665_1 54 ATATATGTGTGTATATATACACACATATATGTGTGTATATATAT 97
i i i i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATAT 94
Matrix = Unknown
Transitions / transversions = 1.00 (19/0)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0)
+ 267 23.6 0.0 0.0 X_145288810_145289166_INS 17 71 (286) C MLT1E1A LTR/ERVL-MaLR (341) 339 285 321
ANNOTATION EVIDENCE:
267 23.64 0.00 0.00 X_145288810_145289166_INS 17 71 286 C MLT1E1A LTR/ERVL-MaLR 285 339 341
267 23.64 0.00 0.00 X_145288810_145289166_INS 17 71 (286) C MLT1E1A#LTR/ERVL-MaLR (341) 339 285 m_b3s502i2
X_145288810_1 17 GGATCTTGCACAACATAGAAGCTTACGTCTTCAAGGTCAAGTGGAGAATA 66
vi iv i v i v i ivv v
C MLT1E1A#LTR/E 339 GGCCCTCTCACAACATGGCAGCTTGCTTCTTCAAGGCCAGCAGGAGAATC 290
X_145288810_1 67 TCTCT 71
C MLT1E1A#LTR/E 289 TCTCT 285
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.53
Transitions / transversions = 0.86 (6/7)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 692 15.3 0.7 10.7 X_145288810_145289166_INS 94 247 (110) C MLT1E1A LTR/ERVL-MaLR (540) 140 1 321
ANNOTATION EVIDENCE:
692 15.28 0.65 10.71 X_145288810_145289166_INS 94 247 110 C MLT1E1A LTR/ERVL-MaLR 1 140 540
692 15.28 0.65 10.71 X_145288810_145289166_INS 94 247 (110) C MLT1E1A#LTR/ERVL-MaLR (540) 140 1 m_b3s502i3
X_145288810_1 94 ATATCTTGTAAGATAATCACAAGGAGTGACTATCCCGTCACTCTTTACCA 143
vv vv i- - i ----------
C MLT1E1A#LTR/E 140 ATATAATGTAACCTAATCACG-GGAGTGA-TATCCCATCA---------- 103
X_145288810_1 144 TATTCACAGGTCTTACCCCCATACTCAAGGGGTGGAAATTATACAGAGCA 193
i-- v i v ii i i
C MLT1E1A#LTR/E 102 TATTCACAGGTCC--CGCCCACACTCAAGGGGAGGGGATTATACAGGGCG 55
X_145288810_1 194 TGTAAACCAACTGGGCAGGAATCTTGGGGACCAT-TTAAAATTCTGTCTA 242
v i-v i i - i i
C MLT1E1A#LTR/E 54 TGTACACCAG-GGGGCGGGAATCTTGGGGGCCATCTTAGAATTCTGCCTA 6
X_145288810_1 243 CCACA 247
C MLT1E1A#LTR/E 5 CCACA 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.58
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.10 (16 / 153), avg. gap size = 1.00 (16 / 16)
+ 286 10.4 0.0 0.0 X_145332319_145332373_INS 1 48 (7) + L1M2 LINE/L1 4578 4625 (1518) 322
ANNOTATION EVIDENCE:
286 10.42 0.00 0.00 X_145332319_145332373_INS 1 48 7 + L1M2_orf2 LINE/L1 2469 2516 775
286 10.42 0.00 0.00 X_145332319_145332373_INS 1 48 (7) L1M2_orf2#LINE/L1 2469 2516 (775) m_b3s551i4
X_145332319_1 1 ATTCAATGCAAACCCTATCAAAACACCAATGTCATTCTTCAAAGCAAT 48
v i v v v
L1M2_orf2#LIN 2469 ATTCAATGCAATCCCTATCAAAATACCAATGACATTCTTCACAGAAAT 2516
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.23
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 35 6.8 0.0 0.0 X_145342990_145343050_INS 2 48 (13) + (ATATATACAC)n Simple_repeat 1 47 (0) 323
ANNOTATION EVIDENCE:
35 6.83 0.00 0.00 X_145342990_145343050_INS 2 48 13 + (ATATATACAC)n Simple_repeat 1 47 0
35 6.83 0.00 0.00 X_145342990_145343050_INS 2 48 (13) (ATATATACAC)n#Simple_repeat 1 47 (0) c_b3s251i40
X_145342990_1 2 ATATATACACATATATATGTATATATACACATATATACACATATATA 48
iii
(ATATATACAC)n 1 ATATATACACATATATACACATATATACACATATATACACATATATA 47
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 43 7.2 0.0 0.0 X_145422612_145422672_INS 2 61 (0) + (TTCT)n Simple_repeat 1 60 (0) 324
ANNOTATION EVIDENCE:
43 7.16 0.00 0.00 X_145422612_145422672_INS 2 61 0 + (TTCT)n Simple_repeat 1 60 0
43 7.16 0.00 0.00 X_145422612_145422672_INS 2 61 (0) (TTCT)n#Simple_repeat 1 60 (0) m_b3s252i32
X_145422612_1 2 TTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCTTTCTTTCTTT 51
i i i i
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50
X_145422612_1 52 CTTTCTTTCT 61
(TTCT)n#Simpl 51 CTTTCTTTCT 60
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 85 4.5 1.7 1.7 X_145464265_145464385_INS 2 121 (0) + (GAGG)n Simple_repeat 1 120 (0) 325
ANNOTATION EVIDENCE:
85 4.51 1.67 1.67 X_145464265_145464385_INS 2 121 0 + (GAGG)n Simple_repeat 1 120 0
85 4.51 1.67 1.67 X_145464265_145464385_INS 2 121 (0) (GAGG)n#Simple_repeat 1 120 (0) m_b3s252i31
X_145464265_1 2 GAGGGAGGGAGGGAGGGAGGGAAGGAAGGAAGGGAGGGAGGGAGGGA-GG 50
- i i -
(GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGG-AGGGAGGGAGGGAGGGAGGGAGGGAGGG 49
X_145464265_1 51 AAGGAGGGAGGGAGGGAGGGA-GGAAGGAAGGAGGGAGGGAGGGAGGGAG 99
i - i i
(GAGG)n#Simpl 50 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 99
X_145464265_1 100 GGAGGGAAGGGAGGGAGGGAGG 121
-
(GAGG)n#Simpl 100 GGAGGG-AGGGAGGGAGGGAGG 120
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.00 (4 / 4)
+ 84 20.3 0.0 0.0 X_145473644_145473804_INS 1 156 (5) + (AT)n Simple_repeat 1 156 (0) 326
ANNOTATION EVIDENCE:
84 20.27 0.00 0.00 X_145473644_145473804_INS 1 156 5 + (AT)n Simple_repeat 1 156 0
84 20.27 0.00 0.00 X_145473644_145473804_INS 1 156 (5) (AT)n#Simple_repeat 1 156 (0) m_b3s252i30
X_145473644_1 1 ATGTATATATATACACATATATGTATATATACATATATATGTGTATATAT 50
i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_145473644_1 51 ACACACATATATATGTATATATACATATATGTGTATATATACACACACAT 100
i i i i i i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_145473644_1 101 ATGTATATATACATATATGTGTATATATATACACATATATGTATATATAC 150
i i i i i i i i
(AT)n#Simple_ 101 ATATATATATATATATATATATATATATATATATATATATATATATATAT 150
X_145473644_1 151 ATATAT 156
(AT)n#Simple_ 151 ATATAT 156
Matrix = Unknown
Transitions / transversions = 1.00 (26/0)
Gap_init rate = 0.00 (0 / 155), avg. gap size = 0.0 (0 / 0)
+ 267 14.3 0.0 0.0 X_145475238_145475308_INS 21 69 (2) C L1M1 LINE/L1 (5001) 2564 2516 327
ANNOTATION EVIDENCE:
267 14.29 0.00 0.00 X_145475238_145475308_INS 21 69 2 C L1M1_5end LINE/L1 2516 2564 1111
267 14.29 0.00 0.00 X_145475238_145475308_INS 21 69 (2) C L1M1_5end#LINE/L1 (1111) 2564 2516 m_b3s551i5
X_145475238_1 21 ACTCTCTTCCCCTGTCTTTTTCTCTACCTATTCTTTAAGGCCAAAAACT 69
i v i i vi v
C L1M1_5end#LIN 2564 ACTTTCTACCCCTATCTCTTTCTCTACCTCCTCTTTAAGGCCAATAACT 2516
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.98
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 2790 2.6 0.0 0.0 X_145539104_145539431_INS 17 325 (3) + AluY SINE/Alu 1 309 (2) 328
ANNOTATION EVIDENCE:
2790 2.59 0.00 0.00 X_145539104_145539431_INS 17 325 3 + AluY SINE/Alu 1 309 2
2790 2.59 0.00 0.00 X_145539104_145539431_INS 17 325 (3) AluY#SINE/Alu 1 309 (2) c_b3s352i10
X_145539104_1 17 GGCCGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGA 66
i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_145539104_1 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 116
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_145539104_1 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_145539104_1 167 GGGCGCCTGTAGGCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 216
v i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_145539104_1 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 266
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_145539104_1 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_145539104_1 317 AAAAAAAAA 325
AluY#SINE/Alu 301 AAAAAAAAA 309
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.74
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.00 (0 / 308), avg. gap size = 0.0 (0 / 0)
+ 47 5.9 0.0 0.0 X_145727192_145727246_INS 1 54 (1) + (TA)n Simple_repeat 1 54 (0) 329
ANNOTATION EVIDENCE:
47 5.89 0.00 0.00 X_145727192_145727246_INS 1 54 1 + (TA)n Simple_repeat 1 54 0
47 5.89 0.00 0.00 X_145727192_145727246_INS 1 54 (1) (TA)n#Simple_repeat 1 54 (0) c_b3s251i39
X_145727192_1 1 TATATATATATATATACATATATATATATATATACACATATATATATATA 50
i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_145727192_1 51 TATA 54
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 2839 2.2 0.0 0.0 X_145758632_145758961_INS 19 329 (1) + AluY SINE/Alu 1 311 (0) 330
ANNOTATION EVIDENCE:
2839 2.25 0.00 0.00 X_145758632_145758961_INS 19 329 1 + AluY SINE/Alu 1 311 0
2839 2.25 0.00 0.00 X_145758632_145758961_INS 19 329 (1) AluY#SINE/Alu 1 311 (0) c_b3s352i11
X_145758632_1 19 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 68
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_145758632_1 69 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 118
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_145758632_1 119 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 168
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_145758632_1 169 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 218
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_145758632_1 219 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 268
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_145758632_1 269 CAGCCTGGGTGACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAA 318
i i
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_145758632_1 319 AAAAAAAAAAA 329
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 51 26.1 0.0 0.0 X_145893813_145894127_INS 4 116 (199) + (TA)n Simple_repeat 1 113 (0) 331
ANNOTATION EVIDENCE:
51 26.13 0.00 0.00 X_145893813_145894127_INS 4 116 199 + (TA)n Simple_repeat 1 113 0
51 26.13 0.00 0.00 X_145893813_145894127_INS 4 116 (199) (TA)n#Simple_repeat 1 113 (0) m_b3s252i28
X_145893813_1 4 TACATATATGTGTATATACGTATATACACATATATATGTGTACATATATG 53
i i i ii i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_145893813_1 54 TGTATATATGTATATACACATATATATGTGTATATATGTATATACACATA 103
i i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_145893813_1 104 TATATGTGTACAT 116
i i i
(TA)n#Simple_ 101 TATATATATATAT 113
Matrix = Unknown
Transitions / transversions = 1.00 (23/0)
Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.0 (0 / 0)
+ 241 21.8 3.4 1.1 X_145893813_145894127_INS 117 204 (111) + L1MD3 LINE/L1 6579 6668 (1327) 332
ANNOTATION EVIDENCE:
241 21.83 3.41 1.11 X_145893813_145894127_INS 117 204 111 + L1MD3_3end LINE/L1 1326 1415 1327
241 21.83 3.41 1.11 X_145893813_145894127_INS 117 204 (111) L1MD3_3end#LINE/L1 1326 1415 (1327) m_b3s551i6
X_145893813_1 117 ATAT-GTGTGTACATATATGTATATACACACACATATACACACATATATG 165
- i v vi i v v -i ? iv v i ? ?
L1MD3_3end#LI 1326 ATATCGTATGAACTCATGTTTATTT-TANACGGATATACAAATANANATG 1374
X_145893813_1 166 TACACATATATATGT--GTATATACATATACACACATATAT 204
v i i iv -- i i
L1MD3_3end#LI 1375 TAAATATACATGGGTTAGTATACACATATACATACATATAT 1415
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.73
Transitions / transversions = 1.38 (11/8)
Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.33 (4 / 3)
+ 41 30.6 0.0 0.0 X_145893813_145894127_INS 211 315 (0) + (AT)n Simple_repeat 1 105 (0) 333
ANNOTATION EVIDENCE:
41 30.55 0.00 0.00 X_145893813_145894127_INS 211 315 0 + (AT)n Simple_repeat 1 105 0
41 30.55 0.00 0.00 X_145893813_145894127_INS 211 315 (0) (AT)n#Simple_repeat 1 105 (0) m_b3s252i29
X_145893813_1 211 ATATATGTGTGTATATACATATATACACATATATGTACACATATATATGT 260
i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_145893813_1 261 GTATATACGTATATACACATATATGTACACATATGTGTGTATATATGTGT 310
i ii i i i i i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_145893813_1 311 GTATA 315
i
(AT)n#Simple_ 101 ATATA 105
Matrix = Unknown
Transitions / transversions = 1.00 (24/0)
Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.0 (0 / 0)
+ 43 26.6 0.0 0.0 X_145893886_145893988_INS 2 98 (5) + (AT)n Simple_repeat 1 97 (0) 334
ANNOTATION EVIDENCE:
43 26.58 0.00 0.00 X_145893886_145893988_INS 2 98 5 + (AT)n Simple_repeat 1 97 0
43 26.58 0.00 0.00 X_145893886_145893988_INS 2 98 (5) (AT)n#Simple_repeat 1 97 (0) m_b3s252i27
X_145893886_1 2 ATATATATGTGTGTATATGTGTGTGTATATACATATATGTGTATATACGT 51
i i i i i i i i i i ii
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_145893886_1 52 ATATACACATATATGTGTGTATATATGTGTATATATATACATATATA 98
i i i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATA 97
Matrix = Unknown
Transitions / transversions = 1.00 (20/0)
Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0)
+ 941 1.0 0.0 0.0 X_146005361_146005501_INS 7 140 (1) C AluY SINE/Alu (0) 311 178 335
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 X_146005361_146005501_INS 7 36 105 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 X_146005361_146005501_INS 7 36 (105) (T)n#Simple_repeat 1 30 (0) c_b3s251i38
X_146005361_1 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
(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)
941 0.96 0.00 0.00 X_146005361_146005501_INS 37 140 1 C AluY SINE/Alu 178 281 30
941 0.96 0.00 0.00 X_146005361_146005501_INS 37 140 (1) C AluY#SINE/Alu (30) 281 178 m_b3s356i0
X_146005361_1 37 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 86
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_146005361_1 87 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 136
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_146005361_1 137 GCCT 140
C AluY#SINE/Alu 181 GCCT 178
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.97
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0)
+ 32 11.4 0.0 2.0 X_14607828_14607879_INS 1 51 (1) + (AT)n Simple_repeat 1 50 (0) 336
ANNOTATION EVIDENCE:
32 11.39 0.00 2.00 X_14607828_14607879_INS 1 51 1 + (AT)n Simple_repeat 1 50 0
32 11.39 0.00 2.00 X_14607828_14607879_INS 1 51 (1) (AT)n#Simple_repeat 1 50 (0) m_b1s252i120
X_14607828_14 1 ATATACATATATATATATATGTATAGTGTATATATATACACATATATATA 50
i i - i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATA-TATATATATATATATATATATATA 49
X_14607828_14 51 T 51
(AT)n#Simple_ 50 T 50
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 26 17.7 0.0 0.0 X_146133844_146133903_INS 3 54 (6) + (ATATAC)n Simple_repeat 1 52 (0) 337
ANNOTATION EVIDENCE:
26 17.68 0.00 0.00 X_146133844_146133903_INS 3 54 6 + (ATATAC)n Simple_repeat 1 52 0
26 17.68 0.00 0.00 X_146133844_146133903_INS 3 54 (6) (ATATAC)n#Simple_repeat 1 52 (0) m_b3s252i26
X_146133844_1 3 ATACACATATACAAATACATATGTGTATATATACACATATACAAATACAT 52
i v iii i i v
(ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATACATATACATATACAT 50
X_146133844_1 53 AT 54
(ATATAC)n#Sim 51 AT 52
Matrix = Unknown
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 23 30.1 0.0 0.0 X_146133844_146133903_INS 55 60 (0) + (AT)n Simple_repeat 3 60 (0) 338
ANNOTATION EVIDENCE:
23 30.12 0.00 0.00 X_146133844_146133903_INS 1 60 0 + (AT)n Simple_repeat 1 60 0
23 30.12 0.00 0.00 X_146133844_146133903_INS 1 60 (0) (AT)n#Simple_repeat 1 60 (0) m_b3s252i25
X_146133844_1 1 ATATACACATATACAAATACATATGTGTATATATACACATATACAAATAC 50
i i i v i i i i i i v i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_146133844_1 51 ATATGTGTAT 60
i i
(AT)n#Simple_ 51 ATATATATAT 60
Matrix = Unknown
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 25 22.3 0.0 0.0 X_146175931_146175981_INS 2 51 (0) + (TA)n Simple_repeat 1 50 (0) 339
ANNOTATION EVIDENCE:
25 22.31 0.00 0.00 X_146175931_146175981_INS 2 51 0 + (TA)n Simple_repeat 1 50 0
25 22.31 0.00 0.00 X_146175931_146175981_INS 2 51 (0) (TA)n#Simple_repeat 1 50 (0) m_b3s252i24
X_146175931_1 2 TATATATATATATGTGTGTGTGTGTGTGTGTATATATATATATATATATA 51
i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 38 21.6 0.0 0.0 X_146233875_146233949_INS 2 75 (0) + (AT)n Simple_repeat 1 74 (0) 340
ANNOTATION EVIDENCE:
38 21.64 0.00 0.00 X_146233875_146233949_INS 2 75 0 + (AT)n Simple_repeat 1 74 0
38 21.64 0.00 0.00 X_146233875_146233949_INS 2 75 (0) (AT)n#Simple_repeat 1 74 (0) m_b3s252i23
X_146233875_1 2 ATATATGTGTATATATGTACATATATGTATACATATATGTGTATATATGT 51
i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_146233875_1 52 ACATATATGTATACATATATACAT 75
i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATAT 74
Matrix = Unknown
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 423 15.8 0.0 0.0 X_146313280_146313387_INS 1 76 (32) + L1MA6 LINE/L1 5931 6006 (294) 341
ANNOTATION EVIDENCE:
423 15.79 0.00 0.00 X_146313280_146313387_INS 1 76 32 + L1MA6_3end LINE/L1 678 753 294
423 15.79 0.00 0.00 X_146313280_146313387_INS 1 76 (32) L1MA6_3end#LINE/L1 678 753 (294) m_b3s551i7
X_146313280_1 1 AGTCTAAGAAAGTTGATCTCATAGGAGTAGAGAGGAGAATGATGGTTACC 50
i i i v ii
L1MA6_3end#LI 678 AATCTAAAAAAGTTGATCTCATAGAAGTAGAGAGTAGAATAGTGGTTACC 727
X_146313280_1 51 AGAGTCTGGGGAAGGGAAGGGAAAGG 76
v i v i i i
L1MA6_3end#LI 728 AGAGGCTGGGGAGGGTAGGGGGAGGG 753
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.23
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0)
+ 98 0.0 7.8 0.0 X_146430562_146430677_INS 2 116 (0) + (AT)n Simple_repeat 1 124 (0) 342
ANNOTATION EVIDENCE:
98 0.00 7.83 0.00 X_146430562_146430677_INS 2 116 0 + (AT)n Simple_repeat 1 124 0
98 0.00 7.83 0.00 X_146430562_146430677_INS 2 116 (0) (AT)n#Simple_repeat 1 124 (0) c_b3s251i37
X_146430562_1 2 ATATATATATATATAT-TATATATATAT-TATATATATA-ATATATATAT 48
- - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_146430562_1 49 AT-TATATATATAT-TATATATATA-ATATATATATATA-ATATATATAT 94
- - - -
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_146430562_1 95 A-ATATATATATAT-TATATATAT 116
- -
(AT)n#Simple_ 101 ATATATATATATATATATATATAT 124
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (9 / 114), avg. gap size = 1.00 (9 / 9)
+ 349 6.2 17.2 0.0 X_146660776_146660840_INS 2 65 (0) + L1P4 LINE/L1 4382 4456 (1690) 343
ANNOTATION EVIDENCE:
349 6.25 17.19 0.00 X_146660776_146660840_INS 2 65 0 + L1P4_orf2 LINE/L1 2273 2347 947
349 6.25 17.19 0.00 X_146660776_146660840_INS 2 65 (0) L1P4_orf2#LINE/L1 2273 2347 (947) m_b3s551i8
X_146660776_1 2 CATTTACAATAGCCACAAAAAAA---------CTAGGAATTCATCTAACC 42
--------- v
L1P4_orf2#LIN 2273 CATTTACAATAGCCACAAAAAAAATAAAATACCTAGGAATACATCTAACC 2322
X_146660776_1 43 AAAGAGGTGAAAGA--ACTACAAAG 65
i --v i
L1P4_orf2#LIN 2323 AAGGAGGTGAAAGATCTCTACAAGG 2347
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.54
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.03 (2 / 63), avg. gap size = 5.50 (11 / 2)
+ 2436 2.5 0.0 2.5 X_146851040_146851370_INS 7 329 (2) C AluY SINE/Alu (0) 311 1 344
ANNOTATION EVIDENCE:
32 2.92 0.00 0.00 X_146851040_146851370_INS 7 41 290 + (T)n Simple_repeat 1 35 0
32 2.92 0.00 0.00 X_146851040_146851370_INS 7 41 (290) (T)n#Simple_repeat 1 35 (0) c_b3s251i36
X_146851040_1 7 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
2436 2.49 0.00 2.49 X_146851040_146851370_INS 42 329 2 C AluY SINE/Alu 1 281 30
2436 2.49 0.00 2.49 X_146851040_146851370_INS 42 329 (2) C AluY#SINE/Alu (30) 281 1 c_b3s352i12
X_146851040_1 42 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 91
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_146851040_1 92 GCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCAGGCCATTCTCC 141
i v
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_146851040_1 142 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 191
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_146851040_1 192 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 241
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_146851040_1 242 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 291
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_146851040_1 292 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 329
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 36 2.7 0.0 0.0 X_146888809_146888878_INS 1 38 (32) + (AGGAG)n Simple_repeat 1 38 (0) 345
ANNOTATION EVIDENCE:
36 2.70 0.00 0.00 X_146888809_146888878_INS 1 38 32 + (AGGAG)n Simple_repeat 1 38 0
36 2.70 0.00 0.00 X_146888809_146888878_INS 1 38 (32) (AGGAG)n#Simple_repeat 1 38 (0) c_b3s251i35
X_146888809_1 1 AGGAGGGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGG 38
i
(AGGAG)n#Simp 1 AGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGG 38
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 15 7.5 0.0 6.7 X_146888809_146888878_INS 39 70 (0) + (GGAGG)n Simple_repeat 1 30 (0) 346
ANNOTATION EVIDENCE:
15 7.49 0.00 6.67 X_146888809_146888878_INS 39 70 0 + (GGAGG)n Simple_repeat 1 30 0
15 7.49 0.00 6.67 X_146888809_146888878_INS 39 70 (0) (GGAGG)n#Simple_repeat 1 30 (0) m_b3s252i22
X_146888809_1 39 GGAAGGGAGGGGAGGGGGGATGGGAGGGGAGG 70
i -- v
(GGAGG)n#Simp 1 GGAGGGGAGGGGA--GGGGAGGGGAGGGGAGG 30
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2)
+ 83 0.0 2.4 1.2 X_147120313_147120397_INS 1 85 (0) + (AAAG)n Simple_repeat 1 86 (0) 347
ANNOTATION EVIDENCE:
83 0.00 2.35 1.16 X_147120313_147120397_INS 1 85 0 + (AAAG)n Simple_repeat 1 86 0
83 0.00 2.35 1.16 X_147120313_147120397_INS 1 85 (0) (AAAG)n#Simple_repeat 1 86 (0) c_b3s251i34
X_147120313_1 1 AAAGAAAGAAAGAAAGAAAGAAAG--AGAAAGAAAAGAAAGAAAGAAAGA 48
-- -
(AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGA 49
X_147120313_1 49 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 85
(AAAG)n#Simpl 50 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 86
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.50 (3 / 2)
+ 51 5.5 9.3 1.6 X_147277531_147277654_INS 3 120 (4) + (TA)n Simple_repeat 1 127 (0) 348
ANNOTATION EVIDENCE:
51 5.55 9.32 1.57 X_147277531_147277654_INS 3 120 4 + (TA)n Simple_repeat 1 127 0
51 5.55 9.32 1.57 X_147277531_147277654_INS 3 120 (4) (TA)n#Simple_repeat 1 127 (0) c_b3s251i33
X_147277531_1 3 TATATATATA-ACATATA-ATATA-ATATAT-TATATGT-TATATATATA 47
- i - - - i -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_147277531_1 48 -ACATATATATA-ATATAT-TATATGT-TATATATATA-ACATATATATC 92
- i - - i - - i -
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATAT- 99
X_147277531_1 93 ATATATATATA-ACATATATATCATATAT 120
- i -
(TA)n#Simple_ 100 ATATATATATATATATATATAT-ATATAT 127
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.11 (13 / 117), avg. gap size = 1.00 (13 / 13)
+ 46 25.5 0.0 0.0 X_147662554_147662661_INS 7 106 (2) + (AT)n Simple_repeat 1 100 (0) 349
ANNOTATION EVIDENCE:
46 25.54 0.00 0.00 X_147662554_147662661_INS 7 106 2 + (AT)n Simple_repeat 1 100 0
46 25.54 0.00 0.00 X_147662554_147662661_INS 7 106 (2) (AT)n#Simple_repeat 1 100 (0) m_b3s252i21
X_147662554_1 7 ATATATACACATATGTGTATATATGTATATATACACACATATATACACAT 56
i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_147662554_1 57 ATGTGTATATGTATATATACACATATATACACATATGTGTATATGTATAT 106
i i i i i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
Matrix = Unknown
Transitions / transversions = 1.00 (20/0)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0)
+ 234 21.4 3.4 5.8 X_147662937_147663154_INS 25 113 (105) C Tigger17 DNA/TcMar-Tigger (310) 2363 2277 350
ANNOTATION EVIDENCE:
234 21.45 3.37 5.75 X_147662937_147663154_INS 25 113 105 C Tigger17 DNA/TcMar-Tigger 2277 2363 310
234 21.45 3.37 5.75 X_147662937_147663154_INS 25 113 (105) C Tigger17#DNA/TcMar-Tigger (310) 2363 2277 m_b3s502i4
X_147662937_1 25 GTGTACACACACACACGTATA-TATACGTATACGTGTACACACACACGTA 73
ii i i - i ii i - -ii ? i
C Tigger17#DNA/ 2363 GTACACACACACGCACGTACAGTACACACACAC-TGTACA-GTACNCGCA 2316
X_147662937_1 74 TATATACGTA-TACGTGTACACACACACGTATATAC-GTATA 113
i -i i - - i? i - i - i
C Tigger17#DNA/ 2315 CA-GTACGCAGTAC-TGTGNACACATAC-TGTATACTGTACA 2277
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.98
Transitions / transversions = 1.00 (18/0)
Gap_init rate = 0.09 (8 / 88), avg. gap size = 1.00 (8 / 8)
+ 28 21.7 0.0 5.2 X_147662937_147663154_INS 132 212 (6) + (TATACG)n Simple_repeat 1 77 (0) 351
ANNOTATION EVIDENCE:
28 21.73 0.00 5.19 X_147662937_147663154_INS 132 212 6 + (TATACG)n Simple_repeat 1 77 0
28 21.73 0.00 5.19 X_147662937_147663154_INS 132 212 (6) (TATACG)n#Simple_repeat 1 77 (0) m_b3s252i20
X_147662937_1 132 TATACGTATACGTGTACACACACATACACGTATATACGTATACGTGTACA 181
i ii i i i -- i i
(TATACG)n#Sim 1 TATACGTATACGTATACGTATACGTATACG--TATACGTATACGTATACG 48
X_147662937_1 182 CACACATACACGTATATACGTATACGTGTAC 212
i i i i -- i
(TATACG)n#Sim 49 TATACGTATACG--TATACGTATACGTATAC 77
Matrix = Unknown
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.00 (4 / 4)
+ 53 2.0 0.0 0.0 X_147843944_147843994_INS 1 50 (1) + (TA)n Simple_repeat 1 50 (0) 352
ANNOTATION EVIDENCE:
53 2.04 0.00 0.00 X_147843944_147843994_INS 1 50 1 + (TA)n Simple_repeat 1 50 0
53 2.04 0.00 0.00 X_147843944_147843994_INS 1 50 (1) (TA)n#Simple_repeat 1 50 (0) c_b3s251i32
X_147843944_1 1 TATATATATATATATATATATATATACATATATATATATATATATATATA 50
i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 8.8 2.8 X_148500058_148500126_INS 1 68 (1) + (AT)n Simple_repeat 1 72 (0) 353
ANNOTATION EVIDENCE:
44 0.00 8.82 2.78 X_148500058_148500126_INS 1 68 1 + (AT)n Simple_repeat 1 72 0
44 0.00 8.82 2.78 X_148500058_148500126_INS 1 68 (1) (AT)n#Simple_repeat 1 72 (0) c_b3s251i31
X_148500058_1 1 ATATATCATATATATA-ATATATAT-TATAT-TATATATATATCATATAT 47
- - - - -
(AT)n#Simple_ 1 ATATAT-ATATATATATATATATATATATATATATATATATAT-ATATAT 48
X_148500058_1 48 ATA-ATATATAT-TATAT-TATAT 68
- - -
(AT)n#Simple_ 49 ATATATATATATATATATATATAT 72
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.12 (8 / 67), avg. gap size = 1.00 (8 / 8)
+ 2684 3.5 0.0 2.3 X_148539112_148539435_INS 6 322 (2) + AluY SINE/Alu 1 310 (1) 354
ANNOTATION EVIDENCE:
2684 3.55 0.00 2.26 X_148539112_148539435_INS 6 322 2 + AluY SINE/Alu 1 310 1
2684 3.55 0.00 2.26 X_148539112_148539435_INS 6 322 (2) AluY#SINE/Alu 1 310 (1) c_b3s352i13
X_148539112_1 6 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 55
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_148539112_1 56 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 105
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_148539112_1 106 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCAGGCGCGGTGGC 155
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_148539112_1 156 GGGCGCCTGTAGTCCCAGTTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 205
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_148539112_1 206 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 255
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_148539112_1 256 CGCAGTCTGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 305
-------i
AluY#SINE/Alu 251 C-------AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_148539112_1 306 AAAAAAAAAAAAAAGAA 322
i
AluY#SINE/Alu 294 AAAAAAAAAAAAAAAAA 310
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.43
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.02 (7 / 316), avg. gap size = 1.00 (7 / 7)
+ 415 11.9 0.0 0.0 X_148572255_148572444_INS 132 190 (0) C MLT1C2 LTR/ERVL-MaLR (2) 459 401 355
ANNOTATION EVIDENCE:
415 11.86 0.00 0.00 X_148572255_148572444_INS 132 190 0 C MLT1C2 LTR/ERVL-MaLR 401 459 2
415 11.86 0.00 0.00 X_148572255_148572444_INS 132 190 (0) C MLT1C2#LTR/ERVL-MaLR (2) 459 401 m_b3s502i5
X_148572255_1 132 TGTTAATTTCCTGTGGCTGCCATAACAAAATATCACAAACTGGGTGGCTG 181
i i iv i ? i v
C MLT1C2#LTR/ER 459 TATTAGTTTCCTAGGGCTGCCGTAACAAANTACCACAAACTGGGTGGCTT 410
X_148572255_1 182 AAAACAACA 190
C MLT1C2#LTR/ER 409 AAAACAACA 401
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.46
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 24 15.0 0.0 5.5 X_148980194_148980254_INS 4 61 (0) + (ATAT)n Simple_repeat 1 55 (0) 356
ANNOTATION EVIDENCE:
24 14.97 0.00 5.45 X_148980194_148980254_INS 4 61 0 + (ATAT)n Simple_repeat 1 55 0
24 14.97 0.00 5.45 X_148980194_148980254_INS 4 61 (0) (ATAT)n#Simple_repeat 1 55 (0) m_b3s252i19
X_148980194_1 4 ATATATATCTGATATATATGAGATATATATAGATATATAGATGATAGATA 53
v - - v v v - v
(ATAT)n#Simpl 1 ATATATATAT-ATATATAT-ATATATATATATATATATATAT-ATATATA 47
X_148980194_1 54 GATAGATA 61
v v
(ATAT)n#Simpl 48 TATATATA 55
Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3)
+ 36 20.3 1.4 0.0 X_149009183_149009256_INS 1 72 (2) + (TA)n Simple_repeat 1 73 (0) 357
ANNOTATION EVIDENCE:
36 20.27 1.39 0.00 X_149009183_149009256_INS 1 72 2 + (TA)n Simple_repeat 1 73 0
36 20.27 1.39 0.00 X_149009183_149009256_INS 1 72 (2) (TA)n#Simple_repeat 1 73 (0) m_b3s252i18
X_149009183_1 1 TATATACACATACATATATACACATACATATATACACATACATATATATA 50
i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_149009183_1 51 CACATATATATATACATA-ATAT 72
i i i -
(TA)n#Simple_ 51 TATATATATATATATATATATAT 73
Matrix = Unknown
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1)
+ 12 14.2 12.8 0.0 X_149010391_149010443_INS 2 48 (5) + (GGCAG)n Simple_repeat 1 53 (0) 358
ANNOTATION EVIDENCE:
12 14.20 12.77 0.00 X_149010391_149010443_INS 2 48 5 + (GGCAG)n Simple_repeat 1 53 0
12 14.20 12.77 0.00 X_149010391_149010443_INS 2 48 (5) (GGCAG)n#Simple_repeat 1 53 (0) m_b3s252i17
X_149010391_1 2 GGCATGGC--GGCCGGGCATGGC--GGCCGGGCAGGGC--GGCCGGGCAT 45
v -- v v -- v -- v v
(GGCAG)n#Simp 1 GGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAG 50
X_149010391_1 46 GGC 48
(GGCAG)n#Simp 51 GGC 53
Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.07 (3 / 46), avg. gap size = 2.00 (6 / 3)
+ 30 0.0 8.2 3.9 X_149168968_149169019_INS 2 50 (2) + (AT)n Simple_repeat 1 51 (0) 359
ANNOTATION EVIDENCE:
30 0.00 8.16 3.92 X_149168968_149169019_INS 2 50 2 + (AT)n Simple_repeat 1 51 0
30 0.00 8.16 3.92 X_149168968_149169019_INS 2 50 (2) (AT)n#Simple_repeat 1 51 (0) c_b3s251i30
X_149168968_1 2 ATATATATATA-ATATATGATATATA-ATA-ATATAT-TATATATCATAT 47
- - - - - -
(AT)n#Simple_ 1 ATATATATATATATATAT-ATATATATATATATATATATATATAT-ATAT 48
X_149168968_1 48 ATA 50
(AT)n#Simple_ 49 ATA 51
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.12 (6 / 48), avg. gap size = 1.00 (6 / 6)
+ 2241 3.3 4.3 1.1 X_14917236_14917560_INS 19 325 (0) C AluY SINE/Alu (0) 311 3 360
ANNOTATION EVIDENCE:
39 0.00 0.00 0.00 X_14917236_14917560_INS 19 54 271 + (T)n Simple_repeat 1 36 0
39 0.00 0.00 0.00 X_14917236_14917560_INS 19 54 (271) (T)n#Simple_repeat 1 36 (0) c_b1s251i160
X_14917236_14 19 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 54
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
2241 3.29 4.35 1.05 X_14917236_14917560_INS 55 325 0 C AluY SINE/Alu 3 282 29
2241 3.29 4.35 1.05 X_14917236_14917560_INS 55 325 (0) C AluY#SINE/Alu (29) 282 3 c_b1s352i8
X_14917236_14 55 GAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTACAGTGGCGCAGCCT 104
i i iii
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_14917236_14 105 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 154
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_14917236_14 155 GCCTCTCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAA 204
-
C AluY#SINE/Alu 182 GCCTC-CCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAA 134
X_14917236_14 205 TTTTTTTTTTATTTTTAGTAGAGACGGGGTTTCACCG------------T 242
-- v ------------
C AluY#SINE/Alu 133 --TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGAT 86
X_14917236_14 243 GGTCTCGATCTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAGTG 292
i
C AluY#SINE/Alu 85 GGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 36
X_14917236_14 293 CTGGGATTACAAGCGTGAGCCACCGCGCCCGGC 325
i
C AluY#SINE/Alu 35 CTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.36
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.01 (4 / 270), avg. gap size = 3.75 (15 / 4)
+ 30 8.3 5.9 0.0 X_149224314_149224369_INS 6 56 (0) + (TA)n Simple_repeat 1 54 (0) 361
ANNOTATION EVIDENCE:
30 8.35 5.88 0.00 X_149224314_149224369_INS 6 56 0 + (TA)n Simple_repeat 1 54 0
30 8.35 5.88 0.00 X_149224314_149224369_INS 6 56 (0) (TA)n#Simple_repeat 1 54 (0) m_b3s252i16
X_149224314_1 6 TATATA-ATATATATATAGTTATATA-ATATATATATATA-ATAGTTATA 52
- vv - - vv
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_149224314_1 53 TATA 56
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3)
+ 2793 2.0 0.0 0.0 X_149451308_149451628_INS 18 321 (0) + AluY SINE/Alu 1 304 (7) 362
ANNOTATION EVIDENCE:
2793 1.97 0.00 0.00 X_149451308_149451628_INS 18 321 0 + AluY SINE/Alu 1 304 7
2793 1.97 0.00 0.00 X_149451308_149451628_INS 18 321 (0) AluY#SINE/Alu 1 304 (7) c_b3s352i14
X_149451308_1 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_149451308_1 68 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAATGG 117
i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_149451308_1 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_149451308_1 168 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 217
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_149451308_1 218 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 267
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_149451308_1 268 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_149451308_1 318 AAAA 321
AluY#SINE/Alu 301 AAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 303), avg. gap size = 0.0 (0 / 0)
+ 74 9.7 0.0 0.0 X_149562397_149562508_INS 2 112 (0) + (T)n Simple_repeat 1 111 (0) 363
ANNOTATION EVIDENCE:
74 9.69 0.00 0.00 X_149562397_149562508_INS 2 112 0 + (T)n Simple_repeat 1 111 0
74 9.69 0.00 0.00 X_149562397_149562508_INS 2 112 (0) (T)n#Simple_repeat 1 111 (0) c_b3s251i29
X_149562397_1 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_149562397_1 52 TTTTTGTTTTTTTTTTTTGGGGGGGTTTTTGTTTTTTTTTTATTTTTTTT 101
v vvvvvvv v v
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 100
X_149562397_1 102 TTTTTTTTTTT 112
(T)n#Simple_r 101 TTTTTTTTTTT 111
Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.0 (0 / 0)
+ 54 0.0 3.6 0.0 X_149584386_149584441_INS 1 56 (0) + (TTCT)n Simple_repeat 1 58 (0) 364
ANNOTATION EVIDENCE:
54 0.00 3.57 0.00 X_149584386_149584441_INS 1 56 0 + (TTCT)n Simple_repeat 1 58 0
54 0.00 3.57 0.00 X_149584386_149584441_INS 1 56 (0) (TTCT)n#Simple_repeat 1 58 (0) c_b3s251i28
X_149584386_1 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TT-TTTCTTTCTTTCTTT 48
- -
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50
X_149584386_1 49 CTTTCTTT 56
(TTCT)n#Simpl 51 CTTTCTTT 58
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2)
+ 2451 2.5 0.0 2.5 X_149839774_149840116_INS 16 343 (0) C AluY SINE/Alu (0) 311 1 365
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_149839774_149840116_INS 16 55 288 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_149839774_149840116_INS 16 55 (288) (T)n#Simple_repeat 1 40 (0) c_b3s251i27
X_149839774_1 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 55
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2451 2.49 0.00 2.49 X_149839774_149840116_INS 56 343 0 C AluY SINE/Alu 1 281 30
2451 2.49 0.00 2.49 X_149839774_149840116_INS 56 343 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i15
X_149839774_1 56 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 105
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_149839774_1 106 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 155
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_149839774_1 156 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 205
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_149839774_1 206 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 255
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_149839774_1 256 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 305
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_149839774_1 306 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 343
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 1598 1.2 0.0 0.0 X_149959289_149959477_INS 17 189 (0) + AluY SINE/Alu 131 303 (8) 366
ANNOTATION EVIDENCE:
1598 1.16 0.00 0.00 X_149959289_149959477_INS 17 189 0 + AluY SINE/Alu 131 303 8
1598 1.16 0.00 0.00 X_149959289_149959477_INS 17 189 (0) AluY#SINE/Alu 131 303 (8) m_b3s356i1
X_149959289_1 17 AATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGG 66
i
AluY#SINE/Alu 131 AATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGG 180
X_149959289_1 67 CTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCC 116
AluY#SINE/Alu 181 CTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCC 230
X_149959289_1 117 GAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT 166
v
AluY#SINE/Alu 231 GAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT 280
X_149959289_1 167 CAAAAAAAAAAAAAAAAAAAAAA 189
AluY#SINE/Alu 281 CAAAAAAAAAAAAAAAAAAAAAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.17
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 172), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 0.0 X_150145808_150145860_INS 14 53 (0) + (GAAA)n Simple_repeat 1 40 (0) 367
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_150145808_150145860_INS 14 53 0 + (GAAA)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_150145808_150145860_INS 14 53 (0) (GAAA)n#Simple_repeat 1 40 (0) c_b3s251i26
X_150145808_1 14 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 53
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 47 0.0 4.0 0.0 X_150185116_150185166_INS 1 50 (1) + (CTTT)n Simple_repeat 1 52 (0) 368
ANNOTATION EVIDENCE:
47 0.00 4.00 0.00 X_150185116_150185166_INS 1 50 1 + (CTTT)n Simple_repeat 1 52 0
47 0.00 4.00 0.00 X_150185116_150185166_INS 1 50 (1) (CTTT)n#Simple_repeat 1 52 (0) c_b3s251i25
X_150185116_1 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TT-TTTCTTTCT 48
- -
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50
X_150185116_1 49 TT 50
(CTTT)n#Simpl 51 TT 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2)
+ 104 1.5 0.0 9.4 X_150241210_150241373_INS 1 163 (1) + (TATGTATA)n Simple_repeat 1 149 (0) 369
ANNOTATION EVIDENCE:
104 1.50 0.00 9.40 X_150241210_150241373_INS 1 163 1 + (TATGTATA)n Simple_repeat 1 149 0
104 1.50 0.00 9.40 X_150241210_150241373_INS 1 163 (1) (TATGTATA)n#Simple_repeat 1 149 (0) c_b3s251i24
X_150241210_1 1 TATGTATATATGTATATATATGTATATATGTGTATATATGTATATATGTA 50
-- --
(TATGTATA)n#S 1 TATGTATATATG--TATATATGTATATA--TGTATATATGTATATATGTA 46
X_150241210_1 51 TATATGTATATGTGTATATATGTATATATGTATATATGTATATATATGTG 100
i -- --
(TATGTATA)n#S 47 TATATGTATATATGTATATATGTATATATGTATATATG--TATATA--TG 92
X_150241210_1 101 TATATATGTATATATGTGTATATATGTGTATATGTGTATATATGTGTATA 150
-- -- i --
(TATGTATA)n#S 93 TATATATGTATATA--TGTATATA--TGTATATATGTATATA--TGTATA 136
X_150241210_1 151 TATGTATATATGT 163
(TATGTATA)n#S 137 TATGTATATATGT 149
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.09 (14 / 162), avg. gap size = 1.00 (14 / 14)
+ 378 14.7 1.5 0.0 X_150317596_150317674_INS 12 79 (0) C L1MA4A LINE/L1 (204) 6099 6031 370
ANNOTATION EVIDENCE:
378 14.71 1.47 0.00 X_150317596_150317674_INS 12 79 0 C L1MA4A_3end LINE/L1 778 846 204
378 14.71 1.47 0.00 X_150317596_150317674_INS 12 79 (0) C L1MA4A_3end#LINE/L1 (204) 846 778 m_b3s551i9
X_150317596_1 12 AGTCACCCTACACTGCTGTCAAACATT-GAATTTATTCCTTCCATCTTAC 60
v i i - i i v
C L1MA4A_3end#L 846 AGTCACCCTACTCTGCTATCGAACATTAGAACTTATTCCTTCTATCTAAC 797
X_150317596_1 61 TGTAGGATTGTACTCTTTA 79
v v i v
C L1MA4A_3end#L 796 TGTATGTTTGTACCCATTA 778
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.77
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)
+ 2885 1.0 0.0 0.0 X_15031975_15032310_INS 2 336 (0) + AluY SINE/Alu 1 311 (0) 371
ANNOTATION EVIDENCE:
15 13.86 0.00 0.00 X_15031975_15032310_INS 313 336 0 + (A)n Simple_repeat 1 24 0
15 13.86 0.00 0.00 X_15031975_15032310_INS 313 336 (0) (A)n#Simple_repeat 1 24 (0) m_b1s252i119
X_15031975_15 313 AAAAAAAGAAAAAAACAAAGAAAA 336
i v i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24
Matrix = Unknown
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
2885 0.96 0.00 0.00 X_15031975_15032310_INS 2 312 24 + AluY SINE/Alu 1 311 0
2885 0.96 0.00 0.00 X_15031975_15032310_INS 2 312 (24) AluY#SINE/Alu 1 311 (0) c_b1s352i9
X_15031975_15 2 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 51
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_15031975_15 52 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 101
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_15031975_15 102 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 151
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_15031975_15 152 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 201
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_15031975_15 202 GAACCCGGGAGGCGGAGCTGGCAGTGAGCCGAGAGCGCGCCACTGCACTC 251
v v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_15031975_15 252 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 301
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_15031975_15 302 AAAAAAAAAAA 312
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.97
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 45 6.0 0.0 0.0 X_15039999_15040050_INS 1 52 (0) + (TA)n Simple_repeat 1 52 (0) 372
ANNOTATION EVIDENCE:
45 6.04 0.00 0.00 X_15039999_15040050_INS 1 52 0 + (TA)n Simple_repeat 1 52 0
45 6.04 0.00 0.00 X_15039999_15040050_INS 1 52 (0) (TA)n#Simple_repeat 1 52 (0) c_b1s251i159
X_15039999_15 1 TATATATATATATATATATATATTTATATATTTATATATTTATATATATA 50
v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_15039999_15 51 TA 52
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2567 1.4 0.0 1.8 X_15050725_15051052_INS 12 328 (0) C AluY SINE/Alu (0) 311 1 373
ANNOTATION EVIDENCE:
33 0.00 0.00 0.00 X_15050725_15051052_INS 12 42 286 + (T)n Simple_repeat 1 31 0
33 0.00 0.00 0.00 X_15050725_15051052_INS 12 42 (286) (T)n#Simple_repeat 1 31 (0) c_b1s251i158
X_15050725_15 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
2567 1.43 0.00 1.78 X_15050725_15051052_INS 43 328 0 C AluY SINE/Alu 1 281 30
2567 1.43 0.00 1.78 X_15050725_15051052_INS 43 328 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i10
X_15050725_15 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 92
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_15050725_15 93 CGGCTCACTGCAAGCTCCGCCTCCTGGGTTCACACCATTCTCCTGCCTCA 142
i i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_15050725_15 143 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 192
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_15050725_15 193 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 242
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_15050725_15 243 CTCGATCTGATCTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAG 292
----- i
C AluY#SINE/Alu 81 CTCG-----ATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 37
X_15050725_15 293 TGCTGGGATTACAGGCGTGAGCCACCGTGCCCGGCC 328
i
C AluY#SINE/Alu 36 TGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.14
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.02 (5 / 285), avg. gap size = 1.00 (5 / 5)
+ 2683 2.3 0.0 2.6 X_150537383_150537708_INS 8 323 (3) + AluY SINE/Alu 1 308 (3) 374
ANNOTATION EVIDENCE:
2683 2.28 0.00 2.60 X_150537383_150537708_INS 8 323 3 + AluY SINE/Alu 1 308 3
2683 2.28 0.00 2.60 X_150537383_150537708_INS 8 323 (3) AluY#SINE/Alu 1 308 (3) c_b3s352i16
X_150537383_1 8 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 57
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_150537383_1 58 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 107
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_150537383_1 108 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGCGGTGG 157
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATAC-AAAAAATTAGCCGGGCGTGGTGG 149
X_150537383_1 158 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 207
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_150537383_1 208 TGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGT 257
i i --
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA-- 247
X_150537383_1 258 CCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 307
----- i
AluY#SINE/Alu 248 C-----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
X_150537383_1 308 AAAAAAAAAAAAAAAA 323
AluY#SINE/Alu 293 AAAAAAAAAAAAAAAA 308
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.03 (8 / 315), avg. gap size = 1.00 (8 / 8)
+ 120 8.7 3.0 1.9 X_150542113_150542315_INS 1 203 (0) + (TATTATA)n Simple_repeat 1 205 (0) 375
ANNOTATION EVIDENCE:
120 8.74 2.96 1.95 X_150542113_150542315_INS 1 203 0 + (TATTATA)n Simple_repeat 1 205 0
120 8.74 2.96 1.95 X_150542113_150542315_INS 1 203 (0) (TATTATA)n#Simple_repeat 1 205 (0) m_b3s252i15
X_150542113_1 1 TATTATATATTATA-A-TATATATTATATAATATATTATAATATATAATA 48
- - v - v v
(TATTATA)n#Si 1 TATTATATATTATATATTATATATTATATATTATA-TATTATATATTATA 49
X_150542113_1 49 TATATTATATTATA-A-TATATAATATATATTATATATTATAATATATTA 96
vv - - v - vv
(TATTATA)n#Si 50 TATTATATATTATATATTATATATTATATATTATATATTAT-ATATTATA 98
X_150542113_1 97 TATAATATATTATATTATATATTATAATATATAATATATTATATATTATA 146
v vv - v v
(TATTATA)n#Si 99 TATTATATATTATATATTATA-TATTATATATTATATATTATATATTATA 147
X_150542113_1 147 TAATAATATATAATATATTATA-A-TATATATTATATAATATATATTATA 194
- v v - - v
(TATTATA)n#Si 148 T-ATTATATATTATATATTATATATTATATATTATATATTATATATTATA 196
X_150542113_1 195 TATTATATA 203
(TATTATA)n#Si 197 TATTATATA 205
Matrix = Unknown
Transitions / transversions = 0.00 (0/16)
Gap_init rate = 0.05 (10 / 202), avg. gap size = 1.00 (10 / 10)
+ 38 4.8 0.0 0.0 X_150682937_150682987_INS 8 51 (0) + (TCTT)n Simple_repeat 1 44 (0) 376
ANNOTATION EVIDENCE:
38 4.77 0.00 0.00 X_150682937_150682987_INS 8 51 0 + (TCTT)n Simple_repeat 1 44 0
38 4.77 0.00 0.00 X_150682937_150682987_INS 8 51 (0) (TCTT)n#Simple_repeat 1 44 (0) c_b3s251i23
X_150682937_1 8 TCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTTTCTTTCTTTCTT 51
i i
(TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 44
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 61 1.4 3.8 2.5 X_150865566_150865665_INS 21 99 (1) + (TCCT)n Simple_repeat 1 80 (0) 377
ANNOTATION EVIDENCE:
61 1.35 3.80 2.50 X_150865566_150865665_INS 21 99 1 + (TCCT)n Simple_repeat 1 80 0
61 1.35 3.80 2.50 X_150865566_150865665_INS 21 99 (1) (TCCT)n#Simple_repeat 1 80 (0) c_b3s251i22
X_150865566_1 21 TCCTTCTTTCCTTCC-TCCTTCCCTTCCCTT-C-TCCTTCCTTCCTTCCT 67
i - - - - -
(TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTT-CCTT-CCTTCCTTCCTTCCTTCCTTCCT 48
X_150865566_1 68 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 99
(TCCT)n#Simpl 49 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 80
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.00 (5 / 5)
+ 30 16.7 0.0 3.5 X_150911513_150911573_INS 1 60 (1) + (TA)n Simple_repeat 1 58 (0) 378
ANNOTATION EVIDENCE:
30 16.72 0.00 3.45 X_150911513_150911573_INS 1 60 1 + (TA)n Simple_repeat 1 58 0
30 16.72 0.00 3.45 X_150911513_150911573_INS 1 60 (1) (TA)n#Simple_repeat 1 58 (0) m_b3s252i14
X_150911513_1 1 TATATATATGTGTGAGTGTATATATATATATATATATATATACACACACA 50
i i - - i i i i i
(TA)n#Simple_ 1 TATATATATATAT-A-TATATATATATATATATATATATATATATATATA 48
X_150911513_1 51 CATATATATA 60
i
(TA)n#Simple_ 49 TATATATATA 58
Matrix = Unknown
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2)
+ 2880 0.7 0.0 0.0 X_151218754_151219073_INS 17 320 (0) + AluY SINE/Alu 1 304 (7) 379
ANNOTATION EVIDENCE:
2880 0.66 0.00 0.00 X_151218754_151219073_INS 17 320 0 + AluY SINE/Alu 1 304 7
2880 0.66 0.00 0.00 X_151218754_151219073_INS 17 320 (0) AluY#SINE/Alu 1 304 (7) c_b3s352i17
X_151218754_1 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_151218754_1 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 116
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_151218754_1 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_151218754_1 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_151218754_1 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCACCACTGCACTC 266
i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_151218754_1 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_151218754_1 317 AAAA 320
AluY#SINE/Alu 301 AAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.36
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 303), avg. gap size = 0.0 (0 / 0)
+ 2629 1.1 0.0 0.0 X_151261523_151261855_INS 8 333 (0) C AluY SINE/Alu (0) 311 1 380
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 X_151261523_151261855_INS 8 52 281 + (T)n Simple_repeat 1 45 0
50 0.00 0.00 0.00 X_151261523_151261855_INS 8 52 (281) (T)n#Simple_repeat 1 45 (0) c_b3s251i21
X_151261523_1 8 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 52
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
2629 1.07 0.00 0.00 X_151261523_151261855_INS 53 333 0 C AluY SINE/Alu 1 281 30
2629 1.07 0.00 0.00 X_151261523_151261855_INS 53 333 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i18
X_151261523_1 53 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 102
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_151261523_1 103 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCCCCTGCCTCA 152
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_151261523_1 153 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 202
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_151261523_1 203 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 252
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_151261523_1 253 CTCGATCTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTG 302
i
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_151261523_1 303 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 333
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.75
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 29 11.1 0.0 7.4 X_151351125_151351185_INS 2 59 (2) + (AT)n Simple_repeat 1 54 (0) 381
ANNOTATION EVIDENCE:
29 11.06 0.00 7.41 X_151351125_151351185_INS 2 59 2 + (AT)n Simple_repeat 1 54 0
29 11.06 0.00 7.41 X_151351125_151351185_INS 2 59 (2) (AT)n#Simple_repeat 1 54 (0) m_b3s252i13
X_151351125_1 2 ATATATAGTGTATATATACACTATATATACATATATAGTGTATATATACA 51
- i i - i - i i
(AT)n#Simple_ 1 ATATATA-TATATATATATA-TATATATATATATATA-TATATATATATA 47
X_151351125_1 52 CTATATAT 59
-
(AT)n#Simple_ 48 -TATATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4)
+ 127 13.3 0.0 8.6 X_151351194_151351485_INS 2 292 (0) + (TA)n Simple_repeat 1 268 (0) 382
ANNOTATION EVIDENCE:
127 13.33 0.00 8.58 X_151351194_151351485_INS 2 292 0 + (TA)n Simple_repeat 1 268 0
127 13.33 0.00 8.58 X_151351194_151351485_INS 2 292 (0) (TA)n#Simple_repeat 1 268 (0) m_b3s252i12
X_151351194_1 2 TATAGTGTATATATACACTATATATACACTATATATGTATAGTATATATA 51
- i i - i - i -
(TA)n#Simple_ 1 TATA-TATATATATATA-TATATATATA-TATATATATATA-TATATATA 46
X_151351194_1 52 CACTATATATAGTATATATACACTATATATATAGTGTATATACACTATAT 101
i - - i - - i i -
(TA)n#Simple_ 47 TA-TATATATA-TATATATATA-TATATATATA-TATATATATA-TATAT 91
X_151351194_1 102 ATATAGTATATATACACTACATATATAGTATATATACACTATATATACAC 151
- i - i - i - i -
(TA)n#Simple_ 92 ATATA-TATATATATA-TATATATATA-TATATATATA-TATATATATA- 136
X_151351194_1 152 TATATATGTATATATATACATATATAGTGTATATATAGTGTATATATACA 201
i i - i - i i
(TA)n#Simple_ 137 TATATATATATATATATATATATATA-TATATATATA-TATATATATATA 184
X_151351194_1 202 CTGTATATGTATATATAGTGTATATATACACTATATATACACTGTATATG 251
- i i - i i - i - i i
(TA)n#Simple_ 185 -TATATATATATATATA-TATATATATATA-TATATATATA-TATATATA 230
X_151351194_1 252 TATATATAGTGTATATATACACTATACACTGTATATGTATA 292
- i i - i - i i
(TA)n#Simple_ 231 TATATATA-TATATATATATA-TATATA-TATATATATATA 268
Matrix = Unknown
Transitions / transversions = 1.00 (29/0)
Gap_init rate = 0.08 (23 / 290), avg. gap size = 1.00 (23 / 23)
+ 2582 2.1 0.0 0.0 X_151363926_151364259_INS 17 334 (0) C AluY SINE/Alu (0) 311 2 383
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 X_151363926_151364259_INS 17 53 281 + (T)n Simple_repeat 1 37 0
40 0.00 0.00 0.00 X_151363926_151364259_INS 17 53 (281) (T)n#Simple_repeat 1 37 (0) c_b3s251i20
X_151363926_1 17 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 53
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
2582 2.11 0.00 0.00 X_151363926_151364259_INS 54 334 0 C AluY SINE/Alu 2 282 29
2582 2.11 0.00 0.00 X_151363926_151364259_INS 54 334 (0) C AluY#SINE/Alu (29) 282 2 c_b3s352i19
X_151363926_1 54 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 103
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_151363926_1 104 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 153
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_151363926_1 154 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 203
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_151363926_1 204 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 253
v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_151363926_1 254 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 303
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_151363926_1 304 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 334
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.82
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 15 25.5 1.9 1.9 X_151443902_151443966_INS 7 59 (6) + (TATT)n Simple_repeat 1 53 (0) 384
ANNOTATION EVIDENCE:
15 25.49 1.89 1.89 X_151443902_151443966_INS 7 59 6 + (TATT)n Simple_repeat 1 53 0
15 25.49 1.89 1.89 X_151443902_151443966_INS 7 59 (6) (TATT)n#Simple_repeat 1 53 (0) m_b3s252i11
X_151443902_1 7 TATATATTTACATATTTATTT-TAAATGTAAAATATATATTTACATATTT 55
v iv - vv - v vv v iv
(TATT)n#Simpl 1 TATTTATTTATTTATTTATTTATTTAT-TTATTTATTTATTTATTTATTT 49
X_151443902_1 56 ATTT 59
(TATT)n#Simpl 50 ATTT 53
Matrix = Unknown
Transitions / transversions = 0.22 (2/9)
Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2)
+ 26 2.2 8.3 2.0 X_151454579_151454643_INS 14 61 (4) + (AGTAT)n Simple_repeat 1 51 (0) 385
ANNOTATION EVIDENCE:
26 2.20 8.33 1.96 X_151454579_151454643_INS 14 61 4 + (AGTAT)n Simple_repeat 1 51 0
26 2.20 8.33 1.96 X_151454579_151454643_INS 14 61 (4) (AGTAT)n#Simple_repeat 1 51 (0) c_b3s251i19
X_151454579_1 14 AGTATAGTATAGTATA-TA-AGT-TA-TATACTATAAGTATAGTATAGTA 59
- - - - v -
(AGTAT)n#Simp 1 AGTATAGTATAGTATAGTATAGTATAGTATAGTAT-AGTATAGTATAGTA 49
X_151454579_1 60 TA 61
(AGTAT)n#Simp 50 TA 51
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5)
+ 2596 3.6 0.0 2.3 X_151831761_151832074_INS 4 314 (0) C AluY SINE/Alu (7) 304 1 386
ANNOTATION EVIDENCE:
2596 3.62 0.00 2.30 X_151831761_151832074_INS 4 314 0 C AluY SINE/Alu 1 304 7
2596 3.62 0.00 2.30 X_151831761_151832074_INS 4 314 (0) C AluY#SINE/Alu (7) 304 1 c_b3s352i20
X_151831761_1 4 TTTTGTTCTTTCTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 53
v i i
C AluY#SINE/Alu 304 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 255
X_151831761_1 54 GCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGC 103
i ----- -- i
C AluY#SINE/Alu 254 GCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGC 212
X_151831761_1 104 TTCCCGGGTTCACACCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 153
i i
C AluY#SINE/Alu 211 CTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 162
X_151831761_1 154 TACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAG 203
i
C AluY#SINE/Alu 161 TACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAG 112
X_151831761_1 204 ACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATG 253
v i
C AluY#SINE/Alu 111 ACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTG 62
X_151831761_1 254 ATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 303
i
C AluY#SINE/Alu 61 ATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 12
X_151831761_1 304 CGCGCCCGGCC 314
C AluY#SINE/Alu 11 CGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.48
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.02 (7 / 310), avg. gap size = 1.00 (7 / 7)
+ 2755 2.6 0.0 0.3 X_152001790_152002109_INS 16 320 (0) + AluY SINE/Alu 1 304 (7) 387
ANNOTATION EVIDENCE:
2755 2.63 0.00 0.33 X_152001790_152002109_INS 16 320 0 + AluY SINE/Alu 1 304 7
2755 2.63 0.00 0.33 X_152001790_152002109_INS 16 320 (0) AluY#SINE/Alu 1 304 (7) c_b3s352i21
X_152001790_1 16 GGCCGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGA 65
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_152001790_1 66 GGCGGGCGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 115
i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_152001790_1 116 TGAAACCCTGTCTCTACTAAAAATACAAAAAAATTAGCCGGCCGTGATGG 165
i - v i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_152001790_1 166 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 215
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_152001790_1 216 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCACACCACTGCACT 265
i i
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_152001790_1 266 CCAGCCTGGGCAACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 315
i
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_152001790_1 316 AAAAA 320
AluY#SINE/Alu 300 AAAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.16
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (1 / 304), avg. gap size = 1.00 (1 / 1)
+ 22 27.5 0.0 0.0 X_152195175_152195227_INS 2 53 (0) + (TA)n Simple_repeat 1 52 (0) 388
ANNOTATION EVIDENCE:
22 27.50 0.00 0.00 X_152195175_152195227_INS 2 53 0 + (TA)n Simple_repeat 1 52 0
22 27.50 0.00 0.00 X_152195175_152195227_INS 2 53 (0) (TA)n#Simple_repeat 1 52 (0) m_b3s252i10
X_152195175_1 2 TATATATATGTGTGTGTATATATATGTGTATATGTGTGTATATGTATATG 51
i i i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_152195175_1 52 TA 53
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 48 0.0 0.0 0.0 X_152850039_152850091_INS 10 53 (0) + (AGGG)n Simple_repeat 1 44 (0) 389
ANNOTATION EVIDENCE:
48 0.00 0.00 0.00 X_152850039_152850091_INS 10 53 0 + (AGGG)n Simple_repeat 1 44 0
48 0.00 0.00 0.00 X_152850039_152850091_INS 10 53 (0) (AGGG)n#Simple_repeat 1 44 (0) c_b3s251i18
X_152850039_1 10 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 53
(AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 44
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 2777 1.6 0.0 0.3 X_152883200_152883522_INS 18 323 (0) + AluY SINE/Alu 1 305 (6) 390
ANNOTATION EVIDENCE:
2777 1.64 0.00 0.33 X_152883200_152883522_INS 18 323 0 + AluY SINE/Alu 1 305 6
2777 1.64 0.00 0.33 X_152883200_152883522_INS 18 323 (0) AluY#SINE/Alu 1 305 (6) c_b3s352i22
X_152883200_1 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_152883200_1 68 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 117
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_152883200_1 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTAGTGG 167
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_152883200_1 168 CGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCG 217
i
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_152883200_1 218 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACT 267
v
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_152883200_1 268 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_152883200_1 318 AAAAAA 323
AluY#SINE/Alu 300 AAAAAA 305
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (1 / 305), avg. gap size = 1.00 (1 / 1)
+ 82 3.7 1.6 5.0 X_152885760_152885898_INS 4 128 (11) + (TGTATATA)n Simple_repeat 1 121 (0) 391
ANNOTATION EVIDENCE:
82 3.66 1.60 4.96 X_152885760_152885898_INS 4 128 11 + (TGTATATA)n Simple_repeat 1 121 0
82 3.66 1.60 4.96 X_152885760_152885898_INS 4 128 (11) (TGTATATA)n#Simple_repeat 1 121 (0) c_b3s251i17
X_152885760_1 4 TGTATATATGTATATATGTATATATGTGTGTGTGTATATATGTATATATG 53
i i i
(TGTATATA)n#S 1 TGTATATATGTATATATGTATATATGTATATATGTATATATGTATATATG 50
X_152885760_1 54 TATATATG--TGTATGTATATATGTATATATGTGTATATATGTATATATG 101
-- i -- --
(TGTATATA)n#S 51 TATATATGTATATATGTATATATGTATATA--TGTATATATGTATATA-- 96
X_152885760_1 102 TGTGTATATATGTATATATGTATATAT 128
--
(TGTATATA)n#S 97 --TGTATATATGTATATATGTATATAT 121
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.14 (8 / 7)
+ 15 18.3 0.0 5.0 X_15293656_15293706_INS 10 51 (0) + (TGTACA)n Simple_repeat 1 40 (0) 392
ANNOTATION EVIDENCE:
15 18.27 0.00 5.00 X_15293656_15293706_INS 10 51 0 + (TGTACA)n Simple_repeat 1 40 0
15 18.27 0.00 5.00 X_15293656_15293706_INS 10 51 (0) (TGTACA)n#Simple_repeat 1 40 (0) m_b1s252i118
X_15293656_15 10 TGTATATATGCATGTACATGTATATACATACATGTACTTGTA 51
i i i i --i v
(TGTACA)n#Sim 1 TGTACATGTACATGTACATGTACAT--GTACATGTACATGTA 40
Matrix = Unknown
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2)
+ 37 19.6 0.0 0.0 X_15301088_15301162_INS 2 75 (0) + (TATA)n Simple_repeat 1 74 (0) 393
ANNOTATION EVIDENCE:
37 19.60 0.00 0.00 X_15301088_15301162_INS 2 75 0 + (TATA)n Simple_repeat 1 74 0
37 19.60 0.00 0.00 X_15301088_15301162_INS 2 75 (0) (TATA)n#Simple_repeat 1 74 (0) m_b1s252i117
X_15301088_15 2 TATATATATACGTATATATATATACGTATATGTATGTATATATATACGTA 51
ii ii i i ii
(TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_15301088_15 52 TATATATATACGTATATGTATGTA 75
ii i i
(TATA)n#Simpl 51 TATATATATATATATATATATATA 74
Matrix = Unknown
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 74 10.2 0.0 0.0 X_153260157_153260275_INS 10 117 (2) + (TG)n Simple_repeat 1 108 (0) 394
ANNOTATION EVIDENCE:
74 10.24 0.00 0.00 X_153260157_153260275_INS 10 117 2 + (TG)n Simple_repeat 1 108 0
74 10.24 0.00 0.00 X_153260157_153260275_INS 10 117 (2) (TG)n#Simple_repeat 1 108 (0) c_b3s251i16
X_153260157_1 10 TGTGTGCGTGTGTGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTG 59
i ii
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50
X_153260157_1 60 TGCGTGTGTGCGTGTGTGCATGTGTGCGTGTGTGTGTGTGTGCATGTGTG 109
i i ii i ii
(TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100
X_153260157_1 110 TGTGTGTG 117
(TG)n#Simple_ 101 TGTGTGTG 108
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0)
+ 52 0.0 0.0 0.0 X_153900623_153900674_INS 1 47 (5) + (TCT)n Simple_repeat 1 47 (0) 395
ANNOTATION EVIDENCE:
52 0.00 0.00 0.00 X_153900623_153900674_INS 1 47 5 + (TCT)n Simple_repeat 1 47 0
52 0.00 0.00 0.00 X_153900623_153900674_INS 1 47 (5) (TCT)n#Simple_repeat 1 47 (0) c_b3s251i15
X_153900623_1 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 47
(TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 2501 2.8 0.0 2.4 X_15419482_15419783_INS 8 301 (1) C AluY SINE/Alu (3) 308 22 396
ANNOTATION EVIDENCE:
2501 2.79 0.00 2.44 X_15419482_15419783_INS 8 301 1 C AluY SINE/Alu 22 308 3
2501 2.79 0.00 2.44 X_15419482_15419783_INS 8 301 (1) C AluY#SINE/Alu (3) 308 22 c_b1s352i11
X_15419482_15 8 TTTCTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 57
i
C AluY#SINE/Alu 308 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 259
X_15419482_15 58 CCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCT 107
i ----- -- i
C AluY#SINE/Alu 258 CCAGGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCT 216
X_15419482_15 108 CCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTG 157
i
C AluY#SINE/Alu 215 CCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTG 166
X_15419482_15 158 GGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGT 207
i
C AluY#SINE/Alu 165 GGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGT 116
X_15419482_15 208 AGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 257
v
C AluY#SINE/Alu 115 AGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 66
X_15419482_15 258 CATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGG 301
i i
C AluY#SINE/Alu 65 CGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGG 22
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.88
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.02 (7 / 293), avg. gap size = 1.00 (7 / 7)
+ 2545 2.5 0.0 0.3 X_154275425_154275764_INS 9 340 (0) C AluY SINE/Alu (0) 311 2 397
ANNOTATION EVIDENCE:
56 0.00 0.00 0.00 X_154275425_154275764_INS 9 58 282 + (T)n Simple_repeat 1 50 0
56 0.00 0.00 0.00 X_154275425_154275764_INS 9 58 (282) (T)n#Simple_repeat 1 50 (0) c_b3s251i14
X_154275425_1 9 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 58
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
2545 2.45 0.00 0.35 X_154275425_154275764_INS 59 340 0 C AluY SINE/Alu 2 282 29
2545 2.45 0.00 0.35 X_154275425_154275764_INS 59 340 (0) C AluY#SINE/Alu (29) 282 2 c_b3s352i23
X_154275425_1 59 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 108
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_154275425_1 109 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 158
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_154275425_1 159 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 208
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_154275425_1 209 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 258
- v i
C AluY#SINE/Alu 132 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 84
X_154275425_1 259 TCTCGATCTCTTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 308
i
C AluY#SINE/Alu 83 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 34
X_154275425_1 309 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 340
C AluY#SINE/Alu 33 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.18
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 281), avg. gap size = 1.00 (1 / 1)
+ 2421 2.5 0.0 2.5 X_154448065_154448384_INS 11 320 (0) C AluY SINE/Alu (0) 311 4 398
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_154448065_154448384_INS 11 35 285 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_154448065_154448384_INS 11 35 (285) (T)n#Simple_repeat 1 25 (0) c_b3s251i13
X_154448065_1 11 TTTTTTTTTTTTTTTTTTTTTTTTT 35
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2421 2.52 0.00 2.52 X_154448065_154448384_INS 36 320 0 C AluY SINE/Alu 4 281 30
2421 2.52 0.00 2.52 X_154448065_154448384_INS 36 320 (0) C AluY#SINE/Alu (30) 281 4 c_b3s352i24
X_154448065_1 36 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 85
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_154448065_1 86 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 135
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_154448065_1 136 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 185
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_154448065_1 186 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 235
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_154448065_1 236 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 285
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_154448065_1 286 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 320
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.56
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 284), avg. gap size = 1.00 (7 / 7)
+ 2474 1.8 0.7 0.4 X_154511616_154511932_INS 12 317 (0) C AluY SINE/Alu (0) 311 1 399
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_154511616_154511932_INS 12 37 280 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_154511616_154511932_INS 12 37 (280) (T)n#Simple_repeat 1 26 (0) c_b3s251i12
X_154511616_1 12 TTTTTTTTTTTTTTTTTTTTTTTTTT 37
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2474 1.80 0.71 0.36 X_154511616_154511932_INS 38 317 0 C AluY SINE/Alu 1 281 30
2474 1.80 0.71 0.36 X_154511616_154511932_INS 38 317 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i25
X_154511616_1 38 GAGACGGAGTCTCGCT--GTCGCCCAGGCTGGAGTGCAGTGGCGCAATCT 85
-- i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_154511616_1 86 CGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTC 135
i i i -
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGG-TTCACGCCATTCTCCTGCCTC 183
X_154511616_1 136 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAA 185
v
C AluY#SINE/Alu 182 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAA 133
X_154511616_1 186 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 235
C AluY#SINE/Alu 132 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_154511616_1 236 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 285
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_154511616_1 286 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 317
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.16
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.01 (2 / 279), avg. gap size = 1.50 (3 / 2)
+ 692 9.1 0.0 0.0 X_154778194_154778318_INS 1 88 (37) + AluSx SINE/Alu 194 281 (31) 400
ANNOTATION EVIDENCE:
692 9.09 0.00 0.00 X_154778194_154778318_INS 1 88 37 + AluSx SINE/Alu 194 281 31
692 9.09 0.00 0.00 X_154778194_154778318_INS 1 88 (37) AluSx#SINE/Alu 194 281 (31) m_b3s357i0
X_154778194_1 1 AATCGCTTGAACCCAGGAGGCAAAGGTTGCAGTGAGCTGAGATTGCGCCA 50
i ii i i
AluSx#SINE/Al 194 AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCA 243
X_154778194_1 51 CTGCACTCCAGCCTGGGCGACAGAGTGAGACTCTGCCT 88
i i i
AluSx#SINE/Al 244 CTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT 281
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.05
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0)
+ 72 0.0 0.0 0.0 X_154845795_154845883_INS 29 89 (0) + (CT)n Simple_repeat 1 61 (0) 401
ANNOTATION EVIDENCE:
72 0.00 0.00 0.00 X_154845795_154845883_INS 29 89 0 + (CT)n Simple_repeat 1 61 0
72 0.00 0.00 0.00 X_154845795_154845883_INS 29 89 (0) (CT)n#Simple_repeat 1 61 (0) c_b3s251i11
X_154845795_1 29 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 78
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50
X_154845795_1 79 CTCTCTCTCTC 89
(CT)n#Simple_ 51 CTCTCTCTCTC 61
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 26 0.0 0.0 0.0 X_154930274_154930328_INS 5 29 (26) + (T)n Simple_repeat 1 25 (0) 402
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_154930274_154930328_INS 5 29 26 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_154930274_154930328_INS 5 29 (26) (T)n#Simple_repeat 1 25 (0) c_b3s251i10
X_154930274_1 5 TTTTTTTTTTTTTTTTTTTTTTTTT 29
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 55 0.0 0.0 0.0 X_155007297_155007347_INS 2 48 (3) + (TA)n Simple_repeat 1 47 (0) 403
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 X_155007297_155007347_INS 2 48 3 + (TA)n Simple_repeat 1 47 0
55 0.00 0.00 0.00 X_155007297_155007347_INS 2 48 (3) (TA)n#Simple_repeat 1 47 (0) c_b3s251i9
X_155007297_1 2 TATATATATATATATATATATATATATATATATATATATATATATAT 48
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATAT 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 2690 2.9 0.0 2.3 X_155190895_155191228_INS 18 334 (0) + AluY SINE/Alu 1 310 (1) 404
ANNOTATION EVIDENCE:
2690 2.91 0.00 2.26 X_155190895_155191228_INS 18 334 0 + AluY SINE/Alu 1 310 1
2690 2.91 0.00 2.26 X_155190895_155191228_INS 18 334 (0) AluY#SINE/Alu 1 310 (1) c_b3s352i26
X_155190895_1 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_155190895_1 68 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 117
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_155190895_1 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_155190895_1 168 GGGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGTCAGGAGAATGGCGT 217
i v
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_155190895_1 218 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 267
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_155190895_1 268 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 317
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_155190895_1 318 AAAAAAAAAAAAAAAAA 334
AluY#SINE/Alu 294 AAAAAAAAAAAAAAAAA 310
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.76
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.02 (7 / 316), avg. gap size = 1.00 (7 / 7)
+ 75 12.7 0.0 0.0 X_155238906_155239025_INS 1 120 (0) + (GTGTGT)n Simple_repeat 1 120 (0) 405
ANNOTATION EVIDENCE:
75 12.70 0.00 0.00 X_155238906_155239025_INS 1 120 0 + (GTGTGT)n Simple_repeat 1 120 0
75 12.70 0.00 0.00 X_155238906_155239025_INS 1 120 (0) (GTGTGT)n#Simple_repeat 1 120 (0) m_b3s252i9
X_155238906_1 1 GTGTGTCTGTGTGTGTGTTTGTGTGTGTATGTCTGTGTGTGTGTGTTTAT 50
v v i v v i
(GTGTGT)n#Sim 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50
X_155238906_1 51 GTGTGGGTGTTTGTGTGTGTTGGTGTATGTGTGTGTTTGTGTGGGTGTGT 100
v v vv i v v
(GTGTGT)n#Sim 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100
X_155238906_1 101 GTCTGTGTGTGTGTGTGTGT 120
v
(GTGTGT)n#Sim 101 GTGTGTGTGTGTGTGTGTGT 120
Matrix = Unknown
Transitions / transversions = 0.27 (3/11)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0)
+ 2850 1.9 0.0 0.0 X_15626851_15627179_INS 15 325 (4) + AluY SINE/Alu 1 311 (0) 406
ANNOTATION EVIDENCE:
2850 1.93 0.00 0.00 X_15626851_15627179_INS 15 325 4 + AluY SINE/Alu 1 311 0
2850 1.93 0.00 0.00 X_15626851_15627179_INS 15 325 (4) AluY#SINE/Alu 1 311 (0) c_b1s352i12
X_15626851_15 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_15626851_15 65 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCAGCTAAAACGG 114
ii v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_15626851_15 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_15626851_15 165 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 214
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_15626851_15 215 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 264
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_15626851_15 265 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 314
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_15626851_15 315 AAAAAAAAAAA 325
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.66
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 2202 2.1 0.0 0.0 X_15806775_15807067_INS 16 293 (0) C AluY SINE/Alu (0) 311 40 407
ANNOTATION EVIDENCE:
39 0.00 0.00 0.00 X_15806775_15807067_INS 16 51 242 + (T)n Simple_repeat 1 36 0
39 0.00 0.00 0.00 X_15806775_15807067_INS 16 51 (242) (T)n#Simple_repeat 1 36 (0) c_b1s251i157
X_15806775_15 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
2202 2.07 0.00 0.00 X_15806775_15807067_INS 52 293 0 C AluY SINE/Alu 40 281 30
2202 2.07 0.00 0.00 X_15806775_15807067_INS 52 293 (0) C AluY#SINE/Alu (30) 281 40 c_b1s352i13
X_15806775_15 52 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 101
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_15806775_15 102 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 151
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_15806775_15 152 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 201
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_15806775_15 202 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 251
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_15806775_15 252 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCA 293
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCA 40
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.71
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 241), avg. gap size = 0.0 (0 / 0)
+ 23 7.7 0.0 8.7 X_16558661_16558712_INS 2 51 (1) + GA-rich Low_complexity 1 46 (0) 408
ANNOTATION EVIDENCE:
23 7.66 0.00 8.70 X_16558661_16558712_INS 2 51 1 + (AGGAA)n Simple_repeat 1 46 0
23 7.66 0.00 8.70 X_16558661_16558712_INS 2 51 (1) (AGGAA)n#Simple_repeat 1 46 (0) m_b1s252i115
X_16558661_16 2 AGGAGAGGAGAGGAGAGGAAAGGAAAAAGGAAAGGAAAAAGGAAAGGAAA 51
i i i -- --
(AGGAA)n#Simp 1 AGGAAAGGAAAGGAAAGGAAAGG--AAAGGAAAGG--AAAGGAAAGGAAA 46
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4)
13 11.37 6.98 4.55 X_16558661_16558712_INS 5 47 5 + (AGAGGAA)n Simple_repeat 1 44 0
13 11.37 6.98 4.55 X_16558661_16558712_INS 5 47 (5) (AGAGGAA)n#Simple_repeat 1 44 (0) m_b1s252i116
X_16558661_16 5 AGAGGAGAGGAGAGGAA-AGGAAAAAGG-AA-AGGAAAAAGGAAAG 47
- i - i - i - - i
(AGAGGAA)n#Si 1 AGAGGA-AAGAG-GAAAGAGGAAAGAGGAAAGAGGAAAGAGGAAAG 44
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5)
+ 2770 1.6 0.0 0.7 X_16970860_16971175_INS 10 316 (0) + AluY SINE/Alu 1 305 (6) 409
ANNOTATION EVIDENCE:
2770 1.64 0.00 0.66 X_16970860_16971175_INS 10 316 0 + AluY SINE/Alu 1 305 6
2770 1.64 0.00 0.66 X_16970860_16971175_INS 10 316 (0) AluY#SINE/Alu 1 305 (6) c_b1s352i14
X_16970860_16 10 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 59
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_16970860_16 60 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 109
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_16970860_16 110 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCGTAGTG 159
-- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA--AATTAGCCGGGCGTGGTG 148
X_16970860_16 160 GCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGC 209
i
AluY#SINE/Alu 149 GCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGC 198
X_16970860_16 210 GTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCAC 259
v
AluY#SINE/Alu 199 GTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCAC 248
X_16970860_16 260 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 309
AluY#SINE/Alu 249 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 298
X_16970860_16 310 AAAAAAA 316
AluY#SINE/Alu 299 AAAAAAA 305
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (2 / 306), avg. gap size = 1.00 (2 / 2)
+ 85 2.4 0.0 0.0 X_17068260_17068344_INS 2 85 (0) + (CTTC)n Simple_repeat 1 84 (0) 410
ANNOTATION EVIDENCE:
85 2.44 0.00 0.00 X_17068260_17068344_INS 2 85 0 + (CTTC)n Simple_repeat 1 84 0
85 2.44 0.00 0.00 X_17068260_17068344_INS 2 85 (0) (CTTC)n#Simple_repeat 1 84 (0) c_b1s251i156
X_17068260_17 2 CTTCCTTCCTTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 51
i i
(CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50
X_17068260_17 52 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 85
(CTTC)n#Simpl 51 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 84
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0)
+ 2563 2.1 0.0 0.0 X_17349495_17349833_INS 16 339 (0) C AluY SINE/Alu (0) 311 1 411
ANNOTATION EVIDENCE:
47 0.00 0.00 0.00 X_17349495_17349833_INS 16 58 281 + (T)n Simple_repeat 1 43 0
47 0.00 0.00 0.00 X_17349495_17349833_INS 16 58 (281) (T)n#Simple_repeat 1 43 (0) c_b1s251i155
X_17349495_17 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 58
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
2563 2.14 0.00 0.00 X_17349495_17349833_INS 59 339 0 C AluY SINE/Alu 1 281 30
2563 2.14 0.00 0.00 X_17349495_17349833_INS 59 339 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i15
X_17349495_17 59 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 108
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_17349495_17 109 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 158
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_17349495_17 159 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 208
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_17349495_17 209 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTTTTAGCCGGGATGGT 258
i v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_17349495_17 259 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 308
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_17349495_17 309 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 339
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.51
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 1789 0.5 0.0 0.0 X_17607771_17607991_INS 25 221 (0) C L1HS LINE/L1 (0) 6155 5959 412
ANNOTATION EVIDENCE:
1789 0.51 0.00 0.00 X_17607771_17607991_INS 25 221 0 C L1HS_3end LINE/L1 706 902 0
1789 0.51 0.00 0.00 X_17607771_17607991_INS 25 221 (0) C L1HS_3end#LINE/L1 (0) 902 706 m_b1s551i3
X_17607771_17 25 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 74
C L1HS_3end#LIN 902 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 853
X_17607771_17 75 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 124
C L1HS_3end#LIN 852 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 803
X_17607771_17 125 CTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 174
i
C L1HS_3end#LIN 802 CTAACGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 753
X_17607771_17 175 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCT 221
C L1HS_3end#LIN 752 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCT 706
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.05
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 196), avg. gap size = 0.0 (0 / 0)
+ 2839 1.6 0.0 0.0 X_17808562_17808885_INS 17 324 (0) + AluY SINE/Alu 1 308 (3) 413
ANNOTATION EVIDENCE:
2839 1.62 0.00 0.00 X_17808562_17808885_INS 17 324 0 + AluY SINE/Alu 1 308 3
2839 1.62 0.00 0.00 X_17808562_17808885_INS 17 324 (0) AluY#SINE/Alu 1 308 (3) c_b1s352i16
X_17808562_17 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_17808562_17 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 116
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_17808562_17 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_17808562_17 167 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 216
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_17808562_17 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 266
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_17808562_17 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_17808562_17 317 AAAAAAAA 324
AluY#SINE/Alu 301 AAAAAAAA 308
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.34
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 307), avg. gap size = 0.0 (0 / 0)
+ 2227 2.8 0.0 0.4 X_18594857_18595152_INS 9 296 (0) C AluY SINE/Alu (0) 311 36 414
ANNOTATION EVIDENCE:
38 2.56 0.00 0.00 X_18594857_18595152_INS 9 48 248 + (T)n Simple_repeat 1 40 0
38 2.56 0.00 0.00 X_18594857_18595152_INS 9 48 (248) (T)n#Simple_repeat 1 40 (0) c_b1s251i154
X_18594857_18 9 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2227 2.78 0.00 0.40 X_18594857_18595152_INS 49 296 0 C AluY SINE/Alu 36 282 29
2227 2.78 0.00 0.40 X_18594857_18595152_INS 49 296 (0) C AluY#SINE/Alu (29) 282 36 c_b1s352i17
X_18594857_18 49 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 98
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_18594857_18 99 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 148
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_18594857_18 149 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 198
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_18594857_18 199 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 248
- v i
C AluY#SINE/Alu 132 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 84
X_18594857_18 249 TCTCGATCTCTTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 296
i
C AluY#SINE/Alu 83 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 36
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.48
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 247), avg. gap size = 1.00 (1 / 1)
+ 2466 2.8 0.0 2.5 X_18847561_18847886_INS 13 326 (0) C AluY SINE/Alu (0) 311 2 415
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_18847561_18847886_INS 13 38 288 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_18847561_18847886_INS 13 38 (288) (T)n#Simple_repeat 1 26 (0) c_b1s251i153
X_18847561_18 13 TTTTTTTTTTTTTTTTTTTTTTTTTT 38
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2466 2.80 0.00 2.45 X_18847561_18847886_INS 39 326 0 C AluY SINE/Alu 2 282 29
2466 2.80 0.00 2.45 X_18847561_18847886_INS 39 326 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i18
X_18847561_18 39 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 88
i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_18847561_18 89 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 138
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_18847561_18 139 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 188
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_18847561_18 189 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 238
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_18847561_18 239 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 288
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_18847561_18 289 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 326
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 56 1.3 9.1 0.0 X_18875878_18875960_INS 2 78 (5) + (AT)n Simple_repeat 1 84 (0) 416
ANNOTATION EVIDENCE:
56 1.31 9.09 0.00 X_18875878_18875960_INS 2 78 5 + (AT)n Simple_repeat 1 84 0
56 1.31 9.09 0.00 X_18875878_18875960_INS 2 78 (5) (AT)n#Simple_repeat 1 84 (0) c_b1s251i152
X_18875878_18 2 ATATATATAT-TATA-ATATAT-TTTATATATATATATATA-ATATATAT 47
- - - v -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_18875878_18 48 AT-TATA-ATATAT-TATATATATATATATATAT 78
- - -
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATAT 84
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.09 (7 / 76), avg. gap size = 1.00 (7 / 7)
+ 313 18.0 0.0 0.0 X_18886932_18887057_INS 40 56 (70) C 7SLRNA srpRNA (4) 316 300 417
ANNOTATION EVIDENCE:
313 18.03 0.00 0.00 X_18886932_18887057_INS 40 56 70 C 7SLRNA SINE/Alu 300 316 4
313 18.03 0.00 0.00 X_18886932_18887057_INS 40 56 (70) C 7SLRNA#SINE/Alu (4) 316 300 m_b1s502i1
X_18886932_18 40 TTTTTTTCCCTAATTTC 56
iii vv v
C 7SLRNA#SINE/A 316 TTTTTTTTTTTTTTTTA 300
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.31
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)
+ 26 0.0 0.0 0.0 X_18886932_18887057_INS 57 81 (45) + (T)n Simple_repeat 1 25 (0) 418
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_18886932_18887057_INS 57 81 45 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_18886932_18887057_INS 57 81 (45) (T)n#Simple_repeat 1 25 (0) c_b1s251i151
X_18886932_18 57 TTTTTTTTTTTTTTTTTTTTTTTTT 81
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 313 18.0 0.0 0.0 X_18886932_18887057_INS 82 124 (2) C 7SLRNA srpRNA (21) 299 257 417
ANNOTATION EVIDENCE:
313 18.03 0.00 0.00 X_18886932_18887057_INS 82 124 2 C 7SLRNA SINE/Alu 257 299 21
313 18.03 0.00 0.00 X_18886932_18887057_INS 82 124 (2) C 7SLRNA#SINE/Alu (21) 299 257 m_b1s502i1
X_18886932_18 82 GAGACGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCGGTGGC 124
i i v i i
C 7SLRNA#SINE/A 299 GAGACGGGGTCTCGCTATGTTGCCCAGGCTGGAGTGCAGTGGC 257
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.31
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 24 17.2 0.0 9.4 X_18899577_18899649_INS 1 70 (3) + (AT)n Simple_repeat 1 64 (0) 419
ANNOTATION EVIDENCE:
24 17.18 0.00 9.38 X_18899577_18899649_INS 1 70 3 + (AT)n Simple_repeat 1 64 0
24 17.18 0.00 9.38 X_18899577_18899649_INS 1 70 (3) (AT)n#Simple_repeat 1 64 (0) m_b1s252i114
X_18899577_18 1 ATATGATCTACAGATCATATATATATATGATCTACAGATCATATATATAT 50
- v i v - - v i v -
(AT)n#Simple_ 1 ATAT-ATATATATAT-ATATATATATAT-ATATATATAT-ATATATATAT 46
X_18899577_18 51 ATGATCTACAGATCATATAT 70
- v i v -
(AT)n#Simple_ 47 AT-ATATATATAT-ATATAT 64
Matrix = Unknown
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.00 (6 / 6)
+ 380 13.5 0.0 0.0 X_19092459_19092513_INS 3 54 (1) C 7SLRNA srpRNA (259) 61 10 420
ANNOTATION EVIDENCE:
380 13.46 0.00 0.00 X_19092459_19092513_INS 3 54 1 C 7SLRNA SINE/Alu 10 61 259
380 13.46 0.00 0.00 X_19092459_19092513_INS 3 54 (1) C 7SLRNA#SINE/Alu (259) 61 10 m_b1s502i2
X_19092459_19 3 GATCCTCCTGCCTCAGCCTCCTGAGTAGCTGAGACTACAGGCATGTACCA 52
i i i ii ii
C 7SLRNA#SINE/A 61 GATCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCA 12
X_19092459_19 53 CC 54
C 7SLRNA#SINE/A 11 CC 10
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.84
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 137 15.0 0.0 2.1 X_19092662_19092910_INS 2 249 (0) + (TTCTTC)n Simple_repeat 1 243 (0) 421
ANNOTATION EVIDENCE:
137 15.04 0.00 2.06 X_19092662_19092910_INS 2 249 0 + (TTCTTC)n Simple_repeat 1 243 0
137 15.04 0.00 2.06 X_19092662_19092910_INS 2 249 (0) (TTCTTC)n#Simple_repeat 1 243 (0) m_b1s252i113
X_19092662_19 2 TTCTTCTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCT 51
- i
(TTCTTC)n#Sim 1 TTCTTC-TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT 49
X_19092662_19 52 CCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCC 101
i i i i i i i i i
(TTCTTC)n#Sim 50 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 99
X_19092662_19 102 TTCTCCTTCTCCTTCTTCTTCCTTCTTCTTCTCCTTCTCCTTCTCCTTCT 151
i i - i i i
(TTCTTC)n#Sim 100 TTCTTCTTCTTCTTCTTCTT-CTTCTTCTTCTTCTTCTTCTTCTTCTTCT 148
X_19092662_19 152 CCTTCTCCTTCTCCTTCTTCTTCTTCCTTCTTCTTCCTTCTTCTTCTTCT 201
i i i - -
(TTCTTC)n#Sim 149 TCTTCTTCTTCTTCTTCTTCTTCTT-CTTCTTCTT-CTTCTTCTTCTTCT 196
X_19092662_19 202 TCCTCTTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTTC 249
i - i i i i i i i i i i i i
(TTCTTC)n#Sim 197 TCTTCTT-CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 243
Matrix = Unknown
Transitions / transversions = 1.00 (31/0)
Gap_init rate = 0.02 (5 / 247), avg. gap size = 1.00 (5 / 5)
+ 2887 0.3 0.0 0.0 X_19279526_19279833_INS 6 308 (0) C AluY SINE/Alu (7) 304 2 422
ANNOTATION EVIDENCE:
2887 0.33 0.00 0.00 X_19279526_19279833_INS 6 308 0 C AluY SINE/Alu 2 304 7
2887 0.33 0.00 0.00 X_19279526_19279833_INS 6 308 (0) C AluY#SINE/Alu (7) 304 2 c_b1s352i19
X_19279526_19 6 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 55
C AluY#SINE/Alu 304 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 255
X_19279526_19 56 GCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGG 105
C AluY#SINE/Alu 254 GCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGG 205
X_19279526_19 106 GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 155
C AluY#SINE/Alu 204 GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 155
X_19279526_19 156 GCCCGCTACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 205
i
C AluY#SINE/Alu 154 GCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 105
X_19279526_19 206 TTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCC 255
C AluY#SINE/Alu 104 TTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCC 55
X_19279526_19 256 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 305
C AluY#SINE/Alu 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 5
X_19279526_19 306 GGC 308
C AluY#SINE/Alu 4 GGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.33
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 2664 2.3 0.0 2.3 X_19357178_19357502_INS 16 325 (0) + AluY SINE/Alu 1 303 (8) 423
ANNOTATION EVIDENCE:
2664 2.31 0.00 2.31 X_19357178_19357502_INS 16 325 0 + AluY SINE/Alu 1 303 8
2664 2.31 0.00 2.31 X_19357178_19357502_INS 16 325 (0) AluY#SINE/Alu 1 303 (8) c_b1s352i20
X_19357178_19 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_19357178_19 66 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 115
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_19357178_19 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_19357178_19 166 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 215
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_19357178_19 216 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 265
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_19357178_19 266 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 315
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_19357178_19 316 AAAAAAAAAA 325
AluY#SINE/Alu 294 AAAAAAAAAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 1.00 (7 / 7)
+ 2850 1.9 0.0 0.0 X_19492628_19492955_INS 2 312 (16) + AluY SINE/Alu 1 311 (0) 424
ANNOTATION EVIDENCE:
2850 1.93 0.00 0.00 X_19492628_19492955_INS 2 312 16 + AluY SINE/Alu 1 311 0
2850 1.93 0.00 0.00 X_19492628_19492955_INS 2 312 (16) AluY#SINE/Alu 1 311 (0) c_b1s352i21
X_19492628_19 2 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 51
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_19492628_19 52 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 101
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_19492628_19 102 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 151
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_19492628_19 152 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCAT 201
i i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_19492628_19 202 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 251
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_19492628_19 252 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 301
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_19492628_19 302 AAAAAAAAAAA 312
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 21 14.8 0.0 4.3 X_19572495_19572546_INS 3 51 (1) + A-rich Low_complexity 1 47 (0) 425
ANNOTATION EVIDENCE:
21 14.83 0.00 4.26 X_19572495_19572546_INS 3 51 1 + (ATATAAA)n Simple_repeat 1 47 0
21 14.83 0.00 4.26 X_19572495_19572546_INS 3 51 (1) (ATATAAA)n#Simple_repeat 1 47 (0) m_b1s252i112
X_19572495_19 3 ATATATCATATTAAAATATAATATATATCATATTAAAATATAATATATA 51
vv - v vv - v
(ATATAAA)n#Si 1 ATATAAAATA-TAAAATATAAAATATAAAATA-TAAAATATAAAATATA 47
Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2)
+ 2432 3.4 0.0 2.8 X_20174402_20174733_INS 13 332 (0) C AluY SINE/Alu (0) 311 2 426
ANNOTATION EVIDENCE:
28 3.33 0.00 0.00 X_20174402_20174733_INS 13 43 289 + (T)n Simple_repeat 1 31 0
28 3.33 0.00 0.00 X_20174402_20174733_INS 13 43 (289) (T)n#Simple_repeat 1 31 (0) c_b1s251i150
X_20174402_20 13 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTT 43
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
2432 3.43 0.00 2.75 X_20174402_20174733_INS 44 332 0 C AluY SINE/Alu 2 282 29
2432 3.43 0.00 2.75 X_20174402_20174733_INS 44 332 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i22
X_20174402_20 44 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 93
i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_20174402_20 94 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 143
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_20174402_20 144 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 193
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_20174402_20 194 GGCTAATTTTTTGTATTTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCC 243
- v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTAT-TTTTAGTAGAGACGGGGTTTCACCGTGTTAGCC 91
X_20174402_20 244 AGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCA 293
i i
C AluY#SINE/Alu 90 AGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCA 41
X_20174402_20 294 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 332
C AluY#SINE/Alu 40 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.57
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.03 (8 / 288), avg. gap size = 1.00 (8 / 8)
+ 85 9.4 0.0 0.0 X_20738609_20738733_INS 8 124 (1) + (TA)n Simple_repeat 1 117 (0) 427
ANNOTATION EVIDENCE:
85 9.37 0.00 0.00 X_20738609_20738733_INS 8 124 1 + (TA)n Simple_repeat 1 117 0
85 9.37 0.00 0.00 X_20738609_20738733_INS 8 124 (1) (TA)n#Simple_repeat 1 117 (0) c_b1s251i149
X_20738609_20 8 TATATATATATATATACGTATATATATATATGTATATATGTATATATATA 57
ii i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_20738609_20 58 TATATACATATATATATACACACACATATATATATATATATATACATATA 107
i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_20738609_20 108 TATATATATATATATAT 124
(TA)n#Simple_ 101 TATATATATATATATAT 117
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 116), avg. gap size = 0.0 (0 / 0)
+ 2607 2.7 0.3 2.3 X_20923168_20923491_INS 17 324 (0) + AluY SINE/Alu 1 302 (9) 428
ANNOTATION EVIDENCE:
2607 2.66 0.32 2.32 X_20923168_20923491_INS 17 324 0 + AluY SINE/Alu 1 302 9
2607 2.66 0.32 2.32 X_20923168_20923491_INS 17 324 (0) AluY#SINE/Alu 1 302 (9) c_b1s352i23
X_20923168_20 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_20923168_20 67 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 116
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_20923168_20 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGT 166
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_20923168_20 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_20923168_20 217 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 266
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_20923168_20 267 CGCAGTCCGGCCTGGGCGACAG-GCGAGACTCCGTCTCAAAAAAAAAAAA 315
----- i -
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_20923168_20 316 AAAAAAAAA 324
AluY#SINE/Alu 294 AAAAAAAAA 302
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.03 (8 / 307), avg. gap size = 1.00 (8 / 8)
+ 2735 2.2 0.0 2.2 X_21015835_21016168_INS 4 321 (13) + AluY SINE/Alu 1 311 (0) 429
ANNOTATION EVIDENCE:
2735 2.25 0.00 2.25 X_21015835_21016168_INS 4 321 13 + AluY SINE/Alu 1 311 0
2735 2.25 0.00 2.25 X_21015835_21016168_INS 4 321 (13) AluY#SINE/Alu 1 311 (0) c_b1s352i24
X_21015835_21 4 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 53
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_21015835_21 54 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 103
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_21015835_21 104 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 153
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_21015835_21 154 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 203
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_21015835_21 204 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 253
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_21015835_21 254 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 303
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_21015835_21 304 AAAAAAAAAAAAAAAAAA 321
AluY#SINE/Alu 294 AAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.00 (7 / 7)
+ 22 21.1 3.5 0.0 X_21218988_21219045_INS 1 58 (0) + (TATGTA)n Simple_repeat 1 60 (0) 430
ANNOTATION EVIDENCE:
22 21.14 3.45 0.00 X_21218988_21219045_INS 1 58 0 + (TATGTA)n Simple_repeat 1 60 0
22 21.14 3.45 0.00 X_21218988_21219045_INS 1 58 (0) (TATGTA)n#Simple_repeat 1 60 (0) m_b1s252i110
X_21218988_21 1 TATGTATACACATATGTATACACATATGTATA--TATATATATGTATATG 48
iii iii -- i i i i
(TATGTA)n#Sim 1 TATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATA 50
X_21218988_21 49 TGTATATGTA 58
(TATGTA)n#Sim 51 TGTATATGTA 60
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.02 (1 / 57), avg. gap size = 2.00 (2 / 1)
+ 2122 0.8 0.0 0.0 X_21280597_21280933_INS 33 337 (0) + L1P1 LINE/L1 5153 5457 (698) 431
ANNOTATION EVIDENCE:
2122 1.59 0.00 0.00 X_21280597_21280933_INS 33 283 54 + L1P1_orf2 LINE/L1 3044 3294 0
2122 1.59 0.00 0.00 X_21280597_21280933_INS 33 283 (54) L1P1_orf2#LINE/L1 3044 3294 (0) m_b1s551i4
X_21280597_21 33 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGG 82
L1P1_orf2#LIN 3044 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGG 3093
X_21280597_21 83 CAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGG 132
iv
L1P1_orf2#LIN 3094 CAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGG 3143
X_21280597_21 133 GCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAA 182
L1P1_orf2#LIN 3144 GCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAA 3193
X_21280597_21 183 CAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTCA 232
i
L1P1_orf2#LIN 3194 CAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCA 3243
X_21280597_21 233 AAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATC 282
i
L1P1_orf2#LIN 3244 AAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATC 3293
X_21280597_21 283 A 283
L1P1_orf2#LIN 3294 A 3294
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.25
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 250), avg. gap size = 0.0 (0 / 0)
1741 0.49 0.00 0.00 X_21280597_21280933_INS 134 337 0 + L1HS_3end LINE/L1 1 204 698
1741 0.49 0.00 0.00 X_21280597_21280933_INS 134 337 (0) L1HS_3end#LINE/L1 1 204 (698) m_b1s551i5
X_21280597_21 134 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 183
L1HS_3end#LIN 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
X_21280597_21 184 AAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTCAA 233
i
L1HS_3end#LIN 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
X_21280597_21 234 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 283
L1HS_3end#LIN 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 150
X_21280597_21 284 CTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCAC 333
L1HS_3end#LIN 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCAC 200
X_21280597_21 334 ACCA 337
L1HS_3end#LIN 201 ACCA 204
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.05
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 203), avg. gap size = 0.0 (0 / 0)
+ 27 15.5 0.0 0.0 X_21322921_21322973_INS 4 48 (5) + (TA)n Simple_repeat 1 45 (0) 432
ANNOTATION EVIDENCE:
27 15.51 0.00 0.00 X_21322921_21322973_INS 4 48 5 + (TA)n Simple_repeat 1 45 0
27 15.51 0.00 0.00 X_21322921_21322973_INS 4 48 (5) (TA)n#Simple_repeat 1 45 (0) m_b1s252i109
X_21322921_21 4 TATATATATATATACACATATGTGTATATATATATATACACATAT 48
i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 2713 2.6 0.0 2.2 X_21884406_21884760_INS 15 355 (0) + AluY SINE/Alu 1 311 (0) 433
ANNOTATION EVIDENCE:
21 0.00 0.00 0.00 X_21884406_21884760_INS 333 355 0 + (A)n Simple_repeat 1 23 0
21 0.00 0.00 0.00 X_21884406_21884760_INS 333 355 (0) (A)n#Simple_repeat 1 23 (0) m_b1s252i108
X_21884406_21 333 AAAAAAAAAAAAAAAAAAAAAAA 355
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
2713 2.58 0.00 2.25 X_21884406_21884760_INS 15 332 23 + AluY SINE/Alu 1 311 0
2713 2.58 0.00 2.25 X_21884406_21884760_INS 15 332 (23) AluY#SINE/Alu 1 311 (0) c_b1s352i25
X_21884406_21 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_21884406_21 65 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 114
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_21884406_21 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_21884406_21 165 GGGCGCCTGTAGTCCCAGCTACTGGGGAGGCTGAGGCAGGAGAATGGCGT 214
v
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_21884406_21 215 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 264
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_21884406_21 265 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 314
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_21884406_21 315 AAAAAAAAAAAAAAAAAA 332
AluY#SINE/Alu 294 AAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.73
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.00 (7 / 7)
+ 1164 2.7 0.0 4.8 X_22324316_22324508_INS 2 193 (0) C AluY SINE/Alu (0) 311 136 434
ANNOTATION EVIDENCE:
43 0.00 0.00 0.00 X_22324316_22324508_INS 2 40 153 + (T)n Simple_repeat 1 39 0
43 0.00 0.00 0.00 X_22324316_22324508_INS 2 40 (153) (T)n#Simple_repeat 1 39 (0) c_b1s251i148
X_22324316_22 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
1164 2.74 0.00 4.79 X_22324316_22324508_INS 41 193 0 C AluY SINE/Alu 136 281 30
1164 2.74 0.00 4.79 X_22324316_22324508_INS 41 193 (0) C AluY#SINE/Alu (30) 281 136 m_b1s356i0
X_22324316_22 41 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 90
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_22324316_22 91 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 140
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_22324316_22 141 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 190
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_22324316_22 191 GGC 193
C AluY#SINE/Alu 138 GGC 136
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.17
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.05 (7 / 152), avg. gap size = 1.00 (7 / 7)
+ 41 0.0 0.0 4.4 X_22332288_22332338_INS 1 47 (4) + (AGGGAGG)n Simple_repeat 1 45 (0) 435
ANNOTATION EVIDENCE:
41 0.00 0.00 4.44 X_22332288_22332338_INS 1 47 4 + (AGGGAGG)n Simple_repeat 1 45 0
41 0.00 0.00 4.44 X_22332288_22332338_INS 1 47 (4) (AGGGAGG)n#Simple_repeat 1 45 (0) c_b1s251i147
X_22332288_22 1 AGGGAGGAGGGAGGAGGAGAGGAGGGAGGAGGAGAGGAGGGAGGAGG 47
- -
(AGGGAGG)n#Si 1 AGGGAGGAGGGAGGAGG-GAGGAGGGAGGAGG-GAGGAGGGAGGAGG 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2)
+ 2607 2.1 0.0 0.0 X_22365071_22365404_INS 9 334 (0) C AluY SINE/Alu (0) 311 2 436
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 X_22365071_22365404_INS 9 53 281 + (T)n Simple_repeat 1 45 0
50 0.00 0.00 0.00 X_22365071_22365404_INS 9 53 (281) (T)n#Simple_repeat 1 45 (0) c_b1s251i146
X_22365071_22 9 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 53
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
2607 2.10 0.00 0.00 X_22365071_22365404_INS 54 334 0 C AluY SINE/Alu 2 282 29
2607 2.10 0.00 0.00 X_22365071_22365404_INS 54 334 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i26
X_22365071_22 54 GAGACGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 103
i
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_22365071_22 104 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 153
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_22365071_22 154 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 203
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_22365071_22 204 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 253
v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_22365071_22 254 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 303
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_22365071_22 304 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 334
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.49
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2426 2.9 0.0 2.5 X_22504994_22505320_INS 7 327 (0) C AluY SINE/Alu (0) 311 1 437
ANNOTATION EVIDENCE:
30 3.13 0.00 0.00 X_22504994_22505320_INS 7 39 288 + (T)n Simple_repeat 1 33 0
30 3.13 0.00 0.00 X_22504994_22505320_INS 7 39 (288) (T)n#Simple_repeat 1 33 (0) c_b1s251i145
X_22504994_22 7 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
2426 2.85 0.00 2.49 X_22504994_22505320_INS 40 327 0 C AluY SINE/Alu 1 281 30
2426 2.85 0.00 2.49 X_22504994_22505320_INS 40 327 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i27
X_22504994_22 40 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 89
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_22504994_22 90 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 139
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_22504994_22 140 TGCCTCAGCCTCCCGAGTAGCTGGGACCACAGGCGCCCGCCACCGCGCCC 189
i i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_22504994_22 190 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 239
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_22504994_22 240 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 289
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_22504994_22 290 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 327
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.92
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 453 5.2 0.0 0.0 X_22631237_22631294_INS 1 58 (0) + L1P1 LINE/L1 3954 4011 (2135) 438
ANNOTATION EVIDENCE:
453 5.17 0.00 0.00 X_22631237_22631294_INS 1 58 0 + L1P1_orf2 LINE/L1 1845 1902 1392
453 5.17 0.00 0.00 X_22631237_22631294_INS 1 58 (0) L1P1_orf2#LINE/L1 1845 1902 (1392) m_b1s551i6
X_22631237_22 1 AACTCTCAATAAATTAGGAAGTGATGGGACGTATCTCAAAACAATAAGAG 50
v v i
L1P1_orf2#LIN 1845 AACTCTCAATAAATTAGGTATTGATGGGACGTATCTCAAAATAATAAGAG 1894
X_22631237_22 51 CTATCTAT 58
L1P1_orf2#LIN 1895 CTATCTAT 1902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.36
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 55 1.4 0.0 5.3 X_22682814_22682894_INS 2 81 (0) + (GAAA)n Simple_repeat 1 76 (0) 439
ANNOTATION EVIDENCE:
55 1.40 0.00 5.26 X_22682814_22682894_INS 2 81 0 + (GAAA)n Simple_repeat 1 76 0
55 1.40 0.00 5.26 X_22682814_22682894_INS 2 81 (0) (GAAA)n#Simple_repeat 1 76 (0) m_b1s252i107
X_22682814_22 2 GAAAGAAAGGAAAGAAAGAAAGGAAAGAAAGGAAAGAAAGGAAAGAAAGG 51
- - - - i
(GAAA)n#Simpl 1 GAAAGAAA-GAAAGAAAGAAA-GAAAGAAA-GAAAGAAA-GAAAGAAAGA 46
X_22682814_22 52 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 81
(GAAA)n#Simpl 47 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 76
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4)
+ 65 0.0 0.0 0.0 X_22796598_22796663_INS 9 66 (0) + (T)n Simple_repeat 1 58 (0) 440
ANNOTATION EVIDENCE:
65 0.00 0.00 0.00 X_22796598_22796663_INS 9 66 0 + (T)n Simple_repeat 1 58 0
65 0.00 0.00 0.00 X_22796598_22796663_INS 9 66 (0) (T)n#Simple_repeat 1 58 (0) c_b1s251i144
X_22796598_22 9 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 58
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_22796598_22 59 TTTTTTTT 66
(T)n#Simple_r 51 TTTTTTTT 58
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 20 10.8 0.0 7.0 X_22806308_22806377_INS 6 51 (19) + A-rich Low_complexity 1 43 (0) 441
ANNOTATION EVIDENCE:
20 10.78 0.00 6.98 X_22806308_22806377_INS 6 51 19 + (TTAAA)n Simple_repeat 1 43 0
20 10.78 0.00 6.98 X_22806308_22806377_INS 6 51 (19) (TTAAA)n#Simple_repeat 1 43 (0) m_b1s252i106
X_22806308_22 6 TTAAATTAGAAATTTAATTTAATTAAATTTAATTAAAATTAAAATA 51
-- v v v - v
(TTAAA)n#Simp 1 TTAAATT--AAATTAAATTAAATTAAATTAAATT-AAATTAAATTA 43
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3)
+ 61 9.3 1.8 2.8 X_22916737_22916847_INS 2 111 (0) + (ATAATAT)n Simple_repeat 1 108 (0) 442
ANNOTATION EVIDENCE:
61 9.28 1.83 2.78 X_22916737_22916847_INS 2 110 1 + (ATAATAT)n Simple_repeat 1 108 0
61 9.28 1.83 2.78 X_22916737_22916847_INS 2 110 (1) (ATAATAT)n#Simple_repeat 1 108 (0) m_b1s252i104
X_22916737_22 2 ATTATATATTAATATATAATATATAATTATATATTATATATTATATATTA 51
v - - v v v
(ATAATAT)n#Si 1 ATAATATA-TAATATATAATATATAA-TATATAATATATAATATATAATA 48
X_22916737_22 52 TACAATATATAATTATATATTATATAATATA-ATTACATATTATATAATA 100
i - v - v i v
(ATAATAT)n#Si 49 TATAATATATAA-TATATAATATATAATATATAATATATAATATATAATA 97
X_22916737_22 101 TATAAT-TATA 110
-
(ATAATAT)n#Si 98 TATAATATATA 108
Matrix = Unknown
Transitions / transversions = 0.29 (2/7)
Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.00 (5 / 5)
51 12.06 8.33 0.00 X_22916737_22916847_INS 4 111 0 + (TA)n Simple_repeat 1 117 0
51 12.06 8.33 0.00 X_22916737_22916847_INS 4 111 (0) (TA)n#Simple_repeat 1 117 (0) m_b1s252i105
X_22916737_22 4 TATATATTAATATATA-ATATATAATTATATAT-TATATAT-TATATAT- 49
vv - vv - - -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_22916737_22 50 TATACA-ATATATAATTATATAT-TATATA-ATATAATTACATAT-TATA 95
i - vv - - vv i -
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_22916737_22 96 TA-ATATATAATTATAT 111
- vv
(TA)n#Simple_ 101 TATATATATATATATAT 117
Matrix = Unknown
Transitions / transversions = 0.20 (2/10)
Gap_init rate = 0.08 (9 / 107), avg. gap size = 1.00 (9 / 9)
+ 42 0.0 7.5 0.0 X_22957239_22957291_INS 1 53 (0) + (ATATATGTAT)n Simple_repeat 1 57 (0) 443
ANNOTATION EVIDENCE:
42 0.00 7.55 0.00 X_22957239_22957291_INS 1 53 0 + (ATATATGTAT)n Simple_repeat 1 57 0
42 0.00 7.55 0.00 X_22957239_22957291_INS 1 53 (0) (ATATATGTAT)n#Simple_repeat 1 57 (0) c_b1s251i143
X_22957239_22 1 ATATATGTATATATATG--TATATATGTATATATATG--TATATATGTAT 46
-- --
(ATATATGTAT)n 1 ATATATGTATATATATGTATATATATGTATATATATGTATATATATGTAT 50
X_22957239_22 47 ATATATG 53
(ATATATGTAT)n 51 ATATATG 57
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 52), avg. gap size = 2.00 (4 / 2)
+ 2577 2.4 0.0 2.4 X_22960237_22960551_INS 16 315 (0) + AluY SINE/Alu 1 293 (18) 444
ANNOTATION EVIDENCE:
2577 2.39 0.00 2.39 X_22960237_22960551_INS 16 315 0 + AluY SINE/Alu 1 293 18
2577 2.39 0.00 2.39 X_22960237_22960551_INS 16 315 (0) AluY#SINE/Alu 1 293 (18) c_b1s352i28
X_22960237_22 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_22960237_22 66 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 115
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_22960237_22 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_22960237_22 166 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 215
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_22960237_22 216 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 265
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_22960237_22 266 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 315
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.49
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 299), avg. gap size = 1.00 (7 / 7)
+ 2760 2.3 0.0 0.3 X_23057689_23058006_INS 10 318 (0) C AluY SINE/Alu (3) 308 1 445
ANNOTATION EVIDENCE:
2760 2.28 0.00 0.32 X_23057689_23058006_INS 10 318 0 C AluY SINE/Alu 1 308 3
2760 2.28 0.00 0.32 X_23057689_23058006_INS 10 318 (0) C AluY#SINE/Alu (3) 308 1 c_b1s352i29
X_23057689_23 10 TTTTCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 59
i
C AluY#SINE/Alu 308 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 259
X_23057689_23 60 CCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTC 109
v
C AluY#SINE/Alu 258 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTC 209
X_23057689_23 110 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTAC 159
i
C AluY#SINE/Alu 208 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 159
X_23057689_23 160 AGGCGCCCGCCACTACGCCCGGCTAATTTTTTTGTATTTTTAGTAGAGAC 209
i -
C AluY#SINE/Alu 158 AGGCGCCCGCCACCACGCCCGGCTAATT-TTTTGTATTTTTAGTAGAGAC 110
X_23057689_23 210 GGGGTTTCACCGTTTTAGCCGGGATGGCCTCGATCTCCTGACCTCGTGAT 259
v i i
C AluY#SINE/Alu 109 GGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGAT 60
X_23057689_23 260 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 309
C AluY#SINE/Alu 59 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
X_23057689_23 310 CGCCCGGCC 318
C AluY#SINE/Alu 9 CGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.01
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (1 / 308), avg. gap size = 1.00 (1 / 1)
+ 50 0.0 0.0 0.0 X_23628490_23628542_INS 1 45 (8) + (AGGA)n Simple_repeat 1 45 (0) 446
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 X_23628490_23628542_INS 1 45 8 + (AGGA)n Simple_repeat 1 45 0
50 0.00 0.00 0.00 X_23628490_23628542_INS 1 45 (8) (AGGA)n#Simple_repeat 1 45 (0) c_b1s251i142
X_23628490_23 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 45
(AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 79 0.0 4.8 0.0 X_23777840_23777930_INS 1 84 (7) + (AAGA)n Simple_repeat 1 88 (0) 447
ANNOTATION EVIDENCE:
79 0.00 4.76 0.00 X_23777840_23777930_INS 1 84 7 + (AAGA)n Simple_repeat 1 88 0
79 0.00 4.76 0.00 X_23777840_23777930_INS 1 84 (7) (AAGA)n#Simple_repeat 1 88 (0) c_b1s251i141
X_23777840_23 1 AAGAAAGAAAGAAAG--AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 48
--
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
X_23777840_23 49 GAAAGAAAGAAAGAAAGAAAGAAAG-AA-AAAGAAAGA 84
- -
(AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 88
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.33 (4 / 3)
+ 39 16.2 0.0 0.0 X_23798243_23798311_INS 2 66 (3) + (AT)n Simple_repeat 1 65 (0) 448
ANNOTATION EVIDENCE:
39 16.21 0.00 0.00 X_23798243_23798311_INS 2 66 3 + (AT)n Simple_repeat 1 65 0
39 16.21 0.00 0.00 X_23798243_23798311_INS 2 66 (3) (AT)n#Simple_repeat 1 65 (0) m_b1s252i103
X_23798243_23 2 ATATATATGTGTATATATATGTGTATATATACACATATATATGTGTATAT 51
i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_23798243_23 52 ATATGTATATATATA 66
i
(AT)n#Simple_ 51 ATATATATATATATA 65
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 16 0.0 0.0 0.0 X_24000777_24001437_INS 2 18 (643) + (A)n Simple_repeat 1 17 (0) 449
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 X_24000777_24001437_INS 2 18 371 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 X_24000777_24001437_INS 2 18 (371) (A)n#Simple_repeat 1 17 (0) m_b1s252i102
X_24000777_24 2 AAAAAAAAAAAAAAAAA 18
(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)
+ 209 26.1 5.6 1.1 X_24000777_24001437_INS 249 337 (324) C L2 LINE/L2 (936) 2483 2391 450
ANNOTATION EVIDENCE:
209 26.12 5.62 1.08 X_24000777_24001437_INS 249 337 52 C L2 LINE/L2 2391 2483 599
209 26.12 5.62 1.08 X_24000777_24001437_INS 249 337 (52) C L2#LINE/L2 (599) 2483 2391 m_b1s601i0
X_24000777_24 249 TTTGGGGGAGTAGACAATGTATTCAGATTTGCACTTGTTCAGTTTGAAAT 298
i i v iv v vi i v v v v i
C L2#LINE/L2 2483 TTTGAGGGGGAAGATCAGGAGTTCGGTTTTGGACATGTTAAGTTTGAGAT 2434
X_24000777_24 299 TCCAAT---ACAAC--AGTGAGAGATGTTCAGGAGATGGTTGGA 337
v v --- v -- - iv v iii
C L2#LINE/L2 2433 GCCTATTAGACATCCAAGTG-GAGATGTCGAGTAGGCAGTTGGA 2391
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 29.09
Transitions / transversions = 0.77 (10/13)
Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.00 (6 / 3)
+ 1880 11.8 3.7 0.7 X_24000777_24001437_INS 388 660 (1) + AluSx SINE/Alu 1 281 (31) 451
ANNOTATION EVIDENCE:
1880 11.80 3.66 0.71 X_24000777_24001437_INS 388 660 1 + AluSx SINE/Alu 1 281 31
1880 11.80 3.66 0.71 X_24000777_24001437_INS 388 660 (1) AluSx#SINE/Alu 1 281 (31) c_b1s352i30
X_24000777_24 388 GGCTGGGTGCAGTGGCTCACACCTGTAACACCAACACGTTGGGAGGCCGA 437
i i i i iv i v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_24000777_24 438 A-CGGGTGGATCATCTGAGGTCAGGAGTTCGAGACCAGCCTGTCCAACAT 486
i- i i v
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
X_24000777_24 487 GGTGAAACCCCGTCTCTACTAAAAATACAAAA-TTACCTGGGCATGGTGG 535
- v i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
X_24000777_24 536 CACATGCACCTGTAATCCCAGCTACTTGGGATGCTGAAGCAGGAGAATCA 585
i -- i i v i i
AluSx#SINE/Al 151 CGC--GCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG 198
X_24000777_24 586 CTTGAACCCAGAAGGTGGAGGTTGCAGTGAGCCAAGACCACACCACTGCA 635
i i i i i i i
AluSx#SINE/Al 199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248
X_24000777_24 636 TTCCAGC--------CAGAGCAAGGCTCTGTCT 660
i -------- i i i
AluSx#SINE/Al 249 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT 281
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 6.11
Transitions / transversions = 5.40 (27/5)
Gap_init rate = 0.02 (5 / 272), avg. gap size = 2.40 (12 / 5)
+ 24 22.9 0.0 0.0 X_24064608_24064664_INS 2 50 (7) + (AT)n Simple_repeat 1 49 (0) 452
ANNOTATION EVIDENCE:
24 22.89 0.00 0.00 X_24064608_24064664_INS 2 50 7 + (AT)n Simple_repeat 1 49 0
24 22.89 0.00 0.00 X_24064608_24064664_INS 2 50 (7) (AT)n#Simple_repeat 1 49 (0) m_b1s252i101
X_24064608_24 2 ATATACACATATATGTATATACACACATATATACACATATATGTATATA 50
i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 38 9.8 0.0 0.0 X_24378607_24378667_INS 1 55 (6) + (CA)n Simple_repeat 1 55 (0) 453
ANNOTATION EVIDENCE:
38 9.75 0.00 0.00 X_24378607_24378667_INS 1 55 6 + (CA)n Simple_repeat 1 55 0
38 9.75 0.00 0.00 X_24378607_24378667_INS 1 55 (6) (CA)n#Simple_repeat 1 55 (0) c_b1s251i140
X_24378607_24 1 CACACACACACGTACACACATACACACACACTGACACACACACACACACA 50
ii i vv
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50
X_24378607_24 51 CACAC 55
(CA)n#Simple_ 51 CACAC 55
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 439 5.2 0.0 0.0 X_24451541_24451650_INS 13 110 (0) C AluSx SINE/Alu (0) 312 225 454
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_24451541_24451650_INS 13 52 58 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_24451541_24451650_INS 13 52 (58) (T)n#Simple_repeat 1 40 (0) c_b1s251i139
X_24451541_24 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 52
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
439 5.17 0.00 0.00 X_24451541_24451650_INS 53 110 0 C AluSx SINE/Alu 225 282 30
439 5.17 0.00 0.00 X_24451541_24451650_INS 53 110 (0) C AluSx#SINE/Alu (30) 282 225 m_b1s357i0
X_24451541_24 53 GAGACGGAGTCTCGCTCTGTGGCCCAGGCGGGAGTGCAGTGGCGCAATCT 102
v v i
C AluSx#SINE/Al 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_24451541_24 103 CGGCTCAC 110
C AluSx#SINE/Al 232 CGGCTCAC 225
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.72
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 2809 2.2 0.0 0.0 X_2451748_2452090_INS 18 328 (15) + AluY SINE/Alu 1 311 (0) 455
ANNOTATION EVIDENCE:
2809 2.25 0.00 0.00 X_2451748_2452090_INS 18 328 15 + AluY SINE/Alu 1 311 0
2809 2.25 0.00 0.00 X_2451748_2452090_INS 18 328 (15) AluY#SINE/Alu 1 311 (0) c_b1s352i31
X_2451748_245 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_2451748_245 68 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 117
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_2451748_245 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_2451748_245 168 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 217
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_2451748_245 218 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 267
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_2451748_245 268 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAC 317
v
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_2451748_245 318 AAAAAACAAAA 328
v
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.99
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 2592 2.7 0.0 2.4 X_24799747_24800067_INS 17 321 (0) + AluY SINE/Alu 2 299 (12) 456
ANNOTATION EVIDENCE:
2592 2.68 0.00 2.35 X_24799747_24800067_INS 17 321 0 + AluY SINE/Alu 2 299 12
2592 2.68 0.00 2.35 X_24799747_24800067_INS 17 321 (0) AluY#SINE/Alu 2 299 (12) c_b1s352i32
X_24799747_24 17 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 66
AluY#SINE/Alu 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
X_24799747_24 67 GCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGT 116
i i v
AluY#SINE/Alu 52 GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGT 101
X_24799747_24 117 GAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCG 166
i
AluY#SINE/Alu 102 GAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCG 151
X_24799747_24 167 GGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTG 216
AluY#SINE/Alu 152 GGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTG 201
X_24799747_24 217 AACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCC 266
i i v -
AluY#SINE/Alu 202 AACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC- 250
X_24799747_24 267 GCAGTCCGACCTGGGCGACAGAGAGAGACTCCGTCTCAAAAAAAAAAAAA 316
- ----- v
AluY#SINE/Alu 251 -CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAA 294
X_24799747_24 317 AAAAA 321
AluY#SINE/Alu 295 AAAAA 299
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.80
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.02 (7 / 304), avg. gap size = 1.00 (7 / 7)
+ 2424 3.6 0.0 2.5 X_24842817_24843150_INS 13 333 (1) C AluY SINE/Alu (0) 311 1 457
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_24842817_24843150_INS 13 45 289 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_24842817_24843150_INS 13 45 (289) (T)n#Simple_repeat 1 33 (0) c_b1s251i138
X_24842817_24 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(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)
2424 3.56 0.00 2.49 X_24842817_24843150_INS 46 333 1 C AluY SINE/Alu 1 281 30
2424 3.56 0.00 2.49 X_24842817_24843150_INS 46 333 (1) C AluY#SINE/Alu (30) 281 1 c_b1s352i33
X_24842817_24 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCAGACTGCGGACTGCAGTGGC 95
i------- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCT-------GGAGTGCAGTGGC 239
X_24842817_24 96 GCAATCTCGGCTCACTGCAAGCTCCACTTCCTGGGTTCACGCCATTCTCC 145
i i i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_24842817_24 146 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 195
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_24842817_24 196 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 245
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_24842817_24 246 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 295
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_24842817_24 296 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 333
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.99
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 59 0.0 0.0 0.0 X_24940009_24940059_INS 2 51 (0) + (TG)n Simple_repeat 1 50 (0) 458
ANNOTATION EVIDENCE:
59 0.00 0.00 0.00 X_24940009_24940059_INS 2 51 0 + (TG)n Simple_repeat 1 50 0
59 0.00 0.00 0.00 X_24940009_24940059_INS 2 51 (0) (TG)n#Simple_repeat 1 50 (0) c_b1s251i137
X_24940009_24 2 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 51
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 2398 10.4 0.3 0.0 X_2496936_2497332_INS 7 315 (82) C AluSx SINE/Alu (2) 310 1 459
ANNOTATION EVIDENCE:
2398 10.36 0.32 0.00 X_2496936_2497332_INS 7 315 82 C AluSx SINE/Alu 1 310 2
2398 10.36 0.32 0.00 X_2496936_2497332_INS 7 315 (82) C AluSx#SINE/Alu (2) 310 1 c_b1s352i34
X_2496936_249 7 TTTTTTTTTCTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCA 56
i i ii i
C AluSx#SINE/Al 310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCG 261
X_2496936_249 57 CCCAGGCTGGAGTGCAATGGCGCGATCTCGGCTCACCGCAACCTCTGCCT 106
i i i
C AluSx#SINE/Al 260 CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT 211
X_2496936_249 107 CCCAGGTTCAAGTAATTCTCCTGCCTCAGCTTCCCAAGTAGCTGGGACTA 156
i ii i i i
C AluSx#SINE/Al 210 CCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTA 161
X_2496936_249 157 CAGGCATGTGTCACCATGTCCAGC-AAATTTTGTATTTTTAGTAGAGACG 205
ii i i i i i - v
C AluSx#SINE/Al 160 CAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACG 111
X_2496936_249 206 GGGTTTCGCCATGGTGGCCGGGCTGGTCTCAAACTCCTGACCTCAGGTGA 255
i v i i
C AluSx#SINE/Al 110 GGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGA 61
X_2496936_249 256 TCCACCCGCATCGGCCTCCCAAAGTGCTGGGATTACAGGCATGTGCCACC 305
i v i v
C AluSx#SINE/Al 60 TCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 11
X_2496936_249 306 ACGCCCAGCC 315
i i
C AluSx#SINE/Al 10 GCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.58
Transitions / transversions = 7.00 (28/4)
Gap_init rate = 0.00 (1 / 308), avg. gap size = 1.00 (1 / 1)
+ 2578 3.1 0.0 0.0 X_25060124_25060440_INS 12 317 (0) C AluY SINE/Alu (0) 311 2 460
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_25060124_25060440_INS 12 36 281 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_25060124_25060440_INS 12 36 (281) (T)n#Simple_repeat 1 25 (0) c_b1s251i136
X_25060124_25 12 TTTTTTTTTTTTTTTTTTTTTTTTT 36
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2578 3.10 0.00 0.00 X_25060124_25060440_INS 37 317 0 C AluY SINE/Alu 2 282 29
2578 3.10 0.00 0.00 X_25060124_25060440_INS 37 317 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i35
X_25060124_25 37 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 86
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_25060124_25 87 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 136
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_25060124_25 137 GCCTCCCAAGTAGCTGGGACTACAGGCGCCTGCCACTACGCCCGGCTAAT 186
i i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_25060124_25 187 TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTTTTAGCCGGGATGGT 236
i v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_25060124_25 237 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 286
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_25060124_25 287 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 317
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.21
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2563 2.1 0.0 0.0 X_25159302_25159623_INS 11 322 (0) C AluY SINE/Alu (0) 311 1 461
ANNOTATION EVIDENCE:
33 0.00 0.00 0.00 X_25159302_25159623_INS 11 41 281 + (T)n Simple_repeat 1 31 0
33 0.00 0.00 0.00 X_25159302_25159623_INS 11 41 (281) (T)n#Simple_repeat 1 31 (0) c_b1s251i135
X_25159302_25 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
2563 2.14 0.00 0.00 X_25159302_25159623_INS 42 322 0 C AluY SINE/Alu 1 281 30
2563 2.14 0.00 0.00 X_25159302_25159623_INS 42 322 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i36
X_25159302_25 42 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 91
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_25159302_25 92 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 141
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_25159302_25 142 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 191
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_25159302_25 192 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTTTTAGCCGGGATGGT 241
i v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_25159302_25 242 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 291
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_25159302_25 292 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 322
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.51
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2445 2.5 0.0 2.5 X_2528858_2529200_INS 16 343 (0) C AluY SINE/Alu (0) 311 1 462
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_2528858_2529200_INS 16 55 288 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_2528858_2529200_INS 16 55 (288) (T)n#Simple_repeat 1 40 (0) c_b1s251i134
X_2528858_252 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 55
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2445 2.49 0.00 2.49 X_2528858_2529200_INS 56 343 0 C AluY SINE/Alu 1 281 30
2445 2.49 0.00 2.49 X_2528858_2529200_INS 56 343 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i37
X_2528858_252 56 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 105
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_2528858_252 106 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 155
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_2528858_252 156 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 205
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_2528858_252 206 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 255
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_2528858_252 256 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 305
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_2528858_252 306 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 343
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 341 0.0 0.0 0.0 X_25395187_25395257_INS 29 65 (6) C tRNA-Arg-AGA tRNA (37) 37 1 463
ANNOTATION EVIDENCE:
341 0.00 0.00 0.00 X_25395187_25395257_INS 29 65 6 C tRNA-Arg-AGA tRNA 1 37 37
341 0.00 0.00 0.00 X_25395187_25395257_INS 29 65 (6) C tRNA-Arg-AGA#tRNA (37) 37 1 m_b1s502i3
X_25395187_25 29 TAGAAGTCCAATGCGCTATCCATTGCGCCACAGAGCC 65
C tRNA-Arg-AGA# 37 TAGAAGTCCAATGCGCTATCCATTGCGCCACAGAGCC 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 2101 3.2 0.0 4.4 X_25631452_25631746_INS 8 295 (0) C AluY SINE/Alu (0) 311 31 464
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_25631452_25631746_INS 8 33 262 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_25631452_25631746_INS 8 33 (262) (T)n#Simple_repeat 1 26 (0) c_b1s251i133
X_25631452_25 8 TTTTTTTTTTTTTTTTTTTTTTTTTT 33
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2101 3.19 0.00 4.38 X_25631452_25631746_INS 34 295 0 C AluY SINE/Alu 31 281 30
2101 3.19 0.00 4.38 X_25631452_25631746_INS 34 295 (0) C AluY#SINE/Alu (30) 281 31 c_b1s352i38
X_25631452_25 34 GAGACGGAGTCTCGCTCTGTCGCCCCGGCGGGAGTGCGGACTGCAGTGGC 83
v v -------
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGC-------AGTGGC 239
X_25631452_25 84 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 133
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_25631452_25 134 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 183
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_25631452_25 184 GGCTAATTTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTA 233
---- v
C AluY#SINE/Alu 138 GGCTAATT----TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTA 93
X_25631452_25 234 GCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTC 283
i i
C AluY#SINE/Alu 92 GCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTC 43
X_25631452_25 284 CCAAAGTGCTGG 295
C AluY#SINE/Alu 42 CCAAAGTGCTGG 31
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.14
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.04 (11 / 261), avg. gap size = 1.00 (11 / 11)
+ 26 0.0 3.5 0.0 X_25760159_25760219_INS 32 60 (1) + (ATATA)n Simple_repeat 1 30 (0) 465
ANNOTATION EVIDENCE:
26 0.00 3.45 0.00 X_25760159_25760219_INS 32 60 1 + (ATATA)n Simple_repeat 1 30 0
26 0.00 3.45 0.00 X_25760159_25760219_INS 32 60 (1) (ATATA)n#Simple_repeat 1 30 (0) c_b1s251i132
X_25760159_25 32 ATATAATAT-ATATAATATAATATAATATA 60
-
(ATATA)n#Simp 1 ATATAATATAATATAATATAATATAATATA 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1)
+ 32 9.8 0.0 3.5 X_25842783_25842843_INS 2 60 (1) + (TATATAT)n Simple_repeat 1 57 (0) 466
ANNOTATION EVIDENCE:
32 9.75 0.00 3.51 X_25842783_25842843_INS 2 60 1 + (TATATAT)n Simple_repeat 1 57 0
32 9.75 0.00 3.51 X_25842783_25842843_INS 2 60 (1) (TATATAT)n#Simple_repeat 1 57 (0) m_b1s252i100
X_25842783_25 2 TATATCATATATATTATATATGATATATTCTATATCATATATATTATATA 51
vv v v --
(TATATAT)n#Si 1 TATATATTATATATTATATATTATATATTATATAT--TATATATTATATA 48
X_25842783_25 52 TGATATATT 60
v
(TATATAT)n#Si 49 TTATATATT 57
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2)
+ 2735 2.3 0.0 2.3 X_25978448_25978780_INS 17 333 (0) + AluY SINE/Alu 1 310 (1) 467
ANNOTATION EVIDENCE:
2735 2.26 0.00 2.26 X_25978448_25978780_INS 17 333 0 + AluY SINE/Alu 1 310 1
2735 2.26 0.00 2.26 X_25978448_25978780_INS 17 333 (0) AluY#SINE/Alu 1 310 (1) c_b1s352i39
X_25978448_25 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_25978448_25 67 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 116
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_25978448_25 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_25978448_25 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_25978448_25 217 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 266
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_25978448_25 267 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 316
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_25978448_25 317 AAAAAAAAAAAAAAAAA 333
AluY#SINE/Alu 294 AAAAAAAAAAAAAAAAA 310
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 316), avg. gap size = 1.00 (7 / 7)
+ 436 21.2 1.5 0.2 X_26034424_26034536_INS 9 112 (1) + L1M3 LINE/L1 2627 2732 (3408) 468
ANNOTATION EVIDENCE:
322 23.22 3.96 1.94 X_26034424_26034536_INS 9 109 4 + L1PB_orf2 LINE/L1 518 620 2674
322 23.22 3.96 1.94 X_26034424_26034536_INS 9 109 (4) L1PB_orf2#LINE/L1 518 620 (2674) m_b1s551i7
X_26034424_26 9 AACAAGT---CTTAAGACAG-CATATACAGAACATTCCATCCAACACTTG 54
i --- -- -i v i i vii
L1PB_orf2#LIN 518 AACAAATGGACTTAA--CAGATATTTACAGAACATTCTACCCAACAACCG 565
X_26034424_26 55 TAGAATATATATTCTTTACAAGAGTACATGAAACATTTTCCACAATCAAT 104
i i v v ?v ii i ? i vi vi i
L1PB_orf2#LIN 566 CAGAATATACATTCTATTCANCAGCGCATGGAACNTTCTCCAAGATAGAC 615
X_26034424_26 105 CACAT 109
i
L1PB_orf2#LIN 616 CATAT 620
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.44
Transitions / transversions = 2.29 (16/7)
Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.50 (6 / 4)
436 20.88 1.10 0.00 X_26034424_26034536_INS 22 112 1 + L1M3_orf2 LINE/L1 532 623 2665
436 20.88 1.10 0.00 X_26034424_26034536_INS 22 112 (1) L1M3_orf2#LINE/L1 532 623 (2665) m_b1s551i8
X_26034424_26 22 ACAG-CATATACAGAACATTCCATCCAACACTTGTAGAATATATATTCTT 70
- i viv i i i
L1M3_orf2#LIN 532 ACAGACATATACAGAACATTCCACCCAACAGCAGCAGAATACACATTCTT 581
X_26034424_26 71 TACAAGAGTACATGAAACATTTTCCACAATCAATCACATATT 112
iv v i i i i vi vi i
L1M3_orf2#LIN 582 CTCAAGCGCACACGGAACATTCTCCAGGATAGATCACATGTT 623
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.70
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1)
+ 2404 2.9 0.0 2.5 X_26420216_26420572_INS 11 357 (0) C AluY SINE/Alu (0) 311 2 469
ANNOTATION EVIDENCE:
62 1.70 0.00 0.00 X_26420216_26420572_INS 11 70 287 + (T)n Simple_repeat 1 60 0
62 1.70 0.00 0.00 X_26420216_26420572_INS 11 70 (287) (T)n#Simple_repeat 1 60 (0) c_b1s251i131
X_26420216_26 11 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 60
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_26420216_26 61 TTTTTTTTTT 70
(T)n#Simple_r 51 TTTTTTTTTT 60
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
2404 2.86 0.00 2.50 X_26420216_26420572_INS 71 357 0 C AluY SINE/Alu 2 281 30
2404 2.86 0.00 2.50 X_26420216_26420572_INS 71 357 (0) C AluY#SINE/Alu (30) 281 2 c_b1s352i40
X_26420216_26 71 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 120
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_26420216_26 121 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 170
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_26420216_26 171 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 220
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_26420216_26 221 GGCTAATTTTTTGTATTTTTAGTAGAGTCGGGGTTTCACCTTGTTAGCCA 270
v v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_26420216_26 271 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 320
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_26420216_26 321 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 357
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.92
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.02 (7 / 286), avg. gap size = 1.00 (7 / 7)
+ 33 0.0 2.0 6.4 X_26444053_26444105_INS 4 52 (1) + (TCTATGCCAA)n Simple_repeat 1 47 (0) 470
ANNOTATION EVIDENCE:
33 0.00 2.04 6.38 X_26444053_26444105_INS 4 52 1 + (TCTATGCCAA)n Simple_repeat 1 47 0
33 0.00 2.04 6.38 X_26444053_26444105_INS 4 52 (1) (TCTATGCCAA)n#Simple_repeat 1 47 (0) c_b1s251i130
X_26444053_26 4 TCTATGCC-ATCTATGCCATATCTATGCCAATCTATGCCATTATCTATGC 52
- - --
(TCTATGCCAA)n 1 TCTATGCCAATCTATGCCA-ATCTATGCCAATCTATGCCA--ATCTATGC 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4)
+ 15 30.2 1.4 2.8 X_26444710_26444786_INS 3 12 (65) + (AGTAT)n Simple_repeat 1 18 (53) 471
ANNOTATION EVIDENCE:
15 30.21 1.39 2.82 X_26444710_26444786_INS 3 74 3 + (AGTAT)n Simple_repeat 1 71 0
15 30.21 1.39 2.82 X_26444710_26444786_INS 3 74 (3) (AGTAT)n#Simple_repeat 1 71 (0) m_b1s252i98
X_26444710_26 3 AGTATAGTATA-AAAAAAAAAGTATAGTATAAAAAAAAAAAAAAAAAAGT 51
-v v iv v -- iv v iv v iv v
(AGTAT)n#Simp 1 AGTATAGTATAGTATAGTATAGTATAGTAT--AGTATAGTATAGTATAGT 48
X_26444710_26 52 ATAGTATAAAAAAGTATAGTATA 74
iv v
(AGTAT)n#Simp 49 ATAGTATAGTATAGTATAGTATA 71
Matrix = Unknown
Transitions / transversions = 0.42 (5/12)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3)
+ 20 18.3 0.0 0.0 X_26444710_26444786_INS 13 49 (28) + A-rich Low_complexity 1 37 (0) 472
ANNOTATION EVIDENCE:
20 18.27 0.00 0.00 X_26444710_26444786_INS 13 49 28 + (A)n Simple_repeat 1 37 0
20 18.27 0.00 0.00 X_26444710_26444786_INS 13 49 (28) (A)n#Simple_repeat 1 37 (0) m_b1s252i99
X_26444710_26 13 AAAAAAAAAAGTATAGTATAAAAAAAAAAAAAAAAAA 49
iv v iv v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 15 30.2 1.4 2.8 X_26444710_26444786_INS 50 74 (3) + (AGTAT)n Simple_repeat 19 71 (0) 471
ANNOTATION EVIDENCE:
15 30.21 1.39 2.82 X_26444710_26444786_INS 3 74 3 + (AGTAT)n Simple_repeat 1 71 0
15 30.21 1.39 2.82 X_26444710_26444786_INS 3 74 (3) (AGTAT)n#Simple_repeat 1 71 (0) m_b1s252i98
X_26444710_26 3 AGTATAGTATA-AAAAAAAAAGTATAGTATAAAAAAAAAAAAAAAAAAGT 51
-v v iv v -- iv v iv v iv v
(AGTAT)n#Simp 1 AGTATAGTATAGTATAGTATAGTATAGTAT--AGTATAGTATAGTATAGT 48
X_26444710_26 52 ATAGTATAAAAAAGTATAGTATA 74
iv v
(AGTAT)n#Simp 49 ATAGTATAGTATAGTATAGTATA 71
Matrix = Unknown
Transitions / transversions = 0.42 (5/12)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3)
+ 2499 2.9 0.0 0.0 X_26481460_26481774_INS 13 315 (0) C AluY SINE/Alu (0) 311 6 473
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_26481460_26481774_INS 13 39 276 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 X_26481460_26481774_INS 13 39 (276) (T)n#Simple_repeat 1 27 (0) c_b1s251i129
X_26481460_26 13 TTTTTTTTTTTTTTTTTTTTTTTTTTT 39
(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)
2499 2.90 0.00 0.00 X_26481460_26481774_INS 40 315 0 C AluY SINE/Alu 6 281 30
2499 2.90 0.00 0.00 X_26481460_26481774_INS 40 315 (0) C AluY#SINE/Alu (30) 281 6 c_b1s352i41
X_26481460_26 40 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 89
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_26481460_26 90 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 139
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_26481460_26 140 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTATGCCCGGCTAAT 189
i i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_26481460_26 190 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCTGGGATGGT 239
v ii
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_26481460_26 240 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCAGCCTCCCAAAGTGCTG 289
i
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_26481460_26 290 GGATTACAGGCGTGAGCCACCGCGCC 315
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCC 6
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.95
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 275), avg. gap size = 0.0 (0 / 0)
+ 29 0.0 7.8 3.8 X_2668757_2668817_INS 8 58 (3) + (CACACATG)n Simple_repeat 1 53 (0) 474
ANNOTATION EVIDENCE:
29 0.00 7.84 3.77 X_2668757_2668817_INS 8 58 3 + (CACACATG)n Simple_repeat 1 53 0
29 0.00 7.84 3.77 X_2668757_2668817_INS 8 58 (3) (CACACATG)n#Simple_repeat 1 53 (0) c_b1s251i128
X_2668757_266 8 CACACATGAACACACATGCACAC--GCACACATGCACAC--GCACACATG 53
-- -- --
(CACACATG)n#S 1 CACACATG--CACACATGCACACATGCACACATGCACACATGCACACATG 48
X_2668757_266 54 CACAC 58
(CACACATG)n#S 49 CACAC 53
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.50 (6 / 4)
+ 2699 1.7 0.0 0.0 X_26941750_26942062_INS 21 313 (0) + AluY SINE/Alu 1 293 (18) 475
ANNOTATION EVIDENCE:
2699 1.71 0.00 0.00 X_26941750_26942062_INS 21 313 0 + AluY SINE/Alu 1 293 18
2699 1.71 0.00 0.00 X_26941750_26942062_INS 21 313 (0) AluY#SINE/Alu 1 293 (18) c_b1s352i42
X_26941750_26 21 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 70
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_26941750_26 71 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 120
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_26941750_26 121 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 170
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_26941750_26 171 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 220
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_26941750_26 221 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 270
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_26941750_26 271 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 313
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 292), avg. gap size = 0.0 (0 / 0)
+ 2782 1.0 0.0 0.0 X_26943061_26943370_INS 12 310 (0) + AluY SINE/Alu 1 299 (12) 476
ANNOTATION EVIDENCE:
2782 1.00 0.00 0.00 X_26943061_26943370_INS 12 310 0 + AluY SINE/Alu 1 299 12
2782 1.00 0.00 0.00 X_26943061_26943370_INS 12 310 (0) AluY#SINE/Alu 1 299 (12) c_b1s352i43
X_26943061_26 12 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 61
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_26943061_26 62 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 111
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_26943061_26 112 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 161
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_26943061_26 162 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 211
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_26943061_26 212 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 261
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_26943061_26 262 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 310
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.01
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 780 6.3 0.0 7.1 X_27476612_27476737_INS 2 121 (5) + SVA_A Retroposon/SVA 497 608 (779) 477
ANNOTATION EVIDENCE:
780 6.28 0.00 7.14 X_27476612_27476737_INS 2 121 5 + SVA_A Retroposon/SVA 497 608 779
780 6.28 0.00 7.14 X_27476612_27476737_INS 2 121 (5) SVA_A#Retroposon/SVA 497 608 (779) m_b1s502i4
X_27476612_27 2 GTCTGGGATGTGAGGAGCGTCTCTGCCTGGCCGCCCCGTCTGGGAGTCTC 51
? i i -----
SVA_A#Retropo 497 GTCTGGGANGTGAGGAGCGCCTCTGCCCGGCCGCCCCGTCTGGGA----- 541
X_27476612_27 52 GGAAGTGAGGAGCACCTCTGCCCGGCCGCCACCCTGTCTGGGAAGTGAGG 101
--- i i i
SVA_A#Retropo 542 ---AGTGAGGAGCGCCTCTGCCCGGCCGCCGCCCCGTCTGGGAAGTGAGG 588
X_27476612_27 102 AGCGCCTCTGCCCAGCCACC 121
i i
SVA_A#Retropo 589 AGCGCCTCTGCCCGGCCGCC 608
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.46
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.00 (8 / 8)
+ 2477 2.2 0.0 0.0 X_27501953_27502237_INS 14 285 (0) + AluY SINE/Alu 33 304 (7) 478
ANNOTATION EVIDENCE:
2477 2.21 0.00 0.00 X_27501953_27502237_INS 14 285 0 + AluY SINE/Alu 33 304 7
2477 2.21 0.00 0.00 X_27501953_27502237_INS 14 285 (0) AluY#SINE/Alu 33 304 (7) c_b1s352i44
X_27501953_27 14 AGGACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGA 63
v
AluY#SINE/Alu 33 AGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGA 82
X_27501953_27 64 CCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAA 113
i v
AluY#SINE/Alu 83 CCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAA 132
X_27501953_27 114 TTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCT 163
i i
AluY#SINE/Alu 133 TTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCT 182
X_27501953_27 164 GAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGA 213
AluY#SINE/Alu 183 GAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGA 232
X_27501953_27 214 GATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 263
i
AluY#SINE/Alu 233 GATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 282
X_27501953_27 264 AAAAAAAAAAAAAAAAAAAAAA 285
AluY#SINE/Alu 283 AAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.56
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 271), avg. gap size = 0.0 (0 / 0)
+ 20 0.0 0.0 0.0 X_27515666_27515722_INS 1 25 (32) + (CTTC)n Simple_repeat 1 25 (0) 479
ANNOTATION EVIDENCE:
20 0.00 0.00 0.00 X_27515666_27515722_INS 1 25 1 + (CTTC)n Simple_repeat 1 25 0
20 0.00 0.00 0.00 X_27515666_27515722_INS 1 25 (1) (CTTC)n#Simple_repeat 1 25 (0) m_b1s252i97
X_27515666_27 1 CTTCCTTCCTTCCTTCCTTCCTTCC 25
(CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCC 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 34 0.0 0.0 0.0 X_27515666_27515722_INS 26 57 (0) + (TTCT)n Simple_repeat 1 32 (0) 480
ANNOTATION EVIDENCE:
34 0.00 0.00 0.00 X_27515666_27515722_INS 26 57 0 + (TTCT)n Simple_repeat 1 32 0
34 0.00 0.00 0.00 X_27515666_27515722_INS 26 57 (0) (TTCT)n#Simple_repeat 1 32 (0) c_b1s251i127
X_27515666_27 26 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 57
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 32
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 20 9.7 1.9 8.2 X_27546110_27546162_INS 2 53 (0) + (ATTAA)n Simple_repeat 1 49 (0) 481
ANNOTATION EVIDENCE:
20 9.70 1.92 8.16 X_27546110_27546162_INS 2 53 0 + (ATTAA)n Simple_repeat 1 49 0
20 9.70 1.92 8.16 X_27546110_27546162_INS 2 53 (0) (ATTAA)n#Simple_repeat 1 49 (0) m_b1s252i96
X_27546110_27 2 ATTAAATTAAATTTTTAATTTAATT-AATTAAATTAAATTTTTAATTTAA 50
-- v v - -- v v
(ATTAA)n#Simp 1 ATTAAATTAAA--TTAAATTAAATTAAATTAAATTAAA--TTAAATTAAA 46
X_27546110_27 51 TTA 53
(ATTAA)n#Simp 47 TTA 49
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.10 (5 / 51), avg. gap size = 1.00 (5 / 5)
+ 55 3.7 0.0 0.0 X_27551296_27551351_INS 1 56 (0) + (AG)n Simple_repeat 1 56 (0) 482
ANNOTATION EVIDENCE:
55 3.71 0.00 0.00 X_27551296_27551351_INS 1 56 0 + (AG)n Simple_repeat 1 56 0
55 3.71 0.00 0.00 X_27551296_27551351_INS 1 56 (0) (AG)n#Simple_repeat 1 56 (0) c_b1s251i126
X_27551296_27 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAAAGAGAGAGAGAG 50
i i
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50
X_27551296_27 51 AGAGAG 56
(AG)n#Simple_ 51 AGAGAG 56
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 67 3.1 0.0 0.0 X_27566007_27566072_INS 1 66 (0) + (TC)n Simple_repeat 1 66 (0) 483
ANNOTATION EVIDENCE:
67 3.13 0.00 0.00 X_27566007_27566072_INS 1 66 0 + (TC)n Simple_repeat 1 66 0
67 3.13 0.00 0.00 X_27566007_27566072_INS 1 66 (0) (TC)n#Simple_repeat 1 66 (0) c_b1s251i125
X_27566007_27 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTC 50
i
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50
X_27566007_27 51 TCTCTCTCTTTCTCTC 66
i
(TC)n#Simple_ 51 TCTCTCTCTCTCTCTC 66
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 2456 3.5 0.0 2.4 X_27653948_27654283_INS 20 336 (0) C AluY SINE/Alu (0) 311 2 484
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_27653948_27654283_INS 20 48 288 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_27653948_27654283_INS 20 48 (288) (T)n#Simple_repeat 1 29 (0) c_b1s251i124
X_27653948_27 20 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
(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)
2456 3.45 0.00 2.41 X_27653948_27654283_INS 49 336 0 C AluY SINE/Alu 2 282 29
2456 3.45 0.00 2.41 X_27653948_27654283_INS 49 336 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i45
X_27653948_27 49 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 98
i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_27653948_27 99 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 148
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_27653948_27 149 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 198
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_27653948_27 199 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 248
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_27653948_27 249 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 298
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_27653948_27 299 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 336
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.58
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 36 0.0 0.0 0.0 X_28085694_28085756_INS 1 31 (32) + (CA)n Simple_repeat 1 31 (0) 485
ANNOTATION EVIDENCE:
36 0.00 0.00 0.00 X_28085694_28085756_INS 1 31 32 + (CA)n Simple_repeat 1 31 0
36 0.00 0.00 0.00 X_28085694_28085756_INS 1 31 (32) (CA)n#Simple_repeat 1 31 (0) c_b1s251i123
X_28085694_28 1 CACACACACACACACACACACACACACACAC 31
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACAC 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 1932 1.0 0.0 0.0 X_28417025_28417281_INS 48 253 (4) + AluY SINE/Alu 106 311 (0) 486
ANNOTATION EVIDENCE:
1932 0.97 0.00 0.00 X_28417025_28417281_INS 48 253 4 + AluY SINE/Alu 106 311 0
1932 0.97 0.00 0.00 X_28417025_28417281_INS 48 253 (4) AluY#SINE/Alu 106 311 (0) m_b1s356i1
X_28417025_28 48 CCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 97
i
AluY#SINE/Alu 106 CCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCG 155
X_28417025_28 98 CCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACC 147
i
AluY#SINE/Alu 156 CCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACC 205
X_28417025_28 148 CGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCC 197
AluY#SINE/Alu 206 CGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCC 255
X_28417025_28 198 TGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAA 247
AluY#SINE/Alu 256 TGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAA 305
X_28417025_28 248 AAAAAA 253
AluY#SINE/Alu 306 AAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.54
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 205), avg. gap size = 0.0 (0 / 0)
+ 2420 2.8 0.0 3.1 X_28446498_28446823_INS 11 326 (0) C AluY SINE/Alu (0) 311 2 487
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_28446498_28446823_INS 11 36 290 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_28446498_28446823_INS 11 36 (290) (T)n#Simple_repeat 1 26 (0) c_b1s251i122
X_28446498_28 11 TTTTTTTTTTTTTTTTTTTTTTTTTT 36
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2420 2.80 0.00 3.15 X_28446498_28446823_INS 37 326 0 C AluY SINE/Alu 2 282 29
2420 2.80 0.00 3.15 X_28446498_28446823_INS 37 326 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i46
X_28446498_28 37 GAGACGGAGTCTCGCTCTGTCGCCCAGGTGGGACTGCGGACTGCAGTGGC 86
----- -- v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 240
X_28446498_28 87 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 136
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_28446498_28 137 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 186
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_28446498_28 187 GGCTAATTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGC 236
-- v
C AluY#SINE/Alu 139 GGCTAATTTTTT--GTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGC 92
X_28446498_28 237 CAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCC 286
i i
C AluY#SINE/Alu 91 CAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCC 42
X_28446498_28 287 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 326
C AluY#SINE/Alu 41 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (9 / 289), avg. gap size = 1.00 (9 / 9)
+ 2639 0.7 0.0 0.0 X_28679659_28679995_INS 12 337 (0) C AluY SINE/Alu (0) 311 1 488
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 X_28679659_28679995_INS 12 56 281 + (T)n Simple_repeat 1 45 0
50 0.00 0.00 0.00 X_28679659_28679995_INS 12 56 (281) (T)n#Simple_repeat 1 45 (0) c_b1s251i121
X_28679659_28 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 56
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
2639 0.71 0.00 0.00 X_28679659_28679995_INS 57 337 0 C AluY SINE/Alu 1 281 30
2639 0.71 0.00 0.00 X_28679659_28679995_INS 57 337 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i47
X_28679659_28 57 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 106
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_28679659_28 107 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 156
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_28679659_28 157 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 206
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_28679659_28 207 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGT 256
v
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_28679659_28 257 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 306
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_28679659_28 307 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 337
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.72
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2485 2.9 0.0 0.4 X_28683661_28683981_INS 15 321 (0) C AluY SINE/Alu (0) 311 2 489
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_28683661_28683981_INS 15 40 281 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_28683661_28683981_INS 15 40 (281) (T)n#Simple_repeat 1 26 (0) c_b1s251i120
X_28683661_28 15 TTTTTTTTTTTTTTTTTTTTTTTTTT 40
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2485 2.86 0.00 0.36 X_28683661_28683981_INS 41 321 0 C AluY SINE/Alu 2 281 30
2485 2.86 0.00 0.36 X_28683661_28683981_INS 41 321 (0) C AluY#SINE/Alu (30) 281 2 c_b1s352i48
X_28683661_28 41 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 90
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_28683661_28 91 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 140
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_28683661_28 141 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 190
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_28683661_28 191 TTTTTTGTATTTTTAGTAGAGACGAGGTTTCACCGTTTTAGCCGGGATGG 240
- i v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_28683661_28 241 CCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 290
i
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_28683661_28 291 GGGATTACAGGTGTGAGCCACCGCGCCCGGC 321
i
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.25
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 2863 0.7 0.0 0.0 X_28882588_28882906_INS 17 319 (0) + AluY SINE/Alu 1 303 (8) 490
ANNOTATION EVIDENCE:
2863 0.66 0.00 0.00 X_28882588_28882906_INS 17 319 0 + AluY SINE/Alu 1 303 8
2863 0.66 0.00 0.00 X_28882588_28882906_INS 17 319 (0) AluY#SINE/Alu 1 303 (8) c_b1s352i49
X_28882588_28 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_28882588_28 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 116
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_28882588_28 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_28882588_28 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGGGAATGGCGT 216
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_28882588_28 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 266
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_28882588_28 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_28882588_28 317 AAA 319
AluY#SINE/Alu 301 AAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.66
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 2745 1.7 0.0 0.0 X_29121638_29121948_INS 16 311 (0) + AluY SINE/Alu 1 296 (15) 491
ANNOTATION EVIDENCE:
2745 1.69 0.00 0.00 X_29121638_29121948_INS 16 311 0 + AluY SINE/Alu 1 296 15
2745 1.69 0.00 0.00 X_29121638_29121948_INS 16 311 (0) AluY#SINE/Alu 1 296 (15) c_b1s352i50
X_29121638_29 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_29121638_29 66 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 115
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_29121638_29 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_29121638_29 166 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 215
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_29121638_29 216 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCACTC 265
i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_29121638_29 266 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 311
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 296
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.09
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 295), avg. gap size = 0.0 (0 / 0)
+ 30 7.7 0.0 0.0 X_2914617_2914670_INS 13 54 (0) + (CCTT)n Simple_repeat 1 42 (0) 492
ANNOTATION EVIDENCE:
30 7.71 0.00 0.00 X_2914617_2914670_INS 13 54 0 + (CCTT)n Simple_repeat 1 42 0
30 7.71 0.00 0.00 X_2914617_2914670_INS 13 54 (0) (CCTT)n#Simple_repeat 1 42 (0) c_b1s251i119
X_2914617_291 13 CCTTCCTTCCTTCCCTCCTTCCTTCCTTCTTTCCTTTCTTCC 54
i i i
(CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 42
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
+ 2794 0.0 0.0 0.0 X_29270133_29270440_INS 17 308 (0) + AluY SINE/Alu 1 292 (19) 493
ANNOTATION EVIDENCE:
2794 0.00 0.00 0.00 X_29270133_29270440_INS 17 308 0 + AluY SINE/Alu 1 292 19
2794 0.00 0.00 0.00 X_29270133_29270440_INS 17 308 (0) AluY#SINE/Alu 1 292 (19) c_b1s352i51
X_29270133_29 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_29270133_29 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 116
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_29270133_29 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 166
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_29270133_29 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_29270133_29 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 266
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_29270133_29 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 308
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 291), avg. gap size = 0.0 (0 / 0)
+ 5508 0.8 0.0 0.0 X_29372124_29372731_INS 4 608 (0) + L1HS LINE/L1 5551 6155 (0) 494
ANNOTATION EVIDENCE:
5508 0.83 0.00 0.00 X_29372124_29372731_INS 4 608 0 + L1HS_3end LINE/L1 298 902 0
5508 0.83 0.00 0.00 X_29372124_29372731_INS 4 608 (0) L1HS_3end#LINE/L1 298 902 (0) m_b1s551i9
X_29372124_29 4 AAAATAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCT 53
v
L1HS_3end#LIN 298 AAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCT 347
X_29372124_29 54 AGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACC 103
L1HS_3end#LIN 348 AGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACC 397
X_29372124_29 104 CAAATGAGTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTT 153
v v
L1HS_3end#LIN 398 CAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTT 447
X_29372124_29 154 ATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCC 203
L1HS_3end#LIN 448 ATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCC 497
X_29372124_29 204 AACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAAT 253
L1HS_3end#LIN 498 AACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAAT 547
X_29372124_29 254 ACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGG 303
L1HS_3end#LIN 548 ACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGG 597
X_29372124_29 304 ATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAAC 353
L1HS_3end#LIN 598 ATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAAC 647
X_29372124_29 354 CAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCAC 403
L1HS_3end#LIN 648 CAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCAC 697
X_29372124_29 404 ATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGG 453
L1HS_3end#LIN 698 ATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGG 747
X_29372124_29 454 GGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACAC 503
L1HS_3end#LIN 748 GGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACAC 797
X_29372124_29 504 ATTAGTGGGTGCAGTGCACCAGCATGGCACATGTATACATATGTAACTAA 553
i i
L1HS_3end#LIN 798 GTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAA 847
X_29372124_29 554 CCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAA 603
L1HS_3end#LIN 848 CCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAA 897
X_29372124_29 604 AAAAA 608
L1HS_3end#LIN 898 AAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.53
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 604), avg. gap size = 0.0 (0 / 0)
+ 47 7.4 0.0 0.0 X_29508969_29509035_INS 6 63 (4) + (TA)n Simple_repeat 1 58 (0) 495
ANNOTATION EVIDENCE:
47 7.42 0.00 0.00 X_29508969_29509035_INS 6 63 4 + (TA)n Simple_repeat 1 58 0
47 7.42 0.00 0.00 X_29508969_29509035_INS 6 63 (4) (TA)n#Simple_repeat 1 58 (0) c_b1s251i118
X_29508969_29 6 TATATATATATATATATACGTATATATATATATATATATACGTATATATA 55
ii ii
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_29508969_29 56 TATATATA 63
(TA)n#Simple_ 51 TATATATA 58
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 35 9.5 1.8 0.0 X_29525501_29525560_INS 4 60 (0) + (CTCCC)n Simple_repeat 1 58 (0) 496
ANNOTATION EVIDENCE:
35 9.49 1.75 0.00 X_29525501_29525560_INS 4 60 0 + (CTCCC)n Simple_repeat 1 58 0
35 9.49 1.75 0.00 X_29525501_29525560_INS 4 60 (0) (CTCCC)n#Simple_repeat 1 58 (0) m_b1s252i95
X_29525501_29 4 CTCCCCT-CCCTTCCCTCCCCTTCTCTGCCCTCCCCTCCCCTCCCTTCCC 52
- i i i v i
(CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCC 50
X_29525501_29 53 CTCCCCTC 60
(CTCCC)n#Simp 51 CTCCCCTC 58
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1)
+ 2722 1.7 0.0 0.3 X_2961686_2961997_INS 13 312 (0) C AluY SINE/Alu (12) 299 1 497
ANNOTATION EVIDENCE:
2722 1.68 0.00 0.33 X_2961686_2961997_INS 13 312 0 C AluY SINE/Alu 1 299 12
2722 1.68 0.00 0.33 X_2961686_2961997_INS 13 312 (0) C AluY#SINE/Alu (12) 299 1 c_b1s352i52
X_2961686_296 13 TTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 62
C AluY#SINE/Alu 299 TTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 250
X_2961686_296 63 AGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCA 112
v
C AluY#SINE/Alu 249 AGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCA 200
X_2961686_296 113 CGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCCG 162
i
C AluY#SINE/Alu 199 CGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCG 150
X_2961686_296 163 CCACTACGCCCGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGTTTCA 212
i -
C AluY#SINE/Alu 149 CCACCACGCCCGGCTAATT-TTTTGTATTTTTAGTAGAGACGGGGTTTCA 101
X_2961686_296 213 CCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 262
v i
C AluY#SINE/Alu 100 CCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 51
X_2961686_296 263 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 312
C AluY#SINE/Alu 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.38
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (1 / 299), avg. gap size = 1.00 (1 / 1)
+ 43 3.1 6.1 0.0 X_29784814_29784879_INS 1 66 (0) + (TATATAA)n Simple_repeat 1 70 (0) 498
ANNOTATION EVIDENCE:
43 3.10 6.06 0.00 X_29784814_29784879_INS 1 66 0 + (TATATAA)n Simple_repeat 1 70 0
43 3.10 6.06 0.00 X_29784814_29784879_INS 1 66 (0) (TATATAA)n#Simple_repeat 1 70 (0) m_b1s252i93
X_29784814_29 1 TATATAATATATAA-ATATAATATATAATATATAA-ATATAAAGTAT-AT 47
- - vi -
(TATATAA)n#Si 1 TATATAATATATAATATATAATATATAATATATAATATATAATATATAAT 50
X_29784814_29 48 AT-TAATATATAATATATAA 66
-
(TATATAA)n#Si 51 ATATAATATATAATATATAA 70
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4)
+ 32 7.3 0.0 0.0 X_29821023_29821073_INS 4 47 (4) + (ATATGTGTAC)n Simple_repeat 1 44 (0) 499
ANNOTATION EVIDENCE:
32 7.33 0.00 0.00 X_29821023_29821073_INS 4 47 4 + (ATATGTGTAC)n Simple_repeat 1 44 0
32 7.33 0.00 0.00 X_29821023_29821073_INS 4 47 (4) (ATATGTGTAC)n#Simple_repeat 1 44 (0) c_b1s251i117
X_29821023_29 4 ATATGTGTACATATGTATACATATATGTATATATGTGTACATAT 47
i i i
(ATATGTGTAC)n 1 ATATGTGTACATATGTGTACATATGTGTACATATGTGTACATAT 44
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 2523 3.0 4.0 0.0 X_29885128_29885447_INS 13 311 (9) + AluY SINE/Alu 1 311 (0) 500
ANNOTATION EVIDENCE:
2523 3.01 4.01 0.00 X_29885128_29885447_INS 13 311 9 + AluY SINE/Alu 1 311 0
2523 3.01 4.01 0.00 X_29885128_29885447_INS 13 311 (9) AluY#SINE/Alu 1 311 (0) c_b1s352i53
X_29885128_29 13 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 62
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_29885128_29 63 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCA------------CGG 100
------------
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_29885128_29 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCAGTGGC 150
ii
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_29885128_29 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_29885128_29 201 GAACCCAGAAGGCGGAGCTTGCAGTGAGCGGAGATCGCGCCACAGCACTC 250
i i v v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_29885128_29 251 CCGCCTGGGCGACAGAACGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
v i
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_29885128_29 301 AAAAAAACAAA 311
v
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.76
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (1 / 298), avg. gap size = 12.00 (12 / 1)
+ 54 5.0 0.0 0.0 X_2991571_2991677_INS 1 62 (45) + (AGTATAT)n Simple_repeat 1 62 (0) 501
ANNOTATION EVIDENCE:
54 5.02 0.00 0.00 X_2991571_2991677_INS 1 62 45 + (AGTATAT)n Simple_repeat 1 62 0
54 5.02 0.00 0.00 X_2991571_2991677_INS 1 62 (45) (AGTATAT)n#Simple_repeat 1 62 (0) c_b1s251i116
X_2991571_299 1 AGTATATAGTATATAGTATATAGTATATAGTATATAGTATATACTATATA 50
v
(AGTATAT)n#Si 1 AGTATATAGTATATAGTATATAGTATATAGTATATAGTATATAGTATATA 50
X_2991571_299 51 CTATATATTATA 62
v v
(AGTATAT)n#Si 51 GTATATAGTATA 62
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 25 7.4 7.0 0.0 X_2991571_2991677_INS 63 106 (1) + (AT)n Simple_repeat 1 47 (0) 502
ANNOTATION EVIDENCE:
23 7.89 0.00 4.76 X_2991571_2991677_INS 63 106 1 + (AATATAT)n Simple_repeat 1 42 0
23 7.89 0.00 4.76 X_2991571_2991677_INS 63 106 (1) (AATATAT)n#Simple_repeat 1 42 (0) m_b1s252i91
X_2991571_299 63 AATATATACATATATTTATATGTTATATATAATATATAATATAT 106
- - v i v
(AATATAT)n#Si 1 AATATATA-ATATA-TAATATATAATATATAATATATAATATAT 42
Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2)
25 7.37 6.98 0.00 X_2991571_2991677_INS 64 106 1 + (AT)n Simple_repeat 1 46 0
25 7.37 6.98 0.00 X_2991571_2991677_INS 64 106 (1) (AT)n#Simple_repeat 1 46 (0) m_b1s252i92
X_2991571_299 64 ATATATACATATATTTATATGT-TATATATA-ATATATA-ATATAT 106
i v i - - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT 46
Matrix = Unknown
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3)
+ 29 4.7 4.5 0.0 X_3003322_3003376_INS 12 55 (0) + (TATACATA)n Simple_repeat 1 46 (0) 503
ANNOTATION EVIDENCE:
29 4.69 4.55 0.00 X_3003322_3003376_INS 12 55 0 + (TATACATA)n Simple_repeat 1 46 0
29 4.69 4.55 0.00 X_3003322_3003376_INS 12 55 (0) (TATACATA)n#Simple_repeat 1 46 (0) c_b1s251i115
X_3003322_300 12 TATACATATATACATATATAC-TATATA-TTGTATACATATATACA 55
- -v i
(TATACATA)n#S 1 TATACATATATACATATATACATATATACATATATACATATATACA 46
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2)
+ 27 4.6 0.0 8.2 X_30036477_30036532_INS 2 54 (2) + (ATATATA)n Simple_repeat 1 49 (0) 504
ANNOTATION EVIDENCE:
27 4.58 0.00 8.16 X_30036477_30036532_INS 2 54 2 + (ATATATA)n Simple_repeat 1 49 0
27 4.58 0.00 8.16 X_30036477_30036532_INS 2 54 (2) (ATATATA)n#Simple_repeat 1 49 (0) m_b1s252i90
X_30036477_30 2 ATATATTATATATAATATATATGATATATAATACGTATTATATATAATAT 51
v -- -- v
(ATATATA)n#Si 1 ATATATAATATATAATATATA--ATATATAATA--TATAATATATAATAT 46
X_30036477_30 52 ATA 54
(ATATATA)n#Si 47 ATA 49
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4)
+ 2604 1.4 0.0 0.0 X_3020244_3020561_INS 13 318 (0) C AluY SINE/Alu (0) 311 1 505
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_3020244_3020561_INS 13 37 281 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_3020244_3020561_INS 13 37 (281) (T)n#Simple_repeat 1 25 (0) c_b1s251i114
X_3020244_302 13 TTTTTTTTTTTTTTTTTTTTTTTTT 37
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2604 1.42 0.00 0.00 X_3020244_3020561_INS 38 318 0 C AluY SINE/Alu 1 281 30
2604 1.42 0.00 0.00 X_3020244_3020561_INS 38 318 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i54
X_3020244_302 38 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCT 87
i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_3020244_302 88 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 137
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_3020244_302 138 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 187
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_3020244_302 188 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 237
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_3020244_302 238 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 287
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_3020244_302 288 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 318
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.79
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2760 3.0 0.0 0.0 X_30346692_30346997_INS 1 305 (1) C AluY SINE/Alu (6) 305 1 506
ANNOTATION EVIDENCE:
2760 2.95 0.00 0.00 X_30346692_30346997_INS 1 305 1 C AluY SINE/Alu 1 305 6
2760 2.95 0.00 0.00 X_30346692_30346997_INS 1 305 (1) C AluY#SINE/Alu (6) 305 1 c_b1s352i55
X_30346692_30 1 TTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTTTTGCCCA 50
i v i
C AluY#SINE/Alu 305 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 256
X_30346692_30 51 GGCTGGAGTGCAGTGGCGCGATCTCTGCTCACTGCAAGCTCCGCCTCCCG 100
v
C AluY#SINE/Alu 255 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCG 206
X_30346692_30 101 GGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGG 150
i i
C AluY#SINE/Alu 205 GGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 156
X_30346692_30 151 TGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTCAGTAGAGACGGGG 200
i i
C AluY#SINE/Alu 155 CGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGG 106
X_30346692_30 201 TTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGC 250
C AluY#SINE/Alu 105 TTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGC 56
X_30346692_30 251 CTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 300
i
C AluY#SINE/Alu 55 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 6
X_30346692_30 301 CGGCC 305
C AluY#SINE/Alu 5 CGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.49
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 304), avg. gap size = 0.0 (0 / 0)
+ 58 0.0 0.0 0.0 X_30501933_30501985_INS 1 52 (1) + (GAAA)n Simple_repeat 1 52 (0) 507
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_30501933_30501985_INS 1 52 1 + (GAAA)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_30501933_30501985_INS 1 52 (1) (GAAA)n#Simple_repeat 1 52 (0) c_b1s251i113
X_30501933_30 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
X_30501933_30 51 AA 52
(GAAA)n#Simpl 51 AA 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2821 1.6 0.0 0.0 X_3064238_3064545_INS 3 308 (0) + AluY SINE/Alu 1 306 (5) 508
ANNOTATION EVIDENCE:
2821 1.63 0.00 0.00 X_3064238_3064545_INS 3 308 0 + AluY SINE/Alu 1 306 5
2821 1.63 0.00 0.00 X_3064238_3064545_INS 3 308 (0) AluY#SINE/Alu 1 306 (5) c_b1s352i56
X_3064238_306 3 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 52
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_3064238_306 53 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 102
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_3064238_306 103 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 152
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_3064238_306 153 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 202
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_3064238_306 203 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 252
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_3064238_306 253 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 302
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_3064238_306 303 AAAAAA 308
AluY#SINE/Alu 301 AAAAAA 306
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.35
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 305), avg. gap size = 0.0 (0 / 0)
+ 2680 1.7 0.7 0.3 X_30665959_30666272_INS 15 314 (0) C AluY SINE/Alu (9) 302 2 509
ANNOTATION EVIDENCE:
2680 1.68 0.67 0.33 X_30665959_30666272_INS 15 314 0 C AluY SINE/Alu 2 302 9
2680 1.68 0.67 0.33 X_30665959_30666272_INS 15 314 (0) C AluY#SINE/Alu (9) 302 2 c_b1s352i57
X_30665959_30 15 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCT--GTCGCCCAGGC 62
--
C AluY#SINE/Alu 302 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 253
X_30665959_30 63 TGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGG 112
i i i i -
C AluY#SINE/Alu 252 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGG- 204
X_30665959_30 113 TTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCG 162
C AluY#SINE/Alu 203 TTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCG 154
X_30665959_30 163 CCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTT 212
v
C AluY#SINE/Alu 153 CCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTT 104
X_30665959_30 213 TCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCC 262
C AluY#SINE/Alu 103 TCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCC 54
X_30665959_30 263 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 312
C AluY#SINE/Alu 53 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
X_30665959_30 313 GC 314
C AluY#SINE/Alu 3 GC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.08
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.01 (2 / 299), avg. gap size = 1.50 (3 / 2)
+ 60 10.7 0.0 8.3 X_30807647_30807784_INS 4 134 (4) + (TGCCT)n Simple_repeat 1 121 (0) 510
ANNOTATION EVIDENCE:
60 10.69 0.00 8.26 X_30807647_30807784_INS 4 134 4 + (TGCCT)n Simple_repeat 1 121 0
60 10.69 0.00 8.26 X_30807647_30807784_INS 4 134 (4) (TGCCT)n#Simple_repeat 1 121 (0) m_b1s252i89
X_30807647_30 4 TGCCTTGCCTTGCCTTGTTCCTTGCCTTGTTCTGTGCCTTACCTTGCCTT 53
-- -i - i
(TGCCT)n#Simp 1 TGCCTTGCCTTGCCTTG--CCTTGCCTTG-CCT-TGCCTTGCCTTGCCTT 46
X_30807647_30 54 GCCTTATGCCTTGCTTTGGCTTGCCTTGACTTGGGCCTTGCCTTGCTGTG 103
- - i v v -- iv
(TGCCT)n#Simp 47 GCC-T-TGCCTTGCCTTGCCTTGCCTTGCCTT--GCCTTGCCTTGCCTTG 92
X_30807647_30 104 CCTCACTTTCTGCCTTGCCTTGCCTTGCTTT 134
ii -i - i
(TGCCT)n#Simp 93 CCTTGC-CT-TGCCTTGCCTTGCCTTGCCTT 121
Matrix = Unknown
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.00 (10 / 10)
+ 28 11.1 0.0 9.4 X_30811558_30811636_INS 2 71 (8) + (TTGCC)n Simple_repeat 1 64 (0) 511
ANNOTATION EVIDENCE:
28 11.05 0.00 9.38 X_30811558_30811636_INS 2 71 8 + (TTGCC)n Simple_repeat 1 64 0
28 11.05 0.00 9.38 X_30811558_30811636_INS 2 71 (8) (TTGCC)n#Simple_repeat 1 64 (0) m_b1s252i88
X_30811558_30 2 TTGCCTTGCCTTGTTACTTGCCTTCCCTTGGCTTGTGCCTTGCCTTGCTT 51
--v v - i - --
(TTGCC)n#Simp 1 TTGCCTTGCCTTG--CCTTGCCTTGCCTT-GCCT-TGCCTTGCCTTGC-- 44
X_30811558_30 52 TTTGCCTTGCCTTGAATTGC 71
i vv
(TTGCC)n#Simp 45 CTTGCCTTGCCTTGCCTTGC 64
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.00 (6 / 6)
+ 45 10.2 1.0 6.6 X_30812870_30812966_INS 1 96 (1) + (TTGCC)n Simple_repeat 1 91 (0) 512
ANNOTATION EVIDENCE:
45 10.15 1.04 6.59 X_30812870_30812966_INS 1 96 1 + (TTGCC)n Simple_repeat 1 91 0
45 10.15 1.04 6.59 X_30812870_30812966_INS 1 96 (1) (TTGCC)n#Simple_repeat 1 91 (0) m_b1s252i87
X_30812870_30 1 TTGCCTTGCCTTGCCTTGTAACTTGCCTTGCCTTGCCATTCCTTGTCTT- 49
--v v v i -
(TTGCC)n#Simp 1 TTGCCTTGCCTTGCCTTG--CCTTGCCTTGCCTTGCCTTGCCTTGCCTTG 48
X_30812870_30 50 CCTGTGCCTTGATTTGCCTTACCTTGTGCCTTGTCTTGCCTTGGCCT 96
- vi i - - i -
(TTGCC)n#Simp 49 CCT-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTT-GCCT 91
Matrix = Unknown
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.07 (7 / 95), avg. gap size = 1.00 (7 / 7)
+ 149 13.5 0.5 9.7 X_30813476_30813869_INS 2 394 (0) + (TGCCT)n Simple_repeat 1 360 (0) 513
ANNOTATION EVIDENCE:
149 13.52 0.51 9.72 X_30813476_30813869_INS 2 394 0 + (TGCCT)n Simple_repeat 1 360 0
149 13.52 0.51 9.72 X_30813476_30813869_INS 2 394 (0) (TGCCT)n#Simple_repeat 1 360 (0) m_b1s252i86
X_30813476_30 2 TGCCTTGCCTTGTGCCTTGGCTTGCCTTGCCTTGCTTTGCCCTGCACTTT 51
- - v i i - -
(TGCCT)n#Simp 1 TGCCTTGCC-T-TGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGC-C-TT 46
X_30813476_30 52 GCATTGCCTTGCTTTGCCTTGTGCCTTGCCTTGCCTTGTGCCTTGCCATG 101
v i - - - - v
(TGCCT)n#Simp 47 GCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCC-T-TGCCTTGCCTTG 92
X_30813476_30 102 GCTTGTCTTGCTTTGCCTTTTGCCTTGTCTTACACTGTGCCTTGCCTTGC 151
v i i -- i i - -
(TGCCT)n#Simp 93 CCTTGCCTTGCCTTGCC--TTGCCTTGCCTTGC-CT-TGCCTTGCCTTGC 138
X_30813476_30 152 CTTGTGCCTTGCTTTGCCTT-TGTT-CCTTGGTTTGTTCTGTGCCTTACT 199
- - i -iv - vi -i - i i
(TGCCT)n#Simp 139 C-T-TGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTG-CCT-TGCCTTGCC 184
X_30813476_30 200 TTGCCTTGCCTCGTGCCTTGCTTTGGCTTGCCTTGACTTGGGCCTTGCCT 249
-- i v v --
(TGCCT)n#Simp 185 TTGCCTTGCCT--TGCCTTGCCTTGCCTTGCCTTGCCTT--GCCTTGCCT 230
X_30813476_30 250 TGCTATACCTTGATTTCTGTCTTGCCTTGACTTTCCCTGCCTTGTGCCTT 299
iv i -ii - i v v i - -
(TGCCT)n#Simp 231 TGCCTTGCCTTG-CCT-TGCCTTGCCTTGCCTTGCCTTGCC-T-TGCCTT 276
X_30813476_30 300 GCCTTGCCTTGATTTTTGCTTTGCCTTGCCATTTCCTTATGGCTTGCCCT 349
--ii i - v - - v i
(TGCCT)n#Simp 277 GCCTTGCCTTG--CCTTGCCTTGCCTTGCC-TTGCC-T-TGCCTTGCCTT 321
X_30813476_30 350 GACTTGCCTTGCCCCTTGCCCCTTGCCTTGCTTTTTGCCTTCCCT 394
v -- -- --i v
(TGCCT)n#Simp 322 GCCTTGCCTTG--CCTTG--CCTTGCCTTGC--CTTGCCTTGCCT 360
Matrix = Unknown
Transitions / transversions = 1.67 (25/15)
Gap_init rate = 0.09 (37 / 392), avg. gap size = 1.00 (37 / 37)
+ 308 12.5 0.7 9.5 X_30813476_30814243_INS 2 768 (0) + (TGCCT)n Simple_repeat 1 705 (0) 514
ANNOTATION EVIDENCE:
308 12.50 0.65 9.50 X_30813476_30814243_INS 2 768 0 + (TGCCT)n Simple_repeat 1 705 0
308 12.50 0.65 9.50 X_30813476_30814243_INS 2 768 (0) (TGCCT)n#Simple_repeat 1 705 (0) m_b1s252i85
X_30813476_30 2 TGCCTTGCCTTGTGCCTTGGCTTGCCTTGCCTTGCTTTGCCCTGCACTTT 51
- - v i i - -
(TGCCT)n#Simp 1 TGCCTTGCC-T-TGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGC-C-TT 46
X_30813476_30 52 GCCTTGCCTTGCTTTGCCTTGTGCCTTGCCTTGCCTTGCTTTGTGCATTG 101
i - - -i - v
(TGCCT)n#Simp 47 GCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGC-CT-TGCCTTG 92
X_30813476_30 102 CCTTGACTTGCTTTGTGCCTTGCCTTGCCTTGCCTTGTGCCTTGCCTTGC 151
v -i - - -
(TGCCT)n#Simp 93 CCTTGCCTTGC-CT-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGC 138
X_30813476_30 152 CTTCCACCTTGTCTTGCCTTACTTTGCCTTGTGCCTTGCCTTGCTTTGCC 201
--i i i i - - i
(TGCCT)n#Simp 139 CTT--GCCTTGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCC 184
X_30813476_30 202 TTGCCATGCCTTGTGCCTTGTGCCTTGCCTTGCATTGCTTTGCCTTGTCT 251
v - - - - v i - i
(TGCCT)n#Simp 185 TTGCCTTGCC-T-TGCC-T-TGCCTTGCCTTGCCTTGCCTTGCCTTG-CC 229
X_30813476_30 252 TGTGCCTTGCCCTGCTTTGCCTTGACTTG-TTTG--TTGATTTGCCTTGC 298
- i i v -i -- vi
(TGCCT)n#Simp 230 T-TGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGC 278
X_30813476_30 299 CTTGATACTTGCCTTCCCTTAGCTTGTGCCTTGCCTTCGCTTGTGCCTTG 348
--v v - i - - i -
(TGCCT)n#Simp 279 CTTG--CCTTGCCTTGCCTT-GCCT-TGCCTTGCCTT-GCCT-TGCCTTG 322
X_30813476_30 349 GGTTGCCTTGCCTTGTGCCTTGGTGTCCCTTACCTTGTGCCTTACCTTGT 398
vv - - viv v i - - i i
(TGCCT)n#Simp 323 CCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGC 368
X_30813476_30 399 CTTGCCTTGCCCCTTGCATTGCCTTGCCTTGTCCCTTGCCTTGCCTTGTA 448
-- v -- --
(TGCCT)n#Simp 369 CTTGCCTTG--CCTTGCCTTGCCTTGCCTTG--CCTTGCCTTGCCTTG-- 412
X_30813476_30 449 ACTTGCCTTGCCTTGTGCCTTGCCATGGCTTGTCTTGCTTTGCCTTTTGC 498
v - - v v i i --
(TGCCT)n#Simp 413 CCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCCTTGCCTTGCC--TTGC 458
X_30813476_30 499 CTTGTCTTACACTGTGCCTTGCCTTGCCTTGTGCCTTGCTTTGCCTT-TG 547
i i - - - - i -iv
(TGCCT)n#Simp 459 CTTGCCTTGC-CT-TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCC 504
X_30813476_30 548 TT-CCTTGGTTTGTTCTGTGCCTTACTTTGCCTTGCCTCGTGCCTTGCTT 596
- vi -i - i i -- i
(TGCCT)n#Simp 505 TTGCCTTGCCTTG-CCT-TGCCTTGCCTTGCCTTGCCT--TGCCTTGCCT 550
X_30813476_30 597 TGGCTTGCCTTGACTTGGGCCTTGCCTTGCTATACCTTGATTTCTGTCTT 646
v v -- iv i -ii - i
(TGCCT)n#Simp 551 TGCCTTGCCTTGCCTT--GCCTTGCCTTGCCTTGCCTTG-CCT-TGCCTT 596
X_30813476_30 647 GCCTTGACTTTCCCTGCCTTGTGCCTTGCCTTGCCTTGATTTTTGCTTTG 696
v v i - - --ii i
(TGCCT)n#Simp 597 GCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTG--CCTTGCCTTG 642
X_30813476_30 697 CCTTGCCATTTCCTTATGGCTTGCCCTGACTTGCCTTGCCCCTTGCCCCT 746
- v - - v i v -- --
(TGCCT)n#Simp 643 CCTTGCC-TTGCC-T-TGCCTTGCCTTGCCTTGCCTTG--CCTTG--CCT 685
X_30813476_30 747 TGCCTTGCTTTTTGCCTTCCCT 768
--i v
(TGCCT)n#Simp 686 TGCCTTGC--CTTGCCTTGCCT 705
Matrix = Unknown
Transitions / transversions = 1.52 (44/29)
Gap_init rate = 0.09 (71 / 766), avg. gap size = 1.01 (72 / 71)
+ 121 13.8 1.0 8.1 X_30819803_30820110_INS 4 308 (0) + (TGCCT)n Simple_repeat 1 285 (0) 515
ANNOTATION EVIDENCE:
121 13.85 0.98 8.07 X_30819803_30820110_INS 4 308 0 + (TGCCT)n Simple_repeat 1 285 0
121 13.85 0.98 8.07 X_30819803_30820110_INS 4 308 (0) (TGCCT)n#Simple_repeat 1 285 (0) m_b1s252i84
X_30819803_30 4 TGCCTTGCCTTTCCTTGTGCCTTGCCTTGCCTTGTGCCTAGCCTTGCCTT 53
v - - - - v
(TGCCT)n#Simp 1 TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTT 46
X_30819803_30 54 ACCTTGCATTGTGTTGTTCCTTGCATTGCCTTGTCTTGAGCCTTGCTTTG 103
i v iv -- v i -- i
(TGCCT)n#Simp 47 GCCTTGCCTTGCCTTG--CCTTGCCTTGCCTTGCCTT--GCCTTGCCTTG 92
X_30819803_30 104 CCTGGCCTTGGCTTGTGCCTTGCCTTACCTTATGCATTGCCTTGTCTTGG 153
v - i - i - - v i -
(TGCCT)n#Simp 93 CCTTGCCTT-GCCT-TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTT-G 137
X_30819803_30 154 CTTGTGCCTTGCCTTTACTTGCCTTCTGAGTTATCATGACTTGCCTTGTG 203
i - vv - - vv ii v v - -
(TGCCT)n#Simp 138 CCT-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCC-T-TG 182
X_30819803_30 204 CCTTGTCTTGCATTGCATTG-CTT-CC-TGCCTTGCCTTGCCTTGCATTG 250
i v v - - - v
(TGCCT)n#Simp 183 CCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTG 232
X_30819803_30 251 CCTTATGTCTTGCCTTGCCTTGCCTTCTGTATTGCCTTGAGTTGGCTTTG 300
- - i - - iv vv - i
(TGCCT)n#Simp 233 CC-T-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTT-GCCTTG 277
X_30819803_30 301 CCTTGCCT 308
(TGCCT)n#Simp 278 CCTTGCCT 285
Matrix = Unknown
Transitions / transversions = 0.74 (14/19)
Gap_init rate = 0.09 (26 / 304), avg. gap size = 1.00 (26 / 26)
+ 218 13.8 0.5 9.1 X_30819803_30820364_INS 4 562 (0) + (TGCCT)n Simple_repeat 1 515 (0) 516
ANNOTATION EVIDENCE:
218 13.79 0.54 9.13 X_30819803_30820364_INS 4 562 0 + (TGCCT)n Simple_repeat 1 515 0
218 13.79 0.54 9.13 X_30819803_30820364_INS 4 562 (0) (TGCCT)n#Simple_repeat 1 515 (0) m_b1s252i83
X_30819803_30 4 TGCCTTGCCTTTCCTTGTGCCTTGCCTTGCCTTGTGCCTAGCCTTGCCTT 53
v - - - - v
(TGCCT)n#Simp 1 TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTT 46
X_30819803_30 54 ACCTTGCATTGTGTTGTTCCTTGCATTGCCTTGTCTTGAGCCTTGCCTTG 103
i v iv -- v i --
(TGCCT)n#Simp 47 GCCTTGCCTTGCCTTG--CCTTGCCTTGCCTTGCCTT--GCCTTGCCTTG 92
X_30819803_30 104 CCCTGCCTTGCCTGGCCTTGGCTTGTGCCTTGCCTGGCCTTGGCTTGTGC 153
i v - i - v - i -
(TGCCT)n#Simp 93 CCTTGCCTTGCCTTGCCTT-GCCT-TGCCTTGCCTTGCCTT-GCCT-TGC 138
X_30819803_30 154 CTGGCCTTGGCTTGTGCCTTGCCTTGGCTTGTGCCATGCCTTGCCTTGTG 203
v - i - - i - v - -
(TGCCT)n#Simp 139 CTTGCCTT-GCCT-TGCCTTGCCTT-GCCT-TGCCTTGCCTTGCC-T-TG 182
X_30819803_30 204 CCTTGCCTTGCTTTGGCTTGTTCCTTGATTTGACTTGCCTTCTGAATTAT 253
i v -- vi v - - vv ii
(TGCCT)n#Simp 183 CCTTGCCTTGCCTTGCCTTG--CCTTGCCTTGCCTTGCC-T-TGCCTTGC 228
X_30819803_30 254 AATGCTTTGCCTCGTGCCTTGCCTTGCCTTGCTTTGTGCCTTGCCTTGCT 303
vv i -- -i - -
(TGCCT)n#Simp 229 CTTGCCTTGCCT--TGCCTTGCCTTGCCTTGC-CT-TGCCTTGCCTTGC- 273
X_30819803_30 304 TTGTGCCTTGCCTTGCCATGTTCCTTGCCTTTCCTTGTCTTGAGCCTTGC 353
i - - - v v i --
(TGCCT)n#Simp 274 CT-TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCCTT--GCCTTGC 318
X_30819803_30 354 TTTGCCTGGCCTTGGCTTGTGCCTTGCCTTACCTTATGCATTGCCTTGTC 403
i v - i - i - - v i
(TGCCT)n#Simp 319 CTTGCCTTGCCTT-GCCT-TGCCTTGCCTTGCC-T-TGCCTTGCCTTGCC 364
X_30819803_30 404 TTGGCTTGTGCCTTGCCTTTACTTGCCTTCTGAGTTATCATGACTTGCCT 453
- i - vv - - vv ii v v -
(TGCCT)n#Simp 365 TT-GCCT-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTTGCC- 409
X_30819803_30 454 TGTGCCTTGTCTTGCATTGCATTG-CTT-CC-TGCCTTGCCTTGCCTTGC 500
- i v v - - -
(TGCCT)n#Simp 410 T-TGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGCCTTGC 458
X_30819803_30 501 ATTGCCTTATGTCTTGCCTTGCCTTGCCTTCTGTATTGCCTTGAGTTGGC 550
v - - i - - iv vv -
(TGCCT)n#Simp 459 CTTGCC-T-TGCCTTGCCTTGCCTTGCC-T-TGCCTTGCCTTGCCTT-GC 503
X_30819803_30 551 TTTGCCTTGCCT 562
i
(TGCCT)n#Simp 504 CTTGCCTTGCCT 515
Matrix = Unknown
Transitions / transversions = 0.84 (27/32)
Gap_init rate = 0.09 (50 / 558), avg. gap size = 1.00 (50 / 50)
+ 24 9.5 0.0 8.0 X_30824680_30824734_INS 1 54 (1) + (CTTGC)n Simple_repeat 1 50 (0) 517
ANNOTATION EVIDENCE:
24 9.48 0.00 8.00 X_30824680_30824734_INS 1 54 1 + (CTTGC)n Simple_repeat 1 50 0
24 9.48 0.00 8.00 X_30824680_30824734_INS 1 54 (1) (CTTGC)n#Simple_repeat 1 50 (0) m_b1s252i82
X_30824680_30 1 CTTGCCTTGCCTTATGCCTTACCTCGCCTCGTGTCTTGCCCTGCCTTGCC 50
- - i i -- i i
(CTTGC)n#Simp 1 CTTGCCTTGCC-T-TGCCTTGCCTTGCCT--TGCCTTGCCTTGCCTTGCC 46
X_30824680_30 51 TTGC 54
(CTTGC)n#Simp 47 TTGC 50
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4)
+ 430 10.0 0.0 0.0 X_30990893_30990965_INS 11 70 (3) C AluSx SINE/Alu (178) 134 75 518
ANNOTATION EVIDENCE:
430 10.00 0.00 0.00 X_30990893_30990965_INS 11 70 3 C AluSx SINE/Alu 75 134 178
430 10.00 0.00 0.00 X_30990893_30990965_INS 11 70 (3) C AluSx#SINE/Alu (178) 134 75 m_b1s357i1
X_30990893_30 11 ATTTTTGTATTTTTAGTAGAGATGGGGTTTTGACATGTTGGCCAAGCTGC 60
i iiv i v
C AluSx#SINE/Al 134 ATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGG 85
X_30990893_30 61 TCTCGAACTC 70
C AluSx#SINE/Al 84 TCTCGAACTC 75
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 9.07
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 16 51.7 0.0 0.0 X_31084985_31085077_INS 1 90 (3) + (TA)n Simple_repeat 1 90 (0) 519
ANNOTATION EVIDENCE:
16 51.70 0.00 0.00 X_31084985_31085077_INS 1 90 3 + (TA)n Simple_repeat 1 90 0
16 51.70 0.00 0.00 X_31084985_31085077_INS 1 90 (3) (TA)n#Simple_repeat 1 90 (0) m_b1s252i81
X_31084985_31 1 TATGTGTATATACACACACACACATGTGTATATACACACATACACACATG 50
i i i i i i i i i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_31084985_31 51 TGTATATACACACATACACACATGTGTATATACACACATA 90
i i i i i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATA 90
Matrix = Unknown
Transitions / transversions = 1.00 (29/0)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0)
+ 21 30.1 0.0 0.0 X_31085660_31085720_INS 1 53 (8) + (TA)n Simple_repeat 1 53 (0) 520
ANNOTATION EVIDENCE:
21 30.15 0.00 0.00 X_31085660_31085720_INS 1 53 8 + (TA)n Simple_repeat 1 53 0
21 30.15 0.00 0.00 X_31085660_31085720_INS 1 53 (8) (TA)n#Simple_repeat 1 53 (0) m_b1s252i80
X_31085660_31 1 TATATATGTGTGTACATATATACGTATGTGTATATATACACATACGTATA 50
i i i i ii i i i i ii
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_31085660_31 51 TAT 53
(TA)n#Simple_ 51 TAT 53
Matrix = Unknown
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 2643 2.1 0.0 0.0 X_31275305_31275610_INS 17 306 (0) + AluY SINE/Alu 15 304 (7) 521
ANNOTATION EVIDENCE:
2643 2.07 0.00 0.00 X_31275305_31275610_INS 17 306 0 + AluY SINE/Alu 15 304 7
2643 2.07 0.00 0.00 X_31275305_31275610_INS 17 306 (0) AluY#SINE/Alu 15 304 (7) c_b1s352i58
X_31275305_31 17 GCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCAC 66
AluY#SINE/Alu 15 GCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCAC 64
X_31275305_31 67 GAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTC 116
i v
AluY#SINE/Alu 65 GAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTC 114
X_31275305_31 117 TACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTC 166
i
AluY#SINE/Alu 115 TACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTC 164
X_31275305_31 167 CCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCG 216
i
AluY#SINE/Alu 165 CCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCG 214
X_31275305_31 217 GAGCTGGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACA 266
v v
AluY#SINE/Alu 215 GAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACA 264
X_31275305_31 267 GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAA 306
AluY#SINE/Alu 265 GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.78
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 289), avg. gap size = 0.0 (0 / 0)
+ 74 5.1 0.0 0.0 X_31302674_31302758_INS 3 85 (0) + (TCTTCC)n Simple_repeat 1 83 (0) 522
ANNOTATION EVIDENCE:
74 5.07 0.00 0.00 X_31302674_31302758_INS 3 85 0 + (TCTTCC)n Simple_repeat 1 83 0
74 5.07 0.00 0.00 X_31302674_31302758_INS 3 85 (0) (TCTTCC)n#Simple_repeat 1 83 (0) c_b1s251i112
X_31302674_31 3 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCTTCCTCTTCCTCTTCCTC 52
i i i i
(TCTTCC)n#Sim 1 TCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTC 50
X_31302674_31 53 TTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTC 85
(TCTTCC)n#Sim 51 TTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTC 83
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 69 2.6 2.5 1.2 X_31311280_31311359_INS 2 80 (0) + (GT)n Simple_repeat 1 80 (0) 523
ANNOTATION EVIDENCE:
69 2.64 2.53 1.25 X_31311280_31311359_INS 2 80 0 + (GT)n Simple_repeat 1 80 0
69 2.64 2.53 1.25 X_31311280_31311359_INS 2 80 (0) (GT)n#Simple_repeat 1 80 (0) c_b1s251i111
X_31311280_31 2 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 51
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50
X_31311280_31 52 GTGTGTGTAGTCTG-GT-TTTGTGTGTGTGT 80
- v - - v
(GT)n#Simple_ 51 GTGTGTGT-GTGTGTGTGTGTGTGTGTGTGT 80
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.00 (3 / 3)
+ 2706 2.6 0.0 2.6 X_31370316_31370651_INS 16 334 (2) + AluY SINE/Alu 1 311 (0) 524
ANNOTATION EVIDENCE:
2706 2.58 0.00 2.57 X_31370316_31370651_INS 16 334 2 + AluY SINE/Alu 1 311 0
2706 2.58 0.00 2.57 X_31370316_31370651_INS 16 334 (2) AluY#SINE/Alu 1 311 (0) c_b1s352i59
X_31370316_31 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_31370316_31 66 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 115
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_31370316_31 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_31370316_31 166 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 215
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_31370316_31 216 GAACCCGGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGT 265
- i i v
AluY#SINE/Alu 201 GAACCC-GGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_31370316_31 266 CCGCAGTCTGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 315
-------i
AluY#SINE/Alu 250 CC-------AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
X_31370316_31 316 AAAAAAAAAAAAAAAAAAA 334
AluY#SINE/Alu 293 AAAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.73
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.03 (8 / 318), avg. gap size = 1.00 (8 / 8)
+ 2532 2.5 0.0 0.0 X_31379302_31379626_INS 12 325 (0) C AluY SINE/Alu (0) 311 2 525
ANNOTATION EVIDENCE:
37 0.00 0.00 0.00 X_31379302_31379626_INS 12 45 280 + (T)n Simple_repeat 1 34 0
37 0.00 0.00 0.00 X_31379302_31379626_INS 12 45 (280) (T)n#Simple_repeat 1 34 (0) c_b1s251i110
X_31379302_31 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(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)
2532 2.50 0.00 0.00 X_31379302_31379626_INS 46 325 0 C AluY SINE/Alu 2 281 30
2532 2.50 0.00 0.00 X_31379302_31379626_INS 46 325 (0) C AluY#SINE/Alu (30) 281 2 c_b1s352i60
X_31379302_31 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 95
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_31379302_31 96 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCCGCCTCA 145
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_31379302_31 146 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 195
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_31379302_31 196 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATTTTAGCCGGGATGGT 245
i v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_31379302_31 246 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 295
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_31379302_31 296 GGATTACAGGCGTGAGCCACCGCGCCCGGC 325
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.88
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 2868 0.7 0.0 0.0 X_31470348_31470664_INS 14 317 (0) + AluY SINE/Alu 1 304 (7) 526
ANNOTATION EVIDENCE:
2868 0.66 0.00 0.00 X_31470348_31470664_INS 14 317 0 + AluY SINE/Alu 1 304 7
2868 0.66 0.00 0.00 X_31470348_31470664_INS 14 317 (0) AluY#SINE/Alu 1 304 (7) c_b1s352i61
X_31470348_31 14 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 63
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_31470348_31 64 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 113
v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_31470348_31 114 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 163
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_31470348_31 164 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 213
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_31470348_31 214 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 263
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_31470348_31 264 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 313
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_31470348_31 314 AAAA 317
AluY#SINE/Alu 301 AAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.66
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 303), avg. gap size = 0.0 (0 / 0)
+ 34 10.7 1.5 3.1 X_3158605_3158670_INS 1 65 (1) + (TTCC)n Simple_repeat 1 64 (0) 527
ANNOTATION EVIDENCE:
34 10.73 1.54 3.12 X_3158605_3158670_INS 1 65 1 + (TTCC)n Simple_repeat 1 64 0
34 10.73 1.54 3.12 X_3158605_3158670_INS 1 65 (1) (TTCC)n#Simple_repeat 1 64 (0) m_b1s252i79
X_3158605_315 1 TTCCTTTCCTCCCTCCCTTCC-TCCTTCCTTCTTTCCTTCCTTCGTTCCT 49
- i i - i v -
(TTCC)n#Simpl 1 TTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC- 48
X_3158605_315 50 TTCCTTCCTTTCCTCC 65
i i
(TTCC)n#Simpl 49 TTCCTTCCTTCCTTCC 64
Matrix = Unknown
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3)
+ 96 7.0 5.9 0.0 X_31587769_31587937_INS 1 169 (0) + (ATATATACGT)n Simple_repeat 1 179 (0) 528
ANNOTATION EVIDENCE:
96 6.97 5.92 0.00 X_31587769_31587937_INS 1 169 0 + (ATATATACGT)n Simple_repeat 1 179 0
96 6.97 5.92 0.00 X_31587769_31587937_INS 1 169 (0) (ATATATACGT)n#Simple_repeat 1 179 (0) c_b1s251i109
X_31587769_31 1 ATATATACGTATATATACGTGTATACACG--TATATACGTATATACACGT 48
i i -- i
(ATATATACGT)n 1 ATATATACGTATATATACGTATATATACGTATATATACGTATATATACGT 50
X_31587769_31 49 ATATATACGTGTATACACGTATATACACGTGTATATACGTATATACACG- 97
i i i i i -
(ATATATACGT)n 51 ATATATACGTATATATACGTATATATACGTATATATACGTATATATACGT 100
X_31587769_31 98 -TATATACGTATATACACG--TATATACGTATATACACG--TATATACGT 142
- i -- i --
(ATATATACGT)n 101 ATATATACGTATATATACGTATATATACGTATATATACGTATATATACGT 150
X_31587769_31 143 ATATACACG--TATATACGTATATATACG 169
i --
(ATATATACGT)n 151 ATATATACGTATATATACGTATATATACG 179
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.04 (6 / 168), avg. gap size = 1.67 (10 / 6)
+ 37 4.8 0.0 0.0 X_31799743_31799814_INS 15 57 (15) + (T)n Simple_repeat 1 43 (0) 529
ANNOTATION EVIDENCE:
37 4.82 0.00 0.00 X_31799743_31799814_INS 15 57 15 + (T)n Simple_repeat 1 43 0
37 4.82 0.00 0.00 X_31799743_31799814_INS 15 57 (15) (T)n#Simple_repeat 1 43 (0) c_b1s251i108
X_31799743_31 15 TTTTTTTTTTTTTTTTTTTTATTTTTTTTATTTTTTTTTTTTT 57
v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 37 9.4 0.0 10.5 X_31827295_31827379_INS 1 84 (1) + (TA)n Simple_repeat 1 76 (0) 530
ANNOTATION EVIDENCE:
37 9.40 0.00 10.53 X_31827295_31827379_INS 1 84 1 + (TA)n Simple_repeat 1 76 0
37 9.40 0.00 10.53 X_31827295_31827379_INS 1 84 (1) (TA)n#Simple_repeat 1 76 (0) m_b1s252i78
X_31827295_31 1 TATATATGAGTTTATATATAAATATATATGAGTTTATATATATATATGAG 50
- - v v - - v - -
(TA)n#Simple_ 1 TATATAT-A-TATATATATATATATATAT-A-TATATATATATATAT-A- 44
X_31827295_31 51 TTTATATATAAATATATATGAGTTTATATATATA 84
v v - - v
(TA)n#Simple_ 45 TATATATATATATATATAT-A-TATATATATATA 76
Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.10 (8 / 83), avg. gap size = 1.00 (8 / 8)
+ 31 11.4 0.0 0.0 X_31863148_31863204_INS 1 49 (8) + (TA)n Simple_repeat 1 49 (0) 531
ANNOTATION EVIDENCE:
31 11.41 0.00 0.00 X_31863148_31863204_INS 1 49 8 + (TA)n Simple_repeat 1 49 0
31 11.41 0.00 0.00 X_31863148_31863204_INS 1 49 (8) (TA)n#Simple_repeat 1 49 (0) c_b1s251i107
X_31863148_31 1 TATATATATATATATGTATATGTGTATACATATATATATATATGTATAT 49
i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATAT 49
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 45 5.9 0.0 0.0 X_31969238_31969291_INS 1 54 (0) + (ATATAT)n Simple_repeat 1 54 (0) 532
ANNOTATION EVIDENCE:
45 5.89 0.00 0.00 X_31969238_31969291_INS 1 54 0 + (ATATAT)n Simple_repeat 1 54 0
45 5.89 0.00 0.00 X_31969238_31969291_INS 1 54 (0) (ATATAT)n#Simple_repeat 1 54 (0) c_b1s251i106
X_31969238_31 1 ATATACATATATATATATATATATATATATATATATGTATATATATATGT 50
i i i
(ATATAT)n#Sim 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_31969238_31 51 ATAT 54
(ATATAT)n#Sim 51 ATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 38 16.5 0.0 0.0 X_32103719_32103791_INS 6 69 (4) + (TA)n Simple_repeat 1 64 (0) 533
ANNOTATION EVIDENCE:
38 16.51 0.00 0.00 X_32103719_32103791_INS 6 69 4 + (TA)n Simple_repeat 1 64 0
38 16.51 0.00 0.00 X_32103719_32103791_INS 6 69 (4) (TA)n#Simple_repeat 1 64 (0) m_b1s252i77
X_32103719_32 6 TATATATATACGTATATATATATACACATATATACGTATATATACATATA 55
ii i i ii i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_32103719_32 56 TACGTATATATATA 69
ii
(TA)n#Simple_ 51 TATATATATATATA 64
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 23 20.8 1.9 0.0 X_3212319_3212372_INS 2 54 (0) + (TCC)n Simple_repeat 1 54 (0) 534
ANNOTATION EVIDENCE:
23 20.75 1.89 0.00 X_3212319_3212372_INS 2 54 0 + (TCC)n Simple_repeat 1 54 0
23 20.75 1.89 0.00 X_3212319_3212372_INS 2 54 (0) (TCC)n#Simple_repeat 1 54 (0) m_b1s252i76
X_3212319_321 2 TCCTTTTCCTCCTTCT-CTCCTTCTCCTCCTCTTTCTCCTCCTCTTCTTC 50
ii i - i i i i i
(TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 50
X_3212319_321 51 TTCC 54
i
(TCC)n#Simple 51 CTCC 54
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1)
+ 2825 0.3 0.0 0.0 X_32155912_32156260_INS 2 309 (40) + L1HS LINE/L1 5846 6153 (2) 535
ANNOTATION EVIDENCE:
2825 0.32 0.00 0.00 X_32155912_32156260_INS 2 309 40 + L1HS_3end LINE/L1 593 900 2
2825 0.32 0.00 0.00 X_32155912_32156260_INS 2 309 (40) L1HS_3end#LINE/L1 593 900 (2) m_b1s551i10
X_32155912_32 2 CATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAA 51
L1HS_3end#LIN 593 CATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAA 642
X_32155912_32 52 AAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAG 101
L1HS_3end#LIN 643 AAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAG 692
X_32155912_32 102 ATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGG 151
L1HS_3end#LIN 693 ATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGG 742
X_32155912_32 152 GTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGAT 201
L1HS_3end#LIN 743 GTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGAT 792
X_32155912_32 202 GACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTA 251
i
L1HS_3end#LIN 793 GACACGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTA 842
X_32155912_32 252 ACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAA 301
L1HS_3end#LIN 843 ACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAA 892
X_32155912_32 302 AAAAAAAA 309
L1HS_3end#LIN 893 AAAAAAAA 900
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.03
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 307), avg. gap size = 0.0 (0 / 0)
+ 27 11.2 0.0 0.0 X_32155912_32156260_INS 311 349 (0) + (A)n Simple_repeat 1 39 (0) 536
ANNOTATION EVIDENCE:
27 11.15 0.00 0.00 X_32155912_32156260_INS 311 349 0 + (A)n Simple_repeat 1 39 0
27 11.15 0.00 0.00 X_32155912_32156260_INS 311 349 (0) (A)n#Simple_repeat 1 39 (0) m_b1s252i75
X_32155912_32 311 AAATAAATAAAAAATAAAATAAAAAAAAAAAAAAAAAAA 349
v v v v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 57 1.7 1.7 0.0 X_3224861_3224922_INS 2 60 (2) + (ATCT)n Simple_repeat 1 60 (0) 537
ANNOTATION EVIDENCE:
57 1.72 1.69 0.00 X_3224861_3224922_INS 2 60 2 + (ATCT)n Simple_repeat 1 60 0
57 1.72 1.69 0.00 X_3224861_3224922_INS 2 60 (2) (ATCT)n#Simple_repeat 1 60 (0) c_b1s251i105
X_3224861_322 2 ATCTATCTATCTCTCTATCTATCTATCTATCTATCTATCTATCTATCTAT 51
v
(ATCT)n#Simpl 1 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 50
X_3224861_322 52 CTATC-ATCT 60
-
(ATCT)n#Simpl 51 CTATCTATCT 60
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)
+ 26 19.6 8.5 1.1 X_32353789_32353872_INS 1 7 (77) + (TA)n Simple_repeat 1 84 (0) 538
ANNOTATION EVIDENCE:
26 19.58 8.54 1.14 X_32353789_32353872_INS 1 82 2 + (TA)n Simple_repeat 1 88 0
26 19.58 8.54 1.14 X_32353789_32353872_INS 1 82 (2) (TA)n#Simple_repeat 1 88 (0) m_b1s252i73
X_32353789_32 1 TATGTATATATA-ACATATA-ACATGT-TATATACATA-ACATATACATG 46
i - i - i i - i - i i -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATAT- 49
X_32353789_32 47 ACATGTATATATA-ACATATA-ACATGT-TATATACATA 82
i i - i - i i - i
(TA)n#Simple_ 50 ATATATATATATATATATATATATATATATATATATATA 88
Matrix = Unknown
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.10 (8 / 81), avg. gap size = 1.00 (8 / 8)
+ 25 15.1 5.6 2.7 X_32353789_32353872_INS 8 78 (6) + (ATATAAC)n Simple_repeat 1 73 (0) 539
ANNOTATION EVIDENCE:
25 15.09 5.63 2.74 X_32353789_32353872_INS 8 78 6 + (ATATAAC)n Simple_repeat 1 73 0
25 15.09 5.63 2.74 X_32353789_32353872_INS 8 78 (6) (ATATAAC)n#Simple_repeat 1 73 (0) m_b1s252i74
X_32353789_32 8 ATATAACATATAACATGTTATATACATAACATAT-AC--ATGACATGT-A 53
-v - i i - -- i i -
(ATATAAC)n#Si 1 ATATAACATATAACAT-ATA-ACATATAACATATAACATATAACATATAA 48
X_32353789_32 54 TATATAACATATAACATGTTATATA 78
i i v i
(ATATAAC)n#Si 49 CATATAACATATAACATATAACATA 73
Matrix = Unknown
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.20 (6 / 5)
+ 20 18.4 4.0 0.0 X_3243846_3243898_INS 2 51 (2) + (ATAA)n Simple_repeat 1 52 (0) 540
ANNOTATION EVIDENCE:
20 18.36 4.00 0.00 X_3243846_3243898_INS 2 51 2 + (ATAA)n Simple_repeat 1 52 0
20 18.36 4.00 0.00 X_3243846_3243898_INS 2 51 (2) (ATAA)n#Simple_repeat 1 52 (0) m_b1s252i72
X_3243846_324 2 ATATATTTATAAATAAATATAT-AAT-AATATATTTATAAATAAATATAT 49
v vv v - - v vv v
(ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT 50
X_3243846_324 50 AA 51
(ATAA)n#Simpl 51 AA 52
Matrix = Unknown
Transitions / transversions = 0.00 (0/8)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2)
+ 119 11.0 2.5 0.5 X_3244209_3244408_INS 1 199 (1) + (TTTATAA)n Simple_repeat 1 203 (0) 541
ANNOTATION EVIDENCE:
119 10.96 2.51 0.49 X_3244209_3244408_INS 1 199 1 + (TTTATAA)n Simple_repeat 1 203 0
119 10.96 2.51 0.49 X_3244209_3244408_INS 1 199 (1) (TTTATAA)n#Simple_repeat 1 203 (0) m_b1s252i71
X_3244209_324 1 TTTATAATATATAATTTATAA-TTATAAATTATAAATTATAATATATAAT 49
v - v v v
(TTTATAA)n#Si 1 TTTATAATTTATAATTTATAATTTATAATTTATAATTTATAATTTATAAT 50
X_3244209_324 50 TTATATATTATAAATTTATAATATATAATTTATATATTATAATTTATAAT 99
vv - v vv
(TTTATAA)n#Si 51 TTATAATTTAT-AATTTATAATTTATAATTTATAATTTATAATTTATAAT 99
X_3244209_324 100 ATATAATTTATAA-TTATAAGTTATATATTATAATTTTTAA-TTATAAGT 147
v - v vv v - v
(TTTATAA)n#Si 100 TTATAATTTATAATTTATAATTTATAATTTATAATTTATAATTTATAATT 149
X_3244209_324 148 TATAATATATAACTTATAA-TTATAAGTTATAATATATAACTTATAA-TT 195
v i - v v i -
(TTTATAA)n#Si 150 TATAATTTATAATTTATAATTTATAATTTATAATTTATAATTTATAATTT 199
X_3244209_324 196 ATAA 199
(TTTATAA)n#Si 200 ATAA 203
Matrix = Unknown
Transitions / transversions = 0.11 (2/18)
Gap_init rate = 0.03 (6 / 198), avg. gap size = 1.00 (6 / 6)
+ 28 10.7 3.9 0.0 X_3247374_3247426_INS 1 51 (2) + (AAGG)n Simple_repeat 1 53 (0) 542
ANNOTATION EVIDENCE:
28 10.71 3.92 0.00 X_3247374_3247426_INS 1 51 2 + (AAGG)n Simple_repeat 1 53 0
28 10.71 3.92 0.00 X_3247374_3247426_INS 1 51 (2) (AAGG)n#Simple_repeat 1 53 (0) m_b1s252i70
X_3247374_324 1 AAGGAA-AAAAGAAGGAAGGAATGAAGGAA-AAAAGAAGGAAGGAAGGAA 48
-i i v -i i
(AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50
X_3247374_324 49 GGA 51
(AAGG)n#Simpl 51 GGA 53
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2)
+ 2659 1.7 0.0 0.0 X_3248615_3248950_INS 13 336 (0) C AluY SINE/Alu (0) 311 2 543
ANNOTATION EVIDENCE:
47 0.00 0.00 0.00 X_3248615_3248950_INS 13 55 281 + (T)n Simple_repeat 1 43 0
47 0.00 0.00 0.00 X_3248615_3248950_INS 13 55 (281) (T)n#Simple_repeat 1 43 (0) c_b1s251i104
X_3248615_324 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 55
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
2659 1.72 0.00 0.00 X_3248615_3248950_INS 56 336 0 C AluY SINE/Alu 2 282 29
2659 1.72 0.00 0.00 X_3248615_3248950_INS 56 336 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i62
X_3248615_324 56 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 105
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_3248615_324 106 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 155
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_3248615_324 156 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 205
i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_3248615_324 206 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGT 255
v
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_3248615_324 256 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 305
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_3248615_324 306 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 336
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.75
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 35 10.3 0.0 8.8 X_32497898_32497972_INS 2 75 (0) + (TA)n Simple_repeat 1 68 (0) 544
ANNOTATION EVIDENCE:
35 10.30 0.00 8.82 X_32497898_32497972_INS 2 75 0 + (TA)n Simple_repeat 1 68 0
35 10.30 0.00 8.82 X_32497898_32497972_INS 2 75 (0) (TA)n#Simple_repeat 1 68 (0) m_b1s252i69
X_32497898_32 2 TATATATATCACGAGATATATATATATATATATATCTCGTGATATATATA 51
- -v v v -i -
(TA)n#Simple_ 1 TATATATAT-A-TATATATATATATATATATATATAT-AT-ATATATATA 46
X_32497898_32 52 TATATATCTCGTGATATATATATA 75
v -i -
(TA)n#Simple_ 47 TATATATAT-AT-ATATATATATA 68
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.08 (6 / 73), avg. gap size = 1.00 (6 / 6)
+ 80 0.0 0.0 2.6 X_32573073_32573170_INS 4 83 (15) + (GAAA)n Simple_repeat 1 78 (0) 545
ANNOTATION EVIDENCE:
80 0.00 0.00 2.56 X_32573073_32573170_INS 4 83 15 + (GAAA)n Simple_repeat 1 78 0
80 0.00 0.00 2.56 X_32573073_32573170_INS 4 83 (15) (GAAA)n#Simple_repeat 1 78 (0) c_b1s251i103
X_32573073_32 4 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGG 53
-
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA-G 49
X_32573073_32 54 AAAGAAAGAAAGGAAAGAAAGAAAGAAAGA 83
-
(GAAA)n#Simpl 50 AAAGAAAGAAA-GAAAGAAAGAAAGAAAGA 78
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2)
+ 2571 2.5 0.0 0.0 X_32745904_32746205_INS 6 289 (13) + AluY SINE/Alu 28 311 (0) 546
ANNOTATION EVIDENCE:
2571 2.46 0.00 0.00 X_32745904_32746205_INS 6 289 13 + AluY SINE/Alu 28 311 0
2571 2.46 0.00 0.00 X_32745904_32746205_INS 6 289 (13) AluY#SINE/Alu 28 311 (0) c_b1s352i63
X_32745904_32 6 ATTCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGAT 55
i
AluY#SINE/Alu 28 ATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGAT 77
X_32745904_32 56 CGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACA 105
i v
AluY#SINE/Alu 78 CGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACA 127
X_32745904_32 106 AAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGG 155
i i
AluY#SINE/Alu 128 AAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGG 177
X_32745904_32 156 AGGCTGAGGCGGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGA 205
i
AluY#SINE/Alu 178 AGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGA 227
X_32745904_32 206 GCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCG 255
v
AluY#SINE/Alu 228 GCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCG 277
X_32745904_32 256 TCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 289
AluY#SINE/Alu 278 TCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.18
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 283), avg. gap size = 0.0 (0 / 0)
+ 57 10.4 0.0 0.0 X_32889105_32889186_INS 1 82 (0) + (A)n Simple_repeat 1 82 (0) 547
ANNOTATION EVIDENCE:
57 10.45 0.00 0.00 X_32889105_32889186_INS 1 82 0 + (A)n Simple_repeat 1 82 0
57 10.45 0.00 0.00 X_32889105_32889186_INS 1 82 (0) (A)n#Simple_repeat 1 82 (0) m_b1s252i68
X_32889105_32 1 AAAAAAAAAAAACAAAAAAAAAAAAAAAAGACTTATAAAAAAAAAAAAAA 50
v i vvv v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_32889105_32 51 AAAAAAAAAAAAAAGAAAAAAAGAAAAAAAAA 82
i i
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 82
Matrix = Unknown
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0)
+ 56 1.6 0.0 0.0 X_32897138_32897201_INS 1 63 (1) + (A)n Simple_repeat 1 63 (0) 548
ANNOTATION EVIDENCE:
56 1.61 0.00 0.00 X_32897138_32897201_INS 1 63 1 + (A)n Simple_repeat 1 63 0
56 1.61 0.00 0.00 X_32897138_32897201_INS 1 63 (1) (A)n#Simple_repeat 1 63 (0) m_b1s252i67
X_32897138_32 1 AAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA 50
v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_32897138_32 51 AAAAAAAAAAAAA 63
(A)n#Simple_r 51 AAAAAAAAAAAAA 63
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 2539 2.9 0.0 0.0 X_32920731_32921050_INS 14 320 (0) C AluY SINE/Alu (0) 311 1 549
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_32920731_32921050_INS 14 39 281 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_32920731_32921050_INS 14 39 (281) (T)n#Simple_repeat 1 26 (0) c_b1s251i102
X_32920731_32 14 TTTTTTTTTTTTTTTTTTTTTTTTTT 39
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2539 2.85 0.00 0.00 X_32920731_32921050_INS 40 320 0 C AluY SINE/Alu 1 281 30
2539 2.85 0.00 0.00 X_32920731_32921050_INS 40 320 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i64
X_32920731_32 40 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 89
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_32920731_32 90 CGGTTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 139
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_32920731_32 140 GCCTCCCAAGTAGCTGGGACTACAGGCGTCCGCCACTACGCCCGGCTAAT 189
i i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_32920731_32 190 TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTTTTAGCCGGGATGGT 239
i v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_32920731_32 240 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 289
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_32920731_32 290 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 320
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.24
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 46 7.0 0.0 0.0 X_33026920_33026990_INS 1 61 (10) + (CGTATATATA)n Simple_repeat 1 61 (0) 550
ANNOTATION EVIDENCE:
46 7.03 0.00 0.00 X_33026920_33026990_INS 1 61 10 + (CGTATATATA)n Simple_repeat 1 61 0
46 7.03 0.00 0.00 X_33026920_33026990_INS 1 61 (10) (CGTATATATA)n#Simple_repeat 1 61 (0) c_b1s251i101
X_33026920_33 1 CGTATATATGTGTATATATACGTATATATACGTATATATGTGTATATATA 50
ii ii
(CGTATATATA)n 1 CGTATATATACGTATATATACGTATATATACGTATATATACGTATATATA 50
X_33026920_33 51 CGTATATATAC 61
(CGTATATATA)n 51 CGTATATATAC 61
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 17 36.5 0.0 0.0 X_33027420_33027474_INS 1 54 (1) + (TA)n Simple_repeat 1 54 (0) 551
ANNOTATION EVIDENCE:
17 36.54 0.00 0.00 X_33027420_33027474_INS 1 54 1 + (TA)n Simple_repeat 1 54 0
17 36.54 0.00 0.00 X_33027420_33027474_INS 1 54 (1) (TA)n#Simple_repeat 1 54 (0) m_b1s252i66
X_33027420_33 1 TATACACATGTGCATATATGTGTATATATACACATATGTGTATGTGTGTA 50
i i i ii i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_33027420_33 51 TATA 54
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 2724 2.3 0.0 0.0 X_33062660_33062969_INS 12 310 (0) C AluY SINE/Alu (12) 299 1 552
ANNOTATION EVIDENCE:
2724 2.34 0.00 0.00 X_33062660_33062969_INS 12 310 0 C AluY SINE/Alu 1 299 12
2724 2.34 0.00 0.00 X_33062660_33062969_INS 12 310 (0) C AluY#SINE/Alu (12) 299 1 c_b1s352i65
X_33062660_33 12 TTTCTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 61
i
C AluY#SINE/Alu 299 TTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 250
X_33062660_33 62 AGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCA 111
v
C AluY#SINE/Alu 249 AGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCA 200
X_33062660_33 112 CGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCCG 161
i
C AluY#SINE/Alu 199 CGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCG 150
X_33062660_33 162 CCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 211
i
C AluY#SINE/Alu 149 CCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 100
X_33062660_33 212 CATTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCT 261
i v i
C AluY#SINE/Alu 99 CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCT 50
X_33062660_33 262 CGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 310
C AluY#SINE/Alu 49 CGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.76
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 46 0.0 0.0 0.0 X_33126985_33127035_INS 2 51 (0) + (A)n Simple_repeat 1 50 (0) 553
ANNOTATION EVIDENCE:
46 0.00 0.00 0.00 X_33126985_33127035_INS 2 51 0 + (A)n Simple_repeat 1 50 0
46 0.00 0.00 0.00 X_33126985_33127035_INS 2 51 (0) (A)n#Simple_repeat 1 50 (0) m_b1s252i65
X_33126985_33 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 89 0.0 0.0 0.0 X_33141332_33141426_INS 11 88 (7) + (CCTAAC)n Simple_repeat 1 78 (0) 554
ANNOTATION EVIDENCE:
89 0.00 0.00 0.00 X_33141332_33141426_INS 11 88 7 + (CCTAAC)n Simple_repeat 1 78 0
89 0.00 0.00 0.00 X_33141332_33141426_INS 11 88 (7) (CCTAAC)n#Simple_repeat 1 78 (0) c_b1s251i100
X_33141332_33 11 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 60
(CCTAAC)n#Sim 1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 50
X_33141332_33 61 TAACCCTAACCCTAACCCTAACCCTAAC 88
(CCTAAC)n#Sim 51 TAACCCTAACCCTAACCCTAACCCTAAC 78
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 39 4.0 3.9 0.0 X_33298068_33298128_INS 9 60 (1) + (GATATCTA)n Simple_repeat 1 54 (0) 555
ANNOTATION EVIDENCE:
39 3.96 3.85 0.00 X_33298068_33298128_INS 9 60 1 + (GATATCTA)n Simple_repeat 1 54 0
39 3.96 3.85 0.00 X_33298068_33298128_INS 9 60 (1) (GATATCTA)n#Simple_repeat 1 54 (0) c_b1s251i99
X_33298068_33 9 GATATCTAGATATCTAGATATCAAG-T-TCTTGATATCTAGATATCTAGA 56
v - - v
(GATATCTA)n#S 1 GATATCTAGATATCTAGATATCTAGATATCTAGATATCTAGATATCTAGA 50
X_33298068_33 57 TATC 60
(GATATCTA)n#S 51 TATC 54
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2)
+ 2547 2.4 0.0 3.4 X_33302850_33303159_INS 2 305 (5) + AluY SINE/Alu 8 301 (10) 556
ANNOTATION EVIDENCE:
2547 2.38 0.00 3.40 X_33302850_33303159_INS 2 305 5 + AluY SINE/Alu 8 301 10
2547 2.38 0.00 3.40 X_33302850_33303159_INS 2 305 (5) AluY#SINE/Alu 8 301 (10) c_b1s352i66
X_33302850_33 2 CGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGT 51
i
AluY#SINE/Alu 8 CGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGC 57
X_33302850_33 52 GGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACC 101
i v
AluY#SINE/Alu 58 GGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACC 107
X_33302850_33 102 CCGTCTCTACTAAAAATACAAAAAAAAATTAGCCGGGCGCGGTGGCGGGC 151
--- i
AluY#SINE/Alu 108 CCGTCTCTACTAAAAATACAAAA---AATTAGCCGGGCGTGGTGGCGGGC 154
X_33302850_33 152 GCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAAC 201
AluY#SINE/Alu 155 GCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAAC 204
X_33302850_33 202 CCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCGCA 251
i i -- ----
AluY#SINE/Alu 205 CCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C---- 248
X_33302850_33 252 GTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 301
- i
AluY#SINE/Alu 249 -TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
X_33302850_33 302 AAAA 305
AluY#SINE/Alu 298 AAAA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.03 (10 / 303), avg. gap size = 1.00 (10 / 10)
+ 2424 3.6 0.0 2.5 X_33766175_33766503_INS 8 328 (1) C AluY SINE/Alu (0) 311 1 557
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_33766175_33766503_INS 8 40 289 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_33766175_33766503_INS 8 40 (289) (T)n#Simple_repeat 1 33 (0) c_b1s251i98
X_33766175_33 8 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
(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)
2424 3.56 0.00 2.49 X_33766175_33766503_INS 41 328 1 C AluY SINE/Alu 1 281 30
2424 3.56 0.00 2.49 X_33766175_33766503_INS 41 328 (1) C AluY#SINE/Alu (30) 281 1 c_b1s352i67
X_33766175_33 41 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCAGACTGCGGACTGCAGTGGC 90
i------- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCT-------GGAGTGCAGTGGC 239
X_33766175_33 91 GCAATCTCGGCTCACTGCAAGCTCCACTTCCTGGGTTCACGCCATTCTCC 140
i i i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_33766175_33 141 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 190
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_33766175_33 191 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 240
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_33766175_33 241 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 290
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_33766175_33 291 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 328
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.99
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 73 0.0 2.5 2.5 X_33937118_33937206_INS 7 87 (2) + (TTTC)n Simple_repeat 1 81 (0) 558
ANNOTATION EVIDENCE:
73 0.00 2.47 2.47 X_33937118_33937206_INS 7 87 2 + (TTTC)n Simple_repeat 1 81 0
73 0.00 2.47 2.47 X_33937118_33937206_INS 7 87 (2) (TTTC)n#Simple_repeat 1 81 (0) c_b1s251i97
X_33937118_33 7 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC--TCTTTCTT 54
--
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_33937118_33 55 TCTTTCTTTCTCCTTCTTTCTTTCTTTCTTTCT 87
--
(TTTC)n#Simpl 51 TCTTTCTTTCT--TTCTTTCTTTCTTTCTTTCT 81
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.33 (4 / 3)
+ 2856 1.3 0.0 0.3 X_34242451_34242768_INS 4 313 (5) + AluY SINE/Alu 1 309 (2) 559
ANNOTATION EVIDENCE:
2856 1.29 0.00 0.32 X_34242451_34242768_INS 4 313 5 + AluY SINE/Alu 1 309 2
2856 1.29 0.00 0.32 X_34242451_34242768_INS 4 313 (5) AluY#SINE/Alu 1 309 (2) c_b1s352i68
X_34242451_34 4 GGCCGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGA 53
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_34242451_34 54 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 103
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_34242451_34 104 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTGATGG 153
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_34242451_34 154 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 203
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_34242451_34 204 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCACT 253
i
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_34242451_34 254 CCAGCCTGGGCCACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 303
v
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_34242451_34 304 AAAAAAAAAA 313
AluY#SINE/Alu 300 AAAAAAAAAA 309
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.01
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (1 / 309), avg. gap size = 1.00 (1 / 1)
+ 2343 1.9 0.0 1.1 X_34293474_34293780_INS 5 307 (0) C AluY SINE/Alu (0) 311 22 560
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_34293474_34293780_INS 5 44 263 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_34293474_34293780_INS 5 44 (263) (T)n#Simple_repeat 1 40 (0) c_b1s251i96
X_34293474_34 5 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2343 1.92 0.00 1.15 X_34293474_34293780_INS 45 307 0 C AluY SINE/Alu 22 281 30
2343 1.92 0.00 1.15 X_34293474_34293780_INS 45 307 (0) C AluY#SINE/Alu (30) 281 22 c_b1s352i69
X_34293474_34 45 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 94
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_34293474_34 95 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 144
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_34293474_34 145 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 194
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_34293474_34 195 TTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGAT 244
--- v i
C AluY#SINE/Alu 131 T---TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGAT 85
X_34293474_34 245 GGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 294
C AluY#SINE/Alu 84 GGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 35
X_34293474_34 295 CTGGGATTACAGG 307
C AluY#SINE/Alu 34 CTGGGATTACAGG 22
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.59
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (3 / 262), avg. gap size = 1.00 (3 / 3)
+ 29 10.8 6.7 0.0 X_3433955_3434018_INS 2 61 (3) + (TATC)n Simple_repeat 1 64 (0) 561
ANNOTATION EVIDENCE:
29 10.84 6.67 0.00 X_3433955_3434018_INS 2 61 3 + (TATC)n Simple_repeat 1 64 0
29 10.84 6.67 0.00 X_3433955_3434018_INS 2 61 (3) (TATC)n#Simple_repeat 1 64 (0) m_b1s252i64
X_3433955_343 2 TATC-ATCTATCTATTTGTCTACCTATC-ACCTAT-TATCTCTCTATCT- 47
- i i i - i - v -
(TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA 50
X_3433955_343 48 TCTATCTTTCTATC 61
v
(TATC)n#Simpl 51 TCTATCTATCTATC 64
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4)
+ 2646 2.6 0.0 2.6 X_34464331_34464661_INS 17 331 (0) + AluY SINE/Alu 1 307 (4) 562
ANNOTATION EVIDENCE:
2646 2.61 0.00 2.61 X_34464331_34464661_INS 17 331 0 + AluY SINE/Alu 1 307 4
2646 2.61 0.00 2.61 X_34464331_34464661_INS 17 331 (0) AluY#SINE/Alu 1 307 (4) c_b1s352i70
X_34464331_34 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_34464331_34 67 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 116
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_34464331_34 117 TGAAACCCCGTCTCTACTAAAAAATACAAAAAATTAGCCGGGCGCGGTGG 166
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAA-ATACAAAAAATTAGCCGGGCGTGGTGG 149
X_34464331_34 167 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 216
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_34464331_34 217 TGAACCCGGGAAGCGGAGATTGCAGTGAGCCGAGATTGCGCCACTGCAGT 266
i v i --
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA-- 247
X_34464331_34 267 CCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 316
----- i
AluY#SINE/Alu 248 C-----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
X_34464331_34 317 AAAAAAAAAAAAAAA 331
AluY#SINE/Alu 293 AAAAAAAAAAAAAAA 307
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.75
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.03 (8 / 314), avg. gap size = 1.00 (8 / 8)
+ 34 13.3 0.0 1.7 X_3464939_3465000_INS 1 61 (1) + (AAGG)n Simple_repeat 1 60 (0) 563
ANNOTATION EVIDENCE:
34 13.28 0.00 1.67 X_3464939_3465000_INS 1 61 1 + (AAGG)n Simple_repeat 1 60 0
34 13.28 0.00 1.67 X_3464939_3465000_INS 1 61 (1) (AAGG)n#Simple_repeat 1 60 (0) m_b1s252i62
X_3464939_346 1 AAGGAAGGAAGGAAGGAAAAGAGGGAGGCAGGGAGGGAGGGAAGGAAGGA 50
- i i i v i i i
(AAGG)n#Simpl 1 AAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 49
X_3464939_346 51 AGGAAGGAAGG 61
(AAGG)n#Simpl 50 AGGAAGGAAGG 60
Matrix = Unknown
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)
+ 1882 0.5 0.0 0.0 X_34738767_34739019_INS 30 253 (0) + L1HS LINE/L1 5949 6155 (0) 564
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 X_34738767_34739019_INS 237 253 0 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 X_34738767_34739019_INS 237 253 (0) (A)n#Simple_repeat 1 17 (0) m_b1s252i61
X_34738767_34 237 AAAAAAAAAAAAAAAAA 253
(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)
1882 0.48 0.00 0.00 X_34738767_34739019_INS 30 236 17 + L1HS_3end LINE/L1 696 902 0
1882 0.48 0.00 0.00 X_34738767_34739019_INS 30 236 (17) L1HS_3end#LINE/L1 696 902 (0) m_b1s551i11
X_34738767_34 30 ACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTC 79
L1HS_3end#LIN 696 ACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTC 745
X_34738767_34 80 GGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGAC 129
L1HS_3end#LIN 746 GGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGAC 795
X_34738767_34 130 ACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACT 179
i
L1HS_3end#LIN 796 ACGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACT 845
X_34738767_34 180 AACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAA 229
L1HS_3end#LIN 846 AACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAA 895
X_34738767_34 230 AAAAAAA 236
L1HS_3end#LIN 896 AAAAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.05
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 206), avg. gap size = 0.0 (0 / 0)
+ 22 2.6 0.0 13.3 X_34793849_34793901_INS 1 51 (2) + (TCCT)n Simple_repeat 1 45 (0) 565
ANNOTATION EVIDENCE:
22 2.62 0.00 13.33 X_34793849_34793901_INS 1 51 2 + (TCCT)n Simple_repeat 1 45 0
22 2.62 0.00 13.33 X_34793849_34793901_INS 1 51 (2) (TCCT)n#Simple_repeat 1 45 (0) m_b1s252i60
X_34793849_34 1 TCCTTCCTTTGTCTTCCTTCCTTTCTCTTCCTTCCTTTCTCTTCCTTCCT 50
- -i - - - -
(TCCT)n#Simpl 1 TCCTTCC-TT-CCTTCCTTCC-TTC-CTTCCTTCC-TTC-CTTCCTTCCT 44
X_34793849_34 51 T 51
(TCCT)n#Simpl 45 T 45
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.12 (6 / 50), avg. gap size = 1.00 (6 / 6)
+ 29 10.3 0.0 0.0 X_3488229_3488279_INS 2 44 (7) + (TA)n Simple_repeat 1 43 (0) 566
ANNOTATION EVIDENCE:
29 10.29 0.00 0.00 X_3488229_3488279_INS 2 44 7 + (TA)n Simple_repeat 1 43 0
29 10.29 0.00 0.00 X_3488229_3488279_INS 2 44 (7) (TA)n#Simple_repeat 1 43 (0) c_b1s251i95
X_3488229_348 2 TATATATATGTATATATATGTATATATGTATATGTATATATAT 44
i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT 43
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 3804 0.7 0.0 0.0 X_34992617_34993040_INS 2 419 (5) + L1HS LINE/L1 5738 6155 (0) 567
ANNOTATION EVIDENCE:
3804 0.72 0.00 0.00 X_34992617_34993040_INS 2 419 5 + L1HS_3end LINE/L1 485 902 0
3804 0.72 0.00 0.00 X_34992617_34993040_INS 2 419 (5) L1HS_3end#LINE/L1 485 902 (0) m_b1s551i12
X_34992617_34 2 AACTCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATA 51
i
L1HS_3end#LIN 485 AACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATA 534
X_34992617_34 52 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTT 101
L1HS_3end#LIN 535 TACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTT 584
X_34992617_34 102 TGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGC 151
L1HS_3end#LIN 585 TGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGC 634
X_34992617_34 152 AAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGA 201
L1HS_3end#LIN 635 AAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGA 684
X_34992617_34 202 ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACT 251
L1HS_3end#LIN 685 ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACT 734
X_34992617_34 252 GTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAA 301
L1HS_3end#LIN 735 GTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAA 784
X_34992617_34 302 TGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATA 351
i
L1HS_3end#LIN 785 TGCTAGATGACACGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATA 834
X_34992617_34 352 CATATGTAACTAACCTGCACAATGTGCACATGTACCCTGAAACTTAGAGT 401
i
L1HS_3end#LIN 835 CATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGT 884
X_34992617_34 402 ATAATAAAAAAAAAAAAA 419
L1HS_3end#LIN 885 ATAATAAAAAAAAAAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.50
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 417), avg. gap size = 0.0 (0 / 0)
+ 85 5.8 0.0 0.0 X_35005408_35005515_INS 2 108 (0) + (A)n Simple_repeat 1 107 (0) 568
ANNOTATION EVIDENCE:
85 5.83 0.00 0.00 X_35005408_35005515_INS 2 108 0 + (A)n Simple_repeat 1 107 0
85 5.83 0.00 0.00 X_35005408_35005515_INS 2 108 (0) (A)n#Simple_repeat 1 107 (0) m_b1s252i59
X_35005408_35 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_35005408_35 52 ATAAAAAAAAAAAAAGAAAAAAAACAAGAATAAACAAAAAAAAAAAAAAA 101
v i v i v v
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100
X_35005408_35 102 AAAAAAA 108
(A)n#Simple_r 101 AAAAAAA 107
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0)
+ 2687 2.6 0.0 2.3 X_35012570_35012893_INS 11 324 (0) C AluY SINE/Alu (4) 307 1 569
ANNOTATION EVIDENCE:
2687 2.61 0.00 2.28 X_35012570_35012893_INS 11 324 0 C AluY SINE/Alu 1 307 4
2687 2.61 0.00 2.28 X_35012570_35012893_INS 11 324 (0) C AluY#SINE/Alu (4) 307 1 c_b1s352i71
X_35012570_35 11 TTCTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC 60
i
C AluY#SINE/Alu 307 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC 258
X_35012570_35 61 CAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTC 110
i ----- -- i
C AluY#SINE/Alu 257 CAGGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTC 215
X_35012570_35 111 CGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGG 160
i
C AluY#SINE/Alu 214 CGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGG 165
X_35012570_35 161 GACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTA 210
i
C AluY#SINE/Alu 164 GACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTA 115
X_35012570_35 211 GAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTC 260
v
C AluY#SINE/Alu 114 GAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTC 65
X_35012570_35 261 ATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGC 310
i i
C AluY#SINE/Alu 64 GTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGC 15
X_35012570_35 311 CACCGCGCCCGGCC 324
C AluY#SINE/Alu 14 CACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.75
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.02 (7 / 313), avg. gap size = 1.00 (7 / 7)
+ 2830 1.9 0.0 0.3 X_35028088_35028417_INS 16 327 (3) + AluY SINE/Alu 1 311 (0) 570
ANNOTATION EVIDENCE:
2830 1.93 0.00 0.32 X_35028088_35028417_INS 16 327 3 + AluY SINE/Alu 1 311 0
2830 1.93 0.00 0.32 X_35028088_35028417_INS 16 327 (3) AluY#SINE/Alu 1 311 (0) c_b1s352i72
X_35028088_35 16 GGCCGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGA 65
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_35028088_35 66 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 115
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_35028088_35 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCAGGCGTGGTGG 165
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_35028088_35 166 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 215
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_35028088_35 216 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCACT 265
i
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_35028088_35 266 CCCACCTGGGCCACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 315
vi v
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_35028088_35 316 AAAAAAAAAAAA 327
AluY#SINE/Alu 300 AAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.36
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 311), avg. gap size = 1.00 (1 / 1)
+ 2815 1.9 0.0 0.0 X_35419171_35419493_INS 16 323 (0) C AluY SINE/Alu (3) 308 1 571
ANNOTATION EVIDENCE:
2815 1.95 0.00 0.00 X_35419171_35419493_INS 16 323 0 C AluY SINE/Alu 1 308 3
2815 1.95 0.00 0.00 X_35419171_35419493_INS 16 323 (0) C AluY#SINE/Alu (3) 308 1 c_b1s352i73
X_35419171_35 16 TTTATTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 65
v
C AluY#SINE/Alu 308 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 259
X_35419171_35 66 CCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTC 115
v
C AluY#SINE/Alu 258 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTC 209
X_35419171_35 116 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTAC 165
i
C AluY#SINE/Alu 208 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 159
X_35419171_35 166 AGGCGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACG 215
i
C AluY#SINE/Alu 158 AGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACG 109
X_35419171_35 216 GGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATC 265
v i
C AluY#SINE/Alu 108 GGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATC 59
X_35419171_35 266 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 315
C AluY#SINE/Alu 58 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
X_35419171_35 316 GCCCGGCC 323
C AluY#SINE/Alu 8 GCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.67
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 307), avg. gap size = 0.0 (0 / 0)
+ 2809 1.6 0.0 1.3 X_35520117_35520448_INS 4 318 (14) + AluY SINE/Alu 1 311 (0) 572
ANNOTATION EVIDENCE:
2809 1.61 0.00 1.29 X_35520117_35520448_INS 4 318 14 + AluY SINE/Alu 1 311 0
2809 1.61 0.00 1.29 X_35520117_35520448_INS 4 318 (14) AluY#SINE/Alu 1 311 (0) c_b1s352i74
X_35520117_35 4 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 53
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_35520117_35 54 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 103
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_35520117_35 104 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAATTAGCCGGGCGTAG 153
---- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA----AATTAGCCGGGCGTGG 146
X_35520117_35 154 TGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATG 203
i
AluY#SINE/Alu 147 TGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATG 196
X_35520117_35 204 GCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGC 253
v
AluY#SINE/Alu 197 GCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGC 246
X_35520117_35 254 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 303
AluY#SINE/Alu 247 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 296
X_35520117_35 304 AAAAAAAAAAAAAAA 318
AluY#SINE/Alu 297 AAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.33
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (4 / 314), avg. gap size = 1.00 (4 / 4)
+ 39 6.3 0.0 0.0 X_35566365_35566415_INS 1 50 (1) + (AAAGGCAAGG)n Simple_repeat 1 50 (0) 573
ANNOTATION EVIDENCE:
39 6.29 0.00 0.00 X_35566365_35566415_INS 1 50 1 + (AAAGGCAAGG)n Simple_repeat 1 50 0
39 6.29 0.00 0.00 X_35566365_35566415_INS 1 50 (1) (AAAGGCAAGG)n#Simple_repeat 1 50 (0) c_b1s251i94
X_35566365_35 1 AAAGGAAAGGAAAGGAAAGGAAAGGCAAGGAAAGGCAAGGCAAGGCAAGG 50
v v v
(AAAGGCAAGG)n 1 AAAGGCAAGGAAAGGCAAGGAAAGGCAAGGAAAGGCAAGGAAAGGCAAGG 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 40 7.5 2.5 5.2 X_35717452_35717533_INS 1 79 (3) + (ATATAAT)n Simple_repeat 1 77 (0) 574
ANNOTATION EVIDENCE:
40 7.46 2.53 5.19 X_35717452_35717533_INS 1 79 3 + (ATATAAT)n Simple_repeat 1 77 0
40 7.46 2.53 5.19 X_35717452_35717533_INS 1 79 (3) (ATATAAT)n#Simple_repeat 1 77 (0) m_b1s252i57
X_35717452_35 1 ATATAATATATGATATGTATAATATATGATATATAATATATGATAATATC 50
- - i i i - v
(ATATAAT)n#Si 1 ATATAATATAT-A-ATATATAATATATAATATATAATATATAAT-ATATA 47
X_35717452_35 51 ATA-AT-ATATGATAATATATAATATATGAT 79
- - - i
(ATATAAT)n#Si 48 ATATATAATAT-ATAATATATAATATATAAT 77
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.00 (6 / 6)
+ 2222 2.7 0.0 2.7 X_35890291_35890596_INS 15 306 (0) C AluY SINE/Alu (0) 311 26 575
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_35890291_35890596_INS 15 43 263 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_35890291_35890596_INS 15 43 (263) (T)n#Simple_repeat 1 29 (0) c_b1s251i93
X_35890291_35 15 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
(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)
2222 2.73 0.00 2.73 X_35890291_35890596_INS 44 306 0 C AluY SINE/Alu 26 281 30
2222 2.73 0.00 2.73 X_35890291_35890596_INS 44 306 (0) C AluY#SINE/Alu (30) 281 26 c_b1s352i75
X_35890291_35 44 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 93
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_35890291_35 94 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 143
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_35890291_35 144 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 193
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_35890291_35 194 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 243
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_35890291_35 244 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 293
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_35890291_35 294 AGTGCTGGGATTA 306
C AluY#SINE/Alu 38 AGTGCTGGGATTA 26
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.70
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (7 / 262), avg. gap size = 1.00 (7 / 7)
+ 2427 3.2 0.0 2.5 X_35987025_35987349_INS 12 325 (0) C AluY SINE/Alu (0) 311 1 576
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_35987025_35987349_INS 12 37 288 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_35987025_35987349_INS 12 37 (288) (T)n#Simple_repeat 1 26 (0) c_b1s251i92
X_35987025_35 12 TTTTTTTTTTTTTTTTTTTTTTTTTT 37
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2427 3.20 0.00 2.49 X_35987025_35987349_INS 38 325 0 C AluY SINE/Alu 1 281 30
2427 3.20 0.00 2.49 X_35987025_35987349_INS 38 325 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i76
X_35987025_35 38 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 87
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_35987025_35 88 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 137
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_35987025_35 138 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCGCGCCC 187
i i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_35987025_35 188 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGTCA 237
v i
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_35987025_35 238 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 287
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_35987025_35 288 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 325
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.95
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 1883 3.1 0.0 5.7 X_3599704_3599945_INS 1 242 (0) C AluY SINE/Alu (18) 293 65 577
ANNOTATION EVIDENCE:
1883 3.06 0.00 5.68 X_3599704_3599945_INS 1 242 0 C AluY SINE/Alu 65 293 18
1883 3.06 0.00 5.68 X_3599704_3599945_INS 1 242 (0) C AluY#SINE/Alu (18) 293 65 c_b1s352i77
X_3599704_359 1 TTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCG 50
i -----
C AluY#SINE/Alu 293 TTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA----- 249
X_3599704_359 51 GACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTC 100
-- i i
C AluY#SINE/Alu 248 G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTC 201
X_3599704_359 101 ACGCCATTCTCCTGCCTCAGCCTCCCCAGTAACTGGGACTACAGGCGCCC 150
v i
C AluY#SINE/Alu 200 ACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCC 151
X_3599704_359 151 GCCACCGCGCCCGGCTAATTTTTTGTATTTTTTTTTTTAGTAGAGACGGG 200
i ------
C AluY#SINE/Alu 150 GCCACCACGCCCGGCTAATTTTTTGTAT------TTTTAGTAGAGACGGG 107
X_3599704_359 201 GTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTC 242
v
C AluY#SINE/Alu 106 GTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTC 65
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.72
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.05 (13 / 241), avg. gap size = 1.00 (13 / 13)
+ 1072 1.6 0.0 0.0 X_36200879_36201060_INS 18 145 (37) + AluY SINE/Alu 183 310 (1) 578
ANNOTATION EVIDENCE:
1072 1.56 0.00 0.00 X_36200879_36201060_INS 18 145 37 + AluY SINE/Alu 183 310 1
1072 1.56 0.00 0.00 X_36200879_36201060_INS 18 145 (37) AluY#SINE/Alu 183 310 (1) m_b1s357i2
X_36200879_36 18 GAGGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCCGA 67
i
AluY#SINE/Alu 183 GAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGA 232
X_36200879_36 68 GATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 117
AluY#SINE/Alu 233 GATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 282
X_36200879_36 118 AAAAAAAAAAAACAAAAAAAAAAAAAAA 145
v
AluY#SINE/Alu 283 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 310
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 0.86
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.0 (0 / 0)
+ 26 8.9 0.0 0.0 X_36200879_36201060_INS 147 182 (0) + (A)n Simple_repeat 1 36 (0) 579
ANNOTATION EVIDENCE:
26 8.91 0.00 0.00 X_36200879_36201060_INS 147 182 0 + (A)n Simple_repeat 1 36 0
26 8.91 0.00 0.00 X_36200879_36201060_INS 147 182 (0) (A)n#Simple_repeat 1 36 (0) m_b1s252i56
X_36200879_36 147 AAAAAAACAAAAAAACAAAAAAAAAAAAAAACAAAA 182
v v v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 2528 2.1 0.0 0.4 X_36428505_36428833_INS 9 329 (0) C AluY SINE/Alu (0) 311 1 580
ANNOTATION EVIDENCE:
43 0.00 0.00 0.00 X_36428505_36428833_INS 9 47 282 + (T)n Simple_repeat 1 39 0
43 0.00 0.00 0.00 X_36428505_36428833_INS 9 47 (282) (T)n#Simple_repeat 1 39 (0) c_b1s251i91
X_36428505_36 9 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 47
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
2528 2.14 0.00 0.36 X_36428505_36428833_INS 48 329 0 C AluY SINE/Alu 1 281 30
2528 2.14 0.00 0.36 X_36428505_36428833_INS 48 329 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i78
X_36428505_36 48 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 97
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_36428505_36 98 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 147
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_36428505_36 148 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 197
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_36428505_36 198 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 247
- v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_36428505_36 248 TCTCGATCTCTTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 297
i
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_36428505_36 298 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 329
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.84
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 281), avg. gap size = 1.00 (1 / 1)
+ 2445 2.5 0.0 2.5 X_36712239_36712580_INS 14 342 (0) C AluY SINE/Alu (0) 311 1 581
ANNOTATION EVIDENCE:
45 0.00 0.00 0.00 X_36712239_36712580_INS 14 54 288 + (T)n Simple_repeat 1 41 0
45 0.00 0.00 0.00 X_36712239_36712580_INS 14 54 (288) (T)n#Simple_repeat 1 41 (0) c_b1s251i90
X_36712239_36 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 54
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
2445 2.49 0.00 2.49 X_36712239_36712580_INS 55 342 0 C AluY SINE/Alu 1 281 30
2445 2.49 0.00 2.49 X_36712239_36712580_INS 55 342 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i79
X_36712239_36 55 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 104
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_36712239_36 105 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 154
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_36712239_36 155 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 204
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_36712239_36 205 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 254
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_36712239_36 255 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 304
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_36712239_36 305 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 342
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 65 11.5 0.9 0.9 X_36738421_36738527_INS 1 107 (0) + (AGG)n Simple_repeat 1 107 (0) 582
ANNOTATION EVIDENCE:
65 11.53 0.93 0.93 X_36738421_36738527_INS 1 107 0 + (AGG)n Simple_repeat 1 107 0
65 11.53 0.93 0.93 X_36738421_36738527_INS 1 107 (0) (AGG)n#Simple_repeat 1 107 (0) m_b1s252i55
X_36738421_36 1 AGGAGAAGGAGGAGGAGGAGGATGA-GAGAATGGAGGAGGAGGAAGAGGA 49
i v - i - i
(AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGA 49
X_36738421_36 50 GAAAAAGGAGGAGGAGGAGAAGGAGGCGGAAGAGGAGGAGAAGGAGGAGG 99
i ii i v i i
(AGG)n#Simple 50 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 99
X_36738421_36 100 AGGAGGAG 107
(AGG)n#Simple 100 AGGAGGAG 107
Matrix = Unknown
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2)
+ 2726 2.0 0.0 0.3 X_36948224_36948542_INS 18 319 (0) + AluY SINE/Alu 1 301 (10) 583
ANNOTATION EVIDENCE:
2726 2.00 0.00 0.33 X_36948224_36948542_INS 18 319 0 + AluY SINE/Alu 1 301 10
2726 2.00 0.00 0.33 X_36948224_36948542_INS 18 319 (0) AluY#SINE/Alu 1 301 (10) c_b1s352i80
X_36948224_36 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_36948224_36 68 GGCGGGCGGATCACGAGGTCAAGAGATCGAGACCATCCCGGCTAAAACGG 117
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_36948224_36 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTAGTGG 167
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_36948224_36 168 CGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCG 217
i
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_36948224_36 218 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACT 267
v
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_36948224_36 268 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_36948224_36 318 AA 319
AluY#SINE/Alu 300 AA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.72
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 301), avg. gap size = 1.00 (1 / 1)
+ 37 19.6 2.9 3.9 X_36955172_36955277_INS 2 106 (0) + GA-rich Low_complexity 1 104 (0) 584
ANNOTATION EVIDENCE:
37 19.58 2.86 3.85 X_36955172_36955277_INS 2 106 0 + (AAGG)n Simple_repeat 1 104 0
37 19.58 2.86 3.85 X_36955172_36955277_INS 2 106 (0) (AAGG)n#Simple_repeat 1 104 (0) m_b1s252i54
X_36955172_36 2 AAGGAAGGAAGGAAGGGA-GAGGGTGGGAGAAGAAGGAAAGAAAGAAAGA 50
i - i vi - i - i i i
(AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGG-AAGGAAGGAAGG 48
X_36955172_36 51 AAGAAAGAAAGAAAGAAAGAGAAAGAAAGAAAGAAGAGAA--AAGAAAGG 98
i i i i - i i i - -- i
(AAGG)n#Simpl 49 AAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAG-GAAGGAAGGAAGG 96
X_36955172_36 99 AAGGAAGG 106
(AAGG)n#Simpl 97 AAGGAAGG 104
Matrix = Unknown
Transitions / transversions = 15.00 (15/1)
Gap_init rate = 0.06 (6 / 104), avg. gap size = 1.17 (7 / 6)
+ 40 7.7 7.2 0.0 X_37294623_37294692_INS 2 70 (0) + (TA)n Simple_repeat 1 74 (0) 585
ANNOTATION EVIDENCE:
40 7.68 7.25 0.00 X_37294623_37294692_INS 2 70 0 + (TA)n Simple_repeat 1 74 0
40 7.68 7.25 0.00 X_37294623_37294692_INS 2 70 (0) (TA)n#Simple_repeat 1 74 (0) m_b1s252i53
X_37294623_37 2 TATATATATATATATAGA-ATATATATATATATAT-TCTATATATAGA-A 48
v - - v v -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_37294623_37 49 TATATAGA-ATATATAGA-ATATA 70
v - v -
(TA)n#Simple_ 51 TATATATATATATATATATATATA 74
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5)
+ 2115 0.5 0.0 0.0 X_37324623_37324859_INS 16 237 (0) + AluY SINE/Alu 83 304 (7) 586
ANNOTATION EVIDENCE:
2115 0.45 0.00 0.00 X_37324623_37324859_INS 16 237 0 + AluY SINE/Alu 83 304 7
2115 0.45 0.00 0.00 X_37324623_37324859_INS 16 237 (0) AluY#SINE/Alu 83 304 (7) m_b1s356i2
X_37324623_37 16 CCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAA 65
AluY#SINE/Alu 83 CCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAA 132
X_37324623_37 66 TTAGCCGGGCGTGGTAGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCT 115
i
AluY#SINE/Alu 133 TTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCT 182
X_37324623_37 116 GAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGA 165
AluY#SINE/Alu 183 GAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGA 232
X_37324623_37 166 GATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 215
AluY#SINE/Alu 233 GATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 282
X_37324623_37 216 AAAAAAAAAAAAAAAAAAAAAA 237
AluY#SINE/Alu 283 AAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.45
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 221), avg. gap size = 0.0 (0 / 0)
+ 26 9.4 8.2 3.1 X_37753059_37753123_INS 1 61 (4) + (TA)n Simple_repeat 1 64 (0) 587
ANNOTATION EVIDENCE:
26 9.36 8.20 3.12 X_37753059_37753123_INS 1 61 4 + (TA)n Simple_repeat 1 64 0
26 9.36 8.20 3.12 X_37753059_37753123_INS 1 61 (4) (TA)n#Simple_repeat 1 64 (0) m_b1s252i52
X_37753059_37 1 TATATAT-TATATAGAGAT-TAGTATATATA-ATCTATATAT-TATATAG 46
- v v - - - v - v
(TA)n#Simple_ 1 TATATATATATATATATATATA-TATATATATATATATATATATATATAT 49
X_37753059_37 47 AGAT-TAGTATATATA 61
v - -
(TA)n#Simple_ 50 ATATATA-TATATATA 64
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.12 (7 / 60), avg. gap size = 1.00 (7 / 7)
+ 36 10.4 0.0 0.0 X_37978177_37978241_INS 1 53 (12) + (TA)n Simple_repeat 1 53 (0) 588
ANNOTATION EVIDENCE:
36 10.45 0.00 0.00 X_37978177_37978241_INS 1 53 12 + (TA)n Simple_repeat 1 53 0
36 10.45 0.00 0.00 X_37978177_37978241_INS 1 53 (12) (TA)n#Simple_repeat 1 53 (0) c_b1s251i89
X_37978177_37 1 TATATATATATATATATATATATGTACGCATATACATATATATATATATA 50
i iii i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_37978177_37 51 TAT 53
(TA)n#Simple_ 51 TAT 53
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 15 8.5 0.0 0.0 X_3860698_3860753_INS 1 25 (31) + (CCCT)n Simple_repeat 1 25 (0) 589
ANNOTATION EVIDENCE:
15 8.48 0.00 0.00 X_3860698_3860753_INS 1 25 4 + (CCCT)n Simple_repeat 1 25 0
15 8.48 0.00 0.00 X_3860698_3860753_INS 1 25 (4) (CCCT)n#Simple_repeat 1 25 (0) m_b1s252i51
X_3860698_386 1 CCCTCCCTCCGTCCCTCCCTCTCTC 25
v i
(CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTC 25
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 30 0.0 0.0 0.0 X_3860698_3860753_INS 26 53 (3) + (CTTT)n Simple_repeat 1 28 (0) 590
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_3860698_3860753_INS 26 53 3 + (CTTT)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_3860698_3860753_INS 26 53 (3) (CTTT)n#Simple_repeat 1 28 (0) c_b1s251i88
X_3860698_386 26 CTTTCTTTCTTTCTTTCTTTCTTTCTTT 53
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 74 3.5 0.0 4.3 X_3896898_3896994_INS 1 97 (0) + (TCTT)n Simple_repeat 1 93 (0) 591
ANNOTATION EVIDENCE:
74 3.48 0.00 4.30 X_3896898_3896994_INS 1 97 0 + (TCTT)n Simple_repeat 1 93 0
74 3.48 0.00 4.30 X_3896898_3896994_INS 1 97 (0) (TCTT)n#Simple_repeat 1 93 (0) c_b1s251i87
X_3896898_389 1 TCTTTCTTTCTTTTCTTTCTGTCCTTTTTTTCTTTCTTTCTTTCTTTCTT 50
- - i i
(TCTT)n#Simpl 1 TCTTTCTTTC-TTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCTTTCTT 48
X_3896898_389 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCTGTCCTTTCTTT 97
- - i
(TCTT)n#Simpl 49 TCTTTCTTTCTTTCTTTCTTTCTTTC-TTTCTTTCT-TTCTTTCTTT 93
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.00 (4 / 4)
+ 46 2.1 0.0 2.0 X_39036114_39036164_INS 1 51 (0) + (AGAA)n Simple_repeat 1 50 (0) 592
ANNOTATION EVIDENCE:
46 2.08 0.00 2.00 X_39036114_39036164_INS 1 51 0 + (AGAA)n Simple_repeat 1 50 0
46 2.08 0.00 2.00 X_39036114_39036164_INS 1 51 (0) (AGAA)n#Simple_repeat 1 50 (0) c_b1s251i86
X_39036114_39 1 AGAAAGAAAGAAAGAAAGAAAGAAAAAAGAGAAAGAAAGAAAGAAAGAAA 50
i -
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAA-AGAAAGAAAGAAAGAAAGAAA 49
X_39036114_39 51 G 51
(AGAA)n#Simpl 50 G 50
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 2545 3.4 0.0 2.4 X_39939314_39939633_INS 20 320 (0) + AluY SINE/Alu 1 294 (17) 593
ANNOTATION EVIDENCE:
2545 3.40 0.00 2.38 X_39939314_39939633_INS 20 320 0 + AluY SINE/Alu 1 294 17
2545 3.40 0.00 2.38 X_39939314_39939633_INS 20 320 (0) AluY#SINE/Alu 1 294 (17) c_b1s352i81
X_39939314_39 20 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 69
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_39939314_39 70 GGCGGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 119
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_39939314_39 120 TGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 169
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_39939314_39 170 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 219
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_39939314_39 220 GAACCCAGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCATTGCAGTC 269
i i i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_39939314_39 270 CGCAGTCCGGCCTGGGCAACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 319
----- i i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_39939314_39 320 A 320
AluY#SINE/Alu 294 A 294
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.90
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.02 (7 / 300), avg. gap size = 1.00 (7 / 7)
+ 1094 8.9 0.0 0.0 X_40063266_40063403_INS 4 138 (0) C AluSx SINE/Alu (161) 151 17 594
ANNOTATION EVIDENCE:
1094 8.89 0.00 0.00 X_40063266_40063403_INS 4 138 0 C AluSx SINE/Alu 17 151 161
1094 8.89 0.00 0.00 X_40063266_40063403_INS 4 138 (0) C AluSx#SINE/Alu (161) 151 17 m_b1s357i3
X_40063266_40 4 GCCACCACACCCGGCTAATTTTTGTATTTTTAGTAGAAACAGGGTTTCGT 53
i i i ii
C AluSx#SINE/Al 151 GCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 102
X_40063266_40 54 CATGTTGACCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCGC 103
i i i
C AluSx#SINE/Al 101 CATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGC 52
X_40063266_40 104 CTTGGTCTCCCAAAATGCTGGGATTACAGGTGTGA 138
i i i i
C AluSx#SINE/Al 51 CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA 17
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.14
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.00 (0 / 134), avg. gap size = 0.0 (0 / 0)
+ 522 10.8 2.6 5.3 X_40070363_40070483_INS 4 120 (1) C SVA_A Retroposon/SVA (680) 707 594 595
ANNOTATION EVIDENCE:
522 10.83 2.56 5.26 X_40070363_40070483_INS 4 120 1 C SVA_A Retroposon/SVA 594 707 680
522 10.83 2.56 5.26 X_40070363_40070483_INS 4 120 (1) C SVA_A#Retroposon/SVA (680) 707 594 m_b1s502i5
X_40070363_40 4 CCCCCCACCTCCCAGATGGGGAAG-TGGCTGGGCGGAGGTGCCCCCCACC 52
i i vi - i i i i ?
C SVA_A#Retropo 707 CCCCCCACCTCCCGGACGGGGCGGCTGGCCGGGCGGAGGCGCTCCTCACN 658
X_40070363_40 53 TCCCTCCCAGACGGGCGGCTGCTGGGCGGAGGGGCTCCTCACTTCTCAGA 102
---- -- v i v ? i
C SVA_A#Retropo 657 TCCC----AGACGGG--GCGGCCGGGCGGAGGCGCTCCTCACNTCCCAGA 614
X_40070363_40 103 CG--GGGCGGCCGGGCAGAG 120
--
C SVA_A#Retropo 613 CGANGGGCGGCCGGGCAGAG 594
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.33
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.07 (8 / 116), avg. gap size = 1.12 (9 / 8)
+ 1039 1.6 0.0 0.0 X_40212736_40212870_INS 14 135 (0) + AluY SINE/Alu 180 301 (10) 596
ANNOTATION EVIDENCE:
1039 1.64 0.00 0.00 X_40212736_40212870_INS 14 135 0 + AluY SINE/Alu 180 301 10
1039 1.64 0.00 0.00 X_40212736_40212870_INS 14 135 (0) AluY#SINE/Alu 180 301 (10) m_b1s357i4
X_40212736_40 14 GTTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGC 63
i
AluY#SINE/Alu 180 GCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGC 229
X_40212736_40 64 CGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTC 113
v
AluY#SINE/Alu 230 CGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTC 279
X_40212736_40 114 TCAAAAAAAAAAAAAAAAAAAA 135
AluY#SINE/Alu 280 TCAAAAAAAAAAAAAAAAAAAA 301
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 1.66
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 20 23.4 1.8 0.0 X_4035495_4035550_INS 1 55 (1) + (ATAT)n Simple_repeat 1 56 (0) 597
ANNOTATION EVIDENCE:
20 23.39 1.82 0.00 X_4035495_4035550_INS 1 55 1 + (ATAT)n Simple_repeat 1 56 0
20 23.39 1.82 0.00 X_4035495_4035550_INS 1 55 (1) (ATAT)n#Simple_repeat 1 56 (0) m_b1s252i50
X_4035495_403 1 ATATCTA-AAATATAGAAATGTATATATGTAAATATCTATATATCTAGAT 49
v - v v v i i v v v v
(ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_4035495_403 50 ATCTAT 55
v
(ATAT)n#Simpl 51 ATATAT 56
Matrix = Unknown
Transitions / transversions = 0.22 (2/9)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)
+ 58 0.0 0.0 0.0 X_40389690_40389743_INS 3 54 (0) + (AAGA)n Simple_repeat 1 52 (0) 598
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_40389690_40389743_INS 3 54 0 + (AAGA)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_40389690_40389743_INS 3 54 (0) (AAGA)n#Simple_repeat 1 52 (0) c_b1s251i85
X_40389690_40 3 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 52
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
X_40389690_40 53 GA 54
(AAGA)n#Simpl 51 GA 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 36 4.3 0.0 4.0 X_40470060_40470112_INS 1 52 (1) + (TATATGTA)n Simple_repeat 1 50 (0) 599
ANNOTATION EVIDENCE:
36 4.34 0.00 4.00 X_40470060_40470112_INS 1 52 1 + (TATATGTA)n Simple_repeat 1 50 0
36 4.34 0.00 4.00 X_40470060_40470112_INS 1 52 (1) (TATATGTA)n#Simple_repeat 1 50 (0) c_b1s251i84
X_40470060_40 1 TATATGTATATATGTATATGTGTATACATATGTATATATGTATATGTGTA 50
i -- i
(TATATGTA)n#S 1 TATATGTATATATGTATATATGTAT--ATATGTATATATGTATATATGTA 48
X_40470060_40 51 TA 52
(TATATGTA)n#S 49 TA 50
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2)
+ 2575 1.8 0.0 0.0 X_40652496_40652818_INS 12 323 (0) C AluY SINE/Alu (0) 311 1 600
ANNOTATION EVIDENCE:
33 0.00 0.00 0.00 X_40652496_40652818_INS 12 42 281 + (T)n Simple_repeat 1 31 0
33 0.00 0.00 0.00 X_40652496_40652818_INS 12 42 (281) (T)n#Simple_repeat 1 31 (0) c_b1s251i83
X_40652496_40 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
2575 1.78 0.00 0.00 X_40652496_40652818_INS 43 323 0 C AluY SINE/Alu 1 281 30
2575 1.78 0.00 0.00 X_40652496_40652818_INS 43 323 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i82
X_40652496_40 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 92
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_40652496_40 93 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 142
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_40652496_40 143 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 192
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_40652496_40 193 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 242
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_40652496_40 243 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 292
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_40652496_40 293 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 323
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.47
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2757 1.7 0.0 0.0 X_40682514_40682830_INS 19 317 (0) + AluY SINE/Alu 1 299 (12) 601
ANNOTATION EVIDENCE:
2757 1.67 0.00 0.00 X_40682514_40682830_INS 19 317 0 + AluY SINE/Alu 1 299 12
2757 1.67 0.00 0.00 X_40682514_40682830_INS 19 317 (0) AluY#SINE/Alu 1 299 (12) c_b1s352i83
X_40682514_40 19 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 68
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_40682514_40 69 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 118
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_40682514_40 119 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 168
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_40682514_40 169 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 218
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_40682514_40 219 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 268
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_40682514_40 269 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.38
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 328 15.9 1.6 0.0 X_40746249_40746311_INS 1 63 (0) C L1PA15 LINE/L1 (172) 5993 5930 602
ANNOTATION EVIDENCE:
328 15.87 1.59 0.00 X_40746249_40746311_INS 1 63 0 C L1PA15_3end LINE/L1 677 740 172
328 15.87 1.59 0.00 X_40746249_40746311_INS 1 63 (0) C L1PA15_3end#LINE/L1 (172) 740 677 m_b1s551i13
X_40746249_40 1 TCTAGTAGTCCTCAGT-TCTGTTGGTCCCCTCTTTGTGTTCATGTGTACT 49
v v i i - v i i
C L1PA15_3end#L 740 TCAAGTAGGCCCCGGTGTCTGTTGTTCCCTTCTTTGTGTCCATGTGTACT 691
X_40746249_40 50 CAATGTTCACCTTC 63
i v i
C L1PA15_3end#L 690 CAATGTTTAGCTCC 677
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.17
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1)
+ 202 23.8 0.0 0.0 X_40806215_40806706_INS 35 466 (26) + (TA)n Simple_repeat 1 432 (0) 603
ANNOTATION EVIDENCE:
17 28.90 0.00 0.00 X_40806215_40806706_INS 35 75 417 + (TG)n Simple_repeat 1 41 0
17 28.90 0.00 0.00 X_40806215_40806706_INS 35 75 (417) (TG)n#Simple_repeat 1 41 (0) m_b1s252i47
X_40806215_40 35 TGTGTGTGTATATATATATGTGTATATATATGTGTGTGTGT 75
i i i i i i i i i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 41
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
202 23.84 0.00 0.00 X_40806215_40806706_INS 43 466 26 + (TA)n Simple_repeat 1 424 0
202 23.84 0.00 0.00 X_40806215_40806706_INS 43 466 (26) (TA)n#Simple_repeat 1 424 (0) m_b1s252i48
X_40806215_40 43 TATATATATATGTGTATATATATGTGTGTGTGTATATATATATTTATATA 92
i i i i i i i v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_40806215_40 93 TGTATATATATTTATATATACGTGTATATATGTATATATGTATATATACG 142
i v ii i i i ii
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_40806215_40 143 TATATATGTATATATAAATATATATGTGTATATATACACATATGTATATA 192
i v i i i i i
(TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150
X_40806215_40 193 TGTATATATACACATATGTATATATGTATATATACACACATATGTATGTA 242
i i i i i i i i i i
(TA)n#Simple_ 151 TATATATATATATATATATATATATATATATATATATATATATATATATA 200
X_40806215_40 243 TATATGTGTGTATATACACATATGTATGCATATATGTGTATATATACACA 292
i i i i i i ii i i i i
(TA)n#Simple_ 201 TATATATATATATATATATATATATATATATATATATATATATATATATA 250
X_40806215_40 293 CACATATGTATATATATTTATATATACACACACATATGTATATATATTTA 342
i i i v i i i i i v
(TA)n#Simple_ 251 TATATATATATATATATATATATATATATATATATATATATATATATATA 300
X_40806215_40 343 TATATACATATATACGTATATATAAATATATACGTATATACGTAAATATA 392
i ii v ii ii v
(TA)n#Simple_ 301 TATATATATATATATATATATATATATATATATATATATATATATATATA 350
X_40806215_40 393 AATATATACACACATATATAAATATATATATACACACACACACGCATATA 442
v i i i v i i i i i iii
(TA)n#Simple_ 351 TATATATATATATATATATATATATATATATATATATATATATATATATA 400
X_40806215_40 443 TATATACACACACATATATATATA 466
i i i i
(TA)n#Simple_ 401 TATATATATATATATATATATATA 424
Matrix = Unknown
Transitions / transversions = 8.11 (73/9)
Gap_init rate = 0.00 (0 / 423), avg. gap size = 0.0 (0 / 0)
+ 24 36.0 0.0 0.0 X_40806215_40806706_INS 400 476 (16) + (AC)n Simple_repeat 1 77 (0) 604 *
ANNOTATION EVIDENCE:
24 35.97 0.00 0.00 X_40806215_40806706_INS 400 476 16 + (AC)n Simple_repeat 1 77 0
24 35.97 0.00 0.00 X_40806215_40806706_INS 400 476 (16) (AC)n#Simple_repeat 1 77 (0) m_b1s252i49
X_40806215_40 400 ACACACATATATAAATATATATATACACACACACACGCATATATATATAC 449
i i i v i i i i i i i i i i i
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50
X_40806215_40 450 ACACACATATATATATACACACACACA 476
i i i i i
(AC)n#Simple_ 51 ACACACACACACACACACACACACACA 77
Matrix = Unknown
Transitions / transversions = 19.00 (19/1)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 26 17.6 5.7 0.0 X_40822029_40822098_INS 1 70 (0) + (TATCATA)n Simple_repeat 1 74 (0) 605
ANNOTATION EVIDENCE:
26 17.64 5.71 0.00 X_40822029_40822098_INS 1 70 0 + (TATCATA)n Simple_repeat 1 74 0
26 17.64 5.71 0.00 X_40822029_40822098_INS 1 70 (0) (TATCATA)n#Simple_repeat 1 74 (0) m_b1s252i46
X_40822029_40 1 TATAATATATCATAT-T-GTATACAATATATGATCTATCATATATCATAT 48
v - -i iv v v
(TATCATA)n#Si 1 TATCATATATCATATATCATATATCATATATCATATATCATATATCATAT 50
X_40822029_40 49 -T-GTATACAATATATGATCTATC 70
- -i iv v v
(TATCATA)n#Si 51 ATCATATATCATATATCATATATC 74
Matrix = Unknown
Transitions / transversions = 0.57 (4/7)
Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4)
+ 59 9.6 5.2 1.7 X_40822608_40822723_INS 1 115 (1) + (ATATGAT)n Simple_repeat 1 119 (0) 606
ANNOTATION EVIDENCE:
59 9.60 5.22 1.68 X_40822608_40822723_INS 1 115 1 + (ATATGAT)n Simple_repeat 1 119 0
59 9.60 5.22 1.68 X_40822608_40822723_INS 1 115 (1) (ATATGAT)n#Simple_repeat 1 119 (0) m_b1s252i44
X_40822608_40 1 ATATGATATATG--ACATGATATGAT-ATATATCATATATGATATATGAC 47
-- i - - v i
(ATATGAT)n#Si 1 ATATGATATATGATATATGATAT-ATGATATATGATATATGATATATGAT 49
X_40822608_40 48 ATATG--ATATGATATGTGATATATGATATGAT-ATATATCATATATCAC 94
-- i - - v v i
(ATATGAT)n#Si 50 ATATGATATATGATATATGATATATGATAT-ATGATATATGATATATGAT 98
X_40822608_40 95 ATATCATATATGAGATATAAT 115
v v i
(ATATGAT)n#Si 99 ATATGATATATGATATATGAT 119
Matrix = Unknown
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.05 (6 / 114), avg. gap size = 1.33 (8 / 6)
+ 30 22.4 0.0 0.0 X_40846128_40846208_INS 6 66 (15) + (TA)n Simple_repeat 1 61 (0) 607
ANNOTATION EVIDENCE:
30 22.37 0.00 0.00 X_40846128_40846208_INS 6 66 15 + (TA)n Simple_repeat 1 61 0
30 22.37 0.00 0.00 X_40846128_40846208_INS 6 66 (15) (TA)n#Simple_repeat 1 61 (0) m_b1s252i43
X_40846128_40 6 TATATATATACACATATATATGCATATACATGTGTATGTGTATATATATA 55
i i ii i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_40846128_40 56 CACATATATAT 66
i i
(TA)n#Simple_ 51 TATATATATAT 61
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 50 2.0 0.0 0.0 X_40877760_40877810_INS 2 51 (0) + (AAAAT)n Simple_repeat 1 50 (0) 608
ANNOTATION EVIDENCE:
50 2.03 0.00 0.00 X_40877760_40877810_INS 2 51 0 + (AAAAT)n Simple_repeat 1 50 0
50 2.03 0.00 0.00 X_40877760_40877810_INS 2 51 (0) (AAAAT)n#Simple_repeat 1 50 (0) c_b1s251i82
X_40877760_40 2 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAAAAAATAAAAT 51
v
(AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAT 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 31 2.0 0.0 12.3 X_41121468_41121531_INS 1 64 (0) + (TCCTT)n Simple_repeat 1 57 (0) 609
ANNOTATION EVIDENCE:
31 2.03 0.00 12.28 X_41121468_41121531_INS 1 64 0 + (TCCTT)n Simple_repeat 1 57 0
31 2.03 0.00 12.28 X_41121468_41121531_INS 1 64 (0) (TCCTT)n#Simple_repeat 1 57 (0) m_b1s252i42
X_41121468_41 1 TCCTTTCGTTTCCTTTCTCCTTTCCTTTCCTTTCTCCTTTCCTTTCTCCT 50
v - - - - - -
(TCCTT)n#Simp 1 TCCTTTCCTTTCC-TT-TCCTTTCCTTTCC-TT-TCCTTTCC-TT-TCCT 44
X_41121468_41 51 TTCCTTTCCCTTTC 64
-
(TCCTT)n#Simp 45 TTCCTTT-CCTTTC 57
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.11 (7 / 63), avg. gap size = 1.00 (7 / 7)
+ 59 0.0 0.0 0.0 X_4145851_4145906_INS 1 53 (3) + (TTTC)n Simple_repeat 1 53 (0) 610
ANNOTATION EVIDENCE:
59 0.00 0.00 0.00 X_4145851_4145906_INS 1 53 3 + (TTTC)n Simple_repeat 1 53 0
59 0.00 0.00 0.00 X_4145851_4145906_INS 1 53 (3) (TTTC)n#Simple_repeat 1 53 (0) c_b1s251i81
X_4145851_414 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_4145851_414 51 TCT 53
(TTTC)n#Simpl 51 TCT 53
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 30 21.1 0.0 0.0 X_41748024_41748082_INS 2 59 (0) + (TA)n Simple_repeat 1 58 (0) 611
ANNOTATION EVIDENCE:
30 21.14 0.00 0.00 X_41748024_41748082_INS 2 59 0 + (TA)n Simple_repeat 1 58 0
30 21.14 0.00 0.00 X_41748024_41748082_INS 2 59 (0) (TA)n#Simple_repeat 1 58 (0) m_b1s252i41
X_41748024_41 2 TATATATATACATGTATGTGTATATATGTATATATATACATGTATGTGTA 51
i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_41748024_41 52 TATATGTA 59
i
(TA)n#Simple_ 51 TATATATA 58
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 833 10.0 1.7 2.9 X_42144907_42145083_INS 1 175 (2) C SVA_A Retroposon/SVA (619) 768 596 612
ANNOTATION EVIDENCE:
833 10.00 1.71 2.89 X_42144907_42145083_INS 1 175 2 C SVA_A Retroposon/SVA 596 768 619
833 10.00 1.71 2.89 X_42144907_42145083_INS 1 175 (2) C SVA_A#Retroposon/SVA (619) 768 596 m_b1s502i6
X_42144907_42 1 GCAGGGGGCTGGCCCCCC-ACCTCCCTCCCGGATGGGGCGGCTGGCCAGG 49
i i - - i i
C SVA_A#Retropo 768 GCGGGGGGCTGACCCCCCCACCTCC-TCCCGGACGGGGCGGCTGGCCGGG 720
X_42144907_42 50 CGGGGGGCTGAGCCCCCCACCTCCCTCCCGGACGGGGCAGCTGGCCGGGC 99
v ---- i
C SVA_A#Retropo 719 CGGGGGGCTGACCCCCCCACCTCCC----GGACGGGGCGGCTGGCCGGGC 674
X_42144907_42 100 AGAGGGGCTCCTCACTTCCCAGTAGGGGTGGCTGGGCAGAGGCGCCCCTC 149
i v ? vv i i i i
C SVA_A#Retropo 673 GGAGGCGCTCCTCACNTCCCAGACGGGGCGGCCGGGCGGAGGCGCTCCTC 624
X_42144907_42 150 ACCTCCCGGAC--AGGGCGGCTGGCCAG 175
? i --? i v
C SVA_A#Retropo 623 ACNTCCCAGACGANGGGCGGCCGGGCAG 596
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.53
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.04 (7 / 174), avg. gap size = 1.14 (8 / 7)
+ 2599 3.2 0.6 1.9 X_42165195_42165514_INS 7 320 (0) C AluY SINE/Alu (0) 311 2 613
ANNOTATION EVIDENCE:
2599 3.24 0.64 1.94 X_42165195_42165514_INS 7 320 0 C AluY SINE/Alu 2 311 0
2599 3.24 0.64 1.94 X_42165195_42165514_INS 7 320 (0) C AluY#SINE/Alu (0) 311 2 c_b1s352i84
X_42165195_42 7 TTTTACTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCT--GT 54
vi --
C AluY#SINE/Alu 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 262
X_42165195_42 55 CGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGC 104
i i
C AluY#SINE/Alu 261 CGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGC 212
X_42165195_42 105 CCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCGGAGTAGCTGGGA 154
i i - v
C AluY#SINE/Alu 211 CTCCCGGG-TTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGA 163
X_42165195_42 155 CTACAGGCGCCCGCCACCTCGCCTGGCTAATTTTTTGTATTTTTTTTTTA 204
v i -----
C AluY#SINE/Alu 162 CTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTT-----A 118
X_42165195_42 205 GTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGAC 254
i
C AluY#SINE/Alu 117 GTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGAC 68
X_42165195_42 255 CTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTG 304
C AluY#SINE/Alu 67 CTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTG 18
X_42165195_42 305 AGCCACCGCGCCCGGC 320
C AluY#SINE/Alu 17 AGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.11
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.02 (7 / 313), avg. gap size = 1.14 (8 / 7)
+ 37 2.8 0.0 0.0 X_42544451_42544501_INS 16 51 (0) + (TA)n Simple_repeat 1 36 (0) 614
ANNOTATION EVIDENCE:
37 2.84 0.00 0.00 X_42544451_42544501_INS 16 51 0 + (TA)n Simple_repeat 1 36 0
37 2.84 0.00 0.00 X_42544451_42544501_INS 16 51 (0) (TA)n#Simple_repeat 1 36 (0) c_b1s251i80
X_42544451_42 16 TATATATATATATATATATATATATTTATATATATA 51
v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATA 36
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 40 0.0 0.0 0.0 X_42815331_42815381_INS 1 34 (17) + (TG)n Simple_repeat 1 34 (0) 615
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 X_42815331_42815381_INS 1 34 17 + (TG)n Simple_repeat 1 34 0
40 0.00 0.00 0.00 X_42815331_42815381_INS 1 34 (17) (TG)n#Simple_repeat 1 34 (0) c_b1s251i79
X_42815331_42 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 34
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 34
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 47 1.9 3.9 0.0 X_42828505_42828556_INS 1 52 (0) + (TA)n Simple_repeat 1 54 (0) 616
ANNOTATION EVIDENCE:
47 1.95 3.85 0.00 X_42828505_42828556_INS 1 52 0 + (TA)n Simple_repeat 1 54 0
47 1.95 3.85 0.00 X_42828505_42828556_INS 1 52 (0) (TA)n#Simple_repeat 1 54 (0) c_b1s251i78
X_42828505_42 1 TATATATATATATATA-AAATATATATATATATA-ATATATATATATATA 48
- v -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_42828505_42 49 TATA 52
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2)
+ 53 3.2 0.0 0.0 X_4287671_4287734_INS 2 64 (0) + (A)n Simple_repeat 1 63 (0) 617
ANNOTATION EVIDENCE:
53 3.25 0.00 0.00 X_4287671_4287734_INS 2 64 0 + (A)n Simple_repeat 1 63 0
53 3.25 0.00 0.00 X_4287671_4287734_INS 2 64 (0) (A)n#Simple_repeat 1 63 (0) m_b1s252i40
X_4287671_428 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAATAAAAAAAAAA 51
v v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_4287671_428 52 AAAAAAAAAAAAA 64
(A)n#Simple_r 51 AAAAAAAAAAAAA 63
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 321 28.2 1.3 0.0 X_43004995_43005075_INS 3 80 (1) + LTR16C LTR/ERVL 196 274 (215) 618
ANNOTATION EVIDENCE:
321 28.21 1.28 0.00 X_43004995_43005075_INS 3 80 1 + LTR16C LTR/ERVL 196 274 215
321 28.21 1.28 0.00 X_43004995_43005075_INS 3 80 (1) LTR16C#LTR/ERVL 196 274 (215) m_b1s502i7
X_43004995_43 3 AACCAATAATTGATGAGAGTTGGTATATAAATATCCCAGCACCATCAACC 52
i i i i i? i v v iv
LTR16C#LTR/ER 196 AACCAATGACTGACGGGAGTTGGTGNATAAATACCCCAGCTCCCTCGCCC 245
X_43004995_43 53 C-AGAGCAGAATAATTTTGAAGGATGTAT 80
-v i ii i i i i vii i
LTR16C#LTR/ER 246 CTCGGGTGGGATAACTCTGAGGCGCGTGT 274
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.11
Transitions / transversions = 3.40 (17/5)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1)
+ 2732 2.3 0.3 0.0 X_43090178_43090494_INS 15 317 (0) + AluY SINE/Alu 1 304 (7) 619
ANNOTATION EVIDENCE:
2732 2.31 0.33 0.00 X_43090178_43090494_INS 15 317 0 + AluY SINE/Alu 1 304 7
2732 2.31 0.33 0.00 X_43090178_43090494_INS 15 317 (0) AluY#SINE/Alu 1 304 (7) c_b1s352i85
X_43090178_43 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_43090178_43 65 GACGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 114
i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_43090178_43 115 TGAAACCCCGTCTCTACTAAAAATACAAAA-ATTAGCCGGGCATGGTGGC 163
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_43090178_43 164 GCGCGCCTGTAGTCCCAGCTACACGGGAGGCTGAGGCAGGAGAATGGCGT 213
v v
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_43090178_43 214 GAACCCGGGAGGCGGAGCTTGCAGTGAGTCGAGATCGCGCCACTGCACTC 263
i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_43090178_43 264 CAGCCTGGGCGACAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAAAAAAA 313
i i
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_43090178_43 314 AAAA 317
AluY#SINE/Alu 301 AAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.74
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (1 / 302), avg. gap size = 1.00 (1 / 1)
+ 2467 3.1 0.0 2.4 X_4327002_4327348_INS 19 347 (0) C AluY SINE/Alu (0) 311 3 620
ANNOTATION EVIDENCE:
35 5.00 0.00 0.00 X_4327002_4327348_INS 19 60 287 + (T)n Simple_repeat 1 42 0
35 5.00 0.00 0.00 X_4327002_4327348_INS 19 60 (287) (T)n#Simple_repeat 1 42 (0) c_b1s251i77
X_4327002_432 19 TTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTT 60
i i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
2467 3.13 0.00 2.43 X_4327002_4327348_INS 61 347 0 C AluY SINE/Alu 3 282 29
2467 3.13 0.00 2.43 X_4327002_4327348_INS 61 347 (0) C AluY#SINE/Alu (29) 282 3 c_b1s352i86
X_4327002_432 61 GAGATGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 110
i i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_4327002_432 111 GCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 160
i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_4327002_432 161 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 210
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_4327002_432 211 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 260
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_4327002_432 261 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 310
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_4327002_432 311 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 347
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.91
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 286), avg. gap size = 1.00 (7 / 7)
+ 46 2.0 2.0 0.0 X_43932963_43933016_INS 2 51 (3) + (TTTC)n Simple_repeat 1 51 (0) 621
ANNOTATION EVIDENCE:
46 2.04 2.00 0.00 X_43932963_43933016_INS 2 51 3 + (TTTC)n Simple_repeat 1 51 0
46 2.04 2.00 0.00 X_43932963_43933016_INS 2 51 (3) (TTTC)n#Simple_repeat 1 51 (0) c_b1s251i76
X_43932963_43 2 TTTCTTTTTTTCTTT-TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
i -
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_43932963_43 51 T 51
(TTTC)n#Simpl 51 T 51
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1)
+ 371 16.7 0.0 0.0 X_43988886_43988951_INS 1 66 (0) C L1MD LINE/L1 (2512) 3634 3569 622
ANNOTATION EVIDENCE:
371 16.67 0.00 0.00 X_43988886_43988951_INS 1 66 0 C L1MD_orf2 LINE/L1 1460 1525 1769
371 16.67 0.00 0.00 X_43988886_43988951_INS 1 66 (0) C L1MD_orf2#LINE/L1 (1769) 1525 1460 m_b1s551i14
X_43988886_43 1 ATGAGTTGGGAAGTATTCCATTCTCTTCAATTTTTTGGAAGAGTTTATGT 50
i v i v i v i
C L1MD_orf2#LIN 1525 ATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTCTGGAAGAGATTGTGT 1476
X_43988886_43 51 AGAATCAGTATTATTT 66
ii i v
C L1MD_orf2#LIN 1475 AGAATTGGTGTTAATT 1460
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.15
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 48 3.9 0.0 0.0 X_4432134_4432186_INS 1 53 (0) + (GAAGAAAG)n Simple_repeat 1 53 (0) 623
ANNOTATION EVIDENCE:
48 3.92 0.00 0.00 X_4432134_4432186_INS 1 53 0 + (GAAGAAAG)n Simple_repeat 1 53 0
48 3.92 0.00 0.00 X_4432134_4432186_INS 1 53 (0) (GAAGAAAG)n#Simple_repeat 1 53 (0) c_b1s251i75
X_4432134_443 1 GAAGAAAGGAAGAAAGGAAGAAAGGAAGAAAGGAAGAAAGAAAGAAAGAA 50
i i
(GAAGAAAG)n#S 1 GAAGAAAGGAAGAAAGGAAGAAAGGAAGAAAGGAAGAAAGGAAGAAAGGA 50
X_4432134_443 51 AGA 53
(GAAGAAAG)n#S 51 AGA 53
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 77 1.4 0.0 0.0 X_44390493_44390563_INS 2 71 (0) + (AC)n Simple_repeat 1 70 (0) 624
ANNOTATION EVIDENCE:
77 1.44 0.00 0.00 X_44390493_44390563_INS 2 71 0 + (AC)n Simple_repeat 1 70 0
77 1.44 0.00 0.00 X_44390493_44390563_INS 2 71 (0) (AC)n#Simple_repeat 1 70 (0) c_b1s251i74
X_44390493_44 2 ACACACACACACACACACACACACACACACACACACACACACACACACAG 51
v
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50
X_44390493_44 52 ACACACACACACACACACAC 71
(AC)n#Simple_ 51 ACACACACACACACACACAC 70
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 56 0.0 0.0 0.0 X_44449533_44449585_INS 1 50 (3) + (CTTT)n Simple_repeat 1 50 (0) 625
ANNOTATION EVIDENCE:
56 0.00 0.00 0.00 X_44449533_44449585_INS 1 50 3 + (CTTT)n Simple_repeat 1 50 0
56 0.00 0.00 0.00 X_44449533_44449585_INS 1 50 (3) (CTTT)n#Simple_repeat 1 50 (0) c_b1s251i73
X_44449533_44 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 763 6.4 0.0 6.4 X_44504456_44504572_INS 1 117 (0) + AluY SINE/Alu 187 296 (15) 626
ANNOTATION EVIDENCE:
763 6.39 0.00 6.36 X_44504456_44504572_INS 1 117 0 + AluY SINE/Alu 187 296 15
763 6.39 0.00 6.36 X_44504456_44504572_INS 1 117 (0) AluY#SINE/Alu 187 296 (15) m_b1s357i5
X_44504456_44 1 CAAGAAAATCTCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATT 50
i i vv i i
AluY#SINE/Alu 187 CAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATC 236
X_44504456_44 51 GCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTC 100
v -- -----
AluY#SINE/Alu 237 GCGCCACTGCACTC--CAG-----CCTGGGCGACAGAGCGAGACTCCGTC 279
X_44504456_44 101 TCAAAAAAAAAAAAAAA 117
AluY#SINE/Alu 280 TCAAAAAAAAAAAAAAA 296
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.77
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7)
+ 2165 2.1 0.0 0.0 X_44561493_44561774_INS 7 282 (0) C AluY SINE/Alu (0) 311 46 627
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_44561493_44561774_INS 7 46 236 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_44561493_44561774_INS 7 46 (236) (T)n#Simple_repeat 1 40 (0) c_b1s251i72
X_44561493_44 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 46
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2165 2.12 0.00 0.00 X_44561493_44561774_INS 47 282 0 C AluY SINE/Alu 46 281 30
2165 2.12 0.00 0.00 X_44561493_44561774_INS 47 282 (0) C AluY#SINE/Alu (30) 281 46 c_b1s352i87
X_44561493_44 47 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCT 96
i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_44561493_44 97 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 146
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_44561493_44 147 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 196
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_44561493_44 197 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 246
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_44561493_44 247 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGC 282
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGC 46
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.37
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 235), avg. gap size = 0.0 (0 / 0)
+ 2503 2.8 0.0 0.3 X_44689770_44690095_INS 11 326 (0) C AluY SINE/Alu (0) 311 3 628
ANNOTATION EVIDENCE:
38 0.00 0.00 0.00 X_44689770_44690095_INS 11 45 281 + (T)n Simple_repeat 1 35 0
38 0.00 0.00 0.00 X_44689770_44690095_INS 11 45 (281) (T)n#Simple_repeat 1 35 (0) c_b1s251i71
X_44689770_44 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
2503 2.82 0.00 0.35 X_44689770_44690095_INS 46 326 0 C AluY SINE/Alu 3 282 29
2503 2.82 0.00 0.35 X_44689770_44690095_INS 46 326 (0) C AluY#SINE/Alu (29) 282 3 c_b1s352i88
X_44689770_44 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 95
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_44689770_44 96 CAGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 145
i
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_44689770_44 146 GCCTCCCAAGTAGCTGGGGCTACAGGCGCCCGCCACTACGCCCGGCTAAT 195
i i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_44689770_44 196 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 245
- v i
C AluY#SINE/Alu 132 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 84
X_44689770_44 246 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 295
C AluY#SINE/Alu 83 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 34
X_44689770_44 296 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 326
C AluY#SINE/Alu 33 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.23
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 2568 1.8 0.0 0.0 X_44908124_44908439_INS 12 316 (0) C AluY SINE/Alu (0) 311 2 629
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_44908124_44908439_INS 12 36 280 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_44908124_44908439_INS 12 36 (280) (T)n#Simple_repeat 1 25 (0) c_b1s251i70
X_44908124_44 12 TTTTTTTTTTTTTTTTTTTTTTTTT 36
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2568 1.79 0.00 0.00 X_44908124_44908439_INS 37 316 0 C AluY SINE/Alu 2 281 30
2568 1.79 0.00 0.00 X_44908124_44908439_INS 37 316 (0) C AluY#SINE/Alu (30) 281 2 c_b1s352i89
X_44908124_44 37 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 86
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_44908124_44 87 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 136
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_44908124_44 137 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 186
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_44908124_44 187 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 236
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_44908124_44 237 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 286
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_44908124_44 287 GGATTACAGGCGTGAGCCACCGCGCCCGGC 316
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 22 13.6 8.2 0.0 X_45193783_45193840_INS 1 53 (5) + (TA)n Simple_repeat 1 57 (0) 630
ANNOTATION EVIDENCE:
22 13.55 8.16 0.00 X_45193783_45193840_INS 1 49 9 + (TA)n Simple_repeat 1 53 0
22 13.55 8.16 0.00 X_45193783_45193840_INS 1 49 (9) (TA)n#Simple_repeat 1 53 (0) m_b1s252i38
X_45193783_45 1 TATAAATATAT-TATATTTTAAAATATA-ATATA-ATATAAATATAT-TA 46
v - v vv v - - v -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_45193783_45 47 TAT 49
(TA)n#Simple_ 51 TAT 53
Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4)
19 16.90 4.26 0.00 X_45193783_45193840_INS 7 53 5 + (TATAT)n Simple_repeat 1 49 0
19 16.90 4.26 0.00 X_45193783_45193840_INS 7 53 (5) (TATAT)n#Simple_repeat 1 49 (0) m_b1s252i39
X_45193783_45 7 TATATTATATTTTAAAATATAATATAATA-TA-AATATATTATATTTTA 53
v vv v v - - v v
(TATAT)n#Simp 1 TATATTATATTATATTATATTATATTATATTATATTATATTATATTATA 49
Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2)
+ 2469 2.8 0.0 2.5 X_45290693_45291025_INS 19 333 (0) C AluY SINE/Alu (0) 311 2 631
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_45290693_45291025_INS 19 45 288 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 X_45290693_45291025_INS 19 45 (288) (T)n#Simple_repeat 1 27 (0) c_b1s251i69
X_45290693_45 19 TTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(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)
2469 2.80 0.00 2.45 X_45290693_45291025_INS 46 333 0 C AluY SINE/Alu 2 282 29
2469 2.80 0.00 2.45 X_45290693_45291025_INS 46 333 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i90
X_45290693_45 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 95
i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_45290693_45 96 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 145
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_45290693_45 146 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 195
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_45290693_45 196 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 245
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_45290693_45 246 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 295
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_45290693_45 296 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 333
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 24 17.9 1.9 1.9 X_4530296_4530357_INS 6 57 (5) + (TA)n Simple_repeat 1 52 (0) 632
ANNOTATION EVIDENCE:
24 17.94 1.92 1.92 X_4530296_4530357_INS 6 57 5 + (TA)n Simple_repeat 1 52 0
24 17.94 1.92 1.92 X_4530296_4530357_INS 6 57 (5) (TA)n#Simple_repeat 1 52 (0) m_b1s252i37
X_4530296_453 6 TATATATATATACA-ATCTGTATATATATATGTTGATCATATATATAACT 54
i - v i i vv - vv
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT-ATATATATATAT 49
X_4530296_453 55 ATA 57
(TA)n#Simple_ 50 ATA 52
Matrix = Unknown
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2)
+ 2550 2.1 0.0 0.0 X_45318871_45319189_INS 11 319 (0) C AluY SINE/Alu (0) 311 1 633
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_45318871_45319189_INS 11 38 281 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_45318871_45319189_INS 11 38 (281) (T)n#Simple_repeat 1 28 (0) c_b1s251i68
X_45318871_45 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 38
(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)
2550 2.14 0.00 0.00 X_45318871_45319189_INS 39 319 0 C AluY SINE/Alu 1 281 30
2550 2.14 0.00 0.00 X_45318871_45319189_INS 39 319 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i91
X_45318871_45 39 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 88
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_45318871_45 89 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 138
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_45318871_45 139 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 188
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_45318871_45 189 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGC 238
v i i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_45318871_45 239 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 288
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_45318871_45 289 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 319
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.84
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 36 11.5 7.7 0.0 X_45580443_45580527_INS 8 85 (0) + (ATATGC)n Simple_repeat 1 84 (0) 634
ANNOTATION EVIDENCE:
36 11.48 7.69 0.00 X_45580443_45580527_INS 8 85 0 + (ATATGC)n Simple_repeat 1 84 0
36 11.48 7.69 0.00 X_45580443_45580527_INS 8 85 (0) (ATATGC)n#Simple_repeat 1 84 (0) m_b1s252i36
X_45580443_45 8 ATATGCATATGCATAT--ATATACACATATATATGCATATGCATAT--AT 53
-- i i ii --
(ATATGC)n#Sim 1 ATATGCATATGCATATGCATATGCATATGCATATGCATATGCATATGCAT 50
X_45580443_45 54 ATACACATATATATGCATATGCATAT--ATATGC 85
i i ii --
(ATATGC)n#Sim 51 ATGCATATGCATATGCATATGCATATGCATATGC 84
Matrix = Unknown
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.04 (3 / 77), avg. gap size = 2.00 (6 / 3)
+ 36 6.2 5.6 2.7 X_45589348_45589427_INS 1 72 (8) + (AT)n Simple_repeat 1 74 (0) 635
ANNOTATION EVIDENCE:
36 6.15 5.56 2.70 X_45589348_45589427_INS 1 72 8 + (AT)n Simple_repeat 1 74 0
36 6.15 5.56 2.70 X_45589348_45589427_INS 1 72 (8) (AT)n#Simple_repeat 1 74 (0) c_b1s251i67
X_45589348_45 1 ATATATATATATATATAT-TTTA-AGACTATATATATATATATATATAT- 47
- v - v - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATA-TATATATATATATATATATATA 49
X_45589348_45 48 TTTA-AGACTATATATATATATATAT 72
v - v -
(AT)n#Simple_ 50 TATATATA-TATATATATATATATAT 74
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6)
+ 49 2.2 0.0 0.0 X_45606303_45606354_INS 7 52 (0) + (TG)n Simple_repeat 1 46 (0) 636
ANNOTATION EVIDENCE:
49 2.21 0.00 0.00 X_45606303_45606354_INS 7 52 0 + (TG)n Simple_repeat 1 46 0
49 2.21 0.00 0.00 X_45606303_45606354_INS 7 52 (0) (TG)n#Simple_repeat 1 46 (0) c_b1s251i66
X_45606303_45 7 TGTGTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTG 52
v
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 46
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 22 29.4 0.0 0.0 X_46078882_46078942_INS 7 60 (1) + (AT)n Simple_repeat 1 54 (0) 637
ANNOTATION EVIDENCE:
22 29.39 0.00 0.00 X_46078882_46078942_INS 7 60 1 + (AT)n Simple_repeat 1 54 0
22 29.39 0.00 0.00 X_46078882_46078942_INS 7 60 (1) (AT)n#Simple_repeat 1 54 (0) m_b1s252i35
X_46078882_46 7 ATATATACACATATGTGTATATATGCACACATATATACACATATGTGTAT 56
i i i i ii i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_46078882_46 57 ATAT 60
(AT)n#Simple_ 51 ATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 2674 3.3 0.0 2.6 X_4619083_4619409_INS 16 327 (0) + AluY SINE/Alu 1 304 (7) 638
ANNOTATION EVIDENCE:
2674 3.30 0.00 2.63 X_4619083_4619409_INS 16 327 0 + AluY SINE/Alu 1 304 7
2674 3.30 0.00 2.63 X_4619083_4619409_INS 16 327 (0) AluY#SINE/Alu 1 304 (7) c_b1s352i92
X_4619083_461 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_4619083_461 66 GGCGGGCGGATCACAAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 115
i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_4619083_461 116 TGAAACCCCGTCTCTACTAAAACTACAAAAAAAAAAAAAATTAGCCGGGC 165
v --------
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA--------AATTAGCCGGGC 142
X_4619083_461 166 ATGGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAG 215
i i
AluY#SINE/Alu 143 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAG 192
X_4619083_461 216 AATGGCGTGAACCCGGGAGGCAGAGCTTGCAGTGAGCCAAGATCGTGCCA 265
i i i
AluY#SINE/Alu 193 AATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCA 242
X_4619083_461 266 CTACACTCCAGCCTGGGTGACAGAGCAAGACTCCGTCTCAAAAAAAAAAA 315
i i i
AluY#SINE/Alu 243 CTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
X_4619083_461 316 AAAAAAAAAAAA 327
AluY#SINE/Alu 293 AAAAAAAAAAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.93
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.03 (8 / 311), avg. gap size = 1.00 (8 / 8)
+ 33 2.0 7.7 0.0 X_46239712_46239764_INS 2 53 (0) + (AAGA)n Simple_repeat 1 56 (0) 639
ANNOTATION EVIDENCE:
33 1.96 7.69 0.00 X_46239712_46239764_INS 2 53 0 + (AAGA)n Simple_repeat 1 56 0
33 1.96 7.69 0.00 X_46239712_46239764_INS 2 53 (0) (AAGA)n#Simple_repeat 1 56 (0) m_b1s252i34
X_46239712_46 2 AAGAAAGAAAGAAAGAAAG--AGAAAGAAAGGAAGAAAGAAAG--AGAAA 47
-- i --
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
X_46239712_46 48 GAAAGA 53
(AAGA)n#Simpl 51 GAAAGA 56
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 2.00 (4 / 2)
+ 36 1.9 3.5 3.5 X_46244196_46244255_INS 3 60 (0) + (TATAATA)n Simple_repeat 1 58 (0) 640
ANNOTATION EVIDENCE:
36 1.87 3.45 3.45 X_46244196_46244255_INS 3 60 0 + (TATAATA)n Simple_repeat 1 58 0
36 1.87 3.45 3.45 X_46244196_46244255_INS 3 60 (0) (TATAATA)n#Simple_repeat 1 58 (0) m_b1s252i33
X_46244196_46 3 TATAATATATAAT-TATAATATATATTATATATAATATATAAT-TATAAT 50
- -- -
(TATAATA)n#Si 1 TATAATATATAATATATAATATATA--ATATATAATATATAATATATAAT 48
X_46244196_46 51 ATATATTATA 60
v
(TATAATA)n#Si 49 ATATAATATA 58
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4)
+ 53 0.0 1.8 1.8 X_46378658_46378714_INS 1 56 (1) + (TAGA)n Simple_repeat 1 56 (0) 641
ANNOTATION EVIDENCE:
53 0.00 1.79 1.79 X_46378658_46378714_INS 1 56 1 + (TAGA)n Simple_repeat 1 56 0
53 0.00 1.79 1.79 X_46378658_46378714_INS 1 56 (1) (TAGA)n#Simple_repeat 1 56 (0) c_b1s251i65
X_46378658_46 1 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAAGATAGAT-GAT 49
- -
(TAGA)n#Simpl 1 TAGATAGATAGATAGATAGATAGATAGATAGATAGAT-AGATAGATAGAT 49
X_46378658_46 50 AGATAGA 56
(TAGA)n#Simpl 50 AGATAGA 56
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2)
+ 3712 1.2 0.2 0.0 X_4659602_4660053_INS 1 12 (440) C L1HS LINE/L1 (2) 6153 6142 642
ANNOTATION EVIDENCE:
3712 1.20 0.24 0.00 X_4659602_4660053_INS 1 12 440 C L1HS_3end LINE/L1 889 900 2
3712 1.20 0.24 0.00 X_4659602_4660053_INS 1 12 (440) C L1HS_3end#LINE/L1 (2) 900 889 m_b1s551i15
X_4659602_466 1 TTTTTTTTTTCA 12
i
C L1HS_3end#LIN 900 TTTTTTTTTTTA 889
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.21
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 11), avg. gap size = 0.0 (0 / 0)
+ 29 0.0 2.8 2.8 X_4659602_4660053_INS 13 48 (404) + (TTTAT)n Simple_repeat 1 36 (0) 643
ANNOTATION EVIDENCE:
29 0.00 2.78 2.78 X_4659602_4660053_INS 13 48 404 + (TTTAT)n Simple_repeat 1 36 0
29 0.00 2.78 2.78 X_4659602_4660053_INS 13 48 (404) (TTTAT)n#Simple_repeat 1 36 (0) c_b1s251i64
X_4659602_466 13 TTTATTTTTATTTTATTTTATTTTATTTT-TTTTATT 48
- -
(TTTAT)n#Simp 1 TTTA-TTTTATTTTATTTTATTTTATTTTATTTTATT 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2)
+ 3712 1.2 0.2 0.0 X_4659602_4660053_INS 49 452 (0) C L1HS LINE/L1 (14) 6141 5737 642
ANNOTATION EVIDENCE:
3712 1.20 0.24 0.00 X_4659602_4660053_INS 49 452 0 C L1HS_3end LINE/L1 484 888 14
3712 1.20 0.24 0.00 X_4659602_4660053_INS 49 452 (0) C L1HS_3end#LINE/L1 (14) 888 484 m_b1s551i15
X_4659602_466 49 -ATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACAT 97
-
C L1HS_3end#LIN 888 TATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACAT 839
X_4659602_466 98 ATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTA 147
vi
C L1HS_3end#LIN 838 ATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACGTGTCATCTA 789
X_4659602_466 148 GCATTAGGTATATCTCCCAATACTATCCCTCCCCCCTCCCCCGACCCCAC 197
i
C L1HS_3end#LIN 788 GCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCAC 739
X_4659602_466 198 CACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCAT 247
C L1HS_3end#LIN 738 CACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCAT 689
X_4659602_466 248 TGTTCAATTCCCACCTATCAGTGAGAATATGCGGTGTTTGGTTTTTTGTT 297
v
C L1HS_3end#LIN 688 TGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTT 639
X_4659602_466 298 CTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCT 347
C L1HS_3end#LIN 638 CTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCT 589
X_4659602_466 348 ACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGT 397
C L1HS_3end#LIN 588 ACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGT 539
X_4659602_466 398 GTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGG 447
C L1HS_3end#LIN 538 GTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGG 489
X_4659602_466 448 GTTGG 452
C L1HS_3end#LIN 488 GTTGG 484
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.21
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (1 / 403), avg. gap size = 1.00 (1 / 1)
+ 16 47.8 0.0 0.0 X_46707212_46707292_INS 3 80 (1) + (TA)n Simple_repeat 1 78 (0) 644
ANNOTATION EVIDENCE:
16 47.78 0.00 0.00 X_46707212_46707292_INS 3 80 1 + (TA)n Simple_repeat 1 78 0
16 47.78 0.00 0.00 X_46707212_46707292_INS 3 80 (1) (TA)n#Simple_repeat 1 78 (0) m_b1s252i32
X_46707212_46 3 TATATACACACATATGTGTGTGTGTATATACACACGTGTGTGTGTATATA 52
i i i i i i i i i i ii i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_46707212_46 53 CACACATATGTGTGTGTGTATATATATA 80
i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATA 78
Matrix = Unknown
Transitions / transversions = 1.00 (24/0)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 532 7.3 0.0 0.0 X_46810804_46810957_INS 1 68 (86) C AluSx SINE/Alu (244) 68 1 645
ANNOTATION EVIDENCE:
532 7.35 0.00 0.00 X_46810804_46810957_INS 1 68 86 C AluSx SINE/Alu 1 68 244
532 7.35 0.00 0.00 X_46810804_46810957_INS 1 68 (86) C AluSx#SINE/Alu (244) 68 1 m_b1s357i6
X_46810804_46 1 TCAAGTGATCCGCCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCAT 50
i i i
C AluSx#SINE/Al 68 TCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 19
X_46810804_46 51 GAGCCACCGCACCCAGCC 68
i i
C AluSx#SINE/Al 18 GAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.10
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 771 3.4 0.0 0.0 X_46810804_46810957_INS 69 154 (0) + AluSx SINE/Alu 24 109 (203) 646
ANNOTATION EVIDENCE:
771 3.37 0.00 0.00 X_46810804_46810957_INS 66 154 0 + AluSx SINE/Alu 21 109 203
771 3.37 0.00 0.00 X_46810804_46810957_INS 66 154 (0) AluSx#SINE/Alu 21 109 (203) m_b1s357i7
X_46810804_46 66 GCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACTTGAGG 115
i i i
AluSx#SINE/Al 21 GCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGG 70
X_46810804_46 116 TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACC 154
AluSx#SINE/Al 71 TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACC 109
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 1.37
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
+ 34 8.0 3.7 0.0 X_46858838_46858893_INS 1 54 (2) + (TA)n Simple_repeat 1 56 (0) 647
ANNOTATION EVIDENCE:
34 8.02 3.70 0.00 X_46858838_46858893_INS 1 54 2 + (TA)n Simple_repeat 1 56 0
34 8.02 3.70 0.00 X_46858838_46858893_INS 1 54 (2) (TA)n#Simple_repeat 1 56 (0) c_b1s251i63
X_46858838_46 1 TATATATACATATATA-ACATATATATATATATATA-ACATATATATACA 48
i - i - i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_46858838_46 49 TATATA 54
(TA)n#Simple_ 51 TATATA 56
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2)
+ 59 0.0 0.0 0.0 X_46950360_46950423_INS 12 64 (0) + (GAAA)n Simple_repeat 1 53 (0) 648
ANNOTATION EVIDENCE:
59 0.00 0.00 0.00 X_46950360_46950423_INS 12 64 0 + (GAAA)n Simple_repeat 1 53 0
59 0.00 0.00 0.00 X_46950360_46950423_INS 12 64 (0) (GAAA)n#Simple_repeat 1 53 (0) c_b1s251i62
X_46950360_46 12 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 61
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50
X_46950360_46 62 AAG 64
(GAAA)n#Simpl 51 AAG 53
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 33 5.2 0.0 0.0 X_47183843_47184043_INS 16 55 (146) + (T)n Simple_repeat 1 40 (0) 649
ANNOTATION EVIDENCE:
33 5.20 0.00 0.00 X_47183843_47184043_INS 16 55 146 + (T)n Simple_repeat 1 40 0
33 5.20 0.00 0.00 X_47183843_47184043_INS 16 55 (146) (T)n#Simple_repeat 1 40 (0) c_b1s251i61
X_47183843_47 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTATTTTT 55
v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 1277 0.7 0.0 1.4 X_47183843_47184043_INS 56 201 (0) C SVA_E Retroposon/SVA (20) 1362 1219 650
ANNOTATION EVIDENCE:
1277 0.69 0.00 1.39 X_47183843_47184043_INS 56 201 0 C SVA_E Retroposon/SVA 1219 1362 20
1277 0.69 0.00 1.39 X_47183843_47184043_INS 56 201 (0) C SVA_E#Retroposon/SVA (20) 1362 1219 m_b1s502i8
X_47183843_47 56 ATTGATCATTCTTGGGTGTTTCTCGCAGAGGGGGATTTGGCAGGGTCATA 105
C SVA_E#Retropo 1362 ATTGATCATTCTTGGGTGTTTCTCGCAGAGGGGGATTTGGCAGGGTCATA 1313
X_47183843_47 106 GGACAATAGTGGAGGGAAGGTCAGCAGATATAAACAAGTGAACAAAGGTC 155
--
C SVA_E#Retropo 1312 GGACAATAGTGGAGGGAAGGTCAGCAG--ATAAACAAGTGAACAAAGGTC 1265
X_47183843_47 156 TCTGGTTTTCCTAGGCAGAGGACCCTGCGGCCTTCCGCAGCGTTTG 201
i
C SVA_E#Retropo 1264 TCTGGTTTTCCTAGGCAGAGGACCCTGCGGCCTTCCGCAGTGTTTG 1219
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.70
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.01 (2 / 145), avg. gap size = 1.00 (2 / 2)
+ 2947 0.6 0.0 0.0 X_4718491_4718820_INS 6 316 (14) + AluY SINE/Alu 1 311 (0) 651
ANNOTATION EVIDENCE:
2947 0.64 0.00 0.00 X_4718491_4718820_INS 6 316 14 + AluY SINE/Alu 1 311 0
2947 0.64 0.00 0.00 X_4718491_4718820_INS 6 316 (14) AluY#SINE/Alu 1 311 (0) c_b1s352i93
X_4718491_471 6 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 55
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_4718491_471 56 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATTCTGGCTAACACGG 105
i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_4718491_471 106 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 155
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_4718491_471 156 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 205
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_4718491_471 206 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 255
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_4718491_471 256 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 305
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_4718491_471 306 AAAAAAAAAAA 316
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.65
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 2461 2.4 4.1 0.3 X_47194610_47194914_INS 16 305 (0) + AluY SINE/Alu 1 301 (10) 652
ANNOTATION EVIDENCE:
2461 2.42 4.14 0.33 X_47194610_47194914_INS 16 305 0 + AluY SINE/Alu 1 301 10
2461 2.42 4.14 0.33 X_47194610_47194914_INS 16 305 (0) AluY#SINE/Alu 1 301 (10) c_b1s352i94
X_47194610_47 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_47194610_47 66 GGCGGGCGGATCATGAGGTCAGGAGATCGAGACCA------------CGG 103
i ------------
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_47194610_47 104 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGCAGTGG 153
- ii
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_47194610_47 154 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGAGAATGGCG 203
i
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_47194610_47 204 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCAGTGCACT 253
v
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_47194610_47 254 CCCGCCTGGGCGACAGAACGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 303
v i
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_47194610_47 304 AA 305
AluY#SINE/Alu 300 AA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.15
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.01 (2 / 289), avg. gap size = 6.50 (13 / 2)
+ 35 2.8 0.0 0.0 X_47213231_47213320_INS 9 45 (45) + (CTTT)n Simple_repeat 1 37 (0) 653
ANNOTATION EVIDENCE:
35 2.76 0.00 0.00 X_47213231_47213320_INS 9 45 45 + (CTTT)n Simple_repeat 1 37 0
35 2.76 0.00 0.00 X_47213231_47213320_INS 9 45 (45) (CTTT)n#Simple_repeat 1 37 (0) c_b1s251i60
X_47213231_47 9 CTTTCTTTCTTTCTTTCTTTCTTTCTGTCTTTCTTTC 45
v
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 37
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 16 0.0 6.9 3.3 X_47213231_47213320_INS 62 90 (0) + (TCTT)n Simple_repeat 1 30 (0) 654
ANNOTATION EVIDENCE:
16 0.00 6.90 3.33 X_47213231_47213320_INS 62 90 0 + (TCTT)n Simple_repeat 1 30 0
16 0.00 6.90 3.33 X_47213231_47213320_INS 62 90 (0) (TCTT)n#Simple_repeat 1 30 (0) m_b1s252i31
X_47213231_47 62 TCTTTC--TCTTTCTTTTCTTTCTTTCTTTC 90
-- -
(TCTT)n#Simpl 1 TCTTTCTTTCTTTC-TTTCTTTCTTTCTTTC 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.50 (3 / 2)
+ 57 1.8 0.0 0.0 X_47519504_47519560_INS 2 57 (0) + (CCTT)n Simple_repeat 1 56 (0) 655
ANNOTATION EVIDENCE:
57 1.81 0.00 0.00 X_47519504_47519560_INS 2 57 0 + (CCTT)n Simple_repeat 1 56 0
57 1.81 0.00 0.00 X_47519504_47519560_INS 2 57 (0) (CCTT)n#Simple_repeat 1 56 (0) c_b1s251i59
X_47519504_47 2 CCTTCCTTCCTTCCTTCCGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 51
v
(CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 50
X_47519504_47 52 TTCCTT 57
(CCTT)n#Simpl 51 TTCCTT 56
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 2706 3.0 0.3 0.0 X_47708079_47708395_INS 15 317 (0) C AluY SINE/Alu (6) 305 2 656
ANNOTATION EVIDENCE:
2706 2.97 0.33 0.00 X_47708079_47708395_INS 15 317 0 C AluY SINE/Alu 2 305 6
2706 2.97 0.33 0.00 X_47708079_47708395_INS 15 317 (0) C AluY#SINE/Alu (6) 305 2 c_b1s352i95
X_47708079_47 15 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTGTCGCCCA 64
i
C AluY#SINE/Alu 305 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 256
X_47708079_47 65 GGCTGGAGTGCAGTGGCGCGATCTCGACTCACTGCAAGCTCCGCCTCCCG 114
i
C AluY#SINE/Alu 255 GGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCG 206
X_47708079_47 115 GGTTCACGCCATTCTCCTGCCTCAGCCTCCTGTGTAGCTGGGACTACAGG 164
i v
C AluY#SINE/Alu 205 GGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 156
X_47708079_47 165 CACGCGCCACCATGCCCGGCTAAT-TTTTGTATTTTTAGTAGAGACGGGG 213
i v i -
C AluY#SINE/Alu 155 CGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGG 106
X_47708079_47 214 TTTCACCGTGTTAGCCAGGATGGTCTCGATCTTCTGACCTCGTGATCCGC 263
i
C AluY#SINE/Alu 105 TTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGC 56
X_47708079_47 264 CCGTCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 313
i
C AluY#SINE/Alu 55 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 6
X_47708079_47 314 CGGC 317
C AluY#SINE/Alu 5 CGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.11
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (1 / 302), avg. gap size = 1.00 (1 / 1)
+ 2676 2.0 0.0 0.3 X_47771485_47771780_INS 1 296 (0) C AluY SINE/Alu (8) 303 9 657
ANNOTATION EVIDENCE:
2676 2.04 0.00 0.34 X_47771485_47771780_INS 1 296 0 C AluY SINE/Alu 9 303 8
2676 2.04 0.00 0.34 X_47771485_47771780_INS 1 296 (0) C AluY#SINE/Alu (8) 303 9 c_b1s352i96
X_47771485_47 1 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGG 50
C AluY#SINE/Alu 303 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGG 254
X_47771485_47 51 CTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGG 100
v
C AluY#SINE/Alu 253 CTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGG 204
X_47771485_47 101 TTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCG 150
i
C AluY#SINE/Alu 203 TTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCG 154
X_47771485_47 151 CCCGCCACTACGCCCGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGT 200
i -
C AluY#SINE/Alu 153 CCCGCCACCACGCCCGGCTAATT-TTTTGTATTTTTAGTAGAGACGGGGT 105
X_47771485_47 201 TTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTTGTGATCCGCC 250
v i i
C AluY#SINE/Alu 104 TTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCC 55
X_47771485_47 251 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 296
C AluY#SINE/Alu 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.44
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (1 / 295), avg. gap size = 1.00 (1 / 1)
+ 272 19.7 0.0 2.8 X_47844451_47844524_INS 1 73 (1) + L1MC LINE/L1 5617 5687 (2355) 658
ANNOTATION EVIDENCE:
272 19.74 0.00 2.82 X_47844451_47844524_INS 1 73 1 + L1MC4_3end LINE/L1 364 434 2355
272 19.74 0.00 2.82 X_47844451_47844524_INS 1 73 (1) L1MC4_3end#LINE/L1 364 434 (2355) m_b1s551i16
X_47844451_47 1 TACAACCCTGCAATCCCACTCCCACGTTTATTTACCTCAGTGAAATGCAA 50
ii v ? i v -- iv ? ? v
L1MC4_3end#LI 364 TATGACCCAGCAATCNCACTCCTAGGT--ATTTACCCAAGNGAANTGAAA 411
X_47844451_47 51 ACTTAGGTAAACCTAAAAGCCTG 73
? v vv vi i
L1MC4_3end#LI 412 ACNTATGTCCACACAAAAACCTG 434
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.55
Transitions / transversions = 0.75 (6/8)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2)
+ 393 8.2 8.2 0.0 X_47876579_47876663_INS 1 85 (0) + SVA_C Retroposon/SVA 705 796 (588) 659
ANNOTATION EVIDENCE:
393 8.24 8.24 0.00 X_47876579_47876663_INS 1 85 0 + SVA_C Retroposon/SVA 705 796 588
393 8.24 8.24 0.00 X_47876579_47876663_INS 1 85 (0) SVA_C#Retroposon/SVA 705 796 (588) m_b1s502i9
X_47876579_47 1 TCAGCCCCT-GCGCAGCCAGCCGCCCTGTCTGGGAGG---TGGGGGG--C 44
i- v i i i --- --
SVA_C#Retropo 705 TCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGAGGTGGGGGGGTC 754
X_47876579_47 45 AGCCCC-CGCCCGGCCAGCCGCCCCATCCGGGAAGTGGGGGG 85
- i i
SVA_C#Retropo 755 AGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGGGGGG 796
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.13
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.75 (7 / 4)
+ 393 8.2 8.2 0.0 X_47998840_47998924_INS 1 85 (0) + SVA_C Retroposon/SVA 705 796 (588) 660
ANNOTATION EVIDENCE:
393 8.24 8.24 0.00 X_47998840_47998924_INS 1 85 0 + SVA_C Retroposon/SVA 705 796 588
393 8.24 8.24 0.00 X_47998840_47998924_INS 1 85 (0) SVA_C#Retroposon/SVA 705 796 (588) m_b1s502i10
X_47998840_47 1 TCAGCCCCT-GCGCAGCCAGCCGCCCTGTCTGGGAGG---TGGGGGG--C 44
i- v i i i --- --
SVA_C#Retropo 705 TCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGAGGTGGGGGGGTC 754
X_47998840_47 45 AGCCCC-CGCCCGGCCAGCCGCCCCATCCGGGAAGTGGGGGG 85
- i i
SVA_C#Retropo 755 AGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGGGGGG 796
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.13
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.75 (7 / 4)
+ 658 9.1 2.4 3.2 X_48082068_48082195_INS 2 126 (2) + SVA_A Retroposon/SVA 632 755 (632) 661
ANNOTATION EVIDENCE:
658 9.09 2.40 3.23 X_48082068_48082195_INS 2 126 2 + SVA_A Retroposon/SVA 632 755 632
658 9.09 2.40 3.23 X_48082068_48082195_INS 2 126 (2) SVA_A#Retroposon/SVA 632 755 (632) m_b1s502i11
X_48082068_48 2 CCTCTGCCAGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCC 51
i v vv ? v i i
SVA_A#Retropo 632 CCTCCGCCCGGCCGCCCCGTCTGGGANGTGAGGAGCGCCTCCGCCCGGCC 681
X_48082068_48 52 AGCTGCCCCGTCCGGGAGGGAGGTGGGGAGGTCAGCCCCCCGCCCGGCCA 101
i ---- i
SVA_A#Retropo 682 AGCCGCCCCGTCC----GGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCA 727
X_48082068_48 102 GCCACCCCGTCCG---GGAGGTGAGGGG 126
i --- i
SVA_A#Retropo 728 GCCGCCCCGTCCGGGAGGAGGTGGGGGG 755
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.62
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.04 (5 / 124), avg. gap size = 1.40 (7 / 5)
+ 33 2.2 0.0 8.0 X_48501435_48501495_INS 8 61 (0) + (TATATATAG)n Simple_repeat 1 50 (0) 662
ANNOTATION EVIDENCE:
33 2.21 0.00 8.00 X_48501435_48501495_INS 8 61 0 + (TATATATAG)n Simple_repeat 1 50 0
33 2.21 0.00 8.00 X_48501435_48501495_INS 8 61 (0) (TATATATAG)n#Simple_repeat 1 50 (0) c_b1s251i58
X_48501435_48 8 TATATATAGTATATATATTCTATATATAGTATATATATGCTATATATAGT 57
--v - -
(TATATATAG)n# 1 TATATATAGTATATATA--GTATATATAGTATATATA-G-TATATATAGT 46
X_48501435_48 58 ATAT 61
(TATATATAG)n# 47 ATAT 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4)
+ 57 0.0 0.0 0.0 X_48799501_48799588_INS 2 50 (38) + (AC)n Simple_repeat 1 49 (0) 663
ANNOTATION EVIDENCE:
57 0.00 0.00 0.00 X_48799501_48799588_INS 2 50 38 + (AC)n Simple_repeat 1 49 0
57 0.00 0.00 0.00 X_48799501_48799588_INS 2 50 (38) (AC)n#Simple_repeat 1 49 (0) c_b1s251i57
X_48799501_48 2 ACACACACACACACACACACACACACACACACACACACACACACACACA 50
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACA 49
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 18 0.0 0.0 0.0 X_48799501_48799588_INS 69 88 (0) + (AC)n Simple_repeat 1 20 (0) 663
ANNOTATION EVIDENCE:
18 0.00 0.00 0.00 X_48799501_48799588_INS 69 88 0 + (AC)n Simple_repeat 1 20 0
18 0.00 0.00 0.00 X_48799501_48799588_INS 69 88 (0) (AC)n#Simple_repeat 1 20 (0) m_b1s252i30
X_48799501_48 69 ACACACACACACACACACAC 88
(AC)n#Simple_ 1 ACACACACACACACACACAC 20
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 371 8.2 0.0 0.0 X_4880807_4880857_INS 2 50 (1) C L1PB1 LINE/L1 (53) 6098 6050 664
ANNOTATION EVIDENCE:
371 8.16 0.00 0.00 X_4880807_4880857_INS 2 50 1 C L1PB1_3end LINE/L1 797 845 53
371 8.16 0.00 0.00 X_4880807_4880857_INS 2 50 (1) C L1PB1_3end#LINE/L1 (53) 845 797 m_b1s551i17
X_4880807_488 2 AAGCTCTTTAGTGGTGATTTGTGAGATTTTTGCGCACCTATCACCCGAG 50
i ? v i i
C L1PB1_3end#LI 845 AAGTTCTTTAGTGGTGATTTNTGAGATTTTGGTGCACCCATCACCCGAG 797
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.95
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 17 5.0 0.0 0.0 X_48971859_48972429_INS 4 24 (547) + (A)n Simple_repeat 1 21 (0) 665
ANNOTATION EVIDENCE:
17 5.00 0.00 0.00 X_48971859_48972429_INS 4 24 267 + (A)n Simple_repeat 1 21 0
17 5.00 0.00 0.00 X_48971859_48972429_INS 4 24 (267) (A)n#Simple_repeat 1 21 (0) m_b1s252i29
X_48971859_48 4 AAAAAAAAAAAAAAAAAAGAA 24
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 2274 8.9 0.0 0.4 X_48971859_48972429_INS 291 571 (0) + AluSx SINE/Alu 1 280 (32) 666
ANNOTATION EVIDENCE:
2274 8.93 0.00 0.36 X_48971859_48972429_INS 291 571 0 + AluSx SINE/Alu 1 280 32
2274 8.93 0.00 0.36 X_48971859_48972429_INS 291 571 (0) AluSx#SINE/Alu 1 280 (32) c_b1s352i97
X_48971859_48 291 GGCCGAGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGA 340
i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_48971859_48 341 GGTGGGAGGATCACTTAAGGTCAGGAGTTCCAAGACCAGCATGGTCAACA 390
i v i i -i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTC-GAGACCAGCCTGGCCAACA 99
X_48971859_48 391 TGGTGAAACCCTGTCTCTACTAAAAACACAAAAATTAGCCAGGTGTGGTG 440
i i i i
AluSx#SINE/Al 100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTG 149
X_48971859_48 441 ACGCTTGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAAAATCGC 490
i vi i
AluSx#SINE/Al 150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199
X_48971859_48 491 TTGAACCTGGGAAGTGGAGGTTGCAGTGAGCTGAGATCACGCCACTGCAC 540
i i i i i
AluSx#SINE/Al 200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249
X_48971859_48 541 TCCAGCCTGGGTGACAGAGTGAGACTCTGTC 571
i i i
AluSx#SINE/Al 250 TCCAGCCTGGGCGACAGAGCGAGACTCCGTC 280
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.94
Transitions / transversions = 7.33 (22/3)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 2669 3.2 0.0 2.2 X_4916690_4917019_INS 12 329 (1) C AluY SINE/Alu (0) 311 1 667
ANNOTATION EVIDENCE:
2669 3.21 0.00 2.25 X_4916690_4917019_INS 12 329 1 C AluY SINE/Alu 1 311 0
2669 3.21 0.00 2.25 X_4916690_4917019_INS 12 329 (1) C AluY#SINE/Alu (0) 311 1 c_b1s352i98
X_4916690_491 12 TTCTTCTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 61
i i
C AluY#SINE/Alu 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 262
X_4916690_491 62 CGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAA 111
i ----- -- i
C AluY#SINE/Alu 261 CGCCCAGGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAA 219
X_4916690_491 112 GCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCCAGTAG 161
i v
C AluY#SINE/Alu 218 GCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAG 169
X_4916690_491 162 CTGGGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTT 211
i
C AluY#SINE/Alu 168 CTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTT 119
X_4916690_491 212 AGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGA 261
v
C AluY#SINE/Alu 118 AGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGA 69
X_4916690_491 262 CCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 311
i i
C AluY#SINE/Alu 68 CCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 19
X_4916690_491 312 GAGCCACCGCGCCCGGCC 329
C AluY#SINE/Alu 18 GAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.39
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.00 (7 / 7)
+ 53 0.0 2.0 0.0 X_4929235_4929286_INS 2 52 (0) + (TTTC)n Simple_repeat 1 52 (0) 668
ANNOTATION EVIDENCE:
53 0.00 1.96 0.00 X_4929235_4929286_INS 2 52 0 + (TTTC)n Simple_repeat 1 52 0
53 0.00 1.96 0.00 X_4929235_4929286_INS 2 52 (0) (TTTC)n#Simple_repeat 1 52 (0) c_b1s251i56
X_4929235_492 2 TTTCTTTCTTTCTTTCTTT-TTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
-
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_4929235_492 51 TC 52
(TTTC)n#Simpl 51 TC 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 48 4.2 0.0 0.0 X_4933131_4933181_INS 1 50 (1) + (TA)n Simple_repeat 1 50 (0) 669
ANNOTATION EVIDENCE:
48 4.17 0.00 0.00 X_4933131_4933181_INS 1 50 1 + (TA)n Simple_repeat 1 50 0
48 4.17 0.00 0.00 X_4933131_4933181_INS 1 50 (1) (TA)n#Simple_repeat 1 50 (0) c_b1s251i55
X_4933131_493 1 TATATATATATACATATATATATATATATATGTATATATATATATATATA 50
i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 2757 2.0 0.0 0.0 X_49411784_49412096_INS 14 313 (0) C AluY SINE/Alu (10) 301 2 670
ANNOTATION EVIDENCE:
2757 2.00 0.00 0.00 X_49411784_49412096_INS 14 313 0 C AluY SINE/Alu 2 301 10
2757 2.00 0.00 0.00 X_49411784_49412096_INS 14 313 (0) C AluY#SINE/Alu (10) 301 2 c_b1s352i99
X_49411784_49 14 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT 63
C AluY#SINE/Alu 301 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT 252
X_49411784_49 64 GGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTT 113
v
C AluY#SINE/Alu 251 GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTT 202
X_49411784_49 114 CACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCC 163
i
C AluY#SINE/Alu 201 CACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCC 152
X_49411784_49 164 CGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTC 213
i
C AluY#SINE/Alu 151 CGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTC 102
X_49411784_49 214 ACCATTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGC 263
i v i
C AluY#SINE/Alu 101 ACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGC 52
X_49411784_49 264 CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 313
C AluY#SINE/Alu 51 CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 299), avg. gap size = 0.0 (0 / 0)
+ 47 7.0 0.0 0.0 X_49471148_49471208_INS 2 61 (0) + (TCT)n Simple_repeat 1 60 (0) 671
ANNOTATION EVIDENCE:
47 7.03 0.00 0.00 X_49471148_49471208_INS 2 61 0 + (TCT)n Simple_repeat 1 60 0
47 7.03 0.00 0.00 X_49471148_49471208_INS 2 61 (0) (TCT)n#Simple_repeat 1 60 (0) c_b1s251i54
X_49471148_49 2 TCTTCTTCTTCTTCTTCTTGTTCTTGTTCTTGTTCTTGTTCTTCTTCTTC 51
v v v v
(TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 50
X_49471148_49 52 TTCTTCTTCT 61
(TCT)n#Simple 51 TTCTTCTTCT 60
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 2665 2.6 0.0 2.3 X_4953832_4954151_INS 9 320 (0) C AluY SINE/Alu (6) 305 1 672
ANNOTATION EVIDENCE:
2665 2.62 0.00 2.30 X_4953832_4954151_INS 9 320 0 C AluY SINE/Alu 1 305 6
2665 2.62 0.00 2.30 X_4953832_4954151_INS 9 320 (0) C AluY#SINE/Alu (6) 305 1 c_b1s352i100
X_4953832_495 9 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 58
C AluY#SINE/Alu 305 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 256
X_4953832_495 59 GGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCG 108
i ----- -- i
C AluY#SINE/Alu 255 GGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCG 213
X_4953832_495 109 CTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCCAGTAGCTGGGA 158
i v
C AluY#SINE/Alu 212 CCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGA 163
X_4953832_495 159 CTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGA 208
i
C AluY#SINE/Alu 162 CTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGA 113
X_4953832_495 209 GACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCAT 258
i
C AluY#SINE/Alu 112 GACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGT 63
X_4953832_495 259 GATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGACTACAGGCGTGAGCCA 308
i i
C AluY#SINE/Alu 62 GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA 13
X_4953832_495 309 CCGCGCCCGGCC 320
C AluY#SINE/Alu 12 CCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.76
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.02 (7 / 311), avg. gap size = 1.00 (7 / 7)
+ 33 15.0 0.0 0.0 X_50625175_50625229_INS 2 55 (0) + (TA)n Simple_repeat 1 54 (0) 673
ANNOTATION EVIDENCE:
33 15.01 0.00 0.00 X_50625175_50625229_INS 2 55 0 + (TA)n Simple_repeat 1 54 0
33 15.01 0.00 0.00 X_50625175_50625229_INS 2 55 (0) (TA)n#Simple_repeat 1 54 (0) m_b1s252i28
X_50625175_50 2 TATATATATATGTATATATATGTGTATATATATATATACACGTATATATA 51
i i i i ii
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_50625175_50 52 TGTA 55
i
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 287 22.1 2.9 0.0 X_5064430_5064533_INS 1 68 (36) + MLT2B1 LTR/ERVL 457 526 (41) 674
ANNOTATION EVIDENCE:
287 22.06 2.94 0.00 X_5064430_5064533_INS 1 68 36 + MLT2B1 LTR/ERVL 410 479 41
287 22.06 2.94 0.00 X_5064430_5064533_INS 1 68 (36) MLT2B1#LTR/ERVL 410 479 (41) m_b1s502i12
X_5064430_506 1 GACTTCTGAGCCTTCCTCATAGTGTGAATCAACTCCTTATAATAAA--TG 48
v i v v v i ii i i -- v
MLT2B1#LTR/ER 410 GACTTCTCAGCCTCCATAATCGCGTGAGCCAATTCCTCATAATAAATCTC 459
X_5064430_506 49 TTGTTATATGACTATATATA 68
vi iv
MLT2B1#LTR/ER 460 TTTCTATATATCTATATATA 479
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.44
Transitions / transversions = 1.14 (8/7)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 2.00 (2 / 1)
+ 799 13.0 0.8 0.0 X_50710534_50710674_INS 9 139 (2) C ALR/Alpha Satellite/centr (0) 171 40 675
ANNOTATION EVIDENCE:
799 12.98 0.76 0.00 X_50710534_50710674_INS 9 139 2 C ALR Satellite/centromeric 40 171 0
799 12.98 0.76 0.00 X_50710534_50710674_INS 9 139 (2) C ALR#Satellite/centromeric (0) 171 40 m_b1s502i13
X_50710534_50 9 CTTCTGTCTAGATTTTATATGAAGATATC-CCGTTTCCAAAGAAATCCTC 57
v i i- v vv ? iv
C ALR#Satellite 171 CTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCGNAGGCCTC 122
X_50710534_50 58 AAAGGTATCCAAATATCTACTTCCAGATTCTACAAAAAGACTGTTTCAAA 107
vvv i v v
C ALR#Satellite 121 AAAGCGCTCCAAATATCCACTTGCAGATTCTACAAAAAGAGTGTTTCAAA 72
X_50710534_50 108 ACGGCTGTGTCAAAAGGAAGGTTCAACTCTGT 139
v v i
C ALR#Satellite 71 ACTGCTCTATCAAAAGGAAGGTTCAACTCTGT 40
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.37
Transitions / transversions = 0.42 (5/12)
Gap_init rate = 0.01 (1 / 130), avg. gap size = 1.00 (1 / 1)
+ 477 16.9 0.0 0.0 X_50780287_50780441_INS 1 77 (78) + AluJb SINE/Alu 103 179 (133) 676
ANNOTATION EVIDENCE:
477 16.88 0.00 0.00 X_50780287_50780441_INS 1 77 78 + AluJb SINE/Alu 103 179 133
477 16.88 0.00 0.00 X_50780287_50780441_INS 1 77 (78) AluJb#SINE/Alu 103 179 (133) m_b1s357i8
X_50780287_50 1 CAAAACCTCTTCTCTACAAAAAGTACAAAAATCAGCCAGACGTGGTGCTG 50
i i v i i i i vi
AluJb#SINE/Al 103 CGAAACCCCGTCTCTACAAAAAATACAAAAATTAGCCGGGCGTGGTGGCG 152
X_50780287_50 51 CACACCTGTAGTCCCAGGTACTCGTGA 77
i i v v
AluJb#SINE/Al 153 CGCGCCTGTAGTCCCAGCTACTCGGGA 179
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 11.99
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 296 30.9 0.0 0.0 X_50780287_50780441_INS 81 148 (7) + SVA_A Retroposon/SVA 166 233 (1154) 677
ANNOTATION EVIDENCE:
296 30.88 0.00 0.00 X_50780287_50780441_INS 81 148 7 + SVA_A Retroposon/SVA 166 233 1154
296 30.88 0.00 0.00 X_50780287_50780441_INS 81 148 (7) SVA_A#Retroposon/SVA 166 233 (1154) m_b1s502i14
X_50780287_50 81 CTGTGACTACAGGCATGCAGCACCACACCTGGCTGATTTTTGTACCTTTT 130
v i i ii iv i i i i i ii v
SVA_A#Retropo 166 CTGGGATTGCAGGCGCGCGCCGCCACGCCCGACTGGTTTTTGTATTTTTG 215
X_50780287_50 131 GCAGAGAAGAGGTTTTGC 148
ii v i i i
SVA_A#Retropo 216 GTGGAGACGGGGTCTCGC 233
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.51
Transitions / transversions = 4.25 (17/4)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 38 2.6 0.0 0.0 X_50817348_50817408_INS 22 61 (0) + (ATATAGGA)n Simple_repeat 1 40 (0) 678
ANNOTATION EVIDENCE:
38 2.56 0.00 0.00 X_50817348_50817408_INS 22 61 0 + (ATATAGGA)n Simple_repeat 1 40 0
38 2.56 0.00 0.00 X_50817348_50817408_INS 22 61 (0) (ATATAGGA)n#Simple_repeat 1 40 (0) c_b1s251i53
X_50817348_50 22 ATATAGGAATATAGGAATGTAGGAATATAGGAATATAGGA 61
i
(ATATAGGA)n#S 1 ATATAGGAATATAGGAATATAGGAATATAGGAATATAGGA 40
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 545 1.6 0.0 0.0 X_50995909_50995970_INS 1 62 (0) C L1P1 LINE/L1 (655) 5500 5439 679
ANNOTATION EVIDENCE:
545 1.61 0.00 0.00 X_50995909_50995970_INS 1 62 0 C L1PA3_3end LINE/L1 186 247 655
545 1.61 0.00 0.00 X_50995909_50995970_INS 1 62 (0) C L1PA3_3end#LINE/L1 (655) 247 186 m_b1s551i18
X_50995909_50 1 AGCACCTGTTGTTTCTTGACTTTTTAATGATTGCCATTCTAACTGGTGTG 50
i
C L1PA3_3end#LI 247 AGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTG 198
X_50995909_50 51 AGATGGTATCTC 62
C L1PA3_3end#LI 197 AGATGGTATCTC 186
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.64
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 472 10.0 0.0 0.0 X_51316838_51316930_INS 1 60 (33) C LTR53 LTR/ERVL (459) 60 1 680
ANNOTATION EVIDENCE:
472 10.00 0.00 0.00 X_51316838_51316930_INS 1 60 33 C LTR53 LTR/ERVL 1 60 459
472 10.00 0.00 0.00 X_51316838_51316930_INS 1 60 (33) C LTR53#LTR/ERVL (459) 60 1 m_b1s502i15
X_51316838_51 1 TTTCACCAGATGTCAAGGCAGCACATAATATTGAGCCTTAACTTTAGGTC 50
i i i
C LTR53#LTR/ERV 60 TTTCACCAGATGTCAAGGCAGCACATAATATTGGGCCTTAATTTTAGGCC 11
X_51316838_51 51 TTATACTGCA 60
i ii
C LTR53#LTR/ERV 10 TTACACCACA 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.16
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 39 3.7 0.0 3.5 X_51434987_51435046_INS 2 60 (0) + (ATATATT)n Simple_repeat 1 57 (0) 681
ANNOTATION EVIDENCE:
39 3.73 0.00 3.51 X_51434987_51435046_INS 2 60 0 + (ATATATT)n Simple_repeat 1 57 0
39 3.73 0.00 3.51 X_51434987_51435046_INS 2 60 (0) (ATATATT)n#Simple_repeat 1 57 (0) m_b1s252i27
X_51434987_51 2 ATATATTATATATAATATATTATATATTATATATATTATATATAATATAT 51
v - - v
(ATATATT)n#Si 1 ATATATTATATATTATATATTATATA-T-TATATATTATATATTATATAT 48
X_51434987_51 52 TATATATTA 60
(ATATATT)n#Si 49 TATATATTA 57
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2)
+ 2808 1.9 0.0 0.0 X_51693775_51694092_INS 12 318 (0) + AluY SINE/Alu 1 307 (4) 682
ANNOTATION EVIDENCE:
2808 1.95 0.00 0.00 X_51693775_51694092_INS 12 318 0 + AluY SINE/Alu 1 307 4
2808 1.95 0.00 0.00 X_51693775_51694092_INS 12 318 (0) AluY#SINE/Alu 1 307 (4) c_b1s352i101
X_51693775_51 12 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 61
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_51693775_51 62 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 111
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_51693775_51 112 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 161
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_51693775_51 162 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 211
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_51693775_51 212 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGGTCCCGCCACTGCACTC 261
i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_51693775_51 262 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 311
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_51693775_51 312 AAAAAAA 318
AluY#SINE/Alu 301 AAAAAAA 307
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.68
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 306), avg. gap size = 0.0 (0 / 0)
+ 47 1.6 3.0 1.5 X_5196725_5196790_INS 1 66 (0) + (GAAA)n Simple_repeat 1 67 (0) 683
ANNOTATION EVIDENCE:
47 1.58 3.03 1.49 X_5196725_5196790_INS 1 66 0 + (GAAA)n Simple_repeat 1 67 0
47 1.58 3.03 1.49 X_5196725_5196790_INS 1 66 (0) (GAAA)n#Simple_repeat 1 67 (0) m_b1s252i26
X_5196725_519 1 GAAAGAAAG--AGAAAGAAAGAAAGAAAGAAAGAAAAGAAAGAAAAAAAG 48
-- - i
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAG 49
X_5196725_519 49 AAAGAAAGAAAGAAAGAA 66
(GAAA)n#Simpl 50 AAAGAAAGAAAGAAAGAA 67
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.50 (3 / 2)
+ 559 3.0 0.0 0.0 X_5206812_5206878_INS 2 67 (0) C LTR12 LTR/ERV1 (641) 185 120 684
ANNOTATION EVIDENCE:
559 3.03 0.00 0.00 X_5206812_5206878_INS 2 67 0 C LTR12 LTR/ERV1 120 185 641
559 3.03 0.00 0.00 X_5206812_5206878_INS 2 67 (0) C LTR12#LTR/ERV1 (641) 185 120 m_b1s502i16
X_5206812_520 2 TTTACAATCTTTTAGCTAGACACAGAGCGCTGATTGTTGCGTTTTTACAG 51
? i v
C LTR12#LTR/ERV 185 TTTACAANCCTTTAGCTAGACACAGAGCGCTGATTGGTGCGTTTTTACAG 136
X_5206812_520 52 AGTGCTGATTGGTGCG 67
C LTR12#LTR/ERV 135 AGTGCTGATTGGTGCG 120
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.14
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 53 6.2 5.9 0.0 X_52609862_52609949_INS 2 86 (2) + (AT)n Simple_repeat 1 90 (0) 685
ANNOTATION EVIDENCE:
53 6.16 5.88 0.00 X_52609862_52609949_INS 2 86 2 + (AT)n Simple_repeat 1 90 0
53 6.16 5.88 0.00 X_52609862_52609949_INS 2 86 (2) (AT)n#Simple_repeat 1 90 (0) c_b1s251i52
X_52609862_52 2 ATATATATA-ATATATATATAT-TATATATATCGATATATAT-TATATAT 48
- - vv -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_52609862_52 49 ATCTATATATA-ATATATATCGATATATAT-TATATATAT 86
v - vv -
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATAT 90
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.00 (5 / 5)
+ 26 23.1 0.0 0.0 X_52762053_52762109_INS 1 54 (3) + (AT)n Simple_repeat 1 54 (0) 686
ANNOTATION EVIDENCE:
26 23.13 0.00 0.00 X_52762053_52762109_INS 1 54 3 + (AT)n Simple_repeat 1 54 0
26 23.13 0.00 0.00 X_52762053_52762109_INS 1 54 (3) (AT)n#Simple_repeat 1 54 (0) m_b1s252i25
X_52762053_52 1 ATATATATGTGTATATATACACATATGTGTATATATGTGTATATATACAC 50
i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_52762053_52 51 ATAT 54
(AT)n#Simple_ 51 ATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 42 37.0 0.0 0.0 X_52762121_52762262_INS 6 139 (3) + (TA)n Simple_repeat 1 134 (0) 687
ANNOTATION EVIDENCE:
42 36.95 0.00 0.00 X_52762121_52762262_INS 6 139 3 + (TA)n Simple_repeat 1 134 0
42 36.95 0.00 0.00 X_52762121_52762262_INS 6 139 (3) (TA)n#Simple_repeat 1 134 (0) m_b1s252i24
X_52762121_52 6 TATATACGTATACACACATATGTGTATATACGTATACACACATATGTGTA 55
ii i i i i i ii i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_52762121_52 56 TATACGTATATACACATATGTGTATATACGTATATACACATATGTGTACG 105
ii i i i i ii i i i i ii
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_52762121_52 106 TATACACACACATATATACATATGTATATATGTA 139
i i i i i i i
(TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATA 134
Matrix = Unknown
Transitions / transversions = 1.00 (35/0)
Gap_init rate = 0.00 (0 / 133), avg. gap size = 0.0 (0 / 0)
+ 47 5.6 0.0 0.0 X_52800497_52800553_INS 2 57 (0) + (T)n Simple_repeat 1 56 (0) 688
ANNOTATION EVIDENCE:
47 5.59 0.00 0.00 X_52800497_52800553_INS 2 57 0 + (T)n Simple_repeat 1 56 0
47 5.59 0.00 0.00 X_52800497_52800553_INS 2 57 (0) (T)n#Simple_repeat 1 56 (0) c_b1s251i51
X_52800497_52 2 TTTTTGTTTTCTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTT 51
v i i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_52800497_52 52 TTTTTT 57
(T)n#Simple_r 51 TTTTTT 56
Matrix = Unknown
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 54 0.0 0.0 0.0 X_53091173_53091224_INS 4 52 (0) + (GAAGA)n Simple_repeat 1 49 (0) 689
ANNOTATION EVIDENCE:
54 0.00 0.00 0.00 X_53091173_53091224_INS 4 52 0 + (GAAGA)n Simple_repeat 1 49 0
54 0.00 0.00 0.00 X_53091173_53091224_INS 4 52 (0) (GAAGA)n#Simple_repeat 1 49 (0) c_b1s251i50
X_53091173_53 4 GAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 52
(GAAGA)n#Simp 1 GAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 49
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 37 8.7 0.0 0.0 X_53775701_53775755_INS 3 52 (3) + (TA)n Simple_repeat 1 50 (0) 690
ANNOTATION EVIDENCE:
37 8.72 0.00 0.00 X_53775701_53775755_INS 3 52 3 + (TA)n Simple_repeat 1 50 0
37 8.72 0.00 0.00 X_53775701_53775755_INS 3 52 (3) (TA)n#Simple_repeat 1 50 (0) c_b1s251i49
X_53775701_53 3 TATATATATATATATACACACATATATATATATGTATATATATATATATA 52
i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 100 14.4 2.3 0.0 X_53776319_53776497_INS 1 176 (3) + (TA)n Simple_repeat 1 180 (0) 691
ANNOTATION EVIDENCE:
100 14.41 2.27 0.00 X_53776319_53776497_INS 1 176 3 + (TA)n Simple_repeat 1 180 0
100 14.41 2.27 0.00 X_53776319_53776497_INS 1 176 (3) (TA)n#Simple_repeat 1 180 (0) m_b1s252i23
X_53776319_53 1 TATATATTTATATATATTTATACATATATATATAAATATATATTTATAAA 50
v v i v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_53776319_53 51 TATATATGTATAAATATATATATTTATACAAATATATATTTATATATATT 100
i v v i v v v
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_53776319_53 101 TAT-TATATAAAAATATATATATTTATATAT-TATAAATGTATATTTATA 148
- v v v - v i v
(TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150
X_53776319_53 149 TA-ATATAAATATATTTTTTTA-ATATATA 176
- v v v v -
(TA)n#Simple_ 151 TATATATATATATATATATATATATATATA 180
Matrix = Unknown
Transitions / transversions = 0.21 (4/19)
Gap_init rate = 0.02 (4 / 175), avg. gap size = 1.00 (4 / 4)
+ 2559 2.4 0.0 2.4 X_5383272_5383584_INS 15 313 (0) + AluY SINE/Alu 1 292 (19) 692
ANNOTATION EVIDENCE:
2559 2.40 0.00 2.40 X_5383272_5383584_INS 15 313 0 + AluY SINE/Alu 1 292 19
2559 2.40 0.00 2.40 X_5383272_5383584_INS 15 313 (0) AluY#SINE/Alu 1 292 (19) c_b1s352i102
X_5383272_538 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_5383272_538 65 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 114
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_5383272_538 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_5383272_538 165 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 214
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_5383272_538 215 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 264
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_5383272_538 265 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 313
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 292
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.49
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 298), avg. gap size = 1.00 (7 / 7)
+ 462 10.8 0.0 0.0 X_53872702_53872783_INS 3 67 (15) + L1MA3 LINE/L1 6187 6251 (54) 693
ANNOTATION EVIDENCE:
462 10.77 0.00 0.00 X_53872702_53872783_INS 3 67 15 + L1MA3_3end LINE/L1 934 998 54
462 10.77 0.00 0.00 X_53872702_53872783_INS 3 67 (15) L1MA3_3end#LINE/L1 934 998 (54) m_b1s551i19
X_53872702_53 3 TGAGGTGATGGATACCTCATTTACCTGGATGTAATTATTACACATTTTAT 52
i iv i i v
L1MA3_3end#LI 934 TGAGGTGATGGATACCCCATTTACCCTGATGTGATTATTACGCATTGTAT 983
X_53872702_53 53 GACTGTATCAAAATA 67
v
L1MA3_3end#LI 984 GCCTGTATCAAAATA 998
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.05
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 56 1.6 0.0 0.0 X_54036275_54036341_INS 5 67 (0) + (A)n Simple_repeat 1 63 (0) 694
ANNOTATION EVIDENCE:
56 1.61 0.00 0.00 X_54036275_54036341_INS 5 67 0 + (A)n Simple_repeat 1 63 0
56 1.61 0.00 0.00 X_54036275_54036341_INS 5 67 (0) (A)n#Simple_repeat 1 63 (0) m_b1s252i22
X_54036275_54 5 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 54
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_54036275_54 55 AAAAAGAAAAAAA 67
i
(A)n#Simple_r 51 AAAAAAAAAAAAA 63
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 2958 0.3 0.0 0.0 X_54065861_54066195_INS 19 329 (6) + AluY SINE/Alu 1 311 (0) 695
ANNOTATION EVIDENCE:
2958 0.32 0.00 0.00 X_54065861_54066195_INS 19 329 6 + AluY SINE/Alu 1 311 0
2958 0.32 0.00 0.00 X_54065861_54066195_INS 19 329 (6) AluY#SINE/Alu 1 311 (0) c_b1s352i103
X_54065861_54 19 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 68
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_54065861_54 69 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 118
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_54065861_54 119 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTAGC 168
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_54065861_54 169 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 218
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_54065861_54 219 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 268
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_54065861_54 269 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 318
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_54065861_54 319 AAAAAAAAAAA 329
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.32
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 50 0.0 0.0 0.0 X_54633573_54633626_INS 7 51 (3) + (TCTT)n Simple_repeat 1 45 (0) 696
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 X_54633573_54633626_INS 7 51 3 + (TCTT)n Simple_repeat 1 45 0
50 0.00 0.00 0.00 X_54633573_54633626_INS 7 51 (3) (TCTT)n#Simple_repeat 1 45 (0) c_b1s251i48
X_54633573_54 7 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 51
(TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 40 0.0 0.0 0.0 X_54657141_54657191_INS 15 51 (0) + (CTTT)n Simple_repeat 1 37 (0) 697
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 X_54657141_54657191_INS 15 51 0 + (CTTT)n Simple_repeat 1 37 0
40 0.00 0.00 0.00 X_54657141_54657191_INS 15 51 (0) (CTTT)n#Simple_repeat 1 37 (0) c_b1s251i47
X_54657141_54 15 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 51
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 2746 2.0 0.0 0.0 X_54835578_54835894_INS 19 317 (0) + AluY SINE/Alu 1 299 (12) 698
ANNOTATION EVIDENCE:
2746 2.01 0.00 0.00 X_54835578_54835894_INS 19 317 0 + AluY SINE/Alu 1 299 12
2746 2.01 0.00 0.00 X_54835578_54835894_INS 19 317 (0) AluY#SINE/Alu 1 299 (12) c_b1s352i104
X_54835578_54 19 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 68
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_54835578_54 69 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAATGG 118
i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_54835578_54 119 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 168
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_54835578_54 169 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 218
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_54835578_54 219 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 268
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_54835578_54 269 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 317
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.42
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 2867 1.3 0.0 0.0 X_55014477_55014799_INS 14 323 (0) + AluY SINE/Alu 1 310 (1) 699
ANNOTATION EVIDENCE:
2867 1.29 0.00 0.00 X_55014477_55014799_INS 14 323 0 + AluY SINE/Alu 1 310 1
2867 1.29 0.00 0.00 X_55014477_55014799_INS 14 323 (0) AluY#SINE/Alu 1 310 (1) c_b1s352i105
X_55014477_55 14 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 63
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_55014477_55 64 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 113
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_55014477_55 114 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 163
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_55014477_55 164 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 213
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_55014477_55 214 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 263
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_55014477_55 264 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 313
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_55014477_55 314 AAAAAAAAAA 323
AluY#SINE/Alu 301 AAAAAAAAAA 310
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.30
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 309), avg. gap size = 0.0 (0 / 0)
+ 56 10.7 1.0 1.0 X_5564092_5564196_INS 3 105 (0) + (TCCA)n Simple_repeat 1 103 (0) 700
ANNOTATION EVIDENCE:
56 10.73 0.97 0.97 X_5564092_5564196_INS 3 105 0 + (TCCA)n Simple_repeat 1 103 0
56 10.73 0.97 0.97 X_5564092_5564196_INS 3 105 (0) (TCCA)n#Simple_repeat 1 103 (0) c_b1s251i46
X_5564092_556 3 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCTAT- 51
ii i -
(TCCA)n#Simpl 1 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 50
X_5564092_556 52 CACTCCATCCATCCATTTATGTATCTATCCATCGTTCCATCCATCCATCC 101
- ii vi i vv
(TCCA)n#Simpl 51 CA-TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 99
X_5564092_556 102 ATCC 105
(TCCA)n#Simpl 100 ATCC 103
Matrix = Unknown
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.02 (2 / 102), avg. gap size = 1.00 (2 / 2)
+ 83 1.3 0.0 0.0 X_56025718_56025796_INS 2 79 (0) + (T)n Simple_repeat 1 78 (0) 701
ANNOTATION EVIDENCE:
83 1.29 0.00 0.00 X_56025718_56025796_INS 2 79 0 + (T)n Simple_repeat 1 78 0
83 1.29 0.00 0.00 X_56025718_56025796_INS 2 79 (0) (T)n#Simple_repeat 1 78 (0) c_b1s251i45
X_56025718_56 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_56025718_56 52 TTTTTTTTTTGTTTTTTTTTTTTTTTTT 79
v
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 78
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 16 0.0 7.7 0.0 X_5605234_5605313_INS 4 29 (51) + (AGAA)n Simple_repeat 1 28 (0) 702
ANNOTATION EVIDENCE:
16 0.00 7.69 0.00 X_5605234_5605313_INS 4 29 51 + (AGAA)n Simple_repeat 1 28 0
16 0.00 7.69 0.00 X_5605234_5605313_INS 4 29 (51) (AGAA)n#Simple_repeat 1 28 (0) m_b1s252i21
X_5605234_560 4 AGAAAGAAAGAAAGAAA-AAAG-AAGAA 29
- -
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAA 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2)
+ 60 2.4 0.0 0.0 X_56088419_56088512_INS 2 94 (0) + (T)n Simple_repeat 1 93 (0) 703
ANNOTATION EVIDENCE:
60 3.25 0.00 0.00 X_56088419_56088512_INS 2 64 30 + (T)n Simple_repeat 1 63 0
60 3.25 0.00 0.00 X_56088419_56088512_INS 2 64 (30) (T)n#Simple_repeat 1 63 (0) c_b1s251i44
X_56088419_56 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT 51
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_56088419_56 52 TTTTTTGTTTTTT 64
v
(T)n#Simple_r 51 TTTTTTTTTTTTT 63
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
19 0.00 0.00 0.00 X_56088419_56088512_INS 74 94 0 + (T)n Simple_repeat 1 21 0
19 0.00 0.00 0.00 X_56088419_56088512_INS 74 94 (0) (T)n#Simple_repeat 1 21 (0) m_b1s252i20
X_56088419_56 74 TTTTTTTTTTTTTTTTTTTTT 94
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 424 6.7 0.0 0.0 X_56104371_56104430_INS 1 60 (0) C L1P1 LINE/L1 (1790) 4356 4297 704
ANNOTATION EVIDENCE:
424 6.67 0.00 0.00 X_56104371_56104430_INS 1 60 0 C L1P1_orf2 LINE/L1 2188 2247 1047
424 6.67 0.00 0.00 X_56104371_56104430_INS 1 60 (0) C L1P1_orf2#LINE/L1 (1047) 2247 2188 m_b1s551i20
X_56104371_56 1 TGTTTGTCTGTTATTGGTGTATAAGAATGCTTGTGATTTTTCTACATTGC 50
vi v
C L1P1_orf2#LIN 2247 TGTTTGTCTGTTATTGGTGTATAAGAATGCTTGTGATTTTTGCACATTGA 2198
X_56104371_56 51 TTTCGTATCC 60
i
C L1P1_orf2#LIN 2197 TTTTGTATCC 2188
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.99
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 55 0.0 1.9 0.0 X_5654123_5654175_INS 1 53 (0) + (TCTT)n Simple_repeat 1 54 (0) 705
ANNOTATION EVIDENCE:
55 0.00 1.89 0.00 X_5654123_5654175_INS 1 53 0 + (TCTT)n Simple_repeat 1 54 0
55 0.00 1.89 0.00 X_5654123_5654175_INS 1 53 (0) (TCTT)n#Simple_repeat 1 54 (0) c_b1s251i43
X_5654123_565 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TTCTTTC 49
-
(TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 50
X_5654123_565 50 TTTC 53
(TCTT)n#Simpl 51 TTTC 54
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1)
+ 78 4.0 0.0 7.1 X_56686703_56686829_INS 8 127 (0) + (AT)n Simple_repeat 1 112 (0) 706
ANNOTATION EVIDENCE:
78 4.00 0.00 7.14 X_56686703_56686829_INS 8 127 0 + (AT)n Simple_repeat 1 112 0
78 4.00 0.00 7.14 X_56686703_56686829_INS 8 127 (0) (AT)n#Simple_repeat 1 112 (0) c_b1s251i42
X_56686703_56 8 ATATATAGTATATATACTATATATATAGTATATATAGTATATATATATAC 57
- - - - -
(AT)n#Simple_ 1 ATATATA-TATATATA-TATATATATA-TATATATA-TATATATATATA- 45
X_56686703_56 58 TATATATACTATATATACATATACATATATATATATATGTATATGTATAT 107
- i i i i
(AT)n#Simple_ 46 TATATATA-TATATATATATATATATATATATATATATATATATATATAT 94
X_56686703_56 108 ATAGTATATATAGTATATAT 127
- -
(AT)n#Simple_ 95 ATA-TATATATA-TATATAT 112
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.00 (8 / 8)
+ 50 4.0 0.0 0.0 X_56765677_56765731_INS 1 52 (3) + (AT)n Simple_repeat 1 52 (0) 707
ANNOTATION EVIDENCE:
50 4.00 0.00 0.00 X_56765677_56765731_INS 1 52 3 + (AT)n Simple_repeat 1 52 0
50 4.00 0.00 0.00 X_56765677_56765731_INS 1 52 (3) (AT)n#Simple_repeat 1 52 (0) c_b1s251i41
X_56765677_56 1 ATATATATATATATATATATATATATATATATATGTATGTATATATATAT 50
i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_56765677_56 51 AT 52
(AT)n#Simple_ 51 AT 52
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2856 3.9 0.0 0.0 X_57038083_57038413_INS 1 331 (0) C L1P2 LINE/L1 (352) 5803 5473 708
ANNOTATION EVIDENCE:
2856 3.93 0.00 0.00 X_57038083_57038413_INS 1 331 0 C L1PA4_3end LINE/L1 220 550 352
2856 3.93 0.00 0.00 X_57038083_57038413_INS 1 331 (0) C L1PA4_3end#LINE/L1 (352) 550 220 m_b1s551i21
X_57038083_57 1 AGTATTCCATGGTGTATATGTGCCACATGTTCTTAATCCAGTCTGTCATT 50
v i
C L1PA4_3end#LI 550 AGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATT 501
X_57038083_57 51 GATGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCAC 100
v i
C L1PA4_3end#LI 500 GTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGC 451
X_57038083_57 101 GATAAACATACATGTGCATGTGTCTTTATAGCAGCATGATTTATAATCCT 150
i i
C L1PA4_3end#LI 450 AATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATCCT 401
X_57038083_57 151 TTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGT 200
C L1PA4_3end#LI 400 TTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGT 351
X_57038083_57 201 TCTAGATGCCTGAGGAATCACTACACCGACTTCCATGATGGTTGAACCAG 250
v i i i ii i
C L1PA4_3end#LI 350 TCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAG 301
X_57038083_57 251 TTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTC 300
C L1PA4_3end#LI 300 TTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTC 251
X_57038083_57 301 TCCAGCACCTGTTGTTTCCTGACTTTTTAAT 331
C L1PA4_3end#LI 250 TCCAGCACCTGTTGTTTCCTGACTTTTTAAT 220
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.19
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 330), avg. gap size = 0.0 (0 / 0)
+ 1031 4.0 0.0 0.0 X_57038857_57038980_INS 1 124 (0) C L1P1 LINE/L1 (1434) 4712 4589 709
ANNOTATION EVIDENCE:
1031 4.03 0.00 0.00 X_57038857_57038980_INS 1 124 0 C L1P1_orf2 LINE/L1 2480 2603 691
1031 4.03 0.00 0.00 X_57038857_57038980_INS 1 124 (0) C L1P1_orf2#LINE/L1 (691) 2603 2480 m_b1s551i22
X_57038857_57 1 CCAGCTTTGTTCTTTTGGTTTAGGATTGACTTGGCAATGCAGGCTCTTTT 50
i i i
C L1P1_orf2#LIN 2603 CCAGCTTTGTTCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTTTT 2554
X_57038857_57 51 TTGGTTCCATATGAACTTTAAAGTACTTTTTTCCAATTCTGTGAAGAAAG 100
v
C L1P1_orf2#LIN 2553 TTGGTTCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAG 2504
X_57038857_57 101 TCATGGGTAGCTTGATGGGGATGG 124
v
C L1P1_orf2#LIN 2503 TCATTGGTAGCTTGATGGGGATGG 2480
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.63
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 0.0 X_5708288_5708350_INS 1 40 (23) + (AAGA)n Simple_repeat 1 40 (0) 710
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_5708288_5708350_INS 1 40 23 + (AAGA)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_5708288_5708350_INS 1 40 (23) (AAGA)n#Simple_repeat 1 40 (0) c_b1s251i40
X_5708288_570 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 40
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 2198 2.1 0.0 0.0 X_57090395_57090646_INS 12 252 (0) C AluY SINE/Alu (7) 304 64 711
ANNOTATION EVIDENCE:
2198 2.07 0.00 0.00 X_57090395_57090646_INS 12 252 0 C AluY SINE/Alu 64 304 7
2198 2.07 0.00 0.00 X_57090395_57090646_INS 12 252 (0) C AluY#SINE/Alu (7) 304 64 c_b1s352i106
X_57090395_57 12 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 61
C AluY#SINE/Alu 304 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 255
X_57090395_57 62 GCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGG 111
v
C AluY#SINE/Alu 254 GCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGG 205
X_57090395_57 112 GTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGC 161
i
C AluY#SINE/Alu 204 GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 155
X_57090395_57 162 GCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 211
i
C AluY#SINE/Alu 154 GCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 105
X_57090395_57 212 TTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCG 252
v i
C AluY#SINE/Alu 104 TTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCG 64
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.72
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 240), avg. gap size = 0.0 (0 / 0)
+ 60 14.4 0.0 0.0 X_57243031_57243131_INS 2 97 (4) + (TA)n Simple_repeat 1 96 (0) 712
ANNOTATION EVIDENCE:
60 14.38 0.00 0.00 X_57243031_57243131_INS 2 97 4 + (TA)n Simple_repeat 1 96 0
60 14.38 0.00 0.00 X_57243031_57243131_INS 2 97 (4) (TA)n#Simple_repeat 1 96 (0) m_b1s252i19
X_57243031_57 2 TATATATATACGTATATATACGTATATATATATACGTATATATATATACG 51
ii ii ii ii
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_57243031_57 52 TATATATATATACGTATATATATATATATATACGTATATATATATA 97
ii ii
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATA 96
Matrix = Unknown
Transitions / transversions = 1.00 (12/0)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 45 0.0 3.5 3.5 X_57558580_57558640_INS 2 59 (2) + (ATATATATGA)n Simple_repeat 1 58 (0) 713
ANNOTATION EVIDENCE:
45 0.00 3.45 3.45 X_57558580_57558640_INS 2 59 2 + (ATATATATGA)n Simple_repeat 1 58 0
45 0.00 3.45 3.45 X_57558580_57558640_INS 2 59 (2) (ATATATATGA)n#Simple_repeat 1 58 (0) c_b1s251i39
X_57558580_57 2 ATATATATGAATATATAT-ACATATATATGAATATATAT-ATATATATAT 49
- - - -
(ATATATATGA)n 1 ATATATATGAATATATATGA-ATATATATGAATATATATGA-ATATATAT 48
X_57558580_57 50 GAATATATAT 59
(ATATATATGA)n 49 GAATATATAT 58
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4)
+ 2575 1.8 0.0 0.0 X_5781741_5782068_INS 12 328 (0) C AluY SINE/Alu (0) 311 1 714
ANNOTATION EVIDENCE:
34 2.84 0.00 0.00 X_5781741_5782068_INS 12 47 281 + (T)n Simple_repeat 1 36 0
34 2.84 0.00 0.00 X_5781741_5782068_INS 12 47 (281) (T)n#Simple_repeat 1 36 (0) c_b1s251i38
X_5781741_578 12 TTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT 47
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
2575 1.78 0.00 0.00 X_5781741_5782068_INS 48 328 0 C AluY SINE/Alu 1 281 30
2575 1.78 0.00 0.00 X_5781741_5782068_INS 48 328 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i107
X_5781741_578 48 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 97
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_5781741_578 98 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 147
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_5781741_578 148 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 197
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_5781741_578 198 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 247
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_5781741_578 248 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 297
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_5781741_578 298 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 328
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.47
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 438 12.2 0.0 0.0 X_57863237_57863309_INS 1 72 (1) C LTR12D LTR/ERV1 (499) 755 690 715
ANNOTATION EVIDENCE:
438 12.12 0.00 0.00 X_57863237_57863309_INS 1 66 7 C LTR12D LTR/ERV1 690 755 499
438 12.12 0.00 0.00 X_57863237_57863309_INS 1 66 (7) C LTR12D#LTR/ERV1 (499) 755 690 m_b1s502i17
X_57863237_57 1 TGATTGGTCCATTTTACAGTGTGCTGATTGGTCCATTGTAGAGAGCACCG 50
v v v v vi i
C LTR12D#LTR/ER 755 TGATTGGTCCATTTTACAGAGAGCTGATTGGTCCATTTTACAGAGAGCTG 706
X_57863237_57 51 ATTGGTCCATTTTACA 66
i
C LTR12D#LTR/ER 705 ATTGGTCCGTTTTACA 690
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.61
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
344 13.73 0.00 0.00 X_57863237_57863309_INS 22 72 1 C LTR12 LTR/ERV1 293 343 483
344 13.73 0.00 0.00 X_57863237_57863309_INS 22 72 (1) C LTR12#LTR/ERV1 (483) 343 293 m_b1s502i18
X_57863237_57 22 TGCTGATTGGTCCATTGTAGAGAGCACCGATTGGTCCATTTTACAAGGCA 71
v v i i ii? i
C LTR12#LTR/ERV 343 TGCTGATTGGTCCATTTTACAGAGCGCTGATTGGTCCATTTTACAGANCG 294
X_57863237_57 72 C 72
C LTR12#LTR/ERV 293 C 293
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.28
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 1271 1.4 0.0 0.0 X_58053518_58053682_INS 8 150 (15) + L1HS LINE/L1 6013 6155 (0) 716
ANNOTATION EVIDENCE:
1271 1.40 0.00 0.00 X_58053518_58053682_INS 8 150 15 + L1HS_3end LINE/L1 760 902 0
1271 1.40 0.00 0.00 X_58053518_58053682_INS 8 150 (15) L1HS_3end#LINE/L1 760 902 (0) m_b1s551i23
X_58053518_58 8 GGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGC 57
i
L1HS_3end#LIN 760 GGATAGCATTGGGAGATATACCTAATGCTAGATGACACGTTAGTGGGTGC 809
X_58053518_58 58 AGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGT 107
L1HS_3end#LIN 810 AGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGT 859
X_58053518_58 108 GCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAATAAAA 150
v
L1HS_3end#LIN 860 GCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.77
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 142), avg. gap size = 0.0 (0 / 0)
+ 333 18.0 0.0 0.0 X_58285473_58285539_INS 7 67 (0) + GSATX Satellite/centr 68 128 (90) 717
ANNOTATION EVIDENCE:
333 18.03 0.00 0.00 X_58285473_58285539_INS 7 67 0 + GSATX Satellite/centromeric 68 128 90
333 18.03 0.00 0.00 X_58285473_58285539_INS 7 67 (0) GSATX#Satellite/centromeric 68 128 (90) m_b1s502i19
X_58285473_58 7 GAGACCCTGGCCTGCACCCAGGGTATGTGTCTCGGCCACAGGGGACACCT 56
v i ? ii ?v i i i
GSATX#Satelli 68 GAGTCCCTGGCTTNCACCCAGGGTGCGTGTCTCNCCCACGGGGGGCACCC 117
X_58285473_58 57 CATAGCATCAA 67
v iv
GSATX#Satelli 118 CAAAGCGGCAA 128
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.65
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 1003 14.3 0.0 0.0 X_58546118_58546460_INS 1 343 (0) + ALR/Alpha Satellite/centr 1 343 (9) 718
ANNOTATION EVIDENCE:
564 17.17 0.00 0.00 X_58546118_58546460_INS 1 99 244 + ALR Satellite/centromeric 64 162 9
564 17.17 0.00 0.00 X_58546118_58546460_INS 1 99 (244) ALR#Satellite/centromeric 64 162 (9) m_b1s502i20
X_58546118_58 1 AGAGCAGTTTTGAAACACTCTTTTTGTAGTATCTGCACGTGTATATTTAG 50
v v v i
ALR#Satellite 64 AGAGCAGTTTTGAAACACTCTTTTTGTAGAATCTGCAAGTGGATATTTGG 113
X_58546118_58 51 AGCTCTTTGAGGCCTATTGAGGAAGTGGAGGCGTCCCCAGATAAAAACT 99
v ?iv v iv iiii ii v
ALR#Satellite 114 AGCGCTTTGAGGCCTNCGGTGGAAAAGGAAATATCTTCACATAAAAACT 162
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.64
Transitions / transversions = 1.12 (9/8)
Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0)
1003 14.79 0.00 0.00 X_58546118_58546460_INS 110 278 65 + ALR Satellite/centromeric 2 170 1
1003 14.79 0.00 0.00 X_58546118_58546460_INS 110 278 (65) ALR#Satellite/centromeric 2 170 (1) m_b1s502i21
X_58546118_58 110 ATTCTGAGCACTTTCGTTGCGATGTGTGCCTTCATCTCATGGAGTTGAAA 159
v v vi v i v v ii v
ALR#Satellite 2 ATTCTCAGAAACTTCTTTGTGATGTGTGCATTCAACTCACAGAGTTGAAC 51
X_58546118_58 160 CTTTCTTTTGTTTGAGCAGTTTTGAAACACTCTTTTTGTAGAATCTGCTA 209
i v v v
ALR#Satellite 52 CTTCCTTTTGATAGAGCAGTTTTGAAACACTCTTTTTGTAGAATCTGCAA 101
X_58546118_58 210 GTGGATATTTACAGCTCTTTCAGGCCTATTGTTGAAGTGGAAATATCTTC 259
iv v v ?iv v iv
ALR#Satellite 102 GTGGATATTTGGAGCGCTTTGAGGCCTNCGGTGGAAAAGGAAATATCTTC 151
X_58546118_58 260 ACATAAAAACTACACAGAA 278
v
ALR#Satellite 152 ACATAAAAACTAGACAGAA 170
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.93
Transitions / transversions = 0.47 (8/17)
Gap_init rate = 0.00 (0 / 168), avg. gap size = 0.0 (0 / 0)
448 8.20 0.00 0.00 X_58546118_58546460_INS 283 343 0 + ALRa Satellite/centromeric 4 64 108
448 8.20 0.00 0.00 X_58546118_58546460_INS 283 343 (0) ALRa#Satellite/centromeric 4 64 (108) m_b1s502i22
X_58546118_58 283 TCTGAGAAACTTCTTTGAGACGTGTGCATTCATCTCACAGAGTTGAAACT 332
v v i i v
ALRa#Satellit 4 TCTGAGAAACTGCTTTGTGATGTGTGCATTCATCTCACAGAGTTAAACCT 53
X_58546118_58 333 TTCTTTTGATT 343
ALRa#Satellit 54 TTCTTTTGATT 64
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.68
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 85 3.6 0.0 0.0 X_5939043_5939137_INS 10 95 (0) + (TC)n Simple_repeat 1 86 (0) 719
ANNOTATION EVIDENCE:
85 3.62 0.00 0.00 X_5939043_5939137_INS 10 95 0 + (TC)n Simple_repeat 1 86 0
85 3.62 0.00 0.00 X_5939043_5939137_INS 10 95 (0) (TC)n#Simple_repeat 1 86 (0) c_b1s251i37
X_5939043_593 10 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 59
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50
X_5939043_593 60 TCTCTCTCTCTCTCTCTCTCTTTCTTTCTTTCTCTC 95
i i i
(TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 86
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)
+ 58 0.0 0.0 0.0 X_6097155_6097207_INS 1 52 (1) + (GGAA)n Simple_repeat 1 52 (0) 720
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_6097155_6097207_INS 1 52 1 + (GGAA)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_6097155_6097207_INS 1 52 (1) (GGAA)n#Simple_repeat 1 52 (0) c_b1s251i36
X_6097155_609 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 50
(GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 50
X_6097155_609 51 AA 52
(GGAA)n#Simpl 51 AA 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 786 0.0 0.0 3.1 X_6115476_6115575_INS 1 100 (0) C AluY SINE/Alu (0) 311 215 721
ANNOTATION EVIDENCE:
786 0.00 0.00 3.09 X_6115476_6115575_INS 1 100 0 C AluY SINE/Alu 215 311 0
786 0.00 0.00 3.09 X_6115476_6115575_INS 1 100 (0) C AluY#SINE/Alu (0) 311 215 m_b1s357i9
X_6115476_611 1 TTTTTTTGTATTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTC 50
---
C AluY#SINE/Alu 311 TTTTTTT---TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTC 265
X_6115476_611 51 TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTC 100
C AluY#SINE/Alu 264 TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTC 215
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.00 (3 / 3)
+ 2326 1.6 0.0 0.0 X_61750416_61750707_INS 9 292 (0) C AluY SINE/Alu (0) 311 42 722
ANNOTATION EVIDENCE:
33 0.00 0.00 0.00 X_61750416_61750707_INS 21 51 241 + (T)n Simple_repeat 1 31 0
33 0.00 0.00 0.00 X_61750416_61750707_INS 21 51 (241) (T)n#Simple_repeat 1 31 (0) c_b1s251i35
X_61750416_61 21 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
2326 1.57 0.00 0.00 X_61750416_61750707_INS 9 20 272 C AluY SINE/Alu 283 294 17
2326 1.57 0.00 0.00 X_61750416_61750707_INS 9 20 (272) C AluY#SINE/Alu (17) 294 283 c_b1s352i108
X_61750416_61 9 TTTTCTTTCTTC 20
i i i
C AluY#SINE/Alu 294 TTTTTTTTTTTT 283
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.61
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 11), avg. gap size = 0.0 (0 / 0)
2326 1.57 0.00 0.00 X_61750416_61750707_INS 52 292 0 C AluY SINE/Alu 42 282 29
2326 1.57 0.00 0.00 X_61750416_61750707_INS 52 292 (0) C AluY#SINE/Alu (29) 282 42 c_b1s352i108
X_61750416_61 52 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 101
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_61750416_61 102 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 151
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_61750416_61 152 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 201
i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_61750416_61 202 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 251
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_61750416_61 252 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCC 292
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCC 42
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.61
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 240), avg. gap size = 0.0 (0 / 0)
+ 284 6.8 0.0 0.0 X_61757730_61757821_INS 1 73 (19) + ALR/Alpha Satellite/centr 1 73 (0) 723
ANNOTATION EVIDENCE:
284 7.50 0.00 0.00 X_61757730_61757821_INS 1 40 52 + ALR Satellite/centromeric 132 171 0
284 7.50 0.00 0.00 X_61757730_61757821_INS 1 40 (52) ALR#Satellite/centromeric 132 171 (0) m_b1s502i23
X_61757730_61 1 GTGAAAAAGGAAATCTCTTCACATAAACACTAGACAGAAG 40
i v v
ALR#Satellite 132 GTGGAAAAGGAAATATCTTCACATAAAAACTAGACAGAAG 171
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.90
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
262 6.06 0.00 0.00 X_61757730_61757821_INS 41 73 19 + ALR Satellite/centromeric 1 33 138
262 6.06 0.00 0.00 X_61757730_61757821_INS 41 73 (19) ALR#Satellite/centromeric 1 33 (138) m_b1s502i24
X_61757730_61 41 CATTCTCAGAAACTTCTTAGTGACGTGTGCATT 73
v i
ALR#Satellite 1 CATTCTCAGAAACTTCTTTGTGATGTGTGCATT 33
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.33
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 1083 0.8 0.0 0.0 X_61762450_61762590_INS 21 141 (0) C L1HS LINE/L1 (0) 6155 6035 724
ANNOTATION EVIDENCE:
1083 0.83 0.00 0.00 X_61762450_61762590_INS 21 141 0 C L1HS_3end LINE/L1 782 902 0
1083 0.83 0.00 0.00 X_61762450_61762590_INS 21 141 (0) C L1HS_3end#LINE/L1 (0) 902 782 m_b1s551i24
X_61762450_61 21 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 70
C L1HS_3end#LIN 902 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 853
X_61762450_61 71 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 120
C L1HS_3end#LIN 852 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 803
X_61762450_61 121 CTAATGTGTCATCTAGCATTA 141
i
C L1HS_3end#LIN 802 CTAACGTGTCATCTAGCATTA 782
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.08
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0)
+ 1259 16.8 7.3 0.0 X_62244534_62244795_INS 1 232 (30) C THE1B LTR/ERVL-MaLR (111) 253 5 725
ANNOTATION EVIDENCE:
1259 16.81 7.33 0.00 X_62244534_62244795_INS 1 232 30 C THE1B LTR/ERVL-MaLR 5 253 111
1259 16.81 7.33 0.00 X_62244534_62244795_INS 1 232 (30) C THE1B#LTR/ERVL-MaLR (111) 253 5 m_b1s502i25
X_62244534_62 1 ATCATGGCAGAATGTGAATGAAGAGCAAAGTCATGTCTTCCATGGTGGCA 50
i v i v i ? i v i
C THE1B#LTR/ERV 253 ATCATGGCGGAAGGCGAAGGAGGAGCAAAGNCACGTCTTACATGGCGGCA 204
X_62244534_62 51 GGCAAGAGAGCTTGTGCAGGGCAATTCCCATTTATAAAACAATCAGATCT 100
? v i v v
C THE1B#LTR/ERV 203 GGCAAGAGAGCNTGTGCAGGGGAACTCCCCTTTATAAAACCATCAGATCT 154
X_62244534_62 101 CATGAGACTT----ACTACCACAAGAACAGGATGGGGGAAA-TCACTCTT 145
i ---- i i v i ii i -i i i ii
C THE1B#LTR/ERV 153 CGTGAGACTTATTCACTATCACGAGAACAGCACGGGAAAGACCCGCCCCC 104
X_62244534_62 146 ATGATTCAATTATCT-CCACCTGAACCTT-----GACACATGAGAATTAT 189
i - v iv i ----- i i
C THE1B#LTR/ERV 103 ATGATTCAATTACCTCCCACCGGGTCCCTCCCACGACACGTGGGAATTAT 54
X_62244534_62 190 ------TATAATTCAAGGTGAGGCTTGGGTGAGGAAACAGGCAAACCAT 232
------ i i ii i v v
C THE1B#LTR/ERV 53 GGGAGCTACAATTCAAGATGAGATTTGGGTGGGGACACAGCCAAACCAT 5
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.99
Transitions / transversions = 2.55 (28/11)
Gap_init rate = 0.02 (5 / 231), avg. gap size = 3.40 (17 / 5)
+ 31 4.2 8.0 0.0 X_62469977_62470027_INS 2 51 (0) + (AT)n Simple_repeat 1 54 (0) 726
ANNOTATION EVIDENCE:
31 4.17 8.00 0.00 X_62469977_62470027_INS 2 51 0 + (AT)n Simple_repeat 1 54 0
31 4.17 8.00 0.00 X_62469977_62470027_INS 2 51 (0) (AT)n#Simple_repeat 1 54 (0) c_b1s251i34
X_62469977_62 2 ATATATATATATATATATA-ATATA-ATGTGTATATATATA-ATATATA- 47
- - i i - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_62469977_62 48 ATAT 51
(AT)n#Simple_ 51 ATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4)
+ 51 11.4 0.0 0.0 X_6252864_6252939_INS 1 76 (0) + (AG)n Simple_repeat 1 76 (0) 727
ANNOTATION EVIDENCE:
51 11.37 0.00 0.00 X_6252864_6252939_INS 1 76 0 + (AG)n Simple_repeat 1 76 0
51 11.37 0.00 0.00 X_6252864_6252939_INS 1 76 (0) (AG)n#Simple_repeat 1 76 (0) m_b1s252i18
X_6252864_625 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGAGAGACCAAGAA 50
iv vvi i
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50
X_6252864_625 51 AGAGGGAGAGACAGAGAGAGAGAGAG 76
i v
(AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAG 76
Matrix = Unknown
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0)
+ 38 0.0 0.0 0.0 X_63175922_63175992_INS 1 33 (38) + (TA)n Simple_repeat 1 33 (0) 728
ANNOTATION EVIDENCE:
38 0.00 0.00 0.00 X_63175922_63175992_INS 1 33 38 + (TA)n Simple_repeat 1 33 0
38 0.00 0.00 0.00 X_63175922_63175992_INS 1 33 (38) (TA)n#Simple_repeat 1 33 (0) c_b1s251i33
X_63175922_63 1 TATATATATATATATATATATATATATATATAT 33
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATAT 33
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 2558 2.8 0.0 0.0 X_6319550_6319872_INS 17 323 (0) C AluY SINE/Alu (0) 311 2 729
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_6319550_6319872_INS 17 42 281 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_6319550_6319872_INS 17 42 (281) (T)n#Simple_repeat 1 26 (0) c_b1s251i32
X_6319550_631 17 TTTTTTTTTTTTTTTTTTTTTTTTTT 42
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2558 2.80 0.00 0.00 X_6319550_6319872_INS 43 323 0 C AluY SINE/Alu 2 282 29
2558 2.80 0.00 0.00 X_6319550_6319872_INS 43 323 (0) C AluY#SINE/Alu (29) 282 2 c_b1s352i109
X_6319550_631 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 92
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_6319550_631 93 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 142
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_6319550_631 143 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 192
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_6319550_631 193 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGC 242
v i i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_6319550_631 243 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 292
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_6319550_631 293 GGATTACAGGCGTGAGCCACCACGCCCGGCC 323
i
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.21
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2305 2.4 0.0 0.0 X_63440800_63441067_INS 16 268 (0) + AluY SINE/Alu 39 291 (20) 730
ANNOTATION EVIDENCE:
2305 2.37 0.00 0.00 X_63440800_63441067_INS 16 268 0 + AluY SINE/Alu 39 291 20
2305 2.37 0.00 0.00 X_63440800_63441067_INS 16 268 (0) AluY#SINE/Alu 39 291 (20) c_b1s352i110
X_63440800_63 16 TTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCC 65
AluY#SINE/Alu 39 TTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCC 88
X_63440800_63 66 CGGCTAAAATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC 115
i v i
AluY#SINE/Alu 89 TGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC 138
X_63440800_63 116 GGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCA 165
i i
AluY#SINE/Alu 139 GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCA 188
X_63440800_63 166 GGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCC 215
v
AluY#SINE/Alu 189 GGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGC 238
X_63440800_63 216 GCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 265
AluY#SINE/Alu 239 GCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAA 288
X_63440800_63 266 AAA 268
AluY#SINE/Alu 289 AAA 291
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.68
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 252), avg. gap size = 0.0 (0 / 0)
+ 70 1.3 0.0 0.0 X_63507879_63507958_INS 2 80 (0) + (A)n Simple_repeat 1 79 (0) 731
ANNOTATION EVIDENCE:
70 1.28 0.00 0.00 X_63507879_63507958_INS 2 80 0 + (A)n Simple_repeat 1 79 0
70 1.28 0.00 0.00 X_63507879_63507958_INS 2 80 (0) (A)n#Simple_repeat 1 79 (0) m_b1s252i17
X_63507879_63 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_63507879_63 52 AAAAAAACAAAAAAAAAAAAAAAAAAAAA 80
v
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 79
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0)
+ 326 14.3 1.6 1.6 X_63682881_63682945_INS 2 65 (0) + L1PREC2 LINE/L1 3556 3619 (2527) 732
ANNOTATION EVIDENCE:
326 14.28 1.56 1.56 X_63682881_63682945_INS 2 65 0 + L1PREC2_orf2 LINE/L1 1447 1510 1784
326 14.28 1.56 1.56 X_63682881_63682945_INS 2 65 (0) L1PREC2_orf2#LINE/L1 1447 1510 (1784) m_b1s551i25
X_63682881_63 2 ATTTACAAAAAAAGAGC-GGTGCAATTCCTACTGAAATTACTCCAAAAAA 50
v i - - i v i i
L1PREC2_orf2# 1447 ATGTACAAAGAA-GAGCTGGTACCATTCCTACTGAAACTATTCCAAAAAA 1495
X_63682881_63 51 ATGAGGAAGATGGAC 65
v i v
L1PREC2_orf2# 1496 TTGAGGAGGAGGGAC 1510
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.96
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2)
+ 932 9.7 4.5 0.0 X_63852192_63852352_INS 3 121 (40) + MLT2A1 LTR/ERVL 265 389 (55) 733
ANNOTATION EVIDENCE:
932 9.70 4.48 0.00 X_63852192_63852352_INS 3 121 40 + MLT2A1 LTR/ERVL 265 389 55
932 9.70 4.48 0.00 X_63852192_63852352_INS 3 121 (40) MLT2A1#LTR/ERVL 265 389 (55) m_b1s502i26
X_63852192_63 3 TCGAACATTGGACTCCAAGTTCTTCAGTTTTGGGACTCATATTGGCTCTC 52
i iv i
MLT2A1#LTR/ER 265 TCGAACATCGGACTCCAAGTTCTTCAGTTTTGGGACTCGGACTGGCTCTC 314
X_63852192_63 53 CTTGCTCCTCAGCTTGTAGACAGCCTATTATGGGACCTTTTGATAATGTA 102
i i i v vi i
MLT2A1#LTR/ER 315 CTTGCTCCTCAGCTTGCAGACGGCCTATTGTGGGACCTTGTGATCGTGTG 364
X_63852192_63 103 AGTTAATAGTTAATAAGC------T 121
v i ------
MLT2A1#LTR/ER 365 AGTTAATACTTAATAAACTCCCCTT 389
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.51
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 6.00 (6 / 1)
+ 29 0.0 0.0 0.0 X_63852192_63852352_INS 122 146 (15) + (TC)n Simple_repeat 1 25 (0) 734
ANNOTATION EVIDENCE:
29 0.00 0.00 0.00 X_63852192_63852352_INS 122 146 15 + (TC)n Simple_repeat 1 25 0
29 0.00 0.00 0.00 X_63852192_63852352_INS 122 146 (15) (TC)n#Simple_repeat 1 25 (0) c_b1s251i31
X_63852192_63 122 TCTCTCTCTCTCTCTCTCTCTCTCT 146
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 932 9.7 4.5 0.0 X_63852192_63852352_INS 147 160 (1) + MLT2A1 LTR/ERVL 390 403 (41) 733
ANNOTATION EVIDENCE:
932 9.70 4.48 0.00 X_63852192_63852352_INS 147 160 1 + MLT2A1 LTR/ERVL 390 403 41
932 9.70 4.48 0.00 X_63852192_63852352_INS 147 160 (1) MLT2A1#LTR/ERVL 390 403 (41) m_b1s502i26
X_63852192_63 147 ATATATATATATAT 160
?
MLT2A1#LTR/ER 390 ATATATATATNTAT 403
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.51
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 13), avg. gap size = 0.0 (0 / 0)
+ 45 0.0 0.0 8.9 X_64113178_64113240_INS 2 62 (1) + (AT)n Simple_repeat 1 56 (0) 735
ANNOTATION EVIDENCE:
45 0.00 0.00 8.93 X_64113178_64113240_INS 2 62 1 + (AT)n Simple_repeat 1 56 0
45 0.00 0.00 8.93 X_64113178_64113240_INS 2 62 (1) (AT)n#Simple_repeat 1 56 (0) c_b1s251i30
X_64113178_64 2 ATATATATATGATATATATATCATATATATATCATATATATGATATATAT 51
- - - -
(AT)n#Simple_ 1 ATATATATAT-ATATATATAT-ATATATATAT-ATATATAT-ATATATAT 46
X_64113178_64 52 ATGATATATAT 62
-
(AT)n#Simple_ 47 AT-ATATATAT 56
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5)
+ 63 0.0 11.2 0.0 X_64174252_64174340_INS 1 89 (0) + (AT)n Simple_repeat 1 99 (0) 736
ANNOTATION EVIDENCE:
63 0.00 11.24 0.00 X_64174252_64174340_INS 1 89 0 + (AT)n Simple_repeat 1 99 0
63 0.00 11.24 0.00 X_64174252_64174340_INS 1 89 (0) (AT)n#Simple_repeat 1 99 (0) c_b1s251i29
X_64174252_64 1 ATATATA-AT-TATATATATATATA-AT-TATATATATATATA-AT-TAT 44
- - - - - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_64174252_64 45 ATATATATATA-AT-TATATATATATATATATATATATA-AT-TATATA 89
- - - -
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATA 99
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.11 (10 / 88), avg. gap size = 1.00 (10 / 10)
+ 2683 2.3 0.0 2.3 X_64217017_64217344_INS 19 328 (0) + AluY SINE/Alu 1 303 (8) 737
ANNOTATION EVIDENCE:
2683 2.31 0.00 2.31 X_64217017_64217344_INS 19 328 0 + AluY SINE/Alu 1 303 8
2683 2.31 0.00 2.31 X_64217017_64217344_INS 19 328 (0) AluY#SINE/Alu 1 303 (8) c_b1s352i111
X_64217017_64 19 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 68
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_64217017_64 69 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 118
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_64217017_64 119 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 168
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_64217017_64 169 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 218
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_64217017_64 219 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 268
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_64217017_64 269 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 318
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_64217017_64 319 AAAAAAAAAA 328
AluY#SINE/Alu 294 AAAAAAAAAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.44
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 1.00 (7 / 7)
+ 2451 2.5 0.0 2.5 X_64487682_64488013_INS 12 332 (0) C AluY SINE/Alu (0) 311 1 738
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_64487682_64488013_INS 12 44 288 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_64487682_64488013_INS 12 44 (288) (T)n#Simple_repeat 1 33 (0) c_b1s251i28
X_64487682_64 12 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(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)
2451 2.49 0.00 2.49 X_64487682_64488013_INS 45 332 0 C AluY SINE/Alu 1 281 30
2451 2.49 0.00 2.49 X_64487682_64488013_INS 45 332 (0) C AluY#SINE/Alu (30) 281 1 c_b1s352i112
X_64487682_64 45 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 94
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_64487682_64 95 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 144
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_64487682_64 145 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 194
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_64487682_64 195 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 244
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_64487682_64 245 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 294
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_64487682_64 295 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 332
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 54 1.7 0.0 6.2 X_64593775_64593844_INS 1 69 (1) + (AT)n Simple_repeat 1 65 (0) 739
ANNOTATION EVIDENCE:
54 1.66 0.00 6.15 X_64593775_64593844_INS 1 69 1 + (AT)n Simple_repeat 1 65 0
54 1.66 0.00 6.15 X_64593775_64593844_INS 1 69 (1) (AT)n#Simple_repeat 1 65 (0) c_b1s251i27
X_64593775_64 1 ATATATATATATATATATATACTATATATATAGTATATATATATAGTTTA 50
- - - v
(AT)n#Simple_ 1 ATATATATATATATATATATA-TATATATATA-TATATATATATA-TATA 47
X_64593775_64 51 TATATATACTATATATATA 69
-
(AT)n#Simple_ 48 TATATATA-TATATATATA 65
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4)
+ 57 0.0 0.0 0.0 X_64668863_64668913_INS 1 51 (0) + (AAGA)n Simple_repeat 1 51 (0) 740
ANNOTATION EVIDENCE:
57 0.00 0.00 0.00 X_64668863_64668913_INS 1 51 0 + (AAGA)n Simple_repeat 1 51 0
57 0.00 0.00 0.00 X_64668863_64668913_INS 1 51 (0) (AAGA)n#Simple_repeat 1 51 (0) c_b1s251i26
X_64668863_64 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
X_64668863_64 51 G 51
(AAGA)n#Simpl 51 G 51
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 1249 4.2 0.0 5.4 X_64840955_64841137_INS 8 183 (0) C AluY SINE/Alu (6) 305 139 741
ANNOTATION EVIDENCE:
1249 4.21 0.00 5.39 X_64840955_64841137_INS 8 183 0 C AluY SINE/Alu 139 305 6
1249 4.21 0.00 5.39 X_64840955_64841137_INS 8 183 (0) C AluY#SINE/Alu (6) 305 139 m_b1s357i10
X_64840955_64 8 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCGCCCA 57
i
C AluY#SINE/Alu 305 TTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA 256
X_64840955_64 58 GGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCTC 107
i ----- -- i i-
C AluY#SINE/Alu 255 GGCTGGA-----G--TGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCC- 214
X_64840955_64 108 TGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGG 157
- i
C AluY#SINE/Alu 213 -GCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGG 165
X_64840955_64 158 GATTACAGGCGCCCGCCACCGCGCCC 183
i i
C AluY#SINE/Alu 164 GACTACAGGCGCCCGCCACCACGCCC 139
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.64
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.05 (9 / 175), avg. gap size = 1.00 (9 / 9)
+ 61 6.5 0.0 2.4 X_64962606_64962692_INS 2 87 (0) + (CCTT)n Simple_repeat 1 84 (0) 742
ANNOTATION EVIDENCE:
61 6.49 0.00 2.38 X_64962606_64962692_INS 2 87 0 + (CCTT)n Simple_repeat 1 84 0
61 6.49 0.00 2.38 X_64962606_64962692_INS 2 87 (0) (CCTT)n#Simple_repeat 1 84 (0) c_b1s251i25
X_64962606_64 2 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTCCTTCC 51
i
(CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 50
X_64962606_64 52 CTCCCTCCCTCCTCCCTCTCCCTTCCTTCCTTCCTT 87
i i i i - -
(CCTT)n#Simpl 51 TTCCTTCCTTCCTTCCT-T-CCTTCCTTCCTTCCTT 84
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2)
+ 64 0.0 4.4 0.0 X_6500246_6500318_INS 2 69 (4) + (TCTA)n Simple_repeat 1 71 (0) 743
ANNOTATION EVIDENCE:
64 0.00 4.41 0.00 X_6500246_6500318_INS 2 69 4 + (TCTA)n Simple_repeat 1 71 0
64 0.00 4.41 0.00 X_6500246_6500318_INS 2 69 (4) (TCTA)n#Simple_repeat 1 71 (0) c_b1s251i24
X_6500246_650 2 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC-ATCTATC 50
-
(TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 50
X_6500246_650 51 TATC-ATCTATC-ATCTATCT 69
- -
(TCTA)n#Simpl 51 TATCTATCTATCTATCTATCT 71
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3)
+ 34 12.1 0.0 0.0 X_65226508_65226563_INS 1 56 (0) + (TA)n Simple_repeat 1 56 (0) 744
ANNOTATION EVIDENCE:
34 12.06 0.00 0.00 X_65226508_65226563_INS 1 56 0 + (TA)n Simple_repeat 1 56 0
34 12.06 0.00 0.00 X_65226508_65226563_INS 1 56 (0) (TA)n#Simple_repeat 1 56 (0) c_b1s251i23
X_65226508_65 1 TATATATATGTGTGTATATATATATATATGTATATATATATGTATATATA 50
i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_65226508_65 51 TGTATA 56
i
(TA)n#Simple_ 51 TATATA 56
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 85 41.2 0.0 0.0 X_65317333_65317651_INS 1 310 (9) + (TA)n Simple_repeat 1 310 (0) 745
ANNOTATION EVIDENCE:
85 41.20 0.00 0.00 X_65317333_65317651_INS 1 310 9 + (TA)n Simple_repeat 1 310 0
85 41.20 0.00 0.00 X_65317333_65317651_INS 1 310 (9) (TA)n#Simple_repeat 1 310 (0) m_b1s252i16
X_65317333_65 1 TATATGTGTATATATGTATATACACACATGTGTGTATATGTGTATATATG 50
i i i i i i i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_65317333_65 51 TATATACACACATGTGTGTATATGTGTATATACACACATGTGTGTATATG 100
i i i i i i i i i i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_65317333_65 101 TGTATATACACACATGTGTGTATATGTGTATATACACACATGTGCGTATA 150
i i i i i i i i i i i i i iii
(TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150
X_65317333_65 151 TGTGTATACATACACACATGTGCGTATATGTGTATATATGTATACATACA 200
i i i i i i i iii i i i i i
(TA)n#Simple_ 151 TATATATATATATATATATATATATATATATATATATATATATATATATA 200
X_65317333_65 201 CACATATGCATATATGTGTATATATGTATACATACACACATATGCATATA 250
i i ii i i i i i i i ii
(TA)n#Simple_ 201 TATATATATATATATATATATATATATATATATATATATATATATATATA 250
X_65317333_65 251 TGTGTGTATATATGTATACATACACACATATGCATATATGTGTGTGTATA 300
i i i i i i i i ii i i i i
(TA)n#Simple_ 251 TATATATATATATATATATATATATATATATATATATATATATATATATA 300
X_65317333_65 301 TGTATACATA 310
i i
(TA)n#Simple_ 301 TATATATATA 310
Matrix = Unknown
Transitions / transversions = 1.00 (87/0)
Gap_init rate = 0.00 (0 / 309), avg. gap size = 0.0 (0 / 0)
+ 96 12.2 0.0 1.9 X_6539831_6539994_INS 2 162 (2) + (GAAG)n Simple_repeat 1 158 (0) 746
ANNOTATION EVIDENCE:
96 12.19 0.00 1.90 X_6539831_6539994_INS 2 162 2 + (GAAG)n Simple_repeat 1 158 0
96 12.19 0.00 1.90 X_6539831_6539994_INS 2 162 (2) (GAAG)n#Simple_repeat 1 158 (0) m_b1s252i15
X_6539831_653 2 GAAGGGAGGGAGGGAAGGAAGGAAGGGAGGGAGGGAAGGAAGGAGGGAAG 51
- i i - i i i
(GAAG)n#Simpl 1 GAA-GGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAG 48
X_6539831_653 52 GAAGGAGGGAAGGAAGGAGGGAAGGAAGGAGGGAGGGAAGGAAGGAAGAA 101
i i i i i
(GAAG)n#Simpl 49 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 98
X_6539831_653 102 AGGAATGAAGGAAGGATGGGAGGGAGGGAAGGAAGGAAGGAGGGAAGGAA 151
v -i i i i
(GAAG)n#Simpl 99 AGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 147
X_6539831_653 152 GGACGGAGGGA 162
v i
(GAAG)n#Simpl 148 GGAAGGAAGGA 158
Matrix = Unknown
Transitions / transversions = 7.50 (15/2)
Gap_init rate = 0.02 (3 / 160), avg. gap size = 1.00 (3 / 3)
+ 36 23.8 0.0 0.0 X_65505790_65505864_INS 2 75 (0) + (AT)n Simple_repeat 1 74 (0) 747
ANNOTATION EVIDENCE:
36 23.77 0.00 0.00 X_65505790_65505864_INS 2 75 0 + (AT)n Simple_repeat 1 74 0
36 23.77 0.00 0.00 X_65505790_65505864_INS 2 75 (0) (AT)n#Simple_repeat 1 74 (0) m_b1s252i14
X_65505790_65 2 ATATATACGTATATATGTGTGTGTATATATATACACATATATACGTATAT 51
ii i i i i i i ii
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_65505790_65 52 ATATGTGTGTATATATATATACAT 75
i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATAT 74
Matrix = Unknown
Transitions / transversions = 1.00 (14/0)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 33 0.0 2.0 6.4 X_65509184_65509243_INS 2 50 (10) + (ATATATAGCT)n Simple_repeat 1 47 (0) 748
ANNOTATION EVIDENCE:
33 0.00 2.04 6.38 X_65509184_65509243_INS 2 50 10 + (ATATATAGCT)n Simple_repeat 1 47 0
33 0.00 2.04 6.38 X_65509184_65509243_INS 2 50 (10) (ATATATAGCT)n#Simple_repeat 1 47 (0) c_b1s251i22
X_65509184_65 2 ATAT-TAGCTATATATAGCTATATATATTAGCTATATATAGCTATATATA 50
- -- -
(ATATATAGCT)n 1 ATATATAGCTATATATAGC--TATATA-TAGCTATATATAGCTATATATA 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4)
+ 37 0.0 0.0 8.2 X_65557596_65557649_INS 1 53 (1) + (ACATATATAT)n Simple_repeat 1 49 (0) 749
ANNOTATION EVIDENCE:
37 0.00 0.00 8.16 X_65557596_65557649_INS 1 53 1 + (ACATATATAT)n Simple_repeat 1 49 0
37 0.00 0.00 8.16 X_65557596_65557649_INS 1 53 (1) (ACATATATAT)n#Simple_repeat 1 49 (0) c_b1s251i21
X_65557596_65 1 ACATATATATACATATATATACACATATATATATACATATATATACATAT 50
-- --
(ACATATATAT)n 1 ACATATATATACATATATAT--AC--ATATATATACATATATATACATAT 46
X_65557596_65 51 ATA 53
(ACATATATAT)n 47 ATA 49
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4)
+ 275 14.0 4.0 0.0 X_65739188_65739241_INS 1 50 (4) C L1PREC2 LINE/L1 (563) 5597 5546 750
ANNOTATION EVIDENCE:
275 14.00 4.00 0.00 X_65739188_65739241_INS 1 50 4 C L1PREC2_3end LINE/L1 293 344 563
275 14.00 4.00 0.00 X_65739188_65739241_INS 1 50 (4) C L1PREC2_3end#LINE/L1 (563) 344 293 m_b1s551i26
X_65739188_65 1 TCTTTGATGAATTTCCACACTGTTT--AACAATGGTTGCACTAATTTACG 48
v iv i --v v i
C L1PREC2_3end# 344 TCTTTGAGGAATCGCCACACTGCTTTCCACAATGGTTGAACTAATTTACA 295
X_65739188_65 49 CT 50
C L1PREC2_3end# 294 CT 293
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.32
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.02 (1 / 49), avg. gap size = 2.00 (2 / 1)
+ 40 0.0 0.0 0.0 X_65977562_65977616_INS 1 34 (21) + (CT)n Simple_repeat 1 34 (0) 751
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 X_65977562_65977616_INS 1 34 21 + (CT)n Simple_repeat 1 34 0
40 0.00 0.00 0.00 X_65977562_65977616_INS 1 34 (21) (CT)n#Simple_repeat 1 34 (0) c_b1s251i20
X_65977562_65 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 34
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 34
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 19 0.0 0.0 0.0 X_65977562_65977616_INS 35 55 (0) + (AT)n Simple_repeat 1 21 (0) 752
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 X_65977562_65977616_INS 35 55 0 + (AT)n Simple_repeat 1 21 0
19 0.00 0.00 0.00 X_65977562_65977616_INS 35 55 (0) (AT)n#Simple_repeat 1 21 (0) m_b1s252i13
X_65977562_65 35 ATATATATATATATATATATA 55
(AT)n#Simple_ 1 ATATATATATATATATATATA 21
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 54 6.0 0.0 0.0 X_66672302_66672372_INS 1 71 (0) + (AAG)n Simple_repeat 1 71 (0) 753
ANNOTATION EVIDENCE:
54 5.98 0.00 0.00 X_66672302_66672372_INS 1 71 0 + (AAG)n Simple_repeat 1 71 0
54 5.98 0.00 0.00 X_66672302_66672372_INS 1 71 (0) (AAG)n#Simple_repeat 1 71 (0) m_b1s252i12
X_66672302_66 1 AAGAAGAAGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAA 50
i i i i
(AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 50
X_66672302_66 51 GAAGAAGAAGAAGAAGAAGAA 71
(AAG)n#Simple 51 GAAGAAGAAGAAGAAGAAGAA 71
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 41 3.6 5.1 1.6 X_67863028_67863096_INS 10 68 (1) + (TA)n Simple_repeat 1 61 (0) 754
ANNOTATION EVIDENCE:
41 3.63 5.08 1.64 X_67863028_67863096_INS 10 68 1 + (TA)n Simple_repeat 1 61 0
41 3.63 5.08 1.64 X_67863028_67863096_INS 10 68 (1) (TA)n#Simple_repeat 1 61 (0) c_b1s251i19
X_67863028_67 10 TATATATATATACATATATATATAT-TATATATATATATA-ATATACAGT 57
i - - i -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA-T 49
X_67863028_67 58 ATATAT-TATAT 68
-
(TA)n#Simple_ 50 ATATATATATAT 61
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4)
+ 47 0.0 0.0 2.2 X_68123802_68123855_INS 1 47 (7) + (CTTT)n Simple_repeat 1 46 (0) 755
ANNOTATION EVIDENCE:
47 0.00 0.00 2.17 X_68123802_68123855_INS 1 47 7 + (CTTT)n Simple_repeat 1 46 0
47 0.00 0.00 2.17 X_68123802_68123855_INS 1 47 (7) (CTTT)n#Simple_repeat 1 46 (0) c_b1s251i18
X_68123802_68 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTTCTTTCT 47
-
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCT 46
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1)
+ 57 0.0 0.0 0.0 X_68675195_68675246_INS 2 52 (0) + (T)n Simple_repeat 1 51 (0) 756
ANNOTATION EVIDENCE:
57 0.00 0.00 0.00 X_68675195_68675246_INS 2 52 0 + (T)n Simple_repeat 1 51 0
57 0.00 0.00 0.00 X_68675195_68675246_INS 2 52 (0) (T)n#Simple_repeat 1 51 (0) c_b1s251i17
X_68675195_68 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_68675195_68 52 T 52
(T)n#Simple_r 51 T 51
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 2752 1.3 0.0 0.7 X_68789575_68789894_INS 19 320 (0) + AluY SINE/Alu 1 300 (11) 757
ANNOTATION EVIDENCE:
2752 1.33 0.00 0.67 X_68789575_68789894_INS 19 320 0 + AluY SINE/Alu 1 300 11
2752 1.33 0.00 0.67 X_68789575_68789894_INS 19 320 (0) AluY#SINE/Alu 1 300 (11) c_b1s352i113
X_68789575_68 19 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 68
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_68789575_68 69 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 118
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_68789575_68 119 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCGTAGTG 168
-- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA--AATTAGCCGGGCGTGGTG 148
X_68789575_68 169 GCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGC 218
i
AluY#SINE/Alu 149 GCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGC 198
X_68789575_68 219 GTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCAC 268
AluY#SINE/Alu 199 GTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCAC 248
X_68789575_68 269 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 318
AluY#SINE/Alu 249 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 298
X_68789575_68 319 AA 320
AluY#SINE/Alu 299 AA 300
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.04
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.01 (2 / 301), avg. gap size = 1.00 (2 / 2)
+ 47 3.7 3.6 0.0 X_68826745_68826801_INS 2 57 (0) + (TA)n Simple_repeat 1 58 (0) 758
ANNOTATION EVIDENCE:
47 3.67 3.57 0.00 X_68826745_68826801_INS 2 57 0 + (TA)n Simple_repeat 1 58 0
47 3.67 3.57 0.00 X_68826745_68826801_INS 2 57 (0) (TA)n#Simple_repeat 1 58 (0) c_b1s251i16
X_68826745_68 2 TATATATATATATAT-TCTATATATAT-TCTATATATATATATATATATA 49
- v - v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_68826745_68 50 TATATATA 57
(TA)n#Simple_ 51 TATATATA 58
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2)
+ 43 0.0 0.0 0.0 X_68865437_68865490_INS 1 37 (17) + (TA)n Simple_repeat 1 37 (0) 759
ANNOTATION EVIDENCE:
43 0.00 0.00 0.00 X_68865437_68865490_INS 1 37 17 + (TA)n Simple_repeat 1 37 0
43 0.00 0.00 0.00 X_68865437_68865490_INS 1 37 (17) (TA)n#Simple_repeat 1 37 (0) c_b1s251i15
X_68865437_68 1 TATATATATATATATATATATATATATATATATATAT 37
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 50 4.0 0.0 0.0 X_68875606_68875658_INS 2 53 (0) + (TA)n Simple_repeat 1 52 (0) 760
ANNOTATION EVIDENCE:
50 3.96 0.00 0.00 X_68875606_68875658_INS 2 53 0 + (TA)n Simple_repeat 1 52 0
50 3.96 0.00 0.00 X_68875606_68875658_INS 2 53 (0) (TA)n#Simple_repeat 1 52 (0) c_b1s251i14
X_68875606_68 2 TATATATATATCTATATATATATATCTATATATATATATATATATATATA 51
v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_68875606_68 52 TA 53
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 504 1.6 0.0 0.0 X_69151404_69151534_INS 13 76 (55) + L1HS LINE/L1 6092 6155 (0) 761
ANNOTATION EVIDENCE:
504 1.56 0.00 0.00 X_69151404_69151534_INS 13 76 55 + L1HS_3end LINE/L1 839 902 0
504 1.56 0.00 0.00 X_69151404_69151534_INS 13 76 (55) L1HS_3end#LINE/L1 839 902 (0) m_b1s551i27
X_69151404_69 13 TGTAACTAACCTGCACAATGAGCACATGTACCCTAAAACTTAGAGTATAA 62
v
L1HS_3end#LIN 839 TGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAA 888
X_69151404_69 63 TAAAAAAAAAAAAA 76
L1HS_3end#LIN 889 TAAAAAAAAAAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.58
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 44 5.7 0.0 0.0 X_69151404_69151534_INS 77 131 (0) + (A)n Simple_repeat 1 55 (0) 762
ANNOTATION EVIDENCE:
44 5.69 0.00 0.00 X_69151404_69151534_INS 77 131 0 + (A)n Simple_repeat 1 55 0
44 5.69 0.00 0.00 X_69151404_69151534_INS 77 131 (0) (A)n#Simple_repeat 1 55 (0) m_b1s252i11
X_69151404_69 77 AATAAAAAAAAAAAATAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAA 126
v v v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_69151404_69 127 AAAAA 131
(A)n#Simple_r 51 AAAAA 55
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 62 1.4 0.0 0.0 X_69416352_69416421_INS 1 70 (0) + (A)n Simple_repeat 1 70 (0) 763
ANNOTATION EVIDENCE:
62 1.44 0.00 0.00 X_69416352_69416421_INS 1 70 0 + (A)n Simple_repeat 1 70 0
62 1.44 0.00 0.00 X_69416352_69416421_INS 1 70 (0) (A)n#Simple_repeat 1 70 (0) m_b1s252i10
X_69416352_69 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAA 50
v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_69416352_69 51 AAAAAAAAAAAAAAAAAAAA 70
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAA 70
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 261 21.4 27.0 0.0 X_69446562_69446678_INS 18 106 (11) + L1ME3D LINE/L1 6117 6229 (13) 764
ANNOTATION EVIDENCE:
261 21.35 26.97 0.00 X_69446562_69446678_INS 18 106 11 + L1ME3D_3end LINE/L1 864 976 13
261 21.35 26.97 0.00 X_69446562_69446678_INS 18 106 (11) L1ME3D_3end#LINE/L1 864 976 (13) m_b1s551i28
X_69446562_69 18 TCTATTTCTTAAGTCAGATGGCAGACACACATGTATTTG---CATTATTA 64
iii i ii ii iiv i i ---i
L1ME3D_3end#L 864 TCTATTTCTTAAGCTGGGTGGTGGGTACATGGGTGTTCGTTTTATTATTA 913
X_69446562_69 65 TTCTTTCAACTCT---------------------TTTATATGCATGATAT 93
v v --------------------- i i
L1ME3D_3end#L 914 TTCTTTAAACTGTACATATACGTTNTATATATTCTTTGTATGTATGATAT 963
X_69446562_69 94 ATTTCATAATTAA 106
i
L1ME3D_3end#L 964 ATTTCACAATTAA 976
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.09
Transitions / transversions = 5.33 (16/3)
Gap_init rate = 0.02 (2 / 88), avg. gap size = 12.00 (24 / 2)
+ 17 0.0 0.0 0.0 X_69456055_69456114_INS 19 37 (23) + (A)n Simple_repeat 1 19 (0) 765
ANNOTATION EVIDENCE:
17 0.00 0.00 0.00 X_69456055_69456114_INS 19 37 23 + (A)n Simple_repeat 1 19 0
17 0.00 0.00 0.00 X_69456055_69456114_INS 19 37 (23) (A)n#Simple_repeat 1 19 (0) m_b1s252i9
X_69456055_69 19 AAAAAAAAAAAAAAAAAAA 37
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 36 12.1 5.6 4.4 X_6945857_6945949_INS 5 93 (0) + (TA)n Simple_repeat 1 90 (0) 766
ANNOTATION EVIDENCE:
36 12.08 5.62 4.44 X_6945857_6945949_INS 5 93 0 + (TA)n Simple_repeat 1 90 0
36 12.08 5.62 4.44 X_6945857_6945949_INS 5 93 (0) (TA)n#Simple_repeat 1 90 (0) m_b1s252i8
X_6945857_694 5 TATATATATAGA-ATATACTAT-TTTCTATATATAGACTATATATAGACT 52
v - - - v v v - v -
(TA)n#Simple_ 1 TATATATATATATATATA-TATATATATATATATATA-TATATATATA-T 47
X_6945857_694 53 ATATATATAGA-ATATAT-TAT-TTTCTATATATAGACTATATA 93
v - - - v v v -
(TA)n#Simple_ 48 ATATATATATATATATATATATATATATATATATATA-TATATA 90
Matrix = Unknown
Transitions / transversions = 0.00 (0/9)
Gap_init rate = 0.10 (9 / 88), avg. gap size = 1.00 (9 / 9)
+ 40 0.0 0.0 0.0 X_69797609_69797660_INS 2 38 (14) + (T)n Simple_repeat 1 37 (0) 767
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 X_69797609_69797660_INS 2 38 14 + (T)n Simple_repeat 1 37 0
40 0.00 0.00 0.00 X_69797609_69797660_INS 2 38 (14) (T)n#Simple_repeat 1 37 (0) c_b1s251i13
X_69797609_69 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 374 11.3 0.0 0.0 X_69899321_69899374_INS 2 54 (0) + SVA_B Retroposon/SVA 521 573 (810) 768
ANNOTATION EVIDENCE:
374 11.32 0.00 0.00 X_69899321_69899374_INS 2 54 0 + SVA_B Retroposon/SVA 521 573 810
374 11.32 0.00 0.00 X_69899321_69899374_INS 2 54 (0) SVA_B#Retroposon/SVA 521 573 (810) m_b1s502i27
X_69899321_69 2 GCCATCCCATCTAGGAAGTGAGGAGCGCCTCTTCCCGGCCGCCATCCCAT 51
ii vi i i
SVA_B#Retropo 521 GCCGCCCAGTCTGGGAAGTGAGGAGCGCCTCTTCCCGGCCGCCATCCCGT 570
X_69899321_69 52 CTG 54
SVA_B#Retropo 571 CTG 573
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.48
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 67 0.0 0.0 0.0 X_70088896_70088956_INS 1 60 (1) + (ATAAA)n Simple_repeat 1 60 (0) 769
ANNOTATION EVIDENCE:
67 0.00 0.00 0.00 X_70088896_70088956_INS 1 60 1 + (ATAAA)n Simple_repeat 1 60 0
67 0.00 0.00 0.00 X_70088896_70088956_INS 1 60 (1) (ATAAA)n#Simple_repeat 1 60 (0) c_b1s251i12
X_70088896_70 1 ATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAA 50
(ATAAA)n#Simp 1 ATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAA 50
X_70088896_70 51 ATAAAATAAA 60
(ATAAA)n#Simp 51 ATAAAATAAA 60
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 29 9.2 5.2 0.0 X_70117005_70117071_INS 8 65 (2) + (AT)n Simple_repeat 1 61 (0) 770
ANNOTATION EVIDENCE:
29 9.17 5.17 0.00 X_70117005_70117071_INS 8 65 2 + (AT)n Simple_repeat 1 61 0
29 9.17 5.17 0.00 X_70117005_70117071_INS 8 65 (2) (AT)n#Simple_repeat 1 61 (0) c_b1s251i11
X_70117005_70 8 ATATATTTATAGATATATAT-TATATATA-ACATATATTTATAGATATAT 55
v v - - i v v
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_70117005_70 56 AT-TATATATA 65
-
(AT)n#Simple_ 51 ATATATATATA 61
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3)
+ 2744 2.2 0.0 2.2 X_70136030_70136382_INS 17 353 (0) + AluY SINE/Alu 1 311 (0) 771
ANNOTATION EVIDENCE:
17 0.00 0.00 0.00 X_70136030_70136382_INS 335 353 0 + (A)n Simple_repeat 1 19 0
17 0.00 0.00 0.00 X_70136030_70136382_INS 335 353 (0) (A)n#Simple_repeat 1 19 (0) m_b1s252i7
X_70136030_70 335 AAAAAAAAAAAAAAAAAAA 353
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
2744 2.25 0.00 2.25 X_70136030_70136382_INS 17 334 19 + AluY SINE/Alu 1 311 0
2744 2.25 0.00 2.25 X_70136030_70136382_INS 17 334 (19) AluY#SINE/Alu 1 311 (0) c_b1s352i114
X_70136030_70 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_70136030_70 67 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 116
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_70136030_70 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_70136030_70 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_70136030_70 217 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 266
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_70136030_70 267 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 316
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_70136030_70 317 AAAAAAAAAAAAAAAAAA 334
AluY#SINE/Alu 294 AAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.40
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.00 (7 / 7)
+ 57 5.1 0.0 0.0 X_70191335_70191396_INS 1 62 (0) + (AT)n Simple_repeat 1 62 (0) 772
ANNOTATION EVIDENCE:
57 5.09 0.00 0.00 X_70191335_70191396_INS 1 62 0 + (AT)n Simple_repeat 1 62 0
57 5.09 0.00 0.00 X_70191335_70191396_INS 1 62 (0) (AT)n#Simple_repeat 1 62 (0) c_b1s251i10
X_70191335_70 1 ATATATATATGTGTATATATATATATATATATACATATATATATATATAT 50
i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_70191335_70 51 ATATATATATAT 62
(AT)n#Simple_ 51 ATATATATATAT 62
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 18 23.8 0.0 2.0 X_70252864_70252917_INS 3 54 (0) + (ATAAT)n Simple_repeat 1 51 (0) 773
ANNOTATION EVIDENCE:
18 23.83 0.00 1.96 X_70252864_70252917_INS 3 54 0 + (ATAAT)n Simple_repeat 1 51 0
18 23.83 0.00 1.96 X_70252864_70252917_INS 3 54 (0) (ATAAT)n#Simple_repeat 1 51 (0) m_b2s252i40
X_70252864_70 3 ATATTATTATATAATATTAAATAATTTTAATTTAATAAAATATTAAATAT 52
v v v v - v v v v v v
(ATAAT)n#Simp 1 ATAATATAATATAATATAATATAA-TATAATATAATATAATATAATATAA 49
X_70252864_70 53 TA 54
(ATAAT)n#Simp 50 TA 51
Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1)
+ 42 5.6 6.6 1.2 X_70291406_70291498_INS 8 83 (10) + (AT)n Simple_repeat 1 80 (0) 774
ANNOTATION EVIDENCE:
42 5.63 6.58 1.25 X_70291406_70291498_INS 8 83 10 + (AT)n Simple_repeat 1 80 0
42 5.63 6.58 1.25 X_70291406_70291498_INS 8 83 (10) (AT)n#Simple_repeat 1 80 (0) c_b2s251i91
X_70291406_70 8 ATATATTTATATTTATATATAT-TATATATATATA-ATAT-TCATATATT 54
v v - - - - v
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT-ATATATA 49
X_70291406_70 55 TATATTTATATATAT-TATATATATA-ATAT 83
v - -
(AT)n#Simple_ 50 TATATATATATATATATATATATATATATAT 80
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6)
+ 41 4.4 0.0 0.0 X_70752619_70752815_INS 11 57 (140) + (T)n Simple_repeat 1 47 (0) 775
ANNOTATION EVIDENCE:
41 4.39 0.00 0.00 X_70752619_70752815_INS 11 57 140 + (T)n Simple_repeat 1 47 0
41 4.39 0.00 0.00 X_70752619_70752815_INS 11 57 (140) (T)n#Simple_repeat 1 47 (0) c_b2s251i90
X_70752619_70 11 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTT 57
i v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 47
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 1276 0.7 0.0 0.0 X_70752619_70752815_INS 58 197 (0) C SVA_E Retroposon/SVA (20) 1362 1223 776
ANNOTATION EVIDENCE:
1276 0.71 0.00 0.00 X_70752619_70752815_INS 58 197 0 C SVA_E Retroposon/SVA 1223 1362 20
1276 0.71 0.00 0.00 X_70752619_70752815_INS 58 197 (0) C SVA_E#Retroposon/SVA (20) 1362 1223 m_b2s502i11
X_70752619_70 58 ATTGATCATTCTTGGGTGTTTCTCGCAGAGGGGGATTTGGCAGGGTCATA 107
C SVA_E#Retropo 1362 ATTGATCATTCTTGGGTGTTTCTCGCAGAGGGGGATTTGGCAGGGTCATA 1313
X_70752619_70 108 GGACAATAGTGGAGGGAAGGTCAGCAGATAAACAAGTGAACAAAGGTCTC 157
C SVA_E#Retropo 1312 GGACAATAGTGGAGGGAAGGTCAGCAGATAAACAAGTGAACAAAGGTCTC 1263
X_70752619_70 158 TGGTTTTCCTAGGCAGAGGACCCTGCGGCCTTCCGCAGCG 197
i
C SVA_E#Retropo 1262 TGGTTTTCCTAGGCAGAGGACCCTGCGGCCTTCCGCAGTG 1223
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.72
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 139), avg. gap size = 0.0 (0 / 0)
+ 13 18.1 6.5 2.1 X_71040507_71040565_INS 13 58 (1) + A-rich Low_complexity 1 48 (0) 777
ANNOTATION EVIDENCE:
13 18.15 6.52 2.08 X_71040507_71040565_INS 13 58 1 + (ATAAA)n Simple_repeat 1 48 0
13 18.15 6.52 2.08 X_71040507_71040565_INS 13 58 (1) (ATAAA)n#Simple_repeat 1 48 (0) m_b2s252i39
X_71040507_71 13 ATAAAAT-AAATAAAAT-ATTTATTTTATTTATAAAAT-AAATAAAATA 58
- - vv vvv -vv -
(ATAAA)n#Simp 1 ATAAAATAAAATAAAATAAAATAAAATA-AAATAAAATAAAATAAAATA 48
Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4)
+ 58 0.0 0.0 0.0 X_71108076_71108128_INS 2 53 (0) + (TTTC)n Simple_repeat 1 52 (0) 778
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_71108076_71108128_INS 2 53 0 + (TTTC)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_71108076_71108128_INS 2 53 (0) (TTTC)n#Simple_repeat 1 52 (0) c_b2s251i89
X_71108076_71 2 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 51
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_71108076_71 52 TC 53
(TTTC)n#Simpl 51 TC 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 33 9.6 0.0 0.0 X_71183873_71183927_INS 5 50 (5) + (AT)n Simple_repeat 1 46 (0) 779
ANNOTATION EVIDENCE:
33 9.55 0.00 0.00 X_71183873_71183927_INS 5 50 5 + (AT)n Simple_repeat 1 46 0
33 9.55 0.00 0.00 X_71183873_71183927_INS 5 50 (5) (AT)n#Simple_repeat 1 46 (0) c_b2s251i88
X_71183873_71 5 ATATATATATATATGTATATACATATATATATGTGTATATATATAT 50
i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT 46
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
+ 71 0.0 0.0 0.0 X_71673373_71673474_INS 6 68 (34) + (GAAG)n Simple_repeat 1 63 (0) 780
ANNOTATION EVIDENCE:
71 0.00 0.00 0.00 X_71673373_71673474_INS 6 68 34 + (GAAG)n Simple_repeat 1 63 0
71 0.00 0.00 0.00 X_71673373_71673474_INS 6 68 (34) (GAAG)n#Simple_repeat 1 63 (0) c_b2s251i87
X_71673373_71 6 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 55
(GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 50
X_71673373_71 56 AGGAAGGAAGGAA 68
(GAAG)n#Simpl 51 AGGAAGGAAGGAA 63
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 28 0.0 0.0 0.0 X_71673373_71673474_INS 69 102 (0) + (AGAA)n Simple_repeat 1 34 (0) 781
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_71673373_71673474_INS 69 102 0 + (AGAA)n Simple_repeat 1 34 0
28 0.00 0.00 0.00 X_71673373_71673474_INS 69 102 (0) (AGAA)n#Simple_repeat 1 34 (0) m_b2s252i38
X_71673373_71 69 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 102
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 34
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 1173 2.6 0.0 5.2 X_71761036_71761229_INS 1 191 (3) C AluY SINE/Alu (0) 311 127 782
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_71761036_71761229_INS 1 28 166 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_71761036_71761229_INS 1 28 (166) (T)n#Simple_repeat 1 28 (0) c_b2s251i86
X_71761036_71 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
(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)
1173 2.58 0.00 5.16 X_71761036_71761229_INS 29 191 3 C AluY SINE/Alu 127 281 30
1173 2.58 0.00 5.16 X_71761036_71761229_INS 29 191 (3) C AluY#SINE/Alu (30) 281 127 m_b2s357i9
X_71761036_71 29 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 78
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_71761036_71 79 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 128
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_71761036_71 129 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 178
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_71761036_71 179 GGCCTAATTTTTT 191
-
C AluY#SINE/Alu 138 GG-CTAATTTTTT 127
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.04
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.05 (8 / 162), avg. gap size = 1.00 (8 / 8)
+ 1736 3.3 0.0 3.3 X_71856515_71856748_INS 14 234 (0) + AluY SINE/Alu 84 297 (14) 783
ANNOTATION EVIDENCE:
1736 3.28 0.00 3.27 X_71856515_71856748_INS 14 234 0 + AluY SINE/Alu 84 297 14
1736 3.28 0.00 3.27 X_71856515_71856748_INS 14 234 (0) AluY#SINE/Alu 84 297 (14) m_b2s357i10
X_71856515_71 14 CATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAT 63
v
AluY#SINE/Alu 84 CATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAT 133
X_71856515_71 64 TAGCCGGGCTCGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTG 113
vi
AluY#SINE/Alu 134 TAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTG 183
X_71856515_71 114 AGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAG 163
i
AluY#SINE/Alu 184 AGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAG 233
X_71856515_71 164 ATTGTGCCACTGCAGTCCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCC 213
i i -- ----- i
AluY#SINE/Alu 234 ATCGCGCCACTGCA--C-----TCCAGCCTGGGCGACAGAGCGAGACTCC 276
X_71856515_71 214 GTCTCAAAAAAAAAAAAAAAA 234
AluY#SINE/Alu 277 GTCTCAAAAAAAAAAAAAAAA 297
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.47
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (7 / 220), avg. gap size = 1.00 (7 / 7)
+ 48 16.1 0.0 0.0 X_7197379_7197458_INS 1 80 (0) + (TG)n Simple_repeat 1 80 (0) 784
ANNOTATION EVIDENCE:
48 16.08 0.00 0.00 X_7197379_7197458_INS 1 80 0 + (TG)n Simple_repeat 1 80 0
48 16.08 0.00 0.00 X_7197379_7197458_INS 1 80 (0) (TG)n#Simple_repeat 1 80 (0) m_b1s252i6
X_7197379_719 1 TGTGTATGTGTGTGTGTGTGTGTGTATATGTGTGTGTGTGTGTATATATA 50
i i i i i i i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50
X_7197379_719 51 TGTGTGTGTATATATATGTGTGTGTGTGTG 80
i i i i
(TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 80
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 2427 2.5 0.3 2.5 X_72238298_72238631_INS 15 334 (0) C AluY SINE/Alu (0) 311 2 785
ANNOTATION EVIDENCE:
37 0.00 0.00 0.00 X_72238298_72238631_INS 15 48 286 + (T)n Simple_repeat 1 34 0
37 0.00 0.00 0.00 X_72238298_72238631_INS 15 48 (286) (T)n#Simple_repeat 1 34 (0) c_b2s251i85
X_72238298_72 15 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48
(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)
2427 2.51 0.35 2.50 X_72238298_72238631_INS 49 334 0 C AluY SINE/Alu 2 281 30
2427 2.51 0.35 2.50 X_72238298_72238631_INS 49 334 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i77
X_72238298_72 49 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 98
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_72238298_72 99 CGACTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 148
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_72238298_72 149 GCCTCCTGTGTAGCTGGGACTACAGGCACGCGCCACCATGCCCGGCTAAT 198
i v i v i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_72238298_72 199 -TTTTGTATTTTTTTTTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 247
- -------
C AluY#SINE/Alu 131 TTTTTGTA-------TTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_72238298_72 248 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGTCTCGGCCTCCCAA 297
i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_72238298_72 298 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 334
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.56
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (8 / 285), avg. gap size = 1.00 (8 / 8)
+ 53 1.7 1.5 3.1 X_72456690_72456783_INS 1 65 (29) + (TTCT)n Simple_repeat 1 64 (0) 786
ANNOTATION EVIDENCE:
53 1.66 1.54 3.12 X_72456690_72456783_INS 1 65 29 + (TTCT)n Simple_repeat 1 64 0
53 1.66 1.54 3.12 X_72456690_72456783_INS 1 65 (29) (TTCT)n#Simple_repeat 1 64 (0) c_b2s251i84
X_72456690_72 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TTCTTTCTTTTTTTCTTT 49
- i
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50
X_72456690_72 50 CTTTCTCTCTCTTTCT 65
- -
(TTCT)n#Simpl 51 CTTTCT-T-TCTTTCT 64
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3)
+ 22 7.4 0.0 0.0 X_72456690_72456783_INS 66 94 (0) + (CT)n Simple_repeat 1 29 (0) 787
ANNOTATION EVIDENCE:
22 7.42 0.00 0.00 X_72456690_72456783_INS 66 94 0 + (CT)n Simple_repeat 1 29 0
22 7.42 0.00 0.00 X_72456690_72456783_INS 66 94 (0) (CT)n#Simple_repeat 1 29 (0) m_b2s252i37
X_72456690_72 66 CTTTCTCTCTCTTTCTCTCTCTCTCTCTC 94
i i
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTC 29
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 369 16.2 4.9 1.2 X_72645851_72645947_INS 17 97 (0) + L1PREC2 LINE/L1 2635 2718 (3428) 788
ANNOTATION EVIDENCE:
369 16.24 4.94 1.19 X_72645851_72645947_INS 17 97 0 + L1PREC2_orf2 LINE/L1 526 609 2685
369 16.24 4.94 1.19 X_72645851_72645947_INS 17 97 (0) L1PREC2_orf2#LINE/L1 526 609 (2685) m_b2s551i15
X_72645851_72 17 GACCTTTATAGACCTTTACAGAACTCTCCCCTCCAAAACAACAGGATA-G 65
v- v i v i ? i -i
L1PREC2_orf2# 526 GACCTG-ATAGACATCTACAGAACTCTCCACCCNAAAACAACAGAATATA 574
X_72645851_72 66 C---CTTCTAATTGCTACATAACACGTACTCTAAA 97
--- v i i ii i
L1PREC2_orf2# 575 CATTCTTCTCATCGCCACATGGCACATACTCTAAA 609
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.43
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.67 (5 / 3)
+ 30 30.8 0.0 0.0 X_73098598_73098688_INS 7 91 (0) + (TA)n Simple_repeat 1 85 (0) 789
ANNOTATION EVIDENCE:
30 30.75 0.00 0.00 X_73098598_73098688_INS 7 91 0 + (TA)n Simple_repeat 1 85 0
30 30.75 0.00 0.00 X_73098598_73098688_INS 7 91 (0) (TA)n#Simple_repeat 1 85 (0) m_b2s252i36
X_73098598_73 7 TATACACATCTATATGTGTATAGATATATAGATGTGTATACACATATAGA 56
i i v i i v v i i i i v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_73098598_73 57 TGTGTATAGATATATAGATTTGTATACACATCTAT 91
i i v v v i i i v
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATAT 85
Matrix = Unknown
Transitions / transversions = 1.62 (13/8)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0)
+ 55 0.0 0.0 0.0 X_73627364_73627414_INS 2 51 (0) + (TTTTA)n Simple_repeat 1 50 (0) 790
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 X_73627364_73627414_INS 2 51 0 + (TTTTA)n Simple_repeat 1 50 0
55 0.00 0.00 0.00 X_73627364_73627414_INS 2 51 (0) (TTTTA)n#Simple_repeat 1 50 (0) c_b2s251i83
X_73627364_73 2 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA 51
(TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 33 15.0 0.0 0.0 X_73655361_73655419_INS 2 55 (4) + (AT)n Simple_repeat 1 54 (0) 791
ANNOTATION EVIDENCE:
33 15.01 0.00 0.00 X_73655361_73655419_INS 2 55 4 + (AT)n Simple_repeat 1 54 0
33 15.01 0.00 0.00 X_73655361_73655419_INS 2 55 (4) (AT)n#Simple_repeat 1 54 (0) m_b2s252i35
X_73655361_73 2 ATATATATGTGTATATATATATGCATATATATGTATATATATGCATATAT 51
i i ii i ii
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_73655361_73 52 ATAT 55
(AT)n#Simple_ 51 ATAT 54
Matrix = Unknown
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 63 0.0 0.0 0.0 X_73659004_73659059_INS 1 56 (0) + (TTTC)n Simple_repeat 1 56 (0) 792
ANNOTATION EVIDENCE:
63 0.00 0.00 0.00 X_73659004_73659059_INS 1 56 0 + (TTTC)n Simple_repeat 1 56 0
63 0.00 0.00 0.00 X_73659004_73659059_INS 1 56 (0) (TTTC)n#Simple_repeat 1 56 (0) c_b2s251i82
X_73659004_73 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50
X_73659004_73 51 TCTTTC 56
(TTTC)n#Simpl 51 TCTTTC 56
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 75 18.6 0.0 0.0 X_73679064_73679198_INS 2 135 (0) + (AT)n Simple_repeat 1 134 (0) 793
ANNOTATION EVIDENCE:
75 18.64 0.00 0.00 X_73679064_73679198_INS 2 135 0 + (AT)n Simple_repeat 1 134 0
75 18.64 0.00 0.00 X_73679064_73679198_INS 2 135 (0) (AT)n#Simple_repeat 1 134 (0) m_b2s252i34
X_73679064_73 2 ATATATATATATATATATATATACACACACATACATATATATATGTATAT 51
i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_73679064_73 52 ATCTGTATATATATGTGTGTATATATATATACATATATATATGTGTGTGT 101
v i i i i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_73679064_73 102 ATATATATATACATATATATGTGTGTGTATATAT 135
i i i i i
(AT)n#Simple_ 101 ATATATATATATATATATATATATATATATATAT 134
Matrix = Unknown
Transitions / transversions = 20.00 (20/1)
Gap_init rate = 0.00 (0 / 133), avg. gap size = 0.0 (0 / 0)
+ 47 5.4 0.0 1.7 X_73971475_73971537_INS 1 61 (2) + (CCTT)n Simple_repeat 1 60 (0) 794
ANNOTATION EVIDENCE:
47 5.36 0.00 1.67 X_73971475_73971537_INS 1 61 2 + (CCTT)n Simple_repeat 1 60 0
47 5.36 0.00 1.67 X_73971475_73971537_INS 1 61 (2) (CCTT)n#Simple_repeat 1 60 (0) c_b2s251i81
X_73971475_73 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCCTTCCTTCCTTCCCTC 50
- i
(CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCC-TTCCTTCCTTCCTTCCTTC 49
X_73971475_73 51 CCTCCCTCCTT 61
i i
(CCTT)n#Simpl 50 CTTCCTTCCTT 60
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)
+ 92 4.9 4.6 0.7 X_74016044_74016178_INS 2 132 (3) + (TA)n Simple_repeat 1 136 (0) 795
ANNOTATION EVIDENCE:
92 4.88 4.58 0.74 X_74016044_74016178_INS 2 132 3 + (TA)n Simple_repeat 1 136 0
92 4.88 4.58 0.74 X_74016044_74016178_INS 2 132 (3) (TA)n#Simple_repeat 1 136 (0) c_b2s251i80
X_74016044_74 2 TATATATATATACATATAT-TATATATATATACATATATA-ATATATATA 49
i - i -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_74016044_74 50 TATACACATATATAT-TATATATAT-TATATATATACATATATAT-TATA 96
i i - - i -
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_74016044_74 97 TATATACTATATATAT-TATATATATATACATATATA 132
- - i
(TA)n#Simple_ 101 TATATA-TATATATATATATATATATATATATATATA 136
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.00 (7 / 7)
+ 427 10.8 5.4 0.0 X_74101446_74101520_INS 2 75 (0) C MER20 DNA/hAT-Charlie (101) 118 41 796
ANNOTATION EVIDENCE:
427 10.81 5.41 0.00 X_74101446_74101520_INS 2 75 0 C MER20 DNA/hAT-Charlie 41 118 101
427 10.81 5.41 0.00 X_74101446_74101520_INS 2 75 (0) C MER20#DNA/hAT-Charlie (101) 118 41 m_b2s502i12
X_74101446_74 2 CCTCTACCCATTAGAAGCCAGTAGCA-CCCCCCAACCCACTTGTG---AC 47
i v - vv v ---
C MER20#DNA/hAT 118 CCTCTACCCACTAGATGCCAGTAGCATCCCCCCCCCCCAGTTGTGACAAC 69
X_74101446_74 48 TAAAAATGTCTCCAGGCACTGCCAAATG 75
i i i
C MER20#DNA/hAT 68 CAAAAATGTCTCCAGACATTGCCAAATG 41
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.71
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.03 (2 / 73), avg. gap size = 2.00 (4 / 2)
+ 135 0.8 0.0 0.0 X_74199184_74199296_INS 2 123 (0) + (T)n Simple_repeat 1 122 (0) 797
ANNOTATION EVIDENCE:
135 0.82 0.00 0.00 X_74199184_74199296_INS 2 123 0 + (T)n Simple_repeat 1 122 0
135 0.82 0.00 0.00 X_74199184_74199296_INS 2 123 (0) (T)n#Simple_repeat 1 122 (0) c_b2s251i79
X_74199184_74 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_74199184_74 52 TTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTT 101
v
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 100
X_74199184_74 102 TTTTTTTTTTTTTTTTTTTTTT 123
(T)n#Simple_r 101 TTTTTTTTTTTTTTTTTTTTTT 122
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 2582 2.1 0.0 0.0 X_74216929_74217251_INS 15 323 (0) C AluY SINE/Alu (0) 311 2 798
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_74216929_74217251_INS 15 42 281 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_74216929_74217251_INS 15 42 (281) (T)n#Simple_repeat 1 28 (0) c_b2s251i78
X_74216929_74 15 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(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)
2582 2.11 0.00 0.00 X_74216929_74217251_INS 43 323 0 C AluY SINE/Alu 2 282 29
2582 2.11 0.00 0.00 X_74216929_74217251_INS 43 323 (0) C AluY#SINE/Alu (29) 282 2 c_b2s352i78
X_74216929_74 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 92
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_74216929_74 93 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 142
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_74216929_74 143 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 192
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_74216929_74 193 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 242
v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_74216929_74 243 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 292
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_74216929_74 293 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 323
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.82
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2644 2.3 0.0 2.3 X_74270550_74270867_INS 12 318 (0) + AluY SINE/Alu 1 300 (11) 799
ANNOTATION EVIDENCE:
2644 2.33 0.00 2.33 X_74270550_74270867_INS 12 318 0 + AluY SINE/Alu 1 300 11
2644 2.33 0.00 2.33 X_74270550_74270867_INS 12 318 (0) AluY#SINE/Alu 1 300 (11) c_b2s352i79
X_74270550_74 12 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 61
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_74270550_74 62 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 111
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_74270550_74 112 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 161
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_74270550_74 162 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 211
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_74270550_74 212 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 261
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_74270550_74 262 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 311
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_74270550_74 312 AAAAAAA 318
AluY#SINE/Alu 294 AAAAAAA 300
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.45
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 306), avg. gap size = 1.00 (7 / 7)
+ 74 4.9 0.0 0.0 X_74323889_74323994_INS 3 86 (20) + (T)n Simple_repeat 1 84 (0) 800
ANNOTATION EVIDENCE:
74 4.92 0.00 0.00 X_74323889_74323994_INS 3 86 20 + (T)n Simple_repeat 1 84 0
74 4.92 0.00 0.00 X_74323889_74323994_INS 3 86 (20) (T)n#Simple_repeat 1 84 (0) c_b2s251i77
X_74323889_74 3 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTGT 52
v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_74323889_74 53 TTTTGTCTTTTTTTTTTTTTTTTTTTTTTTTTTT 86
v i
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 84
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0)
+ 1217 2.0 0.0 0.0 X_74360365_74360556_INS 10 192 (0) C AluY SINE/Alu (0) 311 135 801
ANNOTATION EVIDENCE:
39 0.00 0.00 0.00 X_74360365_74360556_INS 10 45 147 + (T)n Simple_repeat 1 36 0
39 0.00 0.00 0.00 X_74360365_74360556_INS 10 45 (147) (T)n#Simple_repeat 1 36 (0) c_b2s251i76
X_74360365_74 10 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
1217 2.04 0.00 0.00 X_74360365_74360556_INS 46 192 0 C AluY SINE/Alu 135 281 30
1217 2.04 0.00 0.00 X_74360365_74360556_INS 46 192 (0) C AluY#SINE/Alu (30) 281 135 m_b2s357i11
X_74360365_74 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 95
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_74360365_74 96 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 145
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_74360365_74 146 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCT 192
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCT 135
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 1.44
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 36 10.8 1.6 0.0 X_74373592_74373652_INS 1 61 (0) + (TA)n Simple_repeat 1 62 (0) 802
ANNOTATION EVIDENCE:
36 10.78 1.64 0.00 X_74373592_74373652_INS 1 61 0 + (TA)n Simple_repeat 1 62 0
36 10.78 1.64 0.00 X_74373592_74373652_INS 1 61 (0) (TA)n#Simple_repeat 1 62 (0) c_b2s251i75
X_74373592_74 1 TATATATATATATATATATATATATATA-AAATATATATGTGTGTGTGTA 49
- v i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_74373592_74 50 TATATATATATA 61
(TA)n#Simple_ 51 TATATATATATA 62
Matrix = Unknown
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)
+ 16 13.4 2.1 6.7 X_7437574_7437706_INS 87 133 (0) + A-rich Low_complexity 1 45 (0) 803
ANNOTATION EVIDENCE:
16 13.37 2.13 6.67 X_7437574_7437706_INS 87 133 0 + (AAATTAT)n Simple_repeat 1 45 0
16 13.37 2.13 6.67 X_7437574_7437706_INS 87 133 (0) (AAATTAT)n#Simple_repeat 1 45 (0) m_b1s252i5
X_7437574_743 87 AAAATATAAA-AATATTATTATCAATTTATAACATTATAAAATATAAA 133
v -v -v - v - v
(AAATTAT)n#Si 1 AAATTATAAATTATA-AATTAT-AAATTATAA-ATTATAAATTATAAA 45
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4)
+ 611 5.5 0.0 0.0 X_74399026_74399104_INS 6 78 (1) C LTR12C LTR/ERV1 (690) 889 817 804
ANNOTATION EVIDENCE:
611 5.48 0.00 0.00 X_74399026_74399104_INS 6 78 1 C LTR12C LTR/ERV1 817 889 690
611 5.48 0.00 0.00 X_74399026_74399104_INS 6 78 (1) C LTR12C#LTR/ERV1 (690) 889 817 m_b2s502i13
X_74399026_74 6 AGCTAGATACGGAGTGTTGATTGGTGTATTTACAATCCTTGAGCTAGACA 55
i ii i ?
C LTR12C#LTR/ER 889 AGCTAGATACAGAGTGCCGATTGGTGTATTTACAATCCCTNAGCTAGACA 840
X_74399026_74 56 TAAAGGTTCTCCAAGGCCCCACC 78
?
C LTR12C#LTR/ER 839 TAAAGGTTCTCCAAGNCCCCACC 817
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.57
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0)
+ 38 0.0 10.0 0.0 X_74641246_74641298_INS 2 51 (2) + (AT)n Simple_repeat 1 55 (0) 805
ANNOTATION EVIDENCE:
38 0.00 10.00 0.00 X_74641246_74641298_INS 2 51 2 + (AT)n Simple_repeat 1 55 0
38 0.00 10.00 0.00 X_74641246_74641298_INS 2 51 (2) (AT)n#Simple_repeat 1 55 (0) c_b2s251i74
X_74641246_74 2 ATATATATA-ATATATATATA-ATATATAT-TATATA-ATATATAT-TAT 46
- - - - -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_74641246_74 47 ATATA 51
(AT)n#Simple_ 51 ATATA 55
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5)
+ 18 17.9 0.0 0.0 X_74694408_74694458_INS 1 32 (19) + (TA)n Simple_repeat 1 32 (0) 806
ANNOTATION EVIDENCE:
18 17.86 0.00 0.00 X_74694408_74694458_INS 1 32 19 + (TA)n Simple_repeat 1 32 0
18 17.86 0.00 0.00 X_74694408_74694458_INS 1 32 (19) (TA)n#Simple_repeat 1 32 (0) m_b2s252i33
X_74694408_74 1 TATATATATAATTCTCTTTATATATATATATA 32
vv v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATA 32
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 33 12.5 0.0 3.6 X_74826074_74826133_INS 2 59 (1) + (TA)n Simple_repeat 1 56 (0) 807
ANNOTATION EVIDENCE:
33 12.51 0.00 3.57 X_74826074_74826133_INS 2 59 1 + (TA)n Simple_repeat 1 56 0
33 12.51 0.00 3.57 X_74826074_74826133_INS 2 59 (1) (TA)n#Simple_repeat 1 56 (0) m_b2s252i32
X_74826074_74 2 TATATATGTGTATATATACTATACATGTATAGTATATATGTATATATATG 51
i i - i i - i i
(TA)n#Simple_ 1 TATATATATATATATATA-TATATATATATA-TATATATATATATATATA 48
X_74826074_74 52 TATATATA 59
(TA)n#Simple_ 49 TATATATA 56
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2)
+ 2625 2.4 0.0 2.4 X_74885243_74885564_INS 18 322 (0) + AluY SINE/Alu 1 298 (13) 808
ANNOTATION EVIDENCE:
2625 2.36 0.00 2.35 X_74885243_74885564_INS 18 322 0 + AluY SINE/Alu 1 298 13
2625 2.36 0.00 2.35 X_74885243_74885564_INS 18 322 (0) AluY#SINE/Alu 1 298 (13) c_b2s352i80
X_74885243_74 18 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_74885243_74 68 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 117
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_74885243_74 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_74885243_74 168 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 217
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_74885243_74 218 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 267
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_74885243_74 268 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 317
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_74885243_74 318 AAAAA 322
AluY#SINE/Alu 294 AAAAA 298
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.46
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.02 (7 / 304), avg. gap size = 1.00 (7 / 7)
+ 505 11.3 0.0 0.0 X_74928698_74928792_INS 25 95 (0) C L1PB LINE/L1 (2306) 3840 3770 809
ANNOTATION EVIDENCE:
505 11.27 0.00 0.00 X_74928698_74928792_INS 25 95 0 C L1PB_orf2 LINE/L1 1661 1731 1563
505 11.27 0.00 0.00 X_74928698_74928792_INS 25 95 (0) C L1PB_orf2#LINE/L1 (1563) 1731 1661 m_b2s551i16
X_74928698_74 25 GCATATGTTGAATTATCAGTGCATCACTGATATGAAACCCACTTGATCAT 74
i i ii vv v i
C L1PB_orf2#LIN 1731 GCGTATGTTAAACCATCCCTGCATCCCTGGTATGAAACCCACTTGATCAT 1682
X_74928698_74 75 GGTGGATTATCTTTTTGATAT 95
C L1PB_orf2#LIN 1681 GGTGGATTATCTTTTTGATAT 1661
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.79
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 53 1.9 0.0 0.0 X_75176075_75176136_INS 11 62 (0) + (T)n Simple_repeat 1 52 (0) 810
ANNOTATION EVIDENCE:
53 1.95 0.00 0.00 X_75176075_75176136_INS 11 62 0 + (T)n Simple_repeat 1 52 0
53 1.95 0.00 0.00 X_75176075_75176136_INS 11 62 (0) (T)n#Simple_repeat 1 52 (0) c_b2s251i73
X_75176075_75 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTT 60
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_75176075_75 61 TT 62
(T)n#Simple_r 51 TT 52
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 67 1.4 0.0 0.0 X_75180305_75180380_INS 2 76 (0) + (A)n Simple_repeat 1 75 (0) 811
ANNOTATION EVIDENCE:
67 1.35 0.00 0.00 X_75180305_75180380_INS 2 76 0 + (A)n Simple_repeat 1 75 0
67 1.35 0.00 0.00 X_75180305_75180380_INS 2 76 (0) (A)n#Simple_repeat 1 75 (0) m_b2s252i31
X_75180305_75 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_75180305_75 52 AAAAAAAAAAAAAAAAAAAAAACAA 76
v
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAA 75
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 59 1.8 0.0 0.0 X_75196877_75196935_INS 3 59 (0) + (T)n Simple_repeat 1 57 (0) 812
ANNOTATION EVIDENCE:
59 1.78 0.00 0.00 X_75196877_75196935_INS 3 59 0 + (T)n Simple_repeat 1 57 0
59 1.78 0.00 0.00 X_75196877_75196935_INS 3 59 (0) (T)n#Simple_repeat 1 57 (0) c_b2s251i72
X_75196877_75 3 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 52
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_75196877_75 53 GTTTTTT 59
v
(T)n#Simple_r 51 TTTTTTT 57
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 45 0.0 0.0 0.0 X_7520913_7520978_INS 25 65 (1) + (ATAG)n Simple_repeat 1 41 (0) 813
ANNOTATION EVIDENCE:
45 0.00 0.00 0.00 X_7520913_7520978_INS 25 65 1 + (ATAG)n Simple_repeat 1 41 0
45 0.00 0.00 0.00 X_7520913_7520978_INS 25 65 (1) (ATAG)n#Simple_repeat 1 41 (0) c_b1s251i9
X_7520913_752 25 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 65
(ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 41
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 36 12.0 6.9 0.0 X_75242419_75242497_INS 3 74 (5) + (AT)n Simple_repeat 1 77 (0) 814
ANNOTATION EVIDENCE:
36 12.03 6.94 0.00 X_75242419_75242497_INS 3 74 5 + (AT)n Simple_repeat 1 77 0
36 12.03 6.94 0.00 X_75242419_75242497_INS 3 74 (5) (AT)n#Simple_repeat 1 77 (0) m_b2s252i30
X_75242419_75 3 ATATATATAT-TCTATATATAGA-ATATATATATA-ACAAGAATATATAT 49
- v v - - i viv
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_75242419_75 50 AT-TCTATATATAGA-ATATATATATA 74
- v v -
(AT)n#Simple_ 51 ATATATATATATATATATATATATATA 77
Matrix = Unknown
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5)
+ 90 1.2 0.0 0.0 X_75262133_75262217_INS 2 85 (0) + (T)n Simple_repeat 1 84 (0) 815
ANNOTATION EVIDENCE:
90 1.20 0.00 0.00 X_75262133_75262217_INS 2 85 0 + (T)n Simple_repeat 1 84 0
90 1.20 0.00 0.00 X_75262133_75262217_INS 2 85 (0) (T)n#Simple_repeat 1 84 (0) c_b2s251i71
X_75262133_75 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_75262133_75 52 TTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTT 85
v
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 84
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0)
+ 30 4.5 2.0 4.1 X_7540881_7540932_INS 2 51 (1) + (TCCT)n Simple_repeat 1 49 (0) 816
ANNOTATION EVIDENCE:
30 4.54 2.00 4.08 X_7540881_7540932_INS 2 51 1 + (TCCT)n Simple_repeat 1 49 0
30 4.54 2.00 4.08 X_7540881_7540932_INS 2 51 (1) (TCCT)n#Simple_repeat 1 49 (0) c_b1s251i8
X_7540881_754 2 TCCTTCCTTCCTTCC-TCCTTCCCTCTCTTCCTTCCTTCTTTCCTTTCCT 50
- i - i -
(TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCC-TTCCT 48
X_7540881_754 51 T 51
(TCCT)n#Simpl 49 T 49
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3)
+ 32 13.1 0.0 0.0 X_75429228_75429278_INS 1 50 (1) + (TA)n Simple_repeat 1 50 (0) 817
ANNOTATION EVIDENCE:
32 13.08 0.00 0.00 X_75429228_75429278_INS 1 50 1 + (TA)n Simple_repeat 1 50 0
32 13.08 0.00 0.00 X_75429228_75429278_INS 1 50 (1) (TA)n#Simple_repeat 1 50 (0) m_b2s252i29
X_75429228_75 1 TATATATATCTACATATATATCTACATATATATATCTATATATATATCTA 50
v i v i v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 50 1.8 5.2 0.0 X_75787376_75787436_INS 2 59 (2) + (AT)n Simple_repeat 1 61 (0) 818
ANNOTATION EVIDENCE:
50 1.75 5.17 0.00 X_75787376_75787436_INS 2 59 2 + (AT)n Simple_repeat 1 61 0
50 1.75 5.17 0.00 X_75787376_75787436_INS 2 59 (2) (AT)n#Simple_repeat 1 61 (0) c_b2s251i70
X_75787376_75 2 ATATATATATA-ATATATATATAT-TATATATAAATATATATATATATAT 49
- - v
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_75787376_75 50 -TATATATATA 59
-
(AT)n#Simple_ 51 ATATATATATA 61
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3)
+ 30 2.4 0.0 8.5 X_75903996_75904056_INS 2 52 (9) + (TGATCTATA)n Simple_repeat 1 47 (0) 819
ANNOTATION EVIDENCE:
30 2.36 0.00 8.51 X_75903996_75904056_INS 2 52 9 + (TGATCTATA)n Simple_repeat 1 47 0
30 2.36 0.00 8.51 X_75903996_75904056_INS 2 52 (9) (TGATCTATA)n#Simple_repeat 1 47 (0) c_b2s251i69
X_75903996_75 2 TGATCTATATGATCATATATGTGATGTATATGATCTATATGATCATATAT 51
- -- v -
(TGATCTATA)n# 1 TGATCTATATGATC-TATA--TGATCTATATGATCTATATGATC-TATAT 46
X_75903996_75 52 G 52
(TGATCTATA)n# 47 G 47
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4)
+ 31 14.9 0.0 0.0 X_76052972_76053026_INS 2 53 (2) + (TA)n Simple_repeat 1 52 (0) 820
ANNOTATION EVIDENCE:
31 14.91 0.00 0.00 X_76052972_76053026_INS 2 53 2 + (TA)n Simple_repeat 1 52 0
31 14.91 0.00 0.00 X_76052972_76053026_INS 2 53 (2) (TA)n#Simple_repeat 1 52 (0) m_b2s252i28
X_76052972_76 2 TATATCTATATATATGGATCTATATATCTATATATATAGATATATAGATA 51
v iv v v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_76052972_76 52 TA 53
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 0.17 (1/6)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 30 11.8 5.5 0.0 X_7620647_7620702_INS 2 56 (0) + (CT)n Simple_repeat 1 58 (0) 821
ANNOTATION EVIDENCE:
30 11.79 5.45 0.00 X_7620647_7620702_INS 2 56 0 + (CT)n Simple_repeat 1 58 0
30 11.79 5.45 0.00 X_7620647_7620702_INS 2 56 (0) (CT)n#Simple_repeat 1 58 (0) m_b1s252i4
X_7620647_762 2 CTGTCTCTC-CTCTCTGTCTCCCTGTCTCTC-CTCTCTGTCTCCCTCTCT 49
v - v i v - v i
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50
X_7620647_762 50 CTC-CTCT 56
-
(CT)n#Simple_ 51 CTCTCTCT 58
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3)
+ 53 2.0 0.0 0.0 X_76256248_76256300_INS 2 53 (0) + (AGAA)n Simple_repeat 1 52 (0) 822
ANNOTATION EVIDENCE:
53 1.96 0.00 0.00 X_76256248_76256300_INS 2 53 0 + (AGAA)n Simple_repeat 1 52 0
53 1.96 0.00 0.00 X_76256248_76256300_INS 2 53 (0) (AGAA)n#Simple_repeat 1 52 (0) c_b2s251i68
X_76256248_76 2 AGAAAGAAAGGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 51
i
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50
X_76256248_76 52 AA 53
(AGAA)n#Simpl 51 AA 52
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2487 2.1 0.0 1.1 X_76339886_76340212_INS 11 327 (0) C AluY SINE/Alu (0) 311 1 823
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_76339886_76340212_INS 11 43 284 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_76339886_76340212_INS 11 43 (284) (T)n#Simple_repeat 1 33 (0) c_b2s251i67
X_76339886_76 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
(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)
2487 2.13 0.00 1.07 X_76339886_76340212_INS 44 327 0 C AluY SINE/Alu 1 281 30
2487 2.13 0.00 1.07 X_76339886_76340212_INS 44 327 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i81
X_76339886_76 44 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 93
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_76339886_76 94 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 143
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_76339886_76 144 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 193
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_76339886_76 194 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATTTTTTAGCCGGGAT 243
- i-- v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCG--TGTTAGCCAGGAT 85
X_76339886_76 244 GGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 293
C AluY#SINE/Alu 84 GGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 35
X_76339886_76 294 CTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 327
C AluY#SINE/Alu 34 CTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.51
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.01 (3 / 283), avg. gap size = 1.00 (3 / 3)
+ 29 3.2 0.0 0.0 X_76475139_76475192_INS 1 32 (22) + (GAAA)n Simple_repeat 1 32 (0) 824
ANNOTATION EVIDENCE:
29 3.23 0.00 0.00 X_76475139_76475192_INS 1 32 22 + (GAAA)n Simple_repeat 1 32 0
29 3.23 0.00 0.00 X_76475139_76475192_INS 1 32 (22) (GAAA)n#Simple_repeat 1 32 (0) c_b2s251i66
X_76475139_76 1 GAAAGAAAGAAAGAGAGAAAGAAAGAAAGAAA 32
i
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 32
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 2865 1.6 0.0 0.0 X_76574656_76574980_INS 7 317 (8) + AluY SINE/Alu 1 311 (0) 825
ANNOTATION EVIDENCE:
2865 1.61 0.00 0.00 X_76574656_76574980_INS 7 317 8 + AluY SINE/Alu 1 311 0
2865 1.61 0.00 0.00 X_76574656_76574980_INS 7 317 (8) AluY#SINE/Alu 1 311 (0) c_b2s352i82
X_76574656_76 7 GGCCGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGA 56
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_76574656_76 57 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 106
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_76574656_76 107 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 156
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_76574656_76 157 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 206
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_76574656_76 207 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 256
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_76574656_76 257 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 306
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_76574656_76 307 AAAAAAAAAAA 317
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.63
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 57 6.1 0.0 0.0 X_76971618_76971687_INS 1 69 (1) + (T)n Simple_repeat 1 69 (0) 826
ANNOTATION EVIDENCE:
57 6.07 0.00 0.00 X_76971618_76971687_INS 1 69 1 + (T)n Simple_repeat 1 69 0
57 6.07 0.00 0.00 X_76971618_76971687_INS 1 69 (1) (T)n#Simple_repeat 1 69 (0) c_b2s251i65
X_76971618_76 1 TTTTTTTTTTTTTTTTTTTTTTTTAAAATTTTTTTTTTTTTTTTTTTTTT 50
vvvv
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_76971618_76 51 TTTTTTTTTTTTTTTTTTT 69
(T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTT 69
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 52 3.7 0.0 0.0 X_77260761_77260817_INS 2 57 (0) + (CATAT)n Simple_repeat 1 56 (0) 827
ANNOTATION EVIDENCE:
52 3.71 0.00 0.00 X_77260761_77260817_INS 2 57 0 + (CATAT)n Simple_repeat 1 56 0
52 3.71 0.00 0.00 X_77260761_77260817_INS 2 57 (0) (CATAT)n#Simple_repeat 1 56 (0) c_b2s251i64
X_77260761_77 2 CATATCATATCATATCATATCATATCATACCATATCATACCATATCATAT 51
i i
(CATAT)n#Simp 1 CATATCATATCATATCATATCATATCATATCATATCATATCATATCATAT 50
X_77260761_77 52 CATATC 57
(CATAT)n#Simp 51 CATATC 56
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 29 2.2 8.7 0.0 X_77331015_77331140_INS 34 79 (47) + (ATTTCTA)n Simple_repeat 1 50 (0) 828
ANNOTATION EVIDENCE:
29 2.21 8.70 0.00 X_77331015_77331140_INS 34 79 47 + (ATTTCTA)n Simple_repeat 1 50 0
29 2.21 8.70 0.00 X_77331015_77331140_INS 34 79 (47) (ATTTCTA)n#Simple_repeat 1 50 (0) c_b2s251i63
X_77331015_77 34 ATTTCTAATTTCTAATTTCTAA-TT-T-ATTTCTAA-TTATAATTTCTAA 79
- - - - v
(ATTTCTA)n#Si 1 ATTTCTAATTTCTAATTTCTAATTTCTAATTTCTAATTTCTAATTTCTAA 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4)
+ 2746 2.0 0.0 0.0 X_77357579_77357893_INS 16 315 (0) + AluY SINE/Alu 1 300 (11) 829
ANNOTATION EVIDENCE:
2746 2.00 0.00 0.00 X_77357579_77357893_INS 16 315 0 + AluY SINE/Alu 1 300 11
2746 2.00 0.00 0.00 X_77357579_77357893_INS 16 315 (0) AluY#SINE/Alu 1 300 (11) c_b2s352i83
X_77357579_77 16 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 65
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_77357579_77 66 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 115
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_77357579_77 116 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 165
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_77357579_77 166 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 215
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_77357579_77 216 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 265
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_77357579_77 266 CAGCCTGGGCGACAGAGCGAGACTCCTTCTCAAAAAAAAAAAAAAAAAAA 315
v
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.72
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 299), avg. gap size = 0.0 (0 / 0)
+ 59 1.5 0.0 0.0 X_77478470_77478537_INS 2 68 (0) + (A)n Simple_repeat 1 67 (0) 830
ANNOTATION EVIDENCE:
59 1.51 0.00 0.00 X_77478470_77478537_INS 2 68 0 + (A)n Simple_repeat 1 67 0
59 1.51 0.00 0.00 X_77478470_77478537_INS 2 68 (0) (A)n#Simple_repeat 1 67 (0) m_b2s252i27
X_77478470_77 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA 51
v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_77478470_77 52 AAAAAAAAAAAAAAAAA 68
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAA 67
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 1000 5.2 0.1 2.4 X_77521014_77521190_INS 1 176 (1) C SVA_F Retroposon/SVA (520) 855 543 831
ANNOTATION EVIDENCE:
627 9.46 0.57 9.94 X_77521014_77521190_INS 1 176 1 C SVA_F Retroposon/SVA 543 703 672
627 9.46 0.57 9.94 X_77521014_77521190_INS 1 176 (1) C SVA_F#Retroposon/SVA (672) 703 543 m_b2s502i14
X_77521014_77 1 GGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCTGTGCA 50
---- i v i
C SVA_F#Retropo 703 GGGGGGCTGACCCCCCCACCTCCC----GGACGGGGCGGCTGGCCGGGCG 658
X_77521014_77 51 GAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCA 100
v ? i vv i i
C SVA_F#Retropo 657 GAGGCGCTCCTCACNTCCCGGACGGGGCGGCCGGGCGGAGGCGCTCCTCA 608
X_77521014_77 101 CTTCCCAGACGGGGCGGCTGGCCGGGCGGGGG-GCTGACCCCACCACCTC 149
? i ? - - i i- -- i -------
C SVA_F#Retropo 607 CNTCCCGGACGGNG-GGC-GGCCGGGCGGAGACGCT--CCTCA------- 569
X_77521014_77 150 CCTCCTGGATGGGGCGGCTGGCCGGGC 176
i i -
C SVA_F#Retropo 568 CCTCCCGGACGGGGCGGC-GGCCGGGC 543
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.77
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.10 (17 / 175), avg. gap size = 1.00 (17 / 17)
1000 4.61 0.00 1.32 X_77521014_77521190_INS 23 176 1 C SVA_F Retroposon/SVA 704 855 520
1000 4.61 0.00 1.32 X_77521014_77521190_INS 23 176 (1) C SVA_F#Retroposon/SVA (520) 855 704 m_b2s502i15
X_77521014_77 23 CCTCCCGGACGGGGCGGCTGGCTGTGCAGAGGGGCTCCTCACTTCCCAGT 72
- i v
C SVA_F#Retropo 855 CCTCCCGGACGGGGCGG-TGGCCGGGCAGAGGGGCTCCTCACTTCCCAGT 807
X_77521014_77 73 AGGGGCGGCCGGGCAGAGGCGCCCCTCACTTCCCAGACGGGGCGGCTGGC 122
i i
C SVA_F#Retropo 806 AGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCGGACGGGGCGGCTGGC 757
X_77521014_77 123 CGGGCGGGGGGCTGACCCCACCACCTCCCTCCTGGATGGGGCGGCTGGCC 172
v - i i
C SVA_F#Retropo 756 CGGGCGGGGGGCTGACCCCCCCACCT-CCTCCCGGACGGGGCGGCTGGCC 708
X_77521014_77 173 GGGC 176
C SVA_F#Retropo 707 GGGC 704
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.27
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.00 (2 / 2)
+ 114 5.8 4.3 2.1 X_77524603_77524790_INS 2 188 (0) + (ATATAAT)n Simple_repeat 1 191 (0) 832
ANNOTATION EVIDENCE:
114 5.82 4.28 2.09 X_77524603_77524790_INS 2 188 0 + (ATATAAT)n Simple_repeat 1 191 0
114 5.82 4.28 2.09 X_77524603_77524790_INS 2 188 (0) (ATATAAT)n#Simple_repeat 1 191 (0) m_b2s252i26
X_77524603_77 2 ATAT-ATATATAATATATAATATATAATATAT--TAT-T-ATATATATTA 46
- -- - - v
(ATATAAT)n#Si 1 ATATAATATATAATATATAATATATAATATATAATATATAATATATAATA 50
X_77524603_77 47 TAAATTATATAATATATATAATAT-ATATATTATATATAATATAT--TAT 93
v v vv - v --
(ATATAAT)n#Si 51 TATAATATATAATATATAATATATAATATATAATATATAATATATAATAT 100
X_77524603_77 94 ATATTATATAATATATAATATATATAATATATAATATATTATATATAATA 143
v - - v
(ATATAAT)n#Si 101 ATAATATATAATATAT-A-ATATATAATATATAATATATAATATATAATA 148
X_77524603_77 144 TATTATATATTATATAATATATATATAATATATAATATATAATAT 188
v v - -
(ATATAAT)n#Si 149 TATAATATATAATAT-ATA-ATATATAATATATAATATATAATAT 191
Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.05 (10 / 186), avg. gap size = 1.20 (12 / 10)
+ 100 3.5 0.0 0.0 X_77645925_77646043_INS 2 119 (0) + (A)n Simple_repeat 1 118 (0) 833
ANNOTATION EVIDENCE:
100 3.48 0.00 0.00 X_77645925_77646043_INS 2 119 0 + (A)n Simple_repeat 1 118 0
100 3.48 0.00 0.00 X_77645925_77646043_INS 2 119 (0) (A)n#Simple_repeat 1 118 (0) m_b2s252i25
X_77645925_77 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_77645925_77 52 AAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAACCAAACAAAAAAAAAA 101
v vv v
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100
X_77645925_77 102 AAAAAAAAAAAAAAAAAA 119
(A)n#Simple_r 101 AAAAAAAAAAAAAAAAAA 118
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0)
+ 2043 0.4 0.0 0.0 X_77671394_77671642_INS 4 249 (0) + L1HS LINE/L1 5931 6155 (0) 834
ANNOTATION EVIDENCE:
17 5.00 0.00 0.00 X_77671394_77671642_INS 229 249 0 + (A)n Simple_repeat 1 21 0
17 5.00 0.00 0.00 X_77671394_77671642_INS 229 249 (0) (A)n#Simple_repeat 1 21 (0) m_b2s252i24
X_77671394_77 229 AAGAAAAAAAAAAAAAAAAAA 249
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
2043 0.44 0.00 0.00 X_77671394_77671642_INS 4 228 21 + L1HS_3end LINE/L1 678 902 0
2043 0.44 0.00 0.00 X_77671394_77671642_INS 4 228 (21) L1HS_3end#LINE/L1 678 902 (0) m_b2s551i17
X_77671394_77 4 GAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCT 53
L1HS_3end#LIN 678 GAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCT 727
X_77671394_77 54 GGGGACTGTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATA 103
L1HS_3end#LIN 728 GGGGACTGTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATA 777
X_77671394_77 104 TACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCAC 153
i
L1HS_3end#LIN 778 TACCTAATGCTAGATGACACGTTAGTGGGTGCAGCGCACCAGCATGGCAC 827
X_77671394_77 154 ATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAAC 203
L1HS_3end#LIN 828 ATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAAC 877
X_77671394_77 204 TTAGAGTATAATAAAAAAAAAAAAA 228
L1HS_3end#LIN 878 TTAGAGTATAATAAAAAAAAAAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.04
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 224), avg. gap size = 0.0 (0 / 0)
+ 50 2.0 2.0 0.0 X_77799659_77799710_INS 2 52 (0) + (AT)n Simple_repeat 1 52 (0) 835
ANNOTATION EVIDENCE:
50 2.00 1.96 0.00 X_77799659_77799710_INS 2 52 0 + (AT)n Simple_repeat 1 52 0
50 2.00 1.96 0.00 X_77799659_77799710_INS 2 52 (0) (AT)n#Simple_repeat 1 52 (0) c_b2s251i62
X_77799659_77 2 ATATATATGT-TATATATATATATATATATATATATATATATATATATAT 50
i -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_77799659_77 51 AT 52
(AT)n#Simple_ 51 AT 52
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 49 4.1 0.0 0.0 X_78398182_78398238_INS 4 54 (3) + (AT)n Simple_repeat 1 51 (0) 836
ANNOTATION EVIDENCE:
49 4.08 0.00 0.00 X_78398182_78398238_INS 4 54 3 + (AT)n Simple_repeat 1 51 0
49 4.08 0.00 0.00 X_78398182_78398238_INS 4 54 (3) (AT)n#Simple_repeat 1 51 (0) c_b2s251i61
X_78398182_78 4 ATATATATATATACATACATATATATATATATATATATATATATATATAT 53
i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_78398182_78 54 A 54
(AT)n#Simple_ 51 A 51
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 2608 1.1 0.0 0.0 X_78415629_78415953_INS 17 325 (0) C AluY SINE/Alu (0) 311 2 837
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_78415629_78415953_INS 17 45 280 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_78415629_78415953_INS 17 45 (280) (T)n#Simple_repeat 1 29 (0) c_b2s251i60
X_78415629_78 17 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
(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)
2608 1.07 0.00 0.00 X_78415629_78415953_INS 46 325 0 C AluY SINE/Alu 2 281 30
2608 1.07 0.00 0.00 X_78415629_78415953_INS 46 325 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i84
X_78415629_78 46 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 95
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_78415629_78 96 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 145
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_78415629_78 146 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 195
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_78415629_78 196 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGT 245
v
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_78415629_78 246 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGCGCTG 295
i
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_78415629_78 296 GGATTACAGGCGTGAGCCACCGCGCCCGGC 325
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.08
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 413 17.6 0.0 0.0 X_78557128_78557195_INS 1 68 (0) C MER50B LTR/ERV1 (285) 412 345 838
ANNOTATION EVIDENCE:
413 17.65 0.00 0.00 X_78557128_78557195_INS 1 68 0 C MER50B LTR/ERV1 345 412 285
413 17.65 0.00 0.00 X_78557128_78557195_INS 1 68 (0) C MER50B#LTR/ERV1 (285) 412 345 m_b2s502i16
X_78557128_78 1 TATGCTGGCCCCTTTCCTACAATTCTTCCCTTAGGGTGGGTTGCCCACAT 50
v v i i ii i i
C MER50B#LTR/ER 412 TAGGCTCGCCTCTTTCCCATGATTCTTCCCTTAGGGTGGGCTGCCCGCAT 363
X_78557128_78 51 GCACAGTGCCTATCTTAC 68
i ivi
C MER50B#LTR/ER 362 GCGCAGTGCCCTCCTTAC 345
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.09
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 34 0.0 0.0 0.0 X_78578248_78578298_INS 1 32 (19) + (TTCT)n Simple_repeat 1 32 (0) 839
ANNOTATION EVIDENCE:
34 0.00 0.00 0.00 X_78578248_78578298_INS 1 32 19 + (TTCT)n Simple_repeat 1 32 0
34 0.00 0.00 0.00 X_78578248_78578298_INS 1 32 (19) (TTCT)n#Simple_repeat 1 32 (0) c_b2s251i59
X_78578248_78 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 32
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 32
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 15 5.6 0.0 0.0 X_78578248_78578298_INS 33 51 (0) + (CT)n Simple_repeat 1 19 (0) 840
ANNOTATION EVIDENCE:
15 5.56 0.00 0.00 X_78578248_78578298_INS 33 51 0 + (CT)n Simple_repeat 1 19 0
15 5.56 0.00 0.00 X_78578248_78578298_INS 33 51 (0) (CT)n#Simple_repeat 1 19 (0) m_b2s252i23
X_78578248_78 33 CTCTCTCTCTCTCCCTCTC 51
i
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTC 19
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 421 10.2 0.0 0.0 X_78617398_78617462_INS 2 60 (5) C L1P4 LINE/L1 (376) 5787 5729 841
ANNOTATION EVIDENCE:
421 10.17 0.00 0.00 X_78617398_78617462_INS 2 60 5 C L1PA13_3end LINE/L1 476 534 376
421 10.17 0.00 0.00 X_78617398_78617462_INS 2 60 (5) C L1PA13_3end#LINE/L1 (376) 534 476 m_b2s551i18
X_78617398_78 2 TATGTATCGCATTTTCTTTATCCACTCTATCATTGATGGACATTTAGGCT 51
i i v i i
C L1PA13_3end#L 534 TATGTACCACATTTTCTTTATCCAGTCTATCATTGATGGGCATTTAGGTT 485
X_78617398_78 52 GATACCATG 60
v
C L1PA13_3end#L 484 GATTCCATG 476
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.04
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 50 1.8 0.0 0.0 X_78651766_78651823_INS 2 58 (0) + (A)n Simple_repeat 1 57 (0) 842
ANNOTATION EVIDENCE:
50 1.79 0.00 0.00 X_78651766_78651823_INS 2 58 0 + (A)n Simple_repeat 1 57 0
50 1.79 0.00 0.00 X_78651766_78651823_INS 2 58 (0) (A)n#Simple_repeat 1 57 (0) m_b2s252i22
X_78651766_78 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA 51
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_78651766_78 52 AAAAAAA 58
(A)n#Simple_r 51 AAAAAAA 57
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 2541 1.4 0.0 0.0 X_79046461_79046748_INS 14 288 (0) + AluY SINE/Alu 37 311 (0) 843
ANNOTATION EVIDENCE:
2541 1.45 0.00 0.00 X_79046461_79046748_INS 14 288 0 + AluY SINE/Alu 37 311 0
2541 1.45 0.00 0.00 X_79046461_79046748_INS 14 288 (0) AluY#SINE/Alu 37 311 (0) c_b2s352i85
X_79046461_79 14 CTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCAT 63
AluY#SINE/Alu 37 CTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCAT 86
X_79046461_79 64 CCTGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAG 113
v
AluY#SINE/Alu 87 CCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAG 136
X_79046461_79 114 CTGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGG 163
i i
AluY#SINE/Alu 137 CCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGG 186
X_79046461_79 164 CAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATC 213
AluY#SINE/Alu 187 CAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATC 236
X_79046461_79 214 CCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA 263
v
AluY#SINE/Alu 237 GCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA 286
X_79046461_79 264 AAAAAAAAAAAAAAAAAAAAAAAAA 288
AluY#SINE/Alu 287 AAAAAAAAAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.14
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 274), avg. gap size = 0.0 (0 / 0)
+ 1078 3.0 0.0 0.0 X_7909220_7909394_INS 9 175 (0) C AluY SINE/Alu (0) 311 161 844
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 X_7909220_7909394_INS 9 53 122 + (T)n Simple_repeat 1 45 0
50 0.00 0.00 0.00 X_7909220_7909394_INS 9 53 (122) (T)n#Simple_repeat 1 45 (0) c_b1s251i7
X_7909220_790 9 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 53
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
1078 3.05 0.00 0.00 X_7909220_7909394_INS 54 175 0 C AluY SINE/Alu 161 282 29
1078 3.05 0.00 0.00 X_7909220_7909394_INS 54 175 (0) C AluY#SINE/Alu (29) 282 161 m_b1s357i11
X_7909220_790 54 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 103
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_7909220_790 104 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 153
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_7909220_790 154 GCCTCCCAAGTAGCTGGGACTA 175
i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTA 161
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.43
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 22 14.6 0.0 2.6 X_79094940_79094990_INS 1 40 (11) + (AT)n Simple_repeat 1 39 (0) 845
ANNOTATION EVIDENCE:
22 14.55 0.00 2.56 X_79094940_79094990_INS 1 40 11 + (AT)n Simple_repeat 1 39 0
22 14.55 0.00 2.56 X_79094940_79094990_INS 1 40 (11) (AT)n#Simple_repeat 1 39 (0) m_b2s252i21
X_79094940_79 1 ATATATATATACAGTTACAGTGTATATATATATATATATA 40
i vv i - i
(AT)n#Simple_ 1 ATATATATATATATATATA-TATATATATATATATATATA 39
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1)
+ 39 6.8 0.0 0.0 X_7912338_7912392_INS 2 48 (7) + (AT)n Simple_repeat 1 47 (0) 846
ANNOTATION EVIDENCE:
39 6.83 0.00 0.00 X_7912338_7912392_INS 2 48 7 + (AT)n Simple_repeat 1 47 0
39 6.83 0.00 0.00 X_7912338_7912392_INS 2 48 (7) (AT)n#Simple_repeat 1 47 (0) c_b1s251i6
X_7912338_791 2 ATATATACATACACATATATATATATATATATATATATATATATATA 48
i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 40 3.4 4.8 1.5 X_79267668_79267731_INS 1 63 (1) + (AAGA)n Simple_repeat 1 65 (0) 847
ANNOTATION EVIDENCE:
40 3.35 4.76 1.54 X_79267668_79267731_INS 1 63 1 + (AAGA)n Simple_repeat 1 65 0
40 3.35 4.76 1.54 X_79267668_79267731_INS 1 63 (1) (AAGA)n#Simple_repeat 1 65 (0) m_b2s252i20
X_79267668_79 1 AAGAAAGAAAGAAAGAAAGAAAGAATGAAAGAAAAGAAAGAAAG-AAGGA 49
v - - i
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGAA 49
X_79267668_79 50 AGAAAG--AGAAAGAA 63
--
(AAGA)n#Simpl 50 AGAAAGAAAGAAAGAA 65
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.33 (4 / 3)
+ 638 13.9 0.8 1.7 X_79470624_79470741_INS 2 118 (0) + SVA_A Retroposon/SVA 467 582 (805) 848
ANNOTATION EVIDENCE:
638 13.92 0.85 1.72 X_79470624_79470741_INS 2 118 0 + SVA_A Retroposon/SVA 467 582 805
638 13.92 0.85 1.72 X_79470624_79470741_INS 2 118 (0) SVA_A#Retroposon/SVA 467 582 (805) m_b2s502i17
X_79470624_79 2 GTGAGGAGCTCCTCTGCCCGGCAGCAACC-CCGTCTGGGAGGTGAGGAGT 50
vi v -- -i ? i
SVA_A#Retropo 467 GTGAGGAGCGTCTCTGCCCGGCCGC--CCATCGTCTGGGANGTGAGGAGC 514
X_79470624_79 51 GTCTCTGCCCGGTCACCCCATCTGAGAATTGAGGAGCCCCTCTGCCCGGC 100
i i i i i v v
SVA_A#Retropo 515 GCCTCTGCCCGGCCGCCCCGTCTGGGAAGTGAGGAGCGCCTCTGCCCGGC 564
X_79470624_79 101 AGCCACCCCGTCCAGGAA 118
v i ii
SVA_A#Retropo 565 CGCCGCCCCGTCTGGGAA 582
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.83
Transitions / transversions = 2.20 (11/5)
Gap_init rate = 0.03 (3 / 116), avg. gap size = 1.00 (3 / 3)
+ 2489 2.5 0.0 0.4 X_79571253_79571577_INS 1 325 (0) C AluY SINE/Alu (0) 311 2 849
ANNOTATION EVIDENCE:
48 0.00 0.00 0.00 X_79571253_79571577_INS 1 44 281 + (T)n Simple_repeat 1 44 0
48 0.00 0.00 0.00 X_79571253_79571577_INS 1 44 (281) (T)n#Simple_repeat 1 44 (0) c_b2s251i58
X_79571253_79 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
2489 2.50 0.00 0.36 X_79571253_79571577_INS 45 325 0 C AluY SINE/Alu 2 281 30
2489 2.50 0.00 0.36 X_79571253_79571577_INS 45 325 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i86
X_79571253_79 45 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGGGATCT 94
i v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_79571253_79 95 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 144
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_79571253_79 145 GCCTCCCAAGTAGCTGGGACGACAGGCGCCCGCCACTACGCCCGGCTAAT 194
i v i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_79571253_79 195 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 244
- v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_79571253_79 245 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 294
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_79571253_79 295 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 325
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.88
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 1909 1.0 0.0 0.0 X_79750905_79751112_INS 1 208 (0) + L1P1 LINE/L1 5510 5717 (438) 850
ANNOTATION EVIDENCE:
1909 0.96 0.00 0.00 X_79750905_79751112_INS 1 208 0 + L1HS_3end LINE/L1 257 464 438
1909 0.96 0.00 0.00 X_79750905_79751112_INS 1 208 (0) L1HS_3end#LINE/L1 257 464 (438) m_b2s551i19
X_79750905_79 1 GCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTT 50
L1HS_3end#LIN 257 GCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTT 306
X_79750905_79 51 CAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGA 100
L1HS_3end#LIN 307 CAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGA 356
X_79750905_79 101 AATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAATGAGT 150
v v
L1HS_3end#LIN 357 AATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACT 406
X_79750905_79 151 ATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCA 200
L1HS_3end#LIN 407 ATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCA 456
X_79750905_79 201 CTATTCAC 208
L1HS_3end#LIN 457 CTATTCAC 464
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.97
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 207), avg. gap size = 0.0 (0 / 0)
+ 895 2.6 0.0 0.0 X_79790844_79790958_INS 2 115 (0) + L1P1 LINE/L1 5100 5213 (933) 851
ANNOTATION EVIDENCE:
895 2.63 0.00 0.00 X_79790844_79790958_INS 2 115 0 + L1P1_orf2 LINE/L1 2991 3104 190
895 2.63 0.00 0.00 X_79790844_79790958_INS 2 115 (0) L1P1_orf2#LINE/L1 2991 3104 (190) m_b2s551i20
X_79790844_79 2 AAAACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 51
v v
L1P1_orf2#LIN 2991 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3040
X_79790844_79 52 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 101
L1P1_orf2#LIN 3041 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3090
X_79790844_79 102 AGGCAACCTACAAA 115
i
L1P1_orf2#LIN 3091 AGGCAACCTACAGA 3104
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.68
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 113), avg. gap size = 0.0 (0 / 0)
+ 50 2.0 0.0 0.0 X_80299613_80299663_INS 2 51 (0) + (T)n Simple_repeat 1 50 (0) 852
ANNOTATION EVIDENCE:
50 2.03 0.00 0.00 X_80299613_80299663_INS 2 51 0 + (T)n Simple_repeat 1 50 0
50 2.03 0.00 0.00 X_80299613_80299663_INS 2 51 (0) (T)n#Simple_repeat 1 50 (0) c_b2s251i57
X_80299613_80 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTT 51
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 27 2.5 0.0 8.9 X_80566186_80566241_INS 1 49 (7) + (ATATACGT)n Simple_repeat 1 45 (0) 853
ANNOTATION EVIDENCE:
27 2.49 0.00 8.89 X_80566186_80566241_INS 1 49 7 + (ATATACGT)n Simple_repeat 1 45 0
27 2.49 0.00 8.89 X_80566186_80566241_INS 1 49 (7) (ATATACGT)n#Simple_repeat 1 45 (0) c_b2s251i56
X_80566186_80 1 ATATATGTATATACGTATATACGTACATATATACGTATATACGTATATA 49
i ----
(ATATACGT)n#S 1 ATATACGTATATACGTATATACG----TATATACGTATATACGTATATA 45
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4)
+ 2445 2.5 0.0 2.5 X_80916897_80917226_INS 14 330 (0) C AluY SINE/Alu (0) 311 1 854
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_80916897_80917226_INS 14 42 288 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_80916897_80917226_INS 14 42 (288) (T)n#Simple_repeat 1 29 (0) c_b2s251i55
X_80916897_80 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(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)
2445 2.49 0.00 2.49 X_80916897_80917226_INS 43 330 0 C AluY SINE/Alu 1 281 30
2445 2.49 0.00 2.49 X_80916897_80917226_INS 43 330 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i87
X_80916897_80 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 92
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_80916897_80 93 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 142
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_80916897_80 143 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 192
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_80916897_80 193 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 242
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_80916897_80 243 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 292
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_80916897_80 293 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 330
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 2549 2.8 0.0 0.0 X_80948155_80948480_INS 15 325 (1) C AluY SINE/Alu (0) 311 2 855
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 X_80948155_80948480_INS 15 44 282 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 X_80948155_80948480_INS 15 44 (282) (T)n#Simple_repeat 1 30 (0) c_b2s251i54
X_80948155_80 15 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(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)
2549 2.80 0.00 0.00 X_80948155_80948480_INS 45 325 1 C AluY SINE/Alu 2 282 29
2549 2.80 0.00 0.00 X_80948155_80948480_INS 45 325 (1) C AluY#SINE/Alu (29) 282 2 c_b2s352i88
X_80948155_80 45 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 94
v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_80948155_80 95 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCATGCCATTCTCCTGCCTCA 144
i
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_80948155_80 145 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 194
i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_80948155_80 195 TTTGTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 244
v v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 83
X_80948155_80 245 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 294
C AluY#SINE/Alu 82 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 33
X_80948155_80 295 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 325
C AluY#SINE/Alu 32 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.21
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 3474 1.5 0.0 0.0 X_81036944_81037344_INS 8 401 (0) + L1P1 LINE/L1 3627 4020 (2126) 856
ANNOTATION EVIDENCE:
3474 1.52 0.00 0.00 X_81036944_81037344_INS 8 401 0 + L1P1_orf2 LINE/L1 1518 1911 1383
3474 1.52 0.00 0.00 X_81036944_81037344_INS 8 401 (0) L1P1_orf2#LINE/L1 1518 1911 (1383) m_b2s551i21
X_81036944_81 8 TAACTCATTTTATGAGGCCAGCATCATTCTGATACCAAAGCCGGGCAGAG 57
i ?
L1P1_orf2#LIN 1518 TAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAGCCNGGCAGAG 1567
X_81036944_81 58 ACACAACCAAAAAAGAGAATTTTAGACCAATATCCTTGATGAACATTGAT 107
L1P1_orf2#LIN 1568 ACACAACCAAAAAAGAGAATTTTAGACCAATATCCTTGATGAACATTGAT 1617
X_81036944_81 108 GCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAA 157
L1P1_orf2#LIN 1618 GCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAA 1667
X_81036944_81 158 AAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCT 207
L1P1_orf2#LIN 1668 AAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCT 1717
X_81036944_81 208 GGTTCAATATACGCAAATCAATAAATGTAATCCAGCATATAAACAGAGCC 257
i i i
L1P1_orf2#LIN 1718 GGTTCAACATACGCAAATCAATAAACGTAATCCAGCATATAAACAGAACC 1767
X_81036944_81 258 AAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAAGCCTTTGA 307
i
L1P1_orf2#LIN 1768 AAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGA 1817
X_81036944_81 308 CAAAATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTATTG 357
L1P1_orf2#LIN 1818 CAAAATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTATTG 1867
X_81036944_81 358 ATGGGACGTATTTCAAAATAATAAGAGCTATCTATGACAAACCC 401
i
L1P1_orf2#LIN 1868 ATGGGACGTATCTCAAAATAATAAGAGCTATCTATGACAAACCC 1911
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 1.31
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 393), avg. gap size = 0.0 (0 / 0)
+ 34 0.0 3.0 0.0 X_81152269_81152320_INS 2 34 (18) + (AT)n Simple_repeat 1 34 (0) 857
ANNOTATION EVIDENCE:
34 0.00 3.03 0.00 X_81152269_81152320_INS 2 34 18 + (AT)n Simple_repeat 1 34 0
34 0.00 3.03 0.00 X_81152269_81152320_INS 2 34 (18) (AT)n#Simple_repeat 1 34 (0) c_b2s251i53
X_81152269_81 2 ATATATATATATATATATATATATA-ATATATAT 34
-
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1)
+ 20 25.5 0.0 0.0 X_81172612_81172662_INS 1 50 (1) + (ATAT)n Simple_repeat 1 50 (0) 858
ANNOTATION EVIDENCE:
20 25.54 0.00 0.00 X_81172612_81172662_INS 1 50 1 + (ATAT)n Simple_repeat 1 50 0
20 25.54 0.00 0.00 X_81172612_81172662_INS 1 50 (1) (ATAT)n#Simple_repeat 1 50 (0) m_b2s252i19
X_81172612_81 1 ATGTATACATATGTATACATACATGTATACATATATATGTATACATACAT 50
i i i i i i i i i i
(ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 2628 3.3 0.0 2.3 X_81267702_81268028_INS 18 327 (0) + AluY SINE/Alu 1 303 (8) 859
ANNOTATION EVIDENCE:
2628 3.31 0.00 2.31 X_81267702_81268028_INS 18 327 0 + AluY SINE/Alu 1 303 8
2628 3.31 0.00 2.31 X_81267702_81268028_INS 18 327 (0) AluY#SINE/Alu 1 303 (8) c_b2s352i89
X_81267702_81 18 GGCCGGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 67
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_81267702_81 68 GGCGGGTGGATCATGAGGTCAAGAGATCGAGACCATCCTGGCTAACAAGG 117
i i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_81267702_81 118 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 167
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_81267702_81 168 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCAT 217
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_81267702_81 218 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 267
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_81267702_81 268 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 317
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_81267702_81 318 AAAAAAAAAA 327
AluY#SINE/Alu 294 AAAAAAAAAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.84
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 1.00 (7 / 7)
+ 2770 2.0 0.0 0.0 X_81307626_81307944_INS 17 319 (0) + AluY SINE/Alu 1 303 (8) 860
ANNOTATION EVIDENCE:
2770 1.98 0.00 0.00 X_81307626_81307944_INS 17 319 0 + AluY SINE/Alu 1 303 8
2770 1.98 0.00 0.00 X_81307626_81307944_INS 17 319 (0) AluY#SINE/Alu 1 303 (8) c_b2s352i90
X_81307626_81 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_81307626_81 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTATAACGG 116
i vv
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_81307626_81 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_81307626_81 167 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 216
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_81307626_81 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 266
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_81307626_81 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
X_81307626_81 317 AAA 319
AluY#SINE/Alu 301 AAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.70
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 2721 2.0 0.0 0.3 X_81438277_81438590_INS 12 314 (0) C AluY SINE/Alu (9) 302 1 861
ANNOTATION EVIDENCE:
2721 1.99 0.00 0.33 X_81438277_81438590_INS 12 314 0 C AluY SINE/Alu 1 302 9
2721 1.99 0.00 0.33 X_81438277_81438590_INS 12 314 (0) C AluY#SINE/Alu (9) 302 1 c_b2s352i91
X_81438277_81 12 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 61
C AluY#SINE/Alu 302 TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 253
X_81438277_81 62 TGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 111
v
C AluY#SINE/Alu 252 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGT 203
X_81438277_81 112 TCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACGACAGGCGC 161
i v
C AluY#SINE/Alu 202 TCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGC 153
X_81438277_81 162 CCGCCACTACGCCCGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGTT 211
i -
C AluY#SINE/Alu 152 CCGCCACCACGCCCGGCTAATT-TTTTGTATTTTTAGTAGAGACGGGGTT 104
X_81438277_81 212 TCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCC 261
v i
C AluY#SINE/Alu 103 TCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCC 54
X_81438277_81 262 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 311
C AluY#SINE/Alu 53 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
X_81438277_81 312 GCC 314
C AluY#SINE/Alu 3 GCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.71
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (1 / 302), avg. gap size = 1.00 (1 / 1)
+ 2451 2.8 0.0 2.5 X_81524818_81525142_INS 11 325 (0) C AluY SINE/Alu (0) 311 2 862
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 X_81524818_81525142_INS 11 37 288 + (T)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 X_81524818_81525142_INS 11 37 (288) (T)n#Simple_repeat 1 27 (0) c_b2s251i52
X_81524818_81 11 TTTTTTTTTTTTTTTTTTTTTTTTTTT 37
(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)
2451 2.81 0.00 2.46 X_81524818_81525142_INS 38 325 0 C AluY SINE/Alu 2 282 29
2451 2.81 0.00 2.46 X_81524818_81525142_INS 38 325 (0) C AluY#SINE/Alu (29) 282 2 c_b2s352i92
X_81524818_81 38 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 87
----- -- v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 240
X_81524818_81 88 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 137
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_81524818_81 138 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 187
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_81524818_81 188 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 237
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_81524818_81 238 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 287
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_81524818_81 288 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 325
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 2617 3.0 0.0 2.3 X_81706613_81706933_INS 14 321 (0) + AluY SINE/Alu 1 301 (10) 863
ANNOTATION EVIDENCE:
2617 2.99 0.00 2.33 X_81706613_81706933_INS 14 321 0 + AluY SINE/Alu 1 301 10
2617 2.99 0.00 2.33 X_81706613_81706933_INS 14 321 (0) AluY#SINE/Alu 1 301 (10) c_b2s352i93
X_81706613_81 14 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 63
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_81706613_81 64 GGCGAGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 113
i i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_81706613_81 114 TGAAACCCCGTCTCTACTGAAAATACAAAAAATTAGCCGGGCGCGGTGGC 163
i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_81706613_81 164 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 213
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_81706613_81 214 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 263
i i --
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA--C 248
X_81706613_81 264 CGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 313
----- i
AluY#SINE/Alu 249 -----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_81706613_81 314 AAAAAAAA 321
AluY#SINE/Alu 294 AAAAAAAA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.13
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.02 (7 / 307), avg. gap size = 1.00 (7 / 7)
+ 53 0.0 0.0 3.6 X_81709502_81709562_INS 5 61 (0) + (TTATT)n Simple_repeat 1 55 (0) 864
ANNOTATION EVIDENCE:
53 0.00 0.00 3.64 X_81709502_81709562_INS 5 61 0 + (TTATT)n Simple_repeat 1 55 0
53 0.00 0.00 3.64 X_81709502_81709562_INS 5 61 (0) (TTATT)n#Simple_repeat 1 55 (0) c_b2s251i51
X_81709502_81 5 TTATTTTATTTTATTTTATTTTATTTTATTTTATTTTACATTTTATTTTA 54
--
(TTATT)n#Simp 1 TTATTTTATTTTATTTTATTTTATTTTATTTTATTTT--ATTTTATTTTA 48
X_81709502_81 55 TTTTATT 61
(TTATT)n#Simp 49 TTTTATT 55
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2)
+ 2601 1.4 0.0 0.0 X_81969491_81969811_INS 13 321 (0) C AluY SINE/Alu (0) 311 1 865
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_81969491_81969811_INS 13 40 281 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_81969491_81969811_INS 13 40 (281) (T)n#Simple_repeat 1 28 (0) c_b2s251i50
X_81969491_81 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
(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)
2601 1.42 0.00 0.00 X_81969491_81969811_INS 41 321 0 C AluY SINE/Alu 1 281 30
2601 1.42 0.00 0.00 X_81969491_81969811_INS 41 321 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i94
X_81969491_81 41 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 90
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_81969491_81 91 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 140
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_81969491_81 141 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 190
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_81969491_81 191 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGT 240
v
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_81969491_81 241 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 290
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_81969491_81 291 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 321
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.11
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 60 0.0 0.0 0.0 X_82220393_82220446_INS 1 54 (0) + (CTTT)n Simple_repeat 1 54 (0) 866
ANNOTATION EVIDENCE:
60 0.00 0.00 0.00 X_82220393_82220446_INS 1 54 0 + (CTTT)n Simple_repeat 1 54 0
60 0.00 0.00 0.00 X_82220393_82220446_INS 1 54 (0) (CTTT)n#Simple_repeat 1 54 (0) c_b2s251i49
X_82220393_82 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50
(CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50
X_82220393_82 51 TTCT 54
(CTTT)n#Simpl 51 TTCT 54
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 833 0.0 0.0 0.0 X_82253853_82253951_INS 9 99 (0) C 5S rRNA (30) 91 1 867
ANNOTATION EVIDENCE:
833 0.00 0.00 0.00 X_82253853_82253951_INS 9 99 0 C 5S rRNA 1 91 30
833 0.00 0.00 0.00 X_82253853_82253951_INS 9 99 (0) C 5S#rRNA (30) 91 1 m_b2s502i18
X_82253853_82 9 GTCTCCCATCCAAGTACTAACCAGGCCCGACCCTGCTTAGCTTCCGAGAT 58
C 5S#rRNA 91 GTCTCCCATCCAAGTACTAACCAGGCCCGACCCTGCTTAGCTTCCGAGAT 42
X_82253853_82 59 CAGACGAGATCGGGCGCGTTCAGGGTGGTATGGCCGTAGAC 99
C 5S#rRNA 41 CAGACGAGATCGGGCGCGTTCAGGGTGGTATGGCCGTAGAC 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.00
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0)
+ 41 6.3 0.0 0.0 X_82609861_82609912_INS 1 51 (1) + (TCT)n Simple_repeat 1 51 (0) 868
ANNOTATION EVIDENCE:
41 6.26 0.00 0.00 X_82609861_82609912_INS 1 51 1 + (TCT)n Simple_repeat 1 51 0
41 6.26 0.00 0.00 X_82609861_82609912_INS 1 51 (1) (TCT)n#Simple_repeat 1 51 (0) c_b2s251i48
X_82609861_82 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCTCCTTCTCCTTC 50
i i i
(TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 50
X_82609861_82 51 T 51
(TCT)n#Simple 51 T 51
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 36 0.0 3.9 1.9 X_8270616_8270667_INS 1 51 (1) + (AAAG)n Simple_repeat 1 52 (0) 869
ANNOTATION EVIDENCE:
36 0.00 3.92 1.92 X_8270616_8270667_INS 1 51 1 + (AAAG)n Simple_repeat 1 52 0
36 0.00 3.92 1.92 X_8270616_8270667_INS 1 51 (1) (AAAG)n#Simple_repeat 1 52 (0) m_b1s252i3
X_8270616_827 1 AAAGAAAAGAAAGAAAGAAAGAAAG--AGAAAGAAAGAAAGAAAGAAAGA 48
- --
(AAAG)n#Simpl 1 AAAG-AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 49
X_8270616_827 49 AAG 51
(AAAG)n#Simpl 50 AAG 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.50 (3 / 2)
+ 30 13.4 2.0 0.0 X_82953305_82953356_INS 1 51 (1) + (AT)n Simple_repeat 1 52 (0) 870
ANNOTATION EVIDENCE:
30 13.41 1.96 0.00 X_82953305_82953356_INS 1 51 1 + (AT)n Simple_repeat 1 52 0
30 13.41 1.96 0.00 X_82953305_82953356_INS 1 51 (1) (AT)n#Simple_repeat 1 52 (0) m_b2s252i18
X_82953305_82 1 ATATATATATACACACACACATATATATACATATATATATATATA-ATAT 49
i i i i i i -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_82953305_82 50 AT 51
(AT)n#Simple_ 51 AT 52
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 2413 2.9 0.0 2.5 X_8307637_8307976_INS 14 340 (0) C AluY SINE/Alu (0) 311 2 871
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_8307637_8307976_INS 14 53 287 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_8307637_8307976_INS 14 53 (287) (T)n#Simple_repeat 1 40 (0) c_b1s251i5
X_8307637_830 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 53
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
2413 2.86 0.00 2.50 X_8307637_8307976_INS 54 340 0 C AluY SINE/Alu 2 281 30
2413 2.86 0.00 2.50 X_8307637_8307976_INS 54 340 (0) C AluY#SINE/Alu (30) 281 2 c_b1s352i115
X_8307637_830 54 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 103
i ----- --
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 239
X_8307637_830 104 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 153
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_8307637_830 154 TGCCTCAGCCTCCCCAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 203
v i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_8307637_830 204 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 253
v
C AluY#SINE/Alu 138 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 89
X_8307637_830 254 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 303
i i
C AluY#SINE/Alu 88 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 39
X_8307637_830 304 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 340
C AluY#SINE/Alu 38 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.92
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.02 (7 / 286), avg. gap size = 1.00 (7 / 7)
+ 56 19.1 0.0 0.0 X_83269963_83270063_INS 1 101 (0) + (AT)n Simple_repeat 1 101 (0) 872
ANNOTATION EVIDENCE:
56 19.05 0.00 0.00 X_83269963_83270063_INS 1 101 0 + (AT)n Simple_repeat 1 101 0
56 19.05 0.00 0.00 X_83269963_83270063_INS 1 101 (0) (AT)n#Simple_repeat 1 101 (0) m_b2s252i17
X_83269963_83 1 ATATATACACGTATATATATATATATATACACGTATATATATATATACAC 50
i ii i ii i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_83269963_83 51 GTATATATATATATATACACGTATATATATATATATATACACACGTATAT 100
i i ii i i ii
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_83269963_83 101 A 101
(AT)n#Simple_ 101 A 101
Matrix = Unknown
Transitions / transversions = 1.00 (16/0)
Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0)
+ 27 16.0 0.0 6.7 X_83405860_83405927_INS 1 64 (4) + (TA)n Simple_repeat 1 60 (0) 873
ANNOTATION EVIDENCE:
27 15.98 0.00 6.67 X_83405860_83405927_INS 1 64 4 + (TA)n Simple_repeat 1 60 0
27 15.98 0.00 6.67 X_83405860_83405927_INS 1 64 (4) (TA)n#Simple_repeat 1 60 (0) m_b2s252i16
X_83405860_83 1 TATATAGAGAGGATATATATAGGATATATATATAGAGAGGATATATATAG 50
v v -v -v v v -v -
(TA)n#Simple_ 1 TATATATATA-TATATATATA-TATATATATATATATA-TATATATATA- 46
X_83405860_83 51 GATATATATATATA 64
v
(TA)n#Simple_ 47 TATATATATATATA 60
Matrix = Unknown
Transitions / transversions = 0.00 (0/8)
Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.00 (4 / 4)
+ 57 5.1 0.0 0.0 X_83506955_83507017_INS 1 62 (1) + (AT)n Simple_repeat 1 62 (0) 874
ANNOTATION EVIDENCE:
57 5.09 0.00 0.00 X_83506955_83507017_INS 1 62 1 + (AT)n Simple_repeat 1 62 0
57 5.09 0.00 0.00 X_83506955_83507017_INS 1 62 (1) (AT)n#Simple_repeat 1 62 (0) c_b2s251i47
X_83506955_83 1 ATATATATATATATATATATATATGTATATATGTATATATATATATATAT 50
i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_83506955_83 51 ATATGTATATAT 62
i
(AT)n#Simple_ 51 ATATATATATAT 62
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 766 13.1 0.0 0.0 X_84009827_84009948_INS 1 122 (0) C L1MC LINE/L1 (898) 5446 5325 875
ANNOTATION EVIDENCE:
766 13.11 0.00 0.00 X_84009827_84009948_INS 1 122 0 C L1MC2_3end LINE/L1 72 193 898
766 13.11 0.00 0.00 X_84009827_84009948_INS 1 122 (0) C L1MC2_3end#LINE/L1 (898) 193 72 m_b2s551i22
X_84009827_84 1 GGTATCTTATTGTTGTTTTAATTTGCAACTCCTTAATGACTTACGATGTT 50
i i i v i
C L1MC2_3end#LI 193 GGTATCTCATTGTTGTTTTAATTTGCAATTCCCTAATGACATATGATGTT 144
X_84009827_84 51 GAACATCTTTTCATATGCTTATTTGCCAAATTTATATATTCTTCGGTGTG 100
i vv v v i v
C L1MC2_3end#LI 143 GAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTCTTTGGTGAG 94
X_84009827_84 101 ATGTCCGTTCAAGTCTTTTGCC 122
i i ii
C L1MC2_3end#LI 93 GTGTCTGTTCAGATCTTTTGCC 72
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.57
Transitions / transversions = 1.67 (10/6)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 258 2.6 0.0 0.0 X_84163974_84164038_INS 13 50 (15) + L1HS LINE/L1 6118 6155 (0) 876
ANNOTATION EVIDENCE:
258 2.63 0.00 0.00 X_84163974_84164038_INS 13 50 15 + L1HS_3end LINE/L1 865 902 0
258 2.63 0.00 0.00 X_84163974_84164038_INS 13 50 (15) L1HS_3end#LINE/L1 865 902 (0) m_b2s551i23
X_84163974_84 13 TGTACCCTAAAACTTAGAGTATAATAAAAAAAATAAAA 50
v
L1HS_3end#LIN 865 TGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAA 902
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.69
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 1583 4.0 0.0 3.5 X_84209604_84209846_INS 14 243 (0) C AluY SINE/Alu (0) 311 88 877
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_84209604_84209846_INS 14 41 202 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_84209604_84209846_INS 14 41 (202) (T)n#Simple_repeat 1 28 (0) c_b2s251i46
X_84209604_84 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 41
(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)
1583 3.95 0.00 3.45 X_84209604_84209846_INS 42 243 0 C AluY SINE/Alu 88 282 29
1583 3.95 0.00 3.45 X_84209604_84209846_INS 42 243 (0) C AluY#SINE/Alu (29) 282 88 m_b2s357i12
X_84209604_84 42 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 91
i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_84209604_84 92 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 141
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_84209604_84 142 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 191
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_84209604_84 192 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 241
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_84209604_84 242 GG 243
C AluY#SINE/Alu 89 GG 88
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.63
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.03 (7 / 201), avg. gap size = 1.00 (7 / 7)
+ 74 25.5 0.0 0.0 X_84343077_84343260_INS 8 183 (1) + (ATAT)n Simple_repeat 1 176 (0) 878
ANNOTATION EVIDENCE:
74 25.49 0.00 0.00 X_84343077_84343260_INS 8 183 1 + (ATAT)n Simple_repeat 1 176 0
74 25.49 0.00 0.00 X_84343077_84343260_INS 8 183 (1) (ATAT)n#Simple_repeat 1 176 (0) m_b2s252i15
X_84343077_84 8 ATACATATATGTATAAATACGTATTAATACATATATGTATAAATACATAC 57
i i v ii vv i i v i i
(ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_84343077_84 58 ATATTTATACATATATGTATACATACATATTTATACATATATATGTATAA 107
v i i i i v i i v
(ATAT)n#Simpl 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100
X_84343077_84 108 ATACATACATATTTATACATATATACGTATAAATACATACATATTTATAC 157
i i v i ii v i i v i
(ATAT)n#Simpl 101 ATATATATATATATATATATATATATATATATATATATATATATATATAT 150
X_84343077_84 158 ATATATATGTATAAATACGTACATAT 183
i v ii i
(ATAT)n#Simpl 151 ATATATATATATATATATATATATAT 176
Matrix = Unknown
Transitions / transversions = 2.36 (26/11)
Gap_init rate = 0.00 (0 / 175), avg. gap size = 0.0 (0 / 0)
+ 2657 0.4 0.0 0.0 X_84390741_84391063_INS 11 323 (0) C AluY SINE/Alu (0) 311 2 879
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 X_84390741_84391063_INS 11 43 280 + (T)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 X_84390741_84391063_INS 11 43 (280) (T)n#Simple_repeat 1 33 (0) c_b2s251i45
X_84390741_84 11 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
(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)
2657 0.36 0.00 0.00 X_84390741_84391063_INS 44 323 0 C AluY SINE/Alu 2 281 30
2657 0.36 0.00 0.00 X_84390741_84391063_INS 44 323 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i95
X_84390741_84 44 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 93
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_84390741_84 94 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 143
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_84390741_84 144 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 193
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_84390741_84 194 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 243
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_84390741_84 244 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 293
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_84390741_84 294 GGATTACAGGCGTGAGCCACCGCGCCCGGC 323
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.36
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 42 17.3 0.0 0.0 X_8456534_8456629_INS 3 81 (15) + (TCTG)n Simple_repeat 1 79 (0) 880
ANNOTATION EVIDENCE:
42 17.26 0.00 0.00 X_8456534_8456629_INS 3 81 15 + (TCTG)n Simple_repeat 1 79 0
42 17.26 0.00 0.00 X_8456534_8456629_INS 3 81 (15) (TCTG)n#Simple_repeat 1 79 (0) m_b1s252i2
X_8456534_845 3 TCTGTCTGTCTTTCTTTCTGTCCGTCTATTTTTCTGTCTGTCTGTCCATC 52
v v i i i v ii
(TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 50
X_8456534_845 53 CGTCTGCCCGTCTGTCTGTCTGTGTGTCT 81
i i i v
(TCTG)n#Simpl 51 TGTCTGTCTGTCTGTCTGTCTGTCTGTCT 79
Matrix = Unknown
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0)
+ 66 1.6 0.0 0.0 X_84983236_84983299_INS 2 64 (0) + (T)n Simple_repeat 1 63 (0) 881
ANNOTATION EVIDENCE:
66 1.61 0.00 0.00 X_84983236_84983299_INS 2 64 0 + (T)n Simple_repeat 1 63 0
66 1.61 0.00 0.00 X_84983236_84983299_INS 2 64 (0) (T)n#Simple_repeat 1 63 (0) c_b2s251i44
X_84983236_84 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTT 51
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_84983236_84 52 TTTTTTTTTTTTT 64
(T)n#Simple_r 51 TTTTTTTTTTTTT 63
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 302 8.3 2.1 0.0 X_85009478_85009529_INS 4 51 (1) C L1P1 LINE/L1 (2700) 3446 3398 882
ANNOTATION EVIDENCE:
302 8.33 2.08 0.00 X_85009478_85009529_INS 4 51 1 C L1P1_orf2 LINE/L1 1289 1337 1957
302 8.33 2.08 0.00 X_85009478_85009529_INS 4 51 (1) C L1P1_orf2#LINE/L1 (1957) 1337 1289 m_b2s551i24
X_85009478_85 4 ATTTCTTC-TAGATTAGTCTTGGGAGGGTGTATGTGTTGAGGAATTTAT 51
i - i v i
C L1P1_orf2#LIN 1337 ACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCGAGGAATTTAT 1289
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.80
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1)
+ 54 1.9 0.0 0.0 X_85060480_85060533_INS 2 54 (0) + (T)n Simple_repeat 1 53 (0) 883
ANNOTATION EVIDENCE:
54 1.91 0.00 0.00 X_85060480_85060533_INS 2 54 0 + (T)n Simple_repeat 1 53 0
54 1.91 0.00 0.00 X_85060480_85060533_INS 2 54 (0) (T)n#Simple_repeat 1 53 (0) c_b2s251i43
X_85060480_85 2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT 51
v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_85060480_85 52 TTT 54
(T)n#Simple_r 51 TTT 53
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 49 7.2 0.0 0.0 X_85100485_85100544_INS 1 60 (0) + (TA)n Simple_repeat 1 60 (0) 884
ANNOTATION EVIDENCE:
49 7.16 0.00 0.00 X_85100485_85100544_INS 1 60 0 + (TA)n Simple_repeat 1 60 0
49 7.16 0.00 0.00 X_85100485_85100544_INS 1 60 (0) (TA)n#Simple_repeat 1 60 (0) c_b2s251i42
X_85100485_85 1 TATATATATATGTATGTATATATATATATATATATATATATATGTATGTA 50
i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_85100485_85 51 TATATATATA 60
(TA)n#Simple_ 51 TATATATATA 60
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 33 0.0 6.7 6.7 X_85166157_85166223_INS 6 65 (2) + (AT)n Simple_repeat 1 60 (0) 885
ANNOTATION EVIDENCE:
33 0.00 6.67 6.67 X_85166157_85166223_INS 6 65 2 + (AT)n Simple_repeat 1 60 0
33 0.00 6.67 6.67 X_85166157_85166223_INS 6 65 (2) (AT)n#Simple_repeat 1 60 (0) c_b2s251i41
X_85166157_85 6 ATATATATATGA-ATATATATATGA-ATATATATATGA-ATATATATATG 52
- - - - - - -
(AT)n#Simple_ 1 ATATATATAT-ATATATATATAT-ATATATATATAT-ATATATATATAT- 46
X_85166157_85 53 A-ATATATATATAT 65
-
(AT)n#Simple_ 47 ATATATATATATAT 60
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.14 (8 / 59), avg. gap size = 1.00 (8 / 8)
+ 2735 2.0 0.0 0.0 X_8531357_8531668_INS 14 312 (0) C AluY SINE/Alu (12) 299 1 886
ANNOTATION EVIDENCE:
2735 2.01 0.00 0.00 X_8531357_8531668_INS 14 312 0 C AluY SINE/Alu 1 299 12
2735 2.01 0.00 0.00 X_8531357_8531668_INS 14 312 (0) C AluY#SINE/Alu (12) 299 1 c_b1s352i116
X_8531357_853 14 TTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 63
C AluY#SINE/Alu 299 TTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 250
X_8531357_853 64 AGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCA 113
v
C AluY#SINE/Alu 249 AGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCA 200
X_8531357_853 114 CGCCATTCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCG 163
i
C AluY#SINE/Alu 199 CGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCG 150
X_8531357_853 164 CCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 213
i
C AluY#SINE/Alu 149 CCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 100
X_8531357_853 214 CATTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCT 263
i v i
C AluY#SINE/Alu 99 CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCT 50
X_8531357_853 264 CGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 312
C AluY#SINE/Alu 49 CGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.73
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 48 0.0 0.0 0.0 X_85360427_85360479_INS 1 52 (1) + (A)n Simple_repeat 1 52 (0) 887
ANNOTATION EVIDENCE:
48 0.00 0.00 0.00 X_85360427_85360479_INS 1 52 1 + (A)n Simple_repeat 1 52 0
48 0.00 0.00 0.00 X_85360427_85360479_INS 1 52 (1) (A)n#Simple_repeat 1 52 (0) m_b2s252i14
X_85360427_85 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_85360427_85 51 AA 52
(A)n#Simple_r 51 AA 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2744 2.0 0.0 0.0 X_85615795_85616118_INS 15 313 (11) + AluY SINE/Alu 13 311 (0) 888
ANNOTATION EVIDENCE:
2744 2.01 0.00 0.00 X_85615795_85616118_INS 15 313 11 + AluY SINE/Alu 13 311 0
2744 2.01 0.00 0.00 X_85615795_85616118_INS 15 313 (11) AluY#SINE/Alu 13 311 (0) c_b2s352i96
X_85615795_85 15 TGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATC 64
AluY#SINE/Alu 13 TGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATC 62
X_85615795_85 65 ACGAGGTCAGGAGATCGAGACCATCCCAGCTAAAACGGTGAAACCCCGTC 114
ii v
AluY#SINE/Alu 63 ACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTC 112
X_85615795_85 115 TCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG 164
i
AluY#SINE/Alu 113 TCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAG 162
X_85615795_85 165 TCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGG 214
i
AluY#SINE/Alu 163 TCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGG 212
X_85615795_85 215 CGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGA 264
v
AluY#SINE/Alu 213 CGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGA 262
X_85615795_85 265 CAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 313
AluY#SINE/Alu 263 CAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.73
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 55 0.0 0.0 0.0 X_85684547_85684597_INS 1 50 (1) + (CTTTT)n Simple_repeat 1 50 (0) 889
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 X_85684547_85684597_INS 1 50 1 + (CTTTT)n Simple_repeat 1 50 0
55 0.00 0.00 0.00 X_85684547_85684597_INS 1 50 (1) (CTTTT)n#Simple_repeat 1 50 (0) c_b2s251i40
X_85684547_85 1 CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 50
(CTTTT)n#Simp 1 CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 52 0.0 0.0 3.7 X_85801393_85801449_INS 1 56 (1) + (TTC)n Simple_repeat 1 54 (0) 890
ANNOTATION EVIDENCE:
52 0.00 0.00 3.70 X_85801393_85801449_INS 1 56 1 + (TTC)n Simple_repeat 1 54 0
52 0.00 0.00 3.70 X_85801393_85801449_INS 1 56 (1) (TTC)n#Simple_repeat 1 54 (0) c_b2s251i39
X_85801393_85 1 TTCTTCTTCTTCTTCTTCTTCTTCTTCCTTCTTCTTCTTCTTTCTTCTTC 50
- -
(TTC)n#Simple 1 TTCTTCTTCTTCTTCTTCTTCTTCTT-CTTCTTCTTCTTC-TTCTTCTTC 48
X_85801393_85 51 TTCTTC 56
(TTC)n#Simple 49 TTCTTC 54
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2)
+ 50 2.0 0.0 0.0 X_85848401_85848451_INS 2 51 (0) + (TTTTA)n Simple_repeat 1 50 (0) 891
ANNOTATION EVIDENCE:
50 2.03 0.00 0.00 X_85848401_85848451_INS 2 51 0 + (TTTTA)n Simple_repeat 1 50 0
50 2.03 0.00 0.00 X_85848401_85848451_INS 2 51 (0) (TTTTA)n#Simple_repeat 1 50 (0) c_b2s251i38
X_85848401_85 2 TTTTATTTTATTTTATTATATTTTATTTTATTTTATTTTATTTTATTTTA 51
v
(TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA 50
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 30 9.2 0.0 4.2 X_85960053_85960108_INS 2 51 (5) + (AT)n Simple_repeat 1 48 (0) 892
ANNOTATION EVIDENCE:
30 9.24 0.00 4.17 X_85960053_85960108_INS 2 51 5 + (AT)n Simple_repeat 1 48 0
30 9.24 0.00 4.17 X_85960053_85960108_INS 2 51 (5) (AT)n#Simple_repeat 1 48 (0) m_b2s252i13
X_85960053_85 2 ATATATATATATATATCTCACATATATATATATATATCTCACATATATAT 51
v - i v - i
(AT)n#Simple_ 1 ATATATATATATATATAT-ATATATATATATATATATAT-ATATATATAT 48
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2)
+ 2451 2.8 0.0 2.5 X_86077690_86078011_INS 10 322 (0) C AluY SINE/Alu (0) 311 2 893
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 X_86077690_86078011_INS 10 34 288 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 X_86077690_86078011_INS 10 34 (288) (T)n#Simple_repeat 1 25 (0) c_b2s251i37
X_86077690_86 10 TTTTTTTTTTTTTTTTTTTTTTTTT 34
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2451 2.81 0.00 2.46 X_86077690_86078011_INS 35 322 0 C AluY SINE/Alu 2 282 29
2451 2.81 0.00 2.46 X_86077690_86078011_INS 35 322 (0) C AluY#SINE/Alu (29) 282 2 c_b2s352i97
X_86077690_86 35 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 84
----- -- v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 240
X_86077690_86 85 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 134
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_86077690_86 135 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 184
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_86077690_86 185 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 234
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_86077690_86 235 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 284
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
X_86077690_86 285 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 322
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 707 6.2 2.0 3.1 X_86127344_86127462_INS 21 119 (0) + HERVL-int LTR/ERVL 215 312 (5342) 894
ANNOTATION EVIDENCE:
707 6.25 2.02 3.06 X_86127344_86127462_INS 21 119 0 + HERVL LTR/ERVL 215 312 5342
707 6.25 2.02 3.06 X_86127344_86127462_INS 21 119 (0) HERVL#LTR/ERVL 215 312 (5342) m_b2s701i3
X_86127344_86 21 GCTTGTGAGAGGCCAGGAGTTTAGTGACTCTATACATTATATCTTTGACC 70
i v v i
HERVL#LTR/ERV 215 GCTCGTGAGAGGCAAGGAGTTTAGTGACTCTATACATAATACCTTTGACC 264
X_86127344_86 71 ATATGTGGAGAACCAAGGAACATAATG--GTTGGAACTTGGTTGTTCCTA 118
-- i --- i
HERVL#LTR/ERV 265 ATATGTGGAGAACCAAGGAACATAATGAAGCTGG---TTGGTTGCTCCTA 311
X_86127344_86 119 A 119
HERVL#LTR/ERV 312 A 312
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.53
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.25 (5 / 4)
+ 2664 2.3 0.0 2.3 X_86267459_86267784_INS 17 326 (0) + AluY SINE/Alu 1 303 (8) 895
ANNOTATION EVIDENCE:
2664 2.31 0.00 2.31 X_86267459_86267784_INS 17 326 0 + AluY SINE/Alu 1 303 8
2664 2.31 0.00 2.31 X_86267459_86267784_INS 17 326 (0) AluY#SINE/Alu 1 303 (8) c_b2s352i98
X_86267459_86 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_86267459_86 67 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 116
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_86267459_86 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_86267459_86 167 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 216
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_86267459_86 217 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 266
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_86267459_86 267 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 316
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_86267459_86 317 AAAAAAAAAA 326
AluY#SINE/Alu 294 AAAAAAAAAA 303
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 1.00 (7 / 7)
+ 60 0.0 4.7 2.3 X_86460490_86460578_INS 4 89 (0) + (AAAG)n Simple_repeat 1 88 (0) 896
ANNOTATION EVIDENCE:
60 0.00 4.65 2.27 X_86460490_86460578_INS 4 89 0 + (AAAG)n Simple_repeat 1 88 0
60 0.00 4.65 2.27 X_86460490_86460578_INS 4 89 (0) (AAAG)n#Simple_repeat 1 88 (0) m_b2s252i12
X_86460490_86 4 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AA-AAAGAAAGAAAGAA 51
- -
(AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 50
X_86460490_86 52 AGAAAAGAAAG-AA-AAAGAAAGAAAGAAAGAAAAGAAAG 89
- - - -
(AAAG)n#Simpl 51 AG-AAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAAG 88
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.00 (6 / 6)
+ 34 12.1 0.0 0.0 X_86483620_86483681_INS 5 60 (2) + (TA)n Simple_repeat 1 56 (0) 897
ANNOTATION EVIDENCE:
34 12.06 0.00 0.00 X_86483620_86483681_INS 5 60 2 + (TA)n Simple_repeat 1 56 0
34 12.06 0.00 0.00 X_86483620_86483681_INS 5 60 (2) (TA)n#Simple_repeat 1 56 (0) c_b2s251i36
X_86483620_86 5 TATATATGTATATACATATATATATATACGTATATATGTATATACATATA 54
i i ii i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_86483620_86 55 TATATA 60
(TA)n#Simple_ 51 TATATA 56
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 0.0 X_86500634_86501187_INS 5 44 (510) + (T)n Simple_repeat 1 40 (0) 898
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 X_86500634_86501187_INS 5 44 510 + (T)n Simple_repeat 1 40 0
44 0.00 0.00 0.00 X_86500634_86501187_INS 5 44 (510) (T)n#Simple_repeat 1 40 (0) c_b2s251i35
X_86500634_86 5 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 4548 0.6 0.0 0.0 X_86500634_86501187_INS 54 553 (1) C L1HS LINE/L1 (0) 6155 5656 899
ANNOTATION EVIDENCE:
4548 0.60 0.00 0.00 X_86500634_86501187_INS 54 553 1 C L1HS_3end LINE/L1 403 902 0
4548 0.60 0.00 0.00 X_86500634_86501187_INS 54 553 (1) C L1HS_3end#LINE/L1 (0) 902 403 m_b2s551i25
X_86500634_86 54 TTTATTTATTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 103
v v
C L1HS_3end#LIN 902 TTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGT 853
X_86500634_86 104 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 153
C L1HS_3end#LIN 852 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 803
X_86500634_86 154 CTAACGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 203
C L1HS_3end#LIN 802 CTAACGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 753
X_86500634_86 204 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTG 253
C L1HS_3end#LIN 752 CTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTG 703
X_86500634_86 254 TCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGT 303
C L1HS_3end#LIN 702 TCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGT 653
X_86500634_86 304 GTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAAT 353
C L1HS_3end#LIN 652 GTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAAT 603
X_86500634_86 354 TTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGC 403
C L1HS_3end#LIN 602 TTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGC 553
X_86500634_86 404 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 453
C L1HS_3end#LIN 552 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 503
X_86500634_86 454 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCC 503
C L1HS_3end#LIN 502 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCC 453
X_86500634_86 504 GCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATACTC 553
v
C L1HS_3end#LIN 452 GCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTC 403
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.60
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 499), avg. gap size = 0.0 (0 / 0)
+ 2818 0.3 0.0 1.0 X_86595629_86595944_INS 13 316 (0) + AluY SINE/Alu 1 301 (10) 900
ANNOTATION EVIDENCE:
2818 0.33 0.00 1.00 X_86595629_86595944_INS 13 316 0 + AluY SINE/Alu 1 301 10
2818 0.33 0.00 1.00 X_86595629_86595944_INS 13 316 (0) AluY#SINE/Alu 1 301 (10) c_b2s352i99
X_86595629_86 13 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 62
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_86595629_86 63 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 112
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_86595629_86 113 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAAATTAGCCGGGCGTGGT 162
---
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA---AATTAGCCGGGCGTGGT 147
X_86595629_86 163 AGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGG 212
i
AluY#SINE/Alu 148 GGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGG 197
X_86595629_86 213 CGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA 262
AluY#SINE/Alu 198 CGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCA 247
X_86595629_86 263 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 312
AluY#SINE/Alu 248 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 297
X_86595629_86 313 AAAA 316
AluY#SINE/Alu 298 AAAA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.33
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.01 (3 / 303), avg. gap size = 1.00 (3 / 3)
+ 50 4.2 0.0 7.5 X_86619993_86620088_INS 11 96 (0) + (TATAG)n Simple_repeat 1 80 (0) 901
ANNOTATION EVIDENCE:
50 4.22 0.00 7.50 X_86619993_86620088_INS 11 96 0 + (TATAG)n Simple_repeat 1 80 0
50 4.22 0.00 7.50 X_86619993_86620088_INS 11 96 (0) (TATAG)n#Simple_repeat 1 80 (0) c_b2s251i34
X_86619993_86 11 TATAGTATAGTATAACATATAGTATAGTATAACATATAGTATAGTATAGT 60
- -i - -i
(TATAG)n#Simp 1 TATAGTATAGTAT-A-GTATAGTATAGTAT-A-GTATAGTATAGTATAGT 46
X_86619993_86 61 ATAGTATAGTATAACATATAGTATAGTATAGTATAG 96
- -i
(TATAG)n#Simp 47 ATAGTATAGTAT-A-GTATAGTATAGTATAGTATAG 80
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.00 (6 / 6)
+ 967 9.9 0.0 0.7 X_86933643_86933784_INS 1 142 (0) + L1PREC2 LINE/L1 5937 6077 (83) 902
ANNOTATION EVIDENCE:
967 9.93 0.00 0.71 X_86933643_86933784_INS 1 142 0 + L1PREC2_3end LINE/L1 684 824 83
967 9.93 0.00 0.71 X_86933643_86933784_INS 1 142 (0) L1PREC2_3end#LINE/L1 684 824 (83) m_b2s551i26
X_86933643_86 1 AATTATGAGAACTCATGAACACAAAGAAAGGAACAACAGACATTGGGATC 50
v ? i ii i ii
L1PREC2_3end# 684 AATGATGAGAACNCATGGACACAAAGAGGGGAACAACAGACACTGGGGCC 733
X_86933643_86 51 TATTTGAGGGTGGAGTGTGGGAGTAAGGAGAGAAGCAGAAAAAAATAACT 100
i v v i i ? -
L1PREC2_3end# 734 TACTTGAGGGTGGAGGGTGGGAGGAGGGAGAGGANCAG-AAAAAATAACT 782
X_86933643_86 101 ATTGGGTACTAGGCTTAGTAGCTGGGTGACAAAATAATCTGT 142
v i
L1PREC2_3end# 783 ATTGGGTACTAGGCTTAGTACCTGGGTGACGAAATAATCTGT 824
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.18
Transitions / transversions = 2.50 (10/4)
Gap_init rate = 0.01 (1 / 141), avg. gap size = 1.00 (1 / 1)
+ 328 12.2 0.0 0.0 X_87216897_87216958_INS 12 60 (2) + L1PBb LINE/L1 887 935 (5269) 903
ANNOTATION EVIDENCE:
328 12.24 0.00 0.00 X_87216897_87216958_INS 12 60 2 + L1PBb_5end LINE/L1 887 935 123
328 12.24 0.00 0.00 X_87216897_87216958_INS 12 60 (2) L1PBb_5end#LINE/L1 887 935 (123) m_b2s551i27
X_87216897_87 12 AGGCTATAATGGACTATAAATATTAAAGTCATATCTTTAAGGGGAAAAA 60
i ii i i i
L1PBb_5end#LI 887 AGGCTACAATAAACTATAAACATTAAAGTCACATCCTTAAGGGGAAAAA 935
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.05
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 49 12.4 0.0 0.0 X_87223960_87224048_INS 5 86 (3) + (AT)n Simple_repeat 1 82 (0) 904
ANNOTATION EVIDENCE:
49 12.39 0.00 0.00 X_87223960_87224048_INS 5 86 3 + (AT)n Simple_repeat 1 82 0
49 12.39 0.00 0.00 X_87223960_87224048_INS 5 86 (3) (AT)n#Simple_repeat 1 82 (0) c_b2s251i33
X_87223960_87 5 ATATATATGTATATATGTATACATATATATGTGTATATATATATGTATAT 54
i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_87223960_87 55 ATATATGTGTATATATATATGTATATATATAT 86
i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATATAT 82
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0)
+ 54 3.7 0.0 0.0 X_87482085_87482143_INS 4 58 (1) + (TA)n Simple_repeat 1 55 (0) 905
ANNOTATION EVIDENCE:
54 3.74 0.00 0.00 X_87482085_87482143_INS 4 58 1 + (TA)n Simple_repeat 1 55 0
54 3.74 0.00 0.00 X_87482085_87482143_INS 4 58 (1) (TA)n#Simple_repeat 1 55 (0) c_b2s251i32
X_87482085_87 4 TATATATATATATATATATATATATATATATCTATCTATATATATATATA 53
v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_87482085_87 54 TATAT 58
(TA)n#Simple_ 51 TATAT 55
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 78 3.9 0.0 0.0 X_87514246_87514325_INS 1 80 (0) + (AT)n Simple_repeat 1 80 (0) 906
ANNOTATION EVIDENCE:
78 3.86 0.00 0.00 X_87514246_87514325_INS 1 80 0 + (AT)n Simple_repeat 1 80 0
78 3.86 0.00 0.00 X_87514246_87514325_INS 1 80 (0) (AT)n#Simple_repeat 1 80 (0) c_b2s251i31
X_87514246_87 1 ATATATATATATATATATTTATATATATATATATATATATAAATATATAT 50
v v
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_87514246_87 51 ATATATATATATTTATATATATATATATAT 80
v
(AT)n#Simple_ 51 ATATATATATATATATATATATATATATAT 80
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 54 0.0 0.0 0.0 X_87544080_87544139_INS 1 59 (1) + (A)n Simple_repeat 1 59 (0) 907
ANNOTATION EVIDENCE:
54 0.00 0.00 0.00 X_87544080_87544139_INS 1 59 1 + (A)n Simple_repeat 1 59 0
54 0.00 0.00 0.00 X_87544080_87544139_INS 1 59 (1) (A)n#Simple_repeat 1 59 (0) m_b2s252i11
X_87544080_87 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_87544080_87 51 AAAAAAAAA 59
(A)n#Simple_r 51 AAAAAAAAA 59
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 69 1.5 1.4 0.0 X_87634470_87634565_INS 3 71 (25) + (AGAA)n Simple_repeat 1 70 (0) 908
ANNOTATION EVIDENCE:
69 1.47 1.45 0.00 X_87634470_87634565_INS 3 71 25 + (AGAA)n Simple_repeat 1 70 0
69 1.47 1.45 0.00 X_87634470_87634565_INS 3 71 (25) (AGAA)n#Simple_repeat 1 70 (0) c_b2s251i30
X_87634470_87 3 AGAAAG-AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAGAAAGAAAG 51
- i
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50
X_87634470_87 52 AAAGAAAGAAAGAAAGAAAG 71
(AGAA)n#Simpl 51 AAAGAAAGAAAGAAAGAAAG 70
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1)
+ 76 1.2 0.0 0.0 X_87640606_87640691_INS 2 86 (0) + (A)n Simple_repeat 1 85 (0) 909
ANNOTATION EVIDENCE:
76 1.19 0.00 0.00 X_87640606_87640691_INS 2 86 0 + (A)n Simple_repeat 1 85 0
76 1.19 0.00 0.00 X_87640606_87640691_INS 2 86 (0) (A)n#Simple_repeat 1 85 (0) m_b2s252i10
X_87640606_87 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_87640606_87 52 AAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAA 86
i
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 85
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0)
+ 22 20.3 0.0 0.0 X_87783241_87783293_INS 6 47 (6) + (AT)n Simple_repeat 1 42 (0) 910
ANNOTATION EVIDENCE:
22 20.27 0.00 0.00 X_87783241_87783293_INS 6 47 6 + (AT)n Simple_repeat 1 42 0
22 20.27 0.00 0.00 X_87783241_87783293_INS 6 47 (6) (AT)n#Simple_repeat 1 42 (0) m_b2s252i9
X_87783241_87 6 ATATATATGTATATATGTGTGTACACATATATATGTATATAT 47
i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42
Matrix = Unknown
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
+ 2675 2.3 0.0 2.9 X_87976544_87976874_INS 14 331 (0) + AluY SINE/Alu 1 309 (2) 911
ANNOTATION EVIDENCE:
2675 2.27 0.00 2.91 X_87976544_87976874_INS 14 331 0 + AluY SINE/Alu 1 309 2
2675 2.27 0.00 2.91 X_87976544_87976874_INS 14 331 (0) AluY#SINE/Alu 1 309 (2) c_b2s352i100
X_87976544_87 14 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 63
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_87976544_87 64 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 113
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_87976544_87 114 TGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCGCGGTG 163
-- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATAC--AAAAAATTAGCCGGGCGTGGTG 148
X_87976544_87 164 GCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGC 213
AluY#SINE/Alu 149 GCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGC 198
X_87976544_87 214 GTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAG 263
i i v
AluY#SINE/Alu 199 GTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCAC 248
X_87976544_87 264 TCCGCAGTCCCACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA 313
-- -----
AluY#SINE/Alu 249 TC--CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA 291
X_87976544_87 314 AAAAAAAAAAAAAAAAAA 331
AluY#SINE/Alu 292 AAAAAAAAAAAAAAAAAA 309
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (9 / 317), avg. gap size = 1.00 (9 / 9)
+ 2443 2.9 0.0 2.9 X_88028291_88028631_INS 7 341 (0) C AluY SINE/Alu (0) 311 1 912
ANNOTATION EVIDENCE:
51 0.00 0.00 0.00 X_88028291_88028631_INS 7 52 289 + (T)n Simple_repeat 1 46 0
51 0.00 0.00 0.00 X_88028291_88028631_INS 7 52 (289) (T)n#Simple_repeat 1 46 (0) c_b2s251i29
X_88028291_88 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 52
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 46
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)
2443 2.85 0.00 2.85 X_88028291_88028631_INS 53 341 0 C AluY SINE/Alu 1 281 30
2443 2.85 0.00 2.85 X_88028291_88028631_INS 53 341 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i101
X_88028291_88 53 GAGACGGAGTCTCGCTCTGTCGACCAGGCTGGAGTGCAGTGACGCAATCT 102
v i i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_88028291_88 103 CGGCTCACTGCATGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 152
v
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_88028291_88 153 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 202
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_88028291_88 203 TTTTTTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCC 252
-------- v
C AluY#SINE/Alu 131 T--------TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCC 90
X_88028291_88 253 GGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCA 302
i
C AluY#SINE/Alu 89 AGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCA 40
X_88028291_88 303 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 341
C AluY#SINE/Alu 39 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.24
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.03 (8 / 288), avg. gap size = 1.00 (8 / 8)
+ 657 1.4 0.0 0.0 X_88119190_88119262_INS 1 72 (1) + LTR12D LTR/ERV1 685 756 (498) 913
ANNOTATION EVIDENCE:
657 1.39 0.00 0.00 X_88119190_88119262_INS 1 72 1 + LTR12D LTR/ERV1 685 756 498
657 1.39 0.00 0.00 X_88119190_88119262_INS 1 72 (1) LTR12D#LTR/ERV1 685 756 (498) m_b2s502i19
X_88119190_88 1 CTCTCTGTAAAATGGACCAATCAGCTCTCTGTAAAATGGACCAATCAGCT 50
i
LTR12D#LTR/ER 685 CTCTCTGTAAAACGGACCAATCAGCTCTCTGTAAAATGGACCAATCAGCT 734
X_88119190_88 51 CTCTGTAAAATGGACCAATCAG 72
LTR12D#LTR/ER 735 CTCTGTAAAATGGACCAATCAG 756
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 0.14
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 1505 19.9 1.5 0.0 X_88383146_88383412_INS 1 266 (1) C L1PA12 LINE/L1 (5656) 1325 1056 914
ANNOTATION EVIDENCE:
1505 19.92 1.50 0.00 X_88383146_88383412_INS 1 266 1 C L1PA12_5end LINE/L1 1056 1325 1747
1505 19.92 1.50 0.00 X_88383146_88383412_INS 1 266 (1) C L1PA12_5end#LINE/L1 (1747) 1325 1056 m_b2s551i28
X_88383146_88 1 CCTGCTTAAAAAAGCAGCCTGTCCGTGTTTTCATAGGGCAGCTGTGCTGT 50
i i v ii i i
C L1PA12_5end#L 1325 CCCGCTTAAAAAAGCAGTCTGGCCACGTTTTCGTAGAGCAGCTGTGCTGT 1276
X_88383146_88 51 GCTGGGGGTCCATTTTAGCCCCTGGTTGGCTTGGGCACTCCAAAGACCGA 100
ii i i i v i i v v
C L1PA12_5end#L 1275 GCTGGGGGTCCGCTTCAGCCCCCGGTCGCCTCGGACTCTCCAAAGCCCGA 1226
X_88383146_88 101 AGGCTGGAATAGCTA--TCACCAAAACAGAAAAGGTTGAGGTCTGCCCCT 148
ii -- i v v i v v i i
C L1PA12_5end#L 1225 AGGCTGGAACGGCTAAGTCGCCCAAACAGCAAAGATGGCGGCCCGCCCCT 1176
X_88383146_88 149 CCCTCTGGGAGCTAAGTCTCAGGGTGGTTTCACAACTCTATTTTCTGGAA 198
vv i v v v i ivv i i
C L1PA12_5end#L 1175 CCCTCTGGGAGCTCCGTCCCAGGGAGGTTTCAAACCTCTGTCGGCCGGAG 1126
X_88383146_88 199 AACACCAGCAAGTGTGTCTGGAGACCT--GTTGGGAGATCCTGCCCAGTA 246
i ii v v i i-- i i i
C L1PA12_5end#L 1125 AACACCGGCGGGGGTGGCTGGAGGCCCCGGTTGGGAGGTCCCGCCCAGTG 1076
X_88383146_88 247 AGGAGGAACAGAATAAGGGA 266
i i vi
C L1PA12_5end#L 1075 AGGAGGAACGGGATCGGGGA 1056
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.74
Transitions / transversions = 1.94 (35/18)
Gap_init rate = 0.01 (2 / 265), avg. gap size = 2.00 (4 / 2)
+ 50 13.0 0.0 5.4 X_88389591_88389693_INS 1 97 (6) + (TA)n Simple_repeat 1 92 (0) 915
ANNOTATION EVIDENCE:
50 12.96 0.00 5.43 X_88389591_88389693_INS 1 97 6 + (TA)n Simple_repeat 1 92 0
50 12.96 0.00 5.43 X_88389591_88389693_INS 1 97 (6) (TA)n#Simple_repeat 1 92 (0) m_b2s252i8
X_88389591_88 1 TATATATATACACACTATATATATATATACACTATATATATATACACACT 50
i i - i - i i -
(TA)n#Simple_ 1 TATATATATATATA-TATATATATATATATA-TATATATATATATATA-T 47
X_88389591_88 51 ATATATATATACACACACTATATATATACACACTATATATATATATA 97
i i i - i i -
(TA)n#Simple_ 48 ATATATATATATATATA-TATATATATATATA-TATATATATATATA 92
Matrix = Unknown
Transitions / transversions = 1.00 (10/0)
Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.00 (5 / 5)
+ 26 12.8 0.0 4.3 X_88682263_88682313_INS 2 49 (2) + (TA)n Simple_repeat 1 46 (0) 916
ANNOTATION EVIDENCE:
26 12.82 0.00 4.35 X_88682263_88682313_INS 2 49 2 + (TA)n Simple_repeat 1 46 0
26 12.82 0.00 4.35 X_88682263_88682313_INS 2 49 (2) (TA)n#Simple_repeat 1 46 (0) m_b2s252i7
X_88682263_88 2 TATATATATGGCATATATATATACATATATATATGGCATATATATATA 49
-ii i -ii
(TA)n#Simple_ 1 TATATATAT-ATATATATATATATATATATATAT-ATATATATATATA 46
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2)
+ 33 10.9 0.0 0.0 X_88743872_88743926_INS 2 52 (3) + (AT)n Simple_repeat 1 51 (0) 917
ANNOTATION EVIDENCE:
33 10.91 0.00 0.00 X_88743872_88743926_INS 2 52 3 + (AT)n Simple_repeat 1 51 0
33 10.91 0.00 0.00 X_88743872_88743926_INS 2 52 (3) (AT)n#Simple_repeat 1 51 (0) c_b2s251i28
X_88743872_88 2 ATATATATATACACATATATATATACATATATATATACACATATATATAT 51
i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_88743872_88 52 A 52
(AT)n#Simple_ 51 A 51
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 26 14.2 0.0 5.9 X_89162650_89162705_INS 1 54 (2) + (AT)n Simple_repeat 1 51 (0) 918
ANNOTATION EVIDENCE:
26 14.25 0.00 5.88 X_89162650_89162705_INS 1 54 2 + (AT)n Simple_repeat 1 51 0
26 14.25 0.00 5.88 X_89162650_89162705_INS 1 54 (2) (AT)n#Simple_repeat 1 51 (0) m_b2s252i6
X_89162650_89 1 ATATATATACACCATATATATACATATATGGTGTATATATATATGGTATA 50
i -i i -i i -i
(AT)n#Simple_ 1 ATATATATATA-TATATATATATATATAT-ATATATATATATAT-ATATA 47
X_89162650_89 51 TATA 54
(AT)n#Simple_ 48 TATA 51
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3)
+ 517 15.6 8.9 0.0 X_8946489_8946579_INS 1 90 (1) C L1P4 LINE/L1 (1513) 4633 4536 919
ANNOTATION EVIDENCE:
517 15.56 8.89 0.00 X_8946489_8946579_INS 1 90 1 C L1P4_orf2 LINE/L1 2427 2524 770
517 15.56 8.89 0.00 X_8946489_8946579_INS 1 90 (1) C L1P4_orf2#LINE/L1 (770) 2524 2427 m_b1s551i29
X_8946489_894 1 TTTCCAGCTCTATGAAAAATGACATTGGTATCTTGATAGGAATAGCACCG 50
i ii i i vi iii
C L1P4_orf2#LIN 2524 TTTCTAATTCTGTGAAAAATGACGTTGGTAGTTTGATAGGAATAGCGTTG 2475
X_8946489_894 51 AATCTGTAGATTGCCTTGGGCA--------ATTGCAATGATATTGATT 90
i -------- vi i
C L1P4_orf2#LIN 2474 AATCTGTAGATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATT 2427
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.13
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.01 (1 / 89), avg. gap size = 8.00 (8 / 1)
+ 61 3.4 0.0 0.0 X_89559889_89559963_INS 2 62 (13) + (AT)n Simple_repeat 1 61 (0) 920
ANNOTATION EVIDENCE:
61 3.39 0.00 0.00 X_89559889_89559963_INS 2 62 13 + (AT)n Simple_repeat 1 61 0
61 3.39 0.00 0.00 X_89559889_89559963_INS 2 62 (13) (AT)n#Simple_repeat 1 61 (0) c_b2s251i27
X_89559889_89 2 ATATATATATATACATATATATATATATATATATATATACATATATATAT 51
i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_89559889_89 52 ATATATATATA 62
(AT)n#Simple_ 51 ATATATATATA 61
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 34 6.3 4.0 0.0 X_89739958_89740008_INS 2 51 (0) + (TA)n Simple_repeat 1 52 (0) 921
ANNOTATION EVIDENCE:
34 6.29 4.00 0.00 X_89739958_89740008_INS 2 51 0 + (TA)n Simple_repeat 1 52 0
34 6.29 4.00 0.00 X_89739958_89740008_INS 2 51 (0) (TA)n#Simple_repeat 1 52 (0) c_b2s251i26
X_89739958_89 2 TATATATATATAT-TATATATATATGTAAATATACATATATATAT-TATA 49
- i v i -
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_89739958_89 50 TA 51
(TA)n#Simple_ 51 TA 52
Matrix = Unknown
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2)
+ 46 10.0 0.0 0.0 X_90320096_90320168_INS 1 66 (7) + (TA)n Simple_repeat 1 66 (0) 922
ANNOTATION EVIDENCE:
46 10.03 0.00 0.00 X_90320096_90320168_INS 1 66 7 + (TA)n Simple_repeat 1 66 0
46 10.03 0.00 0.00 X_90320096_90320168_INS 1 66 (7) (TA)n#Simple_repeat 1 66 (0) c_b2s251i25
X_90320096_90 1 TATATATATATATGTGTATATATATATATATACACATATATATATATGTG 50
i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_90320096_90 51 TATATATATATATATA 66
(TA)n#Simple_ 51 TATATATATATATATA 66
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 29 2.8 0.0 5.1 X_90359158_90359210_INS 10 50 (3) + (ATATATAC)n Simple_repeat 1 39 (0) 923
ANNOTATION EVIDENCE:
29 2.77 0.00 5.13 X_90359158_90359210_INS 10 50 3 + (ATATATAC)n Simple_repeat 1 39 0
29 2.77 0.00 5.13 X_90359158_90359210_INS 10 50 (3) (ATATATAC)n#Simple_repeat 1 39 (0) c_b2s251i24
X_90359158_90 10 ATATATACATATATACGTATACATACATATATACATATATA 50
-- i
(ATATATAC)n#S 1 ATATATACATATATAC--ATATATACATATATACATATATA 39
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2)
+ 49 0.0 0.0 0.0 X_9050461_9050519_INS 1 44 (15) + (AGA)n Simple_repeat 1 44 (0) 924
ANNOTATION EVIDENCE:
49 0.00 0.00 0.00 X_9050461_9050519_INS 1 44 15 + (AGA)n Simple_repeat 1 44 0
49 0.00 0.00 0.00 X_9050461_9050519_INS 1 44 (15) (AGA)n#Simple_repeat 1 44 (0) c_b1s251i4
X_9050461_905 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 44
(AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 44
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 2106 1.8 0.0 0.0 X_90534137_90534379_INS 16 243 (0) + AluY SINE/Alu 74 301 (10) 925
ANNOTATION EVIDENCE:
2106 1.75 0.00 0.00 X_90534137_90534379_INS 16 243 0 + AluY SINE/Alu 74 301 10
2106 1.75 0.00 0.00 X_90534137_90534379_INS 16 243 (0) AluY#SINE/Alu 74 301 (10) m_b2s356i5
X_90534137_90 16 AGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAA 65
v
AluY#SINE/Alu 74 AGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAA 123
X_90534137_90 66 TACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACT 115
i
AluY#SINE/Alu 124 TACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACT 173
X_90534137_90 116 TGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCA 165
i
AluY#SINE/Alu 174 CGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCA 223
X_90534137_90 166 GTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGAC 215
v
AluY#SINE/Alu 224 GTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGAC 273
X_90534137_90 216 TCCGTCTCAAAAAAAAAAAAAAAAAAAA 243
AluY#SINE/Alu 274 TCCGTCTCAAAAAAAAAAAAAAAAAAAA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.37
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 227), avg. gap size = 0.0 (0 / 0)
+ 2535 2.9 0.0 7.8 X_90550234_90550579_INS 15 346 (0) + AluY SINE/Alu 1 308 (3) 926
ANNOTATION EVIDENCE:
2535 2.94 0.00 7.79 X_90550234_90550579_INS 15 346 0 + AluY SINE/Alu 1 308 3
2535 2.94 0.00 7.79 X_90550234_90550579_INS 15 346 (0) AluY#SINE/Alu 1 308 (3) c_b2s352i102
X_90550234_90 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_90550234_90 65 GGCGGGTGGATCATGAGGTCAGGAGATCTAGACCATCCTGGCTAACAAGG 114
i i v v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_90550234_90 115 TGAAACCCCGTCTCTACTAAAAAAAAAAAAAAAAAAAAAATACAAAAAAT 164
-----------------
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAA-----------------ATACAAAAAAT 133
X_90550234_90 165 TAGCCGGGCGCGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTG 214
i
AluY#SINE/Alu 134 TAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTG 183
X_90550234_90 215 AGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAG 264
i
AluY#SINE/Alu 184 AGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAG 233
X_90550234_90 265 ATTGCGCCACTGCAGTCCGCAGTCCGGCCTGGGCAACAGAGCGAGACTCC 314
i -- ----- i i
AluY#SINE/Alu 234 ATCGCGCCACTGCA--C-----TCCAGCCTGGGCGACAGAGCGAGACTCC 276
X_90550234_90 315 GTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAA 346
AluY#SINE/Alu 277 GTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAA 308
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.78
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.07 (24 / 331), avg. gap size = 1.00 (24 / 24)
+ 118 1.5 0.0 0.0 X_90640606_90640739_INS 2 134 (0) + (A)n Simple_repeat 1 133 (0) 927
ANNOTATION EVIDENCE:
118 1.52 0.00 0.00 X_90640606_90640739_INS 2 134 0 + (A)n Simple_repeat 1 133 0
118 1.52 0.00 0.00 X_90640606_90640739_INS 2 134 (0) (A)n#Simple_repeat 1 133 (0) m_b2s252i5
X_90640606_90 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 51
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
X_90640606_90 52 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA 101
v v
(A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100
X_90640606_90 102 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 134
(A)n#Simple_r 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 133
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
+ 2517 2.5 0.0 0.0 X_90726805_90727097_INS 17 293 (0) + AluY SINE/Alu 28 304 (7) 928
ANNOTATION EVIDENCE:
2517 2.53 0.00 0.00 X_90726805_90727097_INS 17 293 0 + AluY SINE/Alu 28 304 7
2517 2.53 0.00 0.00 X_90726805_90727097_INS 17 293 (0) AluY#SINE/Alu 28 304 (7) c_b2s352i103
X_90726805_90 17 ATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACGAGGTCAGGAGAT 66
i
AluY#SINE/Alu 28 ATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGAT 77
X_90726805_90 67 CGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACA 116
i v
AluY#SINE/Alu 78 CGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACA 127
X_90726805_90 117 AAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGG 166
i i
AluY#SINE/Alu 128 AAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGG 177
X_90726805_90 167 AGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCAGAGCTTGCAGTGA 216
i
AluY#SINE/Alu 178 AGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGA 227
X_90726805_90 217 GCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCG 266
v
AluY#SINE/Alu 228 GCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCG 277
X_90726805_90 267 TCTCAAAAAAAAAAAAAAAAAAAAAAA 293
AluY#SINE/Alu 278 TCTCAAAAAAAAAAAAAAAAAAAAAAA 304
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.57
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 276), avg. gap size = 0.0 (0 / 0)
+ 75 9.5 0.0 0.0 X_90795954_90796057_INS 1 104 (0) + (TA)n Simple_repeat 1 104 (0) 929
ANNOTATION EVIDENCE:
75 9.50 0.00 0.00 X_90795954_90796057_INS 1 104 0 + (TA)n Simple_repeat 1 104 0
75 9.50 0.00 0.00 X_90795954_90796057_INS 1 104 (0) (TA)n#Simple_repeat 1 104 (0) c_b2s251i23
X_90795954_90 1 TATATATATATATATATGTATGTATATATATATATGTATATATATATATA 50
i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_90795954_90 51 TACATATATATATGTATGTATATATATATATATATGTGTGTATATATATA 100
i i i i i i
(TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100
X_90795954_90 101 TATA 104
(TA)n#Simple_ 101 TATA 104
Matrix = Unknown
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0)
+ 41 14.4 0.0 5.0 X_91205588_91205672_INS 2 85 (0) + (AT)n Simple_repeat 1 80 (0) 930
ANNOTATION EVIDENCE:
41 14.40 0.00 5.00 X_91205588_91205672_INS 2 85 0 + (AT)n Simple_repeat 1 80 0
41 14.40 0.00 5.00 X_91205588_91205672_INS 2 85 (0) (AT)n#Simple_repeat 1 80 (0) m_b2s252i4
X_91205588_91 2 ATATATATATATAAATGTGATTGATATATATATATAAATGTGATATATAT 51
v i - vv v i -
(AT)n#Simple_ 1 ATATATATATATATATAT-ATATATATATATATATATATAT-ATATATAT 48
X_91205588_91 52 ATATAAATGTGATATATATATATAAATGTGATAT 85
v i - v i -
(AT)n#Simple_ 49 ATATATATAT-ATATATATATATATATAT-ATAT 80
Matrix = Unknown
Transitions / transversions = 0.67 (4/6)
Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.00 (4 / 4)
+ 2859 1.3 0.0 0.0 X_91556720_91557034_INS 10 315 (0) C AluY SINE/Alu (4) 307 2 931
ANNOTATION EVIDENCE:
2859 1.31 0.00 0.00 X_91556720_91557034_INS 10 315 0 C AluY SINE/Alu 2 307 4
2859 1.31 0.00 0.00 X_91556720_91557034_INS 10 315 (0) C AluY#SINE/Alu (4) 307 2 c_b2s352i104
X_91556720_91 10 TTTTCTTTTTCTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC 59
i i
C AluY#SINE/Alu 307 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC 258
X_91556720_91 60 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCC 109
C AluY#SINE/Alu 257 CAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCC 208
X_91556720_91 110 CGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACA 159
C AluY#SINE/Alu 207 CGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACA 158
X_91556720_91 160 GGCGCCCGCTACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGG 209
i
C AluY#SINE/Alu 157 GGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGG 108
X_91556720_91 210 GGTTTCACCGTGTTAGCCAGAATGGTCTCGATCTCCTGACCTCGTGATCC 259
i
C AluY#SINE/Alu 107 GGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCC 58
X_91556720_91 260 GCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCG 309
C AluY#SINE/Alu 57 GCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCG 8
X_91556720_91 310 CCCGGC 315
C AluY#SINE/Alu 7 CCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.32
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 305), avg. gap size = 0.0 (0 / 0)
+ 68 0.0 0.0 0.0 X_91586290_91586349_INS 1 60 (0) + (CTT)n Simple_repeat 1 60 (0) 932
ANNOTATION EVIDENCE:
68 0.00 0.00 0.00 X_91586290_91586349_INS 1 60 0 + (CTT)n Simple_repeat 1 60 0
68 0.00 0.00 0.00 X_91586290_91586349_INS 1 60 (0) (CTT)n#Simple_repeat 1 60 (0) c_b2s251i22
X_91586290_91 1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT 50
(CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT 50
X_91586290_91 51 TCTTCTTCTT 60
(CTT)n#Simple 51 TCTTCTTCTT 60
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0)
+ 36 4.0 3.9 0.0 X_91666955_91667007_INS 1 52 (1) + (AGG)n Simple_repeat 1 54 (0) 933
ANNOTATION EVIDENCE:
36 4.00 3.85 0.00 X_91666955_91667007_INS 1 52 1 + (AGG)n Simple_repeat 1 54 0
36 4.00 3.85 0.00 X_91666955_91667007_INS 1 52 (1) (AGG)n#Simple_repeat 1 54 (0) m_b2s252i3
X_91666955_91 1 AGGAGGAGG-GG-GGAGGAGGAGGGGGAGGAGGAGGAGGGGGAGGAGGAG 48
- - i i
(AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 50
X_91666955_91 49 GAGG 52
(AGG)n#Simple 51 GAGG 54
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2)
+ 34 4.1 0.0 7.3 X_91745735_91745793_INS 1 59 (0) + (GAAA)n Simple_repeat 1 55 (0) 934
ANNOTATION EVIDENCE:
34 4.08 0.00 7.27 X_91745735_91745793_INS 1 59 0 + (GAAA)n Simple_repeat 1 55 0
34 4.08 0.00 7.27 X_91745735_91745793_INS 1 59 (0) (GAAA)n#Simple_repeat 1 55 (0) m_b2s252i2
X_91745735_91 1 GAGAGAAAGAGAGAAAGAAAGAAAGGGAAAGAAAGAAAGGAAAGAAAGAA 50
i i -- -
(GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAA--GAAAGAAAGAAA-GAAAGAAAGAA 47
X_91745735_91 51 AGAAAAGAA 59
-
(GAAA)n#Simpl 48 AG-AAAGAA 55
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4)
+ 47 0.0 0.0 0.0 X_91831010_91831087_INS 2 41 (37) + (AC)n Simple_repeat 1 40 (0) 935
ANNOTATION EVIDENCE:
47 0.00 0.00 0.00 X_91831010_91831087_INS 2 41 37 + (AC)n Simple_repeat 1 40 0
47 0.00 0.00 0.00 X_91831010_91831087_INS 2 41 (37) (AC)n#Simple_repeat 1 40 (0) c_b2s251i20
X_91831010_91 2 ACACACACACACACACACACACACACACACACACACACAC 41
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACAC 40
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 33 0.0 0.0 0.0 X_91831010_91831087_INS 50 77 (1) + (TA)n Simple_repeat 1 28 (0) 936
ANNOTATION EVIDENCE:
33 0.00 0.00 0.00 X_91831010_91831087_INS 50 77 1 + (TA)n Simple_repeat 1 28 0
33 0.00 0.00 0.00 X_91831010_91831087_INS 50 77 (1) (TA)n#Simple_repeat 1 28 (0) c_b2s251i21
X_91831010_91 50 TATATATATATATATATATATATATATA 77
(TA)n#Simple_ 1 TATATATATATATATATATATATATATA 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 2403 2.5 0.0 3.2 X_91869259_91869586_INS 13 328 (0) C AluY SINE/Alu (0) 311 1 937
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_91869259_91869586_INS 13 38 290 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_91869259_91869586_INS 13 38 (290) (T)n#Simple_repeat 1 26 (0) c_b2s251i19
X_91869259_91 13 TTTTTTTTTTTTTTTTTTTTTTTTTT 38
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2403 2.49 0.00 3.20 X_91869259_91869586_INS 39 328 0 C AluY SINE/Alu 1 281 30
2403 2.49 0.00 3.20 X_91869259_91869586_INS 39 328 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i105
X_91869259_91 39 GAGACGGAGTCTCGCTCTGTCGCCCAGGTGGGACTGCGGACTGCAGTGGC 88
----- -- v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 239
X_91869259_91 89 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 138
i i
C AluY#SINE/Alu 238 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 189
X_91869259_91 139 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 188
i
C AluY#SINE/Alu 188 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 139
X_91869259_91 189 GGCTAATTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGC 238
-- v
C AluY#SINE/Alu 138 GGCTAATTTTTT--GTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGC 91
X_91869259_91 239 CAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCC 288
i i
C AluY#SINE/Alu 90 CAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCC 41
X_91869259_91 289 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 328
C AluY#SINE/Alu 40 AAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.55
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.03 (9 / 289), avg. gap size = 1.00 (9 / 9)
+ 2528 3.2 0.0 0.0 X_91989129_91989452_INS 16 324 (0) C AluY SINE/Alu (0) 311 1 938
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 X_91989129_91989452_INS 16 43 281 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 X_91989129_91989452_INS 16 43 (281) (T)n#Simple_repeat 1 28 (0) c_b2s251i18
X_91989129_91 16 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
(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)
2528 3.20 0.00 0.00 X_91989129_91989452_INS 44 324 0 C AluY SINE/Alu 1 281 30
2528 3.20 0.00 0.00 X_91989129_91989452_INS 44 324 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i106
X_91989129_91 44 GAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGGGATCT 93
i v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_91989129_91 94 CGGTTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 143
i
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_91989129_91 144 GCCTCCCAAGTAGCTGGGACTACAGGCGTCCGCCACTACGCCCGGCTAAT 193
i i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_91989129_91 194 TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTTTTAGCCGGGATGGT 243
i v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_91989129_91 244 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 293
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_91989129_91 294 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 324
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.28
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 48 4.2 0.0 0.0 X_92054941_92054995_INS 3 52 (3) + (AT)n Simple_repeat 1 50 (0) 939
ANNOTATION EVIDENCE:
48 4.17 0.00 0.00 X_92054941_92054995_INS 3 52 3 + (AT)n Simple_repeat 1 50 0
48 4.17 0.00 0.00 X_92054941_92054995_INS 3 52 (3) (AT)n#Simple_repeat 1 50 (0) c_b2s251i17
X_92054941_92 3 ATATATATATATATATATATACGTATATATATATATATATATATATATAT 52
ii
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 580 13.7 1.0 0.0 X_92646266_92646367_INS 1 102 (0) C L1M1 LINE/L1 (3995) 3570 3468 940
ANNOTATION EVIDENCE:
580 13.73 0.98 0.00 X_92646266_92646367_INS 1 102 0 C L1M1_5end LINE/L1 3468 3570 105
580 13.73 0.98 0.00 X_92646266_92646367_INS 1 102 (0) C L1M1_5end#LINE/L1 (105) 3570 3468 m_b2s551i29
X_92646266_92 1 ATTCAATGATATTATTGAAAAGTAAGAACTTAC-CCTGCCACTTTATTAT 49
v v i - i i
C L1M1_5end#LIN 3570 ATTCAATGTTATTATTGATAAGTAAGGACTTACTCCTGCCATTTTGTTAT 3521
X_92646266_92 50 TTGCTTTCTGCCTGTTTTGTGGTCTTCTCTTTATTTTTTGCTTCTTTCCT 99
i vi iv i v i
C L1M1_5end#LIN 3520 TTGTTTTCTGGTTGTTTTGTGGTCTTCTCTTCCTTCTTTCCTTCCTTCCT 3471
X_92646266_92 100 GCC 102
i
C L1M1_5end#LIN 3470 GTC 3468
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.36
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1)
+ 55 0.0 0.0 0.0 X_9272611_9272661_INS 2 51 (0) + (AAGAG)n Simple_repeat 1 50 (0) 941
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 X_9272611_9272661_INS 2 51 0 + (AAGAG)n Simple_repeat 1 50 0
55 0.00 0.00 0.00 X_9272611_9272661_INS 2 51 (0) (AAGAG)n#Simple_repeat 1 50 (0) c_b1s251i3
X_9272611_927 2 AAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAG 51
(AAGAG)n#Simp 1 AAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAG 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 2533 1.8 0.0 0.4 X_92744075_92744397_INS 7 323 (0) C AluY SINE/Alu (0) 311 2 942
ANNOTATION EVIDENCE:
39 0.00 0.00 0.00 X_92744075_92744397_INS 7 42 281 + (T)n Simple_repeat 1 36 0
39 0.00 0.00 0.00 X_92744075_92744397_INS 7 42 (281) (T)n#Simple_repeat 1 36 (0) c_b2s251i16
X_92744075_92 7 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
2533 1.79 0.00 0.36 X_92744075_92744397_INS 43 323 0 C AluY SINE/Alu 2 281 30
2533 1.79 0.00 0.36 X_92744075_92744397_INS 43 323 (0) C AluY#SINE/Alu (30) 281 2 c_b2s352i107
X_92744075_92 43 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 92
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_92744075_92 93 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 142
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_92744075_92 143 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 192
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_92744075_92 193 TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGG 242
- v i
C AluY#SINE/Alu 131 T-TTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG 83
X_92744075_92 243 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 292
C AluY#SINE/Alu 82 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 33
X_92744075_92 293 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 323
C AluY#SINE/Alu 32 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.48
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 58 0.0 0.0 0.0 X_9306432_9306484_INS 2 53 (0) + (AAGG)n Simple_repeat 1 52 (0) 943
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_9306432_9306484_INS 2 53 0 + (AAGG)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_9306432_9306484_INS 2 53 (0) (AAGG)n#Simple_repeat 1 52 (0) c_b1s251i2
X_9306432_930 2 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 51
(AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50
X_9306432_930 52 GG 53
(AAGG)n#Simpl 51 GG 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2668 1.7 0.0 0.0 X_93362069_93362379_INS 18 307 (4) + AluY SINE/Alu 22 311 (0) 944
ANNOTATION EVIDENCE:
2668 1.72 0.00 0.00 X_93362069_93362379_INS 18 307 4 + AluY SINE/Alu 22 311 0
2668 1.72 0.00 0.00 X_93362069_93362379_INS 18 307 (4) AluY#SINE/Alu 22 311 (0) c_b2s352i108
X_93362069_93 18 CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCA 67
AluY#SINE/Alu 22 CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCA 71
X_93362069_93 68 GGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAA 117
i v
AluY#SINE/Alu 72 GGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAA 121
X_93362069_93 118 AATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTA 167
i
AluY#SINE/Alu 122 AATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTA 171
X_93362069_93 168 CTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTG 217
i
AluY#SINE/Alu 172 CTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTG 221
X_93362069_93 218 CAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAG 267
v
AluY#SINE/Alu 222 CAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAG 271
X_93362069_93 268 ACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 307
AluY#SINE/Alu 272 ACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.43
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 289), avg. gap size = 0.0 (0 / 0)
+ 49 0.0 0.0 5.8 X_93398547_93398605_INS 2 56 (3) + (AT)n Simple_repeat 1 52 (0) 945
ANNOTATION EVIDENCE:
49 0.00 0.00 5.77 X_93398547_93398605_INS 2 56 3 + (AT)n Simple_repeat 1 52 0
49 0.00 0.00 5.77 X_93398547_93398605_INS 2 56 (3) (AT)n#Simple_repeat 1 52 (0) c_b2s251i15
X_93398547_93 2 ATATATATATATCATATATATATATATGATATATATATATCATATATATA 51
- - -
(AT)n#Simple_ 1 ATATATATATAT-ATATATATATATAT-ATATATATATAT-ATATATATA 47
X_93398547_93 52 TATAT 56
(AT)n#Simple_ 48 TATAT 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3)
+ 31 0.0 0.0 0.0 X_9340485_9340573_INS 1 37 (52) + (AGAA)n Simple_repeat 1 37 (0) 946
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_9340485_9340573_INS 1 37 1 + (AGAA)n Simple_repeat 1 37 0
31 0.00 0.00 0.00 X_9340485_9340573_INS 1 37 (1) (AGAA)n#Simple_repeat 1 37 (0) m_b1s252i1
X_9340485_934 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 37
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 58 0.0 0.0 0.0 X_9340485_9340573_INS 38 89 (0) + (GAAG)n Simple_repeat 1 52 (0) 947
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 X_9340485_9340573_INS 38 89 0 + (GAAG)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 X_9340485_9340573_INS 38 89 (0) (GAAG)n#Simple_repeat 1 52 (0) c_b1s251i1
X_9340485_934 38 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 87
(GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 50
X_9340485_934 88 AG 89
(GAAG)n#Simpl 51 AG 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 51 3.7 0.0 0.0 X_93554184_93554239_INS 2 56 (0) + (T)n Simple_repeat 1 55 (0) 948
ANNOTATION EVIDENCE:
51 3.74 0.00 0.00 X_93554184_93554239_INS 2 56 0 + (T)n Simple_repeat 1 55 0
51 3.74 0.00 0.00 X_93554184_93554239_INS 2 56 (0) (T)n#Simple_repeat 1 55 (0) c_b2s251i14
X_93554184_93 2 TTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGT 51
v v
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_93554184_93 52 TTTTT 56
(T)n#Simple_r 51 TTTTT 55
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 430 10.2 0.0 0.0 X_93984045_93984103_INS 1 59 (0) C THE1D LTR/ERVL-MaLR (40) 341 283 949
ANNOTATION EVIDENCE:
430 10.17 0.00 0.00 X_93984045_93984103_INS 1 59 0 C THE1D LTR/ERVL-MaLR 283 341 40
430 10.17 0.00 0.00 X_93984045_93984103_INS 1 59 (0) C THE1D#LTR/ERVL-MaLR (40) 341 283 m_b2s502i20
X_93984045_93 1 AGACTGGGTAATTTATAAAGAAAAGTGATTTAGTTGACTCACAGTTCCAC 50
i v i i i
C THE1D#LTR/ERV 341 AGACTGGGTAATTTATAAAGGAAAGAGGTTTAATTGACTCACAGTTCCGC 292
X_93984045_93 51 ATGGGTGGG 59
v
C THE1D#LTR/ERV 291 ATGGCTGGG 283
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.24
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 52 0.0 3.7 0.0 X_94180698_94180751_INS 1 54 (0) + (AAAG)n Simple_repeat 1 56 (0) 950
ANNOTATION EVIDENCE:
52 0.00 3.70 0.00 X_94180698_94180751_INS 1 54 0 + (AAAG)n Simple_repeat 1 56 0
52 0.00 3.70 0.00 X_94180698_94180751_INS 1 54 (0) (AAAG)n#Simple_repeat 1 56 (0) c_b2s251i13
X_94180698_94 1 AAAGAAAGAAAG-AA-AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 48
- -
(AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 50
X_94180698_94 49 AGAAAG 54
(AAAG)n#Simpl 51 AGAAAG 56
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2)
+ 34 13.1 0.0 0.0 X_94189434_94189486_INS 1 52 (1) + (AT)n Simple_repeat 1 52 (0) 951
ANNOTATION EVIDENCE:
34 13.12 0.00 0.00 X_94189434_94189486_INS 1 52 1 + (AT)n Simple_repeat 1 52 0
34 13.12 0.00 0.00 X_94189434_94189486_INS 1 52 (1) (AT)n#Simple_repeat 1 52 (0) m_b2s252i1
X_94189434_94 1 ATATATACACATATATATGTATATATATGTGTATATATATACATATATAT 50
i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_94189434_94 51 AT 52
(AT)n#Simple_ 51 AT 52
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2639 0.7 0.0 0.0 X_94584364_94584687_INS 14 324 (0) C AluY SINE/Alu (0) 311 1 952
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 X_94584364_94584687_INS 14 43 281 + (T)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 X_94584364_94584687_INS 14 43 (281) (T)n#Simple_repeat 1 30 (0) c_b2s251i12
X_94584364_94 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43
(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)
2639 0.71 0.00 0.00 X_94584364_94584687_INS 44 324 0 C AluY SINE/Alu 1 281 30
2639 0.71 0.00 0.00 X_94584364_94584687_INS 44 324 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i109
X_94584364_94 44 GAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGCGATCT 93
i
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_94584364_94 94 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 143
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_94584364_94 144 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 193
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_94584364_94 194 TTTTTGTGTTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 243
i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_94584364_94 244 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 293
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_94584364_94 294 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 324
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.39
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 1477 10.5 7.7 0.0 X_94894754_94895022_INS 1 88 (181) C AluSx SINE/Alu (87) 225 137 953
ANNOTATION EVIDENCE:
1477 10.53 7.66 0.00 X_94894754_94895022_INS 1 88 181 C AluSx SINE/Alu 137 225 87
1477 10.53 7.66 0.00 X_94894754_94895022_INS 1 88 (181) C AluSx#SINE/Alu (87) 225 137 c_b2s352i110
X_94894754_94 1 CTGCAACCTCTGCCTCCCAGGTTCAAGCGATTCTCATGCCTTAGCCTCC- 49
i i v i -
C AluSx#SINE/Al 225 CTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCC 176
X_94894754_94 50 AAGTAGCTGGGATTTCAGGTGCTCACCACCACACCTGGC 88
i v i v i i i
C AluSx#SINE/Al 175 GAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGC 137
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1)
+ 41 0.0 4.4 0.0 X_94894754_94895022_INS 89 133 (136) + (TTAT)n Simple_repeat 1 47 (0) 954
ANNOTATION EVIDENCE:
41 0.00 4.44 0.00 X_94894754_94895022_INS 89 133 136 + (TTAT)n Simple_repeat 1 47 0
41 0.00 4.44 0.00 X_94894754_94895022_INS 89 133 (136) (TTAT)n#Simple_repeat 1 47 (0) c_b2s251i11
X_94894754_94 89 TTATTTATTTATTTATTTATTTATTTATTTATTTA--TATTTATTTA 133
--
(TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 44), avg. gap size = 2.00 (2 / 1)
+ 1477 10.5 7.7 0.0 X_94894754_94895022_INS 134 253 (16) C AluSx SINE/Alu (176) 136 2 953
ANNOTATION EVIDENCE:
1477 10.53 7.66 0.00 X_94894754_94895022_INS 134 253 16 C AluSx SINE/Alu 2 136 176
1477 10.53 7.66 0.00 X_94894754_94895022_INS 134 253 (16) C AluSx#SINE/Alu (176) 136 2 c_b2s352i110
X_94894754_94 134 AATT---------------GAGATGGAGTTTCACTATGTTGGCCAGGCTG 168
--------------- i i i
C AluSx#SINE/Al 136 AATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG 87
X_94894754_94 169 GTCTCGAACTCCTGACCTCAAGTGATCTACCCACCTTGGCCTCCCAAAGT 218
i ii i i
C AluSx#SINE/Al 86 GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGT 37
X_94894754_94 219 GCTGGGATTACAGGCGTGAGCCACTGCACCCAGCC 253
i i i
C AluSx#SINE/Al 36 GCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.01 (1 / 119), avg. gap size = 15.00 (15 / 1)
+ 52 1.7 3.4 0.0 X_94968599_94968668_INS 12 70 (0) + (ATATATATGT)n Simple_repeat 1 61 (0) 955
ANNOTATION EVIDENCE:
52 1.72 3.39 0.00 X_94968599_94968668_INS 12 70 0 + (ATATATATGT)n Simple_repeat 1 61 0
52 1.72 3.39 0.00 X_94968599_94968668_INS 12 70 (0) (ATATATATGT)n#Simple_repeat 1 61 (0) c_b2s251i10
X_94968599_94 12 ATATATATGTATATATATGTATATATATGTATATAT-T-AATATATATGT 59
- -v
(ATATATATGT)n 1 ATATATATGTATATATATGTATATATATGTATATATATGTATATATATGT 50
X_94968599_94 60 ATATATATGTA 70
(ATATATATGT)n 51 ATATATATGTA 61
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2)
+ 57 0.0 0.0 7.6 X_95337562_95337637_INS 5 75 (1) + (AT)n Simple_repeat 1 66 (0) 956
ANNOTATION EVIDENCE:
57 0.00 0.00 7.58 X_95337562_95337637_INS 5 75 1 + (AT)n Simple_repeat 1 66 0
57 0.00 0.00 7.58 X_95337562_95337637_INS 5 75 (1) (AT)n#Simple_repeat 1 66 (0) c_b2s251i9
X_95337562_95 5 ATATATATATATGATATATATATATCATATATATATGATATATATATGAT 54
- - - -
(AT)n#Simple_ 1 ATATATATATAT-ATATATATATAT-ATATATATAT-ATATATATAT-AT 46
X_95337562_95 55 ATATATATATCATATATATAT 75
-
(AT)n#Simple_ 47 ATATATATAT-ATATATATAT 66
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5)
+ 2587 1.4 0.0 0.0 X_95537339_95537658_INS 14 320 (0) C AluY SINE/Alu (0) 311 1 957
ANNOTATION EVIDENCE:
27 0.00 0.00 0.00 X_95537339_95537658_INS 14 39 281 + (T)n Simple_repeat 1 26 0
27 0.00 0.00 0.00 X_95537339_95537658_INS 14 39 (281) (T)n#Simple_repeat 1 26 (0) c_b2s251i8
X_95537339_95 14 TTTTTTTTTTTTTTTTTTTTTTTTTT 39
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
2587 1.42 0.00 0.00 X_95537339_95537658_INS 40 320 0 C AluY SINE/Alu 1 281 30
2587 1.42 0.00 0.00 X_95537339_95537658_INS 40 320 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i111
X_95537339_95 40 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 89
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_95537339_95 90 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 139
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_95537339_95 140 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 189
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_95537339_95 190 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 239
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_95537339_95 240 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 289
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_95537339_95 290 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 320
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.11
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 2700 2.3 0.0 2.3 X_95838690_95839017_INS 15 328 (0) + AluY SINE/Alu 1 307 (4) 958
ANNOTATION EVIDENCE:
2700 2.28 0.00 2.28 X_95838690_95839017_INS 15 328 0 + AluY SINE/Alu 1 307 4
2700 2.28 0.00 2.28 X_95838690_95839017_INS 15 328 (0) AluY#SINE/Alu 1 307 (4) c_b2s352i112
X_95838690_95 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_95838690_95 65 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 114
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_95838690_95 115 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGC 164
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_95838690_95 165 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 214
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_95838690_95 215 GAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTC 264
i i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_95838690_95 265 CGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 314
-- -----
AluY#SINE/Alu 251 --CAG-----CCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA 293
X_95838690_95 315 AAAAAAAAAAAAAA 328
AluY#SINE/Alu 294 AAAAAAAAAAAAAA 307
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.41
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 313), avg. gap size = 1.00 (7 / 7)
+ 2740 2.0 0.0 0.0 X_95906705_95907018_INS 17 314 (0) + AluY SINE/Alu 1 298 (13) 959
ANNOTATION EVIDENCE:
2740 2.01 0.00 0.00 X_95906705_95907018_INS 17 314 0 + AluY SINE/Alu 1 298 13
2740 2.01 0.00 0.00 X_95906705_95907018_INS 17 314 (0) AluY#SINE/Alu 1 298 (13) c_b2s352i113
X_95906705_95 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_95906705_95 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGG 116
i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_95906705_95 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 166
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
X_95906705_95 167 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 216
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
X_95906705_95 217 GAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 266
i v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
X_95906705_95 267 CAGCCTGGGCGACAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAA 314
i
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 298
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.12
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 297), avg. gap size = 0.0 (0 / 0)
+ 49 0.0 0.0 6.8 X_96143570_96143650_INS 2 64 (17) + (TATATATATC)n Simple_repeat 1 59 (0) 960
ANNOTATION EVIDENCE:
49 0.00 0.00 6.78 X_96143570_96143650_INS 2 64 17 + (TATATATATC)n Simple_repeat 1 59 0
49 0.00 0.00 6.78 X_96143570_96143650_INS 2 64 (17) (TATATATATC)n#Simple_repeat 1 59 (0) c_b2s251i7
X_96143570_96 2 TATATATATCTATATATATCTATATATATACAGCTATATATATCTATATA 51
----
(TATATATATC)n 1 TATATATATCTATATATATCTATATATAT----CTATATATATCTATATA 46
X_96143570_96 52 TATCTATATATAT 64
(TATATATATC)n 47 TATCTATATATAT 59
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4)
+ 56 0.0 1.9 0.0 X_96384121_96384174_INS 1 54 (0) + (TTTTC)n Simple_repeat 1 55 (0) 961
ANNOTATION EVIDENCE:
56 0.00 1.85 0.00 X_96384121_96384174_INS 1 54 0 + (TTTTC)n Simple_repeat 1 55 0
56 0.00 1.85 0.00 X_96384121_96384174_INS 1 54 (0) (TTTTC)n#Simple_repeat 1 55 (0) c_b2s251i6
X_96384121_96 1 TTTTCTTTTCTTTTC-TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC 49
-
(TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC 50
X_96384121_96 50 TTTTC 54
(TTTTC)n#Simp 51 TTTTC 55
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1)
+ 46 10.0 0.0 0.0 X_96440424_96440490_INS 1 66 (1) + (AT)n Simple_repeat 1 66 (0) 962
ANNOTATION EVIDENCE:
46 10.03 0.00 0.00 X_96440424_96440490_INS 1 66 1 + (AT)n Simple_repeat 1 66 0
46 10.03 0.00 0.00 X_96440424_96440490_INS 1 66 (1) (AT)n#Simple_repeat 1 66 (0) c_b2s251i5
X_96440424_96 1 ATATATATATGTGTATATATATATATGTATATATATATGTGTATATATAT 50
i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
X_96440424_96 51 ATATGTATATATATAT 66
i
(AT)n#Simple_ 51 ATATATATATATATAT 66
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 2923 0.3 0.0 0.3 X_96522253_96522580_INS 10 321 (7) + AluY SINE/Alu 1 311 (0) 963
ANNOTATION EVIDENCE:
2923 0.32 0.00 0.32 X_96522253_96522580_INS 10 321 7 + AluY SINE/Alu 1 311 0
2923 0.32 0.00 0.32 X_96522253_96522580_INS 10 321 (7) AluY#SINE/Alu 1 311 (0) c_b2s352i114
X_96522253_96 10 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 59
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_96522253_96 60 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 109
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_96522253_96 110 TGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTGGTAG 159
- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAA-AATTAGCCGGGCGTGGTGG 149
X_96522253_96 160 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 209
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
X_96522253_96 210 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 259
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
X_96522253_96 260 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 309
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
X_96522253_96 310 AAAAAAAAAAAA 321
AluY#SINE/Alu 300 AAAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.32
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (1 / 311), avg. gap size = 1.00 (1 / 1)
+ 2847 1.6 0.0 0.0 X_96995229_96995543_INS 8 315 (0) C AluY SINE/Alu (3) 308 1 964
ANNOTATION EVIDENCE:
2847 1.62 0.00 0.00 X_96995229_96995543_INS 8 315 0 C AluY SINE/Alu 1 308 3
2847 1.62 0.00 0.00 X_96995229_96995543_INS 8 315 (0) C AluY#SINE/Alu (3) 308 1 c_b2s352i115
X_96995229_96 8 TTTTATTTTATTTTATTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 57
v v v
C AluY#SINE/Alu 308 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 259
X_96995229_96 58 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTC 107
C AluY#SINE/Alu 258 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTC 209
X_96995229_96 108 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 157
C AluY#SINE/Alu 208 CCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 159
X_96995229_96 158 AGGCGCCCGCTACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACG 207
i
C AluY#SINE/Alu 158 AGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACG 109
X_96995229_96 208 GGGTTTCACCGTGTTAGCCAGAATGGTCTCGATCTCCTGACCTCGTGATC 257
i
C AluY#SINE/Alu 108 GGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATC 59
X_96995229_96 258 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 307
C AluY#SINE/Alu 58 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
X_96995229_96 308 GCCCGGCC 315
C AluY#SINE/Alu 8 GCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.64
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 307), avg. gap size = 0.0 (0 / 0)
+ 390 16.2 0.0 0.0 X_97018038_97018110_INS 1 68 (5) C LTR8A LTR/ERV1 (562) 165 98 965
ANNOTATION EVIDENCE:
390 16.18 0.00 0.00 X_97018038_97018110_INS 1 68 5 C LTR8A LTR/ERV1 98 165 562
390 16.18 0.00 0.00 X_97018038_97018110_INS 1 68 (5) C LTR8A#LTR/ERV1 (562) 165 98 m_b2s502i21
X_97018038_97 1 ATCATTTAAACTATAAACTACATTTCTCCTAAAGTTAGCTAGTCTCATGA 50
v ? i v v i v v
C LTR8A#LTR/ERV 165 ATCATTTAAACTATAAACTAAATNTCTCCCAAAGTTAGCTTGGCCCAAGC 116
X_97018038_97 51 CAAGGAGTGACCAAGGGC 68
v i ii
C LTR8A#LTR/ERV 115 CCAGGAATGATTAAGGGC 98
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.58
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 46 16.6 0.0 0.0 X_9738358_9738437_INS 3 80 (0) + GA-rich Low_complexity 1 78 (0) 966
ANNOTATION EVIDENCE:
46 16.57 0.00 0.00 X_9738358_9738437_INS 3 80 0 + (AG)n Simple_repeat 1 78 0
46 16.57 0.00 0.00 X_9738358_9738437_INS 3 80 (0) (AG)n#Simple_repeat 1 78 (0) m_b1s252i0
X_9738358_973 3 AGAAAAAGAAAAAGAAAAAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAA 52
i i i i i i i i
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50
X_9738358_973 53 AGAAAAAGAAAGAGAGAGAGAGAGAGAG 80
i i i
(AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAG 78
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0)
+ 2598 2.3 0.0 3.6 X_97689057_97689382_INS 15 326 (0) + AluY SINE/Alu 1 301 (10) 967
ANNOTATION EVIDENCE:
2598 2.32 0.00 3.65 X_97689057_97689382_INS 15 326 0 + AluY SINE/Alu 1 301 10
2598 2.32 0.00 3.65 X_97689057_97689382_INS 15 326 (0) AluY#SINE/Alu 1 301 (10) c_b2s352i116
X_97689057_97 15 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 64
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
X_97689057_97 65 GGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 114
i i v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
X_97689057_97 115 TGAAACCCCGTCTCTACTAAAAAAAAATACAAAAAATTAGCCGGGCGCGG 164
---- i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAA----ATACAAAAAATTAGCCGGGCGTGG 146
X_97689057_97 165 TGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATG 214
AluY#SINE/Alu 147 TGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATG 196
X_97689057_97 215 GCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGC 264
i i
AluY#SINE/Alu 197 GCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGC 246
X_97689057_97 265 AGTCCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAA 314
-- ----- i
AluY#SINE/Alu 247 A--C-----TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAA 289
X_97689057_97 315 AAAAAAAAAAAA 326
AluY#SINE/Alu 290 AAAAAAAAAAAA 301
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.45
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.04 (11 / 311), avg. gap size = 1.00 (11 / 11)
+ 27 15.8 0.0 2.0 X_97865290_97865341_INS 2 52 (0) + (AT)n Simple_repeat 1 50 (0) 968
ANNOTATION EVIDENCE:
27 15.84 0.00 2.00 X_97865290_97865341_INS 2 52 0 + (AT)n Simple_repeat 1 50 0
27 15.84 0.00 2.00 X_97865290_97865341_INS 2 52 (0) (AT)n#Simple_repeat 1 50 (0) m_b2s252i0
X_97865290_97 2 ATATATATATATATATATATAAACCATATATTTATATAACCATATACATA 51
v -i v vvi i
(AT)n#Simple_ 1 ATATATATATATATATATATATA-TATATATATATATATATATATATATA 49
X_97865290_97 52 T 52
(AT)n#Simple_ 50 T 50
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 39 2.0 0.0 7.4 X_9791179_9791237_INS 1 58 (1) + (CCTTCT)n Simple_repeat 1 54 (0) 969
ANNOTATION EVIDENCE:
39 2.04 0.00 7.41 X_9791179_9791237_INS 1 58 1 + (CCTTCT)n Simple_repeat 1 54 0
39 2.04 0.00 7.41 X_9791179_9791237_INS 1 58 (1) (CCTTCT)n#Simple_repeat 1 54 (0) c_b1s251i0
X_9791179_979 1 CCTTCTCCTTCTCCCTTCTCCTTCTCCCTTCTCCTTCCCCCTTCTCCTTC 50
- - - i
(CCTTCT)n#Sim 1 CCTTCTCCTTCT-CCTTCTCCTTCT-CCTTCTCCTT-CTCCTTCTCCTTC 47
X_9791179_979 51 TCCCTTCT 58
-
(CCTTCT)n#Sim 48 T-CCTTCT 54
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4)
+ 1747 3.6 0.0 3.2 X_98203215_98203502_INS 15 288 (0) C AluY SINE/Alu (0) 311 71 970
ANNOTATION EVIDENCE:
61 0.00 0.00 0.00 X_98203215_98203502_INS 15 69 219 + (T)n Simple_repeat 1 55 0
61 0.00 0.00 0.00 X_98203215_98203502_INS 15 69 (219) (T)n#Simple_repeat 1 55 (0) c_b2s251i4
X_98203215_98 15 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 64
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
X_98203215_98 65 TTTTT 69
(T)n#Simple_r 51 TTTTT 55
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
1747 3.62 0.00 3.17 X_98203215_98203502_INS 70 288 0 C AluY SINE/Alu 71 282 29
1747 3.62 0.00 3.17 X_98203215_98203502_INS 70 288 (0) C AluY#SINE/Alu (29) 282 71 m_b2s357i13
X_98203215_98 70 GAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGC 119
i ----- --
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
X_98203215_98 120 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 169
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
X_98203215_98 170 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 219
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
X_98203215_98 220 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 269
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
X_98203215_98 270 GGATGGTCTCGATCTCCTG 288
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTG 71
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 3.32
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.03 (7 / 218), avg. gap size = 1.00 (7 / 7)
+ 2664 0.4 0.0 0.0 X_98225059_98225389_INS 10 331 (0) C AluY SINE/Alu (0) 311 1 971
ANNOTATION EVIDENCE:
45 0.00 0.00 0.00 X_98225059_98225389_INS 10 50 281 + (T)n Simple_repeat 1 41 0
45 0.00 0.00 0.00 X_98225059_98225389_INS 10 50 (281) (T)n#Simple_repeat 1 41 (0) c_b2s251i3
X_98225059_98 10 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
2664 0.36 0.00 0.00 X_98225059_98225389_INS 51 331 0 C AluY SINE/Alu 1 281 30
2664 0.36 0.00 0.00 X_98225059_98225389_INS 51 331 (0) C AluY#SINE/Alu (30) 281 1 c_b2s352i117
X_98225059_98 51 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 100
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
X_98225059_98 101 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 150
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
X_98225059_98 151 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTACCACGCCCGGCTAAT 200
i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
X_98225059_98 201 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 250
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
X_98225059_98 251 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 300
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
X_98225059_98 301 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 331
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 0.36
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 402 21.8 12.5 2.0 X_98389435_98390023_INS 9 144 (445) + LTR40A1 LTR/ERVL 197 346 (238) 972
ANNOTATION EVIDENCE:
402 21.76 12.50 2.00 X_98389435_98390023_INS 9 144 445 + LTR40A1 LTR/ERVL 197 346 238
402 21.76 12.50 2.00 X_98389435_98390023_INS 9 144 (445) LTR40A1#LTR/ERVL 197 346 (238) m_b2s502i22
X_98389435_98 9 AAACCCAGGGTCCTGCCCTTCTTTTCCCAAG-GAGAATTTGTTTACATTA 57
i i v v i i i v - i v
LTR40A1#LTR/E 197 AAACCTAGAGACCTTCCCCTCCTCTCCCCAGAGAGGATTTGTTTACATTC 246
X_98389435_98 58 GGGAGGTTAATTGTTTATTCCACTCTC---AGGA--GAGGATGGGGAAAA 102
vi --i vv i v ii v --- -- -? v i
LTR40A1#LTR/E 247 CAGAG--CAAAGGTCTCTCTCTCTCTCTCTAGGAGGGAGGA-NGGGCAGA 293
X_98389435_98 103 TGTA----------TATATAAGCTCCCAGATTCGT-ATTTTGGGGTTCTT 141
i---------- v vi i - i i
LTR40A1#LTR/E 294 TGTGCCAGCNGCCCTATATAAGCTCCGAGTCTCATAATTTCGGGGTTCCT 343
X_98389435_98 142 CTC 144
LTR40A1#LTR/E 344 CTC 346
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.40
Transitions / transversions = 1.42 (17/12)
Gap_init rate = 0.06 (8 / 135), avg. gap size = 2.50 (20 / 8)
+ 2779 2.0 0.0 0.0 X_98620116_98620432_INS 13 316 (1) C AluY SINE/Alu (7) 304 1 973
ANNOTATION EVIDENCE:
2779 1.97 0.00 0.00 X_98620116_98620432_INS 13 316 1 C AluY SINE/Alu 1 304 7
2779 1.97 0.00 0.00 X_98620116_98620432_INS 13 316 (1) C AluY#SINE/Alu (7) 304 1 c_b2s352i118
X_98620116_98 13 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 62
C AluY#SINE/Alu 304 TTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAG 255
X_98620116_98 63 GCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGG 112
v
C AluY#SINE/Alu 254 GCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGG 205
X_98620116_98 113 GTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGC 162
i
C AluY#SINE/Alu 204 GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 155
X_98620116_98 163 GCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 212
i
C AluY#SINE/Alu 154 GCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGT 105
X_98620116_98 213 TTCACCGTTATAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCC 262
vv i
C AluY#SINE/Alu 104 TTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCC 55
X_98620116_98 263 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 312
C AluY#SINE/Alu 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 5
X_98620116_98 313 GGCC 316
C AluY#SINE/Alu 4 GGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.70
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.00 (0 / 303), avg. gap size = 0.0 (0 / 0)
+ 2507 4.1 0.0 0.3 X_98997614_98997936_INS 14 323 (0) C AluY SINE/Alu (0) 311 3 974
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 X_98997614_98997936_INS 14 42 281 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 X_98997614_98997936_INS 14 42 (281) (T)n#Simple_repeat 1 29 (0) c_b2s251i2
X_98997614_98 14 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42
(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)
2507 4.13 0.00 0.34 X_98997614_98997936_INS 43 323 0 C AluY SINE/Alu 3 282 29
2507 4.13 0.00 0.34 X_98997614_98997936_INS 43 323 (0) C AluY#SINE/Alu (29) 282 3 c_b2s352i119
X_98997614_98 43 GAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 92
i v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 233
X_98997614_98 93 CGGCTCATTGCAAGCTCCACCTCCCGGGTTCACGCCATTCTCCTGCCTCA 142
i i
C AluY#SINE/Alu 232 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 183
X_98997614_98 143 GCCTCCCAAGTAGCTGGGACTACAGGCGCCTGCCACTACGCCCGGCTAAT 192
i i i
C AluY#SINE/Alu 182 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 133
X_98997614_98 193 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTTAGCCGGGATGG 242
- v i
C AluY#SINE/Alu 132 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCG-TGTTAGCCAGGATGG 84
X_98997614_98 243 TCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCT 292
i
C AluY#SINE/Alu 83 TCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCT 34
X_98997614_98 293 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 323
C AluY#SINE/Alu 33 GGGATTACAGGCGTGAGCCACCGCGCCCGGC 3
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.64
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 275 4.3 0.0 0.0 X_99084855_99084905_INS 5 51 (0) C L1PB LINE/L1 (2444) 3702 3656 975
ANNOTATION EVIDENCE:
275 4.26 0.00 0.00 X_99084855_99084905_INS 5 51 0 C L1PB_orf2 LINE/L1 1547 1593 1701
275 4.26 0.00 0.00 X_99084855_99084905_INS 5 51 (0) C L1PB_orf2#LINE/L1 (1701) 1593 1547 m_b2s551i30
X_99084855_99 5 TCTGTAGTTTTGTTTTTTGGTTGTGTCCTTTCCTGGTTTTGGTATTA 51
v ? i
C L1PB_orf2#LIN 1593 TCTGTAGTTTTCTTTTTTNGTTATGTCCTTTCCTGGTTTTGGTATTA 1547
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.48
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 36 11.6 0.0 0.0 X_99489030_99489092_INS 6 63 (0) + (TA)n Simple_repeat 1 58 (0) 976
ANNOTATION EVIDENCE:
36 11.59 0.00 0.00 X_99489030_99489092_INS 6 63 0 + (TA)n Simple_repeat 1 58 0
36 11.59 0.00 0.00 X_99489030_99489092_INS 6 63 (0) (TA)n#Simple_repeat 1 58 (0) c_b2s251i1
X_99489030_99 6 TATATATATATATATATATATGTATATGTATGTGTGTGTATATATATATA 55
i i i i i i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_99489030_99 56 TATATATA 63
(TA)n#Simple_ 51 TATATATA 58
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 37 4.1 5.9 0.0 X_99532139_99532196_INS 8 58 (0) + (TA)n Simple_repeat 1 54 (0) 977
ANNOTATION EVIDENCE:
37 4.08 5.88 0.00 X_99532139_99532196_INS 8 58 0 + (TA)n Simple_repeat 1 54 0
37 4.08 5.88 0.00 X_99532139_99532196_INS 8 58 (0) (TA)n#Simple_repeat 1 54 (0) c_b2s251i0
X_99532139_99 8 TATAT-TATAT-TGTATATAT-TGTATATATATATATATATATATATATA 54
- - i - i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
X_99532139_99 55 TATA 58
(TA)n#Simple_ 51 TATA 54
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3)
+ 63 25.8 0.0 0.0 Y_13139020_13139288_INS 1 157 (112) + (TCCAT)n Simple_repeat 1 157 (0) 978
ANNOTATION EVIDENCE:
63 25.81 0.00 0.00 Y_13139020_13139288_INS 1 157 112 + (TCCAT)n Simple_repeat 1 157 0
63 25.81 0.00 0.00 Y_13139020_13139288_INS 1 157 (112) (TCCAT)n#Simple_repeat 1 157 (0) m_b3s252i8
Y_13139020_13 1 TCAATCCCATTCCATTCCACTCCAATCCAATCCACTACACTACACTCCGT 50
v i i v v i v i v i i
(TCCAT)n#Simp 1 TCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCAT 50
Y_13139020_13 51 TCCTTTCCATTACATCATATTCCACTCCACTTCATTCCACGCCAATCGAC 100
v v ivi i i i iv v v i
(TCCAT)n#Simp 51 TCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCAT 100
Y_13139020_13 101 TCCACTCCATTCCATTCCATTTCATTCCAATACACTCCATTACATTATAT 150
i i v v i v vi
(TCCAT)n#Simp 101 TCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCAT 150
Y_13139020_13 151 CCCTTTC 157
i v
(TCCAT)n#Simp 151 TCCATTC 157
Matrix = Unknown
Transitions / transversions = 1.12 (18/16)
Gap_init rate = 0.00 (0 / 156), avg. gap size = 0.0 (0 / 0)
+ 139 27.6 1.0 4.2 Y_13142410_13142991_INS 3 204 (378) + (TTCCA)n Simple_repeat 1 202 (0) 979
ANNOTATION EVIDENCE:
139 27.57 0.97 4.20 Y_13142410_13142991_INS 3 204 316 + (TTCCA)n Simple_repeat 1 202 0
139 27.57 0.97 4.20 Y_13142410_13142991_INS 3 204 (316) (TTCCA)n#Simple_repeat 1 202 (0) m_b3s252i6
Y_13142410_13 3 TTCCATGCCATTCAATTCCATTCCATTCCACTGCAATCCACTCCTCTCCA 52
v v i v v i vi
(TTCCA)n#Simp 1 TTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCA 50
Y_13142410_13 53 CTCCTTTCTATCCCATTCAATTCCAGTCCATTCCAATCCACACCACTTCA 102
i v i i v v v iv i i
(TTCCA)n#Simp 51 TTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCA 100
Y_13142410_13 103 CTCCAATCAATTCCATTCCATCCCATTCCATTCCACTCCATTCCACTCCA 152
i v v i i i
(TTCCA)n#Simp 101 TTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCA 150
Y_13142410_13 153 CTCCACTCCATTCAATTCCATTTCATTCCATTCCACTACATTCCATTCCA 202
i i v i i v
(TTCCA)n#Simp 151 TTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCA 200
Y_13142410_13 203 TT 204
(TTCCA)n#Simp 201 TT 202
Matrix = Unknown
Transitions / transversions = 1.21 (17/14)
Gap_init rate = 0.00 (0 / 201), avg. gap size = 0.0 (0 / 0)
+ 55 4.9 0.0 0.0 Y_13142410_13142991_INS 281 343 (239) + (CCATT)n Simple_repeat 1 63 (0) 980
ANNOTATION EVIDENCE:
55 4.94 0.00 0.00 Y_13142410_13142991_INS 281 343 239 + (CCATT)n Simple_repeat 1 63 0
55 4.94 0.00 0.00 Y_13142410_13142991_INS 281 343 (239) (CCATT)n#Simple_repeat 1 63 (0) c_b3s251i8
Y_13142410_13 281 CCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATGCCATG 330
v v
(CCATT)n#Simp 1 CCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATT 50
Y_13142410_13 331 CCATGCCATTCCA 343
v
(CCATT)n#Simp 51 CCATTCCATTCCA 63
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 139 27.6 1.0 4.2 Y_13142410_13142991_INS 465 580 (2) + (TTCCA)n Simple_repeat 4 120 (0) 981
ANNOTATION EVIDENCE:
139 27.57 0.97 4.20 Y_13142410_13142991_INS 465 580 2 + (TTCCA)n Simple_repeat 384 500 0
139 27.57 0.97 4.20 Y_13142410_13142991_INS 465 580 (2) (TTCCA)n#Simple_repeat 384 500 (0) m_b3s252i7
Y_13142410_13 465 ACATTTCATTTCA--CCAATCCATTTCATTCCACTCCACTCAATTCCACT 512
- i i -- v i i i v i
(TTCCA)n#Simp 384 -CATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATT 432
Y_13142410_13 513 CCACTCCAGTCAATTCCATCCCATTTCATTCCACTCCATTCCACTCCACT 562
i v v i i i i i
(TTCCA)n#Simp 433 CCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCCATT 482
Y_13142410_13 563 TCACTGCACTCCACTCCA 580
i i v i i
(TTCCA)n#Simp 483 CCATTCCATTCCATTCCA 500
Matrix = Unknown
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 1.50 (3 / 2)
+ 34 18.3 1.3 1.3 Y_13143257_13143333_INS 1 77 (0) + (ACTCC)n Simple_repeat 1 77 (0) 982
ANNOTATION EVIDENCE:
34 18.29 1.30 1.30 Y_13143257_13143333_INS 1 77 0 + (ACTCC)n Simple_repeat 1 77 0
34 18.29 1.30 1.30 Y_13143257_13143333_INS 1 77 (0) (ACTCC)n#Simple_repeat 1 77 (0) m_b3s252i5
Y_13143257_13 1 ACTCCACTCCACT-CAATCCAATTATATTCCACTCCATTCCACTCCACTT 49
- v - i vi i i i
(ACTCC)n#Simp 1 ACTCCACTCCACTCCACTCC-ACTCCACTCCACTCCACTCCACTCCACTC 49
Y_13143257_13 50 CTCTGCACTCCACTCCATTTCATTCCAC 77
v v i i i
(ACTCC)n#Simp 50 CACTCCACTCCACTCCACTCCACTCCAC 77
Matrix = Unknown
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2)
+ 55 0.0 0.0 0.0 Y_13704122_13704172_INS 1 50 (1) + (TGGAA)n Simple_repeat 1 50 (0) 983
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 Y_13704122_13704172_INS 1 50 1 + (TGGAA)n Simple_repeat 1 50 0
55 0.00 0.00 0.00 Y_13704122_13704172_INS 1 50 (1) (TGGAA)n#Simple_repeat 1 50 (0) c_b3s251i7
Y_13704122_13 1 TGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAA 50
(TGGAA)n#Simp 1 TGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAA 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 2451 2.8 0.0 2.5 Y_14028527_14028855_INS 13 329 (0) C AluY SINE/Alu (0) 311 2 984
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 Y_14028527_14028855_INS 13 41 288 + (T)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 Y_14028527_14028855_INS 13 41 (288) (T)n#Simple_repeat 1 29 (0) c_b3s251i6
Y_14028527_14 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41
(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)
2451 2.81 0.00 2.46 Y_14028527_14028855_INS 42 329 0 C AluY SINE/Alu 2 282 29
2451 2.81 0.00 2.46 Y_14028527_14028855_INS 42 329 (0) C AluY#SINE/Alu (29) 282 2 c_b3s352i27
Y_14028527_14 42 GAGACGGAGTCTCGCTCTGTCGCCCAGGTCGGACTGCGGACTGCAGTGGC 91
----- -- v
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGG-----CTG--GAGTGCAGTGGC 240
Y_14028527_14 92 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCC 141
i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
Y_14028527_14 142 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 191
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
Y_14028527_14 192 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 241
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
Y_14028527_14 242 GGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAA 291
i i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
Y_14028527_14 292 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 329
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.89
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 58 1.5 0.0 0.0 Y_15309739_15309805_INS 2 67 (0) + (A)n Simple_repeat 1 66 (0) 985
ANNOTATION EVIDENCE:
58 1.53 0.00 0.00 Y_15309739_15309805_INS 2 67 0 + (A)n Simple_repeat 1 66 0
58 1.53 0.00 0.00 Y_15309739_15309805_INS 2 67 (0) (A)n#Simple_repeat 1 66 (0) m_b3s252i4
Y_15309739_15 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA 51
v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
Y_15309739_15 52 AAAAAAAAAAAAAAAA 67
(A)n#Simple_r 51 AAAAAAAAAAAAAAAA 66
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 48 1.9 0.0 0.0 Y_16860749_16860804_INS 2 56 (0) + (A)n Simple_repeat 1 55 (0) 986
ANNOTATION EVIDENCE:
48 1.85 0.00 0.00 Y_16860749_16860804_INS 2 56 0 + (A)n Simple_repeat 1 55 0
48 1.85 0.00 0.00 Y_16860749_16860804_INS 2 56 (0) (A)n#Simple_repeat 1 55 (0) m_b3s252i3
Y_16860749_16 2 AAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA 51
i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
Y_16860749_16 52 AAAAA 56
(A)n#Simple_r 51 AAAAA 55
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 69 4.1 0.0 0.0 Y_17319889_17319967_INS 1 75 (4) + (AAGA)n Simple_repeat 1 75 (0) 987
ANNOTATION EVIDENCE:
69 4.13 0.00 0.00 Y_17319889_17319967_INS 1 75 4 + (AAGA)n Simple_repeat 1 75 0
69 4.13 0.00 0.00 Y_17319889_17319967_INS 1 75 (4) (AAGA)n#Simple_repeat 1 75 (0) c_b3s251i5
Y_17319889_17 1 AAGAAAGAAAGAAAGAAAGATAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
v
(AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50
Y_17319889_17 51 GAAAGGGAGAAAGAAAGAAAGAAAG 75
ii
(AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGAAAG 75
Matrix = Unknown
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 2575 1.8 0.0 0.0 Y_17959570_17959912_INS 13 343 (0) C AluY SINE/Alu (0) 311 1 988
ANNOTATION EVIDENCE:
56 0.00 0.00 0.00 Y_17959570_17959912_INS 13 62 281 + (T)n Simple_repeat 1 50 0
56 0.00 0.00 0.00 Y_17959570_17959912_INS 13 62 (281) (T)n#Simple_repeat 1 50 (0) c_b3s251i4
Y_17959570_17 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 62
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
2575 1.78 0.00 0.00 Y_17959570_17959912_INS 63 343 0 C AluY SINE/Alu 1 281 30
2575 1.78 0.00 0.00 Y_17959570_17959912_INS 63 343 (0) C AluY#SINE/Alu (30) 281 1 c_b3s352i28
Y_17959570_17 63 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCT 112
v
C AluY#SINE/Alu 281 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCT 232
Y_17959570_17 113 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 162
C AluY#SINE/Alu 231 CGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCA 182
Y_17959570_17 163 GCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAAT 212
i i
C AluY#SINE/Alu 181 GCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAAT 132
Y_17959570_17 213 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGT 262
v i
C AluY#SINE/Alu 131 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGT 82
Y_17959570_17 263 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 312
C AluY#SINE/Alu 81 CTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTG 32
Y_17959570_17 313 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 343
C AluY#SINE/Alu 31 GGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.47
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.0 (0 / 0)
+ 43 20.5 0.0 0.0 Y_18050048_18050166_INS 2 119 (0) + (AT)n Simple_repeat 1 118 (0) 989
ANNOTATION EVIDENCE:
43 0.00 0.00 0.00 Y_18050048_18050166_INS 2 38 81 + (AT)n Simple_repeat 1 37 0
43 0.00 0.00 0.00 Y_18050048_18050166_INS 2 38 (81) (AT)n#Simple_repeat 1 37 (0) c_b3s251i3
Y_18050048_18 2 ATATATATATATATATATATATATATATATATATATA 38
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
29 30.76 0.00 0.00 Y_18050048_18050166_INS 46 119 0 + (AT)n Simple_repeat 1 74 0
29 30.76 0.00 0.00 Y_18050048_18050166_INS 46 119 (0) (AT)n#Simple_repeat 1 74 (0) m_b3s252i2
Y_18050048_18 46 ATACATATATGTATATGTGTGTGTATATATATATATACACACACATATAC 95
i i i i i i i i i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
Y_18050048_18 96 ATATATGTATGTGTGTGTGTATAT 119
i i i i i i
(AT)n#Simple_ 51 ATATATATATATATATATATATAT 74
Matrix = Unknown
Transitions / transversions = 1.00 (17/0)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 35 0.0 0.0 0.0 Y_18872264_18872314_INS 1 33 (18) + (TTCT)n Simple_repeat 1 33 (0) 990
ANNOTATION EVIDENCE:
35 0.00 0.00 0.00 Y_18872264_18872314_INS 1 33 18 + (TTCT)n Simple_repeat 1 33 0
35 0.00 0.00 0.00 Y_18872264_18872314_INS 1 33 (18) (TTCT)n#Simple_repeat 1 33 (0) c_b3s251i2
Y_18872264_18 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 33
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 33
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 2443 3.5 0.0 2.5 Y_21611992_21612316_INS 10 325 (0) C AluY SINE/Alu (0) 311 2 991
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 Y_21611992_21612316_INS 10 37 288 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 Y_21611992_21612316_INS 10 37 (288) (T)n#Simple_repeat 1 28 (0) c_b3s251i1
Y_21611992_21 10 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 37
(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)
2443 3.50 0.00 2.45 Y_21611992_21612316_INS 38 325 0 C AluY SINE/Alu 2 282 29
2443 3.50 0.00 2.45 Y_21611992_21612316_INS 38 325 (0) C AluY#SINE/Alu (29) 282 2 c_b3s352i29
Y_21611992_21 38 GAGACGGAGTCTCGCTCTGTTGCCCAGGCCGGACTGCGGACTGCAATGGC 87
i i ----- -- i
C AluY#SINE/Alu 282 GAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA-----G--TGCAGTGGC 240
Y_21611992_21 88 GCAATCTCGGCTCACTGCAAGCTCCGCTTCCTGGGTTCACGCCATTCTCC 137
i i i
C AluY#SINE/Alu 239 GCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCC 190
Y_21611992_21 138 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCC 187
i
C AluY#SINE/Alu 189 TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCC 140
Y_21611992_21 188 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCA 237
v
C AluY#SINE/Alu 139 GGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCA 90
Y_21611992_21 238 GGATGGTCTCGATCTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAA 287
i
C AluY#SINE/Alu 89 GGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAA 40
Y_21611992_21 288 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 325
C AluY#SINE/Alu 39 AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 2
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 2.29
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.02 (7 / 287), avg. gap size = 1.00 (7 / 7)
+ 363 9.1 0.0 1.8 Y_23786195_23786306_INS 1 56 (56) C MER9a1 LTR/ERVK (214) 299 245 992 *
ANNOTATION EVIDENCE:
363 9.10 0.00 1.82 Y_23786195_23786306_INS 1 56 56 C MER9a1 LTR/ERVK 245 299 214
363 9.10 0.00 1.82 Y_23786195_23786306_INS 1 56 (56) C MER9a1#LTR/ERVK (214) 299 245 m_b3s502i6
Y_23786195_23 1 CTTATAGGAAATGAAGGGATGGGCTGAATTAAAGGAATAGGATGGGCTGA 50
i i i v -
C MER9a1#LTR/ER 299 CTTATGGGAAACGAAGGGATGGGCCGAATTAAAGGAATAGGTTGGGCT-A 251
Y_23786195_23 51 ATTAAC 56
i
C MER9a1#LTR/ER 250 GTTAAC 245
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 6.09
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1)
+ 485 6.6 0.0 0.0 Y_23786195_23786306_INS 51 111 (1) C MER9a2 LTR/ERVK (153) 360 300 993
ANNOTATION EVIDENCE:
485 6.56 0.00 0.00 Y_23786195_23786306_INS 51 111 1 C MER9a2 LTR/ERVK 300 360 153
485 6.56 0.00 0.00 Y_23786195_23786306_INS 51 111 (1) C MER9a2#LTR/ERVK (153) 360 300 m_b3s502i7
Y_23786195_23 51 ATTAACAGTAAGCCAGTCATTGGCATTGTTTCTATAGATATCAAATTAAC 100
i i i i
C MER9a2#LTR/ER 360 ATTAACAGCAAGCCAGTCATTAGCATTGTTTCTATAGATATTAGATTAAC 311
Y_23786195_23 101 TAAAAGTATCC 111
C MER9a2#LTR/ER 310 TAAAAGTATCC 300
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.03
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 434 5.5 0.0 0.0 Y_2759969_2760323_INS 1 55 (300) + AluSx SINE/Alu 241 295 (17) 994
ANNOTATION EVIDENCE:
434 5.45 0.00 0.00 Y_2759969_2760323_INS 1 55 300 + AluSx SINE/Alu 241 295 17
434 5.45 0.00 0.00 Y_2759969_2760323_INS 1 55 (300) AluSx#SINE/Alu 241 295 (17) m_b3s357i1
Y_2759969_276 1 CCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCCATTTCAAAAAAAA 50
i i i
AluSx#SINE/Al 241 CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAA 290
Y_2759969_276 51 AAAAA 55
AluSx#SINE/Al 291 AAAAA 295
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.23
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 601 9.9 1.1 0.0 Y_2759969_2760323_INS 67 157 (198) C AluSx SINE/Alu (10) 302 211 995
ANNOTATION EVIDENCE:
601 9.89 1.10 0.00 Y_2759969_2760323_INS 67 157 198 C AluSx SINE/Alu 211 302 10
601 9.89 1.10 0.00 Y_2759969_2760323_INS 67 157 (198) C AluSx#SINE/Alu (10) 302 211 m_b3s357i2
Y_2759969_276 67 TTCTCTTTTTTTTTTTTTTGGAGACAGAGTCTGGCTCTGTCGCCCAGGCT 116
i i v i v
C AluSx#SINE/Al 302 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT 253
Y_2759969_276 117 GGAGTGCAGTGGTGCGATCTGGGCTCACTGC-ACTTCCGTCT 157
i v - i i
C AluSx#SINE/Al 252 GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCT 211
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.40
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1)
+ 582 19.1 6.1 0.0 Y_2759969_2760323_INS 158 288 (67) C L1MB2 LINE/L1 (219) 5952 5814 996
ANNOTATION EVIDENCE:
582 19.08 6.11 0.00 Y_2759969_2760323_INS 158 288 67 C L1MB2_3end LINE/L1 561 699 219
582 19.08 6.11 0.00 Y_2759969_2760323_INS 158 288 (67) C L1MB2_3end#LINE/L1 (219) 699 561 m_b3s551i10
Y_2759969_276 158 ATGAATTTTACTACATTCAGTACCTCTTATAAGTAGAGTTATACA---TT 204
v vi vii v i i i ---
C L1MB2_3end#LI 699 ATGAATTTGACTACTCTAGATACCTCATATAAGTGGAATCATACAGTATT 650
Y_2759969_276 205 TGTCTTTTTGTTACTGGATTGTCACACTTAGCACAATATGCTCAAGGTT- 253
v v i iv i i v -
C L1MB2_3end#LI 649 TGTCTTTTTGTGACTGGCTTATTTCACTTAGCATAATGTCCTCAAGGTTC 600
Y_2759969_276 254 ---CATGTTGCAACATATAA-AAAATTCCCTTCCTTTCT 288
--- i i i i?- i i i
C L1MB2_3end#LI 599 ATCCATGTTGTAGCATGTGNCAGAATTTCCTTCCTTTTT 561
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.79
Transitions / transversions = 2.12 (17/8)
Gap_init rate = 0.03 (4 / 130), avg. gap size = 2.00 (8 / 4)
+ 450 9.5 0.0 0.0 Y_2759969_2760323_INS 291 353 (2) + AluSx SINE/Alu 177 239 (73) 997
ANNOTATION EVIDENCE:
450 9.52 0.00 0.00 Y_2759969_2760323_INS 291 353 2 + AluSx SINE/Alu 177 239 73
450 9.52 0.00 0.00 Y_2759969_2760323_INS 291 353 (2) AluSx#SINE/Alu 177 239 (73) m_b3s357i3
Y_2759969_276 291 GGAGGGTGAGGCAGGAGAATTGCTTGAACCCAGGAGGCAGAGGTTGCAGT 340
v i i i
AluSx#SINE/Al 177 GGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGT 226
Y_2759969_276 341 GAGCTGAGATCAC 353
i i
AluSx#SINE/Al 227 GAGCCGAGATCGC 239
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.42
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 23 21.4 0.0 0.0 Y_28798952_28799007_INS 2 55 (1) + (TGGAA)n Simple_repeat 1 54 (0) 998
ANNOTATION EVIDENCE:
23 21.39 0.00 0.00 Y_28798952_28799007_INS 2 55 1 + (TGGAA)n Simple_repeat 1 54 0
23 21.39 0.00 0.00 Y_28798952_28799007_INS 2 55 (1) (TGGAA)n#Simple_repeat 1 54 (0) m_b3s252i1
Y_28798952_28 2 TGGAGTTGAATGGAATGGAATGGGAAGGAATGGAATTGAACGAAGTTGCA 51
i v i v v i i i v v
(TGGAA)n#Simp 1 TGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAA 50
Y_28798952_28 52 TGGA 55
(TGGAA)n#Simp 51 TGGA 54
Matrix = Unknown
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 368 15.7 10.0 1.7 Y_28802738_28802853_INS 2 111 (5) C HSATII Satellite (7) 163 45 999
ANNOTATION EVIDENCE:
368 15.71 10.00 1.68 Y_28802738_28802853_INS 2 111 5 C HSATII Satellite 45 163 7
368 15.71 10.00 1.68 Y_28802738_28802853_INS 2 111 (5) C HSATII#Satellite (7) 163 45 m_b3s502i8
Y_28802738_28 2 GACTGGAATGGAATGGAA--A----GGAATGGAATCAAATCGAATTTAAT 45
v v -- ----v i v i--
C HSATII#Satell 163 GAATGGAATCGAATGGAATCATCATCGAATGGAATCGAATGGAATC--AT 116
Y_28802738_28 46 TGAATCAAATCAAATTGAATGA--AAAAAATAGAATTGAATGGAATCA-- 91
i vi i v v -- vvi i i --
C HSATII#Satell 115 CGAATGGAATCGAATGGAATCATCATCGAATGGAATCGAATGGAATCATC 66
Y_28802738_28 92 -AATGGAATCGAATGGAATCA 111
-
C HSATII#Satell 65 GAATGGAATCGAATGGAATCA 45
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.58
Transitions / transversions = 0.89 (8/9)
Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.86 (13 / 7)
+ 389 17.5 6.3 5.7 Y_58975548_58975780_INS 9 228 (5) + HSATII Satellite 1 221 (30) 1000
ANNOTATION EVIDENCE:
389 18.93 5.97 1.43 Y_58975548_58975780_INS 9 142 91 + HSATII Satellite 1 140 30
389 18.93 5.97 1.43 Y_58975548_58975780_INS 9 142 (91) HSATII#Satellite 1 140 (30) m_b3s502i9
Y_58975548_58 9 CCATTCCGATCCATTCAAT---TCTAGTCCATTCCATTCGATTACT-TTT 54
viv i --- i v v v iv- i
HSATII#Satell 1 CCATTCGATTCCATTCGATGATTCCATTCGATTCCATTCGATGATGATTC 50
Y_58975548_58 55 CAATAGATTCCATT---TCATTTGATTCCATTCCATTCGA-GTCCATTCC 100
v v --- v iv v - viv
HSATII#Satell 51 CATTCGATTCCATTCGATGATTCCATTCGATTCCATTCGATGATGATTCC 100
Y_58975548_58 101 ATTCCATTCCATTCGATTCCATTCCATTCGATTGCCTTCCAT 142
v --v v v v
HSATII#Satell 101 ATTCGATTCCATTCGAT--GATTCCATTCGATTCCATTCGAT 140
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.95
Transitions / transversions = 0.39 (7/18)
Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.67 (10 / 6)
372 16.38 6.55 9.15 Y_58975548_58975780_INS 61 228 5 + HSATII Satellite 3 166 4
372 16.38 6.55 9.15 Y_58975548_58975780_INS 61 228 (5) HSATII#Satellite 3 166 (4) m_b3s502i10
Y_58975548_58 61 ATTCCATTTCATTTGATTCCATTCCATTCGAGTCCATTCCATTCC-ATTC 109
v i i v-- v v vvi-
HSATII#Satell 3 ATTCGATTCCATTCGATG--ATTCCATTCGATTCCATTCGATGATGATTC 50
Y_58975548_58 110 CATTCGATTCCATTCCATTCGATTGCCTTCCATTCCAGCCCTTTTCACT- 158
v -- v v v ------ iv -
HSATII#Satell 51 CATTCGATTCCATTCGAT--GATTCCATTCGATTCCA------TTCGATG 92
Y_58975548_58 159 -TGAGCCCCTTCCATCCCCTTTCCTTT--TGATTCCATTCCATTCCATTC 205
- ----- i vv i v i-- v
HSATII#Satell 93 ATGA-----TTCCATTCGATTCCATTCGATGATTCCATTCGATTCCATTC 137
Y_58975548_58 206 GA-G-----TCCAGTCCATTCCACTCGAT 228
- ----- v v i
HSATII#Satell 138 GATGATGATTCCATTCGATTCCATTCGAT 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.23
Transitions / transversions = 0.47 (8/17)
Gap_init rate = 0.13 (21 / 167), avg. gap size = 1.24 (26 / 21)
+ 989 10.4 0.8 0.0 Y_59013741_59013874_INS 1 134 (0) C AluY SINE/Alu (120) 191 57 1001
ANNOTATION EVIDENCE:
989 10.45 0.75 0.00 Y_59013741_59013874_INS 1 134 0 C AluY SINE/Alu 57 191 120
989 10.45 0.75 0.00 Y_59013741_59013874_INS 1 134 (0) C AluY#SINE/Alu (120) 191 57 m_b3s357i4
Y_59013741_59 1 TCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCACCTGCCGCCACA 50
i i i i i i
C AluY#SINE/Alu 191 TCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACG 142
Y_59013741_59 51 CCTAGCGAATTTTT-GTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG 99
ii v - i i
C AluY#SINE/Alu 141 CCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAG 92
Y_59013741_59 100 CCAGGATGGTCTCTATCTCTTGACCTCGTGATCTG 134
v i i
C AluY#SINE/Alu 91 CCAGGATGGTCTCGATCTCCTGACCTCGTGATCCG 57
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.94
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1)
+ 56 0.0 0.0 0.0 Y_59030578_59030630_INS 1 48 (5) + (AT)n Simple_repeat 1 48 (0) 1002
ANNOTATION EVIDENCE:
56 0.00 0.00 0.00 Y_59030578_59030630_INS 1 48 5 + (AT)n Simple_repeat 1 48 0
56 0.00 0.00 0.00 Y_59030578_59030630_INS 1 48 (5) (AT)n#Simple_repeat 1 48 (0) c_b3s251i0
Y_59030578_59 1 ATATATATATATATATATATATATATATATATATATATATATATATAT 48
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATAT 48
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 2891 1.3 0.0 0.0 Y_6697544_6697870_INS 17 327 (0) + AluY SINE/Alu 1 311 (0) 1003
ANNOTATION EVIDENCE:
2891 1.29 0.00 0.00 Y_6697544_6697870_INS 17 327 0 + AluY SINE/Alu 1 311 0
2891 1.29 0.00 0.00 Y_6697544_6697870_INS 17 327 (0) AluY#SINE/Alu 1 311 (0) c_b3s352i30
Y_6697544_669 17 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 66
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
Y_6697544_669 67 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGG 116
v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
Y_6697544_669 117 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 166
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
Y_6697544_669 167 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 216
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
Y_6697544_669 217 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 266
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
Y_6697544_669 267 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 316
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
Y_6697544_669 317 AAAAAAAAAAA 327
AluY#SINE/Alu 301 AAAAAAAAAAA 311
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 1.00
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 310), avg. gap size = 0.0 (0 / 0)
+ 664 21.6 0.0 0.0 Y_7034305_7034429_INS 15 125 (0) + AluSx SINE/Alu 3 113 (199) 1004
ANNOTATION EVIDENCE:
664 21.62 0.00 0.00 Y_7034305_7034429_INS 15 125 0 + AluSx SINE/Alu 3 113 199
664 21.62 0.00 0.00 Y_7034305_7034429_INS 15 125 (0) AluSx#SINE/Alu 3 113 (199) m_b3s357i5
Y_7034305_703 15 CTGGGTGCAGTGGCTCACACCTTTGATGTCAACACTTTGGGAGGCTGAGA 64
i i i i v i vi i i i
AluSx#SINE/Al 3 CCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG 52
Y_7034305_703 65 TGGGCAGATCACTTGAGACCAGGAGTTCAAGACAAGCCTGGTTAACATGA 114
i i i ii i v ii i
AluSx#SINE/Al 53 CGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGG 102
Y_7034305_703 115 TAAAACCTTGT 125
i ii
AluSx#SINE/Al 103 TGAAACCCCGT 113
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 16.41
Transitions / transversions = 7.00 (21/3)
Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.0 (0 / 0)
+ 44 12.1 0.0 2.6 Y_8218026_8218104_INS 1 78 (1) + (TTTC)n Simple_repeat 1 76 (0) 1005
ANNOTATION EVIDENCE:
44 12.14 0.00 2.63 Y_8218026_8218104_INS 1 78 1 + (TTTC)n Simple_repeat 1 76 0
44 12.14 0.00 2.63 Y_8218026_8218104_INS 1 78 (1) (TTTC)n#Simple_repeat 1 76 (0) m_b3s252i0
Y_8218026_821 1 TTTCTTTCTTTCTTTCTTTCTTCCTTTCTTTCTCTCTCTCCTCCTCTTTC 50
i i - i -i
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCT-TTCTTTC 48
Y_8218026_821 51 TTTCCTTCTTTCTTTCTTTTCCTCTTTC 78
i iii
(TTTC)n#Simpl 49 TTTCTTTCTTTCTTTCTTTCTTTCTTTC 76
Matrix = Unknown
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2)