Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 57 of 103
Found at i:21700239 original size:123 final size:122
Alignment explanation
Indices: 21700020--21700265 Score: 483
Period size: 123 Copynumber: 2.0 Consensus size: 122
21700010 AAACGGCTAT
21700020 TCGGACATTTTGCATCACATTTCGTGCATTCATATAGATTTATAGAGCCTGAAATAGTTTATGAT
1 TCGGACATTTTGCATCACATTTCGTGCATTCATATAGATTTATAGAGCCTGAAATAGTTTATGAT
21700085 AAATTGACACAATTTATTGAAATTCGTGTCACATATGATGTTGATAATTCTATTTTA
66 AAATTGACACAATTTATTGAAATTCGTGTCACATATGATGTTGATAATTCTATTTTA
21700142 NTCGGACATTTTGCATCACATTTCGTGCATTCATATAGATTTATAGAGCCTGAAATAGTTTATGA
1 -TCGGACATTTTGCATCACATTTCGTGCATTCATATAGATTTATAGAGCCTGAAATAGTTTATGA
21700207 TAAATTGACACAATTTATTGAAATTCGTGTCACATATGATGTTGATAATTCTATTTTA
65 TAAATTGACACAATTTATTGAAATTCGTGTCACATATGATGTTGATAATTCTATTTTA
21700265 T
1 T
21700266 AGAATTATTT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 1 0.01
123 122 0.99
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (122 bp):
TCGGACATTTTGCATCACATTTCGTGCATTCATATAGATTTATAGAGCCTGAAATAGTTTATGAT
AAATTGACACAATTTATTGAAATTCGTGTCACATATGATGTTGATAATTCTATTTTA
Found at i:21701524 original size:14 final size:14
Alignment explanation
Indices: 21701505--21701531 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21701495 TTAGTTTTAA
21701505 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
21701519 TTTTAGTTAATTA
1 TTTTAGTTAATTA
21701532 ATAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:21705371 original size:40 final size:40
Alignment explanation
Indices: 21705311--21705389 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
21705301 TTTGTAAAGG
* *
21705311 CACCAATCGTGGCGAAGTTGAAAACTCCATTGAGGTGAAT
1 CACCAATCGTGGCGAAGTTGAAAACCCCATTAAGGTGAAT
*
21705351 CACCAATCTTGGC-AAGGTTGAAAACCCCATTAAGGTGAA
1 CACCAATCGTGGCGAA-GTTGAAAACCCCATTAAGGTGAA
21705390 AATAGTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (40 bp):
CACCAATCGTGGCGAAGTTGAAAACCCCATTAAGGTGAAT
Found at i:21709185 original size:28 final size:28
Alignment explanation
Indices: 21709152--21709247 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 28
21709142 TTAGCTAGAG
21709152 TAAAAGG-TAAAGAGTTGTGCTAGATCCA
1 TAAAAGGATAAAG-GTTGTGCTAGATCCA
* *
21709180 TAAAAGGCATTGAAGGTTGTGCTTGATCCA
1 TAAAAGG-A-TAAAGGTTGTGCTAGATCCA
* *
21709210 TAAAAGGCATTGTAAATGTTGTGCTTGATCCA
1 TAAAAGG-A---TAAAGGTTGTGCTAGATCCA
21709242 TAAAAG
1 TAAAAG
21709248 ACAATGTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
28 7 0.12
30 23 0.40
31 4 0.07
32 24 0.41
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.29
Consensus pattern (28 bp):
TAAAAGGATAAAGGTTGTGCTAGATCCA
Found at i:21709270 original size:35 final size:32
Alignment explanation
Indices: 21709158--21709281 Score: 135
Period size: 30 Copynumber: 3.8 Consensus size: 32
21709148 AGAGTAAAAG
* *
21709158 GTAAAGAGTTGTGCTAGATCCATAAAAGGCATT
1 GTAAAG-GTTGTGCTTGATCCATAAAAGACATT
*
21709191 G--AAGGTTGTGCTTGATCCATAAAAGGCATT
1 GTAAAGGTTGTGCTTGATCCATAAAAGACATT
*
21709221 GTAAATGTTGTGCTTGATCCATAAAAGACAATGTT
1 GTAAAGGTTGTGCTTGATCCATAAAAGAC-A--TT
* * *
21709256 GTAAAGGTTATGCTTGAGCCTTAAAA
1 GTAAAGGTTGTGCTTGATCCATAAAA
21709282 AGTAGTTTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
30 26 0.33
31 3 0.04
32 24 0.30
33 2 0.03
35 24 0.30
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (32 bp):
GTAAAGGTTGTGCTTGATCCATAAAAGACATT
Found at i:21709740 original size:33 final size:33
Alignment explanation
Indices: 21709703--21709789 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
21709693 TTTTAACGTC
*
21709703 ATATATTTTATTTTTATTTTTTATTATAATCTT
1 ATATATTTTATTTTTATTTTTTAATATAATCTT
* * *
21709736 ATATATTTTATTTTCATTTCTTAATATAATTTT
1 ATATATTTTATTTTTATTTTTTAATATAATCTT
* *
21709769 CTATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
21709790 AATTTTTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 38 0.84
34 7 0.16
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAATATAATCTT
Found at i:21716608 original size:19 final size:17
Alignment explanation
Indices: 21716574--21716612 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
21716564 GATTTGGGAT
*
21716574 TGCTCCCTCTAAATATG
1 TGCTCCCCCTAAATATG
*
21716591 TGCTCCCCCTAAATATA
1 TGCTCCCCCTAAATATG
21716608 TGCTC
1 TGCTC
21716613 TAATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (17 bp):
TGCTCCCCCTAAATATG
Found at i:21718787 original size:42 final size:42
Alignment explanation
Indices: 21718732--21718830 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
21718722 TGTTGATGTG
* * *
21718732 GACCTAGCTATGTGCGAGTAGGAGTGCGCATACGCCGATGAT
1 GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
* ** *
21718774 GACCCGGCTATGTGCGAGTAAGAGTGCGTTTAAGCCGATGCT
1 GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
*
21718816 GACCCAGCCATGTGC
1 GACCCAGCTATGTGC
21718831 TAGTGGGGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.21
Consensus pattern (42 bp):
GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
Found at i:21721601 original size:21 final size:19
Alignment explanation
Indices: 21721571--21721616 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
21721561 GCTGGAGTTG
21721571 AAAGAAGAAGAAAAAGAAGACA
1 AAAG-AGAAGAAAAAGAA-A-A
*
21721593 AAAGAGAAGTAAAAGAAAA
1 AAAGAGAAGAAAAAGAAAA
21721612 AAAGA
1 AAAGA
21721617 AAAGCATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 12 0.52
22 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAGAGAAGAAAAAGAAAA
Found at i:21726262 original size:20 final size:19
Alignment explanation
Indices: 21726239--21726288 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
21726229 AAATTGGGAA
*
21726239 AAAACAGAAAGAAAAAGAAT
1 AAAA-AGAAAGAAAAAGAAG
*
21726259 AAAAATCAAAGAAAAAGAAG
1 AAAAA-GAAAGAAAAAGAAG
21726279 AAAAAAGAAA
1 -AAAAAGAAA
21726289 AATCATCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 5 0.20
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAGAAG
Found at i:21728387 original size:37 final size:37
Alignment explanation
Indices: 21728336--21728417 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
21728326 AATGCAATAT
* * *
21728336 CATCATCATGTGTGCACTCCTTACTCGCACACTTCAA
1 CATCATCATCTGTGCACTCCCTACTCGCACACTCCAA
21728373 CATCATCATCTGTGCACTCCCTACTCGCACACTCCAA
1 CATCATCATCTGTGCACTCCCTACTCGCACACTCCAA
21728410 CATCATCA
1 CATCATCA
21728418 CACAACATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.26, C:0.39, G:0.09, T:0.27
Consensus pattern (37 bp):
CATCATCATCTGTGCACTCCCTACTCGCACACTCCAA
Found at i:21729041 original size:2 final size:2
Alignment explanation
Indices: 21729034--21729074 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
21729024 GGAAAGTCTT
*
21729034 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21729075 AAAATGTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:21729299 original size:20 final size:20
Alignment explanation
Indices: 21729274--21729313 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21729264 AGAAGAAGAA
21729274 GAAGCTACTGGAAAAATGAG
1 GAAGCTACTGGAAAAATGAG
* *
21729294 GAAGCTGCTGGAGAAATGAG
1 GAAGCTACTGGAAAAATGAG
21729314 ATATTTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (20 bp):
GAAGCTACTGGAAAAATGAG
Found at i:21730755 original size:23 final size:22
Alignment explanation
Indices: 21730711--21730755 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21730701 TAGGGGAAAA
*
21730711 AGAAAGTAGAAGAATTTTAGGG
1 AGAAAGTAGAAGAATTTAAGGG
*
21730733 AGAAAGTAGAAGTGATTTAAGGG
1 AGAAAGTAGAAG-AATTTAAGGG
21730756 TAATTTAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (22 bp):
AGAAAGTAGAAGAATTTAAGGG
Found at i:21731584 original size:73 final size:73
Alignment explanation
Indices: 21731494--21731694 Score: 285
Period size: 73 Copynumber: 2.8 Consensus size: 73
21731484 AAAAATTGAG
* * *
21731494 TTCAAAGACAGAGACGACTTAATCGACTAAGAAGCATAGTTAGTTTACTAAGAGCTTACTGCTAC
1 TTCAAAGACAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTTCACTAAGAGCTTACTGCCAC
21731559 AAACTGAA
66 AAACTGAA
* * * * *
21731567 TTCAGAGACAAAGACGACTTAATCCACTAAGAAGCATAGTTAGTACACTAATAGCTTACTGCCAG
1 TTCAAAGACAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTTCACTAAGAGCTTACTGCCAC
* **
21731632 AAATTGGG
66 AAACTGAA
* *
21731640 TTCAAAGACAAAGATGACTTAATCGACTAAGAAGCATAGTTAGTTGACTAAGAGC
1 TTCAAAGACAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTTCACTAAGAGC
21731695 ATTCGATCTG
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (73 bp):
TTCAAAGACAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTTCACTAAGAGCTTACTGCCAC
AAACTGAA
Found at i:21734526 original size:20 final size:20
Alignment explanation
Indices: 21734501--21734538 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21734491 GTCAAATTTT
*
21734501 CTTTAACCGATTATGAACAC
1 CTTTAACCAATTATGAACAC
21734521 CTTTAACCAATTATGAAC
1 CTTTAACCAATTATGAAC
21734539 TTACTGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (20 bp):
CTTTAACCAATTATGAACAC
Found at i:21740433 original size:21 final size:22
Alignment explanation
Indices: 21740408--21740448 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21740398 CCTAGGTGGA
21740408 AAAATTCAAGG-GAAAAGTGTG
1 AAAATTCAAGGAGAAAAGTGTG
*
21740429 AAAATTCAAGGAGATAAGTG
1 AAAATTCAAGGAGAAAAGTG
21740449 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.20
Consensus pattern (22 bp):
AAAATTCAAGGAGAAAAGTGTG
Found at i:21740454 original size:22 final size:21
Alignment explanation
Indices: 21740407--21740454 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21740397 CCCTAGGTGG
*
21740407 AAAAATTCAAGGGAAAAGTGT
1 AAAAATTCAAGGGAAAAGTGA
* *
21740428 GAAAATTCAAGGAGATAAGTGA
1 AAAAATTCAAGG-GAAAAGTGA
21740450 AAAAA
1 AAAAA
21740455 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAAATTCAAGGGAAAAGTGA
Found at i:21743666 original size:31 final size:31
Alignment explanation
Indices: 21743623--21743681 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
21743613 TAATCATAAG
**
21743623 GGCTAATTTAGCTTTAAATAAAAATATAAAA
1 GGCTAATTTAGCTCAAAATAAAAATATAAAA
* *
21743654 GGCTTATTTAGCTCAAAATAAAAGTATA
1 GGCTAATTTAGCTCAAAATAAAAATATA
21743682 TGGGATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (31 bp):
GGCTAATTTAGCTCAAAATAAAAATATAAAA
Found at i:21744388 original size:23 final size:23
Alignment explanation
Indices: 21744369--21744412 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21744359 GTGCAACAGG
21744369 CACAATTATTTATTTCCAACAAA
1 CACAATTATTTATTTCCAACAAA
* *
21744392 CATAATTATTTGTTTCCAACA
1 CACAATTATTTATTTCCAACA
21744413 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (23 bp):
CACAATTATTTATTTCCAACAAA
Found at i:21750549 original size:32 final size:32
Alignment explanation
Indices: 21750513--21750633 Score: 102
Period size: 32 Copynumber: 3.7 Consensus size: 32
21750503 TTGTAGGTTG
21750513 TGGTTGAGCCTTTGAAAAACCACTTTTGATTT
1 TGGTTGAGCCTTTGAAAAACCACTTTTGATTT
** * *
21750545 TGGTTGAGCCCGTGAAAAACCA-TTGTGAAAAGTTG
1 TGGTTGAGCCTTTGAAAAACCACTTTTG---A-TTT
* * *
21750580 TGGTTGAGCCTTTAAAAAACCACTTTGGGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTTGATTT
* *
21750612 TGGTTTA-TCTTGTGAAAAACCA
1 TGGTTGAGCCTT-TGAAAAACCA
21750634 TTGCTAAAGG
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
31 7 0.10
32 37 0.54
34 1 0.01
35 21 0.30
36 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (32 bp):
TGGTTGAGCCTTTGAAAAACCACTTTTGATTT
Found at i:21750598 original size:35 final size:33
Alignment explanation
Indices: 21750509--21750604 Score: 106
Period size: 32 Copynumber: 2.9 Consensus size: 33
21750499 ATTGTTGTAG
*
21750509 GTTGTGGTTGAGCCTTTGAAAAACCACTTTTGA
1 GTTGTGGTTGAGCCTTTGAAAAACCACTTGTGA
* **
21750542 -TTTTGGTTGAGCCCGTGAAAAACCA-TTGTGAAAA
1 GTTGTGGTTGAGCCTTTGAAAAACCACTTGTG---A
*
21750576 GTTGTGGTTGAGCCTTTAAAAAACCACTT
1 GTTGTGGTTGAGCCTTTGAAAAACCACTT
21750605 TGGGTTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
31 4 0.08
32 22 0.44
34 1 0.02
35 21 0.42
36 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (33 bp):
GTTGTGGTTGAGCCTTTGAAAAACCACTTGTGA
Found at i:21750655 original size:67 final size:67
Alignment explanation
Indices: 21750507--21750657 Score: 196
Period size: 67 Copynumber: 2.3 Consensus size: 67
21750497 TCATTGTTGT
* *
21750507 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTTGATTTTGGTTGAGCCCGTGAAAAACCATTGTG
1 AGGTTGTGGTTGAGCCTTTAAAAAACCACTTTGGATTTTGGTTGAGCCCGTGAAAAACCATTGTG
21750572 AA
66 AA
* * * * **
21750574 AAGTTGTGGTTGAGCCTTTAAAAAACCACTTTGGGTTTTGGTTTATCTTGTGAAAAACCATTGCT
1 AGGTTGTGGTTGAGCCTTTAAAAAACCACTTTGGATTTTGGTTGAGCCCGTGAAAAACCATTG-T
21750639 -AA
65 GAA
* *
21750641 AGGTTTTGGCTGAGCCT
1 AGGTTGTGGTTGAGCCT
21750658 ACGAAAAGCC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
67 71 0.99
68 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTTAAAAAACCACTTTGGATTTTGGTTGAGCCCGTGAAAAACCATTGTG
AA
Found at i:21765071 original size:20 final size:20
Alignment explanation
Indices: 21765046--21765086 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21765036 TAATGAATGT
* *
21765046 TTGATGATGATTGATAATAC
1 TTGATGATAATTGAGAATAC
21765066 TTGATGATAATTGAGAATAC
1 TTGATGATAATTGAGAATAC
21765086 T
1 T
21765087 GCTTGAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGATGATAATTGAGAATAC
Found at i:21767649 original size:35 final size:35
Alignment explanation
Indices: 21767610--21767790 Score: 151
Period size: 35 Copynumber: 5.3 Consensus size: 35
21767600 TGATCCCGAT
* *
21767610 AAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTG
1 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTGTG
* * *
21767645 AAAAACCACT-TTG--GGTTTTGGTTGAGCCCGTG
1 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTGTG
* *
21767677 AAAAACCATTG-TGAAAGGTTATGGTTGAGCCTTTG
1 AAAAACCATTGTTG-AAGGTTGTGGTTGAGCCTGTG
* * * *
21767712 AAAAACCACT-TT--AGGTTTTGGTTGATCCCGTG
1 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTGTG
* * * **
21767744 AAAAACCATTGCTAAAGGTTGTGGCTGAGCCTACG
1 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTGTG
*
21767779 AAAAGCCATTGT
1 AAAAACCATTGT
21767791 AAAAGCTTGG
Statistics
Matches: 115, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
32 52 0.45
33 1 0.01
34 3 0.03
35 59 0.51
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (35 bp):
AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTGTG
Found at i:21767667 original size:67 final size:66
Alignment explanation
Indices: 21767588--21767775 Score: 279
Period size: 67 Copynumber: 2.8 Consensus size: 66
21767578 AAGTTGGTTA
*
21767588 TTGGGTTTTGGTTGATCCCGAT-AAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGGTTTTGGTTGATCCCG-TGAAAAACCATTG-TGAAGGTTGTGGTTGAGCCTTTGAAAAACC
21767652 ACT
64 ACT
* *
21767655 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTATGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTG-AAGGTTGTGGTTGAGCCTTTGAAAAACCA
21767720 CT
65 CT
* * *
21767722 TTAGGTTTTGGTTGATCCCGTGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCT
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTG-TGAAGGTTGTGGTTGAGCCT
21767776 ACGAAAAGCC
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
66 3 0.03
67 106 0.96
68 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (66 bp):
TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTGAAGGTTGTGGTTGAGCCTTTGAAAAACCAC
T
Found at i:21767672 original size:32 final size:32
Alignment explanation
Indices: 21767588--21767751 Score: 152
Period size: 32 Copynumber: 4.9 Consensus size: 32
21767578 AAGTTGGTTA
* *
21767588 TTGGGTTTTGGTTGATCCCGAT-AAAAACCATT
1 TTGGGTTTTGGTTGAGCCCG-TGAAAAACCACT
* **
21767620 GTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCACT
1 -TTG--GGTTTTGGTTGAGCCCGTGAAAAACCACT
21767655 TTGGGTTTTGGTTGAGCCCGTGAAAAACCA-T
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCACT
* **
21767686 TGTGAAAGGTTATGGTTGAGCCTTTGAAAAACCACT
1 T-TG---GGTTTTGGTTGAGCCCGTGAAAAACCACT
* *
21767722 TTAGGTTTTGGTTGATCCCGTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCA
21767752 TTGCTAAAGG
Statistics
Matches: 107, Mismatches: 16, Indels: 17
0.76 0.11 0.12
Matches are distributed among these distances:
31 2 0.02
32 49 0.46
33 3 0.03
34 4 0.04
35 47 0.44
36 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (32 bp):
TTGGGTTTTGGTTGAGCCCGTGAAAAACCACT
Found at i:21770966 original size:2 final size:2
Alignment explanation
Indices: 21770954--21770999 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
21770944 AAATAAAAGG
*
21770954 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21770996 TA TA
1 TA TA
21771000 ACTTCATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21771470 original size:21 final size:22
Alignment explanation
Indices: 21771439--21771504 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
21771429 AATTTTAATC
21771439 ATAATAATATTTAA-ATTATAAA
1 ATAATAATA-TTAATATTATAAA
*
21771461 ATAA-AATATTAATATTTTAAA
1 ATAATAATATTAATATTATAAA
**
21771482 ATGCTAATGATTAA-ATTATAAA
1 ATAATAAT-ATTAATATTATAAA
21771504 A
1 A
21771505 AACATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 13 0.35
22 15 0.41
23 5 0.14
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (22 bp):
ATAATAATATTAATATTATAAA
Found at i:21771537 original size:41 final size:43
Alignment explanation
Indices: 21771443--21771541 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 43
21771433 TTAATCATAA
21771443 TAATATTTAAATTATAAAATAAAATATTAATATTTTAAAATGC
1 TAATATTTAAATTATAAAATAAAATATTAATATTTTAAAATGC
* * **
21771486 TAATGA-TTAAATTATAAAA-AACATA-TAATATTTTAAATTTT
1 TAAT-ATTTAAATTATAAAATAAAATATTAATATTTTAAAATGC
21771527 TAATATTTAAATTAT
1 TAATATTTAAATTAT
21771542 CAATTAGTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 1 0.02
41 26 0.52
42 5 0.10
43 17 0.34
44 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (43 bp):
TAATATTTAAATTATAAAATAAAATATTAATATTTTAAAATGC
Found at i:21771644 original size:34 final size:33
Alignment explanation
Indices: 21771605--21771716 Score: 100
Period size: 34 Copynumber: 3.2 Consensus size: 33
21771595 TACAATAAAA
*
21771605 ATTTTAATTTTTTAATTATATATATAATATTAAT
1 ATTTTAATTTTATAA-TATATATATAATATTAAT
* * * *
21771639 ATTTTAAATTTA-AAAATAAATTAAAATTATTAAT
1 ATTTTAATTTTATAATATATA-TATAA-TATTAAT
*
21771673 ATTTTAATTATTATAATATTAAAATATTAATATTAAT
1 ATTTTAATT-TTATAATA-T-ATATA-TAATATTAAT
21771710 ATTTTAA
1 ATTTTAA
21771717 AATGTTAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
32 4 0.06
33 6 0.10
34 25 0.40
35 3 0.05
36 3 0.05
37 17 0.27
38 5 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
ATTTTAATTTTATAATATATATATAATATTAAT
Found at i:21771766 original size:16 final size:15
Alignment explanation
Indices: 21771741--21771774 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
21771731 AATTATAAAT
21771741 AAAATATTAATATTTA
1 AAAATATTAATA-TTA
*
21771757 AAAATGTTAATATTA
1 AAAATATTAATATTA
21771772 AAA
1 AAA
21771775 TGATCAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAAATATTAATATTA
Found at i:21771776 original size:14 final size:14
Alignment explanation
Indices: 21771713--21771776 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
21771703 TATTAATATT
21771713 TTAAAATGTTAATGA
1 TTAAAATGTTAAT-A
21771728 TT-AAAT-TATAA-A
1 TTAAAATGT-TAATA
*
21771740 -TAAAATATTAATA
1 TTAAAATGTTAATA
21771753 TTTAAAAATGTTAATA
1 -TT-AAAATGTTAATA
21771769 TTAAAATG
1 TTAAAATG
21771777 ATCAATGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
11 1 0.02
12 8 0.20
13 3 0.07
14 13 0.32
15 5 0.12
16 11 0.27
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
TTAAAATGTTAATA
Found at i:21772416 original size:27 final size:29
Alignment explanation
Indices: 21772356--21772422 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
21772346 TATTATGAGT
*
21772356 ATTTAT-TTTAATTTATAAAATATTATTA
1 ATTTATATTTAATTTATAAAATATTAATA
*
21772384 AGTTATATTTAA-TT-TAAAATATTAATA
1 ATTTATATTTAATTTATAAAATATTAATA
*
21772411 ATTTATAATTAA
1 ATTTATATTTAA
21772423 AATATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.65
28 7 0.21
29 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
ATTTATATTTAATTTATAAAATATTAATA
Found at i:21773014 original size:73 final size:72
Alignment explanation
Indices: 21772908--21773154 Score: 300
Period size: 73 Copynumber: 3.4 Consensus size: 72
21772898 TTAGCCGACC
* * * *
21772908 AAGAAGCATGGTTAGTCGACTAAGTGCTCACTGCCATAAATGGGGTTCAGAGACAGAGACGACTT
1 AAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCATAAAT-GGGTTCAGAGACAAAGACGACTT
21772973 AATCAACT
65 AATCAACT
21772981 AAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCC-TGAAATTGGGTTCAGAGACAAAGACGACT
1 AAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCAT-AAA-TGGGTTCAGAGACAAAGACGACT
*
21773045 TAATCGACT
64 TAATCAACT
* * * * * * *
21773054 AAGAAGCATTGTTAGTCGACTAAGACCTTATTGTCAAAAACTAGGATCAGAAGACATAAAACGAC
1 AAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCATAAA-TGGGTTCAG-AGACA-AAGACGAC
*
21773119 TTAATCTACT
63 TTAATCAACT
*
21773129 AAGAAGTA-TGTTAGTCGACTAAGAGC
1 AAGAAGCATTGTTAGTCGACTAAGAGC
21773155 ACTCTGTCAA
Statistics
Matches: 153, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
72 1 0.01
73 106 0.69
74 23 0.15
75 23 0.15
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (72 bp):
AAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCATAAATGGGTTCAGAGACAAAGACGACTTA
ATCAACT
Found at i:21790107 original size:200 final size:196
Alignment explanation
Indices: 21789705--21790095 Score: 414
Period size: 200 Copynumber: 1.9 Consensus size: 196
21789695 TTCAATAAAT
* *
21789705 TTTTTATAATTTTATTTTAAATTAAATAAATATTTATGATTAACAATTGATCATATCATAGTAAC
1 TTTTTATAATTTTATTTTAAATCAAATAAACATTTATGATTAACAATTGATCATATCATAGTAAC
* * ** * * *
21789770 TAATGATATGGTATGATAACATAATTACATGACCTTTTATTTCAGCACCATATCTAAATTACTTG
66 TAATAACATGACATGATAACATAATTACATGACCTTTTATATCAACACCATATCTAAATTACGTG
* *
21789835 AATATAAAATGATAAATAGAATTTTGATTAATAATAATTAATCAACTGTTATTAATTAAGTTTAC
131 AATATAAAATGATAAATAGAATTTTAATTAATAATAATTAATCAAC--TCATTAATTAA--TTAC
*
21789900 TAAAA
192 AAAAA
* *
21789905 TTTTTATATTTTTATTTTAAATCAAATAAACATTTATGATTAACAATTGATCATATCATAGTGGA
1 TTTTTATAATTTTATTTTAAATCAAATAAACATTTATGATTAACAATTGATCATATCATAGT-AA
* * * * * *
21789970 -TGATAACGTGACATGATAATATTATTACATGATATTTTCACTTTTGATATCAATATCATATC-A
65 CTAATAACATGACATGATAACATAATTACATG--A----C-CTTTT-ATATCAACACCATATCTA
*
21790033 ACATTGCGTGAATAT-AAATGGATAAATA-ATATTTTAATTAATAATAATTAATCAA-TCATTAA
122 A-ATTACGTGAATATAAAAT-GATAAATAGA-ATTTTAATTAATAATAATTAATCAACTCATTAA
21790095 T
184 T
21790096 CATAAAAAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
200 82 0.52
201 1 0.01
202 1 0.01
205 7 0.04
206 1 0.01
207 12 0.08
208 55 0.35
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (196 bp):
TTTTTATAATTTTATTTTAAATCAAATAAACATTTATGATTAACAATTGATCATATCATAGTAAC
TAATAACATGACATGATAACATAATTACATGACCTTTTATATCAACACCATATCTAAATTACGTG
AATATAAAATGATAAATAGAATTTTAATTAATAATAATTAATCAACTCATTAATTAATTACAAAA
A
Found at i:21791093 original size:48 final size:47
Alignment explanation
Indices: 21791013--21791113 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 47
21791003 ACTTAATAAA
* * * *
21791013 AAATAAAGTTAAAAATGCATGTAATTTCATGAATCATATC-ACTTTTC
1 AAATATAGGTAAAAATGAATATAATTTCATGAATCATATCAAC-TTTC
21791060 ATAATATAGGTAAAAATGAATATAATTTCATGAATCATATCAACTTTC
1 A-AATATAGGTAAAAATGAATATAATTTCATGAATCATATCAACTTTC
21791108 AAATAT
1 AAATAT
21791114 TGTAATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 6 0.12
48 40 0.83
49 2 0.04
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (47 bp):
AAATATAGGTAAAAATGAATATAATTTCATGAATCATATCAACTTTC
Found at i:21793393 original size:7 final size:7
Alignment explanation
Indices: 21793381--21793405 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21793371 TTGAATTTCC
21793381 ATGGCAT
1 ATGGCAT
21793388 ATGGCAT
1 ATGGCAT
21793395 ATGGCAT
1 ATGGCAT
21793402 ATGG
1 ATGG
21793406 GACCTCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (7 bp):
ATGGCAT
Found at i:21794614 original size:2 final size:2
Alignment explanation
Indices: 21794607--21794637 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21794597 ACATGAGTTT
21794607 TA TA 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 TA TA T
21794638 CTAAATGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21799446 original size:32 final size:33
Alignment explanation
Indices: 21799407--21799497 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 33
21799397 TTCTTATCCT
*
21799407 CTCTAACCGACGGC-CATAAAACCC-ACCTTGTC
1 CTCTAACCGACAGCAC-TAAAACCCAACCTTGTC
* *
21799439 CTCTAACCGGCAGCACTAAAACCCAAATCTTGTC
1 CTCTAACCGACAGCACTAAAACCC-AACCTTGTC
**
21799473 CTCTAACCGGTAGCACT-AAACCCAA
1 CTCTAACCGACAGCACTAAAACCCAA
21799498 ACTTTCCCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
32 22 0.42
33 7 0.13
34 23 0.44
ACGTcount: A:0.32, C:0.37, G:0.12, T:0.19
Consensus pattern (33 bp):
CTCTAACCGACAGCACTAAAACCCAACCTTGTC
Found at i:21799471 original size:34 final size:33
Alignment explanation
Indices: 21799438--21799633 Score: 181
Period size: 34 Copynumber: 5.8 Consensus size: 33
21799428 CCCACCTTGT
21799438 CCTCTAACCGGC-AGC-ACTAAAACCCAAATCTTGT-
1 CCTCTAACCGGCGA-CAAC-AAAACCCAAA-CTT-TC
* *
21799472 CCTCTAACCGG-TAGC-ACTAAACCCAAACTTTCC
1 CCTCTAACCGGCGA-CAACAAAACCCAAACTTT-C
21799505 CTCTCTAACCGGCGACAACAAAACCCAAACTTTCC
1 C-CTCTAACCGGCGACAACAAAACCCAAACTTT-C
21799540 CTCTCTAACCGGCGACAACAAAACCCAAACTTTC
1 C-CTCTAACCGGCGACAACAAAACCCAAACTTTC
* *
21799574 CCTTTCAACCGGCAACAACAAAACCCAAATCTTGT-
1 CCTCT-AACCGGCGACAACAAAACCCAAA-CTT-TC
* *
21799609 CCTCTAACCAGCGAC-ACTAAACCCA
1 CCTCTAACCGGCGACAACAAAACCCA
21799634 GGCTTTAACA
Statistics
Matches: 144, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
31 1 0.01
32 3 0.02
33 22 0.15
34 59 0.41
35 58 0.40
36 1 0.01
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.18
Consensus pattern (33 bp):
CCTCTAACCGGCGACAACAAAACCCAAACTTTC
Found at i:21799534 original size:35 final size:35
Alignment explanation
Indices: 21799490--21799602 Score: 201
Period size: 35 Copynumber: 3.3 Consensus size: 35
21799480 CGGTAGCACT
21799490 AAACCCAAACTTTCCCTCTCTAACCGGCGACAACA
1 AAACCCAAACTTTCCCTCTCTAACCGGCGACAACA
21799525 AAACCCAAACTTTCCCTCTCTAACCGGCGACAACA
1 AAACCCAAACTTTCCCTCTCTAACCGGCGACAACA
* *
21799560 AAACCCAAACTTTCCCTTTC-AACCGGCAACAACA
1 AAACCCAAACTTTCCCTCTCTAACCGGCGACAACA
21799594 AAACCCAAA
1 AAACCCAAA
21799603 TCTTGTCCTC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
34 22 0.29
35 54 0.71
ACGTcount: A:0.38, C:0.39, G:0.07, T:0.16
Consensus pattern (35 bp):
AAACCCAAACTTTCCCTCTCTAACCGGCGACAACA
Found at i:21800185 original size:12 final size:12
Alignment explanation
Indices: 21800168--21800205 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
21800158 TACACCTTTT
21800168 TTTTTCATTTCA
1 TTTTTCATTTCA
21800180 TTTTTCATTTTCA
1 TTTTTCA-TTTCA
21800193 -TTTTCATTTCA
1 TTTTTCATTTCA
21800204 TT
1 TT
21800206 CATTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTCATTTCA
Found at i:21800192 original size:6 final size:6
Alignment explanation
Indices: 21800169--21800205 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
21800159 ACACCTTTTT
21800169 TTTTCA -TTTCA TTTTTCA TTTTCA TTTTCA -TTTCA TT
1 TTTTCA TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TT
21800206 CATTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 10 0.36
6 13 0.46
7 5 0.18
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCA
Found at i:21800224 original size:28 final size:29
Alignment explanation
Indices: 21800170--21800223 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
21800160 CACCTTTTTT
*
21800170 TTTCATTTCATTTTTCATTTTCATTTTCA
1 TTTCATTTCATTTTTCATGTTCATTTTCA
*
21800199 TTTCA-TTCATTTTTTATGTT-ATTTT
1 TTTCATTTCATTTTTCATGTTCATTTT
21800224 TTGTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTCATTTCATTTTTCATGTTCATTTTCA
Found at i:21811429 original size:13 final size:13
Alignment explanation
Indices: 21811411--21811435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21811401 ATTTTCAAAA
21811411 ATTTTATAAAATT
1 ATTTTATAAAATT
21811424 ATTTTATAAAAT
1 ATTTTATAAAAT
21811436 CNNNNNNNNN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:21815870 original size:19 final size:19
Alignment explanation
Indices: 21815846--21815882 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21815836 GTTTGCATCA
21815846 TAGTTCAAATAATATAAAG
1 TAGTTCAAATAATATAAAG
*
21815865 TAGTTCAACTAATATAAA
1 TAGTTCAAATAATATAAA
21815883 AATTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (19 bp):
TAGTTCAAATAATATAAAG
Found at i:21815957 original size:42 final size:41
Alignment explanation
Indices: 21815866--21816367 Score: 302
Period size: 42 Copynumber: 11.9 Consensus size: 41
21815856 AATATAAAGT
* * *
21815866 AGTTCAACTAATATAAA--AATTTTATATATTTAAGTTTGCATCA
1 AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAGTTT--A-CA
*
21815909 TAGTTCAAGTAATATAAATTAATTGTACAATTATTAGTTTACA
1 -AGTTCAAGTAATATAAATTAATTTTACAATT-TTAGTTTACA
* * *
21815952 AGTTCAAGTAATATAAA--AATTTTATATATTTAAGATTGCATCA
1 AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAG-TT-TA-CA
*
21815995 TAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACA
1 -AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAGTTTACA
* * * * *
21816038 AGTTCAACTAATATTAA-T-ATGTTATATATTTAAGATTGTATCA
1 AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAG-TT-TA-CA
* *
21816081 TAGTTCAAGCAATATAAATTAATTTTACATTTTTTAGTTTACA
1 -AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAGTTTACA
* * * *
21816124 AGTTCAACTAATATAAA--AATTTTATATATTTAAGATTGCATCA
1 AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAG-TT-TA-CA
*
21816167 TAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACA
1 -AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAGTTTACA
* * * *
21816210 AGTTCAATTGATATAAA--AATTTTA-TATATTTA--AT-CA
1 AGTTCAAGTAATATAAATTAATTTTACAAT-TTTAGTTTACA
* *
21816246 TAGTTCAAGTAATATAAATTAATTTTACATTTATTAATTTACA
1 -AGTTCAAGTAATATAAATTAATTTTACAATT-TTAGTTTACA
* * * *
21816289 AGTTCAACTAATATAAA--AATATTATATATTTAAGTTTGCATCA
1 AGTTCAAGTAATATAAATTAATTTTACA-ATTTTAGTTT--A-CA
*
21816332 TAGTTCCAATTAATATAAATTAATTTTAC--TTTTAGT
1 -AGTT-CAAGTAATATAAATTAATTTTACAATTTTAGT
21816368 AATTTACAAA
Statistics
Matches: 363, Mismatches: 56, Indels: 78
0.73 0.11 0.16
Matches are distributed among these distances:
36 2 0.01
37 16 0.04
38 1 0.00
39 12 0.03
40 59 0.16
41 12 0.03
42 84 0.23
43 18 0.05
44 78 0.21
45 22 0.06
46 53 0.15
47 6 0.02
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (41 bp):
AGTTCAAGTAATATAAATTAATTTTACAATTTTAGTTTACA
Found at i:21816011 original size:86 final size:86
Alignment explanation
Indices: 21815866--21816364 Score: 780
Period size: 86 Copynumber: 5.9 Consensus size: 86
21815856 AATATAAAGT
*
21815866 AGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
* * *
21815931 TTGTACAATTATTAGTTTACA
66 TTTTACATTTTTTAGTTTACA
*
21815952 AGTTCAAGTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
21816017 TTTTACATTTTTTAGTTTACA
66 TTTTACATTTTTTAGTTTACA
* * * * *
21816038 AGTTCAACTAATATTAATATGTTATATATTTAAGATTGTATCATAGTTCAAGCAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
21816103 TTTTACATTTTTTAGTTTACA
66 TTTTACATTTTTTAGTTTACA
21816124 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
21816189 TTTTACATTTTTTAGTTTACA
66 TTTTACATTTTTTAGTTTACA
* *
21816210 AGTTCAATTGATATAAAAATTTTATATATTT---A----ATCATAGTTCAAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
* *
21816268 TTTTACATTTATTAATTTACA
66 TTTTACATTTTTTAGTTTACA
* * *
21816289 AGTTCAACTAATATAAAAATATTATATATTTAAGTTTGCATCATAGTTCCAATTAATATAAATTA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTT-CAAGTAATATAAATTA
21816354 ATTTTAC-TTTT
65 ATTTTACATTTT
21816365 AGTAATTTAC
Statistics
Matches: 379, Mismatches: 26, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
79 73 0.19
83 1 0.00
86 283 0.75
87 22 0.06
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (86 bp):
AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
TTTTACATTTTTTAGTTTACA
Found at i:21816254 original size:79 final size:79
Alignment explanation
Indices: 21816163--21816376 Score: 284
Period size: 79 Copynumber: 2.6 Consensus size: 79
21816153 TTAAGATTGC
* * * *
21816163 ATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAATTGATATAAAA
1 ATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAA
*
21816228 ATTTTATATATTTA
66 ATATTATATATTTA
21816242 ATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAA
1 ATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAA
21816307 ATATTATATATTTAA
66 ATATTATATATTT-A
* * *
21816322 GTTTGCATCATAGTTCCAATTAATATAAATTAATTTTACTTTTAGTAATTTACAA
1 ------ATCATAGTT-CAAGTAATATAAATTAATTTTACATTTATTAATTTACAA
21816377 AAAAAAGAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
79 73 0.61
80 1 0.01
86 9 0.08
87 36 0.30
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (79 bp):
ATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAA
ATATTATATATTTA
Found at i:21816279 original size:45 final size:45
Alignment explanation
Indices: 21816230--21816373 Score: 117
Period size: 45 Copynumber: 3.3 Consensus size: 45
21816220 ATATAAAAAT
*
21816230 TTTATATATTTAATCATAGTTCAAGTAATATAAATTAATTTTACA
1 TTTATATATTTAATCATAGTTCAACTAATATAAATTAATTTTACA
*
21816275 TTTAT-TAATTT-A-CA-AGTTCAACTAATATAAA--AATATTATATA
1 TTTATAT-ATTTAATCATAGTTCAACTAATATAAATTAAT-TT-TACA
** * *
21816317 TTTA-AGT-TTGCATCATAGTTCCAATTAATATAAATTAATTTTACT
1 TTTATA-TATTTAATCATAGTT-CAACTAATATAAATTAATTTTACA
21816362 TTTAGTA-ATTTA
1 TTTA-TATATTTA
21816374 CAAAAAAAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
40 3 0.04
41 4 0.05
42 24 0.31
43 5 0.06
44 6 0.08
45 27 0.35
46 4 0.05
47 4 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (45 bp):
TTTATATATTTAATCATAGTTCAACTAATATAAATTAATTTTACA
Found at i:21825025 original size:19 final size:20
Alignment explanation
Indices: 21824991--21825028 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21824981 GTGAGTGGAA
*
21824991 AAAAATAGGTGAAAAGAAAC
1 AAAAATAAGTGAAAAGAAAC
21825011 AAAAATAAGTG-AAAGAAA
1 AAAAATAAGTGAAAAGAAA
21825029 AAGAAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAAATAAGTGAAAAGAAAC
Found at i:21827953 original size:111 final size:110
Alignment explanation
Indices: 21827737--21828169 Score: 557
Period size: 111 Copynumber: 3.8 Consensus size: 110
21827727 GGTGAGTGAC
*
21827737 TGACTTGTGCAATTCATGTGTTGCTTT-GAGGCTTTTGTTTAGTAGTTTTTTAGGTAATGCATGA
1 TGACTTGTGCAATTCATGTGTTG-TTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGT--TGCATGA
*
21827801 CTGGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGTGCG
63 CTGGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
*
21827849 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGG-TTGCATGACT
* * *
21827914 GGTTTTTATATATTGCATTACCTGTTGTAGCGTGAGTGGTGGCGCA
65 GGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
*
21827960 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGT-GTTTTTTAGGGTTGCGTGA-T
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTA-GGTTGCATGACT
* * *
21828023 CGATTTTTATATATTGCGTTACCTGTTGTTATGTATTACGAGAGTGGTTGCACG
65 -GGTTTTTATATATTGCGTTACCTGTTG-TA-G-----CGAGAGTGGTGGCGCG
* * *
21828077 TGACTTGTGCAATTCATGTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTTACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGG-TTGCATGACT
* * * * *
21828142 GGTTGTTATGTATTACGTGACCTATTGT
65 GGTTTTTATATATTGCGTTACCTGTTGT
21828170 TATATATTGC
Statistics
Matches: 286, Mismatches: 21, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
109 1 0.00
110 40 0.14
111 100 0.35
112 50 0.17
113 1 0.00
117 57 0.20
118 36 0.13
119 1 0.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (110 bp):
TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGTTGCATGACTG
GTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
Found at i:21828129 original size:228 final size:222
Alignment explanation
Indices: 21827737--21828155 Score: 594
Period size: 228 Copynumber: 1.9 Consensus size: 222
21827727 GGTGAGTGAC
*
21827737 TGACTTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTTAGTAGTTTTTTAGGTAATGCATGAC
1 TGACTTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGT-ATGCATGAC
* **
21827802 TGGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGTGCGTGACTTGTGCAATTCATG
65 TGATTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCACGTGACTTGTGCAATTCATG
* * * *
21827867 TGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACTGGTTTTTATATATTGCAT
130 TGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCATGACTGGTTGTTATATATTGCAT
21827932 TACCTGTTGTAGCGTGAGTGGTGGCGCA
195 TACCTGTTGTAGCGTGAGTGGTGGCGCA
*
21827960 TGACTTGTGCAATTCATGTGTTG-TTTAGAGGCTTTTGTTCAGT-GTTTTTTAGGGT-TGCGTGA
1 TGACTTGTGCAATTCATGTGTTGCTTT-GAGGCTTTTGTTCAGTAGTTTTTTA-GGTATGCATGA
*
21828022 -TCGATTTTTATATATTGCGTTACCTGTTGTTATGTATTACGAGAGTGGTTGCACGTGACTTGTG
64 CT-GATTTTTATATATTGCGTTACCTGTTG-TA-G-----CGAGAGTGGTGGCACGTGACTTGTG
* *
21828086 CAATTCATGTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTTACTGGTTGTTAT
121 CAATTCATGTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCATGACTGGTTGTTAT
*
21828151 GTATT
186 ATATT
21828156 ACGTGACCTA
Statistics
Matches: 173, Mismatches: 13, Indels: 15
0.86 0.06 0.07
Matches are distributed among these distances:
220 1 0.01
221 32 0.18
222 13 0.08
223 42 0.24
228 85 0.49
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (222 bp):
TGACTTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGTATGCATGACT
GATTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCACGTGACTTGTGCAATTCATGT
GTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCATGACTGGTTGTTATATATTGCATT
ACCTGTTGTAGCGTGAGTGGTGGCGCA
Found at i:21828222 original size:118 final size:118
Alignment explanation
Indices: 21827960--21828209 Score: 315
Period size: 118 Copynumber: 2.1 Consensus size: 118
21827950 TGGTGGCGCA
* * *
21827960 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGT-GTTTTTTAGGGTTGCGTGATC
1 TGACTTGTGCAATTCATCTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTGATC
* * * * * * **
21828024 GATTTTTATATATTGCGTTACCTGTTGTTATGTATTACGAGAGTGGTTGCACG
66 GATTGTTATATATTACGTGACCTATTGTTATATATTACGAGAGCGGTAACACG
* *
21828077 TGACTTGTGCAATTCATGTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTTA-C
1 TGACTTGTGCAATTCATCTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTGATC
* * * *
21828141 TGGTTGTTATGTATTACGTGACCTATTGTTATATATTGCGAGAGCGGTAACGCG
66 -GATTGTTATATATTACGTGACCTATTGTTATATATTACGAGAGCGGTAACACG
*
21828195 TGACTTGTGCCATTC
1 TGACTTGTGCAATTC
21828210 GCCTCTTATT
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
117 43 0.37
118 72 0.63
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.43
Consensus pattern (118 bp):
TGACTTGTGCAATTCATCTGTAGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTGATC
GATTGTTATATATTACGTGACCTATTGTTATATATTACGAGAGCGGTAACACG
Found at i:21832436 original size:13 final size:13
Alignment explanation
Indices: 21832415--21832453 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
21832405 TTCAATTGAT
*
21832415 ACAAGAAGAAGATA
1 ACAAAAAGAAGA-A
21832429 A-AAAAAGAAGAA
1 ACAAAAAGAAGAA
21832441 ACAAAAAGAAGAA
1 ACAAAAAGAAGAA
21832454 TGGGAGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 20 0.87
14 1 0.04
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (13 bp):
ACAAAAAGAAGAA
Found at i:21834518 original size:23 final size:23
Alignment explanation
Indices: 21834485--21834541 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
21834475 AGAATAGGTG
* * *
21834485 AGTCACACGATGCAAGATCATCT
1 AGTCACGCGATCCAAGATCATAT
* *
21834508 AGTCACGCGATCCCATATCATAT
1 AGTCACGCGATCCAAGATCATAT
21834531 AGTCACGCGAT
1 AGTCACGCGAT
21834542 TCAATAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (23 bp):
AGTCACGCGATCCAAGATCATAT
Found at i:21836252 original size:23 final size:23
Alignment explanation
Indices: 21836189--21836252 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
21836179 AGAATAGGTG
* *
21836189 AGTCACGCGATGCAATAGCAACT
1 AGTCACGCGATCCAATATCAACT
* * *
21836212 AGTCATGCGATCCCATATCATCT
1 AGTCACGCGATCCAATATCAACT
21836235 AGTCACGCGATCCAATAT
1 AGTCACGCGATCCAATAT
21836253 GAATTCATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (23 bp):
AGTCACGCGATCCAATATCAACT
Found at i:21837718 original size:49 final size:49
Alignment explanation
Indices: 21837645--21837813 Score: 275
Period size: 49 Copynumber: 3.4 Consensus size: 49
21837635 CATTCATCAT
* * *
21837645 CATAGCTGGATCATCATCATCATCGGTCTATGTGCACTCCCTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCCTATGTGCACTCCCTACTCGCA
* * *
21837694 CATAGCCGAGTCATCATCACCATCGGCCTATGCGCACTCCCTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCCTATGTGCACTCCCTACTCGCA
21837743 CATAGCCGGGTCATCATCATCATCGGCCTATGTGCACTCCCTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCCTATGTGCACTCCCTACTCGCA
*
21837792 CATAGTCGGGTCATCATCATCA
1 CATAGCCGGGTCATCATCATCA
21837814 CACAAGATTA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 110 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (49 bp):
CATAGCCGGGTCATCATCATCATCGGCCTATGTGCACTCCCTACTCGCA
Found at i:21839450 original size:23 final size:23
Alignment explanation
Indices: 21839418--21839483 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
21839408 ATATCACATG
*
21839418 AATGAATACAAAGAATAATATGTA
1 AATG-ATACAAAGAATAATATGGA
21839442 AATGATACAACAAAGAATAATATGGA
1 AATGAT---ACAAAGAATAATATGGA
*
21839468 GATGATAC--AGAATAAT
1 AATGATACAAAGAATAAT
21839484 GTTAGTGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 8 0.22
23 4 0.11
24 4 0.11
26 21 0.57
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.23
Consensus pattern (23 bp):
AATGATACAAAGAATAATATGGA
Found at i:21839456 original size:26 final size:26
Alignment explanation
Indices: 21839425--21839476 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
21839415 ATGAATGAAT
*
21839425 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
*
21839451 ACAAAGAATAATATGGAGATGATACA
1 ACAAAGAATAATATGGAAATGATACA
21839477 GAATAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAATGATACA
Found at i:21841077 original size:24 final size:24
Alignment explanation
Indices: 21841050--21841097 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21841040 TGCATCGCCC
* *
21841050 GCTGGATCTCCAATTGCATTGACT
1 GCTGGATCTCCAACTACATTGACT
*
21841074 GCTGGATCTCTAACTACATTGACT
1 GCTGGATCTCCAACTACATTGACT
21841098 ACATCTGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (24 bp):
GCTGGATCTCCAACTACATTGACT
Found at i:21841135 original size:63 final size:63
Alignment explanation
Indices: 21841036--21841170 Score: 216
Period size: 63 Copynumber: 2.1 Consensus size: 63
21841026 ACTACGTCTG
* * * *
21841036 CATCTGCATCGCCCGCTGGATCTCCAATTGCATTGACTGCTGGATCTCTAACTACATTGACTA
1 CATCTGCATCGACCGCTGGATCTCCAACTGCATTGACTGCTGAATCTCCAACTACATTGACTA
* *
21841099 CATCTGCATCGACCGCTGGATCTCCAACTGCATTGACTGCTGAATCTCCAACTGCATTGACTG
1 CATCTGCATCGACCGCTGGATCTCCAACTGCATTGACTGCTGAATCTCCAACTACATTGACTA
21841162 CATCTGCAT
1 CATCTGCAT
21841171 ATTCATCTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (63 bp):
CATCTGCATCGACCGCTGGATCTCCAACTGCATTGACTGCTGAATCTCCAACTACATTGACTA
Found at i:21841140 original size:24 final size:24
Alignment explanation
Indices: 21841102--21841162 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
21841092 TTGACTACAT
* * *
21841102 CTGCATCGACCGCTGGATCTCCAA
1 CTGCATTGACTGCTGAATCTCCAA
21841126 CTGCATTGACTGCTGAATCTCCAA
1 CTGCATTGACTGCTGAATCTCCAA
21841150 CTGCATTGACTGC
1 CTGCATTGACTGC
21841163 ATCTGCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (24 bp):
CTGCATTGACTGCTGAATCTCCAA
Found at i:21841348 original size:24 final size:24
Alignment explanation
Indices: 21841298--21841348 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
21841288 GCTAGCACCT
* *
21841298 GAAGCAAGAGGAAGGGCAGCAGTA
1 GAAGCAAGAGGAAGAGCAGCAGGA
*
21841322 GAAGCAAGAGGAAGAGCAGCGGGA
1 GAAGCAAGAGGAAGAGCAGCAGGA
21841346 GAA
1 GAA
21841349 ACACCATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.43, T:0.02
Consensus pattern (24 bp):
GAAGCAAGAGGAAGAGCAGCAGGA
Found at i:21863599 original size:23 final size:22
Alignment explanation
Indices: 21863553--21863599 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
21863543 GTGAAGTTCG
* * *
21863553 TTGAAGTATTATATGTATATTA
1 TTGAAGTATTATATGCAAAATA
21863575 TTGAAGCTATTATATGCAAAATA
1 TTGAAG-TATTATATGCAAAATA
21863598 TT
1 TT
21863600 ATGCCTTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (22 bp):
TTGAAGTATTATATGCAAAATA
Found at i:21864279 original size:19 final size:19
Alignment explanation
Indices: 21864257--21864303 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
21864247 AGTAAACAAA
* *
21864257 CAAAAAAATTCAAAAAATG
1 CAAAGAAATCCAAAAAATG
21864276 CAAAGAAATCCAAAAAATG
1 CAAAGAAATCCAAAAAATG
21864295 CAAAGAAAT
1 CAAAGAAAT
21864304 AATAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.66, C:0.13, G:0.09, T:0.13
Consensus pattern (19 bp):
CAAAGAAATCCAAAAAATG
Found at i:21864303 original size:10 final size:9
Alignment explanation
Indices: 21864259--21864303 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
21864249 TAAACAAACA
*
21864259 AAAAAATTC
1 AAAAAATGC
21864268 AAAAAATGC
1 AAAAAATGC
*
21864277 AAAGAAATCC
1 AAA-AAATGC
21864287 AAAAAATGC
1 AAAAAATGC
21864296 AAAGAAAT
1 AAA-AAAT
21864304 AATAAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 19 0.61
10 12 0.39
ACGTcount: A:0.67, C:0.11, G:0.09, T:0.13
Consensus pattern (9 bp):
AAAAAATGC
Found at i:21872283 original size:17 final size:17
Alignment explanation
Indices: 21872261--21872294 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21872251 GTTCTTGATA
21872261 AAATAA-AACTCCTTATT
1 AAATAATAACT-CTTATT
21872278 AAATAATAACTCTTATT
1 AAATAATAACTCTTATT
21872295 TTATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAACTCTTATT
Found at i:21872500 original size:28 final size:28
Alignment explanation
Indices: 21872469--21872611 Score: 178
Period size: 29 Copynumber: 5.0 Consensus size: 28
21872459 AAATATTTTA
* * *
21872469 TCTTATCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
21872497 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
* *
21872527 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
21872556 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
21872585 TCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
21872612 AAAGCTGCCA
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
28 34 0.34
29 42 0.42
30 14 0.14
31 10 0.10
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:21872539 original size:59 final size:58
Alignment explanation
Indices: 21872446--21872611 Score: 217
Period size: 59 Copynumber: 2.8 Consensus size: 58
21872436 TCTTGTCTGT
* * *
21872446 AATTAAGACAAAAAAATATTTTATCTTATCTAAATTGAGACAAATATGTTTTCTTGACTA
1 AATTAAGAC-AAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
* * *
21872506 AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGGCAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGACTA
* * *
21872565 AATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGTT
1 AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTT
21872612 AAAGCTGCCA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 18 0.19
58 16 0.17
59 51 0.54
60 9 0.10
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (58 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
Found at i:21872561 original size:29 final size:28
Alignment explanation
Indices: 21872436--21872608 Score: 175
Period size: 29 Copynumber: 5.9 Consensus size: 28
21872426 TTAAGACAAC
* *
21872436 TCTTGTCTGTAATTAAGACAAAAAAATATTTT
1 TCTTGTCT-AAATTAAGAC--AAACATA-TTT
* * * *
21872468 ATCTTATCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* *
21872497 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACATA-TTT
*
21872527 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
*
21872556 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
21872585 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
21872609 GTTAAAGCTG
Statistics
Matches: 121, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
28 31 0.26
29 45 0.37
30 20 0.17
31 10 0.08
32 8 0.07
33 7 0.06
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:21872750 original size:56 final size:55
Alignment explanation
Indices: 21872683--21872796 Score: 192
Period size: 56 Copynumber: 2.1 Consensus size: 55
21872673 TGAATTCTAC
* *
21872683 GAAGCTAAGTGGGGAATTTATTTGAACATAGATATTTCAAGCTCCAATAAACTTA
1 GAAGCTAAGTGGGGAATCTATTTGAACATAGATATTCCAAGCTCCAATAAACTTA
*
21872738 NGAAGCTAAGTGGGGAATCTATTTGGACATAGATATTCCAAGCTCCAATAAACTTA
1 -GAAGCTAAGTGGGGAATCTATTTGAACATAGATATTCCAAGCTCCAATAAACTTA
21872794 GAA
1 GAA
21872797 TTATTCTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 3 0.05
56 52 0.95
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (55 bp):
GAAGCTAAGTGGGGAATCTATTTGAACATAGATATTCCAAGCTCCAATAAACTTA
Found at i:21875255 original size:31 final size:30
Alignment explanation
Indices: 21875160--21875255 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 30
21875150 TTGTCTTAAG
* *
21875160 TATCATCAATGCAATATCATTAACTTAAGCA
1 TATCATCAATGCAATATCA-TAACTCAAACA
* * * *
21875191 TATTATCAATGCAA-AT--T-GCTCCGAA-G
1 TATCATCAATGCAATATCATAACT-CAAACA
21875217 TATCATCAATGCAATATCATCAACTCAAACA
1 TATCATCAATGCAATATCAT-AACTCAAACA
21875248 TATCATCA
1 TATCATCA
21875256 CTTTTGTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
26 15 0.31
27 4 0.08
29 1 0.02
30 5 0.10
31 23 0.48
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (30 bp):
TATCATCAATGCAATATCATAACTCAAACA
Found at i:21886195 original size:24 final size:24
Alignment explanation
Indices: 21886160--21886211 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
21886150 ATCAGTCTAT
* *
21886160 TTTTTATTTTTTTTAA-AAAAATA
1 TTTTTATATTTTATAATAAAAATA
*
21886183 TTTTTATAATTTTATAATAAAATTA
1 TTTTTAT-ATTTTATAATAAAAATA
21886208 TTTT
1 TTTT
21886212 ATGATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 7 0.29
25 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTATATTTTATAATAAAAATA
Found at i:21886254 original size:21 final size:22
Alignment explanation
Indices: 21886217--21886259 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
21886207 ATTTTATGAT
*
21886217 TTAATTTATAAATTAAA-ATTA
1 TTAATTTATAAAGTAAAGATTA
21886238 TTAATTTGAT-AAGTAAAGATTA
1 TTAATTT-ATAAAGTAAAGATTA
21886260 AACACATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATTTATAAAGTAAAGATTA
Found at i:21886339 original size:22 final size:21
Alignment explanation
Indices: 21886297--21886347 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
21886287 ATATTATTGG
**
21886297 TAATTAAATTATTAATTTTAT
1 TAATTAAATTATTAAAATTAT
21886318 ATAATTAAA-TATATAAAATTAT
1 -TAATTAAATTAT-TAAAATTAT
21886340 TAAATTAA
1 T-AATTAA
21886348 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTAAATTATTAAAATTAT
Found at i:21886344 original size:8 final size:8
Alignment explanation
Indices: 21886299--21886358 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
21886289 ATTATTGGTA
21886299 ATTAAATT
1 ATTAAATT
21886307 ATT-AATT
1 ATTAAATT
* *
21886314 -TTATATA
1 ATTAAATT
21886321 ATTAAATAT
1 ATTAAAT-T
*
21886330 ATAAAATT
1 ATTAAATT
21886338 ATTAAATT
1 ATTAAATT
21886346 AATTAAAATT
1 -ATT-AAATT
21886356 ATT
1 ATT
21886359 TACTTTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 16 0.39
9 12 0.29
10 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTAAATT
Found at i:21896564 original size:17 final size:17
Alignment explanation
Indices: 21896542--21896578 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21896532 TAATGAGGAT
21896542 TGCTCCCCCTAAGTGTG
1 TGCTCCCCCTAAGTGTG
*
21896559 TGCTCCCCCTTAGTGTG
1 TGCTCCCCCTAAGTGTG
21896576 TGC
1 TGC
21896579 ATATTTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.35, G:0.24, T:0.32
Consensus pattern (17 bp):
TGCTCCCCCTAAGTGTG
Found at i:21897791 original size:31 final size:32
Alignment explanation
Indices: 21897756--21897860 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 32
21897746 CATTTTGATG
** * * *
21897756 ATGTGGCATTAAAATGATTATGTGGC-ATTCC
1 ATGTGGCACCAAAATAATGATGTGGCAATGCC
*
21897787 ATGTGGCACCAATATAATGATGTGGCAATGCC
1 ATGTGGCACCAAAATAATGATGTGGCAATGCC
* * * * * *
21897819 ATGTGGCACTAATACACTGATATGGCAATGCTG
1 ATGTGGCACCAAAATAATGATGTGGCAATGC-C
21897852 ATGTGGCAC
1 ATGTGGCAC
21897861 TAACATGCTG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 21 0.34
32 31 0.51
33 9 0.15
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (32 bp):
ATGTGGCACCAAAATAATGATGTGGCAATGCC
Found at i:21897825 original size:32 final size:32
Alignment explanation
Indices: 21897775--21897860 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
21897765 TAAAATGATT
* *
21897775 ATGTGGC-ATTCCATGTGGCACCAATATAATG
1 ATGTGGCAATGCCATGTGGCACCAATACAATG
* *
21897806 ATGTGGCAATGCCATGTGGCACTAATACACTG
1 ATGTGGCAATGCCATGTGGCACCAATACAATG
* *
21897838 ATATGGCAATGCTGATGTGGCAC
1 ATGTGGCAATGC-CATGTGGCAC
21897861 TAACATGCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 7 0.15
32 31 0.66
33 9 0.19
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (32 bp):
ATGTGGCAATGCCATGTGGCACCAATACAATG
Found at i:21898982 original size:74 final size:73
Alignment explanation
Indices: 21898845--21899040 Score: 270
Period size: 74 Copynumber: 2.7 Consensus size: 73
21898835 AGACAAAATA
* *
21898845 CTCTTAGTTGA-TGAACATACTTCTTAGTCGATTAAGTCGTTTCTGTCTTCTGATCCTAGTTTCT
1 CTCTTAGTCGACT-AACATACTTCTTAGTCGATTAAGTCGTTTCTGTTTTCTGATCCTAGTTTCT
21898909 AGTAGTGAG
65 AGTAGTGAG
*
21898918 CTCTTAGTCGACTAACAATACTTCTTAGTCGATTAAGTCGTCTCTGTTTTCTGAT-CTCAGTTTC
1 CTCTTAGTCGACTAAC-ATACTTCTTAGTCGATTAAGTCGTTTCTGTTTTCTGATCCT-AGTTTC
21898982 TAGTAGTGAG
64 TAGTAGTGAG
* * * * *
21898992 CTCTTAATCGACTAACCATGCTTCTTGGTCGACTAAGTCTTTTCTGTTT
1 CTCTTAGTCGACTAA-CATACTTCTTAGTCGATTAAGTCGTTTCTGTTT
21899041 ATGAACCGGT
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
73 15 0.14
74 94 0.85
75 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (73 bp):
CTCTTAGTCGACTAACATACTTCTTAGTCGATTAAGTCGTTTCTGTTTTCTGATCCTAGTTTCTA
GTAGTGAG
Found at i:21899312 original size:2 final size:2
Alignment explanation
Indices: 21899305--21899334 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21899295 TATGGTGTTA
*
21899305 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21899335 TTTCTTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21905466 original size:23 final size:22
Alignment explanation
Indices: 21905406--21905468 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
21905396 GTTGCGCAAC
* *
21905406 TTAAGAATTGCATGACTGGTTT
1 TTAAAAATTACATGACTGGTTT
*
21905428 TTAAAAATTACGTGACTGGTTT
1 TTAAAAATTACATGACTGGTTT
** *
21905450 ATTTGACATTACATGACTG
1 -TTAAAAATTACATGACTG
21905469 AATATTAGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (22 bp):
TTAAAAATTACATGACTGGTTT
Found at i:21912778 original size:84 final size:84
Alignment explanation
Indices: 21912637--21912838 Score: 309
Period size: 84 Copynumber: 2.4 Consensus size: 84
21912627 TTGACCAAAT
* *
21912637 TCAAGAAGTCATGCAATGACTATAAACTATTCACGCAATGAGCAACTCACTCAATGCCACATCAA
1 TCAAGAAGTCATGCAATGACTACAAACCATTCACGCAATGAGCAACTCACTCAATGCCACATCAA
21912702 CTAG-TAACACAATGCCATA
66 CT-GCTAACACAATGCCATA
* **
21912721 TCAAGAAGTCATGCAATGACTACAAACCATTCACGCAATGAGCAAGTCACAT-AATGCCGTATCA
1 TCAAGAAGTCATGCAATGACTACAAACCATTCACGCAATGAGCAACTCAC-TCAATGCCACATCA
21912785 ACTGCTAACACAATGCCATA
65 ACTGCTAACACAATGCCATA
* *
21912805 TCAAGAAGTCACGCAATGACTACAACCCATTCAC
1 TCAAGAAGTCATGCAATGACTACAAACCATTCAC
21912839 ATAATTCTGT
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
83 1 0.01
84 107 0.98
85 1 0.01
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (84 bp):
TCAAGAAGTCATGCAATGACTACAAACCATTCACGCAATGAGCAACTCACTCAATGCCACATCAA
CTGCTAACACAATGCCATA
Found at i:21912876 original size:68 final size:68
Alignment explanation
Indices: 21912767--21912905 Score: 199
Period size: 68 Copynumber: 2.0 Consensus size: 68
21912757 AATGAGCAAG
* *
21912767 TCACATAATGCCGTATCAACTGCTAACACAATGCCATATCAAGAAGTCACGCAATGACTACAACC
1 TCACATAATGCCGTATCAACTGCTAACACAATGCCATATCAAGAAGTCACACAATGACTACAAAC
21912832 CAT
66 CAT
* * * * *
21912835 TCACATAATTCTGTATCAACTAG-TAACGCAATGCTATATCAAGAAGTCACACAATGACTATAAA
1 TCACATAATGCCGTATCAACT-GCTAACACAATGCCATATCAAGAAGTCACACAATGACTACAAA
21912899 CCAT
65 CCAT
21912903 TCA
1 TCA
21912906 TGCAATAAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
68 62 0.98
69 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.24
Consensus pattern (68 bp):
TCACATAATGCCGTATCAACTGCTAACACAATGCCATATCAAGAAGTCACACAATGACTACAAAC
CAT
Found at i:21912900 original size:152 final size:152
Alignment explanation
Indices: 21912697--21912988 Score: 415
Period size: 152 Copynumber: 1.9 Consensus size: 152
21912687 TCAATGCCAC
** *
21912697 ATCAACTAGTAACACAATGCCATATCAAGAAGTCATGCAATGACTACAAACCATTCACGCAATGA
1 ATCAACTAGTAACACAATGCCATATCAAGAAGTCACACAATGACTACAAACCATTCACGCAATAA
* * *
21912762 GCAAGTCACATAATGCCGTATCAACT-GCTAACACAATGCCATATCAAGAAGTCACGCAATGACT
66 GCAAGTCACACAATGCCATATCAACTAG-TAACACAATGCCATATCAAAAAGTCACGCAATGACT
*
21912826 ACAACCCATTCACATAATTCTGT
130 ACAAACCATTCACATAATTCTGT
* * * *
21912849 ATCAACTAGTAACGCAATGCTATATCAAGAAGTCACACAATGACTATAAACCATTCATGCAATAA
1 ATCAACTAGTAACACAATGCCATATCAAGAAGTCACACAATGACTACAAACCATTCACGCAATAA
* * * * * *
21912914 GTAAGTCACGCAATGTCATATCAACTAGTACCTCAATGCCATATCAAAAAGTCATGCAATGACTA
66 GCAAGTCACACAATGCCATATCAACTAGTAACACAATGCCATATCAAAAAGTCACGCAATGACTA
21912979 CAAACCATTC
131 CAAACCATTC
21912989 TCCCTAAACC
Statistics
Matches: 122, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
152 121 0.99
153 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (152 bp):
ATCAACTAGTAACACAATGCCATATCAAGAAGTCACACAATGACTACAAACCATTCACGCAATAA
GCAAGTCACACAATGCCATATCAACTAGTAACACAATGCCATATCAAAAAGTCACGCAATGACTA
CAAACCATTCACATAATTCTGT
Found at i:21912973 original size:23 final size:23
Alignment explanation
Indices: 21912916--21912974 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
21912906 TGCAATAAGT
* * *
21912916 AAGTCACGCAATGTCATATCAAC
1 AAGTCATGCAATGCCATATCAAA
* *
21912939 TAGTACCT-CAATGCCATATCAAA
1 AAGT-CATGCAATGCCATATCAAA
21912962 AAGTCATGCAATG
1 AAGTCATGCAATG
21912975 ACTACAAACC
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (23 bp):
AAGTCATGCAATGCCATATCAAA
Found at i:21913557 original size:32 final size:32
Alignment explanation
Indices: 21913521--21913669 Score: 122
Period size: 35 Copynumber: 4.5 Consensus size: 32
21913511 TTTACTAGGA
*
21913521 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
** **
21913553 TCAACCACAACATTTCACAA-TGGTTTTTCATGGGC
1 TCAACCA-AA-A-CCCA-AAGTGGTTTTTCAAAGGC
21913588 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * * * *
21913620 TCAATCACAACCTACAATAATGGTTTTTC-ACGAGA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCAAAG-GC
21913655 TCAACCAAAACCCAA
1 TCAACCAAAACCCAA
21913670 CAATTAACTT
Statistics
Matches: 92, Mismatches: 16, Indels: 17
0.74 0.13 0.14
Matches are distributed among these distances:
31 2 0.02
32 31 0.34
33 6 0.07
34 8 0.09
35 43 0.47
36 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.25
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:21913592 original size:67 final size:67
Alignment explanation
Indices: 21913498--21913669 Score: 206
Period size: 67 Copynumber: 2.6 Consensus size: 67
21913488 AGCCAAAACC
*
21913498 TTTCACAATAGTTTTTACTAGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAA
1 TTTCACAATAGTTTTTACTAGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAA
21913563 CA
66 CA
* * * *
21913565 TTTCACAATGGTTTTT-CATGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAATCACA
1 TTTCACAATAGTTTTTAC-TAGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACA
21913629 AC-
65 ACA
* * * * *
21913631 CTACAATAATGGTTTTTCACGA-GATCAACCAAAACCCAA
1 TTTC-ACAATAGTTTTT-ACTAGGATCAACCAAAACCCAA
21913670 CAATTAACTT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
66 3 0.03
67 86 0.96
69 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (67 bp):
TTTCACAATAGTTTTTACTAGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAA
CA
Found at i:21917391 original size:161 final size:160
Alignment explanation
Indices: 21917125--21917446 Score: 617
Period size: 161 Copynumber: 2.0 Consensus size: 160
21917115 AATATTTTCA
21917125 TTAAGTTCAATGAGTTCATCCTAATCAAATAAGTATGCATAATCAAGAAATCAATTTTGAAACAA
1 TTAAGTTCAATGAGTTCATCCTAATCAAATAAGTATGCATAATCAAGAAATCAATTTTGAAACAA
**
21917190 TCATTTAAGCATAAACGTAAAATATATTTCAAGAATTGTTCCTAGATTAGCATTTGAACGTTTCA
66 TCATTTAAGCATAAACGTAAAATATATTTCAAGAATTGTTCCTAGATTAGCATTTGAAAATTTCA
21917255 ATTTTCATGAGAAGATATTTTCTATATATG
131 ATTTTCATGAGAAGATATTTTCTATATATG
21917285 TNTAAGTTCAATGAGTTCATCCTAATCAAATAAGTATGCATAATCAAGAAATCAATTTTGAAACA
1 T-TAAGTTCAATGAGTTCATCCTAATCAAATAAGTATGCATAATCAAGAAATCAATTTTGAAACA
21917350 ATCATTTAAGCATAAACGTAAAATATATTTCAAGAATTGTTCCTAGATTAGCATTTGAAAATTTC
65 ATCATTTAAGCATAAACGTAAAATATATTTCAAGAATTGTTCCTAGATTAGCATTTGAAAATTTC
21917415 AATTTTCATGAGAAGATATTTTCTATATATG
130 AATTTTCATGAGAAGATATTTTCTATATATG
21917446 T
1 T
21917447 ACATGAAAAT
Statistics
Matches: 159, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
160 1 0.01
161 158 0.99
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (160 bp):
TTAAGTTCAATGAGTTCATCCTAATCAAATAAGTATGCATAATCAAGAAATCAATTTTGAAACAA
TCATTTAAGCATAAACGTAAAATATATTTCAAGAATTGTTCCTAGATTAGCATTTGAAAATTTCA
ATTTTCATGAGAAGATATTTTCTATATATG
Found at i:21925205 original size:32 final size:32
Alignment explanation
Indices: 21925169--21925271 Score: 93
Period size: 32 Copynumber: 3.1 Consensus size: 32
21925159 TTTACTAGGA
21925169 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
* ** **
21925201 TCAACCACAACATTTCACAA-TGGTTTTTCACGGGC
1 TCAACTA-AA-A-CCCA-AAGTGGTTTTTCAAAGGC
*
21925236 TCAA-TCAAAACCCAAAGTGGTTTTTCAAAAGC
1 TCAACT-AAAACCCAAAGTGGTTTTTCAAAGGC
21925268 TCAA
1 TCAA
21925272 TCACAACCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
31 2 0.04
32 24 0.44
33 3 0.06
34 3 0.06
35 20 0.37
36 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (32 bp):
TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:21925225 original size:35 final size:34
Alignment explanation
Indices: 21925186--21925297 Score: 104
Period size: 35 Copynumber: 3.3 Consensus size: 34
21925176 AAACCCAAAG
* *
21925186 TGGTTTTTCAAAGGCTCAACCACAACATTTCACAA
1 TGGTTTTTCAAAGGCTCAATCACAACA-TACACAA
** **
21925221 TGGTTTTTCACGGGCTCAATCA-AA-ACCCA-AA
1 TGGTTTTTCAAAGGCTCAATCACAACATACACAA
* *
21925252 GTGGTTTTTCAAAAGCTCAATCACAACCTACAACAA
1 -TGGTTTTTCAAAGGCTCAATCACAACATAC-ACAA
21925288 TGGTTTTTCA
1 TGGTTTTTCA
21925298 CGAGATCAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
31 2 0.03
32 21 0.34
33 3 0.05
34 3 0.05
35 30 0.49
36 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (34 bp):
TGGTTTTTCAAAGGCTCAATCACAACATACACAA
Found at i:21925227 original size:67 final size:66
Alignment explanation
Indices: 21925145--21925317 Score: 199
Period size: 67 Copynumber: 2.6 Consensus size: 66
21925135 TAGCCAAAAC
* *
21925145 CTTTCACAATAGTTTTT-ACTAGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCAC
1 CTTTCACAATGGTTTTTCAC-AGGATCAACTAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCAC
21925209 AA
65 AA
* * *
21925211 CATTTCACAATGGTTTTTCACGGGCTCAA-TCAAAACCCAAAGTGGTTTTTCAAAAGCTCAATCA
1 C-TTTCACAATGGTTTTTCACAGGATCAACT-AAAACCCAAAGTGGTTTTTCAAAAGCTCAACCA
21925275 CAA
64 CAA
* * **
21925278 CCTACAACAATGGTTTTTCAC-GAGATCAACCCAAACCCAA
1 CTTTC-ACAATGGTTTTTCACAG-GATCAACTAAAACCCAA
21925318 CAACTAATTT
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
66 5 0.05
67 84 0.92
68 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (66 bp):
CTTTCACAATGGTTTTTCACAGGATCAACTAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACA
A
Found at i:21925832 original size:65 final size:65
Alignment explanation
Indices: 21925728--21925906 Score: 313
Period size: 65 Copynumber: 2.8 Consensus size: 65
21925718 AATTTACAAA
**
21925728 CAGAGAGCTTTTAGTCGACTGACTTGGTCGACTAAGTTGGTTCTGTTTCAGGTTGCAGATTCTGG
1 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGGTTCTGTTTCAGGTTGCAGATTCTGG
* *
21925793 CAGAGAGCACTTAGTCGACTAATTTGGTCGACTAAGTTGGTTCTGTTTCAGGTTGCAGATTCTGG
1 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGGTTCTGTTTCAGGTTGCAGATTCTGG
*
21925858 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGGTTCTATTTC
1 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGGTTCTGTTTC
21925907 TCAAACTCTT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 107 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (65 bp):
CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGGTTCTGTTTCAGGTTGCAGATTCTGG
Found at i:21926912 original size:54 final size:54
Alignment explanation
Indices: 21926843--21926983 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 54
21926833 ACTCCGGTTG
* *
21926843 TGTGCACGACATGGGGGGATGCACATGAGCTGGGTGAGATGAGATGT-TCGGCTA
1 TGTGCACGATATGGGGGGATGCACATGAGCTGGGTGAGATGAGATGTCT-AGCTA
* * * *
21926897 TGTGCACGATGTGGGGGGATGCACATGAGCTAGGTGAGATGGGGTGTCTAGCTA
1 TGTGCACGATATGGGGGGATGCACATGAGCTGGGTGAGATGAGATGTCTAGCTA
*
21926951 TGTGCACGATATGGGGGGATGCACACGAGCTGG
1 TGTGCACGATATGGGGGGATGCACATGAGCTGG
21926984 ATCCGATGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 76 0.99
55 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (54 bp):
TGTGCACGATATGGGGGGATGCACATGAGCTGGGTGAGATGAGATGTCTAGCTA
Found at i:21936459 original size:5 final size:5
Alignment explanation
Indices: 21936441--21936483 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
21936431 ATTCTATTCT
* *
21936441 ACTTA ACCTG ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
21936484 GGGCCACGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (5 bp):
ACTTA
Found at i:21947588 original size:11 final size:11
Alignment explanation
Indices: 21947574--21947603 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21947564 AATAATATTT
21947574 TATTAATAAAA
1 TATTAATAAAA
*
21947585 TATTATTAAAA
1 TATTAATAAAA
21947596 TATTAATA
1 TATTAATA
21947604 TTTTAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:21948092 original size:19 final size:18
Alignment explanation
Indices: 21948049--21948105 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
21948039 AAATCAAGAT
21948049 TTTTCATTTTCTTTCCCTTG
1 TTTTC-TTTTCTTT-CCTTG
*
21948069 TTTTCTTTTCTTTCCTTT
1 TTTTCTTTTCTTTCCTTG
*
21948087 TCTTTCTTACTCTTTCCTT
1 T-TTTCTT-TTCTTTCCTT
21948106 CTCCTAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.15
19 14 0.42
20 14 0.42
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTCTTTTCTTTCCTTG
Found at i:21948991 original size:54 final size:54
Alignment explanation
Indices: 21948929--21949071 Score: 232
Period size: 54 Copynumber: 2.6 Consensus size: 54
21948919 TGTGTGAGTN
* *
21948929 TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGAGATGTCCAGTTA
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGATGAGATGAGATGTCCAGCTA
* * *
21948983 TGTGCACGATGTGGGGGGATGCACATGAGCTGGATGAGATGGGGTGTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGATGAGATGAGATGTCCAGCTA
*
21949037 TGTGCACGATGTGGGGGGATGCACACGAGCTGGAT
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGAT
21949072 CCGATGTGGT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.20, C:0.15, G:0.43, T:0.22
Consensus pattern (54 bp):
TGTGCACGATGTGGGGGGATGCACATGAGCTGGATGAGATGAGATGTCCAGCTA
Found at i:21952093 original size:18 final size:17
Alignment explanation
Indices: 21952072--21952118 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
21952062 TAGACACTAA
21952072 AAAATAAATAGAATATAT
1 AAAATAAATAGAATA-AT
21952090 AAAATATATATA-AATAAT
1 AAAATA-A-ATAGAATAAT
*
21952108 AAAAAAAATAG
1 AAAATAAATAG
21952119 TACTGGCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 13 0.52
19 5 0.20
20 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAATAAATAGAATAAT
Found at i:21953470 original size:18 final size:19
Alignment explanation
Indices: 21953447--21953488 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
21953437 AAATATTTAC
21953447 TAATAATAAATAAAAT-AA
1 TAATAATAAATAAAATAAA
21953465 TAATAATAAATAAAATAAA
1 TAATAATAAATAAAATAAA
21953484 TAATA
1 TAATA
21953489 CAAAAATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAATAATAAATAAAATAAA
Found at i:21953476 original size:22 final size:21
Alignment explanation
Indices: 21953447--21953488 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
21953437 AAATATTTAC
21953447 TAATAAT-AAATAAAATAATAA
1 TAATAATAAAAT-AAATAATAA
21953468 TAATAAATAAAATAAATAATA
1 TAAT-AATAAAATAAATAATA
21953489 CAAAAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAATAATAAAATAAATAATAA
Found at i:21953503 original size:19 final size:17
Alignment explanation
Indices: 21953447--21953504 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
21953437 AAATATTTAC
*
21953447 TAATAATAAATAAAATAA
1 TAATAAAAAATAAAA-AA
*
21953465 TAATAATAAATAAAATAAA
1 TAATAAAAAAT-AAA-AAA
21953484 TAATACAAAAATACAAAAA
1 TAATA-AAAAATA-AAAAA
21953503 TA
1 TA
21953505 CCATGATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 11 0.31
19 16 0.46
20 8 0.23
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAATAAAAAATAAAAAA
Found at i:21953715 original size:13 final size:13
Alignment explanation
Indices: 21953697--21953760 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
21953687 AAAGTTTTTC
21953697 AATAAAAATAATA
1 AATAAAAATAATA
*
21953710 AATAAACAACAATA
1 AATAAA-AATAATA
*
21953724 GATAAAAA-AA-A
1 AATAAAAATAATA
* * *
21953735 GGATAAAAATCACA
1 -AATAAAAATAATA
21953749 AATAAAAATAAT
1 AATAAAAATAAT
21953761 TCAAATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 1 0.02
12 10 0.24
13 18 0.44
14 12 0.29
ACGTcount: A:0.72, C:0.06, G:0.05, T:0.17
Consensus pattern (13 bp):
AATAAAAATAATA
Found at i:21954027 original size:10 final size:10
Alignment explanation
Indices: 21954012--21954046 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
21954002 AAAAATATAG
21954012 AAATATACAA
1 AAATATACAA
21954022 AAATATACAA
1 AAATATACAA
21954032 AAATAT--AA
1 AAATATACAA
21954040 AAATATA
1 AAATATA
21954047 AAATAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATATACAA
Found at i:21954049 original size:7 final size:8
Alignment explanation
Indices: 21953985--21954062 Score: 59
Period size: 8 Copynumber: 9.1 Consensus size: 8
21953975 TTGTTTACAA
21953985 AAAAATAT
1 AAAAATAT
**
21953993 AATCATAAT
1 AAAAAT-AT
21954002 AAAAATAT
1 AAAAATAT
*
21954010 AGAAATATAC
1 A-AAA-ATAT
21954020 AAAAATAT
1 AAAAATAT
21954028 ACAAAAATAT
1 --AAAAATAT
21954038 AAAAATAT
1 AAAAATAT
*
21954046 -AAAATAA
1 AAAAATAT
21954053 AATAAATAT
1 AA-AAATAT
21954062 A
1 A
21954063 TATATAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
7 6 0.11
8 19 0.35
9 18 0.33
10 12 0.22
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:21954057 original size:18 final size:19
Alignment explanation
Indices: 21953999--21954064 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
21953989 ATATAATCAT
*
21953999 AATAAAAATATAGAAAT-A
1 AATAAAAATATACAAATAA
* *
21954017 TACAAAAATATACAAA-AA
1 AATAAAAATATACAAATAA
*
21954035 TATAAAAATATA-AAATAA
1 AATAAAAATATACAAATAA
*
21954053 AATAAATATATA
1 AATAAAAATATA
21954065 TATAATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.08
18 37 0.93
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (19 bp):
AATAAAAATATACAAATAA
Found at i:21954059 original size:16 final size:15
Alignment explanation
Indices: 21953983--21954062 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 15
21953973 GATTGTTTAC
*
21953983 AAAAAAATATAATCAT
1 AAAAAAATATAA-AAT
21953999 AATAAAAATATAGAAAT
1 AA-AAAAATATA-AAAT
21954016 ATACAAAAATATACAAAAAT
1 A-A-AAAAATAT---AAAAT
*
21954036 ATAAAAATATAAAAT
1 AAAAAAATATAAAAT
21954051 AAAATAAATATA
1 AAAA-AAATATA
21954063 TATATAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
15 8 0.15
16 9 0.17
17 12 0.23
18 18 0.34
20 5 0.09
21 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (15 bp):
AAAAAAATATAAAAT
Found at i:21962234 original size:8 final size:8
Alignment explanation
Indices: 21962221--21962305 Score: 53
Period size: 10 Copynumber: 9.1 Consensus size: 8
21962211 AAATTTTATA
21962221 TATTTTTT
1 TATTTTTT
21962229 TATTTTATTT
1 TA-TTT-TTT
21962239 TATATTTTT
1 TAT-TTTTT
21962248 ATATTTTTGT
1 -TATTTTT-T
21962258 ATATTTTTGT
1 -TATTTTT-T
*
21962268 ATATTTTTA
1 -TATTTTTT
21962277 TATTTTTAT
1 TATTTTT-T
21962286 TATTATTATT
1 TATT-TT-TT
21962296 ATATTTTTT
1 -TATTTTTT
21962305 T
1 T
21962306 GTAAACAATC
Statistics
Matches: 66, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
8 10 0.15
9 17 0.26
10 34 0.52
11 5 0.08
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.75
Consensus pattern (8 bp):
TATTTTTT
Found at i:21962244 original size:20 final size:19
Alignment explanation
Indices: 21962219--21962305 Score: 90
Period size: 18 Copynumber: 4.6 Consensus size: 19
21962209 AAAAATTTTA
21962219 TATATTTTTTTATTTTATTT
1 TATATTTTTTTA-TTTATTT
* *
21962239 TATATTTTTATATTT-TTG
1 TATATTTTTTTATTTATTT
* *
21962257 TATATTTTTGTATAT-TTT
1 TATATTTTTTTATTTATTT
21962275 TATATTTTTATTA-TTATTAT
1 TATATTTTT-TTATTTATT-T
21962295 TATATTTTTTT
1 TATATTTTTTT
21962306 GTAAACAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
18 27 0.47
19 9 0.16
20 21 0.37
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
TATATTTTTTTATTTATTT
Found at i:21962254 original size:28 final size:28
Alignment explanation
Indices: 21962213--21962305 Score: 107
Period size: 28 Copynumber: 3.2 Consensus size: 28
21962203 AGTGACAAAA
*
21962213 ATTTTATATATTTTTTTATTTTATTTTAT
1 ATTTT-TATATTTTTTTATTTTATTATAT
* *
21962242 ATTTTTATATTTTTGTATATTT-TTGTAT
1 ATTTTTATATTTTTTTAT-TTTATTATAT
21962270 ATTTTTATATTTTTATTATTATTATTATAT
1 ATTTTTATATTTTT-TTATT-TTATTATAT
*
21962300 TTTTTT
1 ATTTTT
21962306 GTAAACAATC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 32 0.58
29 13 0.24
30 10 0.18
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (28 bp):
ATTTTTATATTTTTTTATTTTATTATAT
Found at i:21962521 original size:11 final size:11
Alignment explanation
Indices: 21962496--21962587 Score: 62
Period size: 11 Copynumber: 7.8 Consensus size: 11
21962486 TTATCTTTTT
*
21962496 TTATCATTT-A
1 TTATTATTTAA
21962506 TTATTATTTAA
1 TTATTATTTAA
21962517 TTATTATTTATA
1 TTATTATTTA-A
*
21962529 TTGCATTTTTATAA
1 TT--ATTATT-TAA
*
21962543 GTTTATTATTTTA
1 --TTATTATTTAA
21962556 TTATATATTTGAA
1 TTAT-TATTT-AA
*
21962569 TTATT-TTTAT
1 TTATTATTTAA
21962579 TTATTATTT
1 TTATTATTT
21962588 TTATCTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
10 14 0.21
11 21 0.32
12 9 0.14
13 7 0.11
14 11 0.17
15 2 0.03
16 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATTATTTAA
Found at i:21962525 original size:21 final size:18
Alignment explanation
Indices: 21962476--21962630 Score: 70
Period size: 21 Copynumber: 8.1 Consensus size: 18
21962466 TTGTTTTAGA
*
21962476 TTTTTTATTA-TTA-TCT
1 TTTTTTATTATTTATTAT
*
21962492 TTTTTTATCATTTATTAT
1 TTTTTTATTATTTATTAT
21962510 TATTTAATTATTATTTA-TAT
1 T-TTT--TTATTATTTATTAT
*
21962530 TGCATTTTTATAAGTTTATTAT
1 T---TTTTTATTA-TTTATTAT
*
21962552 TTTATTATATATTTGAATTATT
1 TTTTTTAT-TATTT--ATTA-T
21962574 TTTATTTATTATTT-TTAT
1 TTT-TTTATTATTTATTAT
*
21962592 CTTTTTT-TTATCTATTGTTAT
1 -TTTTTTATTA--T-TTATTAT
*
21962613 TTATTTATTATTT-TTAT
1 TTTTTTATTATTTATTAT
21962630 T
1 T
21962631 GAATAACTTT
Statistics
Matches: 111, Mismatches: 8, Indels: 39
0.70 0.05 0.25
Matches are distributed among these distances:
16 9 0.08
17 11 0.10
18 9 0.08
19 20 0.18
20 17 0.15
21 24 0.22
22 17 0.15
23 4 0.04
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTTATTATTTATTAT
Found at i:21962584 original size:13 final size:13
Alignment explanation
Indices: 21962568--21962630 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
21962558 ATATATTTGA
21962568 ATTATTTTTATTT
1 ATTATTTTTATTT
*
21962581 ATTATTTTTATCT
1 ATTATTTTTATTT
*
21962594 -TT-TTTTTATCT
1 ATTATTTTTATTT
*
21962605 ATTGTTATTTATTT
1 ATTATT-TTTATTT
21962619 ATTATTTTTATT
1 ATTATTTTTATT
21962631 GAATAACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
11 9 0.20
12 4 0.09
13 20 0.45
14 11 0.25
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:21962623 original size:11 final size:11
Alignment explanation
Indices: 21962495--21962625 Score: 55
Period size: 11 Copynumber: 11.9 Consensus size: 11
21962485 ATTATCTTTT
*
21962495 TTTATCATTTA
1 TTTATTATTTA
21962506 -TTATTATTTA
1 TTTATTATTTA
*
21962516 ATTATTATTTA
1 TTTATTATTTA
*
21962527 TATTGCATTTTTATAA
1 T-TT--ATTATT-T-A
21962543 GTTTATTATTT-
1 -TTTATTATTTA
21962554 TATTATATATTTGA
1 T-TTAT-TATTT-A
*
21962568 ATTATT-TTTA
1 TTTATTATTTA
21962578 TTTATTA-TT-
1 TTTATTATTTA
*
21962587 TTTA-TCTTT-
1 TTTATTATTTA
*
21962596 TTT-TTATCTA
1 TTTATTATTTA
*
21962606 -TTGTTATTTA
1 TTTATTATTTA
21962616 TTTATTATTT
1 TTTATTATTT
21962626 TTATTGAATA
Statistics
Matches: 92, Mismatches: 11, Indels: 34
0.67 0.08 0.25
Matches are distributed among these distances:
8 1 0.01
9 14 0.15
10 24 0.26
11 25 0.27
12 8 0.09
13 5 0.05
14 10 0.11
15 1 0.01
16 3 0.03
17 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:21962865 original size:29 final size:29
Alignment explanation
Indices: 21962823--21962887 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
21962813 AATATCATGG
*
21962823 TATTT-TTGTATTTTT-GTATTTATTATTT
1 TATTTATTGTATTTTTATTA-TTATTATTT
21962851 ATATTTATT-TATTTTTATTATTATTATTT
1 -TATTTATTGTATTTTTATTATTATTATTT
21962880 TATTTATT
1 TATTTATT
21962888 ATTAGTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 8 0.24
29 21 0.64
30 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (29 bp):
TATTTATTGTATTTTTATTATTATTATTT
Found at i:21963719 original size:74 final size:74
Alignment explanation
Indices: 21963640--21963800 Score: 182
Period size: 74 Copynumber: 2.2 Consensus size: 74
21963630 GACGACGGTT
* * *
21963640 CAGATCTCCC-CTAAACAGCCCTCTT-CTATGCCTAAATCGGACTCTCCCTTCACCAGTACCAAC
1 CAGATCTCCCTCT--ACAGCCCTCTTCCTATACCCAAATCGGACTCTCCCTTCACCAGCACCAAC
21963703 CAACCCCACGC
64 CAACCCCACGC
* ** * * * * *
21963714 CAGATCTCCCTCTGCCTCTCTCTTCCTTTACCCAAATCGGACTCTCCCTTCACCGGCGCCAGCCA
1 CAGATCTCCCTCTACAGCCCTCTTCCTATACCCAAATCGGACTCTCCCTTCACCAGCACCAACCA
21963779 ACCCCACGC
66 ACCCCACGC
*
21963788 CGGATCTCCCTCT
1 CAGATCTCCCTCT
21963801 GCCGCTTCAC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
73 7 0.10
74 64 0.88
75 2 0.03
ACGTcount: A:0.20, C:0.47, G:0.11, T:0.22
Consensus pattern (74 bp):
CAGATCTCCCTCTACAGCCCTCTTCCTATACCCAAATCGGACTCTCCCTTCACCAGCACCAACCA
ACCCCACGC
Found at i:21965127 original size:24 final size:25
Alignment explanation
Indices: 21965087--21965156 Score: 97
Period size: 24 Copynumber: 2.8 Consensus size: 25
21965077 AACATTCATG
* * *
21965087 CAATGTCGTACAAATAACAGTTGCA
1 CAATGTCATACATATAACAGTTACA
21965112 CAATG-CATACATATAACAGTTACA
1 CAATGTCATACATATAACAGTTACA
*
21965136 CATTGTCATACATATAACAGT
1 CAATGTCATACATATAACAGT
21965157 CACGCATTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (25 bp):
CAATGTCATACATATAACAGTTACA
Found at i:21965164 original size:25 final size:25
Alignment explanation
Indices: 21965117--21965212 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
21965107 TTGCACAATG
* * * *
21965117 CATACATATAACAGTTACACATTGT
1 CATACAGATAACAGTCACGCATTGC
*
21965142 CATACATATAACAGTCACGCATTGC
1 CATACAGATAACAGTCACGCATTGC
* * *
21965167 CATATAGATAATAGTCACGCAATGC
1 CATACAGATAACAGTCACGCATTGC
* *
21965192 CCTACAGATAACAATCACGCA
1 CATACAGATAACAGTCACGCA
21965213 ATGACCTGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (25 bp):
CATACAGATAACAGTCACGCATTGC
Done.