Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold145
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1177157
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31
Warning! 98840 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:1003 original size:2 final size:2
Alignment explanation
Indices: 996--1066 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
986 AAGCGCAAAC
996 AG AG AG AG AG AG AG AG 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
1038 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1067 ATATCGGTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4513 original size:1 final size:1
Alignment explanation
Indices: 4509--4544 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
4499 CTTGACAAGC
* *
4509 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4545 TGTTATGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:4526 original size:12 final size:12
Alignment explanation
Indices: 4509--4544 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
4499 CTTGACAAGC
4509 AAAAAAAA-AAA
1 AAAAAAAAGAAA
4520 AAAAAAAAGAAA
1 AAAAAAAAGAAA
4532 AAAAAAAAGAAA
1 AAAAAAAAGAAA
4544 A
1 A
4545 TGTTATGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:5104 original size:15 final size:16
Alignment explanation
Indices: 5069--5107 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
5059 CTTATAAAAA
5069 TCCTGACAATTATAGT
1 TCCTGACAATTATAGT
5085 TCCTGACAATGTA-A-T
1 TCCTGACAAT-TATAGT
5100 TCCTGACA
1 TCCTGACA
5108 CTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 11 0.50
17 2 0.09
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (16 bp):
TCCTGACAATTATAGT
Found at i:13762 original size:2 final size:2
Alignment explanation
Indices: 13755--13799 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
13745 NNNNNNNNAC
13755 AG AG AG AG AG AG AG AG 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
13797 AG A
1 AG A
13800 AAGTGTTTGT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14598 original size:2 final size:2
Alignment explanation
Indices: 14591--14626 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14581 NNNNNNNNNN
14591 AG AG AG AG AG 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
14627 TGTGTGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14631 original size:2 final size:2
Alignment explanation
Indices: 14626--14654 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14616 GAGAGAGAGA
14626 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
14655 GTAAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:15834 original size:21 final size:21
Alignment explanation
Indices: 15820--16014 Score: 257
Period size: 21 Copynumber: 9.3 Consensus size: 21
15810 CACTTTAAAG
* *
15820 TGTAAATTTTACACTTTAATC
1 TGTAAAATTCACACTTTAATC
*
15841 TGT-AGATGTCACACTTTAATC
1 TGTAAAAT-TCACACTTTAATC
* *
15862 TGTAAATTTTACACTTTAATC
1 TGTAAAATTCACACTTTAATC
* *
15883 TGTAAATTTTACACTTTAATC
1 TGTAAAATTCACACTTTAATC
* **
15904 TGTAAAATTCACACTTAAAAG
1 TGTAAAATTCACACTTTAATC
* **
15925 TGTAAAATTCACAGTTTAAAG
1 TGTAAAATTCACACTTTAATC
15946 TGTAAAATTCACACTTTAATC
1 TGTAAAATTCACACTTTAATC
15967 TGTAAAATTCACACTTTAATC
1 TGTAAAATTCACACTTTAATC
15988 TGTAAAATTCACACTTTAATC
1 TGTAAAATTCACACTTTAATC
16009 TGTAAA
1 TGTAAA
16015 NNNNNNNNNN
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
20 2 0.01
21 152 0.97
22 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (21 bp):
TGTAAAATTCACACTTTAATC
Found at i:17775 original size:21 final size:21
Alignment explanation
Indices: 17750--18278 Score: 510
Period size: 21 Copynumber: 25.2 Consensus size: 21
17740 NNNTGTGAAT
17750 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
* *
17771 TTTACAGATTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
* *
17792 TTTACAGATTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
17813 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
* *
17834 TTTACAGATTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
** * * *
17855 TTTACACTTTTAAGTCT-GAA
1 TTTACAGATTAAAGTGTAAAA
*
17875 TTATACAGATTAAAGTGCAAAA
1 TT-TACAGATTAAAGTGTAAAA
** * *
17897 TTTACACTTTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
*
17918 TTTACAGATTAAAGTATAAAA
1 TTTACAGATTAAAGTGTAAAA
* *
17939 TTTACAGATTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
** * * *
17960 TTTACACTTTGAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
17981 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
* *
18002 TTTACGGATTAAAGTGT-GAA
1 TTTACAGATTAAAGTGTAAAA
*
18022 TTTCACAGATTAAAGTGTGAAA
1 TTT-ACAGATTAAAGTGTAAAA
*
18044 TTTACAGATTAATGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
* *
18065 TTTACGGATTAAAGTGTAAAT
1 TTTACAGATTAAAGTGTAAAA
* * * *
18086 TTTAC-GCTTTAAATTGTGAAT
1 TTTACAG-ATTAAAGTGTAAAA
* * *
18107 TTTACAGATAAAAGTAT-GAA
1 TTTACAGATTAAAGTGTAAAA
* ** * *
18127 TTCACACTTTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
** *
18148 TTTACACTTTAAAGTGTAAAT
1 TTTACAGATTAAAGTGTAAAA
*
18169 TTTACAGATTAAAGTGT-GAA
1 TTTACAGATTAAAGTGTAAAA
18189 TCTTACAGATTAAAGTGTAAAA
1 T-TTACAGATTAAAGTGTAAAA
* * *
18211 TTTAAAGATTAAGGTGTAAAG
1 TTTACAGATTAAAGTGTAAAA
** * *
18232 TTTACACTTTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
18253 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
18274 TTTAC
1 TTTAC
18279 GCTTTTAAGT
Statistics
Matches: 415, Mismatches: 84, Indels: 18
0.80 0.16 0.03
Matches are distributed among these distances:
20 24 0.06
21 378 0.91
22 13 0.03
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
TTTACAGATTAAAGTGTAAAA
Found at i:17802 original size:42 final size:42
Alignment explanation
Indices: 17743--18278 Score: 567
Period size: 42 Copynumber: 12.8 Consensus size: 42
17733 NNNNNNNNNN
17743 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
* *
17785 TGTGAATTTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
* * * * ** *
17827 TGTAAAATTTACAGATTAAAGTGTGAATTTTACACTTTTAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
* * * **
17869 TCTGAATTATACAGATTAAAGTGCAAAATTTACACTTTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
*
17911 TGTGAATTTTACAGATTAAAGTATAAAATTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
** * * *
17953 TGTGAATTTTACACTTTGAAGTGTGAATTTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
* * * *
17995 TGTAAAATTTACGGATTAAAGTGT-GAATTTCACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTT-ACAGATTAAAG
* * *
18037 TGTGAAATTTACAGATTAATGTGTAAAATTTACGGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
* * * * * *
18079 TGTAAATTTTAC-GCTTTAAATTGTGAATTTTACAGATAAAAG
1 TGTGAATTTTACAG-ATTAAAGTGTAAAATTTACAGATTAAAG
* * ** * * **
18121 TATGAA-TTCACACTTTAAAGTGTGAATTTTACACTTTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
* *
18162 TGTAAATTTTACAGATTAAAGTGT-GAATCTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAAT-TTACAGATTAAAG
* * * * * **
18204 TGTAAAATTTAAAGATTAAGGTGTAAAGTTTACACTTTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
18246 TGTGAATTTTACAGATTAAAGTGTAAAATTTAC
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTAC
18279 GCTTTTAAGT
Statistics
Matches: 409, Mismatches: 78, Indels: 14
0.82 0.16 0.03
Matches are distributed among these distances:
41 39 0.10
42 363 0.89
43 7 0.02
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (42 bp):
TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAG
Found at i:17842 original size:63 final size:63
Alignment explanation
Indices: 17743--18278 Score: 628
Period size: 63 Copynumber: 8.5 Consensus size: 63
17733 NNNNNNNNNN
17743 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
** *
17806 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACACTTTTAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
* * * **
17869 TCTGAATTATACAGATTAAAGTGCAAAATTTACACTTTAAAGTGTGAATTTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
* * * * * ** *
17932 TATAAAATTTACAGATTAAAGTGTGAATTTTACACTTTGAAGTGTGAATTTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
* * * * * *
17995 TGTAAAATTTACGGATTAAAGTGT-GAATTTCACAGATTAAAGTGTGAAATTTACAGATTAATG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTT-ACAGATTAAAGTGTGAATTTTACAGATTAAAG
* * * * * * *
18058 TGTAAAATTTACGGATTAAAGTGTAAATTTTAC-GCTTTAAATTGTGAATTTTACAGATAAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAG-ATTAAAGTGTGAATTTTACAGATTAAAG
* * ** * * ** *
18121 TATGAA-TTCACACTTTAAAGTGTGAATTTTACACTTTAAAGTGTAAATTTTACAGATTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
* * * * * **
18183 TGTGAATCTTACAGATTAAAGTGTAAAATTTAAAGATTAAGGTGTAAAGTTTACACTTTAAAG
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
18246 TGTGAATTTTACAGATTAAAGTGTAAAATTTAC
1 TGTGAATTTTACAGATTAAAGTGTAAAATTTAC
18279 GCTTTTAAGT
Statistics
Matches: 406, Mismatches: 62, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
62 56 0.14
63 346 0.85
64 4 0.01
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (63 bp):
TGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTGAATTTTACAGATTAAAG
Found at i:21324 original size:11 final size:11
Alignment explanation
Indices: 21308--21333 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21298 AGGGAACCCT
21308 AAAAAATAAAA
1 AAAAAATAAAA
21319 AAAAAATAAAA
1 AAAAAATAAAA
21330 AAAA
1 AAAA
21334 GAAAGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:25145 original size:2 final size:2
Alignment explanation
Indices: 25138--25162 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25128 AAATATTCTT
25138 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
25163 TTGGCATAAA
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:29754 original size:20 final size:19
Alignment explanation
Indices: 29725--29775 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
29715 TTTCAAATTA
29725 CCTATAGGAATATTGATTTT
1 CCTATAGGAATATT-ATTTT
* *
29745 CCTATGGGAAAAATTATTTT
1 CCTATAGG-AATATTATTTT
29765 CCTATAGGAAT
1 CCTATAGGAAT
29776 TTAATTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (19 bp):
CCTATAGGAATATTATTTT
Found at i:30890 original size:4 final size:4
Alignment explanation
Indices: 30883--30980 Score: 196
Period size: 4 Copynumber: 24.5 Consensus size: 4
30873 TGGATGGATG
30883 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
30931 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
30979 GA
1 GA
30981 ACGAACCACT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:37937 original size:2 final size:2
Alignment explanation
Indices: 37930--37964 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37920 TTCAAGTTCT
37930 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
37965 TTTTGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41382 original size:2 final size:2
Alignment explanation
Indices: 41377--41415 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
41367 AATACTCTTT
*
41377 TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41416 GTACCGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:43054 original size:2 final size:2
Alignment explanation
Indices: 43047--43095 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
43037 CGTGCTCGTG
43047 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43089 CT CT CT C
1 CT CT CT C
43096 GTAATCAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:45014 original size:2 final size:2
Alignment explanation
Indices: 45007--45033 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44997 CCCCACCCCN
45007 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
45034 CAACCAGTAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:56752 original size:10 final size:10
Alignment explanation
Indices: 56735--56776 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
56725 AAATTTCCTT
56735 AATAATAATA
1 AATAATAATA
*
56745 AGTAATAAATA
1 AATAAT-AATA
56756 AATAATAATA
1 AATAATAATA
*
56766 AATAGTAATA
1 AATAATAATA
56776 A
1 A
56777 TAACATTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:61711 original size:2 final size:2
Alignment explanation
Indices: 61700--61736 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
61690 TGAACATGAT
61700 TA TA -A 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
61737 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:79104 original size:4 final size:4
Alignment explanation
Indices: 79095--79204 Score: 132
Period size: 4 Copynumber: 27.8 Consensus size: 4
79085 AAAGTATATC
* *
79095 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAC CTAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * *
79143 ATAC ATAC ATAG ATAG ATAC ATAG ATAG ATAC ATAC ATAG ATAC ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
79191 ATAG A-AG AGAG ATA
1 ATAG ATAG ATAG ATA
79205 ATGTAGTTAC
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
3 3 0.03
4 89 0.97
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:83454 original size:17 final size:18
Alignment explanation
Indices: 83422--83455 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
83412 ACCATATCAT
83422 TTCTTGAGAAAATTATTC
1 TTCTTGAGAAAATTATTC
*
83440 TTCTTG-GAAATTTATT
1 TTCTTGAGAAAATTATT
83456 TACCAAAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (18 bp):
TTCTTGAGAAAATTATTC
Found at i:87317 original size:13 final size:13
Alignment explanation
Indices: 87299--87324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87289 ATGTAAGCAA
87299 AAATTGTGTGGTC
1 AAATTGTGTGGTC
87312 AAATTGTGTGGTC
1 AAATTGTGTGGTC
87325 GGATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
AAATTGTGTGGTC
Found at i:93396 original size:21 final size:21
Alignment explanation
Indices: 93372--93628 Score: 218
Period size: 21 Copynumber: 12.2 Consensus size: 21
93362 ATATAATGGT
*
93372 TTCGCGAAAGTTACGCGTTTA
1 TTCGCGAAAGTTTCGCGTTTA
* * * *
93393 TTCGCGTATGCTTCGCGTTAA
1 TTCGCGAAAGTTTCGCGTTTA
* * ** *
93414 TACGCGAAACTAACGTG-TTA
1 TTCGCGAAAGTTTCGCGTTTA
*
93434 TATCGCGAAAGTTTCGAG-TTA
1 T-TCGCGAAAGTTTCGCGTTTA
* **
93455 TATCGCAAAAAATTCGCGTTTA
1 T-TCGCGAAAGTTTCGCGTTTA
* **** *
93477 TTCGCAAAACAAACGAG-TTA
1 TTCGCGAAAGTTTCGCGTTTA
*
93497 TATCG-GAAAAGTTTCGCGATTA
1 T-TCGCG-AAAGTTTCGCGTTTA
*
93519 TTCGCGAAAGTTTCGGGTTTA
1 TTCGCGAAAGTTTCGCGTTTA
* *
93540 TTTGCGAAAGTTACGCG-TTA
1 TTCGCGAAAGTTTCGCGTTTA
93560 TATCGCGAAAGTTTCGCGTTTA
1 T-TCGCGAAAGTTTCGCGTTTA
93582 TTCGCGAAAGTTTCGCGTTTA
1 TTCGCGAAAGTTTCGCGTTTA
93603 TTCGCGAAAGTTTCGCGTTTA
1 TTCGCGAAAGTTTCGCGTTTA
93624 TTCGC
1 TTCGC
93629 AAAAAAAATA
Statistics
Matches: 188, Mismatches: 40, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
20 11 0.06
21 164 0.87
22 13 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (21 bp):
TTCGCGAAAGTTTCGCGTTTA
Found at i:93621 original size:63 final size:63
Alignment explanation
Indices: 93373--93611 Score: 275
Period size: 63 Copynumber: 3.8 Consensus size: 63
93363 TATAATGGTT
* * * * * * *
93373 TCGCGAAAGTTACGCGTTTATTCGCGTATGCTTCGCGTTAATACGCGAAACTAACGTGTTATA
1 TCGCGAAAGTTTCGCGTTTATTCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACGCGTTATA
* * ** * * *
93436 TCGCGAAAGTTTCGAG-TTATATCGCAAAAAATTCGCGTTTATTCGCAAAACAAACGAGTTATA
1 TCGCGAAAGTTTCGCGTTTAT-TCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACGCGTTATA
* * * * *
93499 TCG-GAAAAGTTTCGCGATTATTCGCGAAAGTTTCGGGTTTATTTGCGAAAGTTACGCGTTATA
1 TCGCG-AAAGTTTCGCGTTTATTCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACGCGTTATA
93562 TCGCGAAAGTTTCGCGTTTATTCGCGAAAGTTTCGCGTTTATTCGCGAAA
1 TCGCGAAAGTTTCGCGTTTATTCGCGAAAGTTTCGCGTTTATTCGCGAAA
93612 GTTTCGCGTT
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
62 5 0.03
63 136 0.93
64 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (63 bp):
TCGCGAAAGTTTCGCGTTTATTCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACGCGTTATA
Found at i:93757 original size:21 final size:21
Alignment explanation
Indices: 93712--93803 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
93702 AAAAATTGTT
* * *
93712 GCGAAAAAACGCGTAACTTTA
1 GCGAATAAACGCGAAACTTTC
*
93733 GCGAATAAACGCGAAATTTTC
1 GCGAATAAACGCGAAACTTTC
* * * ** *
93754 GCG-ATATTAGGTGTGATTTTC
1 GCGAATA-AACGCGAAACTTTC
93775 GCGAATAAACGCGAAACTTTC
1 GCGAATAAACGCGAAACTTTC
*
93796 GCGTATAA
1 GCGAATAA
93804 TAATTATTTC
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 3 0.06
21 47 0.89
22 3 0.06
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (21 bp):
GCGAATAAACGCGAAACTTTC
Found at i:99899 original size:108 final size:108
Alignment explanation
Indices: 99705--99903 Score: 258
Period size: 108 Copynumber: 1.8 Consensus size: 108
99695 TGGGGTTGAA
** * * *
99705 TTTTAACATAGGAATATAAAGAATTAATCCTAAAAAATCTTCTTCTTAGAAACTAATCAGCAAGG
1 TTTTAACATAGGAATATAAAGAAGAAATCCTAAAAAATCTTCTTCTCAGAAACCAATCAGCAAGA
99770 AAAGTTGAAACTTGAGTGGAAGCATATGCATCGTTAGGTAGTG
66 AAAGTTGAAACTTGAGTGGAAGCATATGCATCGTTAGGTAGTG
* * * * ** *
99813 TTTTTACATAGGAATATATAGAAGAAATCTTTAAAAATCGTT-TTCTCAGAAACCAATTGGCCAG
1 TTTTAACATAGGAATATAAAGAAGAAATCCTAAAAAATC-TTCTTCTCAGAAACCAATCAGCAAG
99877 AAAAGTTGAAACTT-ATGTGGAAGCATA
65 AAAAGTTGAAACTTGA-GTGGAAGCATA
99904 CTAAAGTAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 1 0.01
108 74 0.96
109 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (108 bp):
TTTTAACATAGGAATATAAAGAAGAAATCCTAAAAAATCTTCTTCTCAGAAACCAATCAGCAAGA
AAAGTTGAAACTTGAGTGGAAGCATATGCATCGTTAGGTAGTG
Found at i:102886 original size:166 final size:166
Alignment explanation
Indices: 102607--103449 Score: 1221
Period size: 166 Copynumber: 5.1 Consensus size: 166
102597 ACGGGGGGGG
* * * *
102607 GGTCGAAGTTTAACAAATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGCAACTAATC
1 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
* * * *
102672 AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCATCAGGTAATGTAGATTCAAATTTGTGAAAAT
66 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* *
102737 CATGAACCCCAGGGGTAGGGTGGGGCCACCATGGGA
131 CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGA
* * *
102773 GATCGAAGTTTTACATAGGAATATATAAAGTAAATCTTTAAAAATCTTCTTCTAAGAAACTAATC
1 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
* * *
102838 GGCCAGGAAAGATGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
66 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
*
102903 CATG-ACCCCCGGGGTAGGGTGGGGCCACAATGGG-
131 CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGA
* * *
102937 GGTCGAAGTTTTACATAGGAATATATAGAGTAATTTTTTTAAAATCTTCTTCTCAGAAACTAATC
1 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
* * * * * *
103002 AGCCAGTAAAGCTAAAACTTGTGTGAAAGCATCCTCAGATAGTGTAGATTCATAGTTATGAAAAT
66 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
*
103067 CATGACCCCCGGGGGTAGGGTGGGGCCACAATGGG-
131 CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGA
* *
103102 GGATCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCCCTGAAACTAAT
1 GG-TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAT
* * * *
103167 CAGCCAGAAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAA
65 CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAA
* * *
103232 TCATGACCCCCGGGGGTAGGTTGGGGCCACAATGGGG
130 TCATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGA
* * * *
103269 GGTCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATT
1 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
* *
103334 AGCCAGGAAAGCTGAACCTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTG-AAAT
66 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* *
103398 CATG-ACCCCTGGGGGTAGGTTTGGGCCAC-ATGGGA
131 CATGAACCCC-GGGGGTAGGGTGGGGCCACAATGGGA
*
103433 GGTCGATGTTTTACATA
1 GGTCGAAGTTTTACATA
103450 CGCAGCACAG
Statistics
Matches: 608, Mismatches: 65, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
164 143 0.24
165 84 0.14
166 379 0.62
167 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (166 bp):
GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGA
Found at i:103022 original size:330 final size:332
Alignment explanation
Indices: 102603--103449 Score: 1317
Period size: 330 Copynumber: 2.6 Consensus size: 332
102593 CACAACGGGG
* *
102603 GGGGGGTCGAAGTTTAACAAATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGCAACT
1 GGGGGGTCGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
* *
102668 AATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCATCAGGTAATGTAGATTCAAATTTGTGA
66 AATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTGA
*
102733 AAATCATGAACCCCAGGGGTAGGGTGGGGCCACCATGGGAGATCGAAGTTTTACATAGGAATATA
131 AAATCATGAACCCCGGGGGTAGGGTGGGGCCACCATGGGAGATCGAAGTTTTACATAGGAATATA
* * *
102798 TAAAGTAAATCTTTAAAAATCTTCTTCTAAGAAACTAATCGGCCAGGAAAGATGACACTTGTGTG
196 TAAAGTAAATCTTTAAAAATCTTCTTCCAAGAAACTAATCAGCCAGAAAAGATGACACTTGTGTG
*
102863 GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC-GGGGTAGGGTGGGG
261 GAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGG
102927 CCACAAT
326 CCACAAT
* * * * *
102934 -GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAATTTTTTTAAAATCTTCTTCTCAGAAACT
1 GGGGGGTCGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
* * * * * *
102998 AATCAGCCAGTAAAGCTAAAACTTGTGTGAAAGCATCCTCAGATAGTGTAGATTCATAGTTATGA
66 AATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTGA
* * *
103063 AAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAATATA
131 AAATCATGAACCCCGGGGGTAGGGTGGGGCCACCATGGGAGATCGAAGTTTTACATAGGAATATA
* ** *
103128 TAGAGTAAATCTTTAAAAATCTTCTTCCCTGAAACTAATCAGCCAGAAAAGCTGACACTTGTGTG
196 TAAAGTAAATCTTTAAAAATCTTCTTCCAAGAAACTAATCAGCCAGAAAAGATGACACTTGTGTG
* *
103193 GATGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGTTGGGG
261 GAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGG
103258 CCACAAT
326 CCACAAT
*
103265 GGGGGGTCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
1 GGGGGGTCGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
* * *
103330 AATTAGCCAGGAAAGCTGAACCTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTG-
66 AATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTGA
* * * *
103394 AAATCATG-ACCCCTGGGGGTAGGTTTGGGCCA-CATGGGAGGTCGATGTTTTACATA
131 AAATCATGAACCCC-GGGGGTAGGGTGGGGCCACCATGGGAGATCGAAGTTTTACATA
103450 CGCAGCACAG
Statistics
Matches: 462, Mismatches: 51, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
330 305 0.66
331 44 0.10
332 113 0.24
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (332 bp):
GGGGGGTCGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
AATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTGA
AAATCATGAACCCCGGGGGTAGGGTGGGGCCACCATGGGAGATCGAAGTTTTACATAGGAATATA
TAAAGTAAATCTTTAAAAATCTTCTTCCAAGAAACTAATCAGCCAGAAAAGATGACACTTGTGTG
GAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGG
CCACAAT
Found at i:110522 original size:21 final size:21
Alignment explanation
Indices: 110496--110549 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
110486 ATCGTTTTAA
110496 ATCGTTCGTGTAACGTG-GGTG
1 ATCGTTCGTGTAACGTGCGG-G
110517 ATCGTTCGTGTAACGTGCGGG
1 ATCGTTCGTGTAACGTGCGGG
*
110538 ATCGTGCGTGTA
1 ATCGTTCGTGTA
110550 TCAGGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.31
Consensus pattern (21 bp):
ATCGTTCGTGTAACGTGCGGG
Found at i:112654 original size:23 final size:24
Alignment explanation
Indices: 112628--112674 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
112618 AATTTTTATT
* *
112628 GGTTATT-TATTTTTTATTTAAAA
1 GGTTATTATATTATTTATTAAAAA
112651 GGTTATTATATTATTTATTAAAAA
1 GGTTATTATATTATTTATTAAAAA
112675 TAAATATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
GGTTATTATATTATTTATTAAAAA
Found at i:113219 original size:46 final size:46
Alignment explanation
Indices: 113152--113263 Score: 215
Period size: 46 Copynumber: 2.4 Consensus size: 46
113142 AAATTGTGAC
*
113152 TGAGTTTGTGTTCAAGTGAGAAAGTTCGTGATCCATTGTGAAATTG
1 TGAGTTTGTGTTCAAGTGAGAAAGTTCGTGATCAATTGTGAAATTG
113198 TGAGTTTGTGTTCAAGTGAGAAAGTTCGTGATCAATTGTGAAATTG
1 TGAGTTTGTGTTCAAGTGAGAAAGTTCGTGATCAATTGTGAAATTG
113244 TGAGTTTGTGTTCAAGTGAG
1 TGAGTTTGTGTTCAAGTGAG
113264 CGTGTAAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.26, C:0.07, G:0.29, T:0.38
Consensus pattern (46 bp):
TGAGTTTGTGTTCAAGTGAGAAAGTTCGTGATCAATTGTGAAATTG
Found at i:116151 original size:22 final size:22
Alignment explanation
Indices: 116125--116185 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
116115 TCAGTAAGTT
*
116125 AGTGATCGTCCGTGTATCGTGC
1 AGTGATCGTTCGTGTATCGTGC
116147 AGTGATCGTTCGTGTATCGTGC
1 AGTGATCGTTCGTGTATCGTGC
116169 -GTGATCGTTCGTGTATC
1 AGTGATCGTTCGTGTATC
116186 AGAATCGTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 17 0.45
22 21 0.55
ACGTcount: A:0.13, C:0.20, G:0.31, T:0.36
Consensus pattern (22 bp):
AGTGATCGTTCGTGTATCGTGC
Found at i:116154 original size:11 final size:10
Alignment explanation
Indices: 116126--116181 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 10
116116 CAGTAAGTTA
*
116126 GTGATCGTCC
1 GTGATCGTGC
116136 GTGTATCGTGC
1 GTG-ATCGTGC
*
116147 AGTGATCGTTC
1 -GTGATCGTGC
116158 GTGTATCGTGC
1 GTG-ATCGTGC
*
116169 GTGATCGTTC
1 GTGATCGTGC
116179 GTG
1 GTG
116182 TATCAGAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 15 0.38
11 21 0.54
12 3 0.08
ACGTcount: A:0.11, C:0.20, G:0.34, T:0.36
Consensus pattern (10 bp):
GTGATCGTGC
Found at i:119027 original size:18 final size:17
Alignment explanation
Indices: 118995--119043 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
118985 AGTTGCACTT
118995 TATTATATAATAAATAA
1 TATTATATAATAAATAA
*
119012 TATTATAATTATAAATAA
1 TATTAT-ATAATAAATAA
119030 T-TATATGATAATAA
1 TAT-TAT-ATAATAA
119044 TTACTTGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TATTATATAATAAATAA
Found at i:119035 original size:21 final size:23
Alignment explanation
Indices: 118996--119041 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
118986 GTTGCACTTT
*
118996 ATTATATAATAAATAATATTATA
1 ATTATATAATAAATAATATGATA
*
119019 ATTATA-AAT-AATTATATGATA
1 ATTATATAATAAATAATATGATA
119040 AT
1 AT
119042 AATTACTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 3 0.14
23 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTATATAATAAATAATATGATA
Found at i:119328 original size:53 final size:53
Alignment explanation
Indices: 119247--119359 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 53
119237 GTCTTATTTA
* * **
119247 TTTTTAAGGGTCTTCCGTTTTCAACGGAAGCCCCTCTTGTTATTCTTTTGTTTC
1 TTTTT-AGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTC
*
119301 TTTTTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTTTTCTTCGGTTTC
1 TTTTTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTC
119354 TTTTTA
1 TTTTTA
119360 TTATTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 49 0.91
54 5 0.09
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (53 bp):
TTTTTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTC
Found at i:120001 original size:31 final size:30
Alignment explanation
Indices: 119964--120032 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
119954 TCGTGAATGT
*
119964 TTTTGTTAATTCGTACTC-AGAATCATTCGGA
1 TTTTGTTAAGTCGTAC-CAAGAATCATTC-GA
* *
119995 TTTTGTTTAGTCGTACCAAGAATTATTCGA
1 TTTTGTTAAGTCGTACCAAGAATCATTCGA
120025 TTTT-TTAA
1 TTTTGTTAA
120033 ATATTTTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.09
30 7 0.21
31 23 0.70
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACCAAGAATCATTCGA
Found at i:122252 original size:161 final size:161
Alignment explanation
Indices: 121270--122237 Score: 1332
Period size: 161 Copynumber: 6.0 Consensus size: 161
121260 CCACCAACAA
* * *
121270 TTTCCGTTCATTTTCTTCGCAGAGGATGAACATATGGAAATGAAATTTGGTATATAGGTTTATCA
1 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* * * *
121335 TGATAATATCAACGCCAAGTTCAATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCC
66 TGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCC
* *
121400 TTGGACTTAGAAAAATTCTAGTTTTTTGCAG
131 TTGGACTTAGAAAAATTCCAGTTATTTGCAG
* * *
121431 TTTCCGCTCATTTTCTTCGCAGAAGATGAACATATTGAAATGAGATTTGGTATTCAGGTTTATCA
1 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* *
121496 TGATACTATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCCACAGAGTTATGGCCC
66 TGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCC
* * *
121561 TTAGACGTAGAAAAATTCCAGTTTTTTGCAG
131 TTGGACTTAGAAAAATTCCAGTTATTTGCAG
* *
121592 TTTCCGCTCATTTTCTTCGCAGAAGATGAACATATTGAAATTAAATTTGGTATACAGGTTTATCA
1 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* * * *
121657 TAATAATATCTAAGTCAAGTTCGATGTTGGGTACAATCGAGCAATTTTCAACAGAGTTATGGCCC
66 TGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCC
* *
121722 TTGGACTTAGAAAAATTCTAGTTTTTTGCAG
131 TTGGACTTAGAAAAATTCCAGTTATTTGCAG
*
121753 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGATATACAGGTTTATCA
1 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* * *
121818 TGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCAAGCAATTTTCGACAGAGTTATAG-CC
66 TGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCC
* *
121882 TGTTGACGTAGAAAAATTCCAGTTATTTGCAG
131 T-TGGACTTAGAAAAATTCCAGTTATTTGCAG
* * * *
121914 TTTCCGCTCATTTTCTTAGGAGAGGATAAACATATTGAAATTAAATTTGGTATACAGGTTTATCA
1 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* *
121979 TGATAATATCAAGGT-AACGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTAT-GCC
66 TGATAATATCTAGGTCAA-GTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCC
** * *
122042 TCTTGGAGATAGAAAAATTCCAGTAATTTGCAA
130 -CTTGGACTTAGAAAAATTCCAGTTATTTGCAG
* * * * * * * * * *
122075 TTTCAGCTCATTTTCTTCGAAGAGGGTGCAGATATGGATATGAAATTTGATATACAGATTTATCC
1 TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* * * ** * *
122140 TAATAATATCTAGGTCAAGTAT-GATTTTAGGTATGATAGAGCAATTTTTGACAGAGTTATGGCC
66 TGATAATATCTAGGTCAAGT-TCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCC
* *
122204 CTTGAACTTAGAAAAATACCAGTTATTTGCAG
130 CTTGGACTTAGAAAAATTCCAGTTATTTGCAG
122236 TT
1 TT
122238 GAAGTTCATT
Statistics
Matches: 722, Mismatches: 78, Indels: 14
0.89 0.10 0.02
Matches are distributed among these distances:
160 6 0.01
161 708 0.98
162 8 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (161 bp):
TTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
TGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCC
TTGGACTTAGAAAAATTCCAGTTATTTGCAG
Found at i:125949 original size:2 final size:2
Alignment explanation
Indices: 125942--125974 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
125932 AGAAATTGGG
125942 TA TA TA TA TA TA TA TA TA T- 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
125975 ATTACTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128988 original size:18 final size:19
Alignment explanation
Indices: 128954--128991 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
128944 TTTAATTTGG
128954 TTTACTTCAATTTAACAAT
1 TTTACTTCAATTTAACAAT
128973 TTTACTTCAA-TTAACAAT
1 TTTACTTCAATTTAACAAT
128991 T
1 T
128992 AACATAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTACTTCAATTTAACAAT
Found at i:131097 original size:37 final size:37
Alignment explanation
Indices: 131039--131345 Score: 366
Period size: 37 Copynumber: 8.3 Consensus size: 37
131029 TGTGTAGCTT
* * * * *
131039 TGTAGCTAACCATTGTGGAACGTTTCTGTAATTTATC
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
*
131076 TGTAGCTGGCCAATGTTGAACGTTTCTATAATTTATG
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
* *
131113 TGTAGCTGACCAATGTTGAGCGTCTCTATAATTTATG
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
*
131150 T-TAGCTGACC-ATTTTGGAACGTTTCTATAATTTATG
1 TGTAGCTGACCAATGTT-GAACGTTTCTATAATTTATG
* * * **
131186 TATAGCTGACCATTGTAGAACGTTTCTATAATAAATG
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
* ** *
131223 TGAAGCTGACCAATGTTGATGGTTCCTATAATTTATG
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
* * * *
131260 TGTAGCTGACTACTGTGGAACGTTTCTATAGTTTATG
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
* * *
131297 TGTAGTTGACCAATGTTGAGCGTTCCTATAATTTATG
1 TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
131334 TGTAGCTGACCA
1 TGTAGCTGACCA
131346 CACTGTGCAA
Statistics
Matches: 225, Mismatches: 42, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
35 4 0.02
36 28 0.12
37 191 0.85
38 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (37 bp):
TGTAGCTGACCAATGTTGAACGTTTCTATAATTTATG
Found at i:131234 original size:110 final size:111
Alignment explanation
Indices: 131039--131345 Score: 422
Period size: 110 Copynumber: 2.8 Consensus size: 111
131029 TGTGTAGCTT
* * * *
131039 TGTAGCTAACCATTGTGGAACGTTTCTGTAATTTATCTGTAGCTGGCCAATGTTGAACGTTTCTA
1 TGTAGCTGACCATTGTGGAACGTTTCTATAATTTATGTGTAGCTGACCAATGTTGAACGTTTCTA
131104 TAATTTATGTGTAGCTGACCAATGTTGA-GCG-TCTCTATAATTTATG
66 TAATTTATGTGTAGCTGACCAATGTTGATG-GTTC-CTATAATTTATG
* * * *
131150 T-TAGCTGACCATTTTGGAACGTTTCTATAATTTATGTATAGCTGACCATTGTAGAACGTTTCTA
1 TGTAGCTGACCATTGTGGAACGTTTCTATAATTTATGTGTAGCTGACCAATGTTGAACGTTTCTA
** *
131214 TAATAAATGTGAAGCTGACCAATGTTGATGGTTCCTATAATTTATG
66 TAATTTATGTGTAGCTGACCAATGTTGATGGTTCCTATAATTTATG
* * * * * *
131260 TGTAGCTGACTACTGTGGAACGTTTCTATAGTTTATGTGTAGTTGACCAATGTTGAGCGTTCCTA
1 TGTAGCTGACCATTGTGGAACGTTTCTATAATTTATGTGTAGCTGACCAATGTTGAACGTTTCTA
131325 TAATTTATGTGTAGCTGACCA
66 TAATTTATGTGTAGCTGACCA
131346 CACTGTGCAA
Statistics
Matches: 169, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
110 94 0.56
111 75 0.44
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (111 bp):
TGTAGCTGACCATTGTGGAACGTTTCTATAATTTATGTGTAGCTGACCAATGTTGAACGTTTCTA
TAATTTATGTGTAGCTGACCAATGTTGATGGTTCCTATAATTTATG
Found at i:132626 original size:37 final size:36
Alignment explanation
Indices: 132499--133061 Score: 433
Period size: 37 Copynumber: 14.8 Consensus size: 36
132489 ATCCACTGTG
*
132499 GAACGTTTCTATAATTTATATGTAGCTGACCAATGAATGTT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-C-AT---TGTT
* * * *
132540 GAACGTTTCCATAATTTATGTTTAACTGACAACATTGCT
1 GAACGTTTCTATAATTTATGTGTAGCTG---ACATTGTT
** * *
132579 GAACGTTTCTATAGGTAATGTGAAGCTGACTATTGTT
1 GAACGTTTCTATAATTTATGTGTAGCTGAC-ATTGTT
* *
132616 GAACGTTTCTATAATTTATGTGTAGCTGACCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-CATTGTT
*
132653 GAACGTTTATATAATTTATGTGTAGCTGGCCACATTGTT
1 GAACGTTTCTATAATTTATGTGTAGCT-G--ACATTGTT
* * * *
132692 GAACGTTTCTATAATTTATTTGTAGCTCACCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-CATTGTT
* *
132729 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTG
1 GAACGTTTCTATAATTTATGTGTAGCTG---ACATTGTT
* * * * * *
132768 GAACGTTTCTACAATCTATATGTAGCTGGCCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCT-GACATTGTT
* * *
132805 GAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-CATTGTT
* *
132842 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTG
1 GAACGTTTCTATAATTTATGTGTAGCTG---ACATTGTT
* * * * *
132881 GAACGTTTCTACAATCTATATGTAGCTGACCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-CATTGTT
* * *
132918 GAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-CATTGTT
* * *
132955 GAATGTTTCTATAATTTATTTGTAGCTGACCACATTGTG
1 GAACGTTTCTATAATTTATGTGTAGCTG---ACATTGTT
* * * * * *
132994 GAAGGTTTCTACAATCTATATGTAGCTGACCAATGAT
1 GAACGTTTCTATAATTTATGTGTAGCTGA-CATTGTT
* *
133031 GAACGTTTCTATTTATTTATGTTTAGCTGAC
1 GAACGTTTCTA-TAATTTATGTGTAGCTGAC
133062 CACCCTGTGC
Statistics
Matches: 428, Mismatches: 71, Indels: 50
0.78 0.13 0.09
Matches are distributed among these distances:
36 6 0.01
37 235 0.55
38 15 0.04
39 139 0.32
40 5 0.01
41 24 0.06
42 2 0.00
43 1 0.00
44 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (36 bp):
GAACGTTTCTATAATTTATGTGTAGCTGACATTGTT
Found at i:132632 original size:76 final size:73
Alignment explanation
Indices: 132499--133089 Score: 583
Period size: 76 Copynumber: 7.8 Consensus size: 73
132489 ATCCACTGTG
* *
132499 GAACGTTTCTATAATTTATATGTAGCTGACCAATGAATGTTGAACGTTTCCATAATTTATGTTTA
1 GAACGTTTCTATAATTTATGTGTAGCTGACC-AT---TGTTGAACGTTTCTATAATTTAT-TTTA
* * *
132564 ACTGACAACATTGCT
61 GCTGAC--CAATGAT
** * * * *
132579 GAACGTTTCTATAGGTAATGTGAAGCTGACTATTGTTGAACGTTTCTATAATTTATGTGTAGCTG
1 GAACGTTTCTATAATTTATGTGTAGCTGACCATTGTTGAACGTTTCTATAATTTAT-TTTAGCTG
132644 ACCAATGAT
65 ACCAATGAT
* *
132653 GAACGTTTATATAATTTATGTGTAGCTGGCCACATTGTTGAACGTTTCTATAATTTATTTGTAGC
1 GAACGTTTCTATAATTTATGTGTAGCT-GAC-CATTGTTGAACGTTTCTATAATTTATTT-TAGC
*
132718 TCACCAATGAT
63 TGACCAATGAT
* * * * *
132729 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
1 GAACGTTTCTATAATTTATGTGTAGCTGA-C-CATTGTTGAACGTTTCTATAATTTAT-TTTAGC
*
132794 TGGCCAATGAT
63 TGACCAATGAT
* * *
132805 GAACGTTTCTATAATTTATTTGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTG
1 GAACGTTTCTATAATTTATGTGTAGCTGACCATTGTTGAACGTTTCTATAATTTATTT-TAGCTG
132870 ACCACATTG-T
65 ACCA-A-TGAT
* * * * *
132880 GGAACGTTTCTACAATCTATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCT
1 -GAACGTTTCTATAATTTATGTGTAGCTGACCATTGTTGAACGTTTCTATAATTTATTT-TAGCT
132945 GACCAATGAT
64 GACCAATGAT
* * * * * * *
132955 GAATGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAAGGTTTCTACAATCTATATGTAGC
1 GAACGTTTCTATAATTTATGTGTAGCTGA-C-CATTGTTGAACGTTTCTATAATTTAT-TTTAGC
133020 TGACCAATGAT
63 TGACCAATGAT
* * * *
133031 GAACGTTTCTATTTATTTATGTTTAGCTGACCACCCTG-TGCAACGTTTTTATAATTTAT
1 GAACGTTTCTA-TAATTTATGTGTAGCTGACCA--TTGTTG-AACGTTTCTATAATTTAT
133090 GTTGAATTGG
Statistics
Matches: 434, Mismatches: 60, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
73 1 0.00
74 84 0.19
75 12 0.03
76 277 0.64
77 33 0.08
79 2 0.00
80 25 0.06
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (73 bp):
GAACGTTTCTATAATTTATGTGTAGCTGACCATTGTTGAACGTTTCTATAATTTATTTTAGCTGA
CCAATGAT
Found at i:132701 original size:113 final size:113
Alignment explanation
Indices: 132499--133089 Score: 735
Period size: 113 Copynumber: 5.2 Consensus size: 113
132489 ATCCACTGTG
* * * * * * *
132499 GAACGTTTCTATAATTTATATGTAGCTGACCA-ATGAATGTTGAACGTTTCCATAATTTATGTTT
1 GAACGTTTCTATAATTTATTTGTAGCTGACCACAT---TGTGGAACGTTTCTACAATCTATATGT
* * * ** * * * * * *
132563 AACTGACAACATTGCTGAACGTTTCTATAGGTAATGTGAAGCTGACTATTGTT
63 AGCTGAC--CAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
* * * * *
132616 GAACGTTTCTATAATTTATGTGTAGCTGACCA-A-TGAT-GAACGTTTATATAATTTATGTGTAG
1 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTG-TGGAACGTTTCTACAATCTATATGTAG
* * *
132678 CTGGCCACATTGTTGAACGTTTCTATAATTTATTTGTAGCTCACCAATGAT
65 CTGACCA-A-TGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
132729 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
1 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
*
132794 TGGCCAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
66 TGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
132842 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
1 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
132907 TGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
66 TGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
* *
132955 GAATGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAAGGTTTCTACAATCTATATGTAGC
1 GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
* *
133020 TGACCAATGATGAACGTTTCTATTTATTTATGTT-TAGCTGACCACCCTG-T
66 TGACCAATGATGAACGTTTCTA-TAATTTAT-TTGTAGCTGACCA--ATGAT
*
133070 GCAACGTTTTTATAATTTAT
1 G-AACGTTTCTATAATTTAT
133090 GTTGAATTGG
Statistics
Matches: 432, Mismatches: 31, Indels: 23
0.89 0.06 0.05
Matches are distributed among these distances:
111 2 0.00
113 325 0.75
114 21 0.05
115 34 0.08
116 18 0.04
117 32 0.07
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (113 bp):
GAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAACGTTTCTACAATCTATATGTAGC
TGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCAATGAT
Found at i:132823 original size:189 final size:187
Alignment explanation
Indices: 132499--133089 Score: 708
Period size: 189 Copynumber: 3.1 Consensus size: 187
132489 ATCCACTGTG
*
132499 GAACGTTTCTATAATTTATATGTAGCTGACCAATGAATGTTGAACGTTTCCATAATTTATGTT-T
1 GAACGTTTCTATAATTTATATGTAGCTGACCAATG-A---TGAACGTTTCTATAATTTAT-TTGT
* * * * ** * *
132563 AACTGACAACATTGCTGAACGTTTCTATAGGTA-ATGTGAAGCTGACTATTGTTGAACGTTTCTA
61 AGCTGACCACATTGATGAACGTTTCTAAATCTATATGT--AGCTGACCAATG-TGAACGTTTCTA
* * *
132627 TAATTTATGTGTAGCTGACCAATGATGAACGTTTATATAATTTATGTGTAGCTGGCCACATTGTT
123 TAATTTATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATGTGTAGCTGACCACATTGTT
* *
132692 GAACGTTTCTATAATTTATTTGTAGCTCACCAATGATGAACGTTTCTATAATTTATTTGTAGCTG
1 GAACGTTTCTATAATTTATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTG
*
132757 ACCACATTG-TGGAACGTTTCTACAATCTATATGTAGCTGGCCAATGATGAACGTTTCTATAATT
66 ACCACATTGAT-GAACGTTTCTA-AATCTATATGTAGCTGACCAATG-TGAACGTTTCTATAATT
* * *
132821 TATTTGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTGACCACATTGTG
128 TATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATGTGTAGCTGACCACATTGTT
* *
132881 GAACGTTTCTACAATCTATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTG
1 GAACGTTTCTATAATTTATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTG
* * * * *
132946 ACCA-A-TGATGAATGTTTCTATAATTTATTTGTAGCTGACCACATTGTGGAAGGTTTCTACAAT
66 ACCACATTGATGAACGTTTCTA-AATCTATATGTAGCTGACCA-A-TGT-GAACGTTTCTATAAT
* * * **
133009 CTATATGTAGCTGACCAATGATGAACGTTTCTATTTATTTATGTTTAGCTGACCACCCTG-T
127 TTATATGTAGCTGACCAATGATGAACGTTTCTA-TAATTTATGTGTAGCTGACCACATTGTT
*
133070 GCAACGTTTTTATAATTTAT
1 G-AACGTTTCTATAATTTAT
133090 GTTGAATTGG
Statistics
Matches: 349, Mismatches: 39, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
187 29 0.08
188 7 0.02
189 236 0.68
190 39 0.11
191 4 0.01
192 1 0.00
193 33 0.09
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (187 bp):
GAACGTTTCTATAATTTATATGTAGCTGACCAATGATGAACGTTTCTATAATTTATTTGTAGCTG
ACCACATTGATGAACGTTTCTAAATCTATATGTAGCTGACCAATGTGAACGTTTCTATAATTTAT
ATGTAGCTGACCAATGATGAACGTTTCTATAATTTATGTGTAGCTGACCACATTGTT
Found at i:134299 original size:1 final size:1
Alignment explanation
Indices: 134295--134373 Score: 77
Period size: 1 Copynumber: 79.0 Consensus size: 1
134285 TGTTTGTTTG
* * ** * ** * *
134295 TTTTTGTTTTTTATTTTTTGGTTCTTTTTTTTTTTTTTTTTGGTTTTGTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
134360 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
134374 GGGGGGGGGG
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.01, C:0.01, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:134312 original size:32 final size:29
Alignment explanation
Indices: 134276--134370 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
134266 GGGGGGGTGT
134276 TTTTTGGGTTGTTTGTTTGTTTTTGTTTTTTA
1 TTTTTGGGTTGTTT-TTT-TTTTT-TTTTTTA
* * *
134308 TTTTTTGGTTCTTTTTTTTTTTTTTTTTG
1 TTTTTGGGTTGTTTTTTTTTTTTTTTTTA
* ** *
134337 GTTTTGTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTGGGTTGTTTTTTTTTTTTTTTTTA
134366 TTTTT
1 TTTTT
134371 TTTGGGGGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 33 0.62
30 5 0.09
31 3 0.06
32 12 0.23
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (29 bp):
TTTTTGGGTTGTTTTTTTTTTTTTTTTTA
Found at i:143025 original size:15 final size:16
Alignment explanation
Indices: 143005--143034 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
142995 CATTATAATC
143005 ACTTTACG-CCTGGTA
1 ACTTTACGTCCTGGTA
143020 ACTTTACGTCCTGGT
1 ACTTTACGTCCTGGT
143035 GATCGACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (16 bp):
ACTTTACGTCCTGGTA
Found at i:146972 original size:21 final size:19
Alignment explanation
Indices: 146938--147002 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
146928 AGTCCTCCAA
146938 TATATCGTAAGTCTTCCTT
1 TATATCGTAAGTCTTCCTT
146957 TATATCGTAAGTGTCTTCCTT
1 TATATCGTAA--GTCTTCCTT
* ** *
146978 TGTATCACAAGTCTTCCAT
1 TATATCGTAAGTCTTCCTT
146997 TATATC
1 TATATC
147003 AAATCTTCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 23 0.59
21 16 0.41
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (19 bp):
TATATCGTAAGTCTTCCTT
Found at i:147011 original size:17 final size:19
Alignment explanation
Indices: 146946--147020 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
146936 AATATATCGT
* **
146946 AAGTCTTCCTTTATATCGT
1 AAGTCTTCCATTATATCAC
* *
146965 AAGTGTCTTCCTTTGTATCAC
1 AA--GTCTTCCATTATATCAC
146986 AAGTCTTCCATTATATCA-
1 AAGTCTTCCATTATATCAC
*
147004 AA-TCTTCCATCATATCA
1 AAGTCTTCCATTATATCA
147021 TGCATATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
17 14 0.29
18 2 0.04
19 16 0.33
21 16 0.33
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (19 bp):
AAGTCTTCCATTATATCAC
Found at i:151789 original size:1 final size:1
Alignment explanation
Indices: 151783--151808 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
151773 TATGTTTTGA
151783 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
151809 GATTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:157171 original size:2 final size:2
Alignment explanation
Indices: 157164--157264 Score: 188
Period size: 2 Copynumber: 51.5 Consensus size: 2
157154 GATAACTCTC
157164 AG AG AG AG AG AG AG AG 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
157206 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
157246 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
157265 ACACGTCCGC
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 95 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:157566 original size:14 final size:14
Alignment explanation
Indices: 157547--157573 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
157537 TTGTGCATGT
157547 GCGACATATTTCAG
1 GCGACATATTTCAG
157561 GCGACATATTTCA
1 GCGACATATTTCA
157574 CTAAGTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
GCGACATATTTCAG
Found at i:178869 original size:17 final size:18
Alignment explanation
Indices: 178843--178876 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
178833 ATTCGTACTC
178843 TTTTTCCTTCTT-TTTTT
1 TTTTTCCTTCTTCTTTTT
*
178860 TTTTTTCTTCTTCTTTT
1 TTTTTCCTTCTTCTTTT
178877 CGATTGGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCCTTCTTCTTTTT
Found at i:186267 original size:19 final size:19
Alignment explanation
Indices: 186243--186282 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
186233 GTTTGCTGTA
186243 GATTTGGAATGCTAAAGAC
1 GATTTGGAATGCTAAAGAC
*
186262 GATTTGGAATGCTAGAGAC
1 GATTTGGAATGCTAAAGAC
186281 GA
1 GA
186283 CTCTCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (19 bp):
GATTTGGAATGCTAAAGAC
Found at i:187648 original size:16 final size:17
Alignment explanation
Indices: 187611--187652 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
187601 TTTCCTGCAA
*
187611 TTCCTGGTTTGTGGGTT
1 TTCCTGGTTTGTGGGAT
*
187628 TTCCTGGTTT-TGTGAT
1 TTCCTGGTTTGTGGGAT
187644 TTCCTGGTT
1 TTCCTGGTT
187653 CAGAAAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.02, C:0.14, G:0.29, T:0.55
Consensus pattern (17 bp):
TTCCTGGTTTGTGGGAT
Found at i:188596 original size:13 final size:12
Alignment explanation
Indices: 188588--188626 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 12
188578 TTTTTTTTCC
188588 TTTTATTTTTTT
1 TTTTATTTTTTT
188600 TTTTATTTTTTTT
1 TTTTA-TTTTTTT
188613 TTTTATTCTTTTT
1 TTTTATT-TTTTT
188626 T
1 T
188627 GGGGGGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.08, C:0.03, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:188596 original size:17 final size:16
Alignment explanation
Indices: 188576--188626 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
188566 TTTGGTCATG
*
188576 TTTTTTTTTTCCTTTT
1 TTTTTTTTTTCATTTT
*
188592 ATTTTTTTTTTTATTTT
1 -TTTTTTTTTTCATTTT
188609 TTTTTTTTATTC-TTTT
1 TTTTTTTT-TTCATTTT
188625 TT
1 TT
188627 GGGGGGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTCATTTT
Found at i:204803 original size:2 final size:2
Alignment explanation
Indices: 204796--204846 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
204786 CTGTGGTCCC
204796 AG AG AG AG AG AG AG AG 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
204838 AG AG AG AG A
1 AG AG AG AG A
204847 TTGGAAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:206183 original size:16 final size:16
Alignment explanation
Indices: 206133--206183 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
206123 TGAAACATCC
*
206133 ATGATATTTAGAATCT
1 ATGATATTAAGAATCT
* *
206149 GATAAT-TTAAAACATCT
1 -ATGATATTAAGA-ATCT
206166 ATGATATTAAGAATCT
1 ATGATATTAAGAATCT
206182 AT
1 AT
206184 TTTAGAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (16 bp):
ATGATATTAAGAATCT
Found at i:206516 original size:2 final size:2
Alignment explanation
Indices: 206509--206534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
206499 CCCCAGTGAA
206509 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
206535 TGTAGACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:218242 original size:175 final size:176
Alignment explanation
Indices: 217969--218407 Score: 747
Period size: 176 Copynumber: 2.5 Consensus size: 176
217959 TTCAAGTCAA
* *
217969 TCAAGACAGGAAGTTGCTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAG
1 TCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAG
* *
218034 GATTTTGATTTCTGAGAATTTATGAAAAAAATACCAGC-TTTGACAAGTAATTTTTGGCAAATAT
66 GATTTTGATTTCTGATAATTTATGAAAAAAATACCAGCTTTTGACAAGTAACTTTTGGCAAATAT
218098 CGCATATAGGGTACCCTTATTGTACGGATAACTCCTCCTGCAGTTT
131 CGCATATAGGGTACCCTTATTGTACGGATAACTCCTCCTGCAGTTT
218144 TCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAG
1 TCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAG
*
218209 GATTTTGATTTCTGATAATTTATGAAAAAAATACCAGCTTTTGACAAGTCACTTTTGGCAAATAT
66 GATTTTGATTTCTGATAATTTATGAAAAAAATACCAGCTTTTGACAAGTAACTTTTGGCAAATAT
*
218274 CGCATATAGGGTACCCTTATTGTGCGGATAACTCCTCCTGCAGTTT
131 CGCATATAGGGTACCCTTATTGTACGGATAACTCCTCCTGCAGTTT
* *
218320 TCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATTTATCAGGGTATGTGTGCATATTGC
1 TCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCA--G-AGGTGTGCATATTGC
*
218385 TAGGATTATT-ATTGCTGATAATT
63 TAGGATT-TTGATTTCTGATAATT
218408 AAAAAAAATG
Statistics
Matches: 250, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
175 100 0.40
176 114 0.46
178 1 0.00
179 33 0.13
180 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (176 bp):
TCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAG
GATTTTGATTTCTGATAATTTATGAAAAAAATACCAGCTTTTGACAAGTAACTTTTGGCAAATAT
CGCATATAGGGTACCCTTATTGTACGGATAACTCCTCCTGCAGTTT
Found at i:219182 original size:168 final size:165
Alignment explanation
Indices: 218826--219660 Score: 933
Period size: 166 Copynumber: 5.1 Consensus size: 165
218816 GGTATTTTTA
** * * *
218826 AAAAATCTTCTTCTCAAAAACTATTCA-GCTTGAAAAGCTTAAACTT-GTGTGGAGGCATCCTCA
1 AAAAATCTTCTTCTCAAAAACTATT-AGGCCAGAAAAGCTCAAA-TTAGAGTGGAAGCATCCTCA
* * * *
218889 GGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGTGGCCACAA-GAGGG
64 GATAGAGTAGATTCAAGTTTGTTCAAATCATGGT-CCCGGGGGTAGGGTGGGGCCACAATG-GGG
*
218953 GGATCAAATTTTACATAGGAATATATAGAGAAAATCTTT
127 GGATCAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
218992 AAAAATCTTCTTCACAAAAACTATCAGGCCAGAAAAGCTTAAATTAAAATGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGA
*
219057 TAGAGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGGTAGGGTGGGGCCACAATTGGGGG
66 TAGAGTAGATTCAAGTTTGTTCAAATCATGGT-CCC-GGGGGTAGGGTGGGGCCACAA-TGGGGG
* *
219122 GATCAAGTTTTACATAGGAATATATAGAGAATATCTTT
128 GATCAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
219160 AAAAATCTTCTTCTCTAAAACTATTAGGCCAGAAAAGCTCAAATTAAAGTGGAAACATCCTCA-A
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGA
* * * * *
219224 GTAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGTGGTATGGTGGGGCCACAATGGGGGA
66 -TAGAGTAGATTCAAGTTTGTTCAAATCATGGTCCC-GGGGGTAGGGTGGGGCCACAATGGGGGG
** *
219289 ATGGATTTTTACATAGGAATATATAGAGAAAATCTAT
129 ATCAATTTTTACATAGGAATATATAGAGAAAATCTTT
** * * * * * * * *
219326 AAAAAAATTCTT-TTAAAAACTGTTTGGCCAAAAAATCTCAAATTGGCGTGTAA-CTATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGC-ATCCTCAG
* *
219389 ATA-ATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCAAAAT-GGGG
65 ATAGA-GTAGATTCAAGTTTGTTCAAATCATGGTCCC-GGGGGTAGGGTGGGGCCACAATGGGGG
* * * *
219452 GATAAATTTTTATATA--CATGTATAGAGAAAATCTTT
128 GATCAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
219488 AAAAATTTTCTTCTC-AAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCCCCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGA
* * * * * *
219552 TCGTA-TAGATTCAAGTTTGTTTAAATAATAGT-CCAGGGGTAGGGTGAGGCCACAAT-GGGGGA
66 TAG-AGTAGATTCAAGTTTGTTCAAATCATGGTCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
*
219614 TGAATTTTTACATAGGAATATATAGAGAAAATCTTT
130 TCAATTTTTACATAGGAATATATAGAGAAAATCTTT
*
219650 AAAAATATTCT
1 AAAAATCTTCT
219661 GGGAAAGTTT
Statistics
Matches: 570, Mismatches: 84, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
160 36 0.06
161 2 0.00
162 117 0.21
163 2 0.00
164 18 0.03
165 92 0.16
166 134 0.24
167 42 0.07
168 126 0.22
169 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGA
TAGAGTAGATTCAAGTTTGTTCAAATCATGGTCCCGGGGGTAGGGTGGGGCCACAATGGGGGGAT
CAATTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:219280 original size:334 final size:324
Alignment explanation
Indices: 218826--219660 Score: 978
Period size: 334 Copynumber: 2.5 Consensus size: 324
218816 GGTATTTTTA
** * * * *
218826 AAAAATCTTCTTCTCAAAAACTATTCA-GCTTGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAG
1 AAAAATCTTCTTCTC-AAAACTATT-AGGCCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCAA
* * * *
218890 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGTGGCCACAAGAGGGGG
63 GTAGTGTAGATTCAAGTTTGTTCAAATCATAGT-CCCAGGGGTAGGGTGAGGCCACAAG-GGGGG
* * *
218955 ATCAAATTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCACAAAAACTATCAGG
126 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATATTCTT-ACAAAAACTATCAGG
* *
219020 CCAGAAAAGCTTAAATTAAAATGGAAGC-ATCCTCAGATAGA-GTAGATTCAAATTTGTTCAAAT
190 CCAAAAAAGCTCAAATTAAAATGGAA-CTATCCTCAGATA-ATGTAGATTCAAATTTGTTCAAAT
* * *
219083 CATGGTCCCCGGGGGGTAGGGTGGGGCCACAATTGGGGGGATCAAGTTTTACATAGGAATATATA
253 CATGGT-CCCGGGGGGTAGGGCGGGGCCA-AAAT-GGGGGATAAAGTTTTACATA--AATATATA
*
219148 GAGAATATCTTT
313 GAGAAAATCTTT
* *
219160 AAAAATCTTCTTCTCTAAAACTATTAGGCCAGAAAAGCTCAAATTAAAGTGGAAACATCCTCAAG
1 AAAAATCTTCTTCTC-AAAACTATTAGGCCAGAAAAGCTCAAATT-GAGTGGAAGCATCCTCAAG
* * * *
219225 TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGTGGTATGGTGGGGCCACAATGGGGGAA
64 TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCAGG-GGTAGGGTGAGGCCACAA-GGGGGGA
* * * ** * **
219290 TGGATTTTTACATAGGAATATATAGAGAAAATCTATAAAAAAATTCTTTTAAAAACTGTTTGGCC
127 TGAATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATATTCTTACAAAAACTATCAGGCC
* **** * *
219355 AAAAAATCTCAAATTGGCGTGTAACTATCCTCAGATAATGTAGATTCAAGTTTGTTCAAATCATG
192 AAAAAAGCTCAAATTAAAATGGAACTATCCTCAGATAATGTAGATTCAAATTTGTTCAAATCATG
* * * * *
219420 GTCCCTGGGGGTAGGGCGGGGCCAAAATGGGGGATAAATTTTTATATACATGTATAGAGAAAATC
257 GTCCCGGGGGGTAGGGCGGGGCCAAAATGGGGGATAAAGTTTTACATAAATATATAGAGAAAATC
219485 TTT
322 TTT
* * * *
219488 AAAAATTTTCTTCTCAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCC-CCAGA
1 AAAAATCTTCTTCTCAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCAAG-
* * * * *
219552 TCGTATAGATTCAAGTTTGTTTAAATAATAGT-CCAGGGGTAGGGTGAGGCCACAATGGGGGATG
64 TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCAGGGGTAGGGTGAGGCCACAAGGGGGGATG
219616 AATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATATTCT
129 AATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATATTCT
219661 GGGAAAGTTT
Statistics
Matches: 431, Mismatches: 62, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
324 49 0.11
325 16 0.04
326 7 0.02
327 65 0.15
328 33 0.08
330 17 0.04
331 3 0.01
332 22 0.05
333 74 0.17
334 144 0.33
335 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (324 bp):
AAAAATCTTCTTCTCAAAACTATTAGGCCAGAAAAGCTCAAATTGAGTGGAAGCATCCTCAAGTA
GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCAGGGGTAGGGTGAGGCCACAAGGGGGGATGAA
TTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATATTCTTACAAAAACTATCAGGCCAAAA
AAGCTCAAATTAAAATGGAACTATCCTCAGATAATGTAGATTCAAATTTGTTCAAATCATGGTCC
CGGGGGGTAGGGCGGGGCCAAAATGGGGGATAAAGTTTTACATAAATATATAGAGAAAATCTTT
Found at i:221103 original size:146 final size:145
Alignment explanation
Indices: 220839--221378 Score: 639
Period size: 146 Copynumber: 3.8 Consensus size: 145
220829 CGCCTGTTCG
* * ** * *
220839 AAATTCATGTCCGGTCCATATCTTTC-TAAGGAGAAATGTTGGAAGTTCTTACCTCACACATAGA
1 AAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
* * *
220903 TTTCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCAGGCAAGGTCAAGGTCAT
66 TTGCTTATAACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT-AGGCAAGGTCAAGGTCAT
220968 TGGCAGAAAAAGTGCA
130 TGGCAGAAAAAGTGCA
*
220984 AAATTCGTGTCCAGTCCATATCTTTCTTATGGAGAAACAGTT-GAAGTTCTTACTTCACACAAAG
1 AAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACA-TTGGAAGTTCTTACTTCACACAAAG
* * * * * * *
221048 ATTGCTTTTGACCTACGGGTTTGTCATGACCTTGACCCAAAGTCATT-----TGGTCAAGGTTAT
65 ATTGCTTATAACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTAGGCAAGGTCAAGGTCAT
221108 TGGCAGAAAAAGTGCA
130 TGGCAGAAAAAGTGCA
* * * *
221124 AAATTTGTGTCTGGTCCATATCTTT-TTAATGGGGAAACATTGGAAGTTCTTACTTCATACAAAG
1 AAATTCGTGTCCGGTCCATATCTTTCTT-ATGGAGAAACATTGGAAGTTCTTACTTCACACAAAG
* * * * * * *
221188 CTTGCTTCTAACCTAAGGGTATGTCGTGACCTTGACCCAGGGTCATTCGGGCAAGGTCAAGGTCG
65 ATTGCTTATAACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT-AGGCAAGGTCAAGGTCA
221253 TTGGCATG-AAAAGTGCA
129 TTGGCA-GAAAAAGTGCA
* * ** * * *
221270 AAATTTGTGTCCGGTCCATATCTTTCTTATGGACAAGTATTGGAAGTTCTTAATTTACATAAAGA
1 AAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
* *
221335 TTGCTTATAACCTGAGAGTGTGTCATGACCTTGACCCAAGGTCA
66 TTGCTTATAACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCA
221379 ATTGAGAGAG
Statistics
Matches: 336, Mismatches: 47, Indels: 23
0.83 0.12 0.06
Matches are distributed among these distances:
139 4 0.01
140 119 0.35
145 24 0.07
146 184 0.55
147 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (145 bp):
AAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
TTGCTTATAACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTAGGCAAGGTCAAGGTCATT
GGCAGAAAAAGTGCA
Found at i:224293 original size:19 final size:20
Alignment explanation
Indices: 224259--224303 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
224249 CCGTGTCGCA
*
224259 CCGTGGCCGCCTGTGTAACT
1 CCGTGGCCGACTGTGTAACT
*
224279 CCGTGGCC-ACTGTGTTACT
1 CCGTGGCCGACTGTGTAACT
224298 CCGTGG
1 CCGTGG
224304 ATATCGTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.09, C:0.33, G:0.31, T:0.27
Consensus pattern (20 bp):
CCGTGGCCGACTGTGTAACT
Found at i:225758 original size:2 final size:2
Alignment explanation
Indices: 225751--225793 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
225741 ACACATACAC
225751 AG AG AG AG AG AG AG AG 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
225793 A
1 A
225794 TATTTTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:226125 original size:2 final size:2
Alignment explanation
Indices: 226118--226151 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
226108 ATACTGGTAT
226118 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
226152 ATATGACGAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:231329 original size:14 final size:15
Alignment explanation
Indices: 231304--231334 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
231294 ATTACTTTAT
231304 TTTGGAAAAAAAAAA
1 TTTGGAAAAAAAAAA
231319 TTTGGAAAAAAAAAA
1 TTTGGAAAAAAAAAA
231334 T
1 T
231335 CGGGCTCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
TTTGGAAAAAAAAAA
Found at i:241264 original size:16 final size:16
Alignment explanation
Indices: 241243--241275 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
241233 GATAAAGGTG
*
241243 GTCTCATAATGGTGAT
1 GTCTCATAAGGGTGAT
241259 GTCTCATAAGGGTGAT
1 GTCTCATAAGGGTGAT
241275 G
1 G
241276 CCTCGTCTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.33
Consensus pattern (16 bp):
GTCTCATAAGGGTGAT
Found at i:241466 original size:21 final size:21
Alignment explanation
Indices: 241442--241583 Score: 203
Period size: 21 Copynumber: 6.8 Consensus size: 21
241432 TCCGTGCAAG
*
241442 AAACCAACCGTACCGTTCACA
1 AAACGAACCGTACCGTTCACA
*
241463 AAACGAAACGTACCGTTCACA
1 AAACGAACCGTACCGTTCACA
* * *
241484 AAGCGTACCATACCGTTCACA
1 AAACGAACCGTACCGTTCACA
*
241505 AAACGAAACGTACCGTTCACA
1 AAACGAACCGTACCGTTCACA
* *
241526 AAGCGAACTGTACCGTTCACA
1 AAACGAACCGTACCGTTCACA
*
241547 AAGCGAACCGTACCGTTCACA
1 AAACGAACCGTACCGTTCACA
241568 AAACGAACCGTACCGT
1 AAACGAACCGTACCGT
241584 GCAAAAAGCG
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 106 1.00
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.15
Consensus pattern (21 bp):
AAACGAACCGTACCGTTCACA
Found at i:242052 original size:17 final size:17
Alignment explanation
Indices: 242010--242052 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
242000 ATTCTCAGGA
*
242010 GAGAGAGAAAGATGAAT
1 GAGAGAGAGAGATGAAT
242027 GAGAGAGAGAGATGAAT
1 GAGAGAGAGAGATGAAT
242044 GAGAGAGAG
1 GAGAGAGAG
242053 GGAGATCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.42, T:0.09
Consensus pattern (17 bp):
GAGAGAGAGAGATGAAT
Found at i:244422 original size:2 final size:2
Alignment explanation
Indices: 244415--244446 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
244405 ATACACTCTC
244415 AG AG AG 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
244447 CTTGTGTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:246060 original size:21 final size:21
Alignment explanation
Indices: 246036--246124 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
246026 ACTGTGCAAG
*
246036 AAGCGTACCGTACCGTTCACA
1 AAGCGAACCGTACCGTTCACA
* *
246057 AAGCGAACTGTACTGTTCACA
1 AAGCGAACCGTACCGTTCACA
* *
246078 AAACGAACCGTACTGTTCACA
1 AAGCGAACCGTACCGTTCACA
* * *
246099 AAGTGAACCGTACCATTCAAA
1 AAGCGAACCGTACCGTTCACA
246120 AAGCG
1 AAGCG
246125 TAACGAACCA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (21 bp):
AAGCGAACCGTACCGTTCACA
Found at i:246071 original size:42 final size:42
Alignment explanation
Indices: 246023--246111 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
246013 TTTAGCAAAG
* *
246023 CGTACTGTGCA-AGAAGCGTACCGTACCGTTCACAAAGCGAAC
1 CGTACTGTGCACA-AAACGAACCGTACCGTTCACAAAGCGAAC
* * * *
246065 TGTACTGTTCACAAAACGAACCGTACTGTTCACAAAGTGAAC
1 CGTACTGTGCACAAAACGAACCGTACCGTTCACAAAGCGAAC
246107 CGTAC
1 CGTAC
246112 CATTCAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (42 bp):
CGTACTGTGCACAAAACGAACCGTACCGTTCACAAAGCGAAC
Found at i:248639 original size:318 final size:326
Alignment explanation
Indices: 248180--249327 Score: 1093
Period size: 318 Copynumber: 3.5 Consensus size: 326
248170 GGTATTTTTC
* ** * *** * *
248180 AAAAATCTTCTTCTCAAAAACTATTCGGCCAG-AAAAGCTTTAACTAGTGTGGAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAAGCTCAAATTAAAATGGAAGCACCCTCA-
* * * *
248244 GTTGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGTGGGTAGGGTGGGGCCACAATAGGGGG
65 G-AGTGTAGA-T--AGTTAG-T-AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
* * * *
248309 ATCAAGTTTTACATATGAATATATAGAGAAAATCTTTTAAGAATCTTCTTCTCATAAACTATTTG
124 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTTAAAAATATTCTTCTCATAAACTATTAG
* * *
248374 GCCAGAAAAGCTCAAATTATAATGATAGCATCCTCAGGTTGTGTAGATTCAAGTTTATTCAAATC
189 GCCAGAAAAGCTCAAATTAAAATGATAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATC
* * **
248439 ATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGTCAT-G-TTTTACATAGGAATATATTTA
254 ATAGTCCCTGGGGGTAGGGCGGGGCCACAAT-GGGGG-AATGGATTTTACATAGGAATATATGGA
248502 GAAAATCTTT
317 GAAAATCTTT
*
248512 AAAAATCTTCTTCTCAAAAACTATTTGGCCAG-AAAAGCTCAAATTAAAATGGAAGCACCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAAGCTCAAATTAAAATGGAAGCACCCTCAG
*
248576 -GT-T-G-T-G-TAG-AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATTAAGT
66 AGTGTAGATAGTTAGTAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGT
* * * *
248634 TTTACATCGGAATATATAGAGAAAATC-TTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAT
131 TTTACATAGGAATATATAGAGAAAATCTTTTAAAAATATTCTTCTCATAAACTATTAGGCCAGAA
* *
248698 AAGCTCAAATTAAAATGAAAGCATCCTCAGGTAG-GTTAGATTCAAGTTTGTTCAAATCATAGCC
196 AAGCTCAAATTAAAATGATAGCATCCTCAGGTAGTG-TAGATTCAAGTTTGTTCAAATCATAGTC
* *
248762 CCTGGGTGTATGGCGGGGCCACAATGGGGGAATGGATTTTTACATAGGAATATATGGAGAAAATC
260 CCTGGGGGTAGGGCGGGGCCACAATGGGGGAATGGA-TTTTACATAGGAATATATGGAGAAAATC
248827 TTT
324 TTT
* * * ** * *
248830 AAAAATCTTTTTCTCAAAAACTATTAGGCTAGAAAAAAAGCTCATATTTGACTGGAAGCATCCTC
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAG--AAAAAGCTCAAATTAAAATGGAAGCACCCTC
* *
248895 AGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGG
64 AG--AGTGTAGA-T--AGTTAG-T-AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGG
* * * * * * * *
248960 GTATGAATTTTTATACAGGAATATATAGAGAAAATCTTTTAAAAAAATTGTT-T-TTAAACTATT
122 GGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTTAAAAATATTCTTCTCATAAACTATT
* * **** * *
249023 AGGCCAGGAAAGCTCAAACTGGCGTG-TAAGCATCCTTAGATAGTGTAGATTCAAGTTTGTTCAA
187 AGGCCAGAAAAGCTCAAATTAAAATGAT-AGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAA
* *
249087 ATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGG-ATGAATTTT---T-----TATA-GA
251 ATCATAGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGAATGGATTTTACATAGGAATATATG-
249142 GAGAAAATCTTT
315 GAGAAAATCTTT
* * * ** * *
249154 AAAAATCTTCTTC-CGAAAACTATTAGGCCAG-GAAAGCCCAAATTTGAGTAGAAGCATCCC-CA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAAGCTCAAATTAAAATGGAAGCA-CCCTCA
* ** * * * *
249216 GATCGTATAGATTCAAGTTTCTTTAAATCATAGTCCC--GGGGTACGATGAGGCCACAAT-GGGG
65 GA--GTGTAGA-T--AG-TT-AGTAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGG
* * *
249278 GATGAATTTTTACATAGGAATATATAGAGGAAATC-TTTAAAAATATTCTT
123 GATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTTAAAAATATTCTT
249328 GGAAAGTTTT
Statistics
Matches: 698, Mismatches: 88, Indels: 76
0.81 0.10 0.09
Matches are distributed among these distances:
315 2 0.00
316 20 0.03
317 146 0.21
318 148 0.21
320 47 0.07
321 34 0.05
322 2 0.00
323 17 0.02
324 30 0.04
325 2 0.00
326 1 0.00
327 1 0.00
328 2 0.00
329 3 0.00
331 2 0.00
332 60 0.09
333 4 0.01
334 94 0.13
335 71 0.10
336 12 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (326 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAAGCTCAAATTAAAATGGAAGCACCCTCAG
AGTGTAGATAGTTAGTAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGT
TTTACATAGGAATATATAGAGAAAATCTTTTAAAAATATTCTTCTCATAAACTATTAGGCCAGAA
AAGCTCAAATTAAAATGATAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATAGTCC
CTGGGGGTAGGGCGGGGCCACAATGGGGGAATGGATTTTACATAGGAATATATGGAGAAAATCTT
T
Found at i:248709 original size:152 final size:158
Alignment explanation
Indices: 248267--249327 Score: 711
Period size: 165 Copynumber: 6.6 Consensus size: 158
248257 AAGTTTGTTC
* * * *
248267 AAATCATGGTCCCCGTGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATATGAATATA
1 AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATA
* * * * *
248332 TAGAGAAAATCTTTTAAGAATCTTCTTCTCATAAACTATTTGGCCAGAAAAGCTCAAATTATAAT
66 TAGAGAAAATC-TTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAAT
* * *
248397 GATAGCATCCTC-AGGTTGTGTAGATTCAAGTTTATT
130 GAAAGCACCCTCGA-G--GT-TAGA-T--AG-TTAGT
*
248433 CAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG-TCATGTTTTACATAGGAATAT
1 -AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATAT
** * *
248497 ATTTAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAATTAAAAT
65 ATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAAT
*
248562 GGAAGCACCCTC-AGGTT-G-T-G-TAG-
130 GAAAGCACCCTCGAGGTTAGATAGTTAGT
* * *
248585 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATTAAGTTTTACATCGGAATATA
1 AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATA
*
248650 TAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGATAAGCTCAAATTAAAATG
66 TAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATG
* *
248715 AAAGCATCCTCAGGTAGGTTAGATTCAAGTTTGTT
131 AAAGCACCCTC--G-AGGTTAGA-T--AGTTAG-T
* * * * ** *
248750 CAAATCATAGCCCCTGGGTGTATGGCGGGGCCACAAT-GGGGGAATGGATTTTTACATAGGAATA
1 -AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG-ATCAAGTTTTACATAGGAATA
* * *
248814 TATGGAGAAAATCTTTAAAAATCTTT-TTCTCAAAAACTATTAGGCTAGAAAAAAAGCTCATATT
64 TATAGAGAAAATCTTTAAAAAT-TTTCTTCTCAAAAACTATTAGGCCAG---AAAAGCTCAAATT
** * * * * *
248878 TGACTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTT
125 AAAATGAAAGCACCCTC-GA-GGT-TAGA-T--AGTTAG-T
* * * * * * *
248919 CAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGTATGAATTTTTATACAGGAATAT
1 -AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATAT
** * ** * * ****
248984 ATAGAGAAAATCTTTTAAAAAAATTGTT-T-TTAAACTATTAGGCCAGGAAAGCTCAAACTGGCG
65 ATAGAGAAAATC-TTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAA
* * * * *
249047 TGTAAGCATCCTTAGATAGTGTAGATTCAAGTTTGTT
129 TGAAAGCA-CCCTCGA-GGT-TAGA-T--AGTTAG-T
* * *
249084 CAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAAT-GGGGGATGAA-TTTT---T-----TAT
1 -AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATAT
* * * * * ** *
249139 AGAGAGAAAATCTTTAAAAATCTTCTTC-CGAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGT
65 ATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAAT
* **
249203 -AGAAGCATCCC-CAGATCGTATAGATTCAAGTTTCTTT
130 GA-AAGCA-CCCTC-GA-GGT-TAGA-T--AG-TT-AGT
* * * * *
249240 AAATCATAGTCCC--GGGGTACGATGAGGCCACAAT-GGGGGATGAATTTTTACATAGGAATATA
1 AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATA
* *
249302 TAGAGGAAATCTTTAAAAATATTCTT
66 TAGAGAAAATCTTTAAAAATTTTCTT
249328 GGAAAGTTTT
Statistics
Matches: 756, Mismatches: 97, Indels: 87
0.80 0.10 0.09
Matches are distributed among these distances:
151 41 0.05
152 88 0.12
153 29 0.04
154 16 0.02
155 79 0.10
156 8 0.01
157 3 0.00
158 1 0.00
159 1 0.00
160 1 0.00
161 1 0.00
162 30 0.04
163 6 0.01
164 10 0.01
165 142 0.19
166 121 0.16
167 43 0.06
168 17 0.02
169 105 0.14
170 14 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (158 bp):
AAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATA
TAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATG
AAAGCACCCTCGAGGTTAGATAGTTAGT
Found at i:248952 original size:169 final size:165
Alignment explanation
Indices: 248585--249321 Score: 826
Period size: 169 Copynumber: 4.5 Consensus size: 165
248575 GGTTGTGTAG
* * *
248585 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGATTAAGTTTTACATCGGAATATA
1 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAAT-GGGGGATGAATTTTTACATAGGAATATA
* ** *
248650 TAGAGAAAATCTTTAAAAAT-TTTCTTCTCAAAAACTATTAGGCCAGATAAGCTCAAATTAAAAT
65 TAGAGAAAATCTTTAAAAATCTTT-TTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGACT
* *
248714 GAAAGCATCCTCAGGTAG-GTTAGATTCAAGTTTGTTC
129 GGAAGCATCCTCAGATAGTG-TAGATTCAAGTTTGTTC
* * * * * *
248751 AAATCATAGCCCCTGGGTGTATGGCGGGGCCACAATGGGGGAATGGATTTTTACATAGGAATATA
1 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGG-ATGAATTTTTACATAGGAATATA
* * *
248816 TGGAGAAAATCTTTAAAAATCTTTTTCTCAAAAACTATTAGGCTAGAAAAAAAGCTCATATTTGA
65 TAGAGAAAATCTTTAAAAATCTTTTTCTCAAAAACTATTAGGCCAG---AAAAGCTCAAATTTGA
248881 CTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTC
127 CTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTC
* * *
248920 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGTATGAATTTTTATACAGGAATATA
1 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAA-TGGGGGATGAATTTTTACATAGGAATATA
** * * * *
248985 TAGAGAAAATCTTTTAAAAAAATTGTTT-T--TAAACTATTAGGCCAGGAAAGCTCAAA-CTGGC
65 TAGAGAAAATC-TTTAAAAATCTT-TTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAC
* *
249046 GTGTAAGCATCCTTAGATAGTGTAGATTCAAGTTTGTTC
128 -TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTC
* *
249085 AAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATGAA-TTTT---T-----TATAG
1 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGATGAATTTTTACATAGGAATATAT
* * * * * *
249141 AGAGAAAATCTTTAAAAATCTTCTTC-CGAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTAG
66 AGAGAAAATCTTTAAAAATCTTTTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGACTGG
* * * * *
249205 AAGCATCCCCAGATCGTATAGATTCAAGTTTCTTT
131 AAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTC
* * * *
249240 AAATCATAGTCCC--GGGGTACGATGAGGCCACAATGGGGGATGAATTTTTACATAGGAATATAT
1 AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGATGAATTTTTACATAGGAATATAT
*
249303 AGAGGAAATCTTTAAAAAT
66 AGAGAAAATCTTTAAAAAT
249322 ATTCTTGGAA
Statistics
Matches: 483, Mismatches: 65, Indels: 50
0.81 0.11 0.08
Matches are distributed among these distances:
153 29 0.06
154 14 0.03
155 81 0.17
156 2 0.00
157 1 0.00
162 22 0.05
163 4 0.01
164 13 0.03
165 84 0.17
166 90 0.19
167 3 0.01
168 14 0.03
169 106 0.22
170 17 0.04
171 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (165 bp):
AAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGATGAATTTTTACATAGGAATATAT
AGAGAAAATCTTTAAAAATCTTTTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGACTGG
AAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTC
Found at i:255759 original size:2 final size:2
Alignment explanation
Indices: 255752--255798 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
255742 CGCCTAAACG
255752 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
255794 TC TC T
1 TC TC T
255799 GTAAGGTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:266784 original size:163 final size:165
Alignment explanation
Indices: 266470--266789 Score: 400
Period size: 163 Copynumber: 2.0 Consensus size: 165
266460 ATCTTGACAT
* * *
266470 TTTGAGGATGCTTGCATAGTTATCCCACAAACTGTTGCATTGTAGTTCTTAAGAAGAAGATTTTA
1 TTTGAGGATCCTTGCATAATAATCCCACAAACTGTTGCATTGTAGTTCTTAAGAAGAAGATTTTA
* * *
266535 AACACTTTGCCTATATACTTCTATGTTAAACTTTGAAACCCTTCTGGGGCCCCAGTGTTGGTCTA
66 AACACTTTGCCTATATACTTCTATGTTAAACTTTGAAACCCTTCTGGGGCCCCAGTATTAGTCCA
* *
266600 AGGGTCACAGCTTTTACAATTTAGAATTTTCACTA
131 AGGGTCACAGATTTAACAATTTAGAATTTTCACTA
* * *
266635 TTTGAGGATCCTTGCATAATAATCTCACAAACTGTTGCATTGTAGTTC-T-CG-AGAATATTTAT
1 TTTGAGGATCCTTGCATAATAATCCCACAAACTGTTGCATTGTAGTTCTTAAGAAGAAGATTT-T
* * * * **
266697 AATCA-TGTTTCCTATATATTTCTATGTTAAACTTTG-AACCCCTCTTGTTGCCCCAGTATTAGT
65 AAACACT-TTGCCTATATACTTCTATGTTAAACTTTGAAACCCTTC-TGGGGCCCCAGTATTAGT
*
266760 CCAGGGGTCAC-GAATTTAACAATTTAGAAT
128 CCAAGGGTCACAG-ATTTAACAATTTAGAAT
266790 CTACAATAGC
Statistics
Matches: 133, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
162 17 0.13
163 71 0.53
164 1 0.01
165 44 0.33
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (165 bp):
TTTGAGGATCCTTGCATAATAATCCCACAAACTGTTGCATTGTAGTTCTTAAGAAGAAGATTTTA
AACACTTTGCCTATATACTTCTATGTTAAACTTTGAAACCCTTCTGGGGCCCCAGTATTAGTCCA
AGGGTCACAGATTTAACAATTTAGAATTTTCACTA
Found at i:267157 original size:166 final size:166
Alignment explanation
Indices: 266879--267681 Score: 974
Period size: 166 Copynumber: 4.9 Consensus size: 166
266869 TTTCCTATAC
* * * * *
266879 TTAAACTTTGAACCCCGCCTGAGGCCCCAATTTTGGTACGGGGGTCACGATTCTTACAATTTATA
1 TTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGGGGGTCACGATTTTTGCAATTTATA
* * * * * *
266944 ATCTTCACTAAATGTTCAAGCTTTTGTGTATATATTGGCATTTCTGGTGCAGTAGTTCTTAAGGA
66 ATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTAAGAA
* *
267009 GAAGATTTTTAATCATTGTTCCTATGTATTTCTATG
131 GAAGATTTTTAAACATTTTTCCTATGTATTTCTATG
* * * *
267045 TTAGACTTTGAACACCGCCTGGGGCCCCAATTTTGGTCCGGGGGTCACGATTTTTGCAATTTAGA
1 TTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGGGGGTCACGATTTTTGCAATTTATA
* * * *
267110 ATCTTCACTATATATACAAGTTTTTATGTAAATATTGGCATTTCTGGTGCAGTGGGTCTTGAGAA
66 ATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTAAGAA
267175 GAAGATTTTTAAAACATTTTTCCTATGTATTTCTATG
131 GAAGATTTTT-AAACATTTTTCCTATGTATTTCTATG
* * * ** * *
267212 TTAAACTTTGAATCCCGCCTGGGGCCCCTGTTTTTGTCCTCGGGTC-CAATTTTTGCAATTTATT
1 TTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGGGGGTCACGATTTTTGCAATTTATA
* * * * *
267276 ATTTTCACAATATATGCAAGCTCTTGTGTAAATATTGGCATTTCTGGTGCAGTGGGTCTTAATAA
66 ATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTC-T--TAA
* *
267341 GAAGAAGATTTTAAAATATTTTTCCTATGTATTTCTATG
128 GAAGAAGATTTTTAAACATTTTTCCTATGTATTTCTATG
* * * * * *
267380 TTAAACTTTGAACCCCGCCTGGGGCCCCTGTTTTTGTCCTGGGGTC-CAATTTTCGCAATTTATT
1 TTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGGGGGTCACGATTTTTGCAATTTATA
* * * * * *
267444 ATTTTCACAATATATGCAAGCTCTTGTGAAAATATTGGCATTTCTGGTTCAGTGGTTCTT-----
66 ATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTAAGAA
* * * *
267504 G-AGATTTTAAAACATTTTTCCTATTTTTTTTTATG
131 GAAGATTTTTAAACATTTTTCCTATGTATTTCTATG
* * * *
267539 TTAAACTTTGAACCCCACCTGGGGCCCCAGTTTTGGTCTGGAGGTCACGATTTTTGCAATTTAAA
1 TTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGGGGGTCACGATTTTTGCAATTTATA
** * * *
267604 ATCTTCACTATATATACAAGCTTTTACGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGATAG
66 ATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTAAGAA
267669 GAAGATTTTTAAA
131 GAAGATTTTTAAA
267682 GACATGTACC
Statistics
Matches: 558, Mismatches: 68, Indels: 22
0.86 0.10 0.03
Matches are distributed among these distances:
159 70 0.13
160 67 0.12
165 2 0.00
166 200 0.36
167 64 0.11
168 141 0.25
169 14 0.03
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (166 bp):
TTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGGGGGTCACGATTTTTGCAATTTATA
ATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTAAGAA
GAAGATTTTTAAACATTTTTCCTATGTATTTCTATG
Found at i:267863 original size:4 final size:4
Alignment explanation
Indices: 267847--267909 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
267837 TGAAAAGTTT
* * * * * *
267847 ACAG ACGG ACAG ACAG ACAG ACGG ACAG ACAG ACGG ACGG ACGG ACGG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
*
267895 ACAG ACAG ACGG ACA
1 ACAG ACAG ACAG ACA
267910 ACGTGTGATC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:267864 original size:12 final size:12
Alignment explanation
Indices: 267847--267909 Score: 90
Period size: 12 Copynumber: 5.2 Consensus size: 12
267837 TGAAAAGTTT
* *
267847 ACAGACGGACAG
1 ACAGACAGACGG
267859 ACAGACAGACGG
1 ACAGACAGACGG
267871 ACAGACAGACGG
1 ACAGACAGACGG
* *
267883 ACGGACGGACGG
1 ACAGACAGACGG
267895 ACAGACAGACGG
1 ACAGACAGACGG
267907 ACA
1 ACA
267910 ACGTGTGATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:267909 original size:8 final size:8
Alignment explanation
Indices: 267847--267900 Score: 72
Period size: 8 Copynumber: 6.8 Consensus size: 8
267837 TGAAAAGTTT
267847 ACAGACGG
1 ACAGACGG
*
267855 ACAGACAG
1 ACAGACGG
267863 ACAGACGG
1 ACAGACGG
*
267871 ACAGACAG
1 ACAGACGG
*
267879 ACGGACGG
1 ACAGACGG
*
267887 ACGGACGG
1 ACAGACGG
267895 ACAGAC
1 ACAGAC
267901 AGACGGACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:271462 original size:13 final size:14
Alignment explanation
Indices: 271440--271472 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
271430 CAATTCAACA
*
271440 ATTGACATTGA-TG
1 ATTGATATTGATTG
271453 ATTGATATTGATTG
1 ATTGATATTGATTG
271467 ATTGAT
1 ATTGAT
271473 TGAATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.45
Consensus pattern (14 bp):
ATTGATATTGATTG
Found at i:276654 original size:163 final size:164
Alignment explanation
Indices: 276241--276662 Score: 690
Period size: 164 Copynumber: 2.6 Consensus size: 164
276231 AGAGTAAAGA
276241 AAATC-TTAAAAATCTTCATTTCAGAAACTGTTAGGCCAGGAAAACTGAAACTTATGTGGAAGCA
1 AAATCTTTAAAAATCTTCATTTCAGAAACTGTTAGGCCAGGAAAACTGAAACTTATGTGGAAGCA
276305 TCCTCAGGCAGTGTATATTCAAAGTTGTGAAAATCATGACCCCCGGGGTAGGATGGGGCAACAAT
66 TCCTCAGGCAGTGTATATTCAAAGTTGTGAAAATCATGACCCCCGGGGTAGGATGGGGCAACAAT
276370 AGGGGTCGAATTTATACATAAGAATATATAGAGT
131 AGGGGTCGAATTTATACATAAGAATATATAGAGT
* *
276404 AAAGCTTTAAAAATCTTCATTTCAGAAACTGTTAAGCCAGGAAAACTGAAACTTATGTGGAAGCA
1 AAATCTTTAAAAATCTTCATTTCAGAAACTGTTAGGCCAGGAAAACTGAAACTTATGTGGAAGCA
*
276469 TCCTCAGGCAGTGTATATTCAAAGTTGTGAAAATCATGACCCCCGGGGTAGGATGGGGCCACAAT
66 TCCTCAGGCAGTGTATATTCAAAGTTGTGAAAATCATGACCCCCGGGGTAGGATGGGGCAACAAT
*
276534 AGGGGTCGAA-TTATACATAGGAATATATAGAGT
131 AGGGGTCGAATTTATACATAAGAATATATAGAGT
* * * *
276567 AAATCTTTAAAAATCTTC-TTCTCAGAAAGC-GTTAGGGCTGGAAAGCTGACACTTATGTGGAAG
1 AAATCTTTAAAAATCTTCATT-TCAGAAA-CTGTTAGGCCAGGAAAACTGAAACTTATGTGGAAG
* * * *
276630 CATCCTCGGGTAGTGAAGATTCAAAGTTGTGAA
64 CATCCTCAGGCAGTGTATATTCAAAGTTGTGAA
276663 NTATCTGTTG
Statistics
Matches: 242, Mismatches: 14, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
162 2 0.01
163 107 0.44
164 133 0.55
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (164 bp):
AAATCTTTAAAAATCTTCATTTCAGAAACTGTTAGGCCAGGAAAACTGAAACTTATGTGGAAGCA
TCCTCAGGCAGTGTATATTCAAAGTTGTGAAAATCATGACCCCCGGGGTAGGATGGGGCAACAAT
AGGGGTCGAATTTATACATAAGAATATATAGAGT
Found at i:294487 original size:190 final size:190
Alignment explanation
Indices: 294161--294532 Score: 672
Period size: 190 Copynumber: 2.0 Consensus size: 190
294151 AAATAGATTT
*
294161 TGACGTCTGCTTTCACATTCGGCATCGGAAAGATAACAGATACCGCAAACTGAGTAAACCATGTA
1 TGACGTCTGCTTTCACATTCGGCATCGGAAAGATAACAGATACCGCAAACTGAGTAAACCATCTA
* *
294226 AACAGCCGTAAAATGCTTCATGTAAATATGATTAGCAGTGTTTTGCATACTCACATAACATTGTT
66 AACAGCCGTAAAATGCTTCACGTAAATATGATTAGCAGTGTTTTGCATACTCACATAACATTGTG
294291 TTGTAAGTTATAGGCTTATTATTTACTTGTAAACTTAGCAGTGTATTTGATCTATCACTG
131 TTGTAAGTTATAGGCTTATTATTTACTTGTAAACTTAGCAGTGTATTTGATCTATCACTG
* * *
294351 TGACGTCTGCTTTCACATTCGGCATCGGAAAGATGACAGATACTGCAAACTGAGTAGACCATCTA
1 TGACGTCTGCTTTCACATTCGGCATCGGAAAGATAACAGATACCGCAAACTGAGTAAACCATCTA
* *
294416 AACAGCCGTAAAATGCTTCACGTAAGTATGATTAGCAGTGTTTTGCATACTCATATAACATTGTG
66 AACAGCCGTAAAATGCTTCACGTAAATATGATTAGCAGTGTTTTGCATACTCACATAACATTGTG
294481 TTGTAAGTTATAGGCTTATTATTTACTTGTAAACTTAGCAGTGTATTTGATC
131 TTGTAAGTTATAGGCTTATTATTTACTTGTAAACTTAGCAGTGTATTTGATC
294533 CGCCACTGAC
Statistics
Matches: 174, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 174 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (190 bp):
TGACGTCTGCTTTCACATTCGGCATCGGAAAGATAACAGATACCGCAAACTGAGTAAACCATCTA
AACAGCCGTAAAATGCTTCACGTAAATATGATTAGCAGTGTTTTGCATACTCACATAACATTGTG
TTGTAAGTTATAGGCTTATTATTTACTTGTAAACTTAGCAGTGTATTTGATCTATCACTG
Found at i:301981 original size:36 final size:36
Alignment explanation
Indices: 301925--303091 Score: 1047
Period size: 36 Copynumber: 32.6 Consensus size: 36
301915 CTAGCCTAAC
* *
301925 TAGTGAG-GAGGTGGAGGTATGTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * * *
301960 TGGTGGGTGGGGTGGTGGTATGTGTCTTGTCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * * *
301996 TAGTG-GATGGGGTAGTGGTATTTGTCCTGACCTAGG
1 TAGTGAG-TGGGGTGGTGGTATGTGTCCTGGCCTGGG
*
302032 TAGTGAGTGGGGTAGTGGTATGTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302068 TAGTG-GTTGGGTGGTGGTATATGACCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302103 TAGTGAAAGGGTAGTGAAAGGTCAGGAGGTATGTGTCCCGGCTTGGG
1 TAGTG--A--GT-G-G---GGT--GGTGGTATGTGTCCTGGCCTGGG
* *
302150 TAGCGAG-GGGGTGGTGGTA--TG-CCT-GAC----
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
** *
302177 TAGTGAGTGGGGAAGTGGTATGTGTTCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * * * *
302213 TAGTGAG-GAGGTGATGGTATTTGTCCTGTCCTTGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* **
302248 TAGTGAGTGGGG-GGTGGTATGTGTCCTGGCCCGAC
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302283 TATTGAGTGGGATGGTGGTATTTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302319 TAGTTAGTGGGGTGGTGGTATGTGTCTTGTCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* *
302355 TAATGA-TAGGGGTGGTGGTATGTGTCCTGTCCTGGG
1 TAGTGAGT-GGGGTGGTGGTATGTGTCCTGGCCTGGG
* * **
302391 TAGTGAGTGGGG-GGTGGTATGTTTCCTGGCCAGAC
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * * *
302426 TATTGAATGGGGCGGTGGTATTTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302462 TAGTTAGTGGGGTGGTGGTATGTGTCTTGTCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* *
302498 TAATGA-TAGGGGTGGTGGTATGTGTCCTGGCCTAGG
1 TAGTGAGT-GGGGTGGTGGTATGTGTCCTGGCCTGGG
**** **
302534 TAGTGAGCAAAGTGGTGGTATGTGTCCTGGCCTGAC
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* *
302570 TAGTGAGTGGGATGGTGGTATTTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * * *
302606 TAGTAAGTGGGGTGGTGGTATTTGCCCTGACCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * * * * **
302642 TACTCA-TAAGGGTGTTTGTATGTGTTTTGGCCTGGG
1 TAGTGAGT-GGGGTGGTGGTATGTGTCCTGGCCTGGG
302678 TAGTGAGT-GGGT-GTGGTATGTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* *
302712 TAGTGAGTGGGGTGGTGGTATGTGTCCTGTCCTAGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* ** * * *
302748 AAGTGAGCAGAGTGGTGGTATGTGTCCTGTCCT-TG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* **
302783 -AGTG-GGGGGGATGGTGGTATGTGTCCTGGCCTGAC
1 TAGTGAGTGGGG-TGGTGGTATGTGTCCTGGCCTGGG
* * *
302818 TAGTGAGTGGGATGGTTGTATGTGTCCTGACCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302854 TAGTGAGTGGGGTGGTGGTATATGCCCTGACCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302890 TAGTGA-TAAGGGTGTTGGTATGTGTTCTGGCCTGGG
1 TAGTGAGT-GGGGTGGTGGTATGTGTCCTGGCCTGGG
*
302926 TAGTGAGT--GGT-GTAGTATGTGTCCTGGCCTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
* * *
302959 TAGTGAGTGGGGTGGTGGTATGTATCCTGTCTTGGG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
** * * *
302995 TAGTGAGCAGAGTGGTGGTATGTGTCCTGTCCTGTG
1 TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
303031 TAGTGAGTGGGGGGATGGTGGTATGTGTCCTGGCCTGGG
1 TAGTGAGT--GGGG-TGGTGGTATGTGTCCTGGCCTGGG
* * *
303070 TAGGGAGTGGGGTTGTGTTATG
1 TAGTGAGTGGGGTGGTGGTATG
303092 CCTGATGATG
Statistics
Matches: 908, Mismatches: 177, Indels: 93
0.77 0.15 0.08
Matches are distributed among these distances:
27 6 0.01
28 10 0.01
30 2 0.00
31 3 0.00
32 4 0.00
33 32 0.04
34 53 0.06
35 140 0.15
36 580 0.64
37 15 0.02
38 2 0.00
39 29 0.03
40 3 0.00
41 1 0.00
42 1 0.00
43 1 0.00
45 4 0.00
47 22 0.02
ACGTcount: A:0.13, C:0.11, G:0.44, T:0.32
Consensus pattern (36 bp):
TAGTGAGTGGGGTGGTGGTATGTGTCCTGGCCTGGG
Found at i:305570 original size:2 final size:2
Alignment explanation
Indices: 305563--305589 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
305553 CCCTTTCCAT
305563 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
305590 NNNNNNNNNN
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:313783 original size:448 final size:440
Alignment explanation
Indices: 312934--314244 Score: 2151
Period size: 443 Copynumber: 2.9 Consensus size: 440
312924 CAGACCCATC
* * * *
312934 TTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAAATCAAAAGTACACCTAA
1 TTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTATTCAAAAGTACACCTAA
312999 GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTATGTCAAAGTATATTCAGGAGTTGA
66 GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTATGTCAAAGTATATTCAGGAGTTGA
* *
313064 ACAATGAAGTTTTTTTCTAATTTGACCTTGAAATAAAAATTTTAAAGGTCAAGGTCAAAAATTTG
131 ACAATGAAG-TTTTTTCTAATATGACCTTGAAATAAAAATTTT-AAGGTCAAGGTCAAAAATTTT
* **
313129 GGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTGAAAAGTCTGTATGTTAAAG
194 GGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGT-TTAAGTCTGTATGTTAAAG
313194 GAGTCTTGTGTTATGGT-CAGGACAATATTTTTTATGAAAAGCTTGACCTTGAAGAACAAAATAG
258 GAGTCTTGTGTTATGGTCCA-GACAATATTTTTTATGAAAAGCTTGACCTTGAAGAACAAAATAG
* * * *
313258 GTCAAGGTCAAAACTTTTGGTGGCTTGCCCTCCTTCTCAATACCATCTTCCTATGTTCCAAGTTT
322 GTCAAGGTCAAAACTTTTGGTGGCGTGCACTCCTTCTCAATACCATCTACCTATG-TCTAAGTTT
*
313323 GAAGTTTTAATGTCAAAGGGTATTAAAGTTATGACCCAGACAACATTTTATTATTTTTTAT
386 GAAGTCTTAATGTCAAAGGGTATTAAAGTTATGACCCAGACAACATTTTATTA-----T-T
*
313384 TTTTTCTTAA-TTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTATTCAAGAGTACACCTAA
1 TTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTATTCAAAAGTACACCTAA
*
313448 GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAAGTATATTCAGGAGTTGA
66 GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTATGTCAAAGTATATTCAGGAGTTGA
* * * *
313513 ACAATGAAGGTTTTTCTAATATGACCTTGAAATAAAAATTCT-AGGTCAAGGTCAAAATTTTTTG
131 ACAATGAAGTTTTTTCTAATATGACCTTGAAATAAAAATTTTAAGGTCAAGGTCAAAAATTTTGG
*
313577 TAAGGTTTAACTAGGTTATATACCATCTATCTATGATACAAGGTTTAAGTCTGTATGTTAAAGGA
196 TAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAA-GTTTAAGTCTGTATGTTAAAGGA
*
313642 GTCTTGTGTTATGGTCCAGACAATATTTTTTTAATGAAAAACTTGACCTTGAAGAACAAAATAGG
260 GTCTTGTGTTATGGTCCAGACAATA-TTTTTT-ATGAAAAGCTTGACCTTGAAGAACAAAATAGG
313707 TCAAGGTCAAAACTTTTGGTGGCGTGCACTCCTTCTCAATACCATCTACCTATGCTCTAAGTTTG
323 TCAAGGTCAAAACTTTTGGTGGCGTGCACTCCTTCTCAATACCATCTACCTATG-TCTAAGTTTG
*
313772 AAGTCTTAATGTCAAAGGGTATAAAAGTTATGACCCAGACAACATTTTATTATT
387 AAGTCTTAATGTCAAAGGGTATTAAAGTTATGACCCAGACAACATTTTATTATT
*
313826 TTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTATTCAATAGTACACCTAA
1 TTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTATTCAAAAGTACACCTAA
313891 GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTATGTCAAAGTATATTCAGGAGTTGA
66 GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTATGTCAAAGTATATTCAGGAGTTGA
*
313956 ACAATGAAGTTTTTTCTAAAATGACCTTGAAATAAAAATTTTAAAGGTCAAGGTCAAAAATTTTG
131 ACAATGAAGTTTTTTCTAATATGACCTTGAAATAAAAATTTT-AAGGTCAAGGTCAAAAATTTTG
* *
314021 GTAAGGTACAACTAGGTTATATACTATCTATCTATGATACAAGTTTAAAGTCTGTATGTTAAAGG
195 GTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGTTT-AAGTCTGTATGTTAAAGG
* *
314086 ATTCTTGTGTTATGGTCCAGACAATATTTTTTATGAATAGCTTGACCTTGAAGAACAAAATAGGT
259 AGTCTTGTGTTATGGTCCAGACAATATTTTTTATGAAAAGCTTGACCTTGAAGAACAAAATAGGT
* *
314151 CAAGGTCAAAACTTTTGGTGGCGTGCACTCCTTCTCAATATCATCTACCTATGTTTCAAGTTTGA
324 CAAGGTCAAAACTTTTGGTGGCGTGCACTCCTTCTCAATACCATCTACCTATGTCT-AAGTTTGA
*
314216 AGTCTTAATGTCAAAGGGTATTTAAGTTA
388 AGTCTTAATGTCAAAGGGTATTAAAGTTA
314245 CGGCTTGGAC
Statistics
Matches: 811, Mismatches: 41, Indels: 25
0.92 0.05 0.03
Matches are distributed among these distances:
442 13 0.02
443 275 0.34
444 10 0.01
445 101 0.12
446 99 0.12
447 10 0.01
448 171 0.21
449 122 0.15
450 10 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (440 bp):
TTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTATTCAAAAGTACACCTAA
GTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTATGTCAAAGTATATTCAGGAGTTGA
ACAATGAAGTTTTTTCTAATATGACCTTGAAATAAAAATTTTAAGGTCAAGGTCAAAAATTTTGG
TAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGTTTAAGTCTGTATGTTAAAGGAG
TCTTGTGTTATGGTCCAGACAATATTTTTTATGAAAAGCTTGACCTTGAAGAACAAAATAGGTCA
AGGTCAAAACTTTTGGTGGCGTGCACTCCTTCTCAATACCATCTACCTATGTCTAAGTTTGAAGT
CTTAATGTCAAAGGGTATTAAAGTTATGACCCAGACAACATTTTATTATT
Found at i:315528 original size:437 final size:437
Alignment explanation
Indices: 314600--315999 Score: 2149
Period size: 437 Copynumber: 3.3 Consensus size: 437
314590 TCTAGCATTA
* ** * * * * * * ** *
314600 ATAACCTTTCACAAAATGGCTCTCATTAAAGGGCTAAAGATAAAAAAATTTAGAGTCCTTTAATC
1 ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTTTGGTT
* * * *
314665 CCCTAACTTAAGGGGCCAGCCCCTTTTTCTTGGA-ATCAAATGAAAGGACATTTAATTCT----G
66 CCCTAATTTTAGGGGCCAGCCCCTTTTTCTT-GATATCAAATGAAAGGTCATTTAATTCTAAACA
* *
314725 AA--------AACAAGTGTTTA-AACATTCGTTACCGTTCTGGAGATATATGAGAAAGAAGGTTT
130 AATTTTGTTCAACAAGTGTTTAGAA-ATTTGTTACCATTCTGGAGATATATGAGAAAGAAGGTTT
*
314781 AAGGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGATGCATA----T
194 TAGGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGATGCATATTGTT
* *
314842 -----C----GTTTGAACAACTTTTCTTCTGTAATGCATTACAAAATATTTTTCCTTTCTGAGAT
259 AAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTACAAAATATTTTTCCTTTCTGAGAT
314898 ATGGGTGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACATAATACATGACCAAA
324 ATGGGTGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACATAATACATGACCAAA
314963 TTGTTACATTGCTTGGATACATAACTGTGAGATAAACATATTTGCTTCT
389 TTGTTACATTGCTTGGATACATAACTGTGAGATAAACATATTTGCTTCT
*
315012 ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAAACTTTAGAGCCCTTTGGTT
1 ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTTTGGTT
315077 CCCTAATTTTAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCTAAACAA
66 CCCTAATTTTAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCTAAACAA
315142 ATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTTA
131 ATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTTA
*
315207 GGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTGTTAA
196 GGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGATGCATATTGTTAA
315272 GAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTACAAAATATTTTTCCTTTCTGAGATAT
261 GAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTACAAAATATTTTTCCTTTCTGAGATAT
*
315337 GGGTGATAAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACATAATACATGACCAAATT
326 GGGTGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACATAATACATGACCAAATT
*
315402 GTTACATTGCTTGGACACATAACTGTGAGATAAACATATTTGCTTCT
391 GTTACATTGCTTGGATACATAACTGTGAGATAAACATATTTGCTTCT
315449 ATAACATTTCACAAAATATCTCTCAGTAATA-GGCTACAGATTAAAGACTTTAGAGCCCTTTGGT
1 ATAACATTTCACAAAATATCTCTCAGTAA-AGGGCTACAGATTAAAGACTTTAGAGCCCTTTGGT
*
315513 TCCCTAATTTTAGGGGCCAGCCCCTTTTTCTTGGTATCAAATGAAAGGTCATTTAATTCTAAACA
65 TCCCTAATTTTAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCTAAACA
*
315578 AATTTTGTTCAACAAGTGTTTAGAAATTTCTTACCATTCTGGAGATATATGAGAAAGAAGGTTTT
130 AATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTT
* *
315643 AGGGGCCGGTCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGAATGCATATTGTTA
195 AGGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGATGCATATTGTTA
* * * * *
315708 AGAACATTAATTTGAACAACTTTTCTTATGTGTTGCATAACAAAATATTTTTTCTTTGTGAGATA
260 AGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTACAAAATATTTTTCCTTTCTGAGATA
* *
315773 TGGATGATCAAAATTGTT-GACTTTTGGCCCCTAAAAACCCTTAATTA-AGTAATACATGACAAA
325 TGGGTGATCAAAATT-TTGGACTTTTGGCCCCTAAAAACCCTTAATTACA-TAATACATGACCAA
** *
315836 ATCATTACATTGCTGGGATACATAACTGTGAGATAAACATATTTGCTTCT
388 ATTGTTACATTGCTTGGATACATAACTGTGAGATAAACATATTTGCTTCT
315886 ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTTTGGTT
1 ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTTTGGTT
* * * * *
315951 CCCTTATTTGAGGGGTCAGCCCTTTTTTCTTGATATCAAATAAAAGGTC
66 CCCTAATTTTAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTC
316000 TTGTAAATAT
Statistics
Matches: 910, Mismatches: 47, Indels: 37
0.92 0.05 0.04
Matches are distributed among these distances:
411 2 0.00
412 107 0.12
416 2 0.00
424 107 0.12
425 2 0.00
428 1 0.00
433 1 0.00
436 2 0.00
437 683 0.75
438 3 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (437 bp):
ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTTTGGTT
CCCTAATTTTAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCTAAACAA
ATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTTA
GGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGATGCATATTGTTAA
GAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTACAAAATATTTTTCCTTTCTGAGATAT
GGGTGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACATAATACATGACCAAATT
GTTACATTGCTTGGATACATAACTGTGAGATAAACATATTTGCTTCT
Found at i:317249 original size:9 final size:9
Alignment explanation
Indices: 317235--317260 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
317225 GGAAGACCCT
317235 AATAAGAAG
1 AATAAGAAG
317244 AATAAGAAG
1 AATAAGAAG
317253 AATAAGAA
1 AATAAGAA
317261 AGTCGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (9 bp):
AATAAGAAG
Found at i:317919 original size:23 final size:24
Alignment explanation
Indices: 317843--318291 Score: 207
Period size: 24 Copynumber: 18.6 Consensus size: 24
317833 GTGAGTGGCA
317843 AGACTGTTAATAAACCAGACAGAT
1 AGACTGTTAATAAACCAGACAGAT
*
317867 AGACTGTTAATAAACCAGACA-ACA
1 AGACTGTTAATAAACCAGACAGA-T
* *
317891 AAACTGTTAAT-AACCAGTCAGAT
1 AGACTGTTAATAAACCAGACAGAT
* *
317914 AGACTGTTAA-AAGAACAG-CAAGCT
1 AGACTGTTAATAA-ACCAGAC-AGAT
*
317938 AGACTGTTTTATAAAACAAACCAGACAGAT
1 AGACTG---T-T--AATAAACCAGACAGAT
** *
317968 AGACTGTTAAT-AACTGGA-AAACT
1 AGACTGTTAATAAACCAGACAGA-T
** * * *
317991 AGACCATTAACAAACTAGACA-ACA
1 AGACTGTTAATAAACCAGACAGA-T
* * *
318015 ATACTGTTAACAAACCAAACAGCAAT
1 AGACTGTTAATAAACCAGACAG--AT
* * * *
318041 ACAC--TTGAT-AACCAGATAGCT
1 AGACTGTTAATAAACCAGACAGAT
**
318062 AGACTGTTAATAAACTGGACAGCA-
1 AGACTGTTAATAAACCAGACAG-AT
* *
318086 AGGCTGTTAAT-AACCAGAGAGCA-
1 AGACTGTTAATAAACCAGACAG-AT
* * * *
318109 AGACTGTTAACAAACAATACA-ACA
1 AGACTGTTAATAAACCAGACAGA-T
* *
318133 ATACTGTTAACAAACCAGACAGAT
1 AGACTGTTAATAAACCAGACAGAT
318157 AGACTGTTAATAAACCAGACAGCA-
1 AGACTGTTAATAAACCAGACAG-AT
* * * *
318181 GGACTTTTGATAAACCAGACA-ACA
1 AGACTGTTAATAAACCAGACAGA-T
* *
318205 ATACTGTTAATAAACCAGACA-AC
1 AGACTGTTAATAAACCAGACAGAT
* * * *
318228 A-ATTATATTAACAAACCAGACAGCT
1 AGA--CTGTTAATAAACCAGACAGAT
318253 AGACTGTTAATAAACCAGACAGCA-
1 AGACTGTTAATAAACCAGACAG-AT
318277 AGACTGTTAATAAAC
1 AGACTGTTAATAAAC
318292 AATCAACAGA
Statistics
Matches: 322, Mismatches: 68, Indels: 70
0.70 0.15 0.15
Matches are distributed among these distances:
21 4 0.01
22 5 0.02
23 65 0.20
24 217 0.67
25 4 0.01
26 5 0.02
27 3 0.01
28 1 0.00
30 15 0.05
31 3 0.01
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.20
Consensus pattern (24 bp):
AGACTGTTAATAAACCAGACAGAT
Found at i:318165 original size:48 final size:48
Alignment explanation
Indices: 317841--318291 Score: 301
Period size: 48 Copynumber: 9.4 Consensus size: 48
317831 GAGTGAGTGG
*
317841 CAAGACTGTTAATAAACCAGACAGATAGACTGTTAATAAACCAGACAA
1 CAAGACTGTTAACAAACCAGACAGATAGACTGTTAATAAACCAGACAA
* * * *
317889 CAAAACTGTTAA-TAACCAGTCAGATAGACTGTTAA-AAGAACAG-CAA
1 CAAGACTGTTAACAAACCAGACAGATAGACTGTTAATAA-ACCAGACAA
* ** *
317935 GCTAGACTGTTTTATAAAACAAACCAGACAGATAGACTGTTAAT-AACTGGAAAA
1 -CAAGACTG---T-T--AACAAACCAGACAGATAGACTGTTAATAAACCAGACAA
* ** * * * * * *
317989 CTAGACCATTAACAAACTAGACA-ACAATACTGTTAACAAACCAAACAG
1 CAAGACTGTTAACAAACCAGACAGA-TAGACTGTTAATAAACCAGACAA
* ** * * * * ** *
318037 CAATACACTTGA-TAACCAGATAGCTAGACTGTTAATAAACTGGACAG
1 CAAGACTGTTAACAAACCAGACAGATAGACTGTTAATAAACCAGACAA
* * * * * *
318084 CAAGGCTGTTAA-TAACCAGAGAGCA-AGACTGTTAACAAACAATACAA
1 CAAGACTGTTAACAAACCAGACAG-ATAGACTGTTAATAAACCAGACAA
* *
318131 CAATACTGTTAACAAACCAGACAGATAGACTGTTAATAAACCAGACAG
1 CAAGACTGTTAACAAACCAGACAGATAGACTGTTAATAAACCAGACAA
* * * * * *
318179 CAGGACTTTTGATAAACCAGACA-ACAATACTGTTAATAAACCAGACAA
1 CAAGACTGTTAACAAACCAGACAGA-TAGACTGTTAATAAACCAGACAA
* * * *
318227 CAATTA-TATTAACAAACCAGACAGCTAGACTGTTAATAAACCAGACAG
1 CAA-GACTGTTAACAAACCAGACAGATAGACTGTTAATAAACCAGACAA
*
318275 CAAGACTGTTAATAAAC
1 CAAGACTGTTAACAAAC
318292 AATCAACAGA
Statistics
Matches: 304, Mismatches: 78, Indels: 42
0.72 0.18 0.10
Matches are distributed among these distances:
46 6 0.02
47 123 0.40
48 136 0.45
49 2 0.01
50 2 0.01
51 1 0.00
53 10 0.03
54 24 0.08
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (48 bp):
CAAGACTGTTAACAAACCAGACAGATAGACTGTTAATAAACCAGACAA
Found at i:318665 original size:24 final size:24
Alignment explanation
Indices: 318638--319278 Score: 603
Period size: 24 Copynumber: 26.7 Consensus size: 24
318628 AACAATTATA
*
318638 TTAACAAACCAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
*
318662 TTAAT-AACCAGACAGCTAGACTG
1 TTAATAAACCAGACAGATAGACTG
* * *
318685 TTTATAAACCAGACAGCA-GGACTT
1 TTAATAAACCAGACAG-ATAGACTG
318709 TTAAT-AACCAGACAGCA-AGACTG
1 TTAATAAACCAGACAG-ATAGACTG
* *
318732 TTAATAAACTAGACAGATAGACTA
1 TTAATAAACCAGACAGATAGACTG
** *
318756 TTAAT-AACCA-TTA-ATA-CCT-
1 TTAATAAACCAGACAGATAGACTG
* *
318775 TTAATAAACCGTTAACAAACCAGACAACAGTACTG
1 TTAATAAA-C-----CAGA-CAGA---TAG-ACTG
* * **
318810 TTAACAAACCAGACAGCA-ATACCC
1 TTAATAAACCAGACAG-ATAGACTG
*
318834 TTAAT-AACCAGATA-ACTAGACTG
1 TTAATAAACCAGACAGA-TAGACTG
* * *
318857 TTAATAAACCAGACAGCACAAACTT
1 TTAATAAACCAGACAG-ATAGACTG
** *
318882 TTAAT-AACCAGTTAGCTAGACTG
1 TTAATAAACCAGACAGATAGACTG
*
318905 TTAAT-AACCAGACA-ACAGGACTG
1 TTAATAAACCAGACAGATA-GACTG
* *
318928 TTAATAAACCAG-CAGCTAGACGG
1 TTAATAAACCAGACAGATAGACTG
* *
318951 TTAATAAAACAGACAGATACACTG
1 TTAATAAACCAGACAGATAGACTG
* *
318975 TTAATAAAACAGATAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
*
318999 TTAATAAAACAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
* *
319023 TTAATAAAACAGACAGATAGACAG
1 TTAATAAACCAGACAGATAGACTG
319047 TTAATAAACCAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
* * * *
319071 TTAATAAAACAAATAGATAGACAG
1 TTAATAAACCAGACAGATAGACTG
319095 TTAATAAACCAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
*
319119 TTAATAAAACAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
*
319143 TTAATAAAACAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
* *
319167 TTAATAAAACAGACAGATACACTG
1 TTAATAAACCAGACAGATAGACTG
*
319191 TTAATAAAACAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
*
319215 TTAATAAAACAGACAGATAGACTG
1 TTAATAAACCAGACAGATAGACTG
* *
319239 TTAATAAAACAGACAGATACACTG
1 TTAATAAACCAGACAGATAGACTG
*
319263 TTAATAAAACAGACAG
1 TTAATAAACCAGACAG
319279 CTAGGGCTCA
Statistics
Matches: 519, Mismatches: 68, Indels: 60
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.01
20 4 0.01
21 5 0.01
22 2 0.00
23 106 0.20
24 364 0.70
25 10 0.02
26 3 0.01
28 4 0.01
29 5 0.01
32 1 0.00
34 3 0.01
35 7 0.01
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
TTAATAAACCAGACAGATAGACTG
Found at i:318674 original size:23 final size:23
Alignment explanation
Indices: 318644--318765 Score: 140
Period size: 23 Copynumber: 5.2 Consensus size: 23
318634 TATATTAACA
318644 AACCAGACAGATAGACTGTTAAT
1 AACCAGACAGATAGACTGTTAAT
* *
318667 AACCAGACAGCTAGACTGTTTAT
1 AACCAGACAGATAGACTGTTAAT
* *
318690 AAACCAGACAGCA-GGACTTTTAAT
1 -AACCAGACAG-ATAGACTGTTAAT
318714 AACCAGACAGCA-AGACTGTTAAT
1 AACCAGACAG-ATAGACTGTTAAT
* *
318737 AAACTAGACAGATAGACTATTAAT
1 -AACCAGACAGATAGACTGTTAAT
318761 AACCA
1 AACCA
318766 TTAATACCTT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
23 47 0.56
24 37 0.44
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (23 bp):
AACCAGACAGATAGACTGTTAAT
Found at i:330923 original size:161 final size:163
Alignment explanation
Indices: 330677--330976 Score: 426
Period size: 161 Copynumber: 1.8 Consensus size: 163
330667 CTCGTATTAC
* ** * *
330677 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTAGTTCTTCAGAAGAAGATTTTTAACATTT
1 AAGCTTTTATGTAAATATTGGCATTTCTAATGCAGTAGTTCTT-A-AAGAAGATTTTTAAAAATT
* * *
330742 TTCCTACATATTTCTATGTTAAATTTTGAATCCTGCCTGGGGCCCCAGTTTTGGTTCT-GGGGTC
64 TTCCTACATATTTCTATGTTAAACTTTGAACCCTGCCTGGGGCCCCAGTTTTAG-TCTAGGGGTC
330806 ACAATTTTTACAATTTAGAATCTTCACTATTTATAT
128 ACAATTTTTACAATTTAGAATCTTCACTATTTATAT
* * *
330842 AAGCTTTTATGTAAATATTGGCTTTTCTAATGCATTGGTTCTT-AAGAAGA-TTTTAAAAATTTT
1 AAGCTTTTATGTAAATATTGGCATTTCTAATGCAGTAGTTCTTAAAGAAGATTTTTAAAAATTTT
** *
330905 CCTATGTATTTCTATGTTAAACTTTGAACCCTGCCTGGGGCCCCAGTTTTAGTCTAGGGGTCACG
66 CCTACATATTTCTATGTTAAACTTTGAACCCTGCCTGGGGCCCCAGTTTTAGTCTAGGGGTCACA
330970 ATTTTTA
131 ATTTTTA
330977 AAACTTTAAT
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
160 3 0.03
161 73 0.61
162 7 0.06
165 37 0.31
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (163 bp):
AAGCTTTTATGTAAATATTGGCATTTCTAATGCAGTAGTTCTTAAAGAAGATTTTTAAAAATTTT
CCTACATATTTCTATGTTAAACTTTGAACCCTGCCTGGGGCCCCAGTTTTAGTCTAGGGGTCACA
ATTTTTACAATTTAGAATCTTCACTATTTATAT
Found at i:335039 original size:2 final size:2
Alignment explanation
Indices: 335032--335081 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
335022 AGATATTCTA
335032 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
335074 CT CT CT CT
1 CT CT CT CT
335082 GAATGTTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:335712 original size:67 final size:67
Alignment explanation
Indices: 335604--335739 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
335594 ACTACACGTG
*
335604 CAACGTGTGGCCTTGCGTTGTCTTGCTACAGAGTGGTGTGATTTTGATGTCTCTGTATGAAGGGT
1 CAACGTGTGGCCTTGCGTTGTCTTGCTACAGAGTGATGTGATTTTGATGTCTCTGTATGAAGGGT
335669 AT
66 AT
*
335671 CAACGTGTGGCCTTGCGTTGTCTTGCTGCAGAGTGATGTGATTTTGATGTCTCTGTATGAAGGGT
1 CAACGTGTGGCCTTGCGTTGTCTTGCTACAGAGTGATGTGATTTTGATGTCTCTGTATGAAGGGT
335736 AT
66 AT
335738 CA
1 CA
335740 CATGACGCTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (67 bp):
CAACGTGTGGCCTTGCGTTGTCTTGCTACAGAGTGATGTGATTTTGATGTCTCTGTATGAAGGGT
AT
Found at i:338481 original size:15 final size:15
Alignment explanation
Indices: 338461--338531 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
338451 ATTTATATTG
338461 CAATATCATATGAAA
1 CAATATCATATGAAA
*
338476 CAATATCATGTGATAA
1 CAATATCATATGA-AA
338492 -AATAATC-TAT-AACA
1 CAAT-ATCATATGAA-A
* *
338506 CAATATCATATTATA
1 CAATATCATATGAAA
338521 CAATATCATAT
1 CAATATCATAT
338532 CATATTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
13 1 0.02
14 5 0.11
15 35 0.74
16 6 0.13
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.32
Consensus pattern (15 bp):
CAATATCATATGAAA
Found at i:338601 original size:28 final size:30
Alignment explanation
Indices: 338568--338630 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
338558 ATCATGATAT
*
338568 AATATCATAATGTA-CA-A-AAATTTTATAC
1 AATATCATAAAGTATCATATAAATTTT-TAC
338596 AATATCATAAAGTATCATATAAATTTTTAC
1 AATATCATAAAGTATCATATAAATTTTTAC
338626 AATAT
1 AATAT
338631 AATATATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 13 0.42
29 2 0.06
30 9 0.29
31 7 0.23
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (30 bp):
AATATCATAAAGTATCATATAAATTTTTAC
Found at i:338668 original size:20 final size:20
Alignment explanation
Indices: 338645--338698 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
338635 TATATGATAT
*
338645 AATATTGTATCATATAAAAC
1 AATAATGTATCATATAAAAC
* * *
338665 AATAGTGTATCATATCATAC
1 AATAATGTATCATATAAAAC
*
338685 AATAATATATCATA
1 AATAATGTATCATA
338699 GGAATCATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (20 bp):
AATAATGTATCATATAAAAC
Found at i:339257 original size:19 final size:19
Alignment explanation
Indices: 339218--339258 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
339208 GGCACCTGCA
* *
339218 CCAAAAACTTTAACCTGCT
1 CCAAAAACCTTAACCTCCT
*
339237 CCAAAAACCTTAGCCTCCT
1 CCAAAAACCTTAACCTCCT
339256 CCA
1 CCA
339259 GCACATGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.22
Consensus pattern (19 bp):
CCAAAAACCTTAACCTCCT
Found at i:341855 original size:33 final size:33
Alignment explanation
Indices: 341816--341885 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
341806 TTGTGTAGCA
341816 CTTTACCCTGAACCCTTTCGCTTGCTGTAGTTG
1 CTTTACCCTGAACCCTTTCGCTTGCTGTAGTTG
341849 CTTTACCCTGAACCCTTTCGCTTGCTGTAGTTG
1 CTTTACCCTGAACCCTTTCGCTTGCTGTAGTTG
341882 CTTT
1 CTTT
341886 CACGCTGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.11, C:0.30, G:0.17, T:0.41
Consensus pattern (33 bp):
CTTTACCCTGAACCCTTTCGCTTGCTGTAGTTG
Found at i:347352 original size:20 final size:20
Alignment explanation
Indices: 347310--347367 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
347300 ATTTCTGATA
*
347310 TCTGATATCAGGAAATCTATTT
1 TCTGATATCAAG-AAT-TATTT
*
347332 TTTGATATCAAGAATTATTT
1 TCTGATATCAAGAATTATTT
*
347352 TCTGATATCAATAATT
1 TCTGATATCAAGAATT
347368 CGAATTACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 19 0.59
21 3 0.09
22 10 0.31
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
TCTGATATCAAGAATTATTT
Found at i:349021 original size:2 final size:2
Alignment explanation
Indices: 349014--349047 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
349004 ACTATTGCAT
349014 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
349048 AAGCACTAAA
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):
TA
Found at i:350463 original size:11 final size:11
Alignment explanation
Indices: 350449--350490 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
350439 ACTAGAGTGG
350449 ACCCAGAGTAA
1 ACCCAGAGTAA
350460 ACCCAGAGTAA
1 ACCCAGAGTAA
350471 ACCCCA-AGTAA
1 A-CCCAGAGTAA
350482 ACCCAGAGT
1 ACCCAGAGT
350491 GGACACAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.14
11 21 0.72
12 4 0.14
ACGTcount: A:0.43, C:0.31, G:0.17, T:0.10
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:350467 original size:22 final size:22
Alignment explanation
Indices: 350442--350509 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
350432 TGGGTTTACT
350442 AGAGTGGACCCAGAGTAAACCC
1 AGAGTGGACCCAGAGTAAACCC
**
350464 AGAGTAAACCCCA-AGTAAACCC
1 AGAGTGGA-CCCAGAGTAAACCC
*
350486 AGAGTGGACACAGAGAGTAAACCC
1 AGAGTGGAC-C-CAGAGTAAACCC
350510 CCATCAGAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 22 0.59
23 5 0.14
24 9 0.24
ACGTcount: A:0.41, C:0.26, G:0.24, T:0.09
Consensus pattern (22 bp):
AGAGTGGACCCAGAGTAAACCC
Found at i:350687 original size:11 final size:11
Alignment explanation
Indices: 350656--350687 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
350646 GCAATTCTTG
*
350656 AGTAAACCCAA
1 AGTAAACCCCA
350667 AGTAAACCCCA
1 AGTAAACCCCA
350678 AGTAAACCCC
1 AGTAAACCCC
350688 GAGTGGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.34, G:0.09, T:0.09
Consensus pattern (11 bp):
AGTAAACCCCA
Found at i:351149 original size:19 final size:19
Alignment explanation
Indices: 351122--351158 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
351112 GAGGGCACCT
*
351122 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
351141 GCTCTAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
351159 TCCTACAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:351370 original size:177 final size:177
Alignment explanation
Indices: 351074--351457 Score: 410
Period size: 177 Copynumber: 2.2 Consensus size: 177
351064 ATGAAGTTTA
* *
351074 TGAAGTTAGGACCAGTAATAACTGAGATATAATCATTAGAGGGCACCTGCTCCAAAAACTTTAAC
1 TGAAGTTAGGACCAGTAATAACTTAGATATAATCATTAAAGGGCACCTGCTCCAAAAACTTTAAC
* * * *
351139 CAGCTCTAAAAACCTTAACCTCCTACAGCATCTGAAACCTTTACCTTAGATTCAGCATTCAAG-C
66 CAGCTCTAAAAACCTTAACCTCCTACAGCATCTGAAACCATGACCTCAGATTCAGCATCCAAGTC
** * * *
351203 TTGTCGGGTGCATCAGTA-TCATAAGATGCA-CTATCCATGC-AAGTTTGG
131 TT-TCAAGTCCATAAGCAGTC--AAGATGCATC-ATCCATGCAAAGTTTGG
* * *
351251 TGAAGTTAGGACCAGTAGTAACTTAGA-A-ATTGCTATTAAAGGGCACCTGCAT-GAAAAACTTT
1 TGAAGTTAGGACCAGTAATAACTTAGATATAAT-C-ATTAAAGGGCACCTGC-TCCAAAAACTTT
* * * *
351313 AA-CATGCTAC-AGAAACCTTAACCTCCTCCAGCATCTGAAATTCATGGCC-CAGATTCAGCATC
63 AACCA-GCT-CTAAAAACCTTAACCTCCTACAGCATCTGAAA-CCATGACCTCAGATTCAGCATC
*
351375 CAAGTCTTTCAAGTCCATAAGCAGGTCCAGATGCATCATCCATGCAAAGTTTGG
125 CAAGTCTTTCAAGTCCATAAGCA-GTCAAGATGCATCATCCATGCAAAGTTTGG
* *
351429 TGAAGATAGGACAAGTAATAACTTAGATA
1 TGAAGTTAGGACCAGTAATAACTTAGATA
351458 CTGGACTTGC
Statistics
Matches: 173, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
175 2 0.01
176 4 0.02
177 122 0.71
178 42 0.24
179 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (177 bp):
TGAAGTTAGGACCAGTAATAACTTAGATATAATCATTAAAGGGCACCTGCTCCAAAAACTTTAAC
CAGCTCTAAAAACCTTAACCTCCTACAGCATCTGAAACCATGACCTCAGATTCAGCATCCAAGTC
TTTCAAGTCCATAAGCAGTCAAGATGCATCATCCATGCAAAGTTTGG
Found at i:363027 original size:24 final size:24
Alignment explanation
Indices: 362995--363115 Score: 233
Period size: 24 Copynumber: 5.0 Consensus size: 24
362985 NNNNNNNNNN
362995 AGTTATCGGGCAGGGATATACGGT
1 AGTTATCGGGCAGGGATATACGGT
363019 AGTTATCGGGCAGGGATATACGGT
1 AGTTATCGGGCAGGGATATACGGT
363043 AGTTATCGGGCAGGGATATACGGT
1 AGTTATCGGGCAGGGATATACGGT
363067 AGTTATCGGGCAGGGATATACGGT
1 AGTTATCGGGCAGGGATATACGGT
*
363091 AGTTATCGGGCAGGGATATATGGT
1 AGTTATCGGGCAGGGATATACGGT
363115 A
1 A
363116 CATCCTTGTT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 96 1.00
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.26
Consensus pattern (24 bp):
AGTTATCGGGCAGGGATATACGGT
Found at i:366814 original size:169 final size:166
Alignment explanation
Indices: 366150--366906 Score: 1119
Period size: 166 Copynumber: 4.5 Consensus size: 166
366140 CTGGCATCCG
*
366150 ATTGGTACAGAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGC
1 ATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGC
* * * *
366215 ATATGCGATAAATAGCTGCTGAGAAATCTTTGACGGAAATTTGTTTTAAAATTTTGGCTCAAAAA
66 ATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCT-TAAAA
* ** * * *
366280 AAAACAAAGTCATTTTTTAACAGGAAGTTGAGGTCCG
130 TAAACAAAGTCATCATTAAACAGGAAGTTGACGTCCA
* *
366317 ATTGATACAAAAATATATCCCACAATATGGCATGCC-AATACAAATAGTGTGTTAAAATTCCAAG
1 ATTGGTACAAAAATATATCCCACAATATGGCATGCCTAA-ACAAATAGTGTGTTAAAATTTCAAG
* *
366381 CATCTGCGTTAAATAGTTGCTGAGAAATCTTTGATGGAAATTTGTTTGAAAATTTTGGCTTAAAA
65 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTTAAAA
* *
366446 TAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCA
130 TAAACAAAGTCATCATTAAACAGGAAGTTGACGTCCA
* * *
366483 ATTGGTACAAAAATATATCCCACGATATGGCATGCCTATACAAATA-TCGTGTAAAAATTTCAAG
1 ATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGT-GTGTTAAAATTTCAAG
*
366547 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAATATTTTGG-TTATAA
65 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTTA-AA
*
366611 ATAAGCAAAGT-ACTCATTAAACAGGAAGTTGACGTCCA
129 ATAAACAAAGTCA-TCATTAAACAGGAAGTTGACGTCCA
* *
366649 ATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGC
1 ATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGC
*
366714 ATCTGCAATATTAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTTAA
66 ATCTGC--GA-TAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTTAA
366779 AATAAACAAAGT-ACTCATTAAACAGGAAGTTGACGTCCA
128 AATAAACAAAGTCA-TCATTAAACAGGAAGTTGACGTCCA
** * * * *
366818 ATTGGTACAAAAATATATCCCATGATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGC
1 ATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGC
366883 ATCTGCGATAAATAGTTGCTGAGA
66 ATCTGCGATAAATAGTTGCTGAGA
366907 TAAATGCGAC
Statistics
Matches: 537, Mismatches: 43, Indels: 21
0.89 0.07 0.03
Matches are distributed among these distances:
165 4 0.01
166 263 0.49
167 116 0.22
168 1 0.00
169 150 0.28
170 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (166 bp):
ATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGC
ATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTTAAAAT
AAACAAAGTCATCATTAAACAGGAAGTTGACGTCCA
Found at i:366924 original size:335 final size:332
Alignment explanation
Indices: 366109--366906 Score: 1192
Period size: 335 Copynumber: 2.4 Consensus size: 332
366099 GTGAATATGC
* * * * * * * *
366109 AAAATAAGCAAAGTCGACATTTAAC-GGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCAC
1 AAAATAAACAAAGTCGTCATTAAACAGG-AAGTTGACGTCCAATTGGTACAAAAATATATCCCAC
* * * * *
366173 AATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATATGCGATAAATAGCTGCTGAG
65 GATATGGCATGCCTTAACAAATA-TGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* ** *
366238 AAATCTTTGACGGAAATTTGTTTTAAAATTTTGGCTCAAAAAAAAACAAAGTCATTTTTTAACAG
129 AAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTCAAAAAAAAACAAAGTCATCATTAAACAG
* * *
366303 GAAGTTGAGGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCCAATACAAATAGTGTG
194 GAAGTTGACGTCCAATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTG
* *
366368 TTAAAATTCCAAGCATCTGCGTTAAATAGTTGCTGAGAAATCTTTGATGGAAATTTGTTTGAAAA
259 TTAAAATTCCAAGCATCTGCATTAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAA
366433 TTTTGGCTT
324 TTTTGGCTT
*
366442 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCAATTGGTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTAAACAGGAAGTTGACGTCCAATTGGTACAAAAATATATCCCACG
366507 ATATGGCATGCC-TATACAAATATCGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
66 ATATGGCATGCCTTA-ACAAATAT-GTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* * * * *
366571 AAATCTTTGACGGAAATTTGTTTGAATATTTTGG-TTATAAATAAGCAAAGT-ACTCATTAAACA
129 AAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTCAAAAAAAAACAAAGTCA-TCATTAAACA
366634 GGAAGTTGACGTCCAATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGT
193 GGAAGTTGACGTCCAATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGT
*
366699 GTTAAAATTTCAAGCATCTGCAATATTAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTG
258 GTTAAAATTCCAAGCATCTGC---ATTAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTG
366764 AAAATTTTGGCTT
320 AAAATTTTGGCTT
*
366777 AAAATAAACAAAGTAC-TCATTAAACAGGAAGTTGACGTCCAATTGGTACAAAAATATATCCCAT
1 AAAATAAACAAAGT-CGTCATTAAACAGGAAGTTGACGTCCAATTGGTACAAAAATATATCCCAC
*
366841 GATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
65 GATATGGCATGCCTTAACAAATA-TGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
366906 A
129 A
366907 TAAATGCGAC
Statistics
Matches: 425, Mismatches: 30, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
331 1 0.00
332 104 0.24
333 142 0.33
334 2 0.00
335 172 0.40
336 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (332 bp):
AAAATAAACAAAGTCGTCATTAAACAGGAAGTTGACGTCCAATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTTAACAAATATGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
ATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTCAAAAAAAAACAAAGTCATCATTAAACAGGA
AGTTGACGTCCAATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTGTT
AAAATTCCAAGCATCTGCATTAAATAGTTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATT
TTGGCTT
Found at i:368323 original size:13 final size:13
Alignment explanation
Indices: 368305--368330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
368295 AGCTTCAATG
368305 TAGCTCCAGTGTA
1 TAGCTCCAGTGTA
368318 TAGCTCCAGTGTA
1 TAGCTCCAGTGTA
368331 GCCCTTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TAGCTCCAGTGTA
Found at i:371056 original size:15 final size:15
Alignment explanation
Indices: 370990--371123 Score: 76
Period size: 15 Copynumber: 8.9 Consensus size: 15
370980 TATTAATGAT
*
370990 GTACATGTTGATGTT
1 GTACATGTTGATGTA
* *
371005 GTTCATGCTGATGTCA
1 GTACATGTTGATGT-A
* *
371021 -TACATTTTGATGAA
1 GTACATGTTGATGTA
* *
371035 TTTCATGTTGATGTA
1 GTACATGTTGATGTA
* * *
371050 GTACATGTTTATTTC
1 GTACATGTTGATGTA
*
371065 GTACAAGTTGATGTA
1 GTACATGTTGATGTA
* * *
371080 GTAAATGCTAATG-A
1 GTACATGTTGATGTA
*
371094 CATACATGTTGATG-A
1 -GTACATGTTGATGTA
*
371109 CATACATGTTGATGT
1 -GTACATGTTGATGT
371124 TATACATGCA
Statistics
Matches: 88, Mismatches: 27, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
14 2 0.02
15 86 0.98
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (15 bp):
GTACATGTTGATGTA
Found at i:378114 original size:20 final size:20
Alignment explanation
Indices: 378091--378154 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
378081 CGACGTTAAT
378091 CTATATTTCACGTCTGTAAA
1 CTATATTTCACGTCTGTAAA
* * *
378111 CTATAGTTAACG-C-GATAAT
1 CTATATTTCACGTCTG-TAAA
* * *
378130 CTATGTTTCACATCTGTTAA
1 CTATATTTCACGTCTGTAAA
378150 CTATA
1 CTATA
378155 GTTAACACTG
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 17 0.55
21 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
CTATATTTCACGTCTGTAAA
Done.