Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 279 of 318
Found at i:88268013 original size:16 final size:16
Alignment explanation
Indices: 88267976--88268014 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
88267966 AATTTGTGTG
88267976 TTATTTTATTTTTTCT
1 TTATTTTATTTTTTCT
*
88267992 TGATTTTATTTTATT-T
1 TTATTTTATTTT-TTCT
88268008 TTATTTT
1 TTATTTT
88268015 TTTCACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTATTTTATTTTTTCT
Found at i:88272453 original size:16 final size:17
Alignment explanation
Indices: 88272418--88272457 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
88272408 AATTTGTGTG
88272418 TTATTTTAATTTTTTCT
1 TTATTTTAATTTTTTCT
88272435 TTATTTT-ATTTTATT-T
1 TTATTTTAATTTT-TTCT
88272451 TTATTTT
1 TTATTTT
88272458 TTTCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATTTTAATTTTTTCT
Found at i:88284213 original size:25 final size:25
Alignment explanation
Indices: 88284185--88284234 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
88284175 AATGAGAAAA
88284185 ATTTTGTTTGATTTGAACCATGTGC
1 ATTTTGTTTGATTTGAACCATGTGC
88284210 ATTTTGTTTGATTTGAACCATGTGC
1 ATTTTGTTTGATTTGAACCATGTGC
88284235 GGGTTGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (25 bp):
ATTTTGTTTGATTTGAACCATGTGC
Found at i:88284704 original size:24 final size:26
Alignment explanation
Indices: 88284665--88284718 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
88284655 TTTCTAGAAG
*
88284665 ATTTAGCTTTTTATTAGTAT-AATAT
1 ATTTAGCTATTTATTAGTATAAATAT
88284690 ATTTAGC-ATTTATTAGTATAAATAT
1 ATTTAGCTATTTATTAGTATAAATAT
88284715 ATTT
1 ATTT
88284719 GTTATTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (26 bp):
ATTTAGCTATTTATTAGTATAAATAT
Found at i:88286852 original size:13 final size:12
Alignment explanation
Indices: 88286826--88286858 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
88286816 TTAGTGTTTA
88286826 ATTA-TATTAGG
1 ATTATTATTAGG
88286837 ATTATTATTAAGG
1 ATTATTATT-AGG
88286850 ATTATTATT
1 ATTATTATT
88286859 TAGATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 4 0.20
13 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (12 bp):
ATTATTATTAGG
Found at i:88286900 original size:10 final size:10
Alignment explanation
Indices: 88286887--88286924 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
88286877 TTATTACCAT
88286887 TTATCTTTAA
1 TTATCTTTAA
88286897 TTATCTTTAA
1 TTATCTTTAA
*
88286907 TTAT-TTGTAT
1 TTATCTT-TAA
88286917 TTATCTTT
1 TTATCTTT
88286925 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:88294463 original size:19 final size:19
Alignment explanation
Indices: 88294437--88294493 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
88294427 TTAACTTTAA
88294437 TTTA-TTTTAATTTATTAT
1 TTTACTTTTAATTTATTAT
* ** *
88294455 TTTTCTTTTTCTTTTTTAT
1 TTTACTTTTAATTTATTAT
*
88294474 TTTAC-TTTATTTTATTAT
1 TTTACTTTTAATTTATTAT
88294492 TT
1 TT
88294494 ACTATTCTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTACTTTTAATTTATTAT
Found at i:88296017 original size:13 final size:12
Alignment explanation
Indices: 88295991--88296023 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
88295981 TTAATGTTTA
88295991 ATTA-TATTAGG
1 ATTATTATTAGG
88296002 ATTATTATTAAGG
1 ATTATTATT-AGG
88296015 ATTATTATT
1 ATTATTATT
88296024 TAGATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 4 0.20
13 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (12 bp):
ATTATTATTAGG
Found at i:88296065 original size:10 final size:10
Alignment explanation
Indices: 88296051--88296089 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
88296041 TTTATTATCG
88296051 TTTATCTTTA
1 TTTATCTTTA
*
88296061 ATTATCTTTA
1 TTTATCTTTA
88296071 TTTAT-TTGTA
1 TTTATCTT-TA
88296081 TTTATCTTT
1 TTTATCTTT
88296090 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:88297759 original size:24 final size:24
Alignment explanation
Indices: 88297696--88297759 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
88297686 TATTTTTATA
* *
88297696 CTAATAAATGTTAAAAATATTATG
1 CTAATAAATGTTAAATATATTACG
* *
88297720 TTAATAAATGCTAAATATATTACG
1 CTAATAAATGTTAAATATATTACG
*
88297744 CTAATAAATATTAAAT
1 CTAATAAATGTTAAAT
88297760 TTTCTAGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTTAAATATATTACG
Found at i:88301508 original size:41 final size:41
Alignment explanation
Indices: 88301457--88301659 Score: 237
Period size: 41 Copynumber: 5.0 Consensus size: 41
88301447 TTGTAAAATA
* * * *
88301457 CAGAGCAATAGCGGCGTTTTTTGCTAAAACGCCGCTAAAAA-
1 CAGAGCATTAGCGGCG-CTTTCGGTAAAACGCCGCTAAAAAC
* ** *
88301498 CAGAGCAATAGCGGCTTTTTCGGTAAAACGCCTCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAAC
* *
88301539 CAGAGCATTAGCGGTGCTTTCGGTAAAACACCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAAC
* *
88301580 CAGAGCATTAGCTGCGCTTTCGGTAAAGCGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAAC
* * * * *
88301621 CAGAGTATTTGCGACGCTTTTGCTAAAACGCCGCTAAAA
1 CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAA
88301660 GTCATATAAC
Statistics
Matches: 140, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 21 0.15
41 119 0.85
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAAC
Found at i:88301846 original size:14 final size:14
Alignment explanation
Indices: 88301824--88301875 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
88301814 TTAATTATCA
*
88301824 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
88301838 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
88301852 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
*
88301866 TTAAGGTTTA
1 TTATGGTTTA
88301876 GGAGTTAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:88301940 original size:7 final size:7
Alignment explanation
Indices: 88301928--88302027 Score: 62
Period size: 7 Copynumber: 14.0 Consensus size: 7
88301918 TAGATATTAT
88301928 GGTTTAG
1 GGTTTAG
88301935 GGTTTAG
1 GGTTTAG
88301942 GGTTTAG
1 GGTTTAG
88301949 GG-TT-G
1 GGTTTAG
88301954 GAGTTTAAG
1 G-GTTT-AG
* *
88301963 GGGTAAG
1 GGTTTAG
*
88301970 GGTTTAA
1 GGTTTAG
*
88301977 GGTTAAG
1 GGTTTAG
*
88301984 TGTTTAG
1 GGTTTAG
*
88301991 TGTTTATG
1 GGTTTA-G
*
88301999 GG-ATAGG
1 GGTTTA-G
*
88302006 GGTTAAG
1 GGTTTAG
88302013 AGGTTTAG
1 -GGTTTAG
88302021 GGTTTAG
1 GGTTTAG
88302028 ATTAATTAGT
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
5 2 0.03
6 3 0.04
7 53 0.75
8 11 0.15
9 2 0.03
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (7 bp):
GGTTTAG
Found at i:88304558 original size:40 final size:39
Alignment explanation
Indices: 88304514--88304706 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
88304504 GTTCAAAACA
* * ** * *
88304514 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
88304554 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
88304594 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
88304633 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
88304672 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
88304707 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:88304625 original size:39 final size:39
Alignment explanation
Indices: 88304544--88304706 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
88304534 TATGGTAACC
* *
88304544 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
88304584 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
88304623 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
88304662 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
88304701 CGCACA
1 CGCACA
88304707 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:88312530 original size:40 final size:39
Alignment explanation
Indices: 88312486--88312678 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
88312476 GTTCAAAACA
* * ** * *
88312486 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
88312526 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
88312566 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
88312605 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
88312644 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
88312679 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:88312597 original size:39 final size:39
Alignment explanation
Indices: 88312516--88312678 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
88312506 TATGGTAACC
* *
88312516 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
88312556 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
88312595 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
88312634 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
88312673 CGCACA
1 CGCACA
88312679 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:88316713 original size:29 final size:29
Alignment explanation
Indices: 88316667--88316758 Score: 175
Period size: 29 Copynumber: 3.1 Consensus size: 29
88316657 TGAGTCTGGA
88316667 ATTCAGCAATTTTTTAATGTAGTCAATGTT
1 ATTCAG-AATTTTTTAATGTAGTCAATGTT
88316697 ATTCAGAATTTTTTAATGTAGTCAATGTT
1 ATTCAGAATTTTTTAATGTAGTCAATGTT
88316726 ATTCAGAATTTTTTAATGTAGTCAATGTT
1 ATTCAGAATTTTTTAATGTAGTCAATGTT
88316755 ATTC
1 ATTC
88316759 CGGTATAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 56 0.90
30 6 0.10
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (29 bp):
ATTCAGAATTTTTTAATGTAGTCAATGTT
Found at i:88318502 original size:43 final size:43
Alignment explanation
Indices: 88318435--88318539 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
88318425 TAAAAATTTT
* * * *
88318435 ATGACCTTTAGTGACATTTTTGGGAGAAGCGCCGCTAAAGGTA
1 ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTA
*
88318478 ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC
1 ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTA
*
88318521 ATGACCTTTAGCGGAGTTT
1 ATGACCTTTAGCGGCGTTT
88318540 TTTTAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTA
Found at i:88327166 original size:12 final size:13
Alignment explanation
Indices: 88327144--88327180 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
88327134 GCGTGCAAAA
88327144 AAATTAT-TAAAT
1 AAATTATATAAAT
88327156 AAATT-TATAAA-
1 AAATTATATAAAT
88327167 AAATTATATAAAT
1 AAATTATATAAAT
88327180 A
1 A
88327181 TTAAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 15 0.68
13 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTATATAAAT
Found at i:88327755 original size:2 final size:2
Alignment explanation
Indices: 88327748--88327791 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
88327738 ATTTGATAAA
88327748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88327790 AT
1 AT
88327792 CTACAACTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88342396 original size:25 final size:24
Alignment explanation
Indices: 88342368--88342425 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
88342358 TTTTTGGAGT
88342368 TTCCTGTTAAAAGCTCTTTATGAGC
1 TTCCTGTTAAAAGCTC-TTATGAGC
* * *
88342393 TTCCTAATT-TAGGCTCTTATGAGC
1 TTCCT-GTTAAAAGCTCTTATGAGC
88342417 TTCCTGTTA
1 TTCCTGTTA
88342426 TAGCCCGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.07
24 13 0.48
25 10 0.37
26 2 0.07
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.43
Consensus pattern (24 bp):
TTCCTGTTAAAAGCTCTTATGAGC
Found at i:88348930 original size:2 final size:2
Alignment explanation
Indices: 88348923--88348978 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
88348913 TTCATATAAT
88348923 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
88348965 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
88348979 TATATATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:88348983 original size:2 final size:2
Alignment explanation
Indices: 88348978--88349006 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
88348968 ACACACACAC
88348978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88349007 AATTCAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88349695 original size:21 final size:24
Alignment explanation
Indices: 88349670--88349716 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 24
88349660 TGCTTTCTCC
88349670 TTCTTTCC-TTCT-TTT-TTTCTT
1 TTCTTTCCTTTCTGTTTCTTTCTT
88349691 TTCTTTCCTTTCTGTTTCTTTCTT
1 TTCTTTCCTTTCTGTTTCTTTCTT
88349715 TT
1 TT
88349717 TCGTTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 3 0.13
24 8 0.35
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (24 bp):
TTCTTTCCTTTCTGTTTCTTTCTT
Found at i:88349754 original size:24 final size:24
Alignment explanation
Indices: 88349709--88349755 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
88349699 TTTCTGTTTC
*
88349709 TTTCTTTTTCGTTTGTTCTTTCTA
1 TTTCTTTTTCGTTTGTTATTTCTA
*
88349733 TTTCTTTTTC-TTTCTTTATTTCT
1 TTTCTTTTTCGTTT-GTTATTTCT
88349756 TATTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTCTTTTTCGTTTGTTATTTCTA
Found at i:88356465 original size:60 final size:59
Alignment explanation
Indices: 88356384--88356523 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 59
88356374 CAGTGTTAAC
*
88356384 TGGGCCTCAACCCATATCAATATTAATCTGGGCCATAGCTCC-TTAC-AGT-ATCAGAGTATAT
1 TGGGCCT-AGCCCATATCAATATTAATCTGGGCCATAGC-CCATTACGAGTCA--AGA-TATAT
* *
88356445 TGGGCCTAGCCCATATCAATATTAATCTGGGTCGTAGCCCTATTACGAGTCAAGATATAT
1 TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCC-ATTACGAGTCAAGATATAT
*
88356505 TGGGCCTTGCCCATATCAA
1 TGGGCCTAGCCCATATCAA
88356524 CATAGTTGGG
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
59 2 0.03
60 51 0.72
61 14 0.20
62 3 0.04
63 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACGAGTCAAGATATAT
Found at i:88356556 original size:19 final size:20
Alignment explanation
Indices: 88356513--88356568 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
88356503 ATTGGGCCTT
*
88356513 GCCCATATCAACATAGTTGG
1 GCCCATATCAACACAGTTGG
* *
88356533 GCCCATTTCAATACAGTT-G
1 GCCCATATCAACACAGTTGG
* *
88356552 GCCCATAACAAAACAGT
1 GCCCATATCAACACAGT
88356569 CTCATATGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (20 bp):
GCCCATATCAACACAGTTGG
Found at i:88357948 original size:4 final size:4
Alignment explanation
Indices: 88357939--88357970 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
88357929 TACCCAAGAC
88357939 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
88357971 AGAAAGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:88359698 original size:21 final size:21
Alignment explanation
Indices: 88359672--88359760 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
88359662 TGTGGGTGTG
*
88359672 TACACGCCTATGAGGAGGCCA
1 TACACGCCTATGTGGAGGCCA
* *
88359693 TACACG-CTAGTGTGAAGG-AA
1 TACACGCCTA-TGTGGAGGCCA
88359713 CTACACGCCTATGTGGAGGCCA
1 -TACACGCCTATGTGGAGGCCA
* * * *
88359735 TACACGCTTGTGTGAAGGCCC
1 TACACGCCTATGTGGAGGCCA
88359756 TACAC
1 TACAC
88359761 ACCCATGCGG
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
20 4 0.07
21 47 0.85
22 4 0.07
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (21 bp):
TACACGCCTATGTGGAGGCCA
Found at i:88359760 original size:42 final size:42
Alignment explanation
Indices: 88359672--88359752 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
88359662 TGTGGGTGTG
88359672 TACACGCCTATGAGGAGGCCATACACGCTAGTGTGAAGGAAC
1 TACACGCCTATGAGGAGGCCATACACGCTAGTGTGAAGGAAC
* *
88359714 TACACGCCTATGTGGAGGCCATACACGCTTGTGTGAAGG
1 TACACGCCTATGAGGAGGCCATACACGCTAGTGTGAAGG
88359753 CCCTACACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (42 bp):
TACACGCCTATGAGGAGGCCATACACGCTAGTGTGAAGGAAC
Found at i:88359773 original size:42 final size:42
Alignment explanation
Indices: 88359685--88359773 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
88359675 ACGCCTATGA
* * *
88359685 GGAGGCCATACACGCTAGTGTGAAGGAACTACACGCCTATGT
1 GGAGGCCATACACGCTAGTGTGAAGGAACTACACACCCATGC
* **
88359727 GGAGGCCATACACGCTTGTGTGAAGGCCCTACACACCCATGC
1 GGAGGCCATACACGCTAGTGTGAAGGAACTACACACCCATGC
88359769 GGAGG
1 GGAGG
88359774 GGGCACATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.27, G:0.30, T:0.17
Consensus pattern (42 bp):
GGAGGCCATACACGCTAGTGTGAAGGAACTACACACCCATGC
Found at i:88363529 original size:28 final size:27
Alignment explanation
Indices: 88363487--88363595 Score: 128
Period size: 28 Copynumber: 3.9 Consensus size: 27
88363477 TACTTGTATC
* **
88363487 TGGCCCATTAAGCCCAATCTTATTCATA
1 TGGCCCATTAGGCCCAATCACATT-ATA
*
88363515 TGGCCCATTAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCC-AATCACAT-TATA
88363544 TGGCCCATTAGGCCCAATCACATTTATA
1 TGGCCCATTAGGCCCAATCACA-TTATA
* *
88363572 TGGCCCGTTAGGCCCATTCACATT
1 TGGCCCATTAGGCCCAATCACATT
88363596 CATAATCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.03
28 44 0.62
29 24 0.34
30 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (27 bp):
TGGCCCATTAGGCCCAATCACATTATA
Found at i:88364977 original size:16 final size:16
Alignment explanation
Indices: 88364956--88364987 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
88364946 AAGTTCGGGA
88364956 TTTCGAGATTTTTGGG
1 TTTCGAGATTTTTGGG
88364972 TTTCGAGATTTTTGGG
1 TTTCGAGATTTTTGGG
88364988 GCATTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.31, T:0.50
Consensus pattern (16 bp):
TTTCGAGATTTTTGGG
Found at i:88367034 original size:60 final size:59
Alignment explanation
Indices: 88366953--88367092 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 59
88366943 CAGTGTTAAC
*
88366953 TGGGCCTCAACCCATATCAATATTAATCTGGGCCATAGCTCC-TTACCGTA-TC-AGAGTATAT
1 TGGGCCT-AGCCCATATCAATATTAATCTGGGCCATAGC-CCATTA-CG-AGTCAAGA-TATAT
* *
88367014 TGGGCCTAGCCCATATCAATATTAATCTGGGTCGTAGCCCTATTACGAGTCAAGATATAT
1 TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCC-ATTACGAGTCAAGATATAT
*
88367074 TGGGCCTTGCCCATATCAA
1 TGGGCCTAGCCCATATCAA
88367093 CACAGTTGGG
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
59 3 0.04
60 55 0.77
61 13 0.18
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACGAGTCAAGATATAT
Found at i:88367125 original size:19 final size:20
Alignment explanation
Indices: 88367082--88367127 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
88367072 ATTGGGCCTT
88367082 GCCCATATCAACACAGTTGG
1 GCCCATATCAACACAGTTGG
* *
88367102 GCCCATTTCAATACAGTT-G
1 GCCCATATCAACACAGTTGG
88367121 GCCCATA
1 GCCCATA
88367128 ATAAAACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
GCCCATATCAACACAGTTGG
Found at i:88380061 original size:24 final size:24
Alignment explanation
Indices: 88380029--88380076 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
88380019 ATAATAGCAT
88380029 TAGATACTTTCCCTTTACAACTGC
1 TAGATACTTTCCCTTTACAACTGC
88380053 TAGATACTTTCCCTTTACAACTGC
1 TAGATACTTTCCCTTTACAACTGC
88380077 AGCTTAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (24 bp):
TAGATACTTTCCCTTTACAACTGC
Found at i:88389143 original size:25 final size:25
Alignment explanation
Indices: 88389090--88389201 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
88389080 TGAGCGTCCC
* *
88389090 ATTATATGGCTCTTTGTGAGCTTCTTG
1 ATTA-ATGGCTCTCTG-GAGCTTCCTG
88389117 ATTAATGGCTCTCTGGAGCTTCCTG
1 ATTAATGGCTCTCTGGAGCTTCCTG
* ** * *
88389142 A-T-ATGGCTCGCTTAAACTTCCCG
1 ATTAATGGCTCTCTGGAGCTTCCTG
* *
88389165 A-TATATGGCTATCCGGAGCTTCCTG
1 ATTA-ATGGCTCTCTGGAGCTTCCTG
88389190 ATTAATGGCTCT
1 ATTAATGGCTCT
88389202 TCGGAGGTAT
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
23 18 0.27
24 1 0.01
25 32 0.48
26 12 0.18
27 4 0.06
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (25 bp):
ATTAATGGCTCTCTGGAGCTTCCTG
Found at i:88395696 original size:14 final size:15
Alignment explanation
Indices: 88395677--88395717 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
88395667 ACTTATAATT
88395677 AAATTAATTAA-TCA
1 AAATTAATTAATTCA
*
88395691 AAATTAATTAATTTA
1 AAATTAATTAATTCA
88395706 AAATTTAATTAA
1 AAA-TTAATTAA
88395718 CTTACCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 5 0.21
16 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTAATTAATTCA
Found at i:88395772 original size:28 final size:28
Alignment explanation
Indices: 88395737--88395792 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
88395727 ATCAAGATTA
88395737 ATAAAATTGGTGAATTCCAATTGTCATT
1 ATAAAATTGGTGAATTCCAATTGTCATT
*
88395765 ATAAAATTGGTGAATTCTAATTGTCATT
1 ATAAAATTGGTGAATTCCAATTGTCATT
88395793 CACCACTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (28 bp):
ATAAAATTGGTGAATTCCAATTGTCATT
Found at i:88396289 original size:13 final size:14
Alignment explanation
Indices: 88396245--88396289 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
88396235 GTCATTATAA
*
88396245 AAATTAATTAAAAC
1 AAATAAATTAAAAC
88396259 AAATAAATTATGAAAC
1 AAATAAATTA--AAAC
88396275 AAA-AAATTAAAAC
1 AAATAAATTAAAAC
88396288 AA
1 AA
88396290 CAAGAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.21
14 9 0.32
15 6 0.21
16 7 0.25
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (14 bp):
AAATAAATTAAAAC
Found at i:88396297 original size:15 final size:13
Alignment explanation
Indices: 88396250--88396289 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 13
88396240 TATAAAAATT
88396250 AATTAAAACAAATA
1 AATTAAAACAAA-A
88396264 AATTATGAAACAAAA
1 AATTA--AAACAAAA
88396279 AATTAAAACAA
1 AATTAAAACAA
88396290 CAAGAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.25
14 5 0.21
15 6 0.25
16 7 0.29
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (13 bp):
AATTAAAACAAAA
Found at i:88398190 original size:41 final size:41
Alignment explanation
Indices: 88398133--88398216 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
88398123 TACTTCATTT
88398133 GTACCCTCACTGACTTTATACATTTAGATATTTTACTACTG
1 GTACCCTCACTGACTTTATACATTTAGATATTTTACTACTG
88398174 GTACCCTCACTGACTTTATACATTTAGATATTTTACTACTG
1 GTACCCTCACTGACTTTATACATTTAGATATTTTACTACTG
88398215 GT
1 GT
88398217 CCAAAAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (41 bp):
GTACCCTCACTGACTTTATACATTTAGATATTTTACTACTG
Found at i:88401043 original size:25 final size:24
Alignment explanation
Indices: 88401001--88401058 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
88400991 TGTATGTACT
* *
88401001 AACTATTATAATATATAATAATTTC
1 AACTATTATAATACATAAT-ATATC
**
88401026 AACTATTATCCTACATAATATATC
1 AACTATTATAATACATAATATATC
88401050 AAC-ATTATA
1 AACTATTATA
88401059 CCACTTAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 5 0.18
24 7 0.25
25 16 0.57
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (24 bp):
AACTATTATAATACATAATATATC
Found at i:88402397 original size:20 final size:21
Alignment explanation
Indices: 88402359--88402398 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
88402349 TATTTTTTTC
**
88402359 TAAAAATAATTTTGGTTTAAA
1 TAAAAATAATTTTAATTTAAA
88402380 TAAAAAT-ATTTTAATTTAA
1 TAAAAATAATTTTAATTTAA
88402399 TAGTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TAAAAATAATTTTAATTTAAA
Found at i:88403021 original size:2 final size:2
Alignment explanation
Indices: 88403014--88403039 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88403004 CCATATTTTG
88403014 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
88403040 TAGTTGTTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88404240 original size:99 final size:99
Alignment explanation
Indices: 88404127--88404323 Score: 299
Period size: 99 Copynumber: 2.0 Consensus size: 99
88404117 GATTGAAATA
* * * *
88404127 TAACCTTTTGTTATTTGGGTGATAGAATATAATATTATCT-AAAAATATATTCTA-TTTAATTAT
1 TAACATTTTATTATTTGAGTGACAGAATATAATATTATCTAAAAAATATATTCTACTTT-ATTAT
88404190 TTTTATTATAAAATTTATTTTTAAATATTTATAAGT
65 TTTTATTAT-AAATTTATTTTTAAATATTTATAAGT
* *
88404226 TAACATTTTATTATTTGAGTGACAGAATGTAATATTATCTAAAAAATATATTTTACTTTATTATT
1 TAACATTTTATTATTTGAGTGACAGAATATAATATTATCTAAAAAATATATTCTACTTTATTATT
*
88404291 TTTATTATAATTTTATTTTTAAATATTTATAAG
66 TTTATTATAAATTTATTTTTAAATATTTATAAG
88404324 CAAAGAAATT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
99 59 0.66
100 27 0.30
101 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (99 bp):
TAACATTTTATTATTTGAGTGACAGAATATAATATTATCTAAAAAATATATTCTACTTTATTATT
TTTATTATAAATTTATTTTTAAATATTTATAAGT
Found at i:88405145 original size:31 final size:31
Alignment explanation
Indices: 88405110--88405179 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
88405100 TTAACAGTCT
* * *
88405110 AGTGACTTAAATAAAAACTTTCAAATATTTC
1 AGTGACTAAAATAAAAACTTCCAAATAGTTC
*
88405141 AGTGACTAAAATGAAAACTTCCAAATAGTTC
1 AGTGACTAAAATAAAAACTTCCAAATAGTTC
88405172 AGTGACTA
1 AGTGACTA
88405180 TTTTGTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.30
Consensus pattern (31 bp):
AGTGACTAAAATAAAAACTTCCAAATAGTTC
Found at i:88407959 original size:13 final size:13
Alignment explanation
Indices: 88407941--88407967 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88407931 TTCTCTTAAT
88407941 AAGGTTTCCTAAA
1 AAGGTTTCCTAAA
88407954 AAGGTTTCCTAAA
1 AAGGTTTCCTAAA
88407967 A
1 A
88407968 GTACTCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AAGGTTTCCTAAA
Found at i:88414134 original size:65 final size:65
Alignment explanation
Indices: 88414055--88414188 Score: 268
Period size: 65 Copynumber: 2.1 Consensus size: 65
88414045 AAATAAATGT
88414055 ATGATCTGTTTGTCAGCATTACAACATGCCATACTTGTATGATGCATTGCATCGGGGCGGGTTTG
1 ATGATCTGTTTGTCAGCATTACAACATGCCATACTTGTATGATGCATTGCATCGGGGCGGGTTTG
88414120 ATGATCTGTTTGTCAGCATTACAACATGCCATACTTGTATGATGCATTGCATCGGGGCGGGTTTG
1 ATGATCTGTTTGTCAGCATTACAACATGCCATACTTGTATGATGCATTGCATCGGGGCGGGTTTG
88414185 ATGA
1 ATGA
88414189 AGTGAAGGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (65 bp):
ATGATCTGTTTGTCAGCATTACAACATGCCATACTTGTATGATGCATTGCATCGGGGCGGGTTTG
Found at i:88417034 original size:28 final size:28
Alignment explanation
Indices: 88417003--88417065 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
88416993 TCCCATATTA
88417003 ATGGGGTATAGGAAAAGTCTCATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
** * *
88417031 ATGGGGTATAGGAAGGGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
88417059 ATGGGGT
1 ATGGGGT
88417066 TAATAATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCTCATAACTT
Found at i:88422448 original size:28 final size:28
Alignment explanation
Indices: 88422416--88422478 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
88422406 TCACATATTA
88422416 ATGGGGTATAAGAAAAGTCTCATAACTT
1 ATGGGGTATAAGAAAAGTCTCATAACTT
* * ** * *
88422444 ATGGGATATAGGAAGGGTTTTATAACTT
1 ATGGGGTATAAGAAAAGTCTCATAACTT
88422472 ATGGGGT
1 ATGGGGT
88422479 TGACAATGAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAAGAAAAGTCTCATAACTT
Found at i:88424152 original size:35 final size:36
Alignment explanation
Indices: 88424075--88424152 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
88424065 ATATCCAAAC
* *
88424075 AATAACAACAACAAAATAGTAACAAAATAATAGTAA
1 AATAACAACAACAAAATAGTAACAAAACAATAGAAA
* * * *
88424111 AA-AACAATAAGAAAATATTTACAAAACAATA-AAA
1 AATAACAACAACAAAATAGTAACAAAACAATAGAAA
88424145 AATAACAA
1 AATAACAA
88424153 GAAAATCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
34 4 0.11
35 29 0.83
36 2 0.06
ACGTcount: A:0.69, C:0.10, G:0.04, T:0.17
Consensus pattern (36 bp):
AATAACAACAACAAAATAGTAACAAAACAATAGAAA
Found at i:88431077 original size:20 final size:21
Alignment explanation
Indices: 88431052--88431092 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
88431042 ATTTGAAGGC
88431052 TAATG-AATTAAAAGCAAATT
1 TAATGAAATTAAAAGCAAATT
**
88431072 TAATGAAATTCCAAGCAAATT
1 TAATGAAATTAAAAGCAAATT
88431093 AACATAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
TAATGAAATTAAAAGCAAATT
Found at i:88431500 original size:32 final size:32
Alignment explanation
Indices: 88431458--88431563 Score: 79
Period size: 33 Copynumber: 3.2 Consensus size: 32
88431448 TTAGAAGAAG
* *
88431458 ATATACATACAAAAAATAATATAAAATCAATA
1 ATATATATACAAAAAATAATAAAAAATCAATA
* *
88431490 ATATATATACATATAAAAAAATAAAAAATTAA-A
1 ATATATATACA-A-AAAATAATAAAAAATCAATA
* * * **
88431523 GGAAATATTTACATAAAATAATAGGAAATCAATA
1 --ATATATATACAAAAAATAATAAAAAATCAATA
*
88431557 ATGTATA
1 ATATATA
88431564 CTTAGAGTAA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
32 14 0.25
33 16 0.29
34 16 0.29
35 9 0.16
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (32 bp):
ATATATATACAAAAAATAATAAAAAATCAATA
Found at i:88433923 original size:18 final size:18
Alignment explanation
Indices: 88433892--88433935 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
88433882 GCTTAAAAAT
*
88433892 TATTTTTATTATAAT-AA
1 TATTTTTATAATAATGAA
88433909 TATTTCTTATAATAATGAA
1 TATTT-TTATAATAATGAA
88433928 TATTTTTA
1 TATTTTTA
88433936 AAAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 12 0.50
19 7 0.29
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTTTTATAATAATGAA
Found at i:88434447 original size:25 final size:25
Alignment explanation
Indices: 88434419--88434467 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
88434409 AAACAAAAAG
88434419 TATAAATTAT-TTCAAAATTATTAAT
1 TATAAATTATATTCAAAATT-TTAAT
*
88434444 TATAAATTATATTCCAAATTTTAA
1 TATAAATTATATTCAAAATTTTAA
88434468 ATACATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (25 bp):
TATAAATTATATTCAAAATTTTAAT
Found at i:88444895 original size:18 final size:19
Alignment explanation
Indices: 88444850--88444897 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
88444840 TGTTTGTTAA
88444850 ATAAATAAAAATGATTAAAT
1 ATAAAT-AAAATGATTAAAT
* *
88444870 AT-ATTAAAAT-TTTAAAT
1 ATAAATAAAATGATTAAAT
88444887 ATAAATAAAAT
1 ATAAATAAAAT
88444898 ACATACATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 2 0.08
20 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAATAAAATGATTAAAT
Found at i:88447061 original size:129 final size:130
Alignment explanation
Indices: 88446918--88447179 Score: 409
Period size: 129 Copynumber: 2.0 Consensus size: 130
88446908 TATGATACAG
* * *
88446918 TTTTTTGTTTTTGCTCTGCTTTTAGCCAAAATATAGGATATGAAATGTGTGGGGGTATTTTAGAA
1 TTTTTTGTTTTTGCTCTGCTTTTAGCCAAAATATAGGACATGAAATGTGTGGAGGTAATTTAGAA
* * * *
88446983 CTATTACTTACATGCTTTTTATTTAGAATAGGTATAACACGAGTCTGATAGCATTTTGAATAGCA
66 CTACTACTTACATGCTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATAGCA
* *
88447048 TTTTTT-TTTTTGCTCTGCTTTTAGCCAAAATATAGGGCATGAAATGTGTGGAGGTAATTTAGAG
1 TTTTTTGTTTTTGCTCTGCTTTTAGCCAAAATATAGGACATGAAATGTGTGGAGGTAATTTAGAA
* * *
88447112 CTACTACTTACATGTTTTTTATTTAGAACAGGTAGAACACGAATTTGATAGCATTTTGAATTGCA
66 CTACTACTTACATGCTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATAGCA
88447177 TTT
1 TTT
88447180 CCTTGGAACA
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 114 0.95
130 6 0.05
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (130 bp):
TTTTTTGTTTTTGCTCTGCTTTTAGCCAAAATATAGGACATGAAATGTGTGGAGGTAATTTAGAA
CTACTACTTACATGCTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATAGCA
Found at i:88447625 original size:15 final size:15
Alignment explanation
Indices: 88447601--88447631 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
88447591 CCTATATGAT
88447601 TACATATATGTTCAA
1 TACATATATGTTCAA
*
88447616 TACATGTATGTTCAA
1 TACATATATGTTCAA
88447631 T
1 T
88447632 TTTTTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (15 bp):
TACATATATGTTCAA
Found at i:88449631 original size:31 final size:28
Alignment explanation
Indices: 88449577--88449637 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
88449567 GATTCGGTCA
* *
88449577 AATAATTTAGTCTTTTTTTAATACTATT
1 AATAATTTACTCTTTTTTTAATACCATT
88449605 AATAATTTACTCTTTTTTTTTAAATACCATT
1 AATAATTTACTC--TTTTTTT-AATACCATT
88449636 AA
1 AA
88449638 GAGATAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.39
30 7 0.25
31 10 0.36
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (28 bp):
AATAATTTACTCTTTTTTTAATACCATT
Found at i:88449752 original size:10 final size:10
Alignment explanation
Indices: 88449676--88449755 Score: 55
Period size: 10 Copynumber: 8.3 Consensus size: 10
88449666 AATATAATTT
88449676 TTTA-AAAAA
1 TTTATAAAAA
88449685 TATT-TAAAAA
1 T-TTATAAAAA
88449695 -TTATAGAAAA
1 TTTATA-AAAA
*
88449705 --TATAGAAA
1 TTTATAAAAA
88449713 TTTATAAAAAA
1 TTTAT-AAAAA
** *
88449724 TACATAAAAG
1 TTTATAAAAA
88449734 TTTAT-AAAA
1 TTTATAAAAA
88449743 TTTATAAAAA
1 TTTATAAAAA
88449753 TTT
1 TTT
88449756 CTTTGAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.09
9 15 0.27
10 28 0.51
11 7 0.13
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:88450538 original size:15 final size:15
Alignment explanation
Indices: 88450518--88450550 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
88450508 GTAGCTTCTA
88450518 TTATAAATTGTCTCG
1 TTATAAATTGTCTCG
*
88450533 TTATAAATTGTCTTG
1 TTATAAATTGTCTCG
88450548 TTA
1 TTA
88450551 GATTATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (15 bp):
TTATAAATTGTCTCG
Found at i:88454582 original size:15 final size:16
Alignment explanation
Indices: 88454564--88454601 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
88454554 TGTTTTATTT
*
88454564 AATATT-AAATATGAA
1 AATATTAAAAGATGAA
88454579 AATATTAAAAGATGAA
1 AATATTAAAAGATGAA
88454595 AGATATT
1 A-ATATT
88454602 TATATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (16 bp):
AATATTAAAAGATGAA
Found at i:88457761 original size:28 final size:26
Alignment explanation
Indices: 88457730--88457783 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
88457720 TCATCAATTA
88457730 TTCAATTCATTCATTCTCATTTCTCAAT
1 TTCAATT-ATTCATT-TCATTTCTCAAT
* *
88457758 TTCAATTTTTTATTTCATTTCTCAAT
1 TTCAATTATTCATTTCATTTCTCAAT
88457784 CAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
27 5 0.21
28 7 0.29
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (26 bp):
TTCAATTATTCATTTCATTTCTCAAT
Found at i:88458177 original size:24 final size:26
Alignment explanation
Indices: 88458126--88458188 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
88458116 ACATATAACC
**
88458126 TCAATTCAATCACAATTTCTCACATTT
1 TCAATTCAATCA-TTTTTCTCACATTT
88458153 TCAATTCAATCATTTTTC-CAC-TTT
1 TCAATTCAATCATTTTTCTCACATTT
88458177 TCAA-TCAA-CATT
1 TCAATTCAATCATT
88458189 CAATCCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 4 0.12
23 4 0.12
24 7 0.21
25 3 0.09
26 4 0.12
27 12 0.35
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (26 bp):
TCAATTCAATCATTTTTCTCACATTT
Found at i:88458228 original size:18 final size:19
Alignment explanation
Indices: 88458205--88458243 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
88458195 ATATATTCAC
88458205 ACATTTTCA-CAATTCAAT
1 ACATTTTCATCAATTCAAT
88458223 ACATTTTCATTCAATTCAAT
1 ACATTTTCA-TCAATTCAAT
88458243 A
1 A
88458244 TCAATACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTTCATCAATTCAAT
Found at i:88458579 original size:43 final size:43
Alignment explanation
Indices: 88458532--88458617 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
88458522 ATTTTTCCAT
88458532 CCCAATTCATACCTTATTTATATTCAATTTTCAACCAAACTTA
1 CCCAATTCATACCTTATTTATATTCAATTTTCAACCAAACTTA
88458575 CCCAATTCATACCTTATTTATATTCAATTTTCAACCAAACTTA
1 CCCAATTCATACCTTATTTATATTCAATTTTCAACCAAACTTA
88458618 AACTTAACTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.40
Consensus pattern (43 bp):
CCCAATTCATACCTTATTTATATTCAATTTTCAACCAAACTTA
Found at i:88459011 original size:8 final size:8
Alignment explanation
Indices: 88458994--88459050 Score: 51
Period size: 8 Copynumber: 6.4 Consensus size: 8
88458984 CTTTTGTTAT
88458994 ATATATATA
1 ATATA-ATA
88459003 ATATAATA
1 ATATAATA
88459011 ATATAATATA
1 ATAT-A-ATA
*
88459021 ATGTAAAATTA
1 A--TATAA-TA
88459032 ATATAATA
1 ATATAATA
88459040 ATATAATA
1 ATATAATA
88459048 ATA
1 ATA
88459051 AAAATCTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 20 0.49
9 10 0.24
10 5 0.12
11 4 0.10
12 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:88459035 original size:16 final size:18
Alignment explanation
Indices: 88458992--88459039 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
88458982 TTCTTTTGTT
88458992 ATATATATATAATATAATA
1 ATATA-ATATAATATAATA
*
88459011 ATATAATATAATGTAA-A
1 ATATAATATAATATAATA
88459028 AT-TAATATAATA
1 ATATAATATAATA
88459040 ATATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 10 0.37
19 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATAATATAATATAATA
Found at i:88463511 original size:43 final size:43
Alignment explanation
Indices: 88463450--88463603 Score: 145
Period size: 43 Copynumber: 3.6 Consensus size: 43
88463440 GGTTATCGAG
* * * * * *
88463450 TTGTGATTACATGTAAGACCATGTTTGGGATATTGCCATTGTA
1 TTGTGATTACGTGTAAGACCATATCTGGGACATTGACATCGTA
88463493 TTGTGATTACGTGTAAGACCATATCTGGGACATTGACATCGTA
1 TTGTGATTACGTGTAAGACCATATCTGGGACATTGACATCGTA
* * * *
88463536 TAT-TGATT-CGTGTAAGATCC-TGTCTGAGACAGTGGCATCG-A
1 T-TGTGATTACGTGTAAGA-CCATATCTGGGACATTGACATCGTA
* *
88463577 TATGTGATAACATGTAAGACCATATCT
1 T-TGTGATTACGTGTAAGACCATATCT
88463604 AGGATATGGC
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
41 4 0.04
42 31 0.33
43 57 0.61
44 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
TTGTGATTACGTGTAAGACCATATCTGGGACATTGACATCGTA
Found at i:88463575 original size:42 final size:43
Alignment explanation
Indices: 88463494--88463603 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
88463484 GCCATTGTAT
* *
88463494 TGTGATTACGTGTAAGACCATATCTGGGACATTGACATCGTATA
1 TGTGATTACGTGTAAGACCATATCTGAGACAGTGACATCG-ATA
* *
88463538 T-TGATT-CGTGTAAGATCC-TGTCTGAGACAGTGGCATCGATA
1 TGTGATTACGTGTAAGA-CCATATCTGAGACAGTGACATCGATA
* *
88463579 TGTGATAACATGTAAGACCATATCT
1 TGTGATTACGTGTAAGACCATATCT
88463604 AGGATATGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
41 4 0.07
42 31 0.56
43 19 0.35
44 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCATATCTGAGACAGTGACATCGATA
Found at i:88466724 original size:41 final size:37
Alignment explanation
Indices: 88466626--88466727 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 37
88466616 CGAAGCAAAT
*
88466626 AATTGACACCCAGTGTCTCATCGGTCAAGCCAAAGTA
1 AATTGACACCCAGTGTCTCATCGATCAAGCCAAAGTA
* ** * * * *
88466663 AATTGATACCCAGTACCTCATTGAATCTATCCGAAGTA
1 AATTGACACCCAGTGTCTCATCG-ATCAAGCCAAAGTA
88466701 ATATAGTGACACCCAGTGTCTCATCGA
1 A-AT--TGACACCCAGTGTCTCATCGA
88466728 CTCGAGGTCG
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
37 19 0.39
38 11 0.22
39 2 0.04
40 1 0.02
41 16 0.33
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (37 bp):
AATTGACACCCAGTGTCTCATCGATCAAGCCAAAGTA
Found at i:88466931 original size:18 final size:19
Alignment explanation
Indices: 88466908--88466946 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
88466898 ATATATTCAC
88466908 ACATTTTCA-CAATTCAAT
1 ACATTTTCATCAATTCAAT
88466926 ACATTTTCATTCAATTCAAT
1 ACATTTTCA-TCAATTCAAT
88466946 A
1 A
88466947 TCAATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTTCATCAATTCAAT
Found at i:88467698 original size:5 final size:5
Alignment explanation
Indices: 88467676--88467764 Score: 74
Period size: 5 Copynumber: 17.2 Consensus size: 5
88467666 TTCTTTTGTT
*
88467676 ATATA TATATA TATATA ATATA ACATA ATAT- -TATA ATAATA ATATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
* * * *
88467722 ATATA ATGTA ACATTA ATATA ATAATA AAATA ATATA TTATA A
1 ATATA ATATA ATA-TA ATATA AT-ATA ATATA ATATA ATATA A
88467765 AAAATCTTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
3 3 0.04
5 41 0.60
6 24 0.35
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:88467717 original size:24 final size:27
Alignment explanation
Indices: 88467676--88467763 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 27
88467666 TTCTTTTGTT
88467676 ATATATATATATATATAATATAACATA
1 ATATATATATATATATAATATAACATA
*
88467703 ATAT-TATA-ATA-ATAATATAATATA
1 ATATATATATATATATAATATAACATA
* * *
88467727 ATGTA-ACAT-TAATATAATAATAAAATA
1 ATATATATATAT-ATATAAT-ATAACATA
88467754 ATATAT-TATA
1 ATATATATATA
88467764 AAAAATCTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
24 18 0.38
25 4 0.08
26 9 0.19
27 17 0.35
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (27 bp):
ATATATATATATATATAATATAACATA
Found at i:88467721 original size:29 final size:30
Alignment explanation
Indices: 88467674--88467753 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
88467664 GTTTCTTTTG
*
88467674 TTATATATATATATATATAATATAACATAATA
1 TTATATATA-ATA-ATATAATATAACATAACA
**
88467706 TTATA-ATAATAATATAATATAATGTAACA
1 TTATATATAATAATATAATATAACATAACA
*
88467735 TTA-ATATAATAATAAAATA
1 TTATATATAATAATATAATA
88467754 ATATATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 31 0.72
30 3 0.07
31 3 0.07
32 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
TTATATATAATAATATAATATAACATAACA
Found at i:88467726 original size:16 final size:16
Alignment explanation
Indices: 88467688--88467758 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
88467678 ATATATATAT
*
88467688 ATATAATATAA-CATA
1 ATATAATATAATAATA
88467703 ATAT--TATAATAATA
1 ATATAATATAATAATA
*
88467717 ATATAATATAAT-GTA
1 ATATAATATAATAATA
*
88467732 ACATTAATATAATAATA
1 ATA-TAATATAATAATA
*
88467749 AAATAATATA
1 ATATAATATA
88467759 TTATAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.11
14 7 0.15
15 8 0.17
16 22 0.48
17 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (16 bp):
ATATAATATAATAATA
Found at i:88467767 original size:16 final size:16
Alignment explanation
Indices: 88467688--88467767 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
88467678 ATATATATAT
88467688 ATATAATATAACATAATA
1 ATATAATATAA-A-AATA
* *
88467706 TTATAATA-ATAATATA
1 ATATAATATA-AAAATA
* * *
88467722 ATATAATGTAACATTA
1 ATATAATATAAAAATA
88467738 ATATAATA-ATAAAATA
1 ATATAATATA-AAAATA
*
88467754 ATATATTATAAAAA
1 ATATAATATAAAAA
88467768 ATCTTAACTA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
15 1 0.02
16 34 0.72
17 4 0.09
18 8 0.17
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (16 bp):
ATATAATATAAAAATA
Found at i:88475090 original size:22 final size:22
Alignment explanation
Indices: 88475065--88475121 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
88475055 TTCTAAGCGG
88475065 TATCGATACCATTTATGAGAAT
1 TATCGATACCATTTATGAGAAT
* **
88475087 TATCTATACCAACTATGAGAAT
1 TATCGATACCATTTATGAGAAT
*
88475109 TATCGATATCATT
1 TATCGATACCATT
88475122 GAATGAGTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
TATCGATACCATTTATGAGAAT
Found at i:88480130 original size:25 final size:25
Alignment explanation
Indices: 88480102--88480168 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
88480092 GCAATACTTT
88480102 TGAAAAGTGCTTTTGAGAAGTGC-TG
1 TGAAAAGTGCTTTTGAG-AGTGCTTG
* *
88480127 TGAAAAAATGCTTTTGAGAGTGCTTT
1 TG-AAAAGTGCTTTTGAGAGTGCTTG
*
88480153 TGAGAAGTGCTTTTGA
1 TGAAAAGTGCTTTTGA
88480169 AAAATTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.36
Consensus pattern (25 bp):
TGAAAAGTGCTTTTGAGAGTGCTTG
Found at i:88480152 original size:12 final size:13
Alignment explanation
Indices: 88480098--88480168 Score: 83
Period size: 13 Copynumber: 5.5 Consensus size: 13
88480088 TTTGGCAATA
*
88480098 CTTTTGAAAAGTG
1 CTTTTGAGAAGTG
88480111 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
* * *
88480124 C-TGTGAAAAAATG
1 CTTTTG-AGAAGTG
88480137 CTTTTGAG-AGTG
1 CTTTTGAGAAGTG
88480149 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
88480162 CTTTTGA
1 CTTTTGA
88480169 AAAATTTAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
12 14 0.29
13 31 0.65
14 3 0.06
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:88482450 original size:72 final size:72
Alignment explanation
Indices: 88482186--88482420 Score: 375
Period size: 72 Copynumber: 3.3 Consensus size: 72
88482176 AAAATCATAT
**
88482186 ATAAACAACTATTGATAAAACTA-ATTTA-GTATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
*
88482249 GACCAAAC
65 AACCAAAC
* *
88482257 ATAAACAACTATTAATAAAAGTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
88482322 ACCAAAC
66 ACCAAAC
* *
88482329 AAAAACAACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
88482394 ACCAAAC
66 ACCAAAC
*
88482401 ATAAATAACTATTGATAAAA
1 ATAAACAACTATTGATAAAA
88482421 TTAGTTTAGC
Statistics
Matches: 150, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
71 24 0.16
72 126 0.84
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:88482874 original size:18 final size:18
Alignment explanation
Indices: 88482853--88482900 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
88482843 TCCATCAATT
88482853 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
88482871 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
88482889 TGAACATCATTT
1 TGAACATCATTT
88482901 CTCACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:88491160 original size:22 final size:22
Alignment explanation
Indices: 88491135--88491183 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
88491125 TAAAAATCAC
*
88491135 AATTTCATATAATGACAACTTA
1 AATTTCAAATAATGACAACTTA
*
88491157 AA-TTCAAATATTGACAACTTA
1 AATTTCAAATAATGACAACTTA
88491178 AATTTC
1 AATTTC
88491184 TTAAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (22 bp):
AATTTCAAATAATGACAACTTA
Found at i:88492038 original size:35 final size:35
Alignment explanation
Indices: 88491980--88492074 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
88491970 ATAAATTTAG
* **
88491980 TATAAATACAATTTAATTTATATTTT-ATTATTTGAT
1 TATAAATATAATTTAA-AAATATTTTGA-TATTTGAT
* *
88492016 T-TAAATATAATTTGTAAAATATTTTGATATTTTAT
1 TATAAATATAATTT-AAAAATATTTTGATATTTGAT
*
88492051 TATGAATATAATTTAAAAATATTT
1 TATAAATATAATTTAAAAATATTT
88492075 AAATTTTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
35 35 0.71
36 14 0.29
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (35 bp):
TATAAATATAATTTAAAAATATTTTGATATTTGAT
Found at i:88492295 original size:21 final size:21
Alignment explanation
Indices: 88492271--88492320 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
88492261 CATTGTTTCT
* *
88492271 AATCTCACCGCTATAGTATCC
1 AATCTCACCGCTACAGTAACC
*
88492292 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
88492313 AATCTCAC
1 AATCTCAC
88492321 TGCCACCGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:88498154 original size:17 final size:18
Alignment explanation
Indices: 88498134--88498207 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
88498124 TTTTAATAAC
88498134 ATTTAAATTTAT-AATTT
1 ATTTAAATTTATAAATTT
* *
88498151 ATTTTATTTTATAAATTT
1 ATTTAAATTTATAAATTT
* *
88498169 GTTTAAATATTTTAAA-TT
1 ATTTAAAT-TTATAAATTT
*
88498187 ATTAACTAATTTATAAATTT
1 ATTTA--AATTTATAAATTT
88498207 A
1 A
88498208 GCTATTCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.23
18 15 0.35
19 12 0.28
20 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
ATTTAAATTTATAAATTT
Found at i:88498481 original size:2 final size:2
Alignment explanation
Indices: 88498474--88498513 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
88498464 CCTTACTTAC
88498474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88498514 AATGGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88499005 original size:20 final size:21
Alignment explanation
Indices: 88498980--88499030 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
88498970 ATTAATTATT
88498980 TATAAAATT-TAATTTAAATA
1 TATAAAATTATAATTTAAATA
*
88499000 TAT-AAATTATATTTTAAATA
1 TATAAAATTATAATTTAAATA
88499020 T-TAAAA-TATAA
1 TATAAAATTATAA
88499031 CCGTTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAAATTATAATTTAAATA
Found at i:88500481 original size:22 final size:22
Alignment explanation
Indices: 88500450--88500499 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
88500440 ATATCCAAAC
* *
88500450 AATAACAACAAAATGATAGTAA
1 AATAATAACAAAATGATAGCAA
*
88500472 TATAATAACAAAATGATAGCAA
1 AATAATAACAAAATGATAGCAA
88500494 AATAAT
1 AATAAT
88500500 GACAGTAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (22 bp):
AATAATAACAAAATGATAGCAA
Found at i:88507362 original size:21 final size:21
Alignment explanation
Indices: 88507338--88507395 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
88507328 AGTGCCTAAA
88507338 ACGACACACGAGGTG-TCTGAT
1 ACGACACACGAGGTGCT-TGAT
88507359 ACGACACACGAGGTGCTTGAT
1 ACGACACACGAGGTGCTTGAT
*
88507380 ACGACACATGAGGTGC
1 ACGACACACGAGGTGC
88507396 CTAAAATACA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.17
Consensus pattern (21 bp):
ACGACACACGAGGTGCTTGAT
Found at i:88507624 original size:18 final size:19
Alignment explanation
Indices: 88507585--88507626 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
88507575 CCCATTTTCA
*
88507585 CAATTCATACAATTTCATT
1 CAATTCATACAATATCATT
88507604 CAATTCA-ACAATAT-ATGT
1 CAATTCATACAATATCAT-T
88507622 CAATT
1 CAATT
88507627 ATTCACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 7 0.33
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (19 bp):
CAATTCATACAATATCATT
Found at i:88507814 original size:15 final size:15
Alignment explanation
Indices: 88507789--88507846 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
88507779 TCATGTATAT
88507789 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
88507805 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
88507820 AATAATTTCAATCAA
1 TATAAATTCAATCAA
88507835 TATAAATTCAAT
1 TATAAATTCAAT
88507847 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:88509129 original size:5 final size:5
Alignment explanation
Indices: 88509116--88509147 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
88509106 TTCTTTAGTT
88509116 TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA T
88509148 TAAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:88509186 original size:8 final size:8
Alignment explanation
Indices: 88509173--88509205 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
88509163 CTTTATTATA
88509173 AATAATAT
1 AATAATAT
88509181 AATAATAT
1 AATAATAT
88509189 AATAATAT
1 AATAATAT
88509197 AATAATAT
1 AATAATAT
88509205 A
1 A
88509206 CTAAACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAATAT
Found at i:88511644 original size:17 final size:18
Alignment explanation
Indices: 88511604--88511673 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 18
88511594 AAATTATGAT
88511604 AATTATACATTTAAAAAC
1 AATTATACATTTAAAAAC
*
88511622 AATTATA-ATTT-AATAC
1 AATTATACATTTAAAAAC
*
88511638 AACTTATTACCCCTTTAAAAAC
1 AA-TTA-TA--CATTTAAAAAC
*
88511660 AATTAGA-ATTTAAA
1 AATTATACATTTAAA
88511674 TTATAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
16 6 0.15
17 13 0.32
18 9 0.22
20 1 0.02
21 6 0.15
22 6 0.15
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (18 bp):
AATTATACATTTAAAAAC
Found at i:88512004 original size:23 final size:24
Alignment explanation
Indices: 88511959--88512005 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
88511949 GAATAGGTTA
*
88511959 AAAATGTTTTTATTATTATTATTT
1 AAAATGTTTTTATTATTAATATTT
88511983 AAAAT-TTTTATATTA-TAATATTT
1 AAAATGTTTT-TATTATTAATATTT
88512006 GAATTGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AAAATGTTTTTATTATTAATATTT
Found at i:88516569 original size:51 final size:52
Alignment explanation
Indices: 88516493--88516602 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 52
88516483 TACTTCATAC
* *
88516493 TTCATCCGGAATTATTACCTTGTTGCTCTAACTTCAATAAGAGCTTAAT-AT
1 TTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAGCTTAATAAT
* * * *
88516544 TTCATCCGGAATAATTACTTTGTTGCTCTAGCTTTAACAAGAGCTTCATAAT
1 TTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAGCTTAATAAT
88516596 TT-ATCCG
1 TTCATCCG
88516603 CATAACTTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 48 0.92
52 4 0.08
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (52 bp):
TTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAGCTTAATAAT
Found at i:88518285 original size:29 final size:29
Alignment explanation
Indices: 88518243--88518302 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
88518233 GCTTGGCCCA
88518243 TAATTATTATTTATTAAAATTTCTAAACT
1 TAATTATTATTTATTAAAATTTCTAAACT
88518272 TAATTATTATTTATTAAAATTTCTAAACT
1 TAATTATTATTTATTAAAATTTCTAAACT
88518301 TA
1 TA
88518303 CTCATTGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATTATTATTTATTAAAATTTCTAAACT
Found at i:88520703 original size:15 final size:15
Alignment explanation
Indices: 88520673--88520701 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88520663 ACTAATAGTA
88520673 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
88520688 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
88520702 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:88524854 original size:88 final size:88
Alignment explanation
Indices: 88524753--88525142 Score: 420
Period size: 88 Copynumber: 4.5 Consensus size: 88
88524743 ATAGGGTGGC
* * * * * *
88524753 CTATCATTTTTAGCCTGTTTCCCTACTACTTAAGGGGTTAAGGCTCACCGTCTTTGATCTGCTCC
1 CTATAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCC
*
88524818 ACTACTGTTTAAGGAGATAAGAT
66 ACTACTATTTAAGGAGATAAGAT
*
88524841 CTATAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCC
1 CTATAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCC
* *
88524906 ACTACTATTTAGGGAGATAAGTT
66 ACTACTATTTAAGGAGATAAGAT
* * * * * *
88524929 TTATAATTTCCT-GCTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGCTGTCTTTGATCTACTC
1 CTATAATTT-CTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTC
*
88524993 CACTACTATTTAAAGAGAT-A-A-
65 CACTACTATTTAAGGAGATAAGAT
* * * ** **
88525014 -TATTATTTCCATCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCGATCTGCTCC
1 CTATAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCC
* *
88525078 ACTACTGTTT-AGG-G--GAGAT
66 ACTACTATTTAAGGAGATAAGAT
* * * * * *
88525097 CTGTATTTTCCAACCTATTACCCTACCGCTTAGGGGGTTAAGGCTC
1 CTATAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
88525143 CACTACTGTA
Statistics
Matches: 261, Mismatches: 35, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.00
82 2 0.01
83 3 0.01
84 101 0.39
87 1 0.00
88 152 0.58
89 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (88 bp):
CTATAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCC
ACTACTATTTAAGGAGATAAGAT
Found at i:88525078 original size:172 final size:176
Alignment explanation
Indices: 88524768--88525096 Score: 468
Period size: 172 Copynumber: 1.9 Consensus size: 176
88524758 ATTTTTAGCC
* * * *
88524768 TGTTTCCCTACTACTTAAGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGTTTAAGGA
1 TGTTACCCTACTACTTAAGGGGTTAAGGCTCACCGTCTTTGATCTACTCCACTACTATTTAAAGA
** *
88524833 GATAAGATCTATAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGA
66 GATAAGA-CTATAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCGA
88524898 TCTGCTCCACTACTATTTA-GGGAGATAAGTTTTATAATTTCCTGCT
130 TCTGCTCCACTACTATTTAGGGGAGATAAGTTTTATAATTTCCTGCT
* * * *
88524944 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGCTGTCTTTGATCTACTCCACTACTATTTAAAGA
1 TGTTACCCTACTACTTAAGGGGTTAAGGCTCACCGTCTTTGATCTACTCCACTACTATTTAAAGA
* * ** *
88525009 GAT-A-A-TATTATTTCCATCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCGAT
66 GATAAGACTATAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCGAT
*
88525071 CTGCTCCACTACTGTTTAGGGGAGAT
131 CTGCTCCACTACTATTTAGGGGAGAT
88525097 CTGTATTTTC
Statistics
Matches: 135, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
172 66 0.49
173 7 0.05
174 1 0.01
175 1 0.01
176 60 0.44
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (176 bp):
TGTTACCCTACTACTTAAGGGGTTAAGGCTCACCGTCTTTGATCTACTCCACTACTATTTAAAGA
GATAAGACTATAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCGAT
CTGCTCCACTACTATTTAGGGGAGATAAGTTTTATAATTTCCTGCT
Found at i:88531605 original size:25 final size:24
Alignment explanation
Indices: 88531557--88531605 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
88531547 GGCTTTAGGG
*
88531557 TTATTTAGGGCTTGGATTTAAGTT
1 TTATTTAGGGCTTAGATTTAAGTT
* *
88531581 TTATTTTGGGCTTTAGATTTGAGTT
1 TTATTTAGGGC-TTAGATTTAAGTT
88531606 AAAAATAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.53
Consensus pattern (24 bp):
TTATTTAGGGCTTAGATTTAAGTT
Found at i:88531746 original size:13 final size:13
Alignment explanation
Indices: 88531728--88531765 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
88531718 AATTATAATC
88531728 TATAAAA-AATTAT
1 TATAAAATAA-TAT
88531741 TATAAAATAATAT
1 TATAAAATAATAT
*
88531754 TATAAACTAATA
1 TATAAAATAATA
88531766 AAATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAAAATAATAT
Found at i:88531940 original size:23 final size:23
Alignment explanation
Indices: 88531912--88531955 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
88531902 TTAAGGATTA
88531912 TTTTGGT-ACTATAATTTAAATTT
1 TTTTGGTAACTA-AATTTAAATTT
*
88531935 TTTTGGTAACTAATTTTAAAT
1 TTTTGGTAACTAAATTTAAAT
88531956 AGTATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (23 bp):
TTTTGGTAACTAAATTTAAATTT
Found at i:88532790 original size:19 final size:19
Alignment explanation
Indices: 88532714--88532790 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
88532704 TTAGTAAATA
*
88532714 ATTTAAAA-TTAAAAAATT
1 ATTTAAAATTTAAAAATTT
* *
88532732 ATAATAATAATTTAAAAAATTA
1 AT-TTAA-AATTT-AAAAATTT
* *
88532754 ATTCTAAAAATT-ATAATTT
1 ATT-TAAAATTTAAAAATTT
88532773 ATTTAAAATTTAAAAATT
1 ATTTAAAATTTAAAAATT
88532791 AAAATATTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
18 9 0.20
19 16 0.36
20 2 0.05
21 6 0.14
22 11 0.25
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAAATTTAAAAATTT
Found at i:88532847 original size:2 final size:2
Alignment explanation
Indices: 88532842--88532874 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
88532832 TTCTCTCAAA
88532842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88532875 ACAAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88534942 original size:17 final size:18
Alignment explanation
Indices: 88534898--88534944 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
88534888 TTTGAAATAA
88534898 AATAAAAATTATACATTT
1 AATAAAAATTATACATTT
88534916 AA-AAATAATTATA-ATTT
1 AATAAA-AATTATACATTT
*
88534933 AATAGAAATTAT
1 AATAAAAATTAT
88534945 GATAGTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AATAAAAATTATACATTT
Found at i:88541325 original size:23 final size:21
Alignment explanation
Indices: 88541273--88541368 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
88541263 CCTGATCAGT
** * *
88541273 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
88541294 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
88541315 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
88541336 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
88541357 AAATACGACACA
1 --ATACGACACA
88541369 TAAAGTGTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:88541781 original size:15 final size:15
Alignment explanation
Indices: 88541756--88541813 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
88541746 TCATATATAT
88541756 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
88541772 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
88541787 AATAATTTCAATCAA
1 TATAAATTCAATCAA
88541802 TATAAATTCAAT
1 TATAAATTCAAT
88541814 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:88544081 original size:62 final size:62
Alignment explanation
Indices: 88544004--88544142 Score: 251
Period size: 62 Copynumber: 2.2 Consensus size: 62
88543994 TAAAACTTGT
* * *
88544004 AACTTTGTAATATAAATTTTGTTATATACATTAAATACATTACAACATTAAAAATTGGAATA
1 AACTTTGTAATATAAATTTTGTTATATAAATTAAAAACATTACAACATTAAAAATTGGAACA
88544066 AACTTTGTAATATAAATTTTGTTATATAAATTAAAAACATTACAACATTAAAAATTGGAACA
1 AACTTTGTAATATAAATTTTGTTATATAAATTAAAAACATTACAACATTAAAAATTGGAACA
88544128 AACTTTGTAATATAA
1 AACTTTGTAATATAA
88544143 TTTAGGTACA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.37
Consensus pattern (62 bp):
AACTTTGTAATATAAATTTTGTTATATAAATTAAAAACATTACAACATTAAAAATTGGAACA
Found at i:88544086 original size:14 final size:14
Alignment explanation
Indices: 88544063--88544097 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
88544053 AAAAATTGGA
*
88544063 ATAAACTTTGTAAT
1 ATAAATTTTGTAAT
*
88544077 ATAAATTTTGTTAT
1 ATAAATTTTGTAAT
88544091 ATAAATT
1 ATAAATT
88544098 AAAAACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
ATAAATTTTGTAAT
Found at i:88546262 original size:18 final size:18
Alignment explanation
Indices: 88546236--88546273 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
88546226 ACTGAAGATG
88546236 CATTAATGT-TTCCATCGT
1 CATTAATGTCTT-CATCGT
*
88546254 CATTCATGTCTTCATCGT
1 CATTAATGTCTTCATCGT
88546272 CA
1 CA
88546274 ATATCATCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
CATTAATGTCTTCATCGT
Found at i:88551571 original size:62 final size:62
Alignment explanation
Indices: 88551469--88551621 Score: 191
Period size: 62 Copynumber: 2.5 Consensus size: 62
88551459 TCCGTGTAGC
* * * * *
88551469 TCACACGGCTTGGGCACATGCCTATGTCCATGCTCTTGTGGTCCTAAATCATAAACTA-TGAG
1 TCACACGGCCTAGGCACATGCCCATGTCCATGCACGTGTGGTCCTAAATCATAAAC-AGTGAG
* *
88551531 TTACACGGTCTAGGCACATGCCCATGTCCATGCACGTGTGGTCCTAAATCATAAACAGTGAG
1 TCACACGGCCTAGGCACATGCCCATGTCCATGCACGTGTGGTCCTAAATCATAAACAGTGAG
* * * *
88551593 TCACGCGGCCTGGGGACACGCCCATGTCC
1 TCACACGGCCTAGGCACATGCCCATGTCC
88551622 TTACCGGTGT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
61 1 0.01
62 76 0.99
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (62 bp):
TCACACGGCCTAGGCACATGCCCATGTCCATGCACGTGTGGTCCTAAATCATAAACAGTGAG
Found at i:88553747 original size:50 final size:50
Alignment explanation
Indices: 88553653--88553929 Score: 446
Period size: 50 Copynumber: 5.5 Consensus size: 50
88553643 CGATGATCAG
* * * *
88553653 GTAGCCGAAGCTACCACTTTTTACTTGCCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
88553704 GTAGCTGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
88553754 GTAGCCGAAGCTATCACTTATCACTTTCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
88553804 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAACT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* * *
88553854 GTAGTCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
88553904 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
88553930 GTTGCCATGG
Statistics
Matches: 210, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 188 0.90
51 22 0.10
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:88556149 original size:10 final size:10
Alignment explanation
Indices: 88556136--88556306 Score: 66
Period size: 10 Copynumber: 17.9 Consensus size: 10
88556126 ATTGATATAA
88556136 ATATATAAAT
1 ATATATAAAT
*
88556146 ATATTTTAAAT
1 ATA-TATAAAT
*
88556157 AT-TATAAAA
1 ATATATAAAT
* *
88556166 ATATAAAAAA
1 ATATATAAAT
88556176 ACTA-ATAAAT
1 A-TATATAAAT
*
88556186 -TATATAAAA
1 ATATATAAAT
88556195 ATATA-AAAT
1 ATATATAAAT
* *
88556204 AAATA-AAAC
1 ATATATAAAT
88556213 ATAT-TAAA-
1 ATATATAAAT
88556221 ATATATAACAT
1 ATATATAA-AT
*
88556232 -TATATAAAA
1 ATATATAAAT
*
88556241 ATTTATTAAA-
1 ATATA-TAAAT
*
88556251 ATTATATAAAA
1 A-TATATAAAT
88556262 ATATA-AAAT
1 ATATATAAAT
88556271 -TA-ATAAA-
1 ATATATAAAT
*
88556278 ACATATTAAA-
1 ATATA-TAAAT
*
88556288 ATATGTAACAT
1 ATATATAA-AT
88556299 -TATATAAA
1 ATATATAAA
88556307 AATTTATTAA
Statistics
Matches: 123, Mismatches: 19, Indels: 39
0.68 0.10 0.22
Matches are distributed among these distances:
7 1 0.01
8 12 0.10
9 40 0.33
10 52 0.42
11 18 0.15
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (10 bp):
ATATATAAAT
Found at i:88556222 original size:19 final size:18
Alignment explanation
Indices: 88556168--88556290 Score: 59
Period size: 17 Copynumber: 7.2 Consensus size: 18
88556158 TTATAAAAAT
88556168 ATAAA-AAAAC-TAATAAA
1 ATAAATAAAACAT-ATAAA
* *
88556185 TTATATAAAA-ATATAAA
1 ATAAATAAAACATATAAA
88556202 ATAAATAAAACATATTAAA
1 ATAAATAAAACATA-TAAA
* *
88556221 AT--ATATAACAT-T-AT
1 ATAAATAAAACATATAAA
***
88556235 ATAAA-AATTTAT-TAAA
1 ATAAATAAAACATATAAA
*
88556251 ATTATATAAAA-ATATAAA
1 A-TAAATAAAACATATAAA
*
88556269 ATTAATAAAACATATTAAA
1 ATAAATAAAACATA-TAAA
88556288 ATA
1 ATA
88556291 TGTAACATTA
Statistics
Matches: 77, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
14 3 0.04
15 5 0.06
16 3 0.04
17 36 0.47
18 18 0.23
19 12 0.16
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAAAACATATAAA
Found at i:88556256 original size:67 final size:67
Alignment explanation
Indices: 88556182--88556337 Score: 285
Period size: 67 Copynumber: 2.3 Consensus size: 67
88556172 AAAAACTAAT
88556182 AAATTATATAAAAATATAAAATAAATAAAACATATTAAAATATATAACATTATATAAAAATTTAT
1 AAATTATATAAAAATATAAAATAAATAAAACATATTAAAATATATAACATTATATAAAAATTTAT
88556247 TA
66 TA
* *
88556249 AAATTATATAAAAATATAAAATTAATAAAACATATTAAAATATGTAACATTATATAAAAATTTAT
1 AAATTATATAAAAATATAAAATAAATAAAACATATTAAAATATATAACATTATATAAAAATTTAT
88556314 TA
66 TA
88556316 AAATTATATAAAAATCATAAAA
1 AAATTATATAAAAAT-ATAAAA
88556338 ATTATTAAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
67 80 0.93
68 6 0.07
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (67 bp):
AAATTATATAAAAATATAAAATAAATAAAACATATTAAAATATATAACATTATATAAAAATTTAT
TA
Found at i:88556320 original size:10 final size:10
Alignment explanation
Indices: 88556214--88556330 Score: 50
Period size: 10 Copynumber: 11.9 Consensus size: 10
88556204 AAATAAAACA
*
88556214 TATTAAAATA
1 TATTAAAATT
*
88556224 TA-TAACATT
1 TATTAAAATT
*
88556233 ATATAAAAATT
1 -TATTAAAATT
88556244 TATTAAAA-T
1 TATTAAAATT
*
88556253 TATATAAAA-A
1 TAT-TAAAATT
88556263 TA-TAAAA-T
1 TATTAAAATT
* **
88556271 TAATAAAACA
1 TATTAAAATT
88556281 TATTAAAA--
1 TATTAAAATT
*
88556289 TATGTAACATT
1 TAT-TAAAATT
*
88556300 ATATAAAAATT
1 -TATTAAAATT
88556311 TATTAAAATT
1 TATTAAAATT
*
88556321 ATATAAAAAT
1 -TATTAAAAT
88556331 CATAAAAATT
Statistics
Matches: 83, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
8 10 0.12
9 18 0.22
10 34 0.41
11 18 0.22
12 3 0.04
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (10 bp):
TATTAAAATT
Done.