Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 35 of 82
Found at i:12834584 original size:13 final size:13
Alignment explanation
Indices: 12834556--12834619 Score: 74
Period size: 13 Copynumber: 4.7 Consensus size: 13
12834546 TTCTCATTTC
*
12834556 TTATTATTTAATTA
1 TTATT-TTTTATTA
12834570 TTATTTTTTATTA
1 TTATTTTTTATTA
*
12834583 TTATATTTTCTATTC
1 TTAT-TTTT-TATTA
*
12834598 TTATTTCTTATTA
1 TTATTTTTTATTA
12834611 TTATTTTTT
1 TTATTTTTT
12834620 CATACTTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
13 23 0.53
14 12 0.28
15 8 0.19
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTTTATTA
Found at i:12834649 original size:43 final size:41
Alignment explanation
Indices: 12834566--12834651 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 41
12834556 TTATTATTTA
* * *
12834566 ATTATTATTTTTTATTATTATATTTTCTATTCTTATTTCTT
1 ATTATTATTTTTTATTATTACATTTTCTATTCTAAGTTCTT
*
12834607 ATTATTATTTTTTCA-TACTTTACATTTTTTATTCTAAGTTCTT
1 ATTATTATTTTTT-ATTA--TTACATTTTCTATTCTAAGTTCTT
12834650 AT
1 AT
12834652 ATTTTCCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 15 0.39
42 1 0.03
43 22 0.58
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.66
Consensus pattern (41 bp):
ATTATTATTTTTTATTATTACATTTTCTATTCTAAGTTCTT
Found at i:12840501 original size:18 final size:18
Alignment explanation
Indices: 12840480--12840514 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12840470 AAAAAAAGAA
12840480 AAGGAAAGAAAA-GAAAAC
1 AAGGAAA-AAAATGAAAAC
12840498 AAGGAAAAAAATGAAAA
1 AAGGAAAAAAATGAAAA
12840515 TCTTGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (18 bp):
AAGGAAAAAAATGAAAAC
Found at i:12845638 original size:49 final size:51
Alignment explanation
Indices: 12845578--12845769 Score: 192
Period size: 55 Copynumber: 3.6 Consensus size: 51
12845568 GTAACTACAC
* * * *
12845578 ATGTGCGGTGTGGGAGTGCACATGCCGGTGATGA-C-A-GGTGATTCCAGCT
1 ATGTGCAGTGTGGGAGTGCACATG-AGCTGATGACCGATGATGATTCCAGCT
*
12845627 ATGTGCAGTGTGGGAGTGCATATGAGCTGATGACCGGTGGATGATGATTCCAGCT
1 ATGTGCAGTGTGGGAGTGCACATGAGCTGATGACC----GATGATGATTCCAGCT
* * *
12845682 ATGTGCAGTGTGGGAGTGCACATGAGCTGATGACTGGTGGATGACTATTCTAGCT
1 ATGTGCAGTGTGGGAGTGCACATGAGCTGATGACCGAT-GATG---ATTCCAGCT
* *
12845737 ATGTGCGGTGTGGGAGTGCACATAAGCTGATGA
1 ATGTGCAGTGTGGGAGTGCACATGAGCTGATGA
12845770 GCCAATGGTT
Statistics
Matches: 121, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
48 7 0.06
49 23 0.19
51 2 0.02
52 4 0.03
54 1 0.01
55 84 0.69
ACGTcount: A:0.21, C:0.15, G:0.37, T:0.27
Consensus pattern (51 bp):
ATGTGCAGTGTGGGAGTGCACATGAGCTGATGACCGATGATGATTCCAGCT
Found at i:12845689 original size:55 final size:56
Alignment explanation
Indices: 12845616--12845769 Score: 249
Period size: 55 Copynumber: 2.8 Consensus size: 56
12845606 TGATGACAGG
*
12845616 TGATTCCAGCTATGTGCAGTGTGGGAGTGCATATGAGCTGATGACCGGTGGATGA-
1 TGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAC
*
12845671 TGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTGATGACTGGTGGATGAC
1 TGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAC
* * *
12845727 T-ATTCTAGCTATGTGCGGTGTGGGAGTGCACATAAGCTGATGA
1 TGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTGATGA
12845770 GCCAATGGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
55 92 0.99
56 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (56 bp):
TGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAC
Found at i:12853711 original size:18 final size:19
Alignment explanation
Indices: 12853685--12853732 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12853675 ATGACAGGTG
*
12853685 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
12853703 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
12853722 AAAATAATATT
1 AAAATAATATT
12853733 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:12860282 original size:36 final size:35
Alignment explanation
Indices: 12860235--12860338 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 35
12860225 TATAAGGCAT
*
12860235 TGTAAAGGTTATAGTTTGATCTCATTAAAAAG-CAAA
1 TGTAAAGGTTAT-GCTTGATCTCATTAAAAAGTC-AA
*
12860271 TGT-AAGAGTTATCGCTTGATCTCATGAAAAAGTCAA
1 TGTAAAG-GTTAT-GCTTGATCTCATTAAAAAGTCAA
*
12860307 TGTAAAGGTTATGACTTGATCCCATTAAAAAG
1 TGTAAAGGTTATG-CTTGATCTCATTAAAAAG
12860339 AAAAAATCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
35 4 0.07
36 51 0.86
37 4 0.07
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (35 bp):
TGTAAAGGTTATGCTTGATCTCATTAAAAAGTCAA
Found at i:12861602 original size:31 final size:31
Alignment explanation
Indices: 12861549--12861666 Score: 127
Period size: 31 Copynumber: 3.8 Consensus size: 31
12861539 TTTAAGGAGA
*
12861549 AGGACTAAATTTAAAAGTAAAGAAAATGTTGG
1 AGGACTAAATTAAAAAG-AAAGAAAATGTTGG
*
12861581 AGG-CTTAAA-TAGAAATGAAAGAAAATGTTGG
1 AGGAC-TAAATTA-AAAAGAAAGAAAATGTTGG
*
12861612 AGGACTAAATTAAAAAGAAAGAAAATGTTGTT
1 AGGACTAAATTAAAAAGAAAGAAAATGTTG-G
* *
12861644 A-AACTAAATT-AAAAGAAAAAAAA
1 AGGACTAAATTAAAAAGAAAGAAAA
12861667 AAGGGTAAGG
Statistics
Matches: 75, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
30 12 0.16
31 48 0.64
32 15 0.20
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (31 bp):
AGGACTAAATTAAAAAGAAAGAAAATGTTGG
Found at i:12862520 original size:30 final size:30
Alignment explanation
Indices: 12862486--12862576 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
12862476 TATATGGAAT
*
12862486 TATAACCTTTTTTTACTTTTTCTATAGAGG
1 TATAACCTTTCTTTACTTTTTCTATAGAGG
* * *
12862516 TATAACCTTTCTCTACCTTTTCTATGGAGG
1 TATAACCTTTCTTTACTTTTTCTATAGAGG
12862546 TATAACCTTTCTTTACCTTTTTCTAATAGAG
1 TATAACCTTTCTTTA-CTTTTTCT-ATAGAG
12862577 TTATGATCGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
30 40 0.77
31 7 0.13
32 5 0.10
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (30 bp):
TATAACCTTTCTTTACTTTTTCTATAGAGG
Found at i:12862675 original size:31 final size:31
Alignment explanation
Indices: 12862509--12862682 Score: 127
Period size: 31 Copynumber: 5.6 Consensus size: 31
12862499 TACTTTTTCT
* * *
12862509 ATAGAGGTATAACCTTTCTCTACCTTTT-CT
1 ATAGAGGTATAACCTTACACTACCTTTTGCA
* * ** *
12862539 ATGGAGGTATAACCTTTCTTTACCTTTTTCTA
1 ATAGAGGTATAACCTTACACTACCTTTTGC-A
* * * * *
12862571 ATAGAGTTATGATCGTACACTA-CTGTTTACA
1 ATAGAGGTATAACCTTACACTACCT-TTTGCA
* * * *
12862602 ACAAAAGTATAACTTTACACTACCTTTTGCA
1 ATAGAGGTATAACCTTACACTACCTTTTGCA
* * *
12862633 ATGGTGGTATAACCTTACACTACCTTTTGTA
1 ATAGAGGTATAACCTTACACTACCTTTTGCA
*
12862664 ATAGAGTTATAACCTTACA
1 ATAGAGGTATAACCTTACA
12862683 ACAGTGGAAT
Statistics
Matches: 109, Mismatches: 31, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
30 26 0.24
31 63 0.58
32 20 0.18
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (31 bp):
ATAGAGGTATAACCTTACACTACCTTTTGCA
Found at i:12866589 original size:40 final size:40
Alignment explanation
Indices: 12866527--12866702 Score: 257
Period size: 40 Copynumber: 4.4 Consensus size: 40
12866517 TGGCACTGAT
*
12866527 TGTGCACAATGTTGGGGG-ATGCACACGATGGTGCCGGCTA
1 TGTGCACAATG-TGGGGGAATGCACACAATGGTGCCGGCTA
* *
12866567 TGTGCACGATGTGGGGGAATGCACACAATGGTGCCGACTA
1 TGTGCACAATGTGGGGGAATGCACACAATGGTGCCGGCTA
*
12866607 TGTGCACAATGTGGGGGGATGCACACAATGGTGCCGGCTA
1 TGTGCACAATGTGGGGGAATGCACACAATGGTGCCGGCTA
* * *
12866647 TATGCACGATGT-GGGGAATGCAGACAATGGTGCCGGCTA
1 TGTGCACAATGTGGGGGAATGCACACAATGGTGCCGGCTA
*
12866686 TGTGCACAATGAGGGGG
1 TGTGCACAATGTGGGGG
12866703 GATGTACATG
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 40 0.33
40 81 0.67
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (40 bp):
TGTGCACAATGTGGGGGAATGCACACAATGGTGCCGGCTA
Found at i:12866681 original size:79 final size:80
Alignment explanation
Indices: 12866527--12866706 Score: 299
Period size: 80 Copynumber: 2.3 Consensus size: 80
12866517 TGGCACTGAT
* * *
12866527 TGTGCACAATGTTGGGGGATGCACACGATGGTGCCGGCTATGTGCACGATGTGGGGGAATGCACA
1 TGTGCACAATGTGGGGGGATGCACACAATGGTGCCGGCTATATGCACGATGTGGGGGAATGCACA
12866592 CAATGGTGCCGACTA
66 CAATGGTGCCGACTA
*
12866607 TGTGCACAATGTGGGGGGATGCACACAATGGTGCCGGCTATATGCACGATGT-GGGGAATGCAGA
1 TGTGCACAATGTGGGGGGATGCACACAATGGTGCCGGCTATATGCACGATGTGGGGGAATGCACA
*
12866671 CAATGGTGCCGGCTA
66 CAATGGTGCCGACTA
*
12866686 TGTGCACAATGAGGGGGGATG
1 TGTGCACAATGTGGGGGGATG
12866707 TACATGAGTC
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 45 0.48
80 49 0.52
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (80 bp):
TGTGCACAATGTGGGGGGATGCACACAATGGTGCCGGCTATATGCACGATGTGGGGGAATGCACA
CAATGGTGCCGACTA
Found at i:12868466 original size:40 final size:38
Alignment explanation
Indices: 12868360--12868466 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 38
12868350 ATAGTGCTTG
* * *
12868360 TGTGCACGATGTGGGGCGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
* * * * *
12868398 TGTGCGCAATGTGGGGGGGATGCACATGATGGCGCCGGCT
1 TGTGCACGATGT-GGGGGGATGTACATGATGGC-ACGGAT
12868438 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
12868467 GTTGGGTGTG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
38 10 0.18
39 17 0.31
40 18 0.33
41 10 0.18
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.22
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
Found at i:12871196 original size:12 final size:12
Alignment explanation
Indices: 12871179--12871220 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
12871169 AAAAGACAAC
12871179 AAAGAAAGAGAA
1 AAAGAAAGAGAA
12871191 AAAGAAAGAGAA
1 AAAGAAAGAGAA
*
12871203 GATA-AAAGAGAA
1 -AAAGAAAGAGAA
12871215 AGAAGA
1 A-AAGA
12871221 GAGTGGGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.04
12 21 0.84
13 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:12871214 original size:18 final size:16
Alignment explanation
Indices: 12871179--12871222 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
12871169 AAAAGACAAC
12871179 AAAGAAAGAGAAAAAG
1 AAAGAAAGAGAAAAAG
*
12871195 AAAGAGAAGATAAAAGAG
1 AAAGA-AAGAGAAAA-AG
12871213 AAAG-AAGAGA
1 AAAGAAAGAGA
12871223 GTGGGGGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (16 bp):
AAAGAAAGAGAAAAAG
Found at i:12871436 original size:15 final size:16
Alignment explanation
Indices: 12871413--12871447 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12871403 GAGAAGAATG
*
12871413 AGAAGGAAAAA-AAAA
1 AGAAAGAAAAAGAAAA
12871428 AGAAAGAAAAAGAAAA
1 AGAAAGAAAAAGAAAA
12871444 AGAA
1 AGAA
12871448 TGAGAGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAGAAAA
Found at i:12871518 original size:18 final size:18
Alignment explanation
Indices: 12871495--12871529 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12871485 GAGAGAAGGC
12871495 AGAAG-AGAAGAAAGAAAA
1 AGAAGAAGAA-AAAGAAAA
12871513 AGAAGAAGAAAAAGAAA
1 AGAAGAAGAAAAAGAAA
12871530 GGGAGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAAAGAAAA
Found at i:12871522 original size:12 final size:13
Alignment explanation
Indices: 12871500--12871528 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12871490 AAGGCAGAAG
12871500 AGAAGAAAGAAAA
1 AGAAGAAAGAAAA
12871513 AGAAG-AAGAAAA
1 AGAAGAAAGAAAA
12871525 AGAA
1 AGAA
12871529 AGGGAGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAGAAAGAAAA
Found at i:12872827 original size:43 final size:43
Alignment explanation
Indices: 12872764--12872875 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
12872754 CATTGACTCG
* *
12872764 GCTATGTGCGAGTAAGGAGTGCGCATAAGTCAAG-GATGACCC-
1 GCTATGTGCGAGTAGGGAGTGCGCATAACTC-AGTGATGACCCA
* *
12872806 GATTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACTCAGTGATGACCCA
* *
12872850 GCCATGTGCAAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
12872876 GAGCTGGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.03
43 57 0.95
44 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACTCAGTGATGACCCA
Found at i:12875046 original size:60 final size:60
Alignment explanation
Indices: 12874869--12875336 Score: 651
Period size: 60 Copynumber: 7.8 Consensus size: 60
12874859 TTGATTGTAA
*
12874869 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
1 AAAGAGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* * * *
12874929 AAA-AGGGGACTTGAAGCCCCGATTTATA-TTGGTGACATGGGTAGTTCCCACAAGTAGGT
1 AAAGA-GGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* * * *
12874988 AAAGAAGGACTTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCTCACGAGTAGGT
1 AAAGAGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* * * *
12875048 AAAGGGGGACTTGAAGCCCCAATTTATATTTGGTGATGTGGGTAGTTCCCACGAGTAGGC
1 AAAGAGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* *
12875108 AAA-AGGGGACCTAAAGCCCCGATTTATATTTGGTGATGTGGGTAGTTCCCACGAGTAGGC
1 AAAGA-GGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* *
12875168 AAAGGGGGACCTGAAGCCTCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
1 AAAGAGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* * *
12875228 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACGAGTAGGT
1 AAAGAGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* * * *
12875288 AAA-AGGGGACCTGAACCCCCGATTCATA--TGGTGGCATGGGTAGTTCCCA
1 AAAGA-GGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCA
12875337 TAAGTAGGTG
Statistics
Matches: 370, Mismatches: 32, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
58 18 0.05
59 53 0.14
60 299 0.81
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (60 bp):
AAAGAGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
Found at i:12875236 original size:180 final size:180
Alignment explanation
Indices: 12874869--12875344 Score: 742
Period size: 180 Copynumber: 2.7 Consensus size: 180
12874859 TTGATTGTAA
12874869 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGCAAAAG
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGCAAAAG
* *
12874934 GGGACTTGAAGCCCCGATTTATA-TTGGTGACATGGGTAGTTCCCACAAGTAGGTAAAGAAGGAC
66 GGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACAAGTAGGCAAAGAAGGAC
* * *
12874998 TTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCTCACGAGTAGGT
131 CTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* * *
12875048 AAAGGGGGACTTGAAGCCCCAATTTATATTTGGTGATGTGGGTAGTTCCCACGAGTAGGCAAAAG
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGCAAAAG
* ** * **
12875113 GGGACCTAAAGCCCCGATTTATATTTGGTGATGTGGGTAGTTCCCACGAGTAGGCAAAGGGGGAC
66 GGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACAAGTAGGCAAAGAAGGAC
*
12875178 CTGAAGCCTCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
131 CTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
* *
12875228 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACGAGTAGGTAAAAG
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGCAAAAG
* * * *
12875293 GGGACCTGAACCCCCGATTCATA--TGGTGGCATGGGTAGTTCCCATAAGTAGG
66 GGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACAAGTAGG
12875345 TGATGATGTC
Statistics
Matches: 268, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
178 24 0.09
179 83 0.31
180 161 0.60
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (180 bp):
AAAGGGGGACCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGCAAAAG
GGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACAAGTAGGCAAAGAAGGAC
CTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGC
Found at i:12876784 original size:59 final size:59
Alignment explanation
Indices: 12876692--12876820 Score: 206
Period size: 59 Copynumber: 2.2 Consensus size: 59
12876682 GTTTATTTGA
* * *
12876692 GAGCATGAGTCTGTTGAGCTTGGTTTAAGATGCTATTGAGCATGATTTGACTTACTAAT
1 GAGCATGAGTTTATTGAGCTTGGTTTAAGATGCTATTGAGCATGAATTGACTTACTAAT
* *
12876751 GAGCATGAGTTTATTGAGCTTGGTTTAAGATGCTGTTGAGCATGAATTGACTTACTAGT
1 GAGCATGAGTTTATTGAGCTTGGTTTAAGATGCTATTGAGCATGAATTGACTTACTAAT
12876810 GAGCAT-AGTTT
1 GAGCATGAGTTT
12876821 TGGATTTTGC
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 5 0.08
59 60 0.92
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (59 bp):
GAGCATGAGTTTATTGAGCTTGGTTTAAGATGCTATTGAGCATGAATTGACTTACTAAT
Found at i:12880878 original size:12 final size:12
Alignment explanation
Indices: 12880861--12880885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12880851 GTATCTTCAA
12880861 AGGTTAAGTGAT
1 AGGTTAAGTGAT
12880873 AGGTTAAGTGAT
1 AGGTTAAGTGAT
12880885 A
1 A
12880886 TTATTGCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AGGTTAAGTGAT
Found at i:12886572 original size:29 final size:28
Alignment explanation
Indices: 12886538--12886694 Score: 179
Period size: 29 Copynumber: 5.4 Consensus size: 28
12886528 TTTAACATGC
12886538 TTGTCTTAATTTAGACAAGAAAATATGT
1 TTGTCTTAATTTAGACAAGAAAATATGT
*
12886566 TTGGTCTTAATTTAGATAAGAAAATATGT
1 TT-GTCTTAATTTAGACAAGAAAATATGT
*
12886595 TTGTCTTAATTTAAGACAAGAAAAATATTTT
1 TTGTCTTAATTT-AGACAAG-AAAATA-TGT
* ** *
12886626 TTGTCTTAATCTAGACAAGAAACCATAT
1 TTGTCTTAATTTAGACAAGAAAATATGT
* *
12886654 TTGTCTCAATTTAGACAAGATAAAATATTT
1 TTGTCTTAATTTAGACAAG--AAAATATGT
*
12886684 TTGCCTTAATT
1 TTGTCTTAATT
12886695 AAAGACAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
28 31 0.28
29 37 0.34
30 28 0.26
31 13 0.12
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (28 bp):
TTGTCTTAATTTAGACAAGAAAATATGT
Found at i:12886633 original size:59 final size:58
Alignment explanation
Indices: 12886538--12886694 Score: 201
Period size: 59 Copynumber: 2.7 Consensus size: 58
12886528 TTTAACATGC
* * * * *
12886538 TTGTCTTAATTTAGACAAG-AAAATATGTTTGGTCTTAATTTAGATAAGAAAATATGT
1 TTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAACATAT
* *
12886595 TTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAAACCATAT
1 TTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAACATAT
* *
12886654 TTGTCTCAATTTAGACAAGATAAAATA-TTTTTGCCTTAATT
1 TTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAATT
12886695 AAAGACAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 12 0.14
58 27 0.31
59 48 0.55
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (58 bp):
TTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAACATAT
Found at i:12886867 original size:17 final size:17
Alignment explanation
Indices: 12886845--12886877 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12886835 ATAATAATAA
12886845 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
12886862 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
12886878 TTATCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:12893897 original size:17 final size:17
Alignment explanation
Indices: 12893852--12893897 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
12893842 TTTCAAGACA
*
12893852 ATTTATAAAATCATTTC
1 ATTTATAAAAACATTTC
* *
12893869 A-TT-TAAACACATTTT
1 ATTTATAAAAACATTTC
12893884 ATTTATAAAAACAT
1 ATTTATAAAAACAT
12893898 AAAGATTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTATAAAAACATTTC
Found at i:12902686 original size:33 final size:32
Alignment explanation
Indices: 12902648--12902711 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
12902638 AATAAGTAAT
*
12902648 ATTATTTAACTTAAAAA-ATATTTAAATTAATTA
1 ATTA-TTAACTTAAAAACATAATTAAA-TAATTA
**
12902681 ATTATTATGTTAAAAACATAATTAAATAATT
1 ATTATTAACTTAAAAACATAATTAAATAATT
12902712 TAGTTAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (32 bp):
ATTATTAACTTAAAAACATAATTAAATAATTA
Found at i:12913102 original size:2 final size:2
Alignment explanation
Indices: 12913095--12913179 Score: 143
Period size: 2 Copynumber: 42.5 Consensus size: 2
12913085 TACTGTGTTG
12913095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
12913137 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12913179 A
1 A
12913180 CGAACAATGT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12913286 original size:61 final size:61
Alignment explanation
Indices: 12913191--12913308 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 61
12913181 GAACAATGTT
12913191 GTGATACTTACAACCGTGCATGTGCAGAGAGGGCAGTGCACATG-TCGGTAATGATGCTATC
1 GTGATACTTACAACCGTGCATGTGCAGAGAGGGCAGTGCACATGCT-GGTAATGATGCTATC
* * *
12913252 GTGATATTTACAACCGTGCTTGTGCGGAGAGGGCAGTGCACATGCTGGTAATGATGC
1 GTGATACTTACAACCGTGCATGTGCAGAGAGGGCAGTGCACATGCTGGTAATGATGC
12913309 ACATAAGCTG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
61 52 0.98
62 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (61 bp):
GTGATACTTACAACCGTGCATGTGCAGAGAGGGCAGTGCACATGCTGGTAATGATGCTATC
Found at i:12916987 original size:28 final size:28
Alignment explanation
Indices: 12916955--12917011 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12916945 AAAACCTAGA
12916955 ATGACTTAATATGGTGATTCAGAGTTTG
1 ATGACTTAATATGGTGATTCAGAGTTTG
12916983 ATGACTTAATATGGTGATTCAGAGTTTG
1 ATGACTTAATATGGTGATTCAGAGTTTG
12917011 A
1 A
12917012 GGATTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.39
Consensus pattern (28 bp):
ATGACTTAATATGGTGATTCAGAGTTTG
Found at i:12924336 original size:44 final size:44
Alignment explanation
Indices: 12924219--12924337 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 44
12924209 ACATTTCAAC
** * * *
12924219 ATCATCATGTTTGTGTGCTCCCCCACATCACGCACATAGGCAAT
1 ATCATCATCATTGTGTGCTCCCCCACATCGCACACAAAGGCAAT
*
12924263 ATCATCACCATTGTGTGCTCCCCCACATCGCACACAAAGGCAAT
1 ATCATCATCATTGTGTGCTCCCCCACATCGCACACAAAGGCAAT
12924307 ATCATCATCATTGTGTGCTCCCCCACATCGC
1 ATCATCATCATTGTGTGCTCCCCCACATCGC
12924338 GCGCAACTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.25
Consensus pattern (44 bp):
ATCATCATCATTGTGTGCTCCCCCACATCGCACACAAAGGCAAT
Found at i:12926207 original size:2 final size:2
Alignment explanation
Indices: 12926200--12926237 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12926190 AATCATCTCC
12926200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12926238 TTGTGTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12926288 original size:2 final size:2
Alignment explanation
Indices: 12926281--12926314 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12926271 TCCATCACTN
12926281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12926315 GTATTTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12926320 original size:81 final size:80
Alignment explanation
Indices: 12926200--12926364 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 80
12926190 AATCATCTCC
12926200 ATATATATATATATATATATATATATATATATATATATTTGTGTATGTACATACACATTTAAGAA
1 ATATATATATATATATATATATATATATATATATATATTTGTGTATGTACATACACATTTAAGAA
12926265 TCATCATCCATCACT
66 TCATCATCCATCACT
*
12926280 NATATATATATATATATATATATATATATATATATGTATTTGTGTATGTACATACACATTTAAGA
1 -ATATATATATATATATATATATATATATATATATATATTTGTGTATGTACATACACATTTAAGA
12926345 ATCATCATCCATCACT
65 ATCATCATCCATCACT
12926361 ATAT
1 ATAT
12926365 GTAGGGACCC
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 4 0.05
81 79 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.42
Consensus pattern (80 bp):
ATATATATATATATATATATATATATATATATATATATTTGTGTATGTACATACACATTTAAGAA
TCATCATCCATCACT
Found at i:12931316 original size:44 final size:44
Alignment explanation
Indices: 12931195--12931317 Score: 192
Period size: 44 Copynumber: 2.8 Consensus size: 44
12931185 TTGCACATTT
** * * *
12931195 CAATATCATCATGTTTGTGTGCTCCCCCACATCCCCCACATAGG
1 CAATATCATCATCATTGTGTGCTCCCCCACATCGCACACAAAGG
*
12931239 CAATATCATCACCATTGTGTGCTCCCCCACATCGCACACAAAGG
1 CAATATCATCATCATTGTGTGCTCCCCCACATCGCACACAAAGG
12931283 CAATATCATCATCATTGTGTGCTCCCCCACATCGC
1 CAATATCATCATCATTGTGTGCTCCCCCACATCGC
12931318 GCGCAACTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.25, C:0.37, G:0.13, T:0.25
Consensus pattern (44 bp):
CAATATCATCATCATTGTGTGCTCCCCCACATCGCACACAAAGG
Found at i:12932156 original size:20 final size:20
Alignment explanation
Indices: 12932131--12932170 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12932121 AGAAGAACAA
12932131 GAAGCTACTGGAAAAATGAG
1 GAAGCTACTGGAAAAATGAG
* *
12932151 GAAGCTGCTGGAGAAATGAG
1 GAAGCTACTGGAAAAATGAG
12932171 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:12936033 original size:67 final size:67
Alignment explanation
Indices: 12935955--12936090 Score: 191
Period size: 67 Copynumber: 2.0 Consensus size: 67
12935945 GAAAAGTTAG
* **
12935955 TTTTGGGTTTTGGTTGATCTTGGGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTATGAAAAGC
1 TTTTGAGTTTTGGTTGATCCCGGGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTATGAAAAGC
12936020 CA
66 CA
* * * * * *
12936022 TTTTGAGTTTTGGTTGATCCCGTGAAAATCCATTGTTAAAGGTTGTGGCTGAGCTTGTGAAATGC
1 TTTTGAGTTTTGGTTGATCCCGGGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTATGAAAAGC
12936087 CA
66 CA
12936089 TT
1 TT
12936091 GTAAAAGCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (67 bp):
TTTTGAGTTTTGGTTGATCCCGGGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTATGAAAAGC
CA
Found at i:12936082 original size:35 final size:35
Alignment explanation
Indices: 12935978--12936097 Score: 104
Period size: 35 Copynumber: 3.5 Consensus size: 35
12935968 TTGATCTTGG
* * *
12935978 GAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTAT
1 GAAAATCCATTGTTAAAGGTTGTGGCTGAGCCTGT
* * * * * *
12936013 GAAAAGCCATT-TT-GA-GTTTTGGTTGATCCCGT
1 GAAAATCCATTGTTAAAGGTTGTGGCTGAGCCTGT
*
12936045 GAAAATCCATTGTTAAAGGTTGTGGCTGAGCTTGT
1 GAAAATCCATTGTTAAAGGTTGTGGCTGAGCCTGT
*
12936080 G-AAATGCCATTGTAAAAG
1 GAAAAT-CCATTGTTAAAG
12936098 CTTGGTGGAA
Statistics
Matches: 65, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
32 22 0.34
33 3 0.05
34 6 0.09
35 34 0.52
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (35 bp):
GAAAATCCATTGTTAAAGGTTGTGGCTGAGCCTGT
Found at i:12937011 original size:21 final size:21
Alignment explanation
Indices: 12936980--12937038 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
12936970 TTGTGAACTT
12936980 AATT-CAT-ATGCTTTTGATG
1 AATTGCATGATGCTTTTGATG
12936999 AATTGCATGATGCTTTTGATG
1 AATTGCATGATGCTTTTGATG
12937020 AATTGCATGATGCTTTTGA
1 AATTGCATGATGCTTTTGA
12937039 GGATTTAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 31 0.82
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.44
Consensus pattern (21 bp):
AATTGCATGATGCTTTTGATG
Found at i:12941114 original size:21 final size:22
Alignment explanation
Indices: 12941072--12941114 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12941062 CCACCAGAGA
*
12941072 GTTTCTCGCTGCAGCGAGATTT
1 GTTTCTCGCTGCAGCGAAATTT
*
12941094 GTTT-TCGCTGCAGGGAAATTT
1 GTTTCTCGCTGCAGCGAAATTT
12941115 CCTTGCTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (22 bp):
GTTTCTCGCTGCAGCGAAATTT
Found at i:12941481 original size:43 final size:42
Alignment explanation
Indices: 12941420--12941552 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 42
12941410 CGGGTCATCA
*
12941420 TCATAGGCTTATGAGCACTCCTTACTCGCACATGGCCAGGTCG
1 TCATAGGCTTATGAGCACTCC-TACTCGCACATAGCCAGGTCG
* * * * *
12941463 TCATCGGCTTATGCGCACTCCCTACTCGTACATAGCCGGGTCA
1 TCATAGGCTTATGAGCACT-CCTACTCGCACATAGCCAGGTCG
* * * *
12941506 TCATTA-GCTCATGTGCACTCCCACATCGCACATAGCTAGGTCG
1 TCA-TAGGCTTATGAGCACTCCTAC-TCGCACATAGCCAGGTCG
12941549 TCAT
1 TCAT
12941553 TATCACACAA
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
42 5 0.07
43 65 0.89
44 3 0.04
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.26
Consensus pattern (42 bp):
TCATAGGCTTATGAGCACTCCTACTCGCACATAGCCAGGTCG
Found at i:12941553 original size:43 final size:43
Alignment explanation
Indices: 12941434--12941554 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
12941424 AGGCTTATGA
* * ** *
12941434 GCACTCCTTACTCGCACATGGCCAGGTCGTCATCGGCTTATGC
1 GCACTCCCTACTCGCACATAGCCAGGTCGTCATTAGCTCATGC
* * * *
12941477 GCACTCCCTACTCGTACATAGCCGGGTCATCATTAGCTCATGT
1 GCACTCCCTACTCGCACATAGCCAGGTCGTCATTAGCTCATGC
*
12941520 GCACTCCC-ACATCGCACATAGCTAGGTCGTCATTA
1 GCACTCCCTAC-TCGCACATAGCCAGGTCGTCATTA
12941555 TCACACAACA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 2 0.03
43 62 0.97
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.26
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAGCCAGGTCGTCATTAGCTCATGC
Found at i:12948272 original size:35 final size:35
Alignment explanation
Indices: 12948161--12948279 Score: 127
Period size: 35 Copynumber: 3.5 Consensus size: 35
12948151 TGATCCCAGA
*
12948161 AAAAACCATTGTTAAAGGTTGTAGCTGAGCTTGTG
1 AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTG
** * * * * *
12948196 AAAAGTCATT-TT-GA-GTTTTGGTTGATCTCGTG
1 AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTG
12948228 AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTG
1 AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTG
* *
12948263 AAAAGCCATTGTAAAAG
1 AAAAACCATTGTTAAAG
12948280 TTTGGCGGAA
Statistics
Matches: 64, Mismatches: 17, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
32 21 0.33
33 3 0.05
34 3 0.05
35 37 0.58
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTG
Found at i:12950027 original size:29 final size:28
Alignment explanation
Indices: 12949980--12950062 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
12949970 TTAGACATGT
*
12949980 AACAA-AAATTTTTTAAACATGGTATGG
1 AACAACAAATTTTTTCAACATGGTATGG
* *
12950007 AACAACAATATTTTTTCAACATGCAGTGTGT
1 AACAACAA-ATTTTTTCAACATG--GTATGG
*
12950038 AACAACAACATTTTTTTCAATATGG
1 AACAACAA-A-TTTTTTCAACATGG
12950063 CGTGTAACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 5 0.11
28 2 0.04
29 13 0.28
30 1 0.02
31 13 0.28
32 12 0.26
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (28 bp):
AACAACAAATTTTTTCAACATGGTATGG
Found at i:12950045 original size:31 final size:28
Alignment explanation
Indices: 12949976--12950053 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 28
12949966 TATTTTAGAC
12949976 ATGTAACAA-AAATTTTTTAAACATGGT
1 ATGTAACAACAAATTTTTTAAACATGGT
* *
12950003 ATGGAACAACAATATTTTTTCAACATGCAGT
1 ATGTAACAACAA-ATTTTTTAAACATG--GT
*
12950034 GTGTAACAACAACATTTTTT
1 ATGTAACAACAA-ATTTTTT
12950054 TCAATATGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 8 0.19
28 2 0.05
29 13 0.31
31 19 0.45
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (28 bp):
ATGTAACAACAAATTTTTTAAACATGGT
Found at i:12953466 original size:37 final size:37
Alignment explanation
Indices: 12953416--12953492 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
12953406 ACTGCAAAAA
12953416 GAGGGTCAAGTGCTAGAGAGAATTCTACGAAAGAATG
1 GAGGGTCAAGTGCTAGAGAGAATTCTACGAAAGAATG
*
12953453 GAGGGTCCAGTGCTAGAGAGAATTCTACGAAAGAATG
1 GAGGGTCAAGTGCTAGAGAGAATTCTACGAAAGAATG
12953490 GAG
1 GAG
12953493 TCGTACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.34, T:0.18
Consensus pattern (37 bp):
GAGGGTCAAGTGCTAGAGAGAATTCTACGAAAGAATG
Found at i:12959745 original size:2 final size:2
Alignment explanation
Indices: 12959733--12959786 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
12959723 AAGTTAGAAC
* * ** *
12959733 GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA AA AA CC NA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12959774 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
12959787 GACTAACCGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.04, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12961937 original size:20 final size:20
Alignment explanation
Indices: 12961889--12961938 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
12961879 TATTTCATGA
*
12961889 CTTTGAAACTGAAACAACAT
1 CTTTGAAATTGAAACAACAT
*
12961909 CTTTGAAATTGAAACAATAT
1 CTTTGAAATTGAAACAACAT
12961929 CTTTGAAATT
1 CTTTGAAATT
12961939 AAAATTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (20 bp):
CTTTGAAATTGAAACAACAT
Found at i:12970652 original size:11 final size:11
Alignment explanation
Indices: 12970638--12970667 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12970628 AATAATATTT
12970638 TATTAATAAAA
1 TATTAATAAAA
*
12970649 TATTATTAAAA
1 TATTAATAAAA
12970660 TATTAATA
1 TATTAATA
12970668 TTTTATTTAG
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:12971257 original size:19 final size:20
Alignment explanation
Indices: 12971230--12971275 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12971220 AGGAGACAAG
*
12971230 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
12971249 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
12971268 ATAATATT
1 ATAATATT
12971276 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:12973107 original size:13 final size:13
Alignment explanation
Indices: 12973089--12973113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12973079 AGAGAAATTG
12973089 TGATTTTATAAAA
1 TGATTTTATAAAA
12973102 TGATTTTATAAA
1 TGATTTTATAAA
12973114 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12974529 original size:15 final size:15
Alignment explanation
Indices: 12974509--12974546 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12974499 CAGATATTTT
12974509 GATTTTAAAGCTTTG
1 GATTTTAAAGCTTTG
* *
12974524 GATTTTAAAGTTTTT
1 GATTTTAAAGCTTTG
12974539 GATTTTAA
1 GATTTTAA
12974547 GGTTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (15 bp):
GATTTTAAAGCTTTG
Found at i:12974632 original size:5 final size:5
Alignment explanation
Indices: 12974592--12974631 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
12974582 CCCCAAGTCC
* *
12974592 AGTTA AGTTA AGATA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
12974632 GATTGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
AGTTA
Found at i:12980180 original size:13 final size:13
Alignment explanation
Indices: 12980162--12980186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12980152 AGAGAAATTG
12980162 TGATTTTATAAAA
1 TGATTTTATAAAA
12980175 TGATTTTATAAA
1 TGATTTTATAAA
12980187 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12982415 original size:61 final size:61
Alignment explanation
Indices: 12982282--12982451 Score: 205
Period size: 61 Copynumber: 2.8 Consensus size: 61
12982272 TAATTGATGT
* * *** *
12982282 AACCGTGCATGTGCGGAATGGGCAGTGCACATGCTGGTTGAATGACAATGTCGTGATAATTAT
1 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGG-T-AATGATGCTGTCGTGATAATTAC
* * * *
12982345 AATCGTGCATGTGCAGAGTGGGTAGTGCACATGCCGGTAATGATGCTGTCGTGATATTTAC
1 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTAC
* * *
12982406 AACCGTGCATGTGTGGAGTGGGCAGTGCACATGCCGATGATGATGC
1 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGC
12982452 ACATGAGCTG
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 58 0.64
62 1 0.01
63 32 0.35
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (61 bp):
AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTAC
Found at i:12985173 original size:11 final size:11
Alignment explanation
Indices: 12985140--12985174 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12985130 CCTAGGGTTC
12985140 TTGTTCTTCCT
1 TTGTTCTTCCT
12985151 TT-TTCTTCCT
1 TTGTTCTTCCT
*
12985161 TTGTTCTTGCT
1 TTGTTCTTCCT
12985172 TTG
1 TTG
12985175 GCCGACCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:12996300 original size:86 final size:85
Alignment explanation
Indices: 12996209--12996496 Score: 255
Period size: 86 Copynumber: 3.3 Consensus size: 85
12996199 GTATTCATAA
12996209 TTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATATGATTAATGATAAATTT
1 TTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATAT-ATTAATGATAAATTT
12996274 GATAAAATATATATCCATTAT
65 GATAAAATATATATCCATTAT
* * * **
12996295 TTTTATTGATTTAC-A-GA-AAAA-T-ATATATGAAAACTATATATATAATATATATAAT-ATTT
1 TTTTATTGATTTACAATAACAAAAGTAATATATG-TAA-TATA-ATA-CATATAT-TAATGATAA
* * * ** * *
12996354 ATTGATGTACAATAAGGAAAAGTATATACATAA
61 ATT--TG-ATAA-AA--TATA-TATCCA-TTAT
* *
12996387 TTTTATTGATTTACAATAACAAAAGTAATATATATAATACAATACATATAATTAATGATAAATTT
1 TTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATAT-ATTAATGATAAATTT
*
12996452 GATGAAATATATATCCATTAT
65 GATAAAATATATATCCATTAT
*
12996473 TTTTATTGATTTACAAAAACAAAA
1 TTTTATTGATTTACAATAACAAAA
12996497 ATTATATGAA
Statistics
Matches: 154, Mismatches: 28, Indels: 40
0.69 0.13 0.18
Matches are distributed among these distances:
81 7 0.05
82 3 0.02
83 8 0.05
84 11 0.07
85 9 0.06
86 41 0.27
87 7 0.05
88 4 0.03
90 4 0.03
91 6 0.04
92 18 0.12
93 9 0.06
94 11 0.07
95 7 0.05
96 3 0.02
97 6 0.04
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (85 bp):
TTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATATATTAATGATAAATTTG
ATAAAATATATATCCATTAT
Found at i:12996394 original size:178 final size:178
Alignment explanation
Indices: 12996017--12996538 Score: 623
Period size: 178 Copynumber: 2.9 Consensus size: 178
12996007 CTACTATATG
*
12996017 TACATAATTTTTATTTATTTACAATAACAAAAGTTATATATATGT-AT-T-A-A-ATATA-TAAT
1 TACATAA-TTTTATTGATTTACAATAACAAAAG-TA-ATATATGTAATATAATACATATATTAAT
* * * * * *
12996076 AATAAAGTTGATGTAATATATATCCATAATTTTTTATTGATTTTAAAAAATAAAAATTATATGAA
63 GATAAATTTGATGAAATATATATCCATTA-TTTTTATTGA-TTTACAAAACAAAAATTATATG--
** ** * *
12996141 AAATTTATATATATATATATATATATAATAATACACTAAATATACAATAAGGAAAATTGTA
124 AAA---ATATATATATA-ATATATATAAT-ATTTA-TTGATATACAATAAGGAAAAGTATA
*
12996202 TTCATAATTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATATGATTAATGA
1 TACATAATTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATAT-ATTAATGA
* * *
12996267 TAAATTTGATAAAATATATATCCATTATTTTTATTGATTTACAGAA-AAATA-TATATGAAAACT
65 TAAATTTGATGAAATATATATCCATTATTTTTATTGATTTACAAAACAAAAATTATATGAAAA-T
*
12996330 ATATATATAATATATATAATATTTATTGATGTACAATAAGGAAAAGTATA
129 ATATATATAATATATATAATATTTATTGATATACAATAAGGAAAAGTATA
* *
12996380 TACATAATTTTATTGATTTACAATAACAAAAGTAATATATATAATACAATACATATAATTAATGA
1 TACATAATTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATAT-ATTAATGA
12996445 TAAATTTGATGAAATATATATCCATTATTTTTATTGATTTACAAAAACAAAAATTATATGAAAAT
65 TAAATTTGATGAAATATATATCCATTATTTTTATTGATTTAC-AAAACAAAAATTATATGAAAAT
*
12996510 -TATATATGAA-ATATATAATTTTTATTGAT
129 ATATATAT-AATATATATAATATTTATTGAT
12996539 TTATAGTAAC
Statistics
Matches: 300, Mismatches: 25, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
178 122 0.41
179 31 0.10
180 19 0.06
181 20 0.07
182 8 0.03
183 7 0.02
184 25 0.08
185 13 0.04
186 5 0.02
187 11 0.04
188 11 0.04
189 28 0.09
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (178 bp):
TACATAATTTTATTGATTTACAATAACAAAAGTAATATATGTAATATAATACATATATTAATGAT
AAATTTGATGAAATATATATCCATTATTTTTATTGATTTACAAAACAAAAATTATATGAAAATAT
ATATATAATATATATAATATTTATTGATATACAATAAGGAAAAGTATA
Found at i:12996402 original size:37 final size:38
Alignment explanation
Indices: 12996337--12996425 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 38
12996327 ACTATATATA
*
12996337 TAATATATATAATATTTATTGATGTACAATAAGGAAAAG
1 TAATATATATAATATTTATTGATGTACAATAA-CAAAAG
* *
12996376 T-ATATACATAAT-TTTATTGATTTACAATAACAAAAG
1 TAATATATATAATATTTATTGATGTACAATAACAAAAG
12996412 TAATATATATAATA
1 TAATATATATAATA
12996426 CAATACATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
36 6 0.14
37 27 0.61
38 10 0.23
39 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.38
Consensus pattern (38 bp):
TAATATATATAATATTTATTGATGTACAATAACAAAAG
Found at i:12999352 original size:25 final size:25
Alignment explanation
Indices: 12999294--12999352 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
12999284 ATGGTTGCAA
*
12999294 CCACAGATATCAACCAATGGCCTAG
1 CCACATATATCAACCAATGGCCTAG
* * *
12999319 CCACGTATATCAACCAGTGGCCTTG
1 CCACATATATCAACCAATGGCCTAG
*
12999344 CTACATATA
1 CCACATATA
12999353 ATCACAGACC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (25 bp):
CCACATATATCAACCAATGGCCTAG
Found at i:13014886 original size:27 final size:28
Alignment explanation
Indices: 13014856--13014909 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
13014846 GTGTCCTGGT
*
13014856 GGTGG-AAAATTACAATTTTGCCCCTAC
1 GGTGGCAAAATTACAATTTTACCCCTAC
*
13014883 GGTGGCAAAATTACCATTTTACCCCTA
1 GGTGGCAAAATTACAATTTTACCCCTA
13014910 TGCTCCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (28 bp):
GGTGGCAAAATTACAATTTTACCCCTAC
Found at i:13015690 original size:174 final size:176
Alignment explanation
Indices: 13015425--13015776 Score: 564
Period size: 175 Copynumber: 2.0 Consensus size: 176
13015415 TTTTGCTCCT
*
13015425 CTCCCTTCATTTTCTTCTTTCCTTTTTCTCTCTCTAGCAGCAGCCACCCTCTCACTTCTCTCTAA
1 CTCCCTTCATTTTCTTCTTTCCTCTTTCTCTCTCTAGCAGCAGCCACCCTCTCACTTCTCTCTAA
* * * *
13015490 ACTTTTCCCTCCGTCGTCCTCTTTCTCCTTCTCTC-CACCTTTCCCTCCACCAATGGCTTGAAGC
66 ACTTTTCCCTCCGTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCCCGCCACCAATGGCTTGAAGC
**
13015554 TCGGTCACCCAAAACCCTAAATATCTCTTCCCTCCACTAGCAATCC
131 TCAATCACCCAAAACCCTAAATATCTCTTCCCTCCACTAGCAATCC
13015600 CTCCCTTCATTTTCTTCTTTCC-CTTTCTCTCTCTAGCAGCAGCCACCCTCTCACTTCTCTCTAA
1 CTCCCTTCATTTTCTTCTTTCCTCTTTCTCTCTCTAGCAGCAGCCACCCTCTCACTTCTCTCTAA
* * ** *
13015664 ACTTTTTCCTTCGTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCCCGCCACCGGTGGCTTGAAGT
66 ACTTTTCCCTCCGTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCCCGCCACCAATGGCTTGAAGC
* *
13015729 TCAATCAGCCAAAACCCTAAATATCTCTTCCCTCCACTGGCAATCC
131 TCAATCACCCAAAACCCTAAATATCTCTTCCCTCCACTAGCAATCC
13015775 CT
1 CT
13015777 AGATCTAACA
Statistics
Matches: 162, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 72 0.44
175 90 0.56
ACGTcount: A:0.16, C:0.41, G:0.08, T:0.35
Consensus pattern (176 bp):
CTCCCTTCATTTTCTTCTTTCCTCTTTCTCTCTCTAGCAGCAGCCACCCTCTCACTTCTCTCTAA
ACTTTTCCCTCCGTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCCCGCCACCAATGGCTTGAAGC
TCAATCACCCAAAACCCTAAATATCTCTTCCCTCCACTAGCAATCC
Found at i:13015915 original size:20 final size:20
Alignment explanation
Indices: 13015890--13015955 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
13015880 TTCCCTCTTG
13015890 ATTTTTTATTTAATTTTATT
1 ATTTTTTATTTAATTTTATT
* *
13015910 ATTTTTTAATTAATTTTGTTT
1 ATTTTTTATTTAATTTT-ATT
* * *
13015931 AATTTTTATTTTTATTATATT
1 ATTTTTTA-TTTAATTTTATT
13015952 ATTT
1 ATTT
13015956 GATTATTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.44
21 14 0.39
22 6 0.17
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTTTTATTTAATTTTATT
Found at i:13015936 original size:21 final size:20
Alignment explanation
Indices: 13015892--13015990 Score: 64
Period size: 20 Copynumber: 5.0 Consensus size: 20
13015882 CCCTCTTGAT
* *
13015892 TTTTTATTTAATTTTATTAT
1 TTTTTAATTAATTTTATTAA
*
13015912 TTTTTAATTAATTTTGTTTAA
1 TTTTTAATTAATTTT-ATTAA
13015933 TTTTT-A-T--TTTTATTATA
1 TTTTTAATTAATTTTATTA-A
* *
13015950 TTATTTGATT-ATTTTATTTA
1 TT-TTTAATTAATTTTATTAA
*
13015970 TTTCTTGATTAATTTTTATTA
1 TTT-TTAATTAA-TTTTATTA
13015991 TATATATTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
16 3 0.05
17 7 0.11
18 3 0.05
19 3 0.05
20 25 0.39
21 16 0.25
22 7 0.11
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTAATTAATTTTATTAA
Found at i:13015991 original size:21 final size:22
Alignment explanation
Indices: 13015936--13015993 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
13015926 TGTTTAATTT
*
13015936 TTATTTTTATTATATTATTTGA
1 TTATTTTTATTATATTACTTGA
*
13015958 TTA-TTTTATT-TATTTCTTGA
1 TTATTTTTATTATATTACTTGA
13015978 TTAATTTTTATTATAT
1 TT-ATTTTTATTATAT
13015994 ATATTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.32
21 8 0.26
22 10 0.32
23 3 0.10
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (22 bp):
TTATTTTTATTATATTACTTGA
Found at i:13017070 original size:29 final size:30
Alignment explanation
Indices: 13017022--13017142 Score: 118
Period size: 30 Copynumber: 4.0 Consensus size: 30
13017012 AACATTTTAA
*
13017022 TTCCATTGGAAAATCATTTT-CAACGGAATT
1 TTCCGTTGG-AAATCATTTTCCAACGGAATT
*
13017052 TTCCGTTGGAAATCCTTTTCCAACGGAATT
1 TTCCGTTGGAAATCATTTTCCAACGGAATT
* * ** **
13017082 TTCCGTTGAAAATGAAGTTCCAATAGAATT
1 TTCCGTTGGAAATCATTTTCCAACGGAATT
* * **
13017112 TTCCTTTGGAAATGAAGTTCCAACGGAATT
1 TTCCGTTGGAAATCATTTTCCAACGGAATT
13017142 T
1 T
13017143 CATTTCCAAC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 9 0.12
30 68 0.88
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (30 bp):
TTCCGTTGGAAATCATTTTCCAACGGAATT
Found at i:13031722 original size:73 final size:73
Alignment explanation
Indices: 13031596--13031736 Score: 230
Period size: 73 Copynumber: 1.9 Consensus size: 73
13031586 TAGTTTTGTC
* *
13031596 AAAAAGTCTTTTTTGTCAAGTCAAAACGATTCAAATTATGGCGTAACACATAACAACTTTTTCAT
1 AAAAAGTCTTTTTTATCAAGTCAAAACGATTCAAATTATGGCGCAACACATAACAACTTTTTCAT
13031661 CTTTTCTA
66 CTTTTCTA
* *
13031669 AAAAAGTCTTTTTTATCAAGTCAAAAC-AGTTCAAATTATGGCGCAACATATAACAGCTTTTTCA
1 AAAAAGTCTTTTTTATCAAGTCAAAACGA-TTCAAATTATGGCGCAACACATAACAACTTTTTCA
13031733 TCTT
65 TCTT
13031737 GATGTGTAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 1 0.02
73 62 0.98
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (73 bp):
AAAAAGTCTTTTTTATCAAGTCAAAACGATTCAAATTATGGCGCAACACATAACAACTTTTTCAT
CTTTTCTA
Found at i:13031800 original size:55 final size:52
Alignment explanation
Indices: 13031740--13032004 Score: 217
Period size: 55 Copynumber: 4.9 Consensus size: 52
13031730 TCATCTTGAT
* * *
13031740 GTGTAACAACTAAATTTTTCAACAAGACGTATAACAACTAAATCTTCAATATCGT
1 GTGTAACAACTAAA-TTTTCAACATGACGTATAACAACTAAATTTTCAA-AT-GC
* *** *
13031795 GTGTAACAACTACATTTTTCAACATGTTTTGTAACAACTAAATTTTCAACATGAC
1 GTGTAACAACTA-AATTTTCAACATGACGTATAACAACTAAATTTTCAA-ATG-C
* * * *
13031850 ATGTAACAACTAAATCTTCAACATGGCGTATAACAACTACATTTTTCAAATGGC
1 GTGTAACAACTAAATTTTCAACATGACGTATAACAACTA-AATTTTCAAAT-GC
* * * * *
13031904 GTGTAACAACTAAATTTTCAACAT-AGCATGTAACAATTACATTTTTCAACATGAT
1 GTGTAACAACTAAATTTTCAACATGA-CGTATAACAACTA-AATTTTCAA-ATG-C
* * * * *
13031959 GTGTAATAACTAAATTTTCAACATGGCATGTAACAACTACATTTTC
1 GTGTAACAACTAAATTTTCAACATGACGTATAACAACTAAATTTTC
13032005 GATGTAATTT
Statistics
Matches: 173, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
54 73 0.42
55 99 0.57
56 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (52 bp):
GTGTAACAACTAAATTTTCAACATGACGTATAACAACTAAATTTTCAAATGC
Found at i:13031801 original size:27 final size:26
Alignment explanation
Indices: 13031740--13032004 Score: 235
Period size: 27 Copynumber: 9.7 Consensus size: 26
13031730 TCATCTTGAT
*
13031740 GTGTAACAACTAAATTTTTCAACAAGAC
1 GTGTAACAACTAAA-TTTTCAACATG-C
* * * *
13031768 GTATAACAACTAAATCTTCAATATCGT
1 GTGTAACAACTAAATTTTCAACAT-GC
* *
13031795 GTGTAACAACTACATTTTTCAACATGTT
1 GTGTAACAACTA-AATTTTCAACATG-C
*
13031823 TTGTAACAACTAAATTTTCAACATGAC
1 GTGTAACAACTAAATTTTCAACATG-C
* *
13031850 ATGTAACAACTAAATCTTCAACATGGC
1 GTGTAACAACTAAATTTTCAACAT-GC
* *
13031877 GTATAACAACTACATTTTTCAA-ATGGC
1 GTGTAACAACTA-AATTTTCAACAT-GC
13031904 GTGTAACAACTAAATTTTCAACATAGC
1 GTGTAACAACTAAATTTTCAACAT-GC
* * * *
13031931 ATGTAACAATTACATTTTTCAACATGAT
1 GTGTAACAACTA-AATTTTCAACATG-C
*
13031959 GTGTAATAACTAAATTTTCAACATGGC
1 GTGTAACAACTAAATTTTCAACAT-GC
* *
13031986 ATGTAACAACTACATTTTC
1 GTGTAACAACTAAATTTTC
13032005 GATGTAATTT
Statistics
Matches: 194, Mismatches: 34, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
26 8 0.04
27 122 0.63
28 64 0.33
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (26 bp):
GTGTAACAACTAAATTTTCAACATGC
Found at i:13031867 original size:82 final size:81
Alignment explanation
Indices: 13031741--13032004 Score: 309
Period size: 82 Copynumber: 3.2 Consensus size: 81
13031731 CATCTTGATG
* * * *
13031741 TGTAACAACTAAATTTTTCAACAAGACGTATAACAACTAAATCTTCAATATCGTGTGTAACAACT
1 TGTAACAACTAAA-TTTTCAACATGACATGTAACAACTAAATCTTCAACAT-GTGTGTAACAACT
***
13031806 ACATTTTTCAACATGTTT
64 ACATTTTTCAACATGGCA
* *
13031824 TGTAACAACTAAATTTTCAACATGACATGTAACAACTAAATCTTCAACATGGCGTATAACAACTA
1 TGTAACAACTAAATTTTCAACATGACATGTAACAACTAAATCTTCAACAT-GTGTGTAACAACTA
*
13031889 CATTTTTCAA-ATGGCG
65 CATTTTTCAACATGGCA
* * * *
13031905 TGTAACAACTAAATTTTCAACAT-AGCATGTAACAATTACATTTTTCAACATGATGTGTAATAAC
1 TGTAACAACTAAATTTTCAACATGA-CATGTAACAACTA-AATCTTCAACATG-TGTGTAACAAC
*
13031969 TA-AATTTTCAACATGGCA
63 TACATTTTTCAACATGGCA
*
13031987 TGTAACAACTACATTTTC
1 TGTAACAACTAAATTTTC
13032005 GATGTAATTT
Statistics
Matches: 158, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
80 1 0.01
81 47 0.30
82 97 0.61
83 13 0.08
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (81 bp):
TGTAACAACTAAATTTTCAACATGACATGTAACAACTAAATCTTCAACATGTGTGTAACAACTAC
ATTTTTCAACATGGCA
Found at i:13032448 original size:24 final size:24
Alignment explanation
Indices: 13032412--13032471 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
13032402 AATTTAAATT
13032412 AAAT-TATTTTTATTTAA-ATATTA
1 AAATATATTTTTA-TTAATATATTA
* *
13032435 AAATATATTTTTATTAATATTTTT
1 AAATATATTTTTATTAATATATTA
13032459 AAATATATTTTTA
1 AAATATATTTTTA
13032472 AAATCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATATATTTTTATTAATATATTA
Found at i:13032466 original size:12 final size:12
Alignment explanation
Indices: 13032435--13032473 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
13032425 TTAAATATTA
13032435 AAATATATTTTT
1 AAATATATTTTT
*
13032447 -ATTAATATTTTT
1 AAAT-ATATTTTT
13032459 AAATATATTTTT
1 AAATATATTTTT
13032471 AAA
1 AAA
13032474 ATCAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATATATTTTT
Found at i:13033936 original size:19 final size:19
Alignment explanation
Indices: 13033912--13033958 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
13033902 TTTTCTTTTG
*
13033912 TTAAGAATGATGACTTCCA
1 TTAAGAATGATGACGTCCA
* * *
13033931 TTAAGAAGGATTACGTCTA
1 TTAAGAATGATGACGTCCA
13033950 TTAAGAATG
1 TTAAGAATG
13033959 TCAAGCCCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (19 bp):
TTAAGAATGATGACGTCCA
Found at i:13038239 original size:20 final size:20
Alignment explanation
Indices: 13038222--13038259 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13038212 CCTCAAATCT
13038222 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
*
13038242 TACTCTAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
13038260 GGGGCCAAAA
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:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:13038729 original size:19 final size:19
Alignment explanation
Indices: 13038662--13038713 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
13038652 TTAATATTTT
13038662 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
13038681 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
13038700 AATATTATTTTATT
1 AATATTATTTTATT
13038714 CTAAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:13042539 original size:16 final size:16
Alignment explanation
Indices: 13042509--13042549 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
13042499 CCTTAAAACA
13042509 ACTTTAAAA-CCAAAG
1 ACTTTAAAATCCAAAG
13042524 ACTTTAAAATCCAAAG
1 ACTTTAAAATCCAAAG
13042540 -CTTTAAAATC
1 ACTTTAAAATC
13042550 AAAATATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (16 bp):
ACTTTAAAATCCAAAG
Found at i:13048565 original size:24 final size:23
Alignment explanation
Indices: 13048525--13048570 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
13048515 TAGAGAAAGG
* *
13048525 AAAAAAAATTATTTTTATTTTTT
1 AAAAAAAATAATATTTATTTTTT
13048548 AAAAAATAATAATATTTATTTTT
1 AAAAAA-AATAATATTTATTTTT
13048571 AAATCACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAAAAAATAATATTTATTTTTT
Found at i:13054010 original size:22 final size:18
Alignment explanation
Indices: 13053985--13054031 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 18
13053975 GTCCTATAAT
13053985 GAACGTGCTCTTCCCATAACTA
1 GAACGTG-TCTT-CCAT-AC-A
13054007 GAACGT-TCTTCCATACA
1 GAACGTGTCTTCCATACA
13054024 GAACGTGT
1 GAACGTGT
13054032 TATCCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.29
18 3 0.12
19 4 0.17
20 4 0.17
22 6 0.25
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
GAACGTGTCTTCCATACA
Found at i:13078383 original size:16 final size:16
Alignment explanation
Indices: 13078323--13078387 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
13078313 TGGGTTTTTT
*
13078323 ATAAATTAATAAAAATA
1 ATAAA-TAATAAAATTA
* *
13078340 ATAAAATTATAAAA-TC
1 AT-AAATAATAAAATTA
* **
13078356 ATAATTTTTAAAATTA
1 ATAAATAATAAAATTA
13078372 ATAAATAATAAAATTA
1 ATAAATAATAAAATTA
13078388 TCTTTTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
15 9 0.24
16 17 0.45
17 9 0.24
18 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATAATAAAATTA
Found at i:13081972 original size:2 final size:2
Alignment explanation
Indices: 13081965--13082011 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
13081955 GGCCCCAAAC
*
13081965 AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13082007 AG AG A
1 AG AG A
13082012 TCAACAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13084088 original size:2 final size:2
Alignment explanation
Indices: 13084083--13084126 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
13084073 AATCAGATTA
13084083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13084125 AT
1 AT
13084127 GTGTGTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13087459 original size:2 final size:2
Alignment explanation
Indices: 13087454--13087483 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13087444 TTACCTTAAC
13087454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13087484 TATTCAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13091999 original size:17 final size:18
Alignment explanation
Indices: 13091965--13092000 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13091955 AAGCCACATG
13091965 TGTTTATGTTTTTCTATA
1 TGTTTATGTTTTTCTATA
*
13091983 TGTTTAT-TTTTTGTATA
1 TGTTTATGTTTTTCTATA
13092000 T
1 T
13092001 AAGTGAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69
Consensus pattern (18 bp):
TGTTTATGTTTTTCTATA
Found at i:13092071 original size:2 final size:2
Alignment explanation
Indices: 13092064--13092090 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13092054 TTCCATATTC
13092064 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13092091 ATTCTTTTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13096716 original size:12 final size:11
Alignment explanation
Indices: 13096701--13096745 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
13096691 TATAAAAGAG
*
13096701 AAAAAAGAAGA
1 AAAAAAGAAAA
*
13096712 AAAAAACAAAA
1 AAAAAAGAAAA
13096723 AAAAAAGAAAA
1 AAAAAAGAAAA
13096734 AGAAAAAGAAAA
1 A-AAAAAGAAAA
13096746 GCCAAACTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:13100497 original size:71 final size:70
Alignment explanation
Indices: 13100332--13100508 Score: 178
Period size: 71 Copynumber: 2.5 Consensus size: 70
13100322 GGTAGCCTAG
* *
13100332 GATCGACTATGGAGGGTTTATAGTCAATCTTGGATCAGAAAGTTTTATGTTTCACCCAATTTTCC
1 GATCGACTATGGAGGG-TTATAGTCAATCTTGGATCAAAAAGTTTCA-GTTTCACCCAATTTTCC
13100397 TTCACAA
64 TTCACAA
* * * * ** *
13100404 GATTGACTATGGAAGGTCTATAGTCGATCTTGGATTAAAAAGTTTGCA-TTTCTTCCATTTTTCC
1 GATCGACTATGGAGGGT-TATAGTCAATCTTGGATCAAAAAGTTT-CAGTTTCACCCAATTTTCC
*
13100468 TTTC-TAA
64 -TTCACAA
* *
13100475 GATCGATTATGGAGGGCTTATAGTCTATCTTGGA
1 GATCGACTATGGAGGG-TTATAGTCAATCTTGGA
13100509 CCATAATGCA
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
71 44 0.51
72 42 0.48
73 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (70 bp):
GATCGACTATGGAGGGTTATAGTCAATCTTGGATCAAAAAGTTTCAGTTTCACCCAATTTTCCTT
CACAA
Found at i:13106863 original size:14 final size:14
Alignment explanation
Indices: 13106844--13106872 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13106834 TCTATAAAAC
13106844 ACACACACACACAT
1 ACACACACACACAT
13106858 ACACACACACACAT
1 ACACACACACACAT
13106872 A
1 A
13106873 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.41, G:0.00, T:0.07
Consensus pattern (14 bp):
ACACACACACACAT
Found at i:13106875 original size:2 final size:2
Alignment explanation
Indices: 13106870--13106907 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13106860 ACACACACAC
13106870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13106908 CATCATGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13106988 original size:43 final size:42
Alignment explanation
Indices: 13106928--13107017 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 42
13106918 ACCATCCCAC
*
13106928 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCC-ACACGCACATAGCTGGGT
*
13106971 CATCATCAGCTCATGTGCACTCCCACACGCATATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
13107013 CATCA
1 CATCA
13107018 GTATCACATA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 21 0.47
43 24 0.53
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.24
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
Found at i:13115306 original size:35 final size:39
Alignment explanation
Indices: 13115218--13115313 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 39
13115208 TATTGAAATG
* * *
13115218 TGCGTGGAGGGAGTGCACATGATAGTATATTGAAGTGTG
1 TGCGTGTAGGGAGTGCACATGATAGTATATTGAACTGTA
* * *
13115257 TGTGTGTAAGGAGTGCACATGAT-G-ATATTG-CCT-TA
1 TGCGTGTAGGGAGTGCACATGATAGTATATTGAACTGTA
13115292 TGCGTGTAGGGAGTGCACATGA
1 TGCGTGTAGGGAGTGCACATGA
13115314 GCTGAGTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 21 0.43
36 1 0.02
37 6 0.12
38 1 0.02
39 20 0.41
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.29
Consensus pattern (39 bp):
TGCGTGTAGGGAGTGCACATGATAGTATATTGAACTGTA
Found at i:13115352 original size:2 final size:2
Alignment explanation
Indices: 13115345--13115369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13115335 GGTATACATG
13115345 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 T
13115370 GCTATAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13116767 original size:19 final size:20
Alignment explanation
Indices: 13116743--13116780 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13116733 CTATAAATAC
13116743 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
13116762 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
13116781 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:13124075 original size:2 final size:2
Alignment explanation
Indices: 13124068--13124109 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
13124058 ATTTTTGAAA
**
13124068 AT AT AT AT GG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13124110 GTTGCATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13125682 original size:17 final size:19
Alignment explanation
Indices: 13125660--13125698 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
13125650 CAAGTGAAAA
13125660 ATTTTA-GAA-AAAATAAT
1 ATTTTATGAATAAAATAAT
*
13125677 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
13125696 ATT
1 ATT
13125699 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:13126144 original size:20 final size:20
Alignment explanation
Indices: 13126119--13126156 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13126109 CCACCTTCAT
13126119 GCACCCAACGCCATTTTCTC
1 GCACCCAACGCCATTTTCTC
13126139 GCACCCAACGCCATTTTC
1 GCACCCAACGCCATTTTC
13126157 ACCTTGCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.45, G:0.11, T:0.24
Consensus pattern (20 bp):
GCACCCAACGCCATTTTCTC
Found at i:13126868 original size:37 final size:37
Alignment explanation
Indices: 13126797--13126888 Score: 127
Period size: 37 Copynumber: 2.5 Consensus size: 37
13126787 TGATGTGGGC
13126797 GGGAGTG--CGTG-TGATGATATTGAAATGTGCGTGTA
1 GGGAGTGCACGTGATGAT-ATATTGAAATGTGCGTGTA
* *
13126832 GGGAGTGCACGTGATGATATATTGAAGTGTGTGTGTA
1 GGGAGTGCACGTGATGATATATTGAAATGTGCGTGTA
*
13126869 GGGAGTGCACATGATGATAT
1 GGGAGTGCACGTGATGATAT
13126889 TACCTTGTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 7 0.14
37 40 0.78
38 4 0.08
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (37 bp):
GGGAGTGCACGTGATGATATATTGAAATGTGCGTGTA
Found at i:13126898 original size:35 final size:36
Alignment explanation
Indices: 13126808--13126917 Score: 127
Period size: 35 Copynumber: 3.1 Consensus size: 36
13126798 GGAGTGCGTG
* * *
13126808 TGATG-ATATTGAAATGTGCGTGTAGGGAGTGCACG
1 TGATGAATATTGAAGTGTGTGTGTAGGGAGTGCACA
13126843 TGATGATATATTGAAGTGTGTGTGTAGGGAGTGCACA
1 TGATGA-ATATTGAAGTGTGTGTGTAGGGAGTGCACA
** *
13126880 TGATG-ATATT-ACCTTGTGTGTGTAGGAAGTGCACA
1 TGATGAATATTGA-AGTGTGTGTGTAGGGAGTGCACA
13126915 TGA
1 TGA
13126918 GCTGAGTAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 1 0.02
35 33 0.50
37 32 0.48
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (36 bp):
TGATGAATATTGAAGTGTGTGTGTAGGGAGTGCACA
Found at i:13126899 original size:37 final size:33
Alignment explanation
Indices: 13126821--13126917 Score: 97
Period size: 37 Copynumber: 2.8 Consensus size: 33
13126811 TGATATTGAA
* *
13126821 ATGTGCGTGTAGGGAGTGCACGTGATGATATATT
1 ATGTGTGTGTAGGGAGTGCACATGATGATATA-T
13126855 GAAGTGTGTGTGTAGGGAGTGCACATGATGATAT-T
1 --A-TGTGTGTGTAGGGAGTGCACATGATGATATAT
*
13126890 ACCTTGTGTGTGTAGGAAGTGCACATGA
1 A---TGTGTGTGTAGGGAGTGCACATGA
13126918 GCTGAGTAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
33 1 0.02
35 24 0.44
36 1 0.02
37 28 0.52
ACGTcount: A:0.25, C:0.09, G:0.35, T:0.31
Consensus pattern (33 bp):
ATGTGTGTGTAGGGAGTGCACATGATGATATAT
Found at i:13129561 original size:29 final size:28
Alignment explanation
Indices: 13129519--13129662 Score: 180
Period size: 29 Copynumber: 5.0 Consensus size: 28
13129509 TGACAGCTTT
13129519 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
13129547 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
13129576 AATATGTTTGTCTTAATTTAAGATAAGGAA
1 AACATGTTTGTCTTAATTT-AGACAA-GAA
* *
13129606 AATATTTTTTGTCTTAATTTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* * *
13129635 TACATATTTGTCTCAAATTTAGACAAGA
1 AACATGTTTGTCT-TAATTTAGACAAGA
13129663 TAAAATATTT
Statistics
Matches: 103, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
28 27 0.26
29 50 0.49
30 12 0.12
31 14 0.14
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:13129627 original size:59 final size:58
Alignment explanation
Indices: 13129519--13129684 Score: 208
Period size: 59 Copynumber: 2.8 Consensus size: 58
13129509 TGACAGCTTT
* * *
13129519 AACATGTTTGTCTTAATTTAGACAA-GAAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGGAAAATATTTTTTGTCTTAATTTAGACAAGAA
* *
13129576 AATATGTTTGTCTTAATTTAAGATAAGGAAAATATTTTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGGAAAATATTTTTTGTCTTAATTTAGACAAGAA
* * * * *
13129635 TACATATTTGTCTCAAATTTAGACAAGATAAAATATTTTTTATCTTAATT
1 AACATGTTTGTCT-TAATTTAGACAAG-GAAAATATTTTTTGTCTTAATT
13129685 ACGGACAAGA
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
57 18 0.19
58 5 0.05
59 45 0.48
60 25 0.27
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGGAAAATATTTTTTGTCTTAATTTAGACAAGAA
Found at i:13129858 original size:17 final size:17
Alignment explanation
Indices: 13129836--13129868 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13129826 ATAATAATAA
13129836 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
13129853 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
13129869 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:13144650 original size:42 final size:42
Alignment explanation
Indices: 13144587--13144708 Score: 199
Period size: 42 Copynumber: 2.9 Consensus size: 42
13144577 TGATGTGGAA
*
13144587 CCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGAC
1 CCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGAC
*
13144629 CCGGCTATGTGCGAGTGGGAGTGAACATAAGCCGTTGCTGAC
1 CCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGAC
* * *
13144671 CCGACTATGTGTGAGTGGGAGTGCGCATAAGCCGTTGC
1 CCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
13144709 ATATGATATG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.22
Consensus pattern (42 bp):
CCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGAC
Found at i:13146911 original size:74 final size:74
Alignment explanation
Indices: 13146790--13147080 Score: 284
Period size: 74 Copynumber: 4.1 Consensus size: 74
13146780 CAAAAAGGCA
* * * * * *
13146790 TTCACTGCAGCGAAATCTAGGGTAAAATTTTGAACCAACCACTTGAGAGTTTTTCACTGCAGTGA
1 TTCACTACAGCGAAATCCAGGGCAAAATTTTGAACCAACCACCTGAGAGTTTCTCACTGCAGCGA
13146855 GAATGCATT
66 GAATGCATT
* *
13146864 TTCACTACAGCAAAATCCAGGGCAAAATTTTGAACCAACAACCTGAGAGTTTCTCGA-TGCAGCG
1 TTCACTACAGCGAAATCCAGGGCAAAATTTTGAACCAACCACCTGAGAGTTTCTC-ACTGCAGCG
13146928 AGAATGCATT
65 AGAATGCATT
* * * * ** *
13146938 TTCGCT-----G---T----TGTAAAATTTTGAACCAACCACCCGAGAGTTTCTCGTTGTAGCGA
1 TTCACTACAGCGAAATCCAGGGCAAAATTTTGAACCAACCACCTGAGAGTTTCTCACTGCAGCGA
13146991 GAATGCATT
66 GAATGCATT
** * * * * *
13147000 TTTGCTGCAACGAAATCCAAGGCAAAATTTTGAACCAACCACTTGAGAGTTTCTCGCTGCAGCGA
1 TTCACTACAGCGAAATCCAGGGCAAAATTTTGAACCAACCACCTGAGAGTTTCTCACTGCAGCGA
13147065 GAATGCATT
66 GAATGCATT
13147074 TTCACTA
1 TTCACTA
13147081 TAATGACAAT
Statistics
Matches: 177, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
62 52 0.29
66 1 0.01
67 1 0.01
70 1 0.01
74 121 0.68
75 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (74 bp):
TTCACTACAGCGAAATCCAGGGCAAAATTTTGAACCAACCACCTGAGAGTTTCTCACTGCAGCGA
GAATGCATT
Found at i:13146963 original size:62 final size:62
Alignment explanation
Indices: 13146887--13147006 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
13146877 AATCCAGGGC
*
13146887 AAAATTTTGAACCAACAACCTGAGAGTTTCTCGATGCAGCGAGAATGCATTTTCGCTGTTGT
1 AAAATTTTGAACCAACAACCCGAGAGTTTCTCGATGCAGCGAGAATGCATTTTCGCTGTTGT
* * * *
13146949 AAAATTTTGAACCAACCACCCGAGAGTTTCTCGTTGTAGCGAGAATGCATTTTTGCTG
1 AAAATTTTGAACCAACAACCCGAGAGTTTCTCGATGCAGCGAGAATGCATTTTCGCTG
13147007 CAACGAAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (62 bp):
AAAATTTTGAACCAACAACCCGAGAGTTTCTCGATGCAGCGAGAATGCATTTTCGCTGTTGT
Found at i:13146993 original size:136 final size:136
Alignment explanation
Indices: 13146811--13147076 Score: 388
Period size: 136 Copynumber: 2.0 Consensus size: 136
13146801 GAAATCTAGG
** * * *
13146811 GTAAAATTTTGAACCAACCACTTGAGAGTTTTTCACTGCAGTGAGAATGCATTTTCACTACAGCA
1 GTAAAATTTTGAACCAACCACCCGAGAGTTTCTCACTGCAGCGAGAATGCATTTTCACTACAACA
*
13146876 AAATCCAGGGCAAAATTTTGAACCAACAACCTGAGAGTTTCTCGATGCAGCGAGAATGCATTTTC
66 AAATCCAAGGCAAAATTTTGAACCAACAACCTGAGAGTTTCTCGATGCAGCGAGAATGCATTTTC
13146941 GCTGTT
131 GCTGTT
** * ** * *
13146947 GTAAAATTTTGAACCAACCACCCGAGAGTTTCTCGTTGTAGCGAGAATGCATTTTTGCTGCAACG
1 GTAAAATTTTGAACCAACCACCCGAGAGTTTCTCACTGCAGCGAGAATGCATTTTCACTACAACA
* * *
13147012 AAATCCAAGGCAAAATTTTGAACCAACCACTTGAGAGTTTCTCGCTGCAGCGAGAATGCATTTTC
66 AAATCCAAGGCAAAATTTTGAACCAACAACCTGAGAGTTTCTCGATGCAGCGAGAATGCATTTTC
13147077 ACTATAATGA
Statistics
Matches: 114, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 114 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (136 bp):
GTAAAATTTTGAACCAACCACCCGAGAGTTTCTCACTGCAGCGAGAATGCATTTTCACTACAACA
AAATCCAAGGCAAAATTTTGAACCAACAACCTGAGAGTTTCTCGATGCAGCGAGAATGCATTTTC
GCTGTT
Found at i:13147407 original size:35 final size:35
Alignment explanation
Indices: 13147361--13147492 Score: 117
Period size: 36 Copynumber: 3.6 Consensus size: 35
13147351 CTCCCAAAGC
13147361 TCATGTGCACTCCCACACTGCACATAGCTAGGTCA
1 TCATGTGCACTCCCACACTGCACATAGCTAGGTCA
* * **
13147396 TCATGTGCACTCCCACACTACACATGGCATAAATCA
1 TCATGTGCACTCCCACACTGCACATAGC-TAGGTCA
* *
13147432 TCGGCGTGTGCACTCCCACACCGCACACTA-CT-GG-CA
1 T---CATGTGCACTCCCACACTGCACA-TAGCTAGGTCA
13147468 CCGTCATGTGCACTCCCACACTGCA
1 ---TCATGTGCACTCCCACACTGCA
13147493 TATGCGCGGT
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
35 26 0.34
36 27 0.35
38 1 0.01
39 22 0.29
40 1 0.01
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (35 bp):
TCATGTGCACTCCCACACTGCACATAGCTAGGTCA
Found at i:13152712 original size:4 final size:4
Alignment explanation
Indices: 13152705--13152741 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
13152695 GTGCACACAC
* *
13152705 ACAT ACAT GCAT ACAT ACAT ACAT ACAT ATAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
13152742 TTTATATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:13154020 original size:15 final size:15
Alignment explanation
Indices: 13153986--13154020 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13153976 TTACTATTAT
*
13153986 ATATATATACTTTTA
1 ATATATATACTTTAA
*
13154001 GTATATATACTTTAA
1 ATATATATACTTTAA
13154016 ATATA
1 ATATA
13154021 AACATGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:13154257 original size:31 final size:33
Alignment explanation
Indices: 13154219--13154289 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
13154209 ACTTGTAATG
13154219 TTTAAGTTG-TTTGA-ATATTTGTTTTTAATTA
1 TTTAAGTTGATTTGAGATATTTGTTTTTAATTA
**
13154250 TTTAAGTTGATATTTGAGATATTTGTTTTTGGTTA
1 TTTAAGTTG--ATTTGAGATATTTGTTTTTAATTA
13154285 TTTAA
1 TTTAA
13154290 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.26
34 5 0.15
35 20 0.59
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.59
Consensus pattern (33 bp):
TTTAAGTTGATTTGAGATATTTGTTTTTAATTA
Found at i:13157386 original size:16 final size:16
Alignment explanation
Indices: 13157367--13157415 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
13157357 AGCTTAATAT
*
13157367 ATATATATATATATAA
1 ATATATACATATATAA
*
13157383 ATATACGTACATATATAC
1 ATATA--TACATATATAA
*
13157401 ATACATACATATATA
1 ATATATACATATATA
13157416 TATGTATGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 15 0.54
18 13 0.46
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATATACATATATAA
Found at i:13163704 original size:36 final size:36
Alignment explanation
Indices: 13163663--13163806 Score: 143
Period size: 36 Copynumber: 4.0 Consensus size: 36
13163653 ACATACAATA
*
13163663 TCATGTCACGCCCCATTGCTGCAGCAAATGATGGAG
1 TCATGTCACACCCCATTGCTGCAGCAAATGATGGAG
13163699 TCATGTCACACCCCATTGC--CATGACAAATGATGGAG
1 TCATGTCACACCCCATTGCTGCA-G-CAAATGATGGAG
* * * *
13163735 TC-TAGTCACGCCCTATTGCTG-AGCAAACGATGGAA
1 TCAT-GTCACACCCCATTGCTGCAGCAAATGATGGAG
* * * * *
13163770 TCTTGTCGCATCCCATTGCGGCAACAAATGATGGAG
1 TCATGTCACACCCCATTGCTGCAGCAAATGATGGAG
13163806 T
1 T
13163807 TTATAATCAT
Statistics
Matches: 88, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
34 2 0.02
35 26 0.30
36 59 0.67
37 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (36 bp):
TCATGTCACACCCCATTGCTGCAGCAAATGATGGAG
Found at i:13163797 original size:71 final size:71
Alignment explanation
Indices: 13163667--13163806 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 71
13163657 ACAATATCAT
* *
13163667 GTCACGCCCCATTGCTGCAGCAAATGATGGAGTCATGTCACACCCCATTGCCATGACAAATGATG
1 GTCACGCCCCATTGCTGCAGCAAACGATGGAATCATGTCACACCCCATTGCCA-GACAAATGATG
13163732 GAGTCTA
65 GAGTCTA
* * * *
13163739 GTCACGCCCTATTGCTG-AGCAAACGATGGAATCTTGTCGCATCCCATTGCGGCA-ACAAATGAT
1 GTCACGCCCCATTGCTGCAGCAAACGATGGAATCATGTCACACCCCATTGC--CAGACAAATGAT
13163802 GGAGT
64 GGAGT
13163807 TTATAATCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 42 0.70
72 16 0.27
73 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (71 bp):
GTCACGCCCCATTGCTGCAGCAAACGATGGAATCATGTCACACCCCATTGCCAGACAAATGATGG
AGTCTA
Found at i:13166537 original size:42 final size:42
Alignment explanation
Indices: 13166478--13166617 Score: 262
Period size: 42 Copynumber: 3.3 Consensus size: 42
13166468 GATCGGGACT
* *
13166478 ATCTATCGAGAGATGAGCTTTGAAACCTTTTATGAAAGCTTC
1 ATCTATCGATAGATGAGCTTTCAAACCTTTTATGAAAGCTTC
13166520 ATCTATCGATAGATGAGCTTTCAAACCTTTTATGAAAGCTTC
1 ATCTATCGATAGATGAGCTTTCAAACCTTTTATGAAAGCTTC
13166562 ATCTATCGATAGATGAGCTTTCAAACCTTTTATGAAAGCTTC
1 ATCTATCGATAGATGAGCTTTCAAACCTTTTATGAAAGCTTC
13166604 ATCTATCGATAGAT
1 ATCTATCGATAGAT
13166618 TTAGCCATCT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 96 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (42 bp):
ATCTATCGATAGATGAGCTTTCAAACCTTTTATGAAAGCTTC
Found at i:13166580 original size:21 final size:21
Alignment explanation
Indices: 13166514--13166581 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
13166504 CTTTTATGAA
13166514 AGCTTCATCTATCGATAGATG
1 AGCTTCATCTATCGATAGATG
* ** *
13166535 AGCTTTCAAACCT-TTTAT-GA-A
1 AGC-TTC--ATCTATCGATAGATG
13166556 AGCTTCATCTATCGATAGATG
1 AGCTTCATCTATCGATAGATG
13166577 AGCTT
1 AGCTT
13166582 TCAAACCTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 5 0.15
21 11 0.33
22 5 0.15
23 3 0.09
24 3 0.09
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (21 bp):
AGCTTCATCTATCGATAGATG
Found at i:13166601 original size:21 final size:21
Alignment explanation
Indices: 13166535--13166602 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
13166525 TCGATAGATG
13166535 AGCTTTCAAACCTTTTATGAA
1 AGCTTTCAAACCTTTTATGAA
* ** *
13166556 AGC-TTC--ATCTATCGATAGATG
1 AGCTTTCAAACCT-TTTAT-GA-A
13166577 AGCTTTCAAACCTTTTATGAA
1 AGCTTTCAAACCTTTTATGAA
13166598 AGCTT
1 AGCTT
13166603 CATCTATCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 5 0.15
21 11 0.33
22 5 0.15
23 3 0.09
24 3 0.09
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (21 bp):
AGCTTTCAAACCTTTTATGAA
Found at i:13170396 original size:43 final size:43
Alignment explanation
Indices: 13170342--13170455 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
13170332 GACTATGTGT
* * **
13170342 GAGTAGGGAGTGCACATAAGCTGAG-GATGACCCGGTTATGTAC
1 GAGTAGGGAGTGCGCATAAGCTG-GTGATGACCCAGCCATGTAC
* * * *
13170385 GAGTAGGGAGTGTGCATAACCCGGTGATGACCCAGCCATGTGC
1 GAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAGCCATGTAC
*
13170428 GAGTAGGGAGTGCGCATGAGCTGGTGAT
1 GAGTAGGGAGTGCGCATAAGCTGGTGAT
13170456 AATGATGATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.20
Consensus pattern (43 bp):
GAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAGCCATGTAC
Found at i:13172078 original size:3 final size:3
Alignment explanation
Indices: 13172070--13172113 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
13172060 TTTCTAGCAA
* *
13172070 AAT AAT AAT AAT AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13172114 GGATTATGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:13178804 original size:36 final size:35
Alignment explanation
Indices: 13178689--13178877 Score: 249
Period size: 34 Copynumber: 5.5 Consensus size: 35
13178679 CTTTAATAGC
* * * * *
13178689 AGATTTTATATGCCAAGGTCAAAACTTCAACA-CT
1 AGATGTTACATGCCAAGGTCAAAGCTTCAGCACCG
* *
13178723 AGATGTTGCATGCCAAGTTCAAAGCTTCAGCACCG
1 AGATGTTACATGCCAAGGTCAAAGCTTCAGCACCG
*
13178758 AGATGTTACATGTCAAGGTCAAAGCTTCAGCACCAG
1 AGATGTTACATGCCAAGGTCAAAGCTTCAGCACC-G
*
13178794 AGATGTTACATGTCAAGGTCAAAGCTTCAGCACC-
1 AGATGTTACATGCCAAGGTCAAAGCTTCAGCACCG
* *
13178828 AGATGTTACATGCCAAGGTCAAAGCTTCATCA-CT
1 AGATGTTACATGCCAAGGTCAAAGCTTCAGCACCG
13178862 AGATGTTACATGCCAA
1 AGATGTTACATGCCAA
13178878 AGCTTCCTTT
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
33 1 0.01
34 72 0.51
35 32 0.23
36 35 0.25
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (35 bp):
AGATGTTACATGCCAAGGTCAAAGCTTCAGCACCG
Found at i:13181510 original size:28 final size:28
Alignment explanation
Indices: 13181479--13181535 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
13181469 TGGAGCATAG
*
13181479 GGGCAAAATGGTAATTTTGCCACC-CCAA
1 GGGCAAAATAGTAATTTT-CCACCACCAA
13181507 GGGCAAAATAGTAATTTTCCACCACCAA
1 GGGCAAAATAGTAATTTTCCACCACCAA
13181535 G
1 G
13181536 ACACTTGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (28 bp):
GGGCAAAATAGTAATTTTCCACCACCAA
Done.