Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 35 of 322
Found at i:10548538 original size:20 final size:21
Alignment explanation
Indices: 10548504--10548542 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10548494 TTATAATATC
*
10548504 ATAAATAATATGAATAAAAAA
1 ATAAATAATAGGAATAAAAAA
10548525 ATAAA-AATAGGAATAAAA
1 ATAAATAATAGGAATAAAA
10548543 GAAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (21 bp):
ATAAATAATAGGAATAAAAAA
Found at i:10549670 original size:49 final size:48
Alignment explanation
Indices: 10549594--10549705 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 48
10549584 AGAAATTTCA
* * **
10549594 GCACTATGTGTGCAAGGTTATGCGGCACTATGTGTGC-A-AAAACTAAGTG
1 GCACTATGTGTGCGAGATTACACGGCACTATGTGTGCGAGAAAAC---GTG
*
10549643 GCACTATGTGTGCGAGATTACATGGCACTATGTGTGCGAGAAAACGTG
1 GCACTATGTGTGCGAGATTACACGGCACTATGTGTGCGAGAAAACGTG
10549691 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
10549706 ATAAGTAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
48 18 0.32
49 32 0.57
50 1 0.02
51 5 0.09
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (48 bp):
GCACTATGTGTGCGAGATTACACGGCACTATGTGTGCGAGAAAACGTG
Found at i:10549673 original size:24 final size:24
Alignment explanation
Indices: 10549617--10549705 Score: 110
Period size: 24 Copynumber: 3.7 Consensus size: 24
10549607 AAGGTTATGC
10549617 GGCACTATGTGTGC-A-AAAACTAAGT
1 GGCACTATGTGTGCGAGAAAAC--A-T
**
10549642 GGCACTATGTGTGCGAGATTACAT
1 GGCACTATGTGTGCGAGAAAACAT
*
10549666 GGCACTATGTGTGCGAGAAAACGT
1 GGCACTATGTGTGCGAGAAAACAT
10549690 GGCACTATGTGTGCGA
1 GGCACTATGTGTGCGA
10549706 ATAAGTAAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
24 38 0.67
25 15 0.26
26 1 0.02
27 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (24 bp):
GGCACTATGTGTGCGAGAAAACAT
Found at i:10549720 original size:49 final size:48
Alignment explanation
Indices: 10549617--10549729 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 48
10549607 AAGGTTATGC
* *
10549617 GGCACTATGTGTGC-AAAAACTAAGTGGCACTATGTGTGCGAGATTACAT
1 GGCACTATGTGTGCGAAAAAC--AGTGGCACTATGTGTGCGAGATAACAA
*
10549666 GGCACTATGTGTGCGAGAAAAC-GTGGCACTATGTGTGCGA-ATAAGTAA
1 GGCACTATGTGTGCGA-AAAACAGTGGCACTATGTGTGCGAGATAA-CAA
10549714 GAGCACTATGTGTGCG
1 G-GCACTATGTGTGCG
10549730 GACTTTCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
47 3 0.05
48 20 0.35
49 28 0.49
50 1 0.02
51 5 0.09
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (48 bp):
GGCACTATGTGTGCGAAAAACAGTGGCACTATGTGTGCGAGATAACAA
Found at i:10556375 original size:24 final size:24
Alignment explanation
Indices: 10556348--10556397 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
10556338 TGAACCATGG
*
10556348 GTTCATGGAATGGTTATTGATATA
1 GTTCATGAAATGGTTATTGATATA
10556372 GTTCATGAAATGGTTATTGATATA
1 GTTCATGAAATGGTTATTGATATA
10556396 GT
1 GT
10556398 GAGATGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (24 bp):
GTTCATGAAATGGTTATTGATATA
Found at i:10557717 original size:91 final size:91
Alignment explanation
Indices: 10557604--10557783 Score: 342
Period size: 91 Copynumber: 2.0 Consensus size: 91
10557594 AATGAGATAA
10557604 TTGAAGTAATGTGGGACAGAGTCAAAATGACTTCTAGATCCCCTGTTCTGTTTTTATAAAATCAC
1 TTGAAGTAATGTGGGACAGAGTCAAAATGACTTCTAGATCCCCTGTTCTGTTTTTATAAAATCAC
*
10557669 TATAAAATGTATAAAAATATTCAAGT
66 TATAAAACGTATAAAAATATTCAAGT
*
10557695 TTGAAGTAATGTGGGATAGAGTCAAAATGACTTCTAGATCCCCTGTTCTGTTTTTATAAAATCAC
1 TTGAAGTAATGTGGGACAGAGTCAAAATGACTTCTAGATCCCCTGTTCTGTTTTTATAAAATCAC
10557760 TATAAAACGTATAAAAATATTCAA
66 TATAAAACGTATAAAAATATTCAA
10557784 ATGATGAAAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (91 bp):
TTGAAGTAATGTGGGACAGAGTCAAAATGACTTCTAGATCCCCTGTTCTGTTTTTATAAAATCAC
TATAAAACGTATAAAAATATTCAAGT
Found at i:10558735 original size:40 final size:40
Alignment explanation
Indices: 10558672--10558858 Score: 275
Period size: 40 Copynumber: 4.7 Consensus size: 40
10558662 CAATTGAGGA
*
10558672 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
10558712 TTATTTCTGGGTTAAGTCCCGAAGGCATTCGTGTTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
10558752 TTATTTTCGGGTTAAGCCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
10558792 CTATTTCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
** * *
10558832 TTACATCCGGGCTAAATCCCGAAGGCA
1 TTATTTCCGGGTTAAGTCCCGAAGGCA
10558859 ATTGGGTTGG
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 131 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (40 bp):
TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:10559040 original size:52 final size:52
Alignment explanation
Indices: 10558962--10559064 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
10558952 ATTAAGTTAA
10558962 GATTGACTATGAGCATGTAAGTATATGGGTTGAAGAGTGAAGTAACATAAGG
1 GATTGACTATGAGCATGTAAGTATATGGGTTGAAGAGTGAAGTAACATAAGG
*
10559014 GATTGACTATGAGCATGTAAGTATATGGGTTGAAGTGTGAAGTAACATAAG
1 GATTGACTATGAGCATGTAAGTATATGGGTTGAAGAGTGAAGTAACATAAG
10559065 TATGTGATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (52 bp):
GATTGACTATGAGCATGTAAGTATATGGGTTGAAGAGTGAAGTAACATAAGG
Found at i:10559046 original size:27 final size:27
Alignment explanation
Indices: 10558964--10559046 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
10558954 TAAGTTAAGA
10558964 TTGACTATGAGCATGTAAGTATATGGG
1 TTGACTATGAGCATGTAAGTATATGGG
* * * *
10558991 TTGA--A-GAGTGAAGTAA-CATAAGGG
1 TTGACTATGAG-CATGTAAGTATATGGG
10559015 ATTGACTATGAGCATGTAAGTATATGGG
1 -TTGACTATGAGCATGTAAGTATATGGG
10559043 TTGA
1 TTGA
10559047 AGTGTGAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
24 9 0.21
25 10 0.24
27 14 0.33
28 9 0.21
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (27 bp):
TTGACTATGAGCATGTAAGTATATGGG
Found at i:10562562 original size:25 final size:25
Alignment explanation
Indices: 10562533--10562580 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10562523 TTATAACATG
* * *
10562533 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
10562558 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
10562581 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:10562664 original size:11 final size:11
Alignment explanation
Indices: 10562628--10562683 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
10562618 CATGGTATGT
10562628 ATGATATGCAC
1 ATGATATGCAC
* *
10562639 ATGACATG--T
1 ATGATATGCAC
10562648 ATGATATGCAC
1 ATGATATGCAC
*
10562659 ATGATATG--T
1 ATGATATGCAC
10562668 ATGATATGCAC
1 ATGATATGCAC
10562679 ATGAT
1 ATGAT
10562684 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:10562683 original size:20 final size:20
Alignment explanation
Indices: 10562617--10562683 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
10562607 ATTTTGATAA
*
10562617 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
10562637 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
10562657 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
10562677 ACATGAT
1 ACATGAT
10562684 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:10562759 original size:24 final size:24
Alignment explanation
Indices: 10562732--10562900 Score: 295
Period size: 24 Copynumber: 7.0 Consensus size: 24
10562722 GGAGGAAGTG
10562732 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
10562756 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
10562780 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
10562804 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
10562828 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
10562852 TAAAAGGGCTTTTGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
10562876 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
10562901 ATGATAAAGC
Statistics
Matches: 140, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
24 129 0.92
25 11 0.08
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:10563129 original size:31 final size:31
Alignment explanation
Indices: 10563094--10563157 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
10563084 CGTTTACAGT
10563094 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
10563125 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
10563156 AA
1 AA
10563158 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:10570709 original size:25 final size:25
Alignment explanation
Indices: 10570680--10570727 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10570670 TTATAATATG
* * *
10570680 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
10570705 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
10570728 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:10570778 original size:9 final size:9
Alignment explanation
Indices: 10570766--10570822 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
10570756 TTTGATAAAC
10570766 ATGATATGT
1 ATGATATGT
*
10570775 ATGATATGCAC
1 ATGATATG--T
*
10570786 ATGACATGT
1 ATGATATGT
*
10570795 ATGATATGCAC
1 ATGATATG--T
10570806 ATGATATGT
1 ATGATATGT
10570815 ATGATATG
1 ATGATATG
10570823 CACATGATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:10570789 original size:20 final size:20
Alignment explanation
Indices: 10570764--10570830 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
10570754 ATTTTGATAA
10570764 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
10570784 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
10570804 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
10570824 ACATGAT
1 ACATGAT
10570831 GTATTCATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:10570811 original size:11 final size:11
Alignment explanation
Indices: 10570775--10570830 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
10570765 CATGATATGT
10570775 ATGATATGCAC
1 ATGATATGCAC
* *
10570786 ATGACATG--T
1 ATGATATGCAC
10570795 ATGATATGCAC
1 ATGATATGCAC
*
10570806 ATGATATG--T
1 ATGATATGCAC
10570815 ATGATATGCAC
1 ATGATATGCAC
10570826 ATGAT
1 ATGAT
10570831 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:10570910 original size:23 final size:24
Alignment explanation
Indices: 10570879--10570997 Score: 181
Period size: 23 Copynumber: 5.0 Consensus size: 24
10570869 GGAGGAAGTG
10570879 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
10570903 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
10570926 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
10570950 TAAAAAGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
10570973 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
10570998 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 41 0.47
24 39 0.44
25 8 0.09
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:10570948 original size:47 final size:47
Alignment explanation
Indices: 10570879--10570997 Score: 179
Period size: 47 Copynumber: 2.5 Consensus size: 47
10570869 GGAGGAAGTG
*
10570879 TAAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTT-TGCCCCAGTTAT
10570926 TAAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTTGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTTGCCCCAGTTAT
*
10570973 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
10570998 ATGATAAAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
47 48 0.72
48 19 0.28
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (47 bp):
TAAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTTGCCCCAGTTAT
Found at i:10571229 original size:31 final size:31
Alignment explanation
Indices: 10571191--10571254 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
10571181 CGTTTACAGT
*
10571191 AAAGGCTTCGGCCCAGTAATATGAAGTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
10571222 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
10571253 AA
1 AA
10571255 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:10574159 original size:32 final size:32
Alignment explanation
Indices: 10574123--10574228 Score: 115
Period size: 32 Copynumber: 3.2 Consensus size: 32
10574113 AAAGGGTAAT
*
10574123 ACTTGAAAAGGTTATGTACACTTTGTGTGTAC
1 ACTTGAAAAGGTTATGTATACTTTGTGTGTAC
* * * *
10574155 ACTTGGAAAGGTTAGGTATACTTTGTATATAC
1 ACTTGAAAAGGTTATGTATACTTTGTGTGTAC
**
10574187 -CATATGAAAAGGAAATGTATACTTTGTGTGTACC
1 AC-T-TGAAAAGGTTATGTATACTTTGTGTGTA-C
10574221 ACTTGAAA
1 ACTTGAAA
10574229 GGAATGCACA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.02
32 28 0.47
33 27 0.46
34 2 0.03
35 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (32 bp):
ACTTGAAAAGGTTATGTATACTTTGTGTGTAC
Found at i:10574221 original size:33 final size:33
Alignment explanation
Indices: 10574123--10574228 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
10574113 AAAGGGTAAT
*
10574123 ACTTGAAAAGGTTATGTACACTTTGTGTGTA-C
1 ACTTGAAAAGGTTATGTATACTTTGTGTGTACC
* * * *
10574155 ACTTGGAAAGGTTAGGTATACTTTGTATATACC
1 ACTTGAAAAGGTTATGTATACTTTGTGTGTACC
**
10574188 A-TATGAAAAGGAAATGTATACTTTGTGTGTACC
1 ACT-TGAAAAGGTTATGTATACTTTGTGTGTACC
10574221 ACTTGAAA
1 ACTTGAAA
10574229 GGAATGCACA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
32 27 0.45
33 32 0.53
34 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (33 bp):
ACTTGAAAAGGTTATGTATACTTTGTGTGTACC
Found at i:10601764 original size:29 final size:29
Alignment explanation
Indices: 10601710--10601824 Score: 88
Period size: 29 Copynumber: 4.0 Consensus size: 29
10601700 GCATGACTAT
* * *
10601710 AATATGATTTGGGACTAATGGCCCATATG
1 AATATGAATTGGGCCTAATGGGCCATATG
* * *
10601739 AATGTGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAATTGGGCCTAATGGGCCATATG
* * * * *
10601768 AATATGAACTGGGTCAAATAGGCCATTTG
1 AATATGAATTGGGCCTAATGGGCCATATG
* * * *
10601797 AATAAG-ATTGGGCATAGTGGGTCATATG
1 AATATGAATTGGGCCTAATGGGCCATATG
10601825 CATGTATGTA
Statistics
Matches: 63, Mismatches: 23, Indels: 1
0.72 0.26 0.01
Matches are distributed among these distances:
28 14 0.22
29 49 0.78
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (29 bp):
AATATGAATTGGGCCTAATGGGCCATATG
Found at i:10607572 original size:16 final size:16
Alignment explanation
Indices: 10607551--10607583 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10607541 TTGTAACGCC
10607551 CCAAAAATCCCGAAAT
1 CCAAAAATCCCGAAAT
*
10607567 CCAAAAATCCTGAAAT
1 CCAAAAATCCCGAAAT
10607583 C
1 C
10607584 TTAAATTTGT
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:0.48, C:0.30, G:0.06, T:0.15
Consensus pattern (16 bp):
CCAAAAATCCCGAAAT
Found at i:10609081 original size:29 final size:29
Alignment explanation
Indices: 10609048--10609148 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 29
10609038 ATATAATTTA
*
10609048 GGCCTAATGGGCCATATGAATGTGAATTG
1 GGCCTAATGGGCCATATGAATATGAATTG
* * * *
10609077 GGCCTAGTGGGCTATAAGAATATGAACTG
1 GGCCTAATGGGCCATATGAATATGAATTG
* *
10609106 GGCC-AGATGGGCCATTTGAATAAG-ATTG
1 GGCCTA-ATGGGCCATATGAATATGAATTG
* *
10609134 GGCCTAGTGGTCCAT
1 GGCCTAATGGGCCAT
10609149 GTGCATGTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
28 15 0.26
29 42 0.74
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
GGCCTAATGGGCCATATGAATATGAATTG
Found at i:10609456 original size:27 final size:25
Alignment explanation
Indices: 10609410--10609463 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
10609400 TAACCATAAT
* *
10609410 TAAGGGAAAAATACCGAAATGCCCC
1 TAAGGGAAAAATACCAAAATACCCC
10609435 TAAGGGCAAAAATGACCAAAATACCCC
1 TAAGGG-AAAAAT-ACCAAAATACCCC
10609462 TA
1 TA
10609464 GGTGTTGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 6 0.24
27 13 0.52
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (25 bp):
TAAGGGAAAAATACCAAAATACCCC
Found at i:10614084 original size:31 final size:31
Alignment explanation
Indices: 10614046--10614162 Score: 180
Period size: 31 Copynumber: 3.8 Consensus size: 31
10614036 GGCCAAAGCC
*
10614046 TCATATCATTGGGCTGAAGCCTTTTCATAAA
1 TCATATCACTGGGCTGAAGCCTTTTCATAAA
10614077 TCATATCACTGGGCTGAAGCCTTTTCATAAA
1 TCATATCACTGGGCTGAAGCCTTTTCATAAA
* * * *
10614108 TAATTTCACTAGGCCGAAGCCTTTTCATAAA
1 TCATATCACTGGGCTGAAGCCTTTTCATAAA
*
10614139 TCATATCATTGGGCTGAAGCCTTT
1 TCATATCACTGGGCTGAAGCCTTT
10614163 ACTGTAAACG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (31 bp):
TCATATCACTGGGCTGAAGCCTTTTCATAAA
Found at i:10614233 original size:42 final size:42
Alignment explanation
Indices: 10614186--10614277 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
10614176 TGGCCCTTAG
*
10614186 GCCCATTTCAATATCACATGTAATGTCAAGGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAAGGAATGTATGCAA
*
10614228 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAAGGAATGTATGCAA
10614270 GCCCATTT
1 GCCCATTT
10614278 GGGGAGACTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAAGGAATGTATGCAA
Found at i:10614499 original size:26 final size:25
Alignment explanation
Indices: 10614422--10614501 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
10614412 CCTCTTTAAT
*
10614422 AACTGGGGCAAAGTCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
**
10614447 AACTGGGGCAAAGCCCTTTTCAATA
1 AACTGGGGCAAAGCCCTTTTCGGTA
10614472 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCA-AAGCCCTTTTCGGTA
10614498 AACT
1 AACT
10614502 TTTCGGTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 32 0.65
26 17 0.35
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:10614539 original size:64 final size:63
Alignment explanation
Indices: 10614437--10614556 Score: 222
Period size: 64 Copynumber: 1.9 Consensus size: 63
10614427 GGGCAAAGTC
10614437 CTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAA
1 CTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAA
*
10614500 CTTTTCGGTAAATTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 CTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
10614557 GCACTTCCTC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (63 bp):
CTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAA
Found at i:10614631 original size:20 final size:20
Alignment explanation
Indices: 10614606--10614700 Score: 142
Period size: 20 Copynumber: 4.8 Consensus size: 20
10614596 TTATGAATAC
*
10614606 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
*
10614626 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
10614646 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10614666 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
10614686 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
10614701 TCCCACGTAT
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
18 8 0.11
20 63 0.86
21 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10614657 original size:11 final size:11
Alignment explanation
Indices: 10614606--10614681 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 11
10614596 TTATGAATAC
10614606 ATCATGTGCAT
1 ATCATGTGCAT
* *
10614617 TTCA--TACAT
1 ATCATGTGCAT
10614626 ATCATGTGCAT
1 ATCATGTGCAT
* *
10614637 TTCA--TACAT
1 ATCATGTGCAT
10614646 ATCATGTGCAT
1 ATCATGTGCAT
*
10614657 ATCA--TACAT
1 ATCATGTGCAT
10614666 ATCATGTGCAT
1 ATCATGTGCAT
10614677 ATCAT
1 ATCAT
10614682 ATCAATCATG
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 22 0.45
11 27 0.55
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:10614698 original size:9 final size:10
Alignment explanation
Indices: 10614623--10614699 Score: 63
Period size: 9 Copynumber: 7.8 Consensus size: 10
10614613 GCATTTCATA
10614623 CATATCATGT
1 CATATCATGT
* *
10614633 GCATTTCAT-A
1 -CATATCATGT
10614643 CATATCATGT
1 CATATCATGT
*
10614653 GCATATCAT-A
1 -CATATCATGT
10614663 CATATCATGT
1 CATATCATGT
*
10614673 GCATATCATAT
1 -CATATCATGT
10614684 CA-ATCATGT
1 CATATCATGT
10614693 -ATATCAT
1 CATATCAT
10614700 ATCCCACGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
8 1 0.02
9 26 0.49
10 2 0.04
11 24 0.45
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (10 bp):
CATATCATGT
Found at i:10615421 original size:27 final size:27
Alignment explanation
Indices: 10615391--10615455 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
10615381 GGGCATATTC
10615391 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
10615418 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
10615445 GTCTTTTTACC
1 GTCATTTTACC
10615456 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:10615539 original size:27 final size:27
Alignment explanation
Indices: 10615487--10615722 Score: 190
Period size: 27 Copynumber: 8.7 Consensus size: 27
10615477 TTCATCCTAC
* * * *
10615487 AAGGGTGTTTTGGTAAATCTACAAACT
1 AAGGGTATTTTAGTAATTTTACAAACT
* * *
10615514 AAGGGTATTTCAGTAATTTTATAAACC
1 AAGGGTATTTTAGTAATTTTACAAACT
* * *
10615541 AATGGTATTTTTA-TAATTTTTAGAAAGT
1 AAGGGTA-TTTTAGTAA-TTTTACAAACT
**
10615569 CAAGGGTATTTCTA-TAATTTTGTAAA-T
1 -AAGGGTATTT-TAGTAATTTTACAAACT
* * *
10615596 CAGGGGTATTTTGGTAATTTTACAAATT
1 -AAGGGTATTTTAGTAATTTTACAAACT
* ** * *
10615624 GAGGGTATTGCAGTAATTTCACAAACC
1 AAGGGTATTTTAGTAATTTTACAAACT
*
10615651 AAGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTAGTAATTTTACAAACT
* * *
10615678 AGGGGTATTTTGGTAATTTTACAAACC
1 AAGGGTATTTTAGTAATTTTACAAACT
10615705 AAGGGTATTTTAGTAATT
1 AAGGGTATTTTAGTAATT
10615723 CACAATCGAG
Statistics
Matches: 166, Mismatches: 37, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.01
27 131 0.79
28 23 0.14
29 11 0.07
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTACAAACT
Found at i:10615657 original size:54 final size:54
Alignment explanation
Indices: 10615486--10615722 Score: 251
Period size: 54 Copynumber: 4.4 Consensus size: 54
10615476 TTTCATCCTA
* * * *
10615486 CAAGGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTCAGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTTACAAAC
* ** * * ** *
10615540 CAATGGTATTTTTATAATTTTTAGAAAGTCAAGGGTATTTCTA-TAATTTTGTAAAT
1 CAAGGGTATTTTGGTAA-TTTTACAAACT-AAGGGTATTTC-AGTAATTTTACAAAC
* * * * *
10615596 CAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTGCAGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTTACAAAC
* **
10615650 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTTACAAAC
*
10615704 CAAGGGTATTTTAGTAATT
1 CAAGGGTATTTTGGTAATT
10615723 CACAATCGAG
Statistics
Matches: 148, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
53 1 0.01
54 95 0.64
55 16 0.11
56 35 0.24
57 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTTACAAAC
Found at i:10615710 original size:81 final size:82
Alignment explanation
Indices: 10615486--10615727 Score: 242
Period size: 81 Copynumber: 3.0 Consensus size: 82
10615476 TTTCATCCTA
* * * * ** * *
10615486 CAAGGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTCAGTAATTTTATAAACCAATGGTATTT
1 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTA-TT
* * *
10615551 TTA-TAATTTTTAGAAAGT
65 TTAGTAA-TTTCACAAAGC
* ** ***
10615569 CAAGGGTATTTCT-ATAATTTTGTAAA-TCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTAT
1 CAAGGGTATTT-TGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAAGGGTAT
**
10615632 TGCAGTAATTTCACAAA-C
64 TTTAGTAATTTCACAAAGC
10615650 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
1 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
10615715 TAGTAA-TTCACAA
66 TAGTAATTTCACAA
10615728 TCGAGGGTAA
Statistics
Matches: 127, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
80 8 0.06
81 59 0.46
82 12 0.09
83 47 0.37
84 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (82 bp):
CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
TAGTAATTTCACAAAGC
Found at i:10615761 original size:27 final size:27
Alignment explanation
Indices: 10615726--10615857 Score: 201
Period size: 27 Copynumber: 4.9 Consensus size: 27
10615716 AGTAATTCAC
* *
10615726 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
10615753 AATTGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
10615780 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
10615807 AATCGAGGGTGAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
10615834 AATCGAGGGTAAAACGGTAATTCT
1 AATCGAGGGTAAAACGGTAATTCT
10615858 ATGGCCCTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:10616894 original size:22 final size:22
Alignment explanation
Indices: 10616845--10616895 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
10616835 ACTATAATAA
* *
10616845 CAAAATAGTAGTAACACAACAG
1 CAAAATAGTAGTAAAAAAACAG
* *
10616867 CGAAATGGTAGTAAAAAAACAG
1 CAAAATAGTAGTAAAAAAACAG
*
10616889 TAAAATA
1 CAAAATA
10616896 ATAACAAAAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.16
Consensus pattern (22 bp):
CAAAATAGTAGTAAAAAAACAG
Found at i:10617765 original size:49 final size:49
Alignment explanation
Indices: 10617698--10617794 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
10617688 TTATGCTTTG
* * *
10617698 CATTTCTAAACTTGGTCTTCCACTGTCTACACTCTTA-TCACTATTTATA
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATTC-CTATTTATA
10617747 CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATTCCTATTTAT
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATTCCTATTTAT
10617795 CCTTTCTAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 42 0.95
50 2 0.05
ACGTcount: A:0.25, C:0.26, G:0.06, T:0.43
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATTCCTATTTATA
Found at i:10619168 original size:16 final size:17
Alignment explanation
Indices: 10619146--10619189 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
10619136 CTTCTCATAA
10619146 TCATTTCTCATATTTTC
1 TCATTTCTCATATTTTC
*
10619163 -CATTTC-AATATTTTC
1 TCATTTCTCATATTTTC
10619178 TCA--TCTCATATT
1 TCATTTCTCATATT
10619190 CATTTCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 13 0.57
16 8 0.35
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (17 bp):
TCATTTCTCATATTTTC
Found at i:10619185 original size:43 final size:43
Alignment explanation
Indices: 10619131--10619216 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
10619121 TCATATCTCA
*
10619131 TTTCTCTTCTCATAATCATTTCTCATATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
* * * *
10619174 TTTCTCATCTCATATTCATTTCTCTTCTTTTTCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
10619217 CAATAACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:10622989 original size:2 final size:2
Alignment explanation
Indices: 10622982--10623011 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10622972 CACTATGTGC
10622982 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
10623012 TGTGGCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10631111 original size:23 final size:20
Alignment explanation
Indices: 10631085--10631130 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
10631075 AATTTTATGA
10631085 ATTTTTTAAATTATATTTAATTT
1 ATTTTTTAAATT-TA-TT-ATTT
*
10631108 ATTTTTTTAATTTATTATTT
1 ATTTTTTAAATTTATTATTT
10631128 ATT
1 ATT
10631131 GTTAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 2 0.09
22 2 0.09
23 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTTAAATTTATTATTT
Found at i:10632213 original size:22 final size:22
Alignment explanation
Indices: 10632186--10632229 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
10632176 TAAGATGGTT
10632186 ATATATAAAATATTAATAAATAAA
1 ATATAT-AAA-ATTAATAAATAAA
*
10632210 ATATATAAAATTATTAAATA
1 ATATATAAAATTAATAAATA
10632230 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATATAAAATTAATAAATAAA
Found at i:10634403 original size:19 final size:19
Alignment explanation
Indices: 10634357--10634404 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
10634347 ATATATATTT
10634357 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
10634375 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
10634394 TAAGTTTTATT
1 TAAATTTTATT
10634405 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:10634466 original size:43 final size:43
Alignment explanation
Indices: 10634418--10634510 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
10634408 ATTCTAGAAA
*
10634418 TATTTT-TATTTTATTTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATGTTTTAGTAGTTTACTAGAATAAGGGAAC
*
10634461 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATGTTTTAGTAGTTTACTAGAATAAGGGAAC
10634504 TATTTTC
1 TATTTTC
10634511 CCAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (43 bp):
TATTTTCTTTTTATGTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:10650644 original size:43 final size:43
Alignment explanation
Indices: 10650592--10650688 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
10650582 TCATATTCTA
10650592 GAAA-TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAG
1 GAAACTATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAG
* *
10650634 GAAACTATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAG
1 GAAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
*
10650677 GGAACTATTTTC
1 GAAACTATTTTC
10650689 CCAATTAGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 4 0.08
43 45 0.90
44 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.49
Consensus pattern (43 bp):
GAAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
Found at i:10651430 original size:10 final size:10
Alignment explanation
Indices: 10651415--10651439 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10651405 GCCTGACACT
10651415 TTTTTTTAAC
1 TTTTTTTAAC
10651425 TTTTTTTAAC
1 TTTTTTTAAC
10651435 TTTTT
1 TTTTT
10651440 ATCCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTTAAC
Found at i:10651606 original size:23 final size:22
Alignment explanation
Indices: 10651523--10651607 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 22
10651513 TATTATTAAT
* * *
10651523 TTTAAAAAATTTGAAATGTATA
1 TTTAAAATATTTAAAATATATA
* *
10651545 TTTAAAATGTTTTATAATATATATT
1 TTTAAAAT-ATTTA-AA-ATATATA
*
10651570 TTTTAAA-ATTTAAAATATATA
1 TTTAAAATATTTAAAATATATA
10651591 TTTAAAATATTATAAAA
1 TTTAAAATATT-TAAAA
10651608 CAAATAATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
21 12 0.24
22 12 0.24
23 12 0.24
24 2 0.04
25 11 0.22
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTAAAATATTTAAAATATATA
Found at i:10651697 original size:21 final size:23
Alignment explanation
Indices: 10651639--10651712 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
10651629 CATATCTTTA
* * *
10651639 AAAATAATATATTTTAAATAATCT
1 AAAATCATA-ATTTTAAATATTAT
10651663 AAAATCATAATTTTAAATATTAT
1 AAAATCATAATTTTAAATATTAT
*
10651686 AAAA-CA-AATTTTAAATATATTT
1 AAAATCATAATTTTAAATAT-TAT
10651708 AAAAT
1 AAAAT
10651713 TTAAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 12 0.27
22 8 0.18
23 16 0.36
24 8 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATCATAATTTTAAATATTAT
Found at i:10651712 original size:18 final size:19
Alignment explanation
Indices: 10651691--10651732 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
10651681 ATTATAAAAC
*
10651691 AAATTTTAAATAT-ATTTA
1 AAATTTAAAATATAATTTA
10651709 AAATTTAAAATATACATTTA
1 AAATTTAAAATATA-ATTTA
10651729 AAAT
1 AAAT
10651733 ATTATAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
20 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTTAAAATATAATTTA
Found at i:10651729 original size:20 final size:18
Alignment explanation
Indices: 10651691--10651837 Score: 64
Period size: 20 Copynumber: 7.3 Consensus size: 18
10651681 ATTATAAAAC
*
10651691 AAATTTTAAATATATTTA
1 AAATTTAAAATATATTTA
10651709 AAATTTAAAATATACATTTA
1 AAATTTAAAATAT--ATTTA
* *
10651729 AAATATTATAAA-ACTAATAA
1 AAAT-TTA-AAATA-TATTTA
10651749 TAAATTTGAAAAATCATATCTTTA
1 -AAATTT--AAAAT-ATA--TTTA
*
10651773 AAATATTAAAAT-TCTTTA
1 AAAT-TTAAAATATATTTA
* *
10651791 TATTATTAAAAATATATTTA
1 -A-AATTTAAAATATATTTA
*
10651811 ATATTTAAAAAATAATATTTA
1 AAATTT--AAAAT-ATATTTA
10651832 AAATTT
1 AAATTT
10651838 TATAAAAAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 35
0.68 0.08 0.24
Matches are distributed among these distances:
18 20 0.20
19 8 0.08
20 27 0.27
21 23 0.23
22 12 0.12
23 5 0.05
24 4 0.04
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
AAATTTAAAATATATTTA
Found at i:10651790 original size:18 final size:18
Alignment explanation
Indices: 10651767--10651801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10651757 AAAAATCATA
10651767 TCTTTAAAATATTAAAAT
1 TCTTTAAAATATTAAAAT
* *
10651785 TCTTTATATTATTAAAA
1 TCTTTAAAATATTAAAA
10651802 ATATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTTTAAAATATTAAAAT
Found at i:10651815 original size:18 final size:21
Alignment explanation
Indices: 10651798--10651837 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10651788 TTATATTATT
10651798 AAAAAT-ATATTTAATATTTA
1 AAAAATAATATTTAATATTTA
*
10651818 AAAAATAATATTTAAAATTT
1 AAAAATAATATTTAATATTT
10651838 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATAATATTTAATATTTA
Found at i:10651822 original size:21 final size:22
Alignment explanation
Indices: 10651798--10651867 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 22
10651788 TTATATTATT
*
10651798 AAAAATATATTT--AATATTTA
1 AAAAATATATTTAAAATTTTTA
10651818 AAAAATAATATTTAAAATTTTATA
1 AAAAAT-ATATTTAAAATTTT-TA
*
10651842 AAAAATATATTATAAAACATTTTA
1 AAAAATATATT-TAAAA-TTTTTA
10651866 AA
1 AA
10651868 TATACATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 6 0.14
21 6 0.14
23 10 0.24
24 17 0.40
25 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATATATTTAAAATTTTTA
Found at i:10651844 original size:23 final size:22
Alignment explanation
Indices: 10651797--10651858 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
10651787 TTTATATTAT
*
10651797 TAAAAAT-ATATTTAATATTTA
1 TAAAAATAATATTTAAAATTTA
10651818 -AAAAATAATATTTAAAATTTTA
1 TAAAAATAATATTTAAAA-TTTA
10651840 TAAAAA-ATATATTATAAAA
1 TAAAAATA-ATATT-TAAAA
10651859 CATTTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 6 0.17
21 9 0.26
22 5 0.14
23 10 0.29
24 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATAATATTTAAAATTTA
Found at i:10651961 original size:13 final size:12
Alignment explanation
Indices: 10651932--10651959 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10651922 GGATAAAGAC
10651932 AAAAGTTAAAAA
1 AAAAGTTAAAAA
10651944 AAAAGTTAAAAA
1 AAAAGTTAAAAA
10651956 AAAA
1 AAAA
10651960 AGAAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAGTTAAAAA
Found at i:10657983 original size:79 final size:81
Alignment explanation
Indices: 10657847--10658031 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
10657837 TTGAATGATG
*
10657847 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
10657911 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
10657926 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
10657988 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
10658006 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10658032 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:10658045 original size:40 final size:40
Alignment explanation
Indices: 10657848--10658031 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
10657838 TGAATGATGT
* * * *
10657848 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
10657888 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
10657928 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
10657966 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
10658007 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
10658032 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:10658053 original size:79 final size:79
Alignment explanation
Indices: 10657900--10658064 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
10657890 GGACTAAGAT
* **
10657900 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
10657965 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
10657979 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
10658042 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
10658058 CCGAAGG
1 CCGAAGG
10658065 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:10661650 original size:37 final size:38
Alignment explanation
Indices: 10661609--10661680 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
10661599 AAGGATAAAA
10661609 TTGGAAAATTGC-AAAATTTACTTAATAAAGCTAGGAC
1 TTGGAAAATTGCAAAAATTTACTTAATAAAGCTAGGAC
10661646 TTGGAAAATTGCAAAAATTTACTTAATAAAGCTAG
1 TTGGAAAATTGCAAAAATTTACTTAATAAAGCTAG
10661681 AACTAAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 12 0.35
38 22 0.65
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (38 bp):
TTGGAAAATTGCAAAAATTTACTTAATAAAGCTAGGAC
Found at i:10663262 original size:35 final size:35
Alignment explanation
Indices: 10663223--10663639 Score: 408
Period size: 35 Copynumber: 12.0 Consensus size: 35
10663213 GTATTATCAA
* * *
10663223 ATCCATACTGAGTTAAGAAACGTAGGTATGGTATC
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* *
10663258 ATCCATACCGAGTTGTGAAATGTAGGTATGGTATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* ** * * *
10663293 AACCATACTAAGTTGTGAAATGTAGGTATGGTATC
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* * *
10663328 ATCCATACTGAGTTGTGAAACATAGGTATGGTATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* * *
10663363 AACCATACCGAGTTGTGAAACATAGGTATGGTATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* * * * *
10663398 AACCATACTGAGCTGTGAAACGTAGGTATGGCATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
*
10663433 -TCCATACCGAGCTATGAAACGTAGGTATGGTATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* ** *
10663467 -TCCATACCGAGCTATGAAACGTAGGTATGGCGTC
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* ** * * * * *
10663501 GTCCATATTGAGCTATGATACATAGGTATGGCATC
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* * **
10663536 GTCCATACTGAGTTATGAAATATAGGTATGGTATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* * * *
10663571 TTCCATACCGAG-CATGAAAAGTAGGTATGGTGTT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
* *
10663605 TTCCATACCGAGTTGTGAAACGTAGGTATGGTATT
1 ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
10663640 TCAATGAGGA
Statistics
Matches: 332, Mismatches: 48, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
34 91 0.27
35 241 0.73
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (35 bp):
ATCCATACCGAGTTATGAAACGTAGGTATGGTATT
Found at i:10663563 original size:173 final size:173
Alignment explanation
Indices: 10663198--10663641 Score: 494
Period size: 173 Copynumber: 2.5 Consensus size: 173
10663188 TGGCAAAGTG
* * * * *
10663198 TGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAACGTAGGTATGGTATCATCCA
1 TGAAATATAGGTATGGTA-T-T--AA-CCATACTGAGCTATGAAACGTAGGTATGGCAT-TTCCA
* * * * * * *
10663263 TACCGAGTTGTGAAATGTAGGTATGGTATTAACCATACTAAGTTGTGAAATGTAGGTATGGTATC
60 TACCGAGTTGTGAAACGTAGGTATGGTATT-TCCATACCAAGCTATGAAACGTAGGTATGGCATC
* * * * *
10663328 ATCCATACTGAGTTGTGAAACATAGGTATGGTATTAACCATACCGAGTTG
124 ATCCATACTGAGCTATGAAACATAGGTATGGCATCAACCATACCGAGTTA
* *
10663378 TGAAACATAGGTATGGTATTAACCATACTGAGCTGTGAAACGTAGGTATGGCATTTCCATACCGA
1 TGAAATATAGGTATGGTATTAACCATACTGAGCTATGAAACGTAGGTATGGCATTTCCATACCGA
* * * * *
10663443 GCTATGAAACGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGGCGTCGTCCATA
66 GTTGTGAAACGTAGGTATGGTATTTCCATACCAAGCTATGAAACGTAGGTATGGCATCATCCATA
* * ** *
10663508 TTGAGCTATGATACATAGGTATGGCATCGTCCATACTGAGTTA
131 CTGAGCTATGAAACATAGGTATGGCATCAACCATACCGAGTTA
** * * **
10663551 TGAAATATAGGTATGGTATTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATACCG
1 TGAAATATAGGTATGGTATTAACCATACTGAGCTATGAAACGTAGGTATGG-CATTTCCATACCG
10663615 AGTTGTGAAACGTAGGTATGGTATTTC
65 AGTTGTGAAACGTAGGTATGGTATTTC
10663642 AATGAGGAAA
Statistics
Matches: 224, Mismatches: 39, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
172 15 0.07
173 130 0.58
174 31 0.14
175 28 0.12
176 2 0.01
178 1 0.00
179 1 0.00
180 16 0.07
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (173 bp):
TGAAATATAGGTATGGTATTAACCATACTGAGCTATGAAACGTAGGTATGGCATTTCCATACCGA
GTTGTGAAACGTAGGTATGGTATTTCCATACCAAGCTATGAAACGTAGGTATGGCATCATCCATA
CTGAGCTATGAAACATAGGTATGGCATCAACCATACCGAGTTA
Found at i:10666190 original size:200 final size:200
Alignment explanation
Indices: 10665847--10666247 Score: 766
Period size: 200 Copynumber: 2.0 Consensus size: 200
10665837 AACAAGCCAT
*
10665847 TCAACAAGCAAGTATAAACCACATCACCAAAGAGCATTAGTACATATATATATACATCACCATAT
1 TCAACAAGCAAGTATAAACCACATCACCAAAGAGCATTAGTACATATATATATACACCACCATAT
10665912 TTTCCAAAATAAGCCAACTCACATGGCTATACACAAACAAAATACTTAACTTTTACAAGCCAACA
66 TTTCCAAAATAAGCCAACTCACATGGCTATACACAAACAAAATACTTAACTTTTACAAGCCAACA
10665977 CAAATGGCCAAATTCATAATAACATATACCAAAATGACCCAAAGTCCCTATGCATGCCATATGTC
131 CAAATGGCCAAATTCATAATAACATATACCAAAATGACCCAAAGTCCCTATGCATGCCATATGTC
10666042 CAAAA
196 CAAAA
10666047 TCAACAAGCAAGTATAAACCACATCACCAAAGAGCATTAGTACATATATATATACACCACCATAT
1 TCAACAAGCAAGTATAAACCACATCACCAAAGAGCATTAGTACATATATATATACACCACCATAT
** *
10666112 TTTCCAAAATAAGCCAACTCACATGTTTGTACACAAACAAAATACTTAACTTTTACAAGCCAACA
66 TTTCCAAAATAAGCCAACTCACATGGCTATACACAAACAAAATACTTAACTTTTACAAGCCAACA
10666177 CAAATGGCCAAATTCATAATAACATATACCAAAATGACCCAAAGTCCCTATGCATGCCATATGTC
131 CAAATGGCCAAATTCATAATAACATATACCAAAATGACCCAAAGTCCCTATGCATGCCATATGTC
10666242 CAAAA
196 CAAAA
10666247 T
1 T
10666248 TTAATTTCAA
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (200 bp):
TCAACAAGCAAGTATAAACCACATCACCAAAGAGCATTAGTACATATATATATACACCACCATAT
TTTCCAAAATAAGCCAACTCACATGGCTATACACAAACAAAATACTTAACTTTTACAAGCCAACA
CAAATGGCCAAATTCATAATAACATATACCAAAATGACCCAAAGTCCCTATGCATGCCATATGTC
CAAAA
Found at i:10667258 original size:21 final size:20
Alignment explanation
Indices: 10667230--10667269 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
10667220 CAAAACTTGT
10667230 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
10667250 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
10667270 AATGCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:10669477 original size:20 final size:20
Alignment explanation
Indices: 10669424--10669465 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10669414 GTTGATACAA
10669424 GGCAAATAAGTTTGTTTAGG
1 GGCAAATAAGTTTGTTTAGG
10669444 GGCAAATAAGTTTGTTTAGG
1 GGCAAATAAGTTTGTTTAGG
10669464 GG
1 GG
10669466 GCAATATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (20 bp):
GGCAAATAAGTTTGTTTAGG
Found at i:10671670 original size:20 final size:20
Alignment explanation
Indices: 10671645--10671687 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
10671635 ATTTTTTTCA
*
10671645 AATCCTAATTTTCACCACTT
1 AATCCTAATTTTCACCACCT
10671665 AATCCTAATTTTCACCACCT
1 AATCCTAATTTTCACCACCT
10671685 AAT
1 AAT
10671688 TTTAGACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (20 bp):
AATCCTAATTTTCACCACCT
Found at i:10688549 original size:29 final size:30
Alignment explanation
Indices: 10688482--10688554 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
10688472 ATGCTTTAAG
* *
10688482 TCTTTGTACTCTTTATATATTTAGAATTTAG
1 TCTTTTTACT-TTTATATATTTAGAATTTAC
**
10688513 TCCCTTTACTTTTAT-T-TTTAGGAATTTAC
1 TCTTTTTACTTTTATATATTTA-GAATTTAC
*
10688542 TCTTTTTATTTTT
1 TCTTTTTACTTTT
10688555 CGAATCTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
28 4 0.12
29 18 0.53
30 5 0.15
31 7 0.21
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (30 bp):
TCTTTTTACTTTTATATATTTAGAATTTAC
Found at i:10690030 original size:22 final size:22
Alignment explanation
Indices: 10689986--10690030 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
10689976 AATTTGATGC
**
10689986 ATATACGAATTATTAGATGTAA
1 ATATACGAATTATTAGAAATAA
10690008 ATATACGAATTATT-GAAAATAA
1 ATATACGAATTATTAG-AAATAA
10690030 A
1 A
10690031 CAGTTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (22 bp):
ATATACGAATTATTAGAAATAA
Found at i:10690415 original size:7 final size:7
Alignment explanation
Indices: 10690390--10690434 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
10690380 TTACTAATGG
*
10690390 AAAAAAT
1 AAAATAT
10690397 AATAAT-T
1 AA-AATAT
10690404 AAAATAT
1 AAAATAT
10690411 AAAATAT
1 AAAATAT
10690418 AAAATAT
1 AAAATAT
10690425 AAAATAT
1 AAAATAT
10690432 AAA
1 AAA
10690435 GAAAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
6 3 0.09
7 30 0.86
8 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATAT
Found at i:10692866 original size:51 final size:51
Alignment explanation
Indices: 10692787--10692886 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
10692777 ATATATATGG
* * * *
10692787 CATCCGAGCTCATTCAGTGGTTCGAGTTCATAATGGATGCGATACATGTAA
1 CATCCGAGCTCATTCAGAGGTCCAAGTTCATAATAGATGCGATACATGTAA
* * * * *
10692838 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATTATAGATGTGTTACATGT
1 CATCCGAGCTCATTCAGAGGTCCAAGTTCATAATAGATGCGATACATGT
10692887 TATAAGGTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (51 bp):
CATCCGAGCTCATTCAGAGGTCCAAGTTCATAATAGATGCGATACATGTAA
Found at i:10695588 original size:22 final size:22
Alignment explanation
Indices: 10695560--10695608 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
10695550 ACCAAAATAG
*
10695560 GAGTTGAACATAAGGCTACTTT
1 GAGTTGAACATAAGGCTACGTT
10695582 GAGTTGAACATAAGGCTACGTT
1 GAGTTGAACATAAGGCTACGTT
10695604 GAGTT
1 GAGTT
10695609 ATTCAAAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (22 bp):
GAGTTGAACATAAGGCTACGTT
Found at i:10697323 original size:45 final size:45
Alignment explanation
Indices: 10697273--10697383 Score: 161
Period size: 45 Copynumber: 2.5 Consensus size: 45
10697263 AGCAGTAGCA
* * *
10697273 GTAACAATAACAGTAACAGTATTCAACACACAAAATG-CTGAATCT
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAATGTC-GAATCG
* *
10697318 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCG
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAATGTCGAATCG
10697363 GTAACAGTAACGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
10697384 ACAGTAATCG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 59 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCAACACACAAAATGTCGAATCG
Found at i:10697378 original size:12 final size:12
Alignment explanation
Indices: 10697361--10697390 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10697351 AGTGTCGAAT
10697361 CGGTAACAGTAA
1 CGGTAACAGTAA
10697373 CGGTAACAGTAA
1 CGGTAACAGTAA
*
10697385 CAGTAA
1 CGGTAA
10697391 TCGGCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:10698479 original size:13 final size:13
Alignment explanation
Indices: 10698442--10698480 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
10698432 TTCTTCTTTA
10698442 TTTTATTTTATTTC
1 TTTTATTTTA-TTC
* *
10698456 ATTTCTTTTATTC
1 TTTTATTTTATTC
10698469 TTTTATTTTATT
1 TTTTATTTTATT
10698481 AACTTTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTATTC
Found at i:10698811 original size:20 final size:22
Alignment explanation
Indices: 10698769--10698818 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
10698759 TTAATTTATT
10698769 TTTAATAATATAAATAATCATAA
1 TTTAATAATATAAAT-ATCATAA
10698792 TTTAATAATATAAAT-T-ATAA
1 TTTAATAATATAAATATCATAA
10698812 TTTAATA
1 TTTAATA
10698819 GAATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
23 15 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATAATATAAATATCATAA
Found at i:10700331 original size:54 final size:54
Alignment explanation
Indices: 10700247--10700438 Score: 325
Period size: 54 Copynumber: 3.6 Consensus size: 54
10700237 TCCCATGGCA
10700247 GGATTA-TCAGTCCAGGCTAAAT-CCTCTATATCATGAACTCATAAGGTGATGTCG
1 GGATTACT-AGTCCAGGCTAAATCCCT-TATATCATGAACTCATAAGGTGATGTCG
10700301 GGATTACTAGTCCAGGCTAAATCCCTTATATCATGAACTCATAAGGTGATGTCG
1 GGATTACTAGTCCAGGCTAAATCCCTTATATCATGAACTCATAAGGTGATGTCG
*
10700355 GGATTACTAGTCCAGGCTAAATCCCTTATATCATGAACTCATAAGGTGATGTTG
1 GGATTACTAGTCCAGGCTAAATCCCTTATATCATGAACTCATAAGGTGATGTCG
* *
10700409 GGATTACCAGTCCAGGCTAAATCCTTTATA
1 GGATTACTAGTCCAGGCTAAATCCCTTATA
10700439 ACAACAAACA
Statistics
Matches: 133, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
54 129 0.97
55 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (54 bp):
GGATTACTAGTCCAGGCTAAATCCCTTATATCATGAACTCATAAGGTGATGTCG
Found at i:10706114 original size:52 final size:52
Alignment explanation
Indices: 10706053--10706151 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
10706043 AATCAGATGG
*
10706053 ACAAATTTTTTATTTTGAGTATGAAAAACAATCCAATTTAATAGAAACATGA
1 ACAAATTTTTTATTTTAAGTATGAAAAACAATCCAATTTAATAGAAACATGA
*
10706105 ACAAATTTTTTATTTTAAGTATGAAAAATAATCCAATTTAATAGAAA
1 ACAAATTTTTTATTTTAAGTATGAAAAACAATCCAATTTAATAGAAA
10706152 TTTTTTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (52 bp):
ACAAATTTTTTATTTTAAGTATGAAAAACAATCCAATTTAATAGAAACATGA
Found at i:10720774 original size:21 final size:21
Alignment explanation
Indices: 10720750--10720789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
10720740 TCGTCTTCAT
* *
10720750 CGTTCAGAACGTCTTCGTTAA
1 CGTTAAGAACGTCGTCGTTAA
*
10720771 CGTTAAGGACGTCGTCGTT
1 CGTTAAGAACGTCGTCGTT
10720790 TTCGTCGACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTAAGAACGTCGTCGTTAA
Found at i:10726053 original size:21 final size:21
Alignment explanation
Indices: 10726019--10726062 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10726009 GGGAGGGTCC
*
10726019 AAGTTACTTCTCTTTTTGTCT
1 AAGTTACTTATCTTTTTGTCT
*
10726040 AAGTTGCTTATCTTTTTGTCT
1 AAGTTACTTATCTTTTTGTCT
10726061 AA
1 AA
10726063 CTCACTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (21 bp):
AAGTTACTTATCTTTTTGTCT
Found at i:10728938 original size:34 final size:34
Alignment explanation
Indices: 10728894--10729000 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
10728884 GCATTTTTTC
10728894 ATACTGTTATTGTAATGGGCTAAAGCCCACACTG
1 ATACTGTTATTGTAATGGGCTAAAGCCCACACTG
* ** *
10728928 TTACTGTTATTGTAATGGGCTAACTCCCATACTG
1 ATACTGTTATTGTAATGGGCTAAAGCCCACACTG
* * * *
10728962 ATACTATTATTGTAATAGGCTAAGGCCCGCACTG
1 ATACTGTTATTGTAATGGGCTAAAGCCCACACTG
10728996 ATACT
1 ATACT
10729001 AGACTGTAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (34 bp):
ATACTGTTATTGTAATGGGCTAAAGCCCACACTG
Found at i:10729239 original size:18 final size:18
Alignment explanation
Indices: 10729216--10729250 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
10729206 TAATTAATTT
10729216 GGATTTCCAAATCTTTTG
1 GGATTTCCAAATCTTTTG
10729234 GGATTTCCAAATCTTTT
1 GGATTTCCAAATCTTTT
10729251 ATTATATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (18 bp):
GGATTTCCAAATCTTTTG
Found at i:10729392 original size:29 final size:29
Alignment explanation
Indices: 10729355--10729414 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
10729345 GAAAGAACAT
10729355 TTTCAAAAACTAATAACAATTCAACATAC
1 TTTCAAAAACTAATAACAATTCAACATAC
*
10729384 TTTCGAAAACTAATAACAATTCAACATAC
1 TTTCAAAAACTAATAACAATTCAACATAC
10729413 TT
1 TT
10729415 AACATTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (29 bp):
TTTCAAAAACTAATAACAATTCAACATAC
Found at i:10732320 original size:43 final size:41
Alignment explanation
Indices: 10732264--10732417 Score: 139
Period size: 43 Copynumber: 3.6 Consensus size: 41
10732254 ATGCTATATT
* ** *
10732264 CCAGATATGGTCTTACATGTTATCACATATCAATGCCACTGTC
1 CCAGACATGGTCTTACATGAAATCA-ATA-CAATGCCAATGTC
* * * * *
10732307 CTAGACAGGGTCTTACACGAAATCAATTAACGATACCAATGTC
1 CCAGACATGGTCTTACATGAAATCAA-T-ACAATGCCAATGTC
*
10732350 CCAGACATGGTCTTAGACAT-AATCTCAATACAATGCCAATGTC
1 CCAGACATGGTCTT--ACATGAA-ATCAATACAATGCCAATGTC
*
10732393 CCAGACATGGTCTTACATGTAATCA
1 CCAGACATGGTCTTACATGAAATCA
10732418 CATCTCGATA
Statistics
Matches: 88, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
41 7 0.08
42 2 0.02
43 68 0.77
44 4 0.05
45 7 0.08
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (41 bp):
CCAGACATGGTCTTACATGAAATCAATACAATGCCAATGTC
Found at i:10743692 original size:11 final size:11
Alignment explanation
Indices: 10743676--10743706 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
10743666 GAGGCGAGCA
10743676 CTAAATTAATT
1 CTAAATTAATT
10743687 CTAAATTAATT
1 CTAAATTAATT
*
10743698 CTAATTTAA
1 CTAAATTAA
10743707 ACATAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (11 bp):
CTAAATTAATT
Found at i:10746251 original size:27 final size:27
Alignment explanation
Indices: 10746218--10746424 Score: 315
Period size: 27 Copynumber: 7.6 Consensus size: 27
10746208 TAAATTGTGC
*
10746218 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
10746245 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
10746273 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
10746300 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
10746328 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10746355 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
10746383 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10746410 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10746425 GACTTAATAT
Statistics
Matches: 168, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
27 91 0.54
28 77 0.46
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:10746282 original size:55 final size:55
Alignment explanation
Indices: 10746218--10746424 Score: 360
Period size: 55 Copynumber: 3.8 Consensus size: 55
10746208 TAAATTGTGC
10746218 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
10746273 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
10746328 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * * *
10746383 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCG
10746425 GACTTAATAT
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:10752260 original size:26 final size:26
Alignment explanation
Indices: 10752230--10752340 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
10752220 AGCATGGCTG
* *
10752230 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
10752256 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
10752283 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
10752310 CCAGATCAGATAAATATGGCATAGACA
1 CCAGAACAGAT-AATGTGGCAGAGCCA
10752337 CCAG
1 CCAG
10752341 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 13 0.17
27 61 0.80
28 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:10753813 original size:24 final size:24
Alignment explanation
Indices: 10753786--10753845 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
10753776 AATCTGCTCT
10753786 TAAATCTTCTCCCTTATCAACTCC
1 TAAATCTTCTCCCTTATCAACTCC
* **
10753810 TAAATCCTCTCCCTTATCTGCTCC
1 TAAATCTTCTCCCTTATCAACTCC
10753834 TAAATCTTCTCC
1 TAAATCTTCTCC
10753846 TGATAGCCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAATCTTCTCCCTTATCAACTCC
Found at i:10760600 original size:20 final size:20
Alignment explanation
Indices: 10760572--10760609 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10760562 TCATGTCAGC
10760572 AAATAATTTTAAAATTATTG
1 AAATAATTTTAAAATTATTG
* *
10760592 AAATTATTTTAAATTTAT
1 AAATAATTTTAAAATTAT
10760610 CATCACCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATAATTTTAAAATTATTG
Found at i:10762802 original size:37 final size:37
Alignment explanation
Indices: 10762731--10762803 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
10762721 TTTTCGGAGC
*
10762731 ACTTGGCGTGTTATCGGTTGGATTAGGTTCTATGAGA
1 ACTTGGCGTGTTATCGGTTGGATTAGCTTCTATGAGA
*
10762768 ACTTGGTGTGTTATCGGTTGGATTAGC-TCTTATGAG
1 ACTTGGCGTGTTATCGGTTGGATTAGCTTC-TATGAG
10762804 CTTTTGGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 31 0.94
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.40
Consensus pattern (37 bp):
ACTTGGCGTGTTATCGGTTGGATTAGCTTCTATGAGA
Found at i:10764707 original size:19 final size:19
Alignment explanation
Indices: 10764683--10764721 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
10764673 GATCCCCTTG
*
10764683 ATTAACACCTACCACAAGA
1 ATTAACACATACCACAAGA
10764702 ATTAACACATACCACAAGA
1 ATTAACACATACCACAAGA
10764721 A
1 A
10764722 ACCACAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.28, G:0.05, T:0.15
Consensus pattern (19 bp):
ATTAACACATACCACAAGA
Found at i:10783881 original size:40 final size:34
Alignment explanation
Indices: 10783812--10783922 Score: 204
Period size: 34 Copynumber: 3.3 Consensus size: 34
10783802 TAATATCAAA
* *
10783812 TATGCAGTAGGGCCTTACCCCATCACAGTATCAG
1 TATGCATTAGGGCCTTAGCCCATCACAGTATCAG
10783846 TATGCATTAGGGCCTTAGCCCATCACAGTATCAG
1 TATGCATTAGGGCCTTAGCCCATCACAGTATCAG
10783880 TATGCATTAGGGCCTTAGCCCATCACAGTATCAG
1 TATGCATTAGGGCCTTAGCCCATCACAGTATCAG
10783914 TATGCATTA
1 TATGCATTA
10783923 TTCAGTAACA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (34 bp):
TATGCATTAGGGCCTTAGCCCATCACAGTATCAG
Found at i:10789068 original size:48 final size:48
Alignment explanation
Indices: 10789007--10789228 Score: 239
Period size: 48 Copynumber: 4.6 Consensus size: 48
10788997 TATGTGTGCT
* * *
10789007 AGTGTAAGGCCATGTCTGTGACATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
* * * * * *
10789055 AGTGTAAGACCATGTTTGGAACATGGCATCGG-TATTGATATGTGTGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCA-CGATATGAGAGCC
* * *** *
10789103 AGTGTAAGACCACGTTTGGGACATGGCATCGACCATTTTACGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
* * * ** *
10789151 AATGTAAGACCATGTCTGGGACATGGCATCGGCCTCGGCATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
10789199 AGTGTAAGACCATGTTTGGGACATGGCATC
1 AGTGTAAGACCATGTTTGGGACATGGCATC
10789229 AGTAATTTAC
Statistics
Matches: 140, Mismatches: 32, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
47 1 0.01
48 138 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
Found at i:10789158 original size:96 final size:96
Alignment explanation
Indices: 10788994--10789228 Score: 299
Period size: 96 Copynumber: 2.4 Consensus size: 96
10788984 GACATTTGGG
* * * * * *
10788994 TGATATGTGTGCTAGTGTAAGGCCATGTCTGTGACATGGCATCGGCCACGATATGAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATACGAGAGCCAATG
* *
10789059 TAAGACCATGTTTGGAACATGGCATCGGTAT
66 TAAGACCATGTCTGGAACATGGCATCGGCAT
* ***
10789090 TGATATGTGTGCTAGTGTAAGACCACGTTTGGGACATGGCATCGACCATTTTACGAGAGCCAATG
1 TGATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATACGAGAGCCAATG
* *
10789155 TAAGACCATGTCTGGGACATGGCATCGGCCT
66 TAAGACCATGTCTGGAACATGGCATCGGCAT
* ** * *
10789186 CGGCATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATC
1 TGATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATC
10789229 AGTAATTTAC
Statistics
Matches: 119, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 119 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (96 bp):
TGATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATACGAGAGCCAATG
TAAGACCATGTCTGGAACATGGCATCGGCAT
Found at i:10795114 original size:31 final size:31
Alignment explanation
Indices: 10795079--10795141 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
10795069 TAAGAAAGGA
*
10795079 AAATTAAGTCCACGTTTTATTGGACCTTATG
1 AAATTAAGTCCACGTTTTATTAGACCTTATG
10795110 AAATTAAGTCCACGTTTTATTAGACCTTATG
1 AAATTAAGTCCACGTTTTATTAGACCTTATG
10795141 A
1 A
10795142 GGTGACAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (31 bp):
AAATTAAGTCCACGTTTTATTAGACCTTATG
Found at i:10800139 original size:6 final size:6
Alignment explanation
Indices: 10800130--10800155 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10800120 ATATGTATAT
10800130 AATAAG AATAAG AATAAG AATAAG AA
1 AATAAG AATAAG AATAAG AATAAG AA
10800156 AGAAAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AATAAG
Found at i:10802625 original size:155 final size:155
Alignment explanation
Indices: 10802028--10802625 Score: 624
Period size: 155 Copynumber: 3.9 Consensus size: 155
10802018 GACTATTTGT
* ** * *
10802028 CGATGAGAGCTGGGCCCAAACTAATTACTTCGGACGTTCTGATGAGGCATTGGGTGCCAAATGGT
1 CGATGAGCGCTGGGTGCAAACTAATTACTTCGAACGTTCTGATGAGGCACTGGGTGCCAAATGGT
* * * * * *
10802093 TACTTCGACTACGTGTCGATGAGTACTAGGAAAAATTTTTGCTTCAGACGTTCCGATGAGTGTTG
66 TACTTCAACTACGTGTCGATGAGTACTAGGCACAATTTTTACTTCGGACATTCCGATGAGTGTTG
*
10802158 GGCACAACATTTACTTCAGTTATAT
131 GGCACAACATTTACTTCAGTTATAC
* * *
10802183 CGATGAGCACTGGGCGCAAACTAATTACTTC-AGACGTTCTGATGAGGCACTGGATGCCAAATGG
1 CGATGAGCGCTGGGTGCAAACTAATTACTTCGA-ACGTTCTGATGAGGCACTGGGTGCCAAATGG
* * * * * *
10802247 TTACTTAAACTACATGTCGATGAGTGCTGGGCACAATTTTTACTTCGGACATTTCGATGAGTGCT
65 TTACTTCAACTACGTGTCGATGAGTACTAGGCACAATTTTTACTTCGGACATTCCGATGAGTGTT
* * **
10802312 GGACACAACATTAACTTTGGTTATAC
130 GGGCACAACATTTACTTCAGTTATAC
* * * * * * * * * *
10802338 CGATAAGTGATGGGTGCAAACTAATTACTTCAAACATTCCGATGAGACACTAGGTGTCAAATAGT
1 CGATGAGCGCTGGGTGCAAACTAATTACTTCGAACGTTCTGATGAGGCACTGGGTGCCAAATGGT
* * * * * * *
10802403 TACTTCAACTACGTGTTGATGAGTGCTAGGCACAATTTTTACTTCGAACGTTTCGATGGGTGATG
66 TACTTCAACTACGTGTCGATGAGTACTAGGCACAATTTTTACTTCGGACATTCCGATGAGTGTTG
* * *
10802468 GGCAAAACATTTACTCCAATTATAC
131 GGCACAACATTTACTTCAGTTATAC
* * *
10802493 CAATGAGCGCTAGGTGCAAACTAATTACTTCGAACGTT-TCGATGAGGCACTGGGTGTCAAATGG
1 CGATGAGCGCTGGGTGCAAACTAATTACTTCGAACGTTCT-GATGAGGCACTGGGTGCCAAATGG
* * * * * * * * * * * *
10802557 ATAATTCGACTATGTTTTGAAGAGTACTGGGCACAATTTTTACTTCGGTCATACCGATAAGCGTT
65 TTACTTCAACTACGTGTCGATGAGTACTAGGCACAATTTTTACTTCGGACATTCCGATGAGTGTT
10802622 GGGC
130 GGGC
10802626 GCAATCTATT
Statistics
Matches: 362, Mismatches: 78, Indels: 6
0.81 0.17 0.01
Matches are distributed among these distances:
155 361 1.00
156 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (155 bp):
CGATGAGCGCTGGGTGCAAACTAATTACTTCGAACGTTCTGATGAGGCACTGGGTGCCAAATGGT
TACTTCAACTACGTGTCGATGAGTACTAGGCACAATTTTTACTTCGGACATTCCGATGAGTGTTG
GGCACAACATTTACTTCAGTTATAC
Found at i:10803075 original size:2 final size:2
Alignment explanation
Indices: 10803068--10803099 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10803058 ATTGTACATA
10803068 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
10803100 GATCATGATA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:10804641 original size:48 final size:46
Alignment explanation
Indices: 10804545--10804762 Score: 189
Period size: 46 Copynumber: 4.7 Consensus size: 46
10804535 TCATTTGTAT
10804545 GCTAGTGTAAGACATGTCTGGGACATGCATCGGTCACATT--G-TGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGAGATGAGA
* *
10804591 GCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGATGAGA
* * * * *
10804639 GCTAGTGTAAGACATGTCTAGGACATGCATCGACCTCGTGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG-AGA
* * * *
10804685 GCCAGTGTAAGACATGTCTGGGACATGCGTCGGC-TATGATATGTG-
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TGAGATGAGA
* *
10804730 TC-AGTGTAAGACCATATCTGGGACATGGCATCG
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
10804763 ACACGTATAG
Statistics
Matches: 142, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
44 9 0.06
45 19 0.13
46 64 0.45
47 27 0.19
48 23 0.16
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAGA
Found at i:10806092 original size:20 final size:21
Alignment explanation
Indices: 10806053--10806092 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10806043 GTTATAACGA
10806053 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
10806074 CCACATGGGCGTG-TGCCCT
1 CCACACGGGCGTGTTGCCCT
10806093 GTTTCAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.30, T:0.23
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:10812494 original size:46 final size:49
Alignment explanation
Indices: 10812444--10812672 Score: 242
Period size: 50 Copynumber: 4.8 Consensus size: 49
10812434 TCGGTCTCGT
*
10812444 GATGT-AAGCCAGTGTAAGA-CATGTCTGGGACAT-GCGTCAGCTAC-GA
1 GATGTGAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACGGA
* *
10812490 GATGT---GTCAGTGAAAGACCATGTCTGGGACATGGCATCAGCACGGA
1 GATGTGAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGGA
**
10812536 GATGTGAAAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGA
1 GATGTG-AAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGGA
* * * **
10812586 GATGTGAGAGCCAGTGTAAGACCATGACTGGGACATGGCGTCGGC-CTCA
1 GATGTGA-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGGA
* *
10812635 -ATTTTGATAGTCAGTGTAAGACCATGTCTGGGACATGG
1 GA-TGTGA-AGCCAGTGTAAGACCATGTCTGGGACATGG
10812673 AATCGGCATT
Statistics
Matches: 158, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
44 10 0.06
45 16 0.10
46 19 0.12
48 1 0.01
49 35 0.22
50 77 0.49
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (49 bp):
GATGTGAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGGA
Found at i:10822108 original size:21 final size:22
Alignment explanation
Indices: 10822062--10822108 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
10822052 TAAATTGATT
*
10822062 TTAAAACTTTAAAATATTCCAA
1 TTAAAACTTTAAAATATTCAAA
* *
10822084 TTAAAATTTTAAAGTATT-AAA
1 TTAAAACTTTAAAATATTCAAA
10822105 TTAA
1 TTAA
10822109 TCAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAACTTTAAAATATTCAAA
Found at i:10831851 original size:15 final size:16
Alignment explanation
Indices: 10831830--10831874 Score: 76
Period size: 15 Copynumber: 2.9 Consensus size: 16
10831820 AACCAAAATA
10831830 AAGAAATCCAAGATAG
1 AAGAAATCCAAGATAG
10831846 AA-AAATCCAAGAT-G
1 AAGAAATCCAAGATAG
10831860 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
10831875 CAGAAGTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.11
15 22 0.81
16 2 0.07
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (16 bp):
AAGAAATCCAAGATAG
Found at i:10841675 original size:111 final size:111
Alignment explanation
Indices: 10841481--10841709 Score: 440
Period size: 111 Copynumber: 2.1 Consensus size: 111
10841471 AAGGTTAGAA
*
10841481 ACTCTTTATGCGACTAAGTCTTTAGCTAACCGTTTAGTGTTGAAACAATGTCTATTTACGTTTCG
1 ACTCTTTATGCGACTAAGTCTTTAGCTAACCGTTTAGTGTTGAAACAACGTCTATTTACGTTTCG
*
10841546 CATGAACGAATGTGAGCTTCTTAGAGATCACATCAGTCAATTCATT
66 CATGAACAAATGTGAGCTTCTTAGAGATCACATCAGTCAATTCATT
10841592 ACTCTTTATGCGACTAAGTCTTTAGCTAACCGTTTAGTGTTGAAACAACGTCTATTTACGTTTCG
1 ACTCTTTATGCGACTAAGTCTTTAGCTAACCGTTTAGTGTTGAAACAACGTCTATTTACGTTTCG
10841657 CATGAACAAATGTGAGCTTCTTAGAGATCACATCAGTCAATTCATT
66 CATGAACAAATGTGAGCTTCTTAGAGATCACATCAGTCAATTCATT
10841703 ACTCTTT
1 ACTCTTT
10841710 TAAATGATTT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 116 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (111 bp):
ACTCTTTATGCGACTAAGTCTTTAGCTAACCGTTTAGTGTTGAAACAACGTCTATTTACGTTTCG
CATGAACAAATGTGAGCTTCTTAGAGATCACATCAGTCAATTCATT
Found at i:10856386 original size:23 final size:23
Alignment explanation
Indices: 10856358--10856405 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
10856348 TTAGGGTTTA
10856358 TTTTAGGTTTTGAAT-TTGGGCTT
1 TTTTAGGTTTTGAATCTTGGG-TT
* *
10856381 TTTTAGTTTTTGCATCTTGGGTT
1 TTTTAGGTTTTGAATCTTGGGTT
10856404 TT
1 TT
10856406 AAATGGGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.10, C:0.06, G:0.23, T:0.60
Consensus pattern (23 bp):
TTTTAGGTTTTGAATCTTGGGTT
Found at i:10870539 original size:22 final size:23
Alignment explanation
Indices: 10870514--10870558 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
10870504 ATATGAAAAT
10870514 TTAAAATTTAC-TTGTTAAATAA
1 TTAAAATTTACATTGTTAAATAA
* *
10870536 TTAACATTTACATTTTTAAATAA
1 TTAAAATTTACATTGTTAAATAA
10870559 ATTACTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATTTACATTGTTAAATAA
Found at i:10871544 original size:31 final size:31
Alignment explanation
Indices: 10871506--10871567 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
10871496 AGTTATTAAG
10871506 ATTATATGTTAATGCATACTTTTCTTTATTT
1 ATTATATGTTAATGCATACTTTTCTTTATTT
10871537 ATTATATGTTAATGCATACTTTTCTTTATTT
1 ATTATATGTTAATGCATACTTTTCTTTATTT
10871568 TTTCCACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (31 bp):
ATTATATGTTAATGCATACTTTTCTTTATTT
Found at i:10875199 original size:35 final size:35
Alignment explanation
Indices: 10875159--10875228 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
10875149 CCAAAGTTAA
10875159 GTTCAGTTCAAGTT-ACCCAGAAAATTGGTTAAGAT
1 GTTCAGTTCAAGTTAACCC-GAAAATTGGTTAAGAT
10875194 GTTCAGTTCAAGTTAACCCGAAAATTGGTTAAGAT
1 GTTCAGTTCAAGTTAACCCGAAAATTGGTTAAGAT
10875229 AAAACATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (35 bp):
GTTCAGTTCAAGTTAACCCGAAAATTGGTTAAGAT
Found at i:10876411 original size:2 final size:2
Alignment explanation
Indices: 10876404--10876428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10876394 AGCCTTTTTG
10876404 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 G
10876429 CGGGAGGAGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10882341 original size:29 final size:28
Alignment explanation
Indices: 10882304--10882359 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
10882294 ATTACATTTT
* *
10882304 ATTATTTTTTAAAATATTTATATTTTAAG
1 ATTAATTTTTAAAATATATAT-TTTTAAG
10882333 ATTAATTTTTAAAATATATATTTTTAA
1 ATTAATTTTTAAAATATATATTTTTAA
10882360 ATATTGAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTAATTTTTAAAATATATATTTTTAAG
Found at i:10882363 original size:14 final size:15
Alignment explanation
Indices: 10882309--10882360 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
10882299 ATTTTATTAT
*
10882309 TTTTTAAAATATTTA
1 TTTTTAAAATATATA
*
10882324 TATTTTAAGAT-TA-A
1 T-TTTTAAAATATATA
10882338 TTTTTAAAATATATA
1 TTTTTAAAATATATA
10882353 TTTTTAAA
1 TTTTTAAA
10882361 TATTGAACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.26
14 4 0.13
15 11 0.35
16 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTTTAAAATATATA
Found at i:10895700 original size:5 final size:5
Alignment explanation
Indices: 10895674--10895731 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
10895664 ATGTGTTAAA
* *
10895674 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
10895723 ATATT ATAT
1 ATATT ATAT
10895732 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:10895710 original size:10 final size:9
Alignment explanation
Indices: 10895675--10895732 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
10895665 TGTGTTAAAA
10895675 TATATATAT
1 TATATATAT
*
10895684 TAAAT-TAT
1 TATATATAT
10895692 TAT-TATAT
1 TATATATAT
10895700 TATAGTATAT
1 TATA-TATAT
10895710 TATAT-TA-
1 TATATATAT
10895717 TATATTATAT
1 TATA-TATAT
10895727 TATATA
1 TATATA
10895733 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:10895722 original size:12 final size:12
Alignment explanation
Indices: 10895677--10895732 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
10895667 TGTTAAAATA
*
10895677 TATATATTAAAT
1 TATATATTATAT
10895689 TAT-TATTATATT
1 TATATATTATA-T
10895701 ATAGTATATTATAT
1 -TA-TATATTATAT
10895715 TATATATTATAT
1 TATATATTATAT
10895727 TATATA
1 TATATA
10895733 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:10897070 original size:18 final size:19
Alignment explanation
Indices: 10897047--10897085 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
10897037 ATATATAGAT
10897047 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
10897065 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
10897084 AT
1 AT
10897086 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:10897432 original size:39 final size:40
Alignment explanation
Indices: 10897325--10897459 Score: 109
Period size: 39 Copynumber: 3.4 Consensus size: 40
10897315 GACCTCGAGT
* **
10897325 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGATAGAGC
** **
10897366 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCA-AG-GC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGG-ATAGAGC
* * *
10897404 CGATGAGACACTGGGTGTCAACTATTACTTCGAAT-TATC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
*
10897443 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
10897460 CCATATTAGT
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
38 20 0.27
39 35 0.47
40 2 0.03
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
Found at i:10903518 original size:152 final size:152
Alignment explanation
Indices: 10903242--10903547 Score: 612
Period size: 152 Copynumber: 2.0 Consensus size: 152
10903232 AATACCCAGT
10903242 ATCCGTCAATTCTCACGAATGATCATTTTACATATATGCACTCCCGTGAACCTCACATCTCATGG
1 ATCCGTCAATTCTCACGAATGATCATTTTACATATATGCACTCCCGTGAACCTCACATCTCATGG
10903307 CGGAATTACTAGTCTAGGTTAAATTCCCCATATCATGAACTCATAAGGTGATGTCGGGATTACCA
66 CGGAATTACTAGTCTAGGTTAAATTCCCCATATCATGAACTCATAAGGTGATGTCGGGATTACCA
10903372 GTCCAGGCTAAATTCCCTTATG
131 GTCCAGGCTAAATTCCCTTATG
10903394 ATCCGTCAATTCTCACGAATGATCATTTTACATATATGCACTCCCGTGAACCTCACATCTCATGG
1 ATCCGTCAATTCTCACGAATGATCATTTTACATATATGCACTCCCGTGAACCTCACATCTCATGG
10903459 CGGAATTACTAGTCTAGGTTAAATTCCCCATATCATGAACTCATAAGGTGATGTCGGGATTACCA
66 CGGAATTACTAGTCTAGGTTAAATTCCCCATATCATGAACTCATAAGGTGATGTCGGGATTACCA
10903524 GTCCAGGCTAAATTCCCTTATG
131 GTCCAGGCTAAATTCCCTTATG
10903546 AT
1 AT
10903548 GACAAACACC
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 154 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (152 bp):
ATCCGTCAATTCTCACGAATGATCATTTTACATATATGCACTCCCGTGAACCTCACATCTCATGG
CGGAATTACTAGTCTAGGTTAAATTCCCCATATCATGAACTCATAAGGTGATGTCGGGATTACCA
GTCCAGGCTAAATTCCCTTATG
Done.