Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 275 of 279
Found at i:89827950 original size:36 final size:37
Alignment explanation
Indices: 89827898--89827978 Score: 123
Period size: 36 Copynumber: 2.2 Consensus size: 37
89827888 GATTACAAAA
89827898 TCATATC-T-TCTAAGATTGCATATCATATCTAAGAT
1 TCATATCATATCTAAGATTGCATATCATATCTAAGAT
*
89827933 T-ATATCATATCTAAGATTGCATATCATATCTCAGAT
1 TCATATCATATCTAAGATTGCATATCATATCTAAGAT
89827969 TGCATATCAT
1 T-CATATCAT
89827979 TGAAGATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
34 5 0.12
35 2 0.05
36 27 0.66
38 7 0.17
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (37 bp):
TCATATCATATCTAAGATTGCATATCATATCTAAGAT
Found at i:89827985 original size:36 final size:36
Alignment explanation
Indices: 89827909--89827986 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
89827899 CATATCTTCT
*
89827909 AAGATTGCATATCATATCTAAGATTATATCATATCT
1 AAGATTGCATATCATATCTAAGATTATATCATATCG
*
89827945 AAGATTGCATATCATATCTCAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCTAAGATT--ATATCATATCG
89827981 AAGATT
1 AAGATT
89827987 ATATTTCCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 30 0.79
37 1 0.03
38 7 0.18
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (36 bp):
AAGATTGCATATCATATCTAAGATTATATCATATCG
Found at i:89828135 original size:21 final size:20
Alignment explanation
Indices: 89828097--89828136 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89828087 TTGGACTTCG
**
89828097 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
89828117 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
89828137 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:89837514 original size:5 final size:5
Alignment explanation
Indices: 89837500--89837541 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
89837490 CCAATTTGTG
*
89837500 AAAA- AAAAT AAAAT AAAAT AAAAT AAAGAA AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AA
89837542 CACACAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 4 0.12
5 26 0.76
6 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:89838445 original size:26 final size:26
Alignment explanation
Indices: 89838416--89838523 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
89838406 TGGTACAAAT
*
89838416 TGATAATGGGTTAGGTAAATGTTCAA
1 TGATAATGGGTTAGGTAAATGTTCCA
** *
89838442 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89838468 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89838494 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
89838520 TGAT
1 TGAT
89838524 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89851415 original size:30 final size:30
Alignment explanation
Indices: 89851379--89851461 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
89851369 ACGGACTCGG
*
89851379 ATACCAAGTTACTCGTCTGAGCTAGAAATT
1 ATACCAAGTTACTCGTCCGAGCTAGAAATT
* * * *
89851409 ATACCAAGCTGCTCGTCCAAG-TTGAAATT
1 ATACCAAGTTACTCGTCCGAGCTAGAAATT
*
89851438 ATACC-AGATTACTTGTCCGAGCTA
1 ATACCAAG-TTACTCGTCCGAGCTA
89851462 AACCTATATC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 2 0.05
29 21 0.51
30 18 0.44
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (30 bp):
ATACCAAGTTACTCGTCCGAGCTAGAAATT
Found at i:89853091 original size:36 final size:36
Alignment explanation
Indices: 89853044--89853116 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
89853034 TAATTGACTT
*
89853044 GGTCCAAATTTTCTGTACCTAAAGCCAACCAAACTC
1 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
89853080 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
1 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
89853116 G
1 G
89853117 CCCTATCTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (36 bp):
GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
Found at i:89855413 original size:26 final size:26
Alignment explanation
Indices: 89855384--89855491 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
89855374 TGGTACAAAT
89855384 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89855410 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89855436 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89855462 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89855488 TGAT
1 TGAT
89855492 GGGCATTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89860816 original size:20 final size:20
Alignment explanation
Indices: 89860791--89860832 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
89860781 GCAAACTACT
89860791 AACATTCCTGAGTTCCTTCC
1 AACATTCCTGAGTTCCTTCC
89860811 AACATTCCTGAGTTCCTTCC
1 AACATTCCTGAGTTCCTTCC
89860831 AA
1 AA
89860833 AAGACCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (20 bp):
AACATTCCTGAGTTCCTTCC
Found at i:89866640 original size:28 final size:28
Alignment explanation
Indices: 89866608--89866667 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
89866598 TAACCTACAT
*
89866608 CTCTCATTGGTGGTAGCTCTACTGATGA
1 CTCTCATTGGCGGTAGCTCTACTGATGA
89866636 CTCTCATTGGCGGTAGCTCTACTGATGA
1 CTCTCATTGGCGGTAGCTCTACTGATGA
89866664 CTCT
1 CTCT
89866668 ACAAGCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (28 bp):
CTCTCATTGGCGGTAGCTCTACTGATGA
Found at i:89877836 original size:17 final size:17
Alignment explanation
Indices: 89877814--89877848 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
89877804 TGCAATTATT
89877814 TTTAT-AATTTATTATAA
1 TTTATAAATTTATT-TAA
89877831 TTTATAAATTTATTTAA
1 TTTATAAATTTATTTAA
89877848 T
1 T
89877849 AAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATAAATTTATTTAA
Found at i:89906942 original size:30 final size:32
Alignment explanation
Indices: 89906908--89906972 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
89906898 AATATTTATA
* *
89906908 TTTTATAATTTTT-AAATAATTAAATTA-AAT
1 TTTTATAATTTTTAAAACAATTAAAATATAAT
*
89906938 TTTTATTATTTTTAAAACAATTAAAATATAAT
1 TTTTATAATTTTTAAAACAATTAAAATATAAT
89906970 TTT
1 TTT
89906973 ATATTTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 12 0.40
31 12 0.40
32 6 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTTATAATTTTTAAAACAATTAAAATATAAT
Found at i:89906978 original size:30 final size:28
Alignment explanation
Indices: 89906907--89906978 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 28
89906897 TAATATTTAT
* *
89906907 ATTTTATAATTTTTAAATAATTAAATTAA
1 ATTTTAT-ATTTTTAAACAATTAAAATAA
89906936 ATTTTTATTATTTTTAAAACAATTAAAATATA
1 A-TTTTA-TATTTTT-AAACAATTAAAATA-A
89906968 ATTTTATATTT
1 ATTTTATATTT
89906979 ACAAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 1 0.03
30 16 0.43
31 18 0.49
32 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTTATATTTTTAAACAATTAAAATAA
Found at i:89907000 original size:16 final size:18
Alignment explanation
Indices: 89906976--89907012 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
89906966 TAATTTTATA
89906976 TTTACAAA-TTT-AAATT
1 TTTACAAATTTTAAAATT
*
89906992 TTTATAAATTTTAAAATT
1 TTTACAAATTTTAAAATT
89907010 TTT
1 TTT
89907013 GAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTACAAATTTTAAAATT
Found at i:89907549 original size:17 final size:17
Alignment explanation
Indices: 89907502--89907549 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
89907492 GTATTTTCAA
*
89907502 TAAAAATATAAAAAATTT
1 TAAAAAT-TAAAAAATCT
89907520 TGAAAAA-TAAAAAATCT
1 T-AAAAATTAAAAAATCT
89907537 TAAAAATTTAAAA
1 TAAAAA-TTAAAA
89907550 TAAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 10 0.38
18 6 0.23
19 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAAAATTAAAAAATCT
Found at i:89918212 original size:15 final size:15
Alignment explanation
Indices: 89918192--89918222 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
89918182 AAGCTATTCA
89918192 AGCAAGTAATTGTCG
1 AGCAAGTAATTGTCG
89918207 AGCAAGTAATTGTCG
1 AGCAAGTAATTGTCG
89918222 A
1 A
89918223 ACCAAGCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
AGCAAGTAATTGTCG
Found at i:89930854 original size:21 final size:23
Alignment explanation
Indices: 89930819--89930861 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
89930809 GGGAAGGTGA
89930819 ATAAAGAATTTTGGG-TTTTTCC
1 ATAAAGAATTTTGGGCTTTTTCC
*
89930841 ATAAAGGA-TTTGGGCTTTTTC
1 ATAAAGAATTTTGGGCTTTTTC
89930862 AGGAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (23 bp):
ATAAAGAATTTTGGGCTTTTTCC
Found at i:89931691 original size:16 final size:18
Alignment explanation
Indices: 89931656--89931689 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89931646 TTCTCCATCT
*
89931656 TGAAGTATTTTTTGAAAA
1 TGAAGTATTTTCTGAAAA
89931674 TGAA-TATTTTCTGAAA
1 TGAAGTATTTTCTGAAA
89931690 TGTTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (18 bp):
TGAAGTATTTTCTGAAAA
Found at i:89939065 original size:90 final size:88
Alignment explanation
Indices: 89938879--89939088 Score: 264
Period size: 90 Copynumber: 2.3 Consensus size: 88
89938869 TAAATCTTTA
* * * *
89938879 TTTTTTTGCACTCAATCGGGTACTTGAATTTTCAAAATGCATAAAAAAGACTCTCAAACTTTTTC
1 TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAACTTTTTC
* *
89938944 AAAAAAAGCAATTAAGCCCCTACT
66 AAAAAAAACAATGAAGCCCCTA-T
*
89938968 TTGTTTTTGCACTCAATTGGGTACTT-AACTTTCAAAATGCATAAAAAAAACCCTTAAACTTTTT
1 TT-TTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAACTTTTT
89939032 CAAAAAAAAAAAAACAATGAAG-CCCT-T
65 C-----AAAAAAAACAATGAAGCCCCTAT
*
89939059 TTTTTTTGCACTCAATTGGGTATTTGAACT
1 TTTTTTTGCACTCAATTGGGTACTTGAACT
89939089 GTGAAATACA
Statistics
Matches: 106, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
89 37 0.35
90 44 0.42
91 7 0.07
93 4 0.04
94 14 0.13
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (88 bp):
TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAACTTTTTC
AAAAAAAACAATGAAGCCCCTAT
Found at i:89939286 original size:19 final size:19
Alignment explanation
Indices: 89939233--89939305 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 19
89939223 ATAAATATCA
89939233 ATAAAAT-TTATAAAAAAAAT
1 ATAAAATATTAT--AAAAAAT
* * *
89939253 ATTAACTTTTAATAAAAAAT
1 ATAAAATATT-ATAAAAAAT
*
89939273 ATAAAATATTAT-AAAATT
1 ATAAAATATTATAAAAAAT
89939291 AT-AAA-ATTATAAAAA
1 ATAAAATATTATAAAAA
89939306 TCATAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 5 0.11
17 7 0.16
18 7 0.16
19 2 0.05
20 19 0.43
21 2 0.05
22 2 0.05
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAATATTATAAAAAAT
Found at i:89939305 original size:17 final size:16
Alignment explanation
Indices: 89939264--89939313 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
89939254 TTAACTTTTA
*
89939264 ATAAAAAATATAAAAT
1 ATAAAAATTATAAAAT
89939280 ATTATAAAATTATAAAATT
1 A-TA-AAAATTATAAAA-T
*
89939299 ATAAAAATCATAAAA
1 ATAAAAATTATAAAA
89939314 AATTGTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 13 0.45
18 13 0.45
19 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATTATAAAAT
Found at i:89939313 original size:8 final size:8
Alignment explanation
Indices: 89939280--89939304 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
89939270 AATATAAAAT
89939280 ATTATAAA
1 ATTATAAA
89939288 ATTATAAA
1 ATTATAAA
89939296 ATTATAAA
1 ATTATAAA
89939304 A
1 A
89939305 ATCATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTATAAA
Found at i:89939343 original size:9 final size:9
Alignment explanation
Indices: 89939264--89939343 Score: 65
Period size: 9 Copynumber: 8.8 Consensus size: 9
89939254 TTAACTTTTA
*
89939264 ATAAAAAAT
1 ATAAAAATT
89939273 ATAAAATATT
1 ATAAAA-ATT
89939283 AT-AAAATT
1 ATAAAAATT
89939291 AT-AAAATT
1 ATAAAAATT
*
89939299 ATAAAAATC
1 ATAAAAATT
89939308 ATAAAAAATT
1 AT-AAAAATT
* **
89939318 GTAAACTTTT
1 ATAAA-AATT
*
89939328 GTAAAAATT
1 ATAAAAATT
89939337 ATAAAAA
1 ATAAAAA
89939344 AAATTTATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
8 13 0.22
9 27 0.47
10 18 0.31
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:89939344 original size:10 final size:10
Alignment explanation
Indices: 89939264--89939344 Score: 50
Period size: 10 Copynumber: 8.8 Consensus size: 10
89939254 TTAACTTTTA
89939264 ATAAAAAA-T
1 ATAAAAAATT
*
89939273 ATAAAATATT
1 ATAAAAAATT
89939283 AT--AAAATT
1 ATAAAAAATT
89939291 AT--AAAATT
1 ATAAAAAATT
*
89939299 AT-AAAAATC
1 ATAAAAAATT
89939308 ATAAAAAATT
1 ATAAAAAATT
* ***
89939318 GTAAACTTTT
1 ATAAAAAATT
*
89939328 GT-AAAAATT
1 ATAAAAAATT
89939337 ATAAAAAA
1 ATAAAAAA
89939345 AATTTATTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
8 15 0.27
9 19 0.34
10 22 0.39
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:89939554 original size:10 final size:10
Alignment explanation
Indices: 89939535--89939699 Score: 55
Period size: 10 Copynumber: 17.2 Consensus size: 10
89939525 TTTTAGTACG
89939535 ATAA-TTTTT
1 ATAATTTTTT
89939544 ATAATTTTTT
1 ATAATTTTTT
* *
89939554 ACAA-ATTTT
1 ATAATTTTTT
*
89939563 A-CATTTCTTT
1 ATAATTT-TTT
*
89939573 A-CATTTTTT
1 ATAATTTTTT
89939582 ATAATTTTCTT
1 ATAATTTT-TT
* *
89939593 ATGA--CTTT
1 ATAATTTTTT
**
89939601 ATAAAATTTT
1 ATAATTTTTT
89939611 ATAATTTTTT
1 ATAATTTTTT
* *
89939621 CT-ATATTTCT
1 ATAAT-TTTTT
*
89939631 AT-A-TATTT
1 ATAATTTTTT
89939639 ATAATTTTTT
1 ATAATTTTTT
**
89939649 ACGA-TTTTT
1 ATAATTTTTT
**
89939658 ATAACATTTT
1 ATAATTTTTT
**
89939668 ATAATTTTAA
1 ATAATTTTTT
89939678 AT-ATTTTTT
1 ATAATTTTTT
*
89939687 AAATATTTTTT
1 ATA-ATTTTTT
89939698 AT
1 AT
89939700 TAAAATTTAA
Statistics
Matches: 113, Mismatches: 30, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
8 11 0.10
9 31 0.27
10 58 0.51
11 13 0.12
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:89939612 original size:29 final size:27
Alignment explanation
Indices: 89939578--89939675 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 27
89939568 TCTTTACATT
89939578 TTTTATAATTTTCTTATGACTTTATAAAA
1 TTTTATAATTTT-TTATGA-TTTATAAAA
* *
89939607 TTTTATAATTTTTTCTAT-ATTTCT-ATA
1 TTTTATAA-TTTTT-TATGATTTATAAAA
* *
89939634 TATTTATAATTTTTTACGATTTTTATAACA
1 T-TTTATAATTTTTTATGA--TTTATAAAA
89939664 TTTTATAATTTT
1 TTTTATAATTTT
89939676 AAATATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
26 2 0.04
27 9 0.16
28 11 0.19
29 25 0.44
30 10 0.18
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTATAATTTTTTATGATTTATAAAA
Found at i:89939674 original size:19 final size:19
Alignment explanation
Indices: 89939535--89939684 Score: 69
Period size: 19 Copynumber: 8.0 Consensus size: 19
89939525 TTTTAGTACG
*
89939535 ATAATTTTTATAATTTTTT
1 ATAATTTTTATAATATTTT
* * * *
89939554 ACAAATTTTA-CATTTCTTT
1 ATAATTTTTATAATAT-TTT
* * *
89939573 ACATTTTTTATAATTTTCTT
1 ATAATTTTTATAATATT-TT
* * *
89939593 ATGA-CTTTATAAAATTTT
1 ATAATTTTTATAATATTTT
*
89939611 ATAATTTTT-TCTATATTTCT
1 ATAATTTTTAT-AATATTT-T
* *
89939631 AT-ATATTTATAATTTTTT
1 ATAATTTTTATAATATTTT
** *
89939649 ACGATTTTTATAACATTTT
1 ATAATTTTTATAATATTTT
89939668 ATAA-TTTTA-AATATTTT
1 ATAATTTTTATAATATTTT
89939685 TTAAATATTT
Statistics
Matches: 97, Mismatches: 26, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
17 7 0.07
18 17 0.18
19 62 0.64
20 11 0.11
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (19 bp):
ATAATTTTTATAATATTTT
Found at i:89939686 original size:11 final size:11
Alignment explanation
Indices: 89939672--89939698 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
89939662 CATTTTATAA
89939672 TTTTAAATATT
1 TTTTAAATATT
89939683 TTTTAAATATT
1 TTTTAAATATT
89939694 TTTTA
1 TTTTA
89939699 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:89941173 original size:164 final size:164
Alignment explanation
Indices: 89940905--89942238 Score: 2632
Period size: 164 Copynumber: 8.1 Consensus size: 164
89940895 AAATTGAATA
89940905 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
*
89940970 TTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
* *
89941035 AGGGTATTTGGTCATTCGGGACTCATGAAAGATA
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89941069 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
*
89941134 CTCAGACCTTCGGAACTAAGTTAGTATTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89941199 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89941233 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
89941298 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89941363 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89941397 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
89941462 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89941527 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89941561 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
89941626 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89941691 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89941725 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
89941790 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89941855 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89941889 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
89941954 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89942019 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89942053 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
1 AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
89942118 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
66 CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
89942183 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
131 AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
89942217 AAATGTAAAGACCCACTCATTT
1 AAATGTAAAGACCCACTCATTT
89942239 TTTTTCAAAA
Statistics
Matches: 1165, Mismatches: 5, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 1165 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (164 bp):
AAATGTAAAGACCCACTCATTTCGAAGGAGAAATATGCCATACCCAGTAAGTTAGGGTCTAACAC
CTCAGACCTTCGGAACTAAGTTAGTCTTTGATTTTTTTAAAATTCATGTATGAAGGTTCAAGAGA
AGGGTATTTGGTCATTCGGGACTCATGAAAAATT
Found at i:89943142 original size:133 final size:133
Alignment explanation
Indices: 89942901--89943381 Score: 734
Period size: 133 Copynumber: 3.6 Consensus size: 133
89942891 GATCTGCTGT
* *
89942901 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTAGTATGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCC
* * *
89942966 TGCTTAGTGAAGATAAGGCCGGTGGCTGAAATCTGCTCCATTGCCGATACATGAAGATAAGA-TT
64 TACTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGAAGATAAGACTT
89943030 -CACTAA
129 GC-C-AA
* * *
89943036 AATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTA
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTA
* *
89943101 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCTATTGCCGATACATGGAGATAAGACTTGC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGAAGATAAGACTTGC
89943166 CAA
131 CAA
* * *
89943169 AATTTGATCTGCTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTA
*
89943234 TTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACAT-AGAGATAAGACTTG
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGA-AGATAAGACTTG
89943298 CCAA
130 CCAA
* * * *
89943302 ATTTTGATCTGCTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCTACTCCTA
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTA
89943367 CTCAGTGAAGATAAG
66 CTCAGTGAAGATAAG
89943382 ACTGATGATA
Statistics
Matches: 320, Mismatches: 23, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
133 276 0.86
134 3 0.01
135 41 0.13
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (133 bp):
AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTA
CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGAAGATAAGACTTGC
CAA
Found at i:89950981 original size:21 final size:21
Alignment explanation
Indices: 89950951--89950994 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
89950941 CTGGCTCATT
89950951 ATGTTGTTCTGTG-ACTCCAGC
1 ATGTTGTTCTG-GAACTCCAGC
*
89950972 ATGTTTTTCTGGAACTCCAGC
1 ATGTTGTTCTGGAACTCCAGC
89950993 AT
1 AT
89950995 TTGATCCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (21 bp):
ATGTTGTTCTGGAACTCCAGC
Found at i:89956247 original size:19 final size:19
Alignment explanation
Indices: 89956200--89956240 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
89956190 TATTTTGTTA
89956200 TTTTATTTTTATTTCATCT
1 TTTTATTTTTATTTCATCT
*
89956219 TTTTATTTTTGTTTCATCT
1 TTTTATTTTTATTTCATCT
89956238 TTT
1 TTT
89956241 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTTTTATTTCATCT
Found at i:89959484 original size:32 final size:32
Alignment explanation
Indices: 89959434--89959498 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
89959424 TGAGCTGGTC
* * *
89959434 CCTACATGAGTCCGGAATGGATAGAGGGTTTG
1 CCTACACGAGTACAGAATGGATAGAGGGTTTG
*
89959466 CCTACACGAGTACAGAATGGATGGAGGGTTTG
1 CCTACACGAGTACAGAATGGATAGAGGGTTTG
89959498 C
1 C
89959499 ATCGATTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (32 bp):
CCTACACGAGTACAGAATGGATAGAGGGTTTG
Found at i:89964191 original size:67 final size:67
Alignment explanation
Indices: 89964113--89964248 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
89964103 ACCCAATTGC
89964113 TTCAATAATTTCTTTTTCTAACTAATCACTAAATTGATAAAATTTTCCTATCAATATTTTCATAC
1 TTCAATAATTTCTTTTTCTAACTAATCACTAAATTGATAAAATTTTCCTATCAATATTTTCATAC
89964178 GA
66 GA
*
89964180 TTCAATAATTTCTTTTTCTAGCTAATCACTAAATTGATAAAATTTTCCTATCAATATTTTCATAC
1 TTCAATAATTTCTTTTTCTAACTAATCACTAAATTGATAAAATTTTCCTATCAATATTTTCATAC
89964245 GA
66 GA
89964247 TT
1 TT
89964249 TTCCTATTAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.46
Consensus pattern (67 bp):
TTCAATAATTTCTTTTTCTAACTAATCACTAAATTGATAAAATTTTCCTATCAATATTTTCATAC
GA
Found at i:89966426 original size:54 final size:54
Alignment explanation
Indices: 89966342--89966455 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 54
89966332 GTTGGCATTC
* *
89966342 ATCAGTCCCCTCGAATTTTACATCTTTCTACAATAATCGAGTCATTGGAGAATCT
1 ATCA-TCCACTCGAATTTTACATCTTTCTACAATAATCGAGTCATTGGAGAAGCT
89966397 ATCATCCACTCGAATTTTACATCTTTCTACAATAATCGAGTCATTGGAGAAGCT
1 ATCATCCACTCGAATTTTACATCTTTCTACAATAATCGAGTCATTGGAGAAGCT
89966451 ATCAT
1 ATCAT
89966456 AGAGAATCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
54 53 0.93
55 4 0.07
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (54 bp):
ATCATCCACTCGAATTTTACATCTTTCTACAATAATCGAGTCATTGGAGAAGCT
Found at i:89972364 original size:22 final size:22
Alignment explanation
Indices: 89972339--89972385 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
89972329 TCCACACCCC
*
89972339 ACCTCGTGCCGCGCCACCGTCG
1 ACCTCGTGCCGCACCACCGTCG
*
89972361 ACCTCGTTCCGCACCACCGTCG
1 ACCTCGTGCCGCACCACCGTCG
89972383 ACC
1 ACC
89972386 GCGCGCCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.51, G:0.21, T:0.15
Consensus pattern (22 bp):
ACCTCGTGCCGCACCACCGTCG
Found at i:89974806 original size:10 final size:10
Alignment explanation
Indices: 89974793--89974818 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
89974783 CATAAAATTA
89974793 AAAAAAAAAG
1 AAAAAAAAAG
89974803 AAAAAAAAAG
1 AAAAAAAAAG
89974813 AAAAAA
1 AAAAAA
89974819 TAATACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:89976344 original size:23 final size:23
Alignment explanation
Indices: 89976318--89976361 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
89976308 GTAAATAGTA
89976318 AAAATA-AATAAAGTATAACAAGC
1 AAAATATAAT-AAGTATAACAAGC
*
89976341 AAAATATAGTAAGTATAACAA
1 AAAATATAATAAGTATAACAA
89976362 TCTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATATAATAAGTATAACAAGC
Found at i:89983275 original size:11 final size:11
Alignment explanation
Indices: 89983259--89983285 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
89983249 TTTTTTATCG
89983259 TCTTCTCTACT
1 TCTTCTCTACT
89983270 TCTTCTCTACT
1 TCTTCTCTACT
89983281 TCTTC
1 TCTTC
89983286 ACCTAGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTTCTCTACT
Found at i:89985828 original size:59 final size:59
Alignment explanation
Indices: 89985736--89985856 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 59
89985726 GCAACTCCGA
* * * * * * *
89985736 AACAGCTCGCGGACTTATGCTCCCAGCTGATGATTAAAGGTTAGATGAGTTAAGCTCAC
1 AACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGCTAGATGAGTAAAGCTCAC
**
89985795 AACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGCTATCTGAGTAAAGCTCAC
1 AACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGCTAGATGAGTAAAGCTCAC
89985854 AAC
1 AAC
89985857 CTTCAGTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (59 bp):
AACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGCTAGATGAGTAAAGCTCAC
Found at i:89985915 original size:163 final size:163
Alignment explanation
Indices: 89985659--89985955 Score: 461
Period size: 163 Copynumber: 1.8 Consensus size: 163
89985649 AGGTTGCAGT
* * * *
89985659 TGATGATTGAAGGTTAGCTAAGTTAAGCTCACAACTTCCAGTTATTTGAGTTAGCTGAGTTAAGC
1 TGATGATTAAAGGCTAGCTAAGTAAAGCTCACAACTTCCAGTTATTTGAGTTAACTGAGTTAAGC
* * *
89985724 TTGCAACTCCGAAACAGCTCGCGGACTTATGCTCCCAGCTGATGATTAAAGGTTAGATGAGTTAA
66 TCGCAACTCCAAAACAGCTCGCGGACTTACGCTCCCAGCTGATGATTAAAGGTTAGATGAGTTAA
89985789 GCTCACAACAGCTCACAGACCTACGCTCCCAAC
131 GCTCACAACAGCTCACAGACCTACGCTCCCAAC
* *
89985822 TGATGATTAAAGGCTATCTGAGTAAAGCTCACAACCTT-CAGTTATTTGAGTTAACTGAGTTAAG
1 TGATGATTAAAGGCTAGCTAAGTAAAGCTCACAA-CTTCCAGTTATTTGAGTTAACTGAGTTAAG
* * * *
89985886 CTCGCAACTCCAAAATAGCTCGTGGACTTACGCTCCTAGCTGATGATTAAAGGTTAGCTGAGTTA
65 CTCGCAACTCCAAAACAGCTCGCGGACTTACGCTCCCAGCTGATGATTAAAGGTTAGATGAGTTA
89985951 AGCTC
130 AGCTC
89985956 GCAAACTCCA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
163 117 0.98
164 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (163 bp):
TGATGATTAAAGGCTAGCTAAGTAAAGCTCACAACTTCCAGTTATTTGAGTTAACTGAGTTAAGC
TCGCAACTCCAAAACAGCTCGCGGACTTACGCTCCCAGCTGATGATTAAAGGTTAGATGAGTTAA
GCTCACAACAGCTCACAGACCTACGCTCCCAAC
Found at i:89985978 original size:104 final size:104
Alignment explanation
Indices: 89985806--89986289 Score: 693
Period size: 104 Copynumber: 4.7 Consensus size: 104
89985796 ACAGCTCACA
* * * * * *
89985806 GACCTACGCTCCCAACTGATGATTAAAGGCTATCTGAGTAAAGCTCACAACCTTCAGTTATTTGA
1 GACCTACGCTCCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGA
89985871 GTTAACTGAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
66 GTTAACTGAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
* * *
89985910 GACTTACGCTCCTAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAAACTCCAGTTATTTGA
1 GACCTACGCTCCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGA
* *
89985975 GTTAGCTAAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
66 GTTAACTGAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
*
89986014 GACCTACGCTTCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGA
1 GACCTACGCTCCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGA
* * *
89986079 GTTACCTGAGTTAAGCTCGCAACTTCGAAATAGCTCGTG
66 GTTAACTGAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
* * * *
89986118 AACCTACGCTCCCAGCTAATAATTAAAGGTTAGCTGAGTTAAGCTCAG-AACCTCTAGTTATTTG
1 GACCTACGCTCCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTC-GCAACCTCCAGTTATTTG
* * * *
89986182 AGTTAACTGAGTTAAGCTTGCAACTTCGAAATAGCTCATG
65 AGTTAACTGAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
* * * * *
89986222 GACCTATGCTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGTAACCTCCAATTA-TTGA
1 GACCTACGCTCCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGA
89986286 GTTA
66 GTTA
89986290 GCTAATTTAA
Statistics
Matches: 345, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
103 9 0.03
104 335 0.97
105 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (104 bp):
GACCTACGCTCCCAGCTGATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGA
GTTAACTGAGTTAAGCTCGCAACTCCAAAATAGCTCGTG
Found at i:89992819 original size:23 final size:23
Alignment explanation
Indices: 89992774--89992852 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 23
89992764 TTATAAAATT
* *
89992774 TAAAATGTATATTTTAAATATTTTA
1 TAAAAT-TATTTTTTTAA-ATTTTA
89992799 TAAAATTATTTTTTTAAA-TTTA
1 TAAAATTATTTTTTTAAATTTTA
*
89992821 -AATATATTA-TTTTTT-AATATTA
1 TAA-A-ATTATTTTTTTAAATTTTA
89992843 TAAAA-TATTT
1 TAAAATTATTT
89992853 AAAATATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
20 2 0.04
21 7 0.15
22 15 0.33
23 7 0.15
24 9 0.20
25 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
TAAAATTATTTTTTTAAATTTTA
Found at i:89992946 original size:21 final size:22
Alignment explanation
Indices: 89992922--89992970 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 22
89992912 TTAATGCATA
89992922 TTTTAAAATTTTTAAATAT-AT
1 TTTTAAAATTTTTAAATATAAT
89992943 TTTT--AATTTTTAAATATAAAT
1 TTTTAAAATTTTTAAATAT-AAT
89992964 TTTTAAA
1 TTTTAAA
89992971 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 13 0.54
21 10 0.42
23 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATTTTTAAATATAAT
Found at i:89992986 original size:14 final size:13
Alignment explanation
Indices: 89992949--89993014 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
89992939 ATATTTTTAA
* *
89992949 TTTTTAAATATAAA
1 TTTTTAAA-ATTAT
89992963 TTTTT-AAATTAT
1 TTTTTAAAATTAT
89992975 TTTTTAAGAATTGTGAT
1 TTTTTAA-AA-T-T-AT
89992992 TTTTTAAAATTAT
1 TTTTTAAAATTAT
*
89993005 TTTTAAAAAT
1 TTTTTAAAAT
89993015 ATTCAAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
12 8 0.18
13 14 0.32
14 8 0.18
15 2 0.05
16 3 0.07
17 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (13 bp):
TTTTTAAAATTAT
Found at i:89993172 original size:13 final size:13
Alignment explanation
Indices: 89993129--89993176 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
89993119 GTTAAAAAAG
89993129 ATTAAAAATATAT
1 ATTAAAAATATAT
89993142 ATTAGAAAATTTATATAT
1 ATT--AAAA---ATATAT
89993160 ATTAAAAATATAT
1 ATTAAAAATATAT
89993173 ATTA
1 ATTA
89993177 TAACTGTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.43
15 4 0.13
16 4 0.13
18 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATTAAAAATATAT
Found at i:89993173 original size:15 final size:16
Alignment explanation
Indices: 89993132--89993174 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
89993122 AAAAAAGATT
89993132 AAAA-ATATATATTAG
1 AAAATATATATATTAG
89993147 AAAATTTATATATATTA-
1 AAAA--TATATATATTAG
89993164 AAAATATATAT
1 AAAATATATAT
89993175 TATAACTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.44
17 4 0.16
18 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATATATATATTAG
Found at i:89993178 original size:18 final size:18
Alignment explanation
Indices: 89993136--89993174 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
89993126 AAGATTAAAA
*
89993136 ATATATATTAGAAAATTT
1 ATATATATTAGAAAATAT
89993154 ATATATATTA-AAAATAT
1 ATATATATTAGAAAATAT
89993171 ATAT
1 ATAT
89993175 TATAACTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATATATTAGAAAATAT
Found at i:89993417 original size:17 final size:16
Alignment explanation
Indices: 89993373--89993417 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
89993363 TTTTGTATTT
*
89993373 TTATATTTTATAGTTA
1 TTATATTTAATAGTTA
*
89993389 TTATAATATAATAGTTAA
1 TTAT-ATTTAATAGTT-A
89993407 TTATATTTAAT
1 TTATATTTAAT
89993418 TTATGTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
TTATATTTAATAGTTA
Found at i:90003636 original size:17 final size:19
Alignment explanation
Indices: 90003611--90003647 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
90003601 AAAAGAAATA
90003611 ATTTCAAT-AATATA-ATT
1 ATTTCAATAAATATATATT
*
90003628 ATTTTAATAAATATATATT
1 ATTTCAATAAATATATATT
90003647 A
1 A
90003648 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTCAATAAATATATATT
Found at i:90005446 original size:27 final size:27
Alignment explanation
Indices: 90005366--90005451 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
90005356 ATTAAATTAA
* * *
90005366 ATTAAAACAATTAACAGCTAAATTCAG
1 ATTATAACAATTAACAACTAAATTCGG
90005393 ATTATAGA-AA-T-ACAAACTAGAAATTCGG
1 ATTATA-ACAATTAAC-AACT--AAATTCGG
90005421 ATTATAACAATTAACAACTAAATTCGG
1 ATTATAACAATTAACAACTAAATTCGG
90005448 ATTA
1 ATTA
90005452 AATAATATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
25 2 0.04
26 4 0.08
27 20 0.41
28 16 0.33
29 5 0.10
30 2 0.04
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (27 bp):
ATTATAACAATTAACAACTAAATTCGG
Found at i:90011705 original size:28 final size:28
Alignment explanation
Indices: 90011665--90011720 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
90011655 TTTTATTACA
90011665 TATATCGTAACTAAATCCATCCATGATC
1 TATATCGTAACTAAATCCATCCATGATC
90011693 TATATCGTAACTAAATCCATCCATGATC
1 TATATCGTAACTAAATCCATCCATGATC
90011721 ATGTATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (28 bp):
TATATCGTAACTAAATCCATCCATGATC
Found at i:90017214 original size:31 final size:31
Alignment explanation
Indices: 90017179--90017242 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
90017169 TTAATTGTTA
*
90017179 TATTTTAATTAAGATGCATGGTAGATAAATT
1 TATTTTAATTAAAATGCATGGTAGATAAATT
90017210 TATTTTAATTAAAATGCATGGTAGATAAATT
1 TATTTTAATTAAAATGCATGGTAGATAAATT
90017241 TA
1 TA
90017243 GGAAAGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (31 bp):
TATTTTAATTAAAATGCATGGTAGATAAATT
Found at i:90017877 original size:44 final size:44
Alignment explanation
Indices: 90017814--90017897 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
90017804 TGTTTAGGGA
90017814 TACTTCGAACTTGAGTCGATGAAGCACTATAAGTGTCGTACTGT
1 TACTTCGAACTTGAGTCGATGAAGCACTATAAGTGTCGTACTGT
* **
90017858 TACTTCG-ACTTTGAGTCGATGAGGCACTATTTGTGTCGTA
1 TACTTCGAAC-TTGAGTCGATGAAGCACTATAAGTGTCGTA
90017898 GTGCTATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (44 bp):
TACTTCGAACTTGAGTCGATGAAGCACTATAAGTGTCGTACTGT
Found at i:90029793 original size:44 final size:44
Alignment explanation
Indices: 90029738--90029934 Score: 183
Period size: 44 Copynumber: 4.5 Consensus size: 44
90029728 TTTCAGCAGC
*
90029738 CTTTAACTCCCTAAGCAATAGGGTAACAAGCTGAAAATTATA-G
1 CTTTAACTCCCTAAGCAATAGGGTAACAAGCTGAAAATTACAGG
* * * *
90029781 ATCTTATCTCCCTAAGCAATAGTGG---CATAGATTGAAAA-CAGCAGG
1 CT-TTAACTCCCTAAGCAATAG-GGTAACA-AG-CTGAAAATTA-CAGG
* * * *
90029826 CTTTAACTCCCTAAACAAAAGGATAACAAGCT-AAAGATTGCAGG
1 CTTTAACTCCCTAAGCAATAGGGTAACAAGCTGAAA-ATTACAGG
90029870 CTTTAACTCCCTAAGCAATAGGGTAACAAGCTGAAAATTACA-G
1 CTTTAACTCCCTAAGCAATAGGGTAACAAGCTGAAAATTACAGG
* *
90029913 ATCTTATCTCCCTAAGCAATAG
1 CT-TTAACTCCCTAAGCAATAG
90029935 TGGAGCAGAT
Statistics
Matches: 122, Mismatches: 19, Indels: 25
0.73 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 10 0.08
44 99 0.81
45 9 0.07
46 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (44 bp):
CTTTAACTCCCTAAGCAATAGGGTAACAAGCTGAAAATTACAGG
Found at i:90030226 original size:84 final size:85
Alignment explanation
Indices: 90029872--90030256 Score: 447
Period size: 85 Copynumber: 4.5 Consensus size: 85
90029862 ATTGCAGGCT
* * * *** * * *
90029872 TTAACTCCCTAAGCAATAGGGTAACAAGCTGAAAA-TTACAGATCTTATCTC-CCTAAGCAATAG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAAATTTACAGATCTGGGCTCGCC-GAGCAGTGG
* *
90029935 TGGAGCAGATCAAAGA-TACATGCC
64 TGGAGCAGGTCGAAGACT-C--GCC
*
90029959 TTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGTGGTG
*
90030024 AAGCAGGTCGAAGACTCGCC
66 GAGCAGGTCGAAGACTCGCC
* * * * * *
90030044 TTAACCCCCTAAGTAGTAGGGTAACAGGTTAAAGTTTACAGATTTGGGCTCGCCAAACAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGTGGTG
* *
90030109 GAGCAGGTCGAAGACTTGTC
66 GAGCAGGTCGAAGACTCGCC
* * *
90030129 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCT-GGCTCTCCGAGTAGTGATG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGTGGTG
*
90030193 GAGCAGGTCGAAGACTCACC
66 GAGCAGGTCGAAGACTCGCC
* *
90030213 TTAACCCCTTAAGCAGTACGGTAACAGGCTAAAA-TTACAGATCT
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCT
90030257 TATCTTCGTT
Statistics
Matches: 260, Mismatches: 35, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
83 10 0.04
84 63 0.24
85 121 0.47
86 4 0.02
87 59 0.23
88 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (85 bp):
TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGTGGTG
GAGCAGGTCGAAGACTCGCC
Found at i:90034015 original size:16 final size:16
Alignment explanation
Indices: 90033994--90034035 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
90033984 TTATTAAATT
*
90033994 ATATATTTTAATTATA
1 ATATATTTTAATAATA
90034010 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
90034025 AT-TATGTTTAA
1 ATATAT-TTTAA
90034036 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:90034020 original size:15 final size:15
Alignment explanation
Indices: 90033985--90034026 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
90033975 TTAAGAATTT
*
90033985 TATTAAATTAT-ATA
1 TATTTAATTATAATA
90033999 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
90034013 TATTTAATAATAAT
1 TATTTAATTATAAT
90034027 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:90034259 original size:45 final size:42
Alignment explanation
Indices: 90034161--90034270 Score: 118
Period size: 45 Copynumber: 2.6 Consensus size: 42
90034151 TTTTCCATTA
90034161 TGCTATTACACCTCTATTCCAT---TTAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTAACCAAACACAAGAT
* * ***
90034200 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATT-AACCAAACACAAGA-T
90034245 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
90034271 CCTCTATTCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 19 0.33
40 1 0.02
43 2 0.04
44 11 0.19
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (42 bp):
TGCTATTACACCTCTATTCCATACATTAACCAAACACAAGAT
Found at i:90034272 original size:16 final size:16
Alignment explanation
Indices: 90034251--90034318 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
90034241 GATTTGCTAT
*
90034251 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
90034267 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
90034283 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
90034299 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
90034315 TACA
1 TACA
90034319 GCGAACAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:90034979 original size:9 final size:8
Alignment explanation
Indices: 90034964--90034989 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
90034954 TTTGGCATTC
90034964 ATTTTTTT
1 ATTTTTTT
90034972 ATTTTTTT
1 ATTTTTTT
90034980 ATTTTTTT
1 ATTTTTTT
90034988 AT
1 AT
90034990 ATACATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:90053608 original size:23 final size:23
Alignment explanation
Indices: 90053554--90053614 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
90053544 GACACATAAA
90053554 GTGCCT-AAA-ACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
90053575 GTGCCTG--ATACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
*
90053596 GTGCCTGAAATACAACACA
1 GTGCCTGAAATACGACACA
90053615 TAAAGTGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.71
23 9 0.26
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (23 bp):
GTGCCTGAAATACGACACACGAG
Found at i:90053622 original size:23 final size:23
Alignment explanation
Indices: 90053541--90053622 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 23
90053531 CTGATCAGTG
*
90053541 TACGACACATAAAGTGCCT-AAA
1 TACGACACACAAAGTGCCTGAAA
* *
90053563 -ACGACACACGAGGTGCCTG--A
1 TACGACACACAAAGTGCCTGAAA
* *
90053583 TACGACACACGAGGTGCCTGAAA
1 TACGACACACAAAGTGCCTGAAA
* *
90053606 TACAACACATAAAGTGC
1 TACGACACACAAAGTGC
90053623 TTGATCAGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 34 0.69
23 14 0.29
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.15
Consensus pattern (23 bp):
TACGACACACAAAGTGCCTGAAA
Found at i:90055779 original size:17 final size:17
Alignment explanation
Indices: 90055759--90055791 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
90055749 TTAACTATTA
90055759 AATTAAATTAATTCATT
1 AATTAAATTAATTCATT
*
90055776 AATTAATTTAATTCAT
1 AATTAAATTAATTCAT
90055792 GTGACAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTAAATTAATTCATT
Found at i:90058527 original size:21 final size:21
Alignment explanation
Indices: 90058503--90058567 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
90058493 AAGTCTAGCT
*
90058503 GAAGCACATAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
*
90058524 GAAGC-C-CGAAG-GCT-AACT
1 GAAGCACAC-AAGTGCTAAACG
90058542 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
90058563 GAAGC
1 GAAGC
90058568 CCGAAGGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 8 0.22
21 13 0.36
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAACG
Found at i:90058555 original size:39 final size:39
Alignment explanation
Indices: 90058492--90058585 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
90058482 TCTGAAACCT
* * *
90058492 GAAGTCTAGCTGAAGCACATAAGTGCTAAACGGAAGCCC
1 GAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAGCCC
90058531 GAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAGCCC
1 GAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAGCCC
90058570 GAAGGCTAACTGAAGC
1 GAAGGCTAACTGAAGC
90058586 TCATCAGAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.13
Consensus pattern (39 bp):
GAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAGCCC
Found at i:90061954 original size:33 final size:30
Alignment explanation
Indices: 90061915--90061974 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
90061905 ATCTATATTA
* *
90061915 TAATAAT-AGTTATATATGTATTAATATTTT
1 TAATAATAATTTATAT-TATATTAATATTTT
*
90061945 TAATAATAATTTATATTATATTATTATTTT
1 TAATAATAATTTATATTATATTAATATTTT
90061975 ATGTATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
TAATAATAATTTATATTATATTAATATTTT
Found at i:90062161 original size:16 final size:17
Alignment explanation
Indices: 90062140--90062172 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
90062130 ATAATTATTG
90062140 TATTAAA-AATATTTTA
1 TATTAAATAATATTTTA
90062156 TATTAAATTAATATTTT
1 TATTAAA-TAATATTTT
90062173 TAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAAATAATATTTTA
Found at i:90064860 original size:68 final size:68
Alignment explanation
Indices: 90064751--90065022 Score: 519
Period size: 68 Copynumber: 4.0 Consensus size: 68
90064741 GAGAATAAAA
*
90064751 ACATAAGCAAAATTTCTA-TCTATCTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAG
1 ACATAAGCAAAATTTCTACT-TATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAG
90064815 GTTT
65 GTTT
90064819 ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
1 ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
90064884 TTT
66 TTT
90064887 ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
1 ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
90064952 TTT
66 TTT
90064955 ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
1 ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
90065020 TTT
66 TTT
90065023 CAGTTTCCCT
Statistics
Matches: 202, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
68 201 1.00
69 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (68 bp):
ACATAAGCAAAATTTCTACTTATTTTTCAAGAGATCTAGGTCTCTCTCTAAACAAGTCCTAAAGG
TTT
Found at i:90066049 original size:16 final size:17
Alignment explanation
Indices: 90066023--90066054 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
90066013 AACTGAAATT
90066023 AAAAAAGGAAAAAGAAG
1 AAAAAAGGAAAAAGAAG
90066040 AAAAAA-GAAAAAGAA
1 AAAAAAGGAAAAAGAA
90066055 AATTTGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAAAAAGAAG
Found at i:90071187 original size:48 final size:48
Alignment explanation
Indices: 90071133--90071229 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
90071123 ACATTAATTC
*
90071133 ATGTAATGAAATGAATTAAATATCAACCTTCAACCATGTTAACAAAAA
1 ATGTAATGAAATGAATTAAATATCAACCTTCAACCATGTTAAAAAAAA
90071181 ATGTAATGAAATGAATTAAATATCAACCTTCAACCATGTTAAAAAAAA
1 ATGTAATGAAATGAATTAAATATCAACCTTCAACCATGTTAAAAAAAA
90071229 A
1 A
90071230 AAAAAAAAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (48 bp):
ATGTAATGAAATGAATTAAATATCAACCTTCAACCATGTTAAAAAAAA
Found at i:90073979 original size:24 final size:24
Alignment explanation
Indices: 90073951--90074008 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
90073941 TTTAGTCTAG
90073951 ATTTAATTATAACATTTTATATAC
1 ATTTAATTATAACATTTTATATAC
*
90073975 ATTTAATTATAACATTTTATTTAC
1 ATTTAATTATAACATTTTATATAC
*
90073999 ACTTATATTA
1 ATTTA-ATTA
90074009 AAAATAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTAATTATAACATTTTATATAC
Found at i:90073991 original size:13 final size:13
Alignment explanation
Indices: 90073951--90073991 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
90073941 TTTAGTCTAG
90073951 ATTTAATTATAAC
1 ATTTAATTATAAC
*
90073964 ATTTTA-TAT-AC
1 ATTTAATTATAAC
90073975 ATTTAATTATAAC
1 ATTTAATTATAAC
90073988 ATTT
1 ATTT
90073992 TATTTACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 11 0.46
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTAATTATAAC
Found at i:90073993 original size:14 final size:14
Alignment explanation
Indices: 90073952--90073993 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
90073942 TTAGTCTAGA
90073952 TTTAATTATAACAT
1 TTTAATTATAACAT
90073966 TTT-A-TAT-ACA-
1 TTTAATTATAACAT
90073976 TTTAATTATAACAT
1 TTTAATTATAACAT
90073990 TTTA
1 TTTA
90073994 TTTACACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 3 0.12
11 4 0.17
12 6 0.25
13 4 0.17
14 7 0.29
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTATAACAT
Found at i:90077755 original size:41 final size:41
Alignment explanation
Indices: 90077678--90077756 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
90077668 GTTTGAAATA
* * ** *
90077678 AAACGCCGCAAAAAACTAAGCAATAGCGGCGTTTTTGGTCG
1 AAACGCCACAAAAAACTAAACAATAGCAACGCTTTTGGTCG
90077719 AAACGCCACAAAAAACTAAACAATAGCAACGCTTTTGG
1 AAACGCCACAAAAAACTAAACAATAGCAACGCTTTTGG
90077757 AAAAACATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
AAACGCCACAAAAAACTAAACAATAGCAACGCTTTTGGTCG
Found at i:90077906 original size:79 final size:78
Alignment explanation
Indices: 90077748--90077969 Score: 309
Period size: 79 Copynumber: 2.8 Consensus size: 78
90077738 ACAATAGCAA
* ** * * *
90077748 CGCTTTTGGAAAAACATCACTATAGATCGAGGTTTTAGCGGTGCTTCTAGAAAAATGCGCTATTG
1 CGCTTTTAGAAAAACGCCACTATAGA--GAGGTTTTAGCGGCGCTTTTAGAAAAACGCGCTATTG
90077813 CTTAGTTTTTAGCGG
64 CTTAGTTTTTAGCGG
** *
90077828 CGCTTTTAGAAAAACGCCACTATAGAGAGGTTTTAGCGGCATTTTTCGAAAAACGCCGCTATTGC
1 CGCTTTTAGAAAAACGCCACTATAGAGAGGTTTTAGCGGCGCTTTTAGAAAAACG-CGCTATTGC
90077893 TTAGTTTTTAGCGG
65 TTAGTTTTTAGCGG
*
90077907 CGTTTTTAGAAAAACGCCACTATAGATAGAGGTTTTAGCGGCGCTTTTAGAAAAACGCGCTAT
1 CGCTTTTAGAAAAACGCCACTATAG--AGAGGTTTTAGCGGCGCTTTTAGAAAAACGCGCTAT
90077970 AGATCGGGGT
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
78 23 0.18
79 47 0.37
80 29 0.23
81 27 0.21
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (78 bp):
CGCTTTTAGAAAAACGCCACTATAGAGAGGTTTTAGCGGCGCTTTTAGAAAAACGCGCTATTGCT
TAGTTTTTAGCGG
Found at i:90077913 original size:40 final size:40
Alignment explanation
Indices: 90077748--90078003 Score: 221
Period size: 40 Copynumber: 6.4 Consensus size: 40
90077738 ACAATAGCAA
* ** * *
90077748 CGCTTTTGGAAAAACATCACTATAGATCGAGGTTTTAGCGG
1 CGCTTTTAGAAAAACGCCGCTATAGCT-GAGGTTTTAGCGG
* * * * * *
90077789 TGCTTCTAGAAAAATG-CGCTATTGCTTAGTTTTTAGCGG
1 CGCTTTTAGAAAAACGCCGCTATAGCTGAGGTTTTAGCGG
* *
90077828 CGCTTTTAGAAAAACGCCACTATAG-AGAGGTTTTAGCGG
1 CGCTTTTAGAAAAACGCCGCTATAGCTGAGGTTTTAGCGG
** * * * *
90077867 CATTTTTCGAAAAACGCCGCTATTGCTTAGTTTTTAGCGG
1 CGCTTTTAGAAAAACGCCGCTATAGCTGAGGTTTTAGCGG
* * *
90077907 CGTTTTTAGAAAAACGCCACTATAGATAGAGGTTTTAGCGG
1 CGCTTTTAGAAAAACGCCGCTATAGCT-GAGGTTTTAGCGG
* * *
90077948 CGCTTTTAGAAAAACG-CGCTATAGATCGGGGTTTTAGCAG
1 CGCTTTTAGAAAAACGCCGCTATAGCT-GAGGTTTTAGCGG
* *
90077988 CACTTTTGGAAAAACG
1 CGCTTTTAGAAAAACG
90078004 TCGCAAAAAA
Statistics
Matches: 172, Mismatches: 40, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
39 55 0.32
40 80 0.47
41 37 0.22
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (40 bp):
CGCTTTTAGAAAAACGCCGCTATAGCTGAGGTTTTAGCGG
Found at i:90079763 original size:12 final size:12
Alignment explanation
Indices: 90079748--90079773 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
90079738 TTCCTATTCG
90079748 CATTCCCACTCC
1 CATTCCCACTCC
90079760 CATTCCCACTCC
1 CATTCCCACTCC
90079772 CA
1 CA
90079774 CATACTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.58, G:0.00, T:0.23
Consensus pattern (12 bp):
CATTCCCACTCC
Found at i:90080873 original size:17 final size:17
Alignment explanation
Indices: 90080847--90080886 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
90080837 ATGCATATGA
90080847 TCTC-TATGTGACCAGT
1 TCTCATATGTGACCAGT
90080863 TCTCATATGTGACCAGT
1 TCTCATATGTGACCAGT
90080880 TCTCATA
1 TCTCATA
90080887 CTTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (17 bp):
TCTCATATGTGACCAGT
Found at i:90098519 original size:290 final size:285
Alignment explanation
Indices: 90097841--90098546 Score: 708
Period size: 290 Copynumber: 2.4 Consensus size: 285
90097831 GATTTCGAGG
* * * * * * * *
90097841 AGAGCCCAAAGGTTCATGGAGTTTGCATAGCACCTCACCAGCAAGGACATATTAACATTTGGCCT
1 AGAGCCC-AAGGTTCATGGAGTTTGGAAAGCGCCTCACCACCAAGGAAATGTTAGCATTTGGACT
** * * * * * *
90097906 TGGCAGGGTTCGAA-CTCATGCCCATAAATGACATTAATAGCTAAGTACACTACCAGTTGTCTAG
65 TGGTGGGGTTCGAACCT-ATGCCCTTAAATGGCATTAGT-GGTAAGTACACTACCACTTGACTAG
* * * * *
90097970 AAAAATGGTGTTTTTTTTTAGGGGAGGTCAGTCTCGCTTTGGGAGACATCTTCTTGGAATGTCGT
128 AAAAAAGGTATTTTTTTTAAGGGGAGATCAGTCTAGCTTTGGGAGACATCTTCTTGGAATGTCGT
* ** * * *
90098035 CTGGGAGCCATTAAACCCCTCAACGGTGGATGTATTGTGCCTGAGATATCTATGTTCGGTTTTAG
193 CTGGGAGCCATCAAACCCCTCAACAATAGAGGTATTGTGCCTGAGATATCTATGTTCGGTTTTAA
** *
90098100 CCTCAAGTTTTTTATCCCAACTTTGAGA
258 CCTCAAGTTTTAGATCCCAACTTTAAGA
* *
90098128 AGAGCCCAAGGATTCATGGAGTTTGTGGAA-CGCCTCACCACTAAGGAAATGTTAGCATTT-GAC
1 AGAGCCCAAGG-TTCATGGAGTTTG-GAAAGCGCCTCACCACCAAGGAAATGTTAGCATTTGGAC
* * * * * *
90098191 ATTAGTGGCGTTCGAACCCATGCCCTTAAATTGCATTAGTGGTTAAGAACACTACCACTTGGCTA
64 -TTGGTGGGGTTCGAACCTATGCCCTTAAATGGCATTAGTGG-TAAGTACACTACCACTTGACTA
* *
90098256 GAAAAAAGGTATCTTTTTGTTAAGGGGAGATCGGTCTAGCTTTGGGAGACATCTT-TTTGAAGTG
127 GAAAAAAGGTAT-TTTTT-TTAAGGGGAGATCAGTCTAGCTTTGGGAGACATCTTCTTGGAA-TG
* * * * * * * *
90098320 TCAT-TCGAGGAGTCGA-CAAACCCTTCAACAATAGAGGTATTGTGCCTGGGGTGTTTGTGCTT-
189 TCGTCT-G-GGAG-CCATCAAACCCCTCAACAATAGAGGTATTGTGCCTGAGATATCTATG-TTC
* * * *
90098382 GGTTTTAACCTTAGGTTTTAGCTCCCGACTTTAAGCA
250 GGTTTTAACCTCAAGTTTTAGATCCCAACTTTAAG-A
* *
90098419 A-AGCCCAAGGTTCATAGAGTTTGGAAAGCGCCTCACCACCAAGGAAATGTTTAGCATTTGGTCT
1 AGAGCCCAAGGTTCATGGAGTTTGGAAAGCGCCTCACCACCAAGGAAATG-TTAGCATTTGGACT
*
90098483 TGGTGGGGTTTGAACCTATGCCCTTAAATGGCATTAGTGAGTAAGTACACTACCACTTGACTAG
65 TGGTGGGGTTCGAACCTATGCCCTTAAATGGCATTAGTG-GTAAGTACACTACCACTTGACTAG
90098547 TCTTTTTGGA
Statistics
Matches: 340, Mismatches: 62, Indels: 31
0.79 0.14 0.07
Matches are distributed among these distances:
286 7 0.02
287 101 0.30
288 16 0.05
289 70 0.21
290 137 0.40
291 9 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (285 bp):
AGAGCCCAAGGTTCATGGAGTTTGGAAAGCGCCTCACCACCAAGGAAATGTTAGCATTTGGACTT
GGTGGGGTTCGAACCTATGCCCTTAAATGGCATTAGTGGTAAGTACACTACCACTTGACTAGAAA
AAAGGTATTTTTTTTAAGGGGAGATCAGTCTAGCTTTGGGAGACATCTTCTTGGAATGTCGTCTG
GGAGCCATCAAACCCCTCAACAATAGAGGTATTGTGCCTGAGATATCTATGTTCGGTTTTAACCT
CAAGTTTTAGATCCCAACTTTAAGA
Found at i:90101880 original size:18 final size:19
Alignment explanation
Indices: 90101851--90101892 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
90101841 GGACTTTATT
*
90101851 TATTGAAAAATATTTTGTA
1 TATTGAAAAATATTTGGTA
90101870 TATTG-AAAATATTTGGTA
1 TATTGAAAAATATTTGGTA
90101888 TATTG
1 TATTG
90101893 TCAATGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (19 bp):
TATTGAAAAATATTTGGTA
Found at i:90109118 original size:105 final size:103
Alignment explanation
Indices: 90108933--90109159 Score: 274
Period size: 105 Copynumber: 2.2 Consensus size: 103
90108923 ATGACACTAG
* * * * * *
90108933 GTATGGTATTGTCCATACTGAGCTATGACATGTAGTATGGTATTTCCCATACCGAGTTGTGAAAC
1 GTATGGTATTATCCATACCGAGCTATAACACGCAGTATGGCATTTCCCATACCGAGTTGTGAAAC
* *
90108998 ATAGGTATGACATTGTCCATATTGAGTTATAAAACATA
66 ATAGGCATGACATTGTCCATATTGAGCTATAAAACATA
* ** *
90109036 TGTATGGTATTATCCATACCGAGCTATAATACGCAGATATGGCATTTCTTATACCGAGTTTTGAA
1 -GTATGGTATTATCCATACCGAGCTATAACACGCAG-TATGGCATTTCCCATACCGAGTTGTGAA
* ** *
90109101 ACGTAGGCATGGTATTGTCCATATTGAGCTATGAAACATA
64 ACATAGGCATGACATTGTCCATATTGAGCTATAAAACATA
*
90109141 GATATGGTATTAACCATAC
1 G-TATGGTATTATCCATAC
90109160 TGAGTTATGA
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
104 30 0.29
105 74 0.71
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (103 bp):
GTATGGTATTATCCATACCGAGCTATAACACGCAGTATGGCATTTCCCATACCGAGTTGTGAAAC
ATAGGCATGACATTGTCCATATTGAGCTATAAAACATA
Found at i:90109148 original size:35 final size:34
Alignment explanation
Indices: 90108919--90109170 Score: 161
Period size: 35 Copynumber: 7.3 Consensus size: 34
90108909 TCCATGGCAA
*
90108919 AGTTATGACAC-TAGGTATGGTATTGTCCATACTG
1 AGTTATGAAACATA-GTATGGTATTGTCCATACTG
* * ** *
90108953 AGCTATGACATGTAGTATGGTATT-TCCCATACCG
1 AGTTATGAAACATAGTATGGTATTGT-CCATACTG
* ** *
90108987 AGTTGTGAAACATAGGTATGACATTGTCCATATTG
1 AGTTATGAAACATA-GTATGGTATTGTCCATACTG
* * *
90109022 AGTTATAAAACATATGTATGGTATTATCCATACCG
1 AGTTATGAAACATA-GTATGGTATTGTCCATACTG
* ** * * *
90109057 AGCTAT-AATACGCAGATATGGCATT-TCTTATACCG
1 AGTTATGAA-ACATAG-TATGGTATTGTC-CATACTG
* * * *
90109092 AGTTTTGAAACGTAGGCATGGTATTGTCCATATTG
1 AGTTATGAAACATA-GTATGGTATTGTCCATACTG
* **
90109127 AGCTATGAAACATAGATATGGTATTAACCATACTG
1 AGTTATGAAACATAG-TATGGTATTGTCCATACTG
90109162 AGTTATGAA
1 AGTTATGAA
90109171 TTGTGGCACT
Statistics
Matches: 166, Mismatches: 41, Indels: 21
0.73 0.18 0.09
Matches are distributed among these distances:
33 1 0.01
34 41 0.25
35 118 0.71
36 6 0.04
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (34 bp):
AGTTATGAAACATAGTATGGTATTGTCCATACTG
Found at i:90113834 original size:35 final size:35
Alignment explanation
Indices: 90113795--90114073 Score: 278
Period size: 35 Copynumber: 8.0 Consensus size: 35
90113785 ATGGCAAAGT
* * * *
90113795 TATGACACATAGGTATAGTATTGTCCATAGTGAGC
1 TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
* * * * *
90113830 TATGACACGTAGGTATAGTATTATCTATACCGAGC
1 TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
* * *
90113865 TAT-AATACGTAGGTATGATATT-TCCCATATTGAGT
1 TATGAA-ACGTAGGTATGGTATTGT-CCATACTGAGC
* *
90113900 TGTGAAACGTAGGTATGATATTGTCCATACTGAGC
1 TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
* * * *
90113935 TATGAAACATATGTATGGTATTATCCATACCGAGC
1 TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
* ** *
90113970 TAT-AATACGTAGTTATGGTATT-TCTCATACCAAGT
1 TATGAA-ACGTAGGTATGGTATTGTC-CATACTGAGC
90114005 TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
1 TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
**
90114040 TATGAAACGTAGGTATGGTATTAACCATACTGAG
1 TATGAAACGTAGGTATGGTATTGTCCATACTGAG
90114074 TTGTGAATCG
Statistics
Matches: 204, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
34 6 0.03
35 191 0.94
36 7 0.03
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (35 bp):
TATGAAACGTAGGTATGGTATTGTCCATACTGAGC
Found at i:90113992 original size:105 final size:105
Alignment explanation
Indices: 90113791--90114069 Score: 389
Period size: 105 Copynumber: 2.7 Consensus size: 105
90113781 ATCCATGGCA
* * * * *
90113791 AAGTTATGACACATAGGTAT-AGTATTGTCCATAGTGAGCTATGACACGTAGGTATAGTATTATC
1 AAGTTATGAAACGTAGGTATGA-TATTGTCCATACTGAGCTATGAAACGTAGGTATGGTATTATC
* **
90113855 TATACCGAGCTATAATACGTAGGTATGATATTTCCCATATT
65 CATACCGAGCTATAATACGTAGGTATGATATTTCCCATACC
* * * *
90113896 GAGTTGTGAAACGTAGGTATGATATTGTCCATACTGAGCTATGAAACATATGTATGGTATTATCC
1 AAGTTATGAAACGTAGGTATGATATTGTCCATACTGAGCTATGAAACGTAGGTATGGTATTATCC
* * *
90113961 ATACCGAGCTATAATACGTAGTTATGGTATTTCTCATACC
66 ATACCGAGCTATAATACGTAGGTATGATATTTCCCATACC
* *
90114001 AAGTTATGAAACGTAGGTATGGTATTGTCCATACTGAGCTATGAAACGTAGGTATGGTATTAACC
1 AAGTTATGAAACGTAGGTATGATATTGTCCATACTGAGCTATGAAACGTAGGTATGGTATTATCC
90114066 ATAC
66 ATAC
90114070 TGAGTTGTGA
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
105 151 0.99
106 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (105 bp):
AAGTTATGAAACGTAGGTATGATATTGTCCATACTGAGCTATGAAACGTAGGTATGGTATTATCC
ATACCGAGCTATAATACGTAGGTATGATATTTCCCATACC
Found at i:90114844 original size:46 final size:46
Alignment explanation
Indices: 90114766--90115683 Score: 1703
Period size: 46 Copynumber: 20.0 Consensus size: 46
90114756 TTATCTTTGA
* * * * * * *
90114766 CATGATGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* ** * *
90114812 CATGTTGCCATGGAATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
90114858 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90114904 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90114950 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90114996 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115042 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115088 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115134 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115180 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115226 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115272 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115318 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115364 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115410 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115456 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115502 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115548 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115594 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
90115640 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
90115684 TTCAGAGAGC
Statistics
Matches: 856, Mismatches: 15, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
45 4 0.00
46 852 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:90122931 original size:21 final size:22
Alignment explanation
Indices: 90122892--90122932 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
90122882 CCGAATTGGT
90122892 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
90122914 CACACGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
90122933 GTGTCTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.44, G:0.29, T:0.17
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:90123520 original size:30 final size:30
Alignment explanation
Indices: 90123453--90123522 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
90123443 TTTAATAGTC
*
90123453 TATAATTTT-ATAATTTTTAAAGGATTAAA
1 TATAATTTTAATAATTTTTAAAGGACTAAA
* *
90123482 TCAAAATTTTAAT-ATTTTTAAAGGGCTAAA
1 T-ATAATTTTAATAATTTTTAAAGGACTAAA
90123512 GTATAATTTTA
1 -TATAATTTTA
90123523 CTTTTACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 1 0.03
30 30 0.88
31 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (30 bp):
TATAATTTTAATAATTTTTAAAGGACTAAA
Found at i:90124737 original size:2 final size:2
Alignment explanation
Indices: 90124730--90124756 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
90124720 ATCGTAATTT
90124730 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
90124757 TTCAATGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90142959 original size:18 final size:18
Alignment explanation
Indices: 90142936--90142976 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
90142926 TTAACCAGAC
* *
90142936 TTTATTAGATGTTTATGT
1 TTTATTAGATATTTATAT
*
90142954 TTTATTAGCTATTTATAT
1 TTTATTAGATATTTATAT
90142972 TTTAT
1 TTTAT
90142977 ATAAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (18 bp):
TTTATTAGATATTTATAT
Found at i:90147446 original size:27 final size:26
Alignment explanation
Indices: 90147398--90147664 Score: 313
Period size: 27 Copynumber: 9.9 Consensus size: 26
90147388 GTGAAGCTGC
* *
90147398 CAGATATTGTGAC-GAAGTCACCAGAAA
1 CAGATATTGTGGCAG-AGCCACCAG-AA
90147425 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
90147451 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAA
* *
90147478 CAGATAATCGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCAGAGCCACCAGAA
*
90147505 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAA
* *
90147532 CAGATAATCGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCAGAGCCACCAGAA
*
90147559 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAA
* *
90147586 CAGATAATCGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCAGAGCCACCAGAA
*
90147613 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAA
90147640 CAGATAATTGTGGC-GTAGCCACCAG
1 CAGAT-ATTGTGGCAG-AGCCACCAG
90147665 GACGCTTCCT
Statistics
Matches: 209, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.08
27 184 0.88
28 9 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:90147492 original size:54 final size:54
Alignment explanation
Indices: 90147416--90147664 Score: 437
Period size: 54 Copynumber: 4.6 Consensus size: 54
90147406 GTGACGAAGT
* * *
90147416 CACCAGAAACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAG-ATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
90147470 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
90147524 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
90147578 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
90147632 CACCAGATCAGATAATTGTGGCGTAGCCACCAG
1 CACCAGATCAGATAATCGTGGCATAGCCACCAG
90147665 GACGCTTCCT
Statistics
Matches: 189, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
53 6 0.03
54 183 0.97
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (54 bp):
CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:90149314 original size:26 final size:26
Alignment explanation
Indices: 90149283--90149390 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
90149273 TGAAATGTCC
*
90149283 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
90149309 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
90149335 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
90149361 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
90149387 ATCA
1 ATCA
90149391 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:90150317 original size:15 final size:15
Alignment explanation
Indices: 90150296--90150332 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
90150286 AACTATTTTA
90150296 AGGTTTAGGGATTAT
1 AGGTTTAGGGATTAT
*
90150311 GGGTTTAGGGATTAT
1 AGGTTTAGGGATTAT
90150326 AGGTTTA
1 AGGTTTA
90150333 AAGGTTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (15 bp):
AGGTTTAGGGATTAT
Found at i:90150830 original size:21 final size:21
Alignment explanation
Indices: 90150806--90150879 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
90150796 GCAAATCTCT
*
90150806 AACCGTAAACCCTAAACTATA
1 AACCTTAAACCCTAAACTATA
*
90150827 AACCTTAAACCATAAA-TATTA
1 AACCTTAAACCCTAAACTA-TA
* * *
90150848 AACCTTGAATCCTAAACCATAA
1 AACCTTAAACCCTAAACTAT-A
*
90150870 AACCCTAAAC
1 AACCTTAAAC
90150880 TATAGATAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.05
21 30 0.73
22 9 0.22
ACGTcount: A:0.49, C:0.27, G:0.03, T:0.22
Consensus pattern (21 bp):
AACCTTAAACCCTAAACTATA
Found at i:90151022 original size:21 final size:21
Alignment explanation
Indices: 90150973--90151025 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
90150963 TATAAAACTT
* * *
90150973 AAAACTATGAACCCTAAATCT
1 AAAACCATAAACCCTAAATCC
* *
90150994 TAATCCATAAACCCTAAATCC
1 AAAACCATAAACCCTAAATCC
90151015 AAAACCATAAA
1 AAAACCATAAA
90151026 ACCTTAAACT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAACCATAAACCCTAAATCC
Found at i:90151386 original size:3 final size:3
Alignment explanation
Indices: 90151378--90151424 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
90151368 ATTAATAGTA
90151378 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
90151425 AAGAGAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:90151781 original size:74 final size:74
Alignment explanation
Indices: 90151679--90151824 Score: 181
Period size: 75 Copynumber: 1.9 Consensus size: 74
90151669 TTTTCACTAG
*
90151679 AAAACGCCACAAACATCTATTAATAGATTGCAAAACGA-CGTC-GTTATAACCTTGTTATTAGTG
1 AAAACGCCACAAACATCTA-TAAGAGATTGCAAAAC-ATCGTCAGTTATAACCTT-TTATTAGTG
90151742 GCGCTTTTTAGA
63 GCGCTTTTTAGA
* * * *
90151754 AAAATGCCACAAAACATCTA-AAGAGATTTCAAAACATCGTCATTTTATAGCCTTTTATTAGTGG
1 AAAACGCCAC-AAACATCTATAAGAGATTGCAAAACATCGTCA-GTTATAACCTTTTATTAGTGG
90151818 CGCTTTT
64 CGCTTTT
90151825 ATAAACACCA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
73 1 0.02
74 17 0.27
75 26 0.42
76 18 0.29
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (74 bp):
AAAACGCCACAAACATCTATAAGAGATTGCAAAACATCGTCAGTTATAACCTTTTATTAGTGGCG
CTTTTTAGA
Found at i:90151814 original size:188 final size:187
Alignment explanation
Indices: 90151541--90151953 Score: 453
Period size: 188 Copynumber: 2.2 Consensus size: 187
90151531 TTTTGAAGCT
**
90151541 TTGTTATTAGTGGCGCTTTTCAAAAAACGCCACAAAACATCTATTAAGAAAATGTAAAATGGCGT
1 TTGTTATTAGTGGCGCTTTTCAAAAAACGCCACAAAACATCTA-TAAGAAAATGTAAAACAGCGT
* * * * *
90151606 CGTTTACATCCTTGTTATTAGTGGCGCTTCTATAAACGCCGCAACAGGTGTGAATTA-TCGGCGT
65 CGTTTACAGCCTTGTTATTAGTGGCGCTTCTATAAACACCACAAAAGGTGTGAAATACT-GGCGT
* * *
90151670 TTTCACTAGAAAACGCCACAAACATCTATTAATAGATTGCAAAACGACGTCGTTATAACC
129 TTTCACCAG-AAACACCACAAAAATCTATTAATAGATTGCAAAACGACGTCGTTATAACC
* * * * *
90151730 TTGTTATTAGTGGCGCTTTTTAGAAAAATGCCACAAAACATCTA-AAG-AGATTTCAAAACATCG
1 TTGTTATTAGTGGCGCTTTTCA-AAAAACGCCACAAAACATCTATAAGAAAATGT-AAAACAGCG
* * *
90151793 TCATTTTATAGCCTT-TTATTAGTGGCGCTTTTATAAACACCACAAAAGGTGTGAAATACTGGCG
64 TC-GTTTACAGCCTTGTTATTAGTGGCGCTTCTATAAACACCACAAAAGGTGTGAAATACTGGCG
** * * *
90151857 TTTTCACCAGAAACACCACAAAAATCTATTACCAGATTGTAAAAACTG-CGTCGTTTGTATCC
128 TTTTCACCAGAAACACCACAAAAATCTATTAATAGATTG-CAAAAC-GACGTCG-TTATAACC
* * *
90151919 TTCTAATTAGTGGC-ATTTT-ATAAAAACGCCACAAA
1 TTGTTATTAGTGGCGCTTTTCA-AAAAACGCCACAAA
90151954 TATTTATTAA
Statistics
Matches: 189, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
187 43 0.23
188 76 0.40
189 50 0.26
190 20 0.11
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (187 bp):
TTGTTATTAGTGGCGCTTTTCAAAAAACGCCACAAAACATCTATAAGAAAATGTAAAACAGCGTC
GTTTACAGCCTTGTTATTAGTGGCGCTTCTATAAACACCACAAAAGGTGTGAAATACTGGCGTTT
TCACCAGAAACACCACAAAAATCTATTAATAGATTGCAAAACGACGTCGTTATAACC
Found at i:90154075 original size:24 final size:24
Alignment explanation
Indices: 90154048--90154094 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
90154038 ATTATTATTG
*
90154048 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
90154072 AAATATTATCGTCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
90154095 TTTAAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:90154331 original size:15 final size:14
Alignment explanation
Indices: 90154309--90154433 Score: 68
Period size: 15 Copynumber: 9.2 Consensus size: 14
90154299 TCAATCTTAT
90154309 TTTAATTAATATAA
1 TTTAATTAATATAA
*
90154323 TTTAGATTAAT-TTA
1 TTTA-ATTAATATAA
*
90154337 TTT-A--AATATTA
1 TTTAATTAATATAA
90154348 TTTAATTAATATAA
1 TTTAATTAATATAA
* * *
90154362 TTTGGATTGAT-TTA
1 TTT-AATTAATATAA
* *
90154376 TCT-A--AATATTA
1 TTTAATTAATATAA
90154387 TTTAATTAATATAA
1 TTTAATTAATATAA
* *
90154401 TTTTTATAAATATAA
1 -TTTAATTAATATAA
*
90154416 TTTAAATTAAAATAA
1 TTT-AATTAATATAA
90154431 TTT
1 TTT
90154434 TTTTCCATGT
Statistics
Matches: 85, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 5 0.06
11 11 0.13
12 4 0.05
14 31 0.36
15 34 0.40
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (14 bp):
TTTAATTAATATAA
Found at i:90154334 original size:19 final size:18
Alignment explanation
Indices: 90154310--90154425 Score: 67
Period size: 19 Copynumber: 6.2 Consensus size: 18
90154300 CAATCTTATT
90154310 TTAATTAATATAATTTAGA
1 TTAATTAATATAATTTA-A
* * *
90154329 TTAATTTATTTAAATATTAT
1 TTAATTAATAT-AAT-TTAA
*
90154349 TTAATTAATATAATTTGGA
1 TTAATTAATATAATTT-AA
* * * *
90154368 TTGATTTATCTAAATATTAT
1 TTAATTAATAT-AAT-TTAA
90154388 TTAATTAATATAATTT--
1 TTAATTAATATAATTTAA
*
90154404 TT-ATAAATATAATTTAAA
1 TTAATTAATATAATTT-AA
90154422 TTAA
1 TTAA
90154426 AATAATTTTT
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
15 12 0.17
16 2 0.03
18 6 0.08
19 24 0.33
20 23 0.32
21 5 0.07
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (18 bp):
TTAATTAATATAATTTAA
Found at i:90154341 original size:24 final size:24
Alignment explanation
Indices: 90154309--90154363 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
90154299 TCAATCTTAT
90154309 TTTAATT-AATATAATTTAGATTAA
1 TTTAATTAAATATAATTTA-ATTAA
* *
90154333 TTTATTTAAATATTATTTAATTAA
1 TTTAATTAAATATAATTTAATTAA
*
90154357 TATAATT
1 TTTAATT
90154364 TGGATTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAATTAAATATAATTTAATTAA
Found at i:90154353 original size:39 final size:39
Alignment explanation
Indices: 90154309--90154403 Score: 163
Period size: 39 Copynumber: 2.4 Consensus size: 39
90154299 TCAATCTTAT
*
90154309 TTTAATTAATATAATTTAGATTAATTTATTTAAATATTA
1 TTTAATTAATATAATTTAGATTAATTTATCTAAATATTA
* *
90154348 TTTAATTAATATAATTTGGATTGATTTATCTAAATATTA
1 TTTAATTAATATAATTTAGATTAATTTATCTAAATATTA
90154387 TTTAATTAATATAATTT
1 TTTAATTAATATAATTT
90154404 TTATAAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (39 bp):
TTTAATTAATATAATTTAGATTAATTTATCTAAATATTA
Found at i:90154354 original size:20 final size:20
Alignment explanation
Indices: 90154329--90154400 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
90154319 ATAATTTAGA
*
90154329 TTAATTTATTTAAATATTAT
1 TTAATTTATATAAATATTAT
*
90154349 TTAATTAATAT-AAT-TTGGA-
1 TTAATTTATATAAATATT--AT
* *
90154368 TTGATTTATCTAAATATTAT
1 TTAATTTATATAAATATTAT
*
90154388 TTAATTAATATAA
1 TTAATTTATATAA
90154401 TTTTTATAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
18 2 0.05
19 12 0.31
20 23 0.59
21 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (20 bp):
TTAATTTATATAAATATTAT
Found at i:90154364 original size:25 final size:25
Alignment explanation
Indices: 90154316--90154364 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
90154306 TATTTTAATT
*
90154316 AATATAATTTAGATTAATTTATTTA
1 AATATAATTTAGATTAATTAATTTA
*
90154341 AATATTATTTA-ATTAATATAATTT
1 AATATAATTTAGATTAAT-TAATTT
90154365 GGATTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATAATTTAGATTAATTAATTTA
Found at i:90154410 original size:29 final size:30
Alignment explanation
Indices: 90154378--90154435 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
90154368 TTGATTTATC
* *
90154378 TAAATATTATTT-AATTAATATAATTTTTA
1 TAAATATAATTTAAATTAAAATAATTTTTA
90154407 TAAATATAATTTAAATTAAAATAATTTTT
1 TAAATATAATTTAAATTAAAATAATTTTT
90154436 TTCCATGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TAAATATAATTTAAATTAAAATAATTTTTA
Found at i:90154723 original size:9 final size:9
Alignment explanation
Indices: 90154706--90154738 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
90154696 TATATACTTG
90154706 AACTTACAT
1 AACTTACAT
*
90154715 AACTCACAT
1 AACTTACAT
90154724 AACTTACAT
1 AACTTACAT
90154733 AACTTA
1 AACTTA
90154739 ATTATACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:90156257 original size:13 final size:14
Alignment explanation
Indices: 90156241--90156269 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
90156231 TTATAAATAT
90156241 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
90156254 TTATAATGGTTTAA
1 TTATAATGGTTTAA
90156268 TT
1 TT
90156270 TGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:90156710 original size:21 final size:21
Alignment explanation
Indices: 90156682--90156744 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
90156672 TAGAGCGGAT
90156682 GCAGCAGCGAGGGAGGCAGCA-
1 GCAGCAGCGAGGGAGGCAG-AG
** *
90156703 TTAGCAGCGAGAGAGGCAGAG
1 GCAGCAGCGAGGGAGGCAGAG
90156724 GCAGCAGCGAGGGAGGCAGAG
1 GCAGCAGCGAGGGAGGCAGAG
90156745 CAAAGCAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.30, C:0.19, G:0.48, T:0.03
Consensus pattern (21 bp):
GCAGCAGCGAGGGAGGCAGAG
Found at i:90157028 original size:31 final size:31
Alignment explanation
Indices: 90156986--90157046 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
90156976 TTTAATTTTT
*
90156986 ATGCTACATTTGCTGTTTTTGGTTGGATTTC
1 ATGCTACATTTGCTGTTATTGGTTGGATTTC
*
90157017 ATGCTATATTTGCTGTTATTGGTTGGATTT
1 ATGCTACATTTGCTGTTATTGGTTGGATTT
90157047 AATGTAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.52
Consensus pattern (31 bp):
ATGCTACATTTGCTGTTATTGGTTGGATTTC
Found at i:90157175 original size:43 final size:43
Alignment explanation
Indices: 90157127--90157409 Score: 386
Period size: 43 Copynumber: 6.6 Consensus size: 43
90157117 AAAAAGCGCT
*
90157127 GCTAAAAGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
1 GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
* *
90157170 GCTAAAAGCCATGACTTTTAGCGGCGCCTCTCCCACAAACGCC
1 GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
** *
90157213 GCTAAAATCCATGACTATTAGCGGCACCTCTCCCACAAACGCC
1 GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
* * * *
90157256 GCTAAAGGCCATGCCTAGTAGCGGCGCTTCTCTCACAAACGCC
1 GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
** * *
90157299 GCTAAAGGCCATGACTATTAGCGGCGTTTCTCCCGCAAAAGCC
1 GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
* * * * *
90157342 GCTAAAGGACATGACTTTTAGCAGCGCTTCTCTCACAAACGCC
1 GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
*
90157385 GCTAAAGGCCATGACTTTTAGCGGC
1 GCTAAAGGCCATGACTATTAGCGGC
90157410 ATTTTTTTAA
Statistics
Matches: 214, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 214 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.20
Consensus pattern (43 bp):
GCTAAAGGCCATGACTATTAGCGGCGCCTCTCCCACAAACGCC
Found at i:90159116 original size:18 final size:18
Alignment explanation
Indices: 90159090--90159126 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
90159080 CCAGACTTTG
90159090 TTAGATATTTATATTTTA
1 TTAGATATTTATATTTTA
*
90159108 TTAGCTATTTATATTTTA
1 TTAGATATTTATATTTTA
90159126 T
1 T
90159127 ATAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
TTAGATATTTATATTTTA
Found at i:90171211 original size:44 final size:44
Alignment explanation
Indices: 90171161--90171251 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
90171151 GTATGTCAAA
* *
90171161 TAATATTAAAATAACCTATACTAATCAGAGTTTAAGT-AGGAAAC
1 TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGA-GAAAC
*
90171205 TAATATTAAAATAACTTACACTAATAAGAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGAGAAAC
90171249 TAA
1 TAA
90171252 AAACAGAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGAGAAAC
Found at i:90174358 original size:17 final size:18
Alignment explanation
Indices: 90174316--90174365 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
90174306 CTTTTGGTAA
90174316 CATATTATATATTGTATAGT
1 CATATTATAT-TT-TATAGT
*
90174336 TA-ATTATATTTTATA-T
1 CATATTATATTTTATAGT
90174352 CATATTAT-TTTTAT
1 CATATTATATTTTAT
90174366 GTCGCATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 8 0.30
17 9 0.33
18 2 0.07
19 7 0.26
20 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
CATATTATATTTTATAGT
Found at i:90177699 original size:54 final size:54
Alignment explanation
Indices: 90177619--90177835 Score: 425
Period size: 54 Copynumber: 4.0 Consensus size: 54
90177609 ACACGCCTAA
90177619 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
1 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
90177673 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
1 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
90177727 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
1 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
*
90177781 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATTGAGGACAT
1 TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
90177835 T
1 T
90177836 CTAATGCTAG
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 162 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (54 bp):
TATTATCAAAGAACAATACGCCCAAGCATTCATCCTGAGGTTAATCGAGGACAT
Found at i:90178802 original size:9 final size:9
Alignment explanation
Indices: 90178782--90178812 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
90178772 AAAATATCTT
90178782 ATTAATTTTA
1 ATTAA-TTTA
90178792 ATTAATTTA
1 ATTAATTTA
90178801 ATTAATTTA
1 ATTAATTTA
90178810 ATT
1 ATT
90178813 TTACTTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:90178832 original size:24 final size:24
Alignment explanation
Indices: 90178783--90178829 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
90178773 AAATATCTTA
**
90178783 TTAATTTTAATTAATTTAATTAAT
1 TTAATTTTAATTAATAAAATTAAT
*
90178807 TTAATTTTACTTAATCAAAATTA
1 TTAATTTTAATTAAT-AAAATTA
90178830 TTTTTTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATTTTAATTAATAAAATTAAT
Found at i:90182590 original size:6 final size:6
Alignment explanation
Indices: 90182579--90182603 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90182569 AAAAAAAGAG
90182579 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
90182604 GAACACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:90182879 original size:16 final size:17
Alignment explanation
Indices: 90182858--90182895 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
90182848 TTCTATATGG
*
90182858 ATTTTACT-TTTATTTT
1 ATTTTACTCTGTATTTT
90182874 ATTTTACTGCTGTATTTT
1 ATTTTACT-CTGTATTTT
90182892 ATTT
1 ATTT
90182896 AAATAAGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.68
Consensus pattern (17 bp):
ATTTTACTCTGTATTTT
Done.