Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 132 of 218
Found at i:40353757 original size:37 final size:37
Alignment explanation
Indices: 40353714--40353784 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40353704 CTTGCCTCTC
40353714 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
40353751 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
40353785 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:40353785 original size:16 final size:16
Alignment explanation
Indices: 40353710--40353770 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
40353700 GCCTCTTGCC
*
40353710 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
40353726 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
40353742 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
40353758 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
40353771 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:40354748 original size:12 final size:12
Alignment explanation
Indices: 40354728--40354753 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40354718 TTTTTTTCGA
40354728 TTTTTTTTGAAT
1 TTTTTTTTGAAT
40354740 TTTTTTTTGAAT
1 TTTTTTTTGAAT
40354752 TT
1 TT
40354754 CTTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:40354847 original size:12 final size:12
Alignment explanation
Indices: 40354830--40354854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40354820 CCAACTCAAA
40354830 ATTTTTTTTTTG
1 ATTTTTTTTTTG
40354842 ATTTTTTTTTTG
1 ATTTTTTTTTTG
40354854 A
1 A
40354855 CTTCCTTTTT
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:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (12 bp):
ATTTTTTTTTTG
Found at i:40356499 original size:30 final size:30
Alignment explanation
Indices: 40356465--40356561 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
40356455 TAAACTAAAA
40356465 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
40356495 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
40356525 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
40356554 ATGAGCTA
1 -TGAGCTA
40356562 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:40359442 original size:20 final size:20
Alignment explanation
Indices: 40359396--40359442 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40359386 AGCTCGTTTC
*
40359396 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40359416 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40359436 CAGCTCA
1 CAGCTCA
40359443 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40362384 original size:30 final size:30
Alignment explanation
Indices: 40362350--40362412 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
40362340 ATCGAAATTC
**
40362350 AAAAAAAAAGTGAAAAAAA-TCGAGCAAAAA
1 AAAAAAAAAGAAAAAAAAAGT-GAGCAAAAA
*
40362380 AAAAAGAAAGAAAAAAAAAGTGAGCAAAAA
1 AAAAAAAAAGAAAAAAAAAGTGAGCAAAAA
40362410 AAA
1 AAA
40362413 TCAAGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (30 bp):
AAAAAAAAAGAAAAAAAAAGTGAGCAAAAA
Found at i:40363443 original size:6 final size:6
Alignment explanation
Indices: 40363415--40363554 Score: 64
Period size: 6 Copynumber: 22.3 Consensus size: 6
40363405 CCATTGAGCG
* * * * * * *
40363415 AGAAAA GGAAAA AGAGAT TGAAAA AGAAAT TGAAAGA AAACAAA AAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGA-AAA A-GAAAA
* * * * * * ** *
40363466 CGAAAA AGAAAA AGAAAT TGCAAA AGAAAA AGAAAT CGAAAA AGTGAG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
40363514 AGAAAA AGAAAA TGAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA AGAAAA AG
40363555 CGAAAAAAGA
Statistics
Matches: 92, Mismatches: 36, Indels: 12
0.66 0.26 0.09
Matches are distributed among these distances:
6 72 0.78
7 13 0.14
8 7 0.08
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:40363443 original size:18 final size:18
Alignment explanation
Indices: 40363416--40363509 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
40363406 CATTGAGCGA
* * *
40363416 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATC
**
40363434 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATC
* *
40363450 G-AAAACAAAAAGAAAAC
1 GAAAAAGAAAAAGAAATC
*
40363467 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATC
*
40363485 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATC
40363503 GAAAAAG
1 GAAAAAG
40363510 TGAGAGAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
15 11 0.18
16 1 0.02
17 1 0.02
18 47 0.78
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATC
Found at i:40363463 original size:11 final size:12
Alignment explanation
Indices: 40363447--40363566 Score: 75
Period size: 12 Copynumber: 9.6 Consensus size: 12
40363437 AAAGAAATTG
40363447 AAAGAAAAC-AA
1 AAAGAAAACGAA
40363458 AAAGAAAACGAA
1 AAAGAAAACGAA
*
40363470 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
40363482 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
40363494 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
40363506 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
40363518 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
40363532 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
40363545 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
40363560 AAAGAAA
1 AAAGAAA
40363567 TTGAAAGAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
11 14 0.16
12 35 0.41
13 11 0.13
14 18 0.21
15 8 0.09
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:40363500 original size:81 final size:83
Alignment explanation
Indices: 40363415--40363569 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 83
40363405 CCATTGAGCG
* ** * *
40363415 AGAAAAGGAAAAAGAGATTGAAAAAGAAATTGAAAGAAAACAAAA-AGAAAACGAAAAA-G-AAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATG-AAGAAAACAAAATAGAAAAAGAAAAACGAAAA
40363477 AAGAAATTGCAAAAGAAAA
65 AAGAAATTGCAAAAGAAAA
* * * *
40363496 AGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAAAAGCGAAAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAA-CGAAAA
40363561 AAGAAATTG
65 AAGAAATTG
40363570 AAAGAGAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 11 0.18
81 37 0.61
83 1 0.02
84 12 0.20
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.08
Consensus pattern (83 bp):
AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAACGAAAAA
AGAAATTGCAAAAGAAAA
Found at i:40363536 original size:14 final size:13
Alignment explanation
Indices: 40363515--40363552 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
40363505 AAAAGTGAGA
40363515 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
40363527 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
40363542 GAAAAAGAAAA
1 GAAAAAGAAAA
40363553 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:40363566 original size:21 final size:21
Alignment explanation
Indices: 40363516--40363566 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
40363506 AAAGTGAGAG
*
40363516 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
40363537 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
40363558 AAAAAGAAA
1 AAAAAGAAA
40363567 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:40363606 original size:33 final size:33
Alignment explanation
Indices: 40363569--40363631 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40363559 AAAAGAAATT
40363569 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
40363602 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
40363632 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:40365305 original size:20 final size:20
Alignment explanation
Indices: 40365259--40365305 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40365249 AGCTCGTTTC
*
40365259 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40365279 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40365299 CAGCTCA
1 CAGCTCA
40365306 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40373245 original size:10 final size:10
Alignment explanation
Indices: 40373230--40373266 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
40373220 GTATGCAATT
*
40373230 TTTTTTTCAA
1 TTTTTTTCGA
40373240 TTTTTTTCGA
1 TTTTTTTCGA
*
40373250 TTTTTTTTGA
1 TTTTTTTCGA
40373260 TTTTTTT
1 TTTTTTT
40373267 GAATCTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.78
Consensus pattern (10 bp):
TTTTTTTCGA
Found at i:40374165 original size:29 final size:29
Alignment explanation
Indices: 40374120--40374191 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
40374110 TGTATTTAGT
*
40374120 ATTGAAGAAAAAA-AAGAAAAAAATTCGGA
1 ATTGAAGAAAAAAGAAGAAAAAAA-TCGAA
40374149 ATT-AAGAAAAAAGAAGAAAAAAATCGAA
1 ATTGAAGAAAAAAGAAGAAAAAAATCGAA
*
40374177 ATTGAAAAAAAAAGA
1 ATTGAAGAAAAAAGA
40374192 GTGATTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 16 0.41
29 23 0.59
ACGTcount: A:0.69, C:0.03, G:0.15, T:0.12
Consensus pattern (29 bp):
ATTGAAGAAAAAAGAAGAAAAAAATCGAA
Found at i:40374168 original size:28 final size:30
Alignment explanation
Indices: 40374120--40374191 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
40374110 TGTATTTAGT
* *
40374120 ATTGAAGAAAAAA-AAGAAAAAAATTCGGA
1 ATTGAAGAAAAAAGAAGAAAAAAAATCGAA
40374149 ATT-AAGAAAAAAGAAG-AAAAAAATCGAA
1 ATTGAAGAAAAAAGAAGAAAAAAAATCGAA
*
40374177 ATTGAAAAAAAAAGA
1 ATTGAAGAAAAAAGA
40374192 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.69, C:0.03, G:0.15, T:0.12
Consensus pattern (30 bp):
ATTGAAGAAAAAAGAAGAAAAAAAATCGAA
Found at i:40379841 original size:46 final size:46
Alignment explanation
Indices: 40379788--40379881 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
40379778 CAAAGAAAAG
*
40379788 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
40379834 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
40379880 AC
1 AC
40379882 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:40380255 original size:19 final size:19
Alignment explanation
Indices: 40380206--40380243 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40380196 TGGCTTAGAA
40380206 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
40380225 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
40380244 TTGACTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:40395467 original size:22 final size:25
Alignment explanation
Indices: 40395432--40395490 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
40395422 GTTGAAAAGT
*
40395432 ATAA-AATAAAATAAATAATGATAATA
1 ATAATAATAAAAT-GAT-ATGATAATA
40395458 ATAATAATAAAATGATATGAT-ATA
1 ATAATAATAAAATGATATGATAATA
40395482 TATAATAAT
1 -ATAATAAT
40395491 GTTTGATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.10
25 13 0.43
26 6 0.20
27 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (25 bp):
ATAATAATAAAATGATATGATAATA
Found at i:40395839 original size:49 final size:48
Alignment explanation
Indices: 40395757--40395914 Score: 273
Period size: 49 Copynumber: 3.2 Consensus size: 48
40395747 CTTACTTTGA
*
40395757 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
40395804 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
40395853 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
40395902 GAATGTGATAAGT
1 GAATGTGA-AAGT
40395915 CCCGAAGGGC
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
47 13 0.12
49 89 0.84
50 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:40396088 original size:37 final size:37
Alignment explanation
Indices: 40396032--40396110 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
40396022 CCGAGCTCTA
* * * * *
40396032 AAGACCTGATGACTACGTGTGGGGATTTTGTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40396069 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40396106 AAGAC
1 AAGAC
40396111 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40407394 original size:24 final size:25
Alignment explanation
Indices: 40407341--40407394 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
40407331 AACAAATTCT
* *
40407341 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
40407366 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
40407389 TTTTTT
1 TTTTTT
40407395 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:40409664 original size:14 final size:14
Alignment explanation
Indices: 40409645--40409671 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40409635 CTAGACCGTA
40409645 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
40409659 TGCAATTTTTTTT
1 TGCAATTTTTTTT
40409672 AAAACTTTTT
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:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:40411979 original size:30 final size:30
Alignment explanation
Indices: 40411939--40412011 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
40411929 CGAGTTTAAA
*
40411939 CTAAA-ATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
40411968 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
40411998 CTAAATATGAGCTA
1 CTAAATATGAGCTA
40412012 GGAGTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:40412022 original size:30 final size:30
Alignment explanation
Indices: 40411958--40412023 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
40411948 GCTAAGTTTT
* *
40411958 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
40411988 AGCTCGTGAGCTAAA-TATGAGCT-AGGAGTG
1 AGCTCGTGAGCTAAAGT-TGAGCTAAGG-GTG
40412018 AGCTCG
1 AGCTCG
40412024 GTTTAGCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:40414154 original size:30 final size:30
Alignment explanation
Indices: 40414111--40414183 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
40414101 CTTTTGTTTC
40414111 AATTTCTTTTTCATCTT-CTTTTTCACTCTCA
1 AATTTC-TTTTCAT-TTCCTTTTTCACTCTCA
* *
40414142 AATTTCTTTTCATTTCCTTTTTCATTTTCA
1 AATTTCTTTTCATTTCCTTTTTCACTCTCA
**
40414172 TTTTTCTTTTCA
1 AATTTCTTTTCA
40414184 AAGGCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 2 0.05
30 29 0.78
31 6 0.16
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (30 bp):
AATTTCTTTTCATTTCCTTTTTCACTCTCA
Found at i:40414193 original size:12 final size:12
Alignment explanation
Indices: 40414178--40414208 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40414168 TTCATTTTTC
40414178 TTTTCAAAGGCT
1 TTTTCAAAGGCT
40414190 TTTTCAAAGGCT
1 TTTTCAAAGGCT
40414202 TTTTCAA
1 TTTTCAA
40414209 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:40414285 original size:6 final size:6
Alignment explanation
Indices: 40414269--40414318 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
40414259 TTTCTTTTTA
*
40414269 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
40414318 T
1 T
40414319 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:40414301 original size:37 final size:37
Alignment explanation
Indices: 40414258--40414328 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40414248 CTTGCCTCTC
40414258 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
40414295 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
40414329 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:40414329 original size:16 final size:16
Alignment explanation
Indices: 40414254--40414314 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
40414244 GCCTCTTGCC
*
40414254 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
40414270 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
40414286 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
40414302 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
40414315 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:40423241 original size:10 final size:10
Alignment explanation
Indices: 40423226--40423252 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40423216 ATAATTAATT
40423226 TTTTTTTCGA
1 TTTTTTTCGA
40423236 TTTTTTTCGA
1 TTTTTTTCGA
40423246 TTTTTTT
1 TTTTTTT
40423253 TACAATCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTCGA
Found at i:40427934 original size:16 final size:17
Alignment explanation
Indices: 40427915--40427948 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40427905 AAAAAAGCAA
40427915 TTGAAAAG-AAAAGTTC
1 TTGAAAAGAAAAAGTTC
40427931 TTGAAAAGAAAAAGTTC
1 TTGAAAAGAAAAAGTTC
40427948 T
1 T
40427949 AGCTGAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (17 bp):
TTGAAAAGAAAAAGTTC
Found at i:40428497 original size:46 final size:46
Alignment explanation
Indices: 40428444--40428537 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
40428434 CAAAGAAAAG
*
40428444 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATACGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATACGATGA
*
40428490 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATACGATGA
40428536 AC
1 AC
40428538 GTCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATACGATGA
Found at i:40432311 original size:12 final size:12
Alignment explanation
Indices: 40432294--40432335 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
40432284 CTAGCTCTCT
40432294 TTTTTTTTACAA
1 TTTTTTTTACAA
40432306 TTTTTTTTCACAA
1 TTTTTTTT-ACAA
*
40432319 TTTGTTTT-CAAA
1 TTTTTTTTAC-AA
40432331 TTTTT
1 TTTTT
40432336 CACAACTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 14 0.54
13 11 0.42
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTTTTTACAA
Found at i:40432311 original size:13 final size:13
Alignment explanation
Indices: 40432293--40432335 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
40432283 ACTAGCTCTC
*
40432293 TTTTTTTTTACAA
1 TTTTTTTTCACAA
40432306 TTTTTTTTCACAA
1 TTTTTTTTCACAA
*
40432319 TTTGTTTTCA-AA
1 TTTTTTTTCACAA
40432331 TTTTT
1 TTTTT
40432336 CACAACTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:40432426 original size:12 final size:12
Alignment explanation
Indices: 40432379--40432425 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
40432369 GGAAACTAGT
40432379 TTTTTTTTCGAA
1 TTTTTTTTCGAA
40432391 TTTTTTTT-GAAA
1 TTTTTTTTCG-AA
*
40432403 TTTTTTTTCGAG
1 TTTTTTTTCGAA
40432415 TTTTTTTTCGA
1 TTTTTTTTCGA
40432426 GAAACTACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.68
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:40432793 original size:46 final size:46
Alignment explanation
Indices: 40432740--40432833 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
40432730 CAAAGAAAAG
*
40432740 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATACGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATACGATGA
*
40432786 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATACGATGA
40432832 AC
1 AC
40432834 ATCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATACGATGA
Found at i:40443848 original size:13 final size:13
Alignment explanation
Indices: 40443832--40443877 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 13
40443822 AAAAAAATAT
40443832 AAAAAAATTCGAA
1 AAAAAAATTCGAA
*
40443845 AAAAAAATTTGAAA
1 AAAAAAATTCG-AA
40443859 AAAAAAATTC-AA
1 AAAAAAATTCGAA
40443871 AAAAAAA
1 AAAAAAA
40443878 AGTTTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 9 0.30
13 10 0.33
14 11 0.37
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:40443851 original size:14 final size:14
Alignment explanation
Indices: 40443832--40443878 Score: 71
Period size: 13 Copynumber: 3.5 Consensus size: 14
40443822 AAAAAAATAT
40443832 AAAAAAATTCG-AA
1 AAAAAAATTCGAAA
*
40443845 AAAAAAATTTGAAA
1 AAAAAAATTCGAAA
40443859 AAAAAAATTC-AAA
1 AAAAAAATTCGAAA
40443872 AAAAAAA
1 AAAAAAA
40443879 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:40444798 original size:21 final size:20
Alignment explanation
Indices: 40444769--40444814 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40444759 AATCTTGAAT
*
40444769 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
40444790 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
40444810 GAAAA
1 GAAAA
40444815 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:40444830 original size:6 final size:6
Alignment explanation
Indices: 40444821--40444856 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
40444811 AAAAAAGAAT
* *
40444821 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
40444857 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:40454097 original size:15 final size:15
Alignment explanation
Indices: 40454077--40454130 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
40454067 ACTCTCCTCA
*
40454077 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
40454092 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
40454107 TTGTTTT-TCTC-TT
1 TTCTTTTCTCTCTTT
40454120 TTCTTTT-TCTC
1 TTCTTTTCTCTC
40454131 GCTCAATAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 12 0.35
14 3 0.09
15 19 0.56
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:40456208 original size:13 final size:13
Alignment explanation
Indices: 40456190--40456232 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
40456180 GAATACAAAC
40456190 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
40456202 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
40456215 --TTTTTTTCG-A
1 TTTTTTTTTCGAA
40456225 TTTTTTTT
1 TTTTTTTT
40456233 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 9 0.32
12 15 0.54
13 3 0.11
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:40464115 original size:27 final size:29
Alignment explanation
Indices: 40464060--40464117 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
40464050 CACAAGTAGG
40464060 AATAAAGAAATAAAAACGAAACAGCAAGA
1 AATAAAGAAATAAAAACGAAACAGCAAGA
* *
40464089 AATAAAGAAA-AGAAATG-AACAGCAAGA
1 AATAAAGAAATAAAAACGAAACAGCAAGA
40464116 AA
1 AA
40464118 AGATAAGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 12 0.44
28 5 0.19
29 10 0.37
ACGTcount: A:0.69, C:0.09, G:0.16, T:0.07
Consensus pattern (29 bp):
AATAAAGAAATAAAAACGAAACAGCAAGA
Found at i:40466341 original size:20 final size:19
Alignment explanation
Indices: 40466318--40466382 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
40466308 AAGCTCAAAC
40466318 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
40466338 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
40466358 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
40466378 GAGCT
1 GAGCT
40466383 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40468428 original size:30 final size:31
Alignment explanation
Indices: 40468394--40468459 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
40468384 CTATTTATGT
* *
40468394 AGGTTGGCCGAATGTGG-GGTTCATTTAGCA
1 AGGTTAGCCGAATGTGGAGATTCATTTAGCA
40468424 AGGTTAGCCGAATGTGGAGATTCATTTAGCA
1 AGGTTAGCCGAATGTGGAGATTCATTTAGCA
40468455 AGGTT
1 AGGTT
40468460 CATGCATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.30
Consensus pattern (31 bp):
AGGTTAGCCGAATGTGGAGATTCATTTAGCA
Found at i:40476352 original size:16 final size:17
Alignment explanation
Indices: 40476320--40476353 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40476310 CATCCAGCAA
*
40476320 CCTTATCAACTAAAAGG
1 CCTTAGCAACTAAAAGG
40476337 CCTTAGCAAC-AAAAGG
1 CCTTAGCAACTAAAAGG
40476353 C
1 C
40476354 AATTTTAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (17 bp):
CCTTAGCAACTAAAAGG
Found at i:40485405 original size:18 final size:19
Alignment explanation
Indices: 40485382--40485424 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
40485372 TCTTTCATTC
*
40485382 TCTTTTTTGAATTTTC-TT
1 TCTTTTTTCAATTTTCTTT
*
40485400 TCTTTTTTCATTTTTCTTT
1 TCTTTTTTCAATTTTCTTT
40485419 TCTTTT
1 TCTTTT
40485425 GTATTTTCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (19 bp):
TCTTTTTTCAATTTTCTTT
Found at i:40485430 original size:18 final size:19
Alignment explanation
Indices: 40485393--40485445 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
40485383 CTTTTTTGAA
*
40485393 TTTTC-TTTCTTTTTTCAT
1 TTTTCTTTTCTTTTGTCAT
40485411 TTTTCTTTTCTTTTGT-AT
1 TTTTCTTTTCTTTTGTCAT
40485429 TTTCGCTCTTTTCTTTT
1 TTT---TCTTTTCTTTT
40485446 TCTCTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.33
19 9 0.30
21 11 0.37
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTCTTTTGTCAT
Found at i:40487959 original size:24 final size:23
Alignment explanation
Indices: 40487905--40487976 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 23
40487895 GGATAATTAA
**
40487905 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
40487928 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
40487952 GAAATGGTA--T-GAATTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
*
40487972 AAAAT
1 GAAAT
40487977 TGGAATGGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 14 0.36
22 1 0.03
23 9 0.23
24 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.29, T:0.39
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:40495344 original size:21 final size:20
Alignment explanation
Indices: 40495320--40495364 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
40495310 TCGTTTCCAG
*
40495320 CTCACTCGAGCTCAAGTTCAA
1 CTCACTCAAGCTCAA-TTCAA
*
40495341 CTCACTCAAGCTCAATTCAG
1 CTCACTCAAGCTCAATTCAA
40495361 CTCA
1 CTCA
40495365 ATCTTTAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.24
Consensus pattern (20 bp):
CTCACTCAAGCTCAATTCAA
Found at i:40495350 original size:15 final size:16
Alignment explanation
Indices: 40495318--40495365 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
40495308 GCTCGTTTCC
40495318 AGCTC-ACTCGAGCTCA
1 AGCTCAACTC-AGCTCA
*
40495334 AGTTCAACTCA-CTCA
1 AGCTCAACTCAGCTCA
*
40495349 AGCTCAATTCAGCTCA
1 AGCTCAACTCAGCTCA
40495365 A
1 A
40495366 TCTTTAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.48
16 10 0.37
17 4 0.15
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.23
Consensus pattern (16 bp):
AGCTCAACTCAGCTCA
Found at i:40496930 original size:20 final size:20
Alignment explanation
Indices: 40496887--40496942 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
40496877 TCGAAAATTC
**
40496887 AAAAAAAAAAAAAAGTGAGC
1 AAAAAAAAAAAAAAGTGAAA
*
40496907 AAAAAAAAAAAAAAGTTAAA
1 AAAAAAAAAAAAAAGTGAAA
40496927 AAAAGAACAAAAAAAA
1 AAAA-AA-AAAAAAAA
40496943 AAGTGAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 21 0.68
21 2 0.06
22 8 0.26
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAAAAGTGAAA
Found at i:40498050 original size:47 final size:46
Alignment explanation
Indices: 40497962--40498062 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
40497952 AGTGTCATGG
*
40497962 AAAAGAAATTGAATTGAAAAAGGATGTGAAAAGAGAAAGAAATCGA
1 AAAAGAAATTGAATTGAAAAAAGATGTGAAAAGAGAAAGAAATCGA
* *
40498008 AAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAA-A-AGAGAAATTGA
1 AAAAGAAATTGA-ATTGAA-AAAAGATGTGA--AAAGAGAAAGAAATCGA
40498055 AAAAGAAA
1 AAAAGAAA
40498063 GAAAAGACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
46 12 0.25
47 28 0.58
48 5 0.10
49 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (46 bp):
AAAAGAAATTGAATTGAAAAAAGATGTGAAAAGAGAAAGAAATCGA
Found at i:40499770 original size:20 final size:20
Alignment explanation
Indices: 40499724--40499770 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40499714 GTCTCGTTTC
*
40499724 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40499744 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40499764 CAGCTCA
1 CAGCTCA
40499771 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40506177 original size:4 final size:4
Alignment explanation
Indices: 40506163--40506198 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
40506153 ATAATAAATT
40506163 TAAA CTAAA TAAA TAAA T-AA TAAA TAAA TAAA TAAA
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
40506199 AATAAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:40506179 original size:19 final size:19
Alignment explanation
Indices: 40506163--40506204 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
40506153 ATAATAAATT
40506163 TAAACTAAATAAATAAATAA
1 TAAA-TAAATAAATAAATAA
40506183 TAAATAAATAAATAAA-AA
1 TAAATAAATAAATAAATAA
40506201 TAAA
1 TAAA
40506205 ACTTTACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAATAAATAAATAAATAA
Found at i:40506186 original size:15 final size:15
Alignment explanation
Indices: 40506168--40506204 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40506158 AAATTTAAAC
40506168 TAAATAAATAAATAA
1 TAAATAAATAAATAA
40506183 TAAATAAATAAATAA
1 TAAATAAATAAATAA
40506198 -AAATAAA
1 TAAATAAA
40506205 ACTTTACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAATAAATAAATAA
Found at i:40507603 original size:23 final size:22
Alignment explanation
Indices: 40507551--40507603 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40507541 TCCATGTCTT
*
40507551 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40507573 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40507596 TTTCTTTT
1 TTTCTTTT
40507604 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40509926 original size:4 final size:4
Alignment explanation
Indices: 40509912--40509944 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
40509902 CATAAAAATT
40509912 TAAA CTAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA
40509945 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:40510827 original size:10 final size:10
Alignment explanation
Indices: 40510812--40510873 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
40510802 TTTGAACCAT
*
40510812 TACCAATTCG
1 TACCAATTCA
*
40510822 TACCAAATACCA
1 TACC-AAT-TCA
*
40510834 TACCATTTCA
1 TACCAATTCA
40510844 TACCAATTCCA
1 TACCAATT-CA
* *
40510855 TACCATTTCG
1 TACCAATTCA
40510865 TACCAATTC
1 TACCAATTC
40510874 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:40510857 original size:21 final size:21
Alignment explanation
Indices: 40510812--40510874 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
40510802 TTTGAACCAT
* *
40510812 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
40510834 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
40510855 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
40510875 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:40511931 original size:15 final size:15
Alignment explanation
Indices: 40511899--40511932 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40511889 GTTCAACGAA
*
40511899 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
40511914 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
40511929 GAGG
1 GAGG
40511933 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:40515627 original size:10 final size:10
Alignment explanation
Indices: 40515612--40515673 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
40515602 TTTGAACCAT
*
40515612 TACCAATTCG
1 TACCAATTCA
*
40515622 TACCAAATACCA
1 TACC-AAT-TCA
*
40515634 TACCATTTCA
1 TACCAATTCA
40515644 TACCAATTCCA
1 TACCAATT-CA
* *
40515655 TACCATTTCG
1 TACCAATTCA
40515665 TACCAATTC
1 TACCAATTC
40515674 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:40515657 original size:21 final size:21
Alignment explanation
Indices: 40515612--40515674 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
40515602 TTTGAACCAT
* *
40515612 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
40515634 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
40515655 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
40515675 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:40522094 original size:15 final size:15
Alignment explanation
Indices: 40522074--40522122 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
40522064 ACTCTCCTCA
40522074 TTCTTTTCTTTCTTT
1 TTCTTTTCTTTCTTT
**
40522089 TTCTTTTCACTC-TT
1 TTCTTTTCTTTCTTT
*
40522103 TT-TGTT-TTTCTTT
1 TTCTTTTCTTTCTTT
40522116 TTCTTTT
1 TTCTTTT
40522123 TCTCGCTCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
12 2 0.08
13 7 0.27
14 7 0.27
15 10 0.38
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (15 bp):
TTCTTTTCTTTCTTT
Found at i:40522122 original size:5 final size:6
Alignment explanation
Indices: 40522082--40522125 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
40522072 CATTCTTTTC
*
40522082 TTTCTT TTTCTT TTCACTCTT TTTGTT TTTCTT TTTCTT TTTCT
1 TTTCTT TTTCTT TT---TCTT TTTCTT TTTCTT TTTCTT TTTCT
40522126 CGCTCAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 27 0.82
9 6 0.18
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:40524221 original size:12 final size:12
Alignment explanation
Indices: 40524200--40524243 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
40524190 GAATACAAAC
40524200 TTTTTCTTTTGAA
1 TTTTT-TTTTGAA
*
40524213 TTTTTTTTTCAA
1 TTTTTTTTTGAA
*
40524225 ATTTTTTTTG-A
1 TTTTTTTTTGAA
40524236 TTTTTTTT
1 TTTTTTTT
40524244 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 8 0.30
12 14 0.52
13 5 0.19
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:40537935 original size:20 final size:20
Alignment explanation
Indices: 40537910--40537964 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
40537900 TGTGGTTCAA
*
40537910 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
40537930 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
40537950 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
40537965 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:40539773 original size:11 final size:11
Alignment explanation
Indices: 40539759--40539800 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
40539749 AAAATAAAGG
40539759 AAAAAAAATTC
1 AAAAAAAATTC
40539770 AAAAAAAATTC
1 AAAAAAAATTC
40539781 AAAAAAAAATTC
1 -AAAAAAAATTC
40539793 AAAAAAAA
1 AAAAAAAA
40539801 AATTGTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:40539774 original size:12 final size:12
Alignment explanation
Indices: 40539759--40539801 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
40539749 AAAATAAAGG
40539759 AAAAAAAATTC-
1 AAAAAAAATTCA
40539770 AAAAAAAATTCA
1 AAAAAAAATTCA
40539782 AAAAAAAATTCA
1 AAAAAAAATTCA
40539794 AAAAAAAA
1 AAAAAAAA
40539802 ATTGTATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:40540823 original size:17 final size:15
Alignment explanation
Indices: 40540803--40540841 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
40540793 GCGAGCGAGA
40540803 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
40540820 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
40540835 AAGATGA
1 AA-ATGA
40540842 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:40542349 original size:20 final size:20
Alignment explanation
Indices: 40542324--40542378 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
40542314 TGTGGTTCAA
*
40542324 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
40542344 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
40542364 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
40542379 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:40544699 original size:20 final size:19
Alignment explanation
Indices: 40544676--40544740 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
40544666 AAGCTCAAAC
40544676 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
40544696 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
40544716 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
40544736 GAGCT
1 GAGCT
40544741 GGGAAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40546187 original size:22 final size:21
Alignment explanation
Indices: 40546156--40546206 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
40546146 ACCTCTTTGA
*
40546156 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCATACC-AAT
*
40546179 ACCATACCATTTCATACCAAT
1 ACCATACCAATTCATACCAAT
*
40546200 TCCATAC
1 ACCATAC
40546207 TATTTCGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCATACCAAT
Found at i:40546206 original size:21 final size:21
Alignment explanation
Indices: 40546161--40546223 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
40546151 TTTGAACCAT
* * *
40546161 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
40546183 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
40546204 TACTATTTCGA-ACCAATTCC
1 TACCATTTC-ATACCAATTCC
40546224 CAAATACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:40548476 original size:30 final size:31
Alignment explanation
Indices: 40548442--40548506 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
40548432 CTATTTATGT
* *
40548442 AGGTTGGCCGAATGTGG-GGTTCATTTAGCA
1 AGGTTAGCCGAATGTGGAGATTCATTTAGCA
40548472 AGGTTAGCCGAATGTGGAGATTCATTTAGCA
1 AGGTTAGCCGAATGTGGAGATTCATTTAGCA
40548503 AGGT
1 AGGT
40548507 GCATGCATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.25, C:0.12, G:0.34, T:0.29
Consensus pattern (31 bp):
AGGTTAGCCGAATGTGGAGATTCATTTAGCA
Found at i:40551762 original size:23 final size:24
Alignment explanation
Indices: 40551721--40551765 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
40551711 TCTGAACAAA
40551721 TTAAATCAAAGTTTAAATGTGTTC
1 TTAAATCAAAGTTTAAATGTGTTC
* *
40551745 TTAAAT-AATGTTTTAATGTGT
1 TTAAATCAAAGTTTAAATGTGT
40551766 CAAGCTAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
TTAAATCAAAGTTTAAATGTGTTC
Found at i:40553618 original size:20 final size:20
Alignment explanation
Indices: 40553572--40553618 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40553562 AGCTCGTTTC
*
40553572 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40553592 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40553612 CAGCTCA
1 CAGCTCA
40553619 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40558047 original size:20 final size:20
Alignment explanation
Indices: 40558001--40558047 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40557991 AGCTCGTTTC
*
40558001 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40558021 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40558041 CAGCTCA
1 CAGCTCA
40558048 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40559549 original size:9 final size:9
Alignment explanation
Indices: 40559535--40559559 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40559525 AGATTTCACA
40559535 AAAGAAAAT
1 AAAGAAAAT
40559544 AAAGAAAAT
1 AAAGAAAAT
40559553 AAAGAAA
1 AAAGAAA
40559560 GTCCTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
AAAGAAAAT
Found at i:40559974 original size:4 final size:4
Alignment explanation
Indices: 40559965--40559996 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
40559955 AAGTTTTATT
40559965 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
40559997 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:40563772 original size:4 final size:4
Alignment explanation
Indices: 40563763--40563790 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40563753 AAGTTTTATT
40563763 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
40563791 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:40574446 original size:2 final size:2
Alignment explanation
Indices: 40574439--40574483 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40574429 GCATGCTTTC
40574439 TA TA TA TA 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
40574481 TA T
1 TA T
40574484 CTTCTAAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40574681 original size:17 final size:17
Alignment explanation
Indices: 40574655--40574692 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40574645 ATCATTGTAA
*
40574655 ATATTTTATTATTTTAC
1 ATATTCTATTATTTTAC
*
40574672 ATATTCTATTATTTTAT
1 ATATTCTATTATTTTAC
40574689 ATAT
1 ATAT
40574693 ATTGCACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTCTATTATTTTAC
Found at i:40579397 original size:67 final size:67
Alignment explanation
Indices: 40579250--40579397 Score: 215
Period size: 67 Copynumber: 2.2 Consensus size: 67
40579240 ACTGGTAGCC
* * * * * *
40579250 TGTTTGCATATATTGGTAGTTTATCTGCATTACCGTTACTGGTGGCTTGTCCGTAATACTAGCAG
1 TGTTTGCATATATTGGCAGTTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAA
40579315 CT
66 CT
**
40579317 TGTTTGTTTATATTGGCAGTTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAA
1 TGTTTGCATATATTGGCAGTTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAA
40579382 CT
66 CT
*
40579384 TGTTTGCACATATT
1 TGTTTGCATATATT
40579398 AACAATTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (67 bp):
TGTTTGCATATATTGGCAGTTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAA
CT
Found at i:40579413 original size:67 final size:67
Alignment explanation
Indices: 40579269--40579416 Score: 179
Period size: 67 Copynumber: 2.2 Consensus size: 67
40579259 ATATTGGTAG
* * * * * *** **
40579269 TTTATCTGCATTACCGTTACTGGTGGCTTGTCCGTAATACTAGCAGCTTGTTTGTTTATATTGGC
1 TTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAACTTGTTTGCACATATTAAC
*
40579334 AG
66 AA
40579336 TTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAACTTGTTTGCACATATTAAC
1 TTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAACTTGTTTGCACATATTAAC
40579401 AA
66 AA
* *
40579403 TTTGTTTGCATTAC
1 TTTATCTGCATTAC
40579417 TATACTGGTG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (67 bp):
TTTATCTGCATTACCATTACTAGTGGCTTGTACATAATACTAGCAACTTGTTTGCACATATTAAC
AA
Found at i:40582715 original size:11 final size:10
Alignment explanation
Indices: 40582696--40582734 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
40582686 ATATATATGT
40582696 TTAAAATTTA
1 TTAAAATTTA
40582706 TTAGAAATTTA
1 TTA-AAATTTA
*
40582717 -TAAAAGTTA
1 TTAAAATTTA
40582726 TTAAAATTT
1 TTAAAATTT
40582735 GATCAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 6 0.24
10 12 0.48
11 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:40582810 original size:29 final size:28
Alignment explanation
Indices: 40582778--40582861 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 28
40582768 TTTTAAAAAA
40582778 TTTATAATATTTTAATAAGTTTTATA-TTT
1 TTTATAAT-TTTTAATAA-TTTTATATTTT
* *
40582807 TTTATATTTTTTTATCAAATTTTAATATTTT
1 TTTATAATTTTTAAT--AATTTT-ATATTTT
*
40582838 TTTATAATTTCATAATAATTTTAT
1 TTTATAATTT-TTAATAATTTTAT
40582862 TAATTCAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
28 6 0.13
29 13 0.29
30 11 0.24
31 12 0.27
32 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTATAATTTTTAATAATTTTATATTTT
Found at i:40582817 original size:10 final size:10
Alignment explanation
Indices: 40582797--40582843 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
40582787 TTTTAATAAG
40582797 TTTTATA-TT
1 TTTTATATTT
40582806 TTTTATATTT
1 TTTTATATTT
**
40582816 TTTTATCAAAT
1 TTTTAT-ATTT
*
40582827 TTTAATATTT
1 TTTTATATTT
40582837 TTTTATA
1 TTTTATA
40582844 ATTTCATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 7 0.23
10 16 0.53
11 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATATTT
Found at i:40582854 original size:21 final size:20
Alignment explanation
Indices: 40582778--40582844 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
40582768 TTTTAAAAAA
**
40582778 TTTATAATATTTTAATA-AGT
1 TTTATAA-ATTTTAATATTTT
* *
40582798 TTTAT-ATTTTTTATATTTT
1 TTTATAAATTTTAATATTTT
40582817 TTTATCAAATTTTAATATTTT
1 TTTAT-AAATTTTAATATTTT
40582838 TTTATAA
1 TTTATAA
40582845 TTTCATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.18
19 7 0.18
20 7 0.18
21 17 0.45
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTATAAATTTTAATATTTT
Found at i:40585940 original size:41 final size:41
Alignment explanation
Indices: 40585879--40586006 Score: 172
Period size: 41 Copynumber: 3.2 Consensus size: 41
40585869 AATACTGTTC
40585879 CAAAATTTATCAGTTCGTATTTTATTTTTAATCTTTTTTTT
1 CAAAATTTATCAGTTCGTATTTTATTTTTAATCTTTTTTTT
* **
40585920 CAAAATTTATCAGCTT-GTATTTTATTTTTAA-C-CTCATTT
1 CAAAATTTATCAG-TTCGTATTTTATTTTTAATCTTTTTTTT
* * *
40585959 CAAAATTTATCTGTTCGTATCTTATTTTTAATATTTTTTTT
1 CAAAATTTATCAGTTCGTATTTTATTTTTAATCTTTTTTTT
40586000 CAAAATT
1 CAAAATT
40586007 GTATACGTAG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.03
39 30 0.41
40 1 0.01
41 39 0.53
42 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (41 bp):
CAAAATTTATCAGTTCGTATTTTATTTTTAATCTTTTTTTT
Found at i:40585984 original size:39 final size:41
Alignment explanation
Indices: 40585879--40585990 Score: 149
Period size: 39 Copynumber: 2.8 Consensus size: 41
40585869 AATACTGTTC
* **
40585879 CAAAATTTATCAGTTCGTATTTTATTTTTAATCTTTTTTTT
1 CAAAATTTATCAGTTCGTATTTTATTTTTAATCTCTCATTT
40585920 CAAAATTTATCAGCTT-GTATTTTATTTTTAA-C-CTCATTT
1 CAAAATTTATCAG-TTCGTATTTTATTTTTAATCTCTCATTT
* *
40585959 CAAAATTTATCTGTTCGTATCTTATTTTTAAT
1 CAAAATTTATCAGTTCGTATTTTATTTTTAAT
40585991 ATTTTTTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.03
39 30 0.48
40 1 0.02
41 28 0.44
42 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.55
Consensus pattern (41 bp):
CAAAATTTATCAGTTCGTATTTTATTTTTAATCTCTCATTT
Found at i:40586995 original size:29 final size:30
Alignment explanation
Indices: 40586937--40586995 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
40586927 GTTAGTATTC
* *
40586937 TTTTATGATAATATTTTTATTCAATTAATG
1 TTTTATGATAATATTTTTACTCAATCAATG
40586967 TTTTATG-TAATATTTTGTACTC-ATCAATG
1 TTTTATGATAATATTTT-TACTCAATCAATG
40586996 CAACAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (30 bp):
TTTTATGATAATATTTTTACTCAATCAATG
Found at i:40588043 original size:28 final size:27
Alignment explanation
Indices: 40587969--40588039 Score: 115
Period size: 28 Copynumber: 2.6 Consensus size: 27
40587959 AAAAAATGAC
*
40587969 ATTAACAAAACTTTTTATTCAATTAAT
1 ATTAACAAAATTTTTTATTCAATTAAT
*
40587996 ACTAACAAAAGTTTTTTATTCAATTAAT
1 ATTAACAAAA-TTTTTTATTCAATTAAT
40588024 ATTAACAAAATTTTTT
1 ATTAACAAAATTTTTT
40588040 TATTAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.38
28 25 0.62
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (27 bp):
ATTAACAAAATTTTTTATTCAATTAAT
Found at i:40591471 original size:16 final size:16
Alignment explanation
Indices: 40591447--40591484 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40591437 TTTGGTTCGC
* *
40591447 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
40591463 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
40591479 TGTAAT
1 TGTAAT
40591485 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:40591568 original size:39 final size:43
Alignment explanation
Indices: 40591463--40591572 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
40591453 GGATTAGAGG
40591463 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGCTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGCT--A
* * ***
40591508 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGCTA
40591548 T-TAATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
40591573 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 21 0.37
40 1 0.02
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGCTA
Found at i:40591738 original size:18 final size:17
Alignment explanation
Indices: 40591717--40591751 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40591707 TTATTATTAA
*
40591717 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40591735 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40591752 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40591904 original size:148 final size:150
Alignment explanation
Indices: 40591633--40591907 Score: 509
Period size: 151 Copynumber: 1.8 Consensus size: 150
40591623 GTAAATGATT
*
40591633 ATTATTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATT
1 ATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATT
*
40591698 TAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
66 TAAACATAA-TATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
40591763 AGCAGAAATTTGTTTTGGTAA
130 AGCAGAAATTTGTTTTGGTAA
40591784 ATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATT
1 ATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATT
40591849 TAAACAT-A-ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
66 TAAACATAATATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
40591908 TTAATATTCT
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
148 50 0.41
150 1 0.01
151 71 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (150 bp):
ATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATT
TAAACATAATATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
GCAGAAATTTGTTTTGGTAA
Found at i:40591946 original size:60 final size:60
Alignment explanation
Indices: 40591880--40592065 Score: 179
Period size: 60 Copynumber: 3.1 Consensus size: 60
40591870 TTATAATTAA
40591880 AATATATAATTTAATAAAATTCTTAATATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAATATTCTTATATGAATTTACTCAAATCAT
* ** * * * * * * *
40591940 AATATATGATACAGTAAAATATAAATTAA-AATAATAATTATTAAAT--ATATTA-T--AATTAA
1 AATATATAATTTAATAAAAT-T--CTTAATATTAAT-ATTCTTATATGAAT-TTACTCAAATCAT
40591999 AATATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAATATTCTTATATGAATTTACTCAAATCAT
40592059 AATATAT
1 AATATAT
40592066 GATACTATAA
Statistics
Matches: 94, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
55 4 0.04
56 8 0.09
57 9 0.10
58 8 0.09
59 14 0.15
60 27 0.29
61 4 0.04
62 8 0.09
63 12 0.13
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:40592015 original size:15 final size:13
Alignment explanation
Indices: 40591954--40592014 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 13
40591944 TATGATACAG
40591954 TAAAATATA-AAT
1 TAAAATATATAAT
*
40591966 TAAAATAATAATTAT
1 TAAAAT-AT-ATAAT
40591981 TAAATATATTATAAT
1 TAAA-ATA-TATAAT
40591996 TAAAATATATAATT
1 TAAAATATATAA-T
40592010 TAAAA
1 TAAAA
40592015 AATTCTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 6 0.15
13 7 0.17
14 10 0.24
15 15 0.37
16 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAAATATATAAT
Found at i:40592148 original size:119 final size:120
Alignment explanation
Indices: 40591854--40592137 Score: 452
Period size: 119 Copynumber: 2.4 Consensus size: 120
40591844 ATATTTAAAC
40591854 ATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT-ATTAATATTCT
1 ATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
40591918 TATATGAATTTACTCAAATCATAATATATGATACAGTAAAATATAAATTAAAATA
66 TATATGAATTTACTCAAATCATAATATATGATACAGTAAAATATAAATTAAAATA
40591973 ATAATTATTAAATATATTATAATTAAAATATATAATTTAA-AAAATTCTTAATAATTAATATTCT
1 ATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
* *** *
40592037 TATATGAATTTACTCAAATCATAATATATGATAC--TATAAATTTTTTTTGAAATA
66 TATATGAATTTACTCAAATCATAATATATGATACAGTA-AAATATAAATTAAAATA
* *
40592091 ATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 A-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
40592138 TAAAATAATT
Statistics
Matches: 154, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
117 2 0.01
118 58 0.38
119 94 0.61
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (120 bp):
ATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
TATATGAATTTACTCAAATCATAATATATGATACAGTAAAATATAAATTAAAATA
Found at i:40593501 original size:14 final size:15
Alignment explanation
Indices: 40593468--40593501 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40593458 AGTGTTCATC
*
40593468 CAAAACAGAACCATA
1 CAAAACAGAAACATA
40593483 CAAAACAGAAACA-A
1 CAAAACAGAAACATA
40593497 CAAAA
1 CAAAA
40593502 TCTGCTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.68, C:0.24, G:0.06, T:0.03
Consensus pattern (15 bp):
CAAAACAGAAACATA
Found at i:40594714 original size:16 final size:15
Alignment explanation
Indices: 40594693--40594726 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40594683 TTTGATAATT
* *
40594693 TGAAAATTTAAGTGC
1 TGAAAAATTAAGTAC
40594708 TGAAAAATTAAGTAC
1 TGAAAAATTAAGTAC
40594723 TGAA
1 TGAA
40594727 TTTTTATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (15 bp):
TGAAAAATTAAGTAC
Found at i:40598078 original size:50 final size:50
Alignment explanation
Indices: 40598004--40598156 Score: 184
Period size: 50 Copynumber: 3.1 Consensus size: 50
40597994 TGTAAAAGTG
*
40598004 AAAATGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC
1 AAAATGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC
* * *
40598053 AAAATGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACATGTATC
1 AAAATGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC
** * * * *
40598103 -GGATGGTAATGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACC
1 AAAATGAT-A-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC
40598154 AAA
1 AAA
40598157 CATCATTGAT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
49 12 0.14
50 38 0.45
51 35 0.41
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (50 bp):
AAAATGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC
Found at i:40598207 original size:45 final size:45
Alignment explanation
Indices: 40598156--40598244 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
40598146 TGTGAACCAA
* *
40598156 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
40598201 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
40598245 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:40606068 original size:20 final size:19
Alignment explanation
Indices: 40606045--40606086 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40606035 TAAAGAAAGT
40606045 AAAT-AAAATGAAAAGTAATG
1 AAATGAAAATG-AAAGTAA-G
*
40606065 AAATGCAAATGAAAGTAAG
1 AAATGAAAATGAAAGTAAG
40606084 AAA
1 AAA
40606087 ATTTGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.17, T:0.17
Consensus pattern (19 bp):
AAATGAAAATGAAAGTAAG
Found at i:40606555 original size:15 final size:16
Alignment explanation
Indices: 40606535--40606564 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40606525 TGGTACCTTG
40606535 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
40606550 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
40606565 AACATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:40614083 original size:21 final size:20
Alignment explanation
Indices: 40614020--40614086 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
40614010 TTGAATCATC
* * *
40614020 TTTTAAATCAAGTTAAAATA
1 TTTTTAATCAAGTTAAATTT
* *
40614040 ATTTTAATCAAGTTAGATTT
1 TTTTTAATCAAGTTAAATTT
*
40614060 TTTTTCAATC-AGTTAAATTG
1 TTTTT-AATCAAGTTAAATTT
40614080 TTTTTAA
1 TTTTTAA
40614087 AATAAGTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.05
20 32 0.84
21 4 0.11
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTTTAATCAAGTTAAATTT
Found at i:40616069 original size:20 final size:20
Alignment explanation
Indices: 40616044--40616095 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 20
40616034 GAAGATATGC
40616044 AATCTTAGATATGA-TTTGT
1 AATCTTAGATATGATTTTGT
40616063 AAATCTTAGAAGATATGATTTTGT
1 -AATCTT---AGATATGATTTTGT
40616087 AATCTTAGA
1 AATCTTAGA
40616096 GATTTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 9 0.32
23 14 0.50
24 5 0.18
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (20 bp):
AATCTTAGATATGATTTTGT
Found at i:40616080 original size:23 final size:22
Alignment explanation
Indices: 40616050--40616108 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
40616040 ATGCAATCTT
40616050 AGATATGATTTGTAAATCTTAG
1 AGATATGATTTGTAAATCTTAG
40616072 AAGATATGATTTTGT-AATCTTAG
1 -AGATATGA-TTTGTAAATCTTAG
*
40616095 AGATTTGATTTGTA
1 AGATATGATTTGTA
40616109 GATAGCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 5 0.15
22 7 0.21
23 16 0.48
24 5 0.15
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (22 bp):
AGATATGATTTGTAAATCTTAG
Found at i:40620033 original size:15 final size:14
Alignment explanation
Indices: 40620012--40620047 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
40620002 ATAATCCTTA
*
40620012 ATAATTATCTTAAT
1 ATAATTATCCTAAT
40620026 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
40620041 ATAATTA
1 ATAATTA
40620048 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:40622960 original size:140 final size:140
Alignment explanation
Indices: 40622706--40623126 Score: 707
Period size: 140 Copynumber: 3.0 Consensus size: 140
40622696 CGAGTTGAAG
* * *
40622706 ACTGCTGCCGGTTTGTTGCAACCTTTGCCTATTCCGGAGCGTCCATGGGAGAGTTTATCCATGAA
1 ACTGCTGCCGGTTTGTTACAACCTTTGCCCATTCCGGAGCGTCCATGGGAGAGTTTATCCATGGA
* *
40622771 CTTTATTGTGGGTTTGCCTAAATTTGATGGGTTTACAAGCATTTTTGTTGTGGTGGACAAGTTTT
66 CTTTATTGTGGGTTTGCCTAAATCTGATGGGTTTGCAAGCATTTTTGTTGTGGTGGACAAGTTTT
*
40622836 TGAAGTATGC
131 CGAAGTATGC
* * *
40622846 ACTGCTGCCGATTTGTTACAACCTTTGCCCATTTCGGAGCGTCCATAGGAGAGTTTATCCATGGA
1 ACTGCTGCCGGTTTGTTACAACCTTTGCCCATTCCGGAGCGTCCATGGGAGAGTTTATCCATGGA
* *
40622911 CTTTATTGTGGGTTTTCCTAAATCTGATGGGTTTGCAAGCATTTATGTTGTGGTGGACAAGTTTT
66 CTTTATTGTGGGTTTGCCTAAATCTGATGGGTTTGCAAGCATTTTTGTTGTGGTGGACAAGTTTT
40622976 CGAAGTATGC
131 CGAAGTATGC
* * *
40622986 ATTGCTGCCGGTTTGTTACAACCTTTACCCATTCCGGAGCGTCCATGGGAGAGTTTATCCACGGA
1 ACTGCTGCCGGTTTGTTACAACCTTTGCCCATTCCGGAGCGTCCATGGGAGAGTTTATCCATGGA
*
40623051 CTTTATTGTGGGTTTGCCTAAATCTGATAGGTTTGCAAGCATTTTTGTTGTGGTGGACAAGTTTT
66 CTTTATTGTGGGTTTGCCTAAATCTGATGGGTTTGCAAGCATTTTTGTTGTGGTGGACAAGTTTT
40623116 CGAAGTATGC
131 CGAAGTATGC
40623126 A
1 A
40623127 ACATTTATTC
Statistics
Matches: 261, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 261 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (140 bp):
ACTGCTGCCGGTTTGTTACAACCTTTGCCCATTCCGGAGCGTCCATGGGAGAGTTTATCCATGGA
CTTTATTGTGGGTTTGCCTAAATCTGATGGGTTTGCAAGCATTTTTGTTGTGGTGGACAAGTTTT
CGAAGTATGC
Found at i:40624347 original size:23 final size:21
Alignment explanation
Indices: 40624303--40624357 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
40624293 ATGTAATCTT
* *
40624303 AGATATGATATGTAAATTTTAG
1 AGATATGAT-TCTAAATCTTAG
40624325 AAGATATGATTCTATAATCTTAG
1 -AGATATGATTCTA-AATCTTAG
*
40624348 AGATTTGATT
1 AGATATGATT
40624358 TGTAGATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (21 bp):
AGATATGATTCTAAATCTTAG
Found at i:40625665 original size:13 final size:13
Alignment explanation
Indices: 40625643--40625674 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40625633 GGCCCGACCC
*
40625643 ATATTAAATATAT
1 ATATTTAATATAT
40625656 ATATTTAATATAT
1 ATATTTAATATAT
40625669 ATATTT
1 ATATTT
40625675 GATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTTAATATAT
Found at i:40629826 original size:95 final size:95
Alignment explanation
Indices: 40629663--40629860 Score: 324
Period size: 95 Copynumber: 2.1 Consensus size: 95
40629653 TTCGGTGGCC
* * *
40629663 TTAGTGGCGTTTTTTGTCTTGCGCTGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGAAAAAAC
1 TTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGAAAAAAC
*
40629728 GCCGCAAAAAATAAAATACAACGGTGTCGT
66 GCCGCAAAAAATAAAATACAACGGCGTCGT
* * * *
40629758 TTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGTGGCGTTTTTAGGAAGAAC
1 TTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGAAAAAAC
40629823 GCCGCAAAAAATAAAATACAACGGCGTCGT
66 GCCGCAAAAAATAAAATACAACGGCGTCGT
40629853 TTAGTGGC
1 TTAGTGGC
40629861 TACGGTGGCG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (95 bp):
TTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGAAAAAAC
GCCGCAAAAAATAAAATACAACGGCGTCGT
Found at i:40629898 original size:113 final size:114
Alignment explanation
Indices: 40629748--40630011 Score: 370
Period size: 113 Copynumber: 2.3 Consensus size: 114
40629738 ATAAAATACA
* * *
40629748 ACGGTGTCGTTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGTGGCGTTTT
1 ACGGTGGCG-TTAGTGGCGTTTTTGGTCTAGCACCGCTAATGGTCTGTGTTTTTAGCGGCGTTTT
* *
40629813 TAGGA-AGAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGG-CT
65 CAGGATA-AACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAATGGCCT
* *
40629862 ACGGTGGCGTTAGTGGCGTTTTTGGTTTGGCACCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTC
1 ACGGTGGCGTTAGTGGCGTTTTTGGTCTAGCACCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTC
40629927 AGGATAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAATGGCCT
66 AGGATAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAATGGCCT
* * ** * * *
40629976 TCAGTGGCCCTAGTGGCATTTTTGGTATAGCGCCGC
1 ACGGTGGCGTTAGTGGCGTTTTTGGTCTAGCACCGC
40630012 AAAAAATAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
113 94 0.71
114 39 0.29
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (114 bp):
ACGGTGGCGTTAGTGGCGTTTTTGGTCTAGCACCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTC
AGGATAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAATGGCCT
Found at i:40631322 original size:391 final size:390
Alignment explanation
Indices: 40630547--40631481 Score: 1331
Period size: 391 Copynumber: 2.4 Consensus size: 390
40630537 GTTCATATAA
* * * *
40630547 TTTTAA-GGTTTAGGGAGTACTATATATATA-TGGATTTATATATGGATTATAGATTAGGGGTTT
1 TTTTAATGG-TTAGGGAGTACTATATATA-AGTGGA--T-T-TAGGGATTATAGATTATGGATTA
* * *
40630610 TGCTTAATTAAGGATTGGCTGGGATTTAAGGTTT-----AGGGG-TTAGGGGTTAGATGTTAGTG
60 TGCTTAATTAAGGGTTGGC-CGGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTTAGTT
* *
40630669 GTTAAGACTTAGGGATTT-TGTGTTTAGGGTTTCAGGGGTCGGGTTACGATTTTGGTTTAGATTA
124 GTTAAGACTTAGGGATTTAAG-GTTTAGGGTTTCAGGGGTCGGGTTACAATTTTGGTTTAGATTA
* * * *
40630733 ATTTTTTTATTTATATTTTAAATATGTTCTTATGTAATTGTAAAATATGTATAATTTAAGGTTTA
188 ATTTTTTTACTTATACTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAAGGTTTA
* *
40630798 ATTAATTATGCCTTTAGAGAGATATATATAATAGATAGAGTACAGAAAATTATTTATATCCTTCA
253 A-TAATTATGCCTTGAGAGAGATATATATAATAGATAGAATACAGAAAATTATTTATATCCTTCA
*
40630863 ATGGTTAATTTAGGCGGGTTTAATAAGATTAAGGTTTAATTGAGATTTTGAATTTTATACAATTA
317 ATGGTTAATTTAGGCGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTA
40630928 ATTAATGCT
382 ATTAATGCT
40630937 TTTTAATGGTTAGGGAGTACTATATATAAGTGGATTTAGGGATTATAGATTATGGATTATGCTTA
1 TTTTAATGGTTAGGGAGTACTATATATAAGTGGATTTAGGGATTATAGATTATGGATTATGCTTA
*
40631002 ACTAAGGGTTGGCCAGGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTTAGTTGTTAAG
66 ATTAAGGGTTGGCC-GGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTTAGTTGTTAAG
* *
40631067 ACTTAGGGATTTAAGGTTTAGGGTTTCAGGGGTCTGGTTATAATTTTGGGTTTAGATTAATTTTT
130 ACTTAGGGATTTAAGGTTTAGGGTTTCAGGGGTCGGGTTACAATTTT-GGTTTAGATTAATTTTT
* *
40631132 TTACTTATACTTTAACTATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTT-A-AATT
194 TTACTTATACTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAAGGTTTAATAATT
* **
40631195 ATGCCTTGAGAGATATATATATATAATAGATAGAATAC-TTAAA-TATTTATATCCCTTCAATGG
259 ATGCCTTGAGAG--AGATATATATAATAGATAGAATACAGAAAATTATTTATAT-CCTTCAATGG
40631258 TTAATTTAGGCGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTA
321 TTAATTTAGGCGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTA
40631323 ATGCT
386 ATGCT
* *
40631328 TTTTAATGTTTAGGGAGTACTATATATATGTGGATTTAGGGATTATAGATTATGGATTATGCTTA
1 TTTTAATGGTTAGGGAGTACTATATATAAGTGGATTTAGGGATTATAGATTATGGATTATGCTTA
* *
40631393 ATTAAGGGTTGGCCGAGATTTGAGATTTAGGGGTTAGGGGTTTAGGGGTTAGATGTTAG-TGATT
66 ATTAAGGGTTGGCCG-GATTTAAGGTTTAGGGG--AGGGGTTTAGGGGTTAGATGTTAGTTG-TT
* * *
40631457 AAGACTGAGGAATTTAGGGTTTAGG
127 AAGACTTAGGGATTTAAGGTTTAGG
40631482 AGAGGACCAA
Statistics
Matches: 495, Mismatches: 32, Indels: 33
0.88 0.06 0.06
Matches are distributed among these distances:
386 49 0.10
387 1 0.00
388 1 0.00
389 1 0.00
390 54 0.11
391 180 0.36
392 91 0.18
393 118 0.24
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (390 bp):
TTTTAATGGTTAGGGAGTACTATATATAAGTGGATTTAGGGATTATAGATTATGGATTATGCTTA
ATTAAGGGTTGGCCGGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTTAGTTGTTAAGA
CTTAGGGATTTAAGGTTTAGGGTTTCAGGGGTCGGGTTACAATTTTGGTTTAGATTAATTTTTTT
ACTTATACTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAAGGTTTAATAATTAT
GCCTTGAGAGAGATATATATAATAGATAGAATACAGAAAATTATTTATATCCTTCAATGGTTAAT
TTAGGCGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCT
Done.