Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 38 of 210
Found at i:12168805 original size:7 final size:7
Alignment explanation
Indices: 12168782--12168812 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
12168772 AGCTTAGGAT
12168782 TTTAGGG
1 TTTAGGG
12168789 TTTAGAGG
1 TTTAG-GG
12168797 TTTAGGG
1 TTTAGGG
12168804 TTTAGGG
1 TTTAGGG
12168811 TT
1 TT
12168813 AAATCCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:12169844 original size:21 final size:22
Alignment explanation
Indices: 12169801--12169846 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
12169791 ACTATTCCGA
*
12169801 TTAAATATGTAAGGCGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
12169823 TTAAATAGGTAAGGCG-TTCTG
1 TTAAATAGGTAAGGCGTTTCTG
12169844 TTA
1 TTA
12169847 TTACAGCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (22 bp):
TTAAATAGGTAAGGCGTTTCTG
Found at i:12169994 original size:54 final size:53
Alignment explanation
Indices: 12169930--12170031 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 53
12169920 TTACAGCACA
12169930 TGATTATGTTGTTATGTTCTGAAATAATTG-AGTGGATTTGAAATAATTTGTTTT
1 TGATTATGTTGTTATGTTCTGAAAT-A-TGCAGTGGATTTGAAATAATTTGTTTT
**
12169984 TGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTT
1 TGATTATGTTGTTATGTTCTGAAATATGCAGTGGATTTGAAATAATTT
12170032 CTGAGGCTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
52 2 0.04
53 18 0.40
54 25 0.56
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (53 bp):
TGATTATGTTGTTATGTTCTGAAATATGCAGTGGATTTGAAATAATTTGTTTT
Found at i:12170208 original size:15 final size:15
Alignment explanation
Indices: 12170188--12170228 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
12170178 TTTGGCGTGG
12170188 AGGTAAATTTTGTAA
1 AGGTAAATTTTGTAA
12170203 AGGTAAATTTTGTAA
1 AGGTAAATTTTGTAA
12170218 AGGTAAATTTT
1 AGGTAAATTTT
12170229 ATGTTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (15 bp):
AGGTAAATTTTGTAA
Found at i:12170267 original size:14 final size:14
Alignment explanation
Indices: 12170248--12170277 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12170238 ATAAAAGGTT
12170248 TTTAGTTAATCATC
1 TTTAGTTAATCATC
12170262 TTTAGTTAATCATC
1 TTTAGTTAATCATC
12170276 TT
1 TT
12170278 GCTGTTCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:12170542 original size:22 final size:22
Alignment explanation
Indices: 12170514--12170666 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
12170504 TTTATTGTTC
*
12170514 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
12170536 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
12170558 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
12170580 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
12170602 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
12170624 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
12170646 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
12170667 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:12171294 original size:9 final size:9
Alignment explanation
Indices: 12171280--12171761 Score: 93
Period size: 9 Copynumber: 56.7 Consensus size: 9
12171270 NNNNNNNNAC
12171280 ACATAACTT
1 ACATAACTT
*
12171289 ACATAACCT
1 ACATAACTT
*
12171298 ACTTAA--T
1 ACATAACTT
*
12171305 ATATAACTT
1 ACATAACTT
*
12171314 GCATAACTT
1 ACATAACTT
* *
12171323 AAATAAGTT
1 ACATAACTT
12171332 ACATAA-TAAT
1 ACATAACT--T
12171342 ACATAA--T
1 ACATAACTT
**
12171349 ACGCAACTT
1 ACATAACTT
*
12171358 ACAT--GTGT
1 ACATAACT-T
*
12171366 AAATAA--T
1 ACATAACTT
*
12171373 ACAGAACTT
1 ACATAACTT
12171382 ACATAACTT
1 ACATAACTT
* * *
12171391 GCATACCCT
1 ACATAACTT
*
12171400 ACATAAATT
1 ACATAACTT
* *
12171409 AAATAAGTT
1 ACATAACTT
12171418 ACATAA-TAAT
1 ACATAACT--T
* *
12171428 ACATACCCT
1 ACATAACTT
*
12171437 ACATAAATT
1 ACATAACTT
* *
12171446 AAATAAGTT
1 ACATAACTT
12171455 ACATAA-TAAT
1 ACATAACT--T
* *
12171465 ACATACCCT
1 ACATAACTT
*
12171474 ACATAAATT
1 ACATAACTT
* *
12171483 AAATAAGTT
1 ACATAACTT
12171492 ACATAA--T
1 ACATAACTT
*
12171499 ACACAACTT
1 ACATAACTT
**
12171508 ACGCAACTT
1 ACATAACTT
12171517 ACATAAC--
1 ACATAACTT
12171524 AC--AACTT
1 ACATAACTT
** *
12171531 ACGCATCTT
1 ACATAACTT
*
12171540 ACATAA--G
1 ACATAACTT
*
12171547 ACACAACTT
1 ACATAACTT
*
12171556 ACAT--GTGT
1 ACATAACT-T
*
12171564 AAATAA--T
1 ACATAACTT
*
12171571 ACATAAATT
1 ACATAACTT
12171580 ACATAACTT
1 ACATAACTT
*
12171589 ACATAA--G
1 ACATAACTT
*
12171596 ACAAAACTT
1 ACATAACTT
*
12171605 TCATAA--T
1 ACATAACTT
*
12171612 ACACAACTT
1 ACATAACTT
**
12171621 ACGCAACTT
1 ACATAACTT
*
12171630 ACATAA--G
1 ACATAACTT
12171637 ACATAACTT
1 ACATAACTT
*
12171646 ACAT--GTGT
1 ACATAACT-T
*
12171654 AAATAA--T
1 ACATAACTT
**
12171661 ACATATTTT
1 ACATAACTT
12171670 ACATAACTT
1 ACATAACTT
*
12171679 ACATAA--G
1 ACATAACTT
*
12171686 ACGTAACTT
1 ACATAACTT
*
12171695 ACATAAGTT
1 ACATAACTT
*
12171704 TCATAA--T
1 ACATAACTT
* *
12171711 ACACATCTT
1 ACATAACTT
**
12171720 ACGCAACTT
1 ACATAACTT
*
12171729 ACACAACTT
1 ACATAACTT
*
12171738 ACACAACTT
1 ACATAACTT
12171747 ACATAACTT
1 ACATAACTT
12171756 ACATAA
1 ACATAA
12171762 TGTATATCTT
Statistics
Matches: 336, Mismatches: 92, Indels: 90
0.65 0.18 0.17
Matches are distributed among these distances:
5 3 0.01
7 69 0.21
8 15 0.04
9 230 0.68
10 19 0.06
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (9 bp):
ACATAACTT
Found at i:12171436 original size:37 final size:37
Alignment explanation
Indices: 12171392--12171499 Score: 216
Period size: 37 Copynumber: 2.9 Consensus size: 37
12171382 ACATAACTTG
12171392 CATACCCTACATAAATTAAATAAGTTACATAATAATA
1 CATACCCTACATAAATTAAATAAGTTACATAATAATA
12171429 CATACCCTACATAAATTAAATAAGTTACATAATAATA
1 CATACCCTACATAAATTAAATAAGTTACATAATAATA
12171466 CATACCCTACATAAATTAAATAAGTTACATAATA
1 CATACCCTACATAAATTAAATAAGTTACATAATA
12171500 CACAACTTAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.30
Consensus pattern (37 bp):
CATACCCTACATAAATTAAATAAGTTACATAATAATA
Found at i:12171441 original size:19 final size:19
Alignment explanation
Indices: 12171417--12171479 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
12171407 TTAAATAAGT
12171417 TACATAATAATACATACCC
1 TACATAATAATACATACCC
* * ***
12171436 TACATAA-ATTAAATAAGT
1 TACATAATAATACATACCC
12171454 TACATAATAATACATACCC
1 TACATAATAATACATACCC
12171473 TACATAA
1 TACATAA
12171480 ATTAAATAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
18 13 0.39
19 20 0.61
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.29
Consensus pattern (19 bp):
TACATAATAATACATACCC
Found at i:12171529 original size:23 final size:25
Alignment explanation
Indices: 12171490--12171557 Score: 104
Period size: 23 Copynumber: 2.8 Consensus size: 25
12171480 ATTAAATAAG
*
12171490 TTACATAATACACAACTTACGCAAC
1 TTACATAAGACACAACTTACGCAAC
*
12171515 TTACAT-A-ACACAACTTACGCATC
1 TTACATAAGACACAACTTACGCAAC
12171538 TTACATAAGACACAACTTAC
1 TTACATAAGACACAACTTAC
12171558 ATGTGTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 21 0.52
24 2 0.05
25 17 0.43
ACGTcount: A:0.43, C:0.28, G:0.04, T:0.25
Consensus pattern (25 bp):
TTACATAAGACACAACTTACGCAAC
Found at i:12171596 original size:49 final size:49
Alignment explanation
Indices: 12171537--12171698 Score: 187
Period size: 49 Copynumber: 3.5 Consensus size: 49
12171527 ACTTACGCAT
*
12171537 CTTACATAAGACACAACTTACATGTGTAAATAATACATAAATTACATAA
1 CTTACATAAGACATAACTTACATGTGTAAATAATACATAAATTACATAA
* * * **
12171586 CTTACATAAGACA-AA---AC-T-T-T-CATAATACACAACTTACGCAA
1 CTTACATAAGACATAACTTACATGTGTAAATAATACATAAATTACATAA
**
12171627 CTTACATAAGACATAACTTACATGTGTAAATAATACATATTTTACATAA
1 CTTACATAAGACATAACTTACATGTGTAAATAATACATAAATTACATAA
*
12171676 CTTACATAAGACGTAACTTACAT
1 CTTACATAAGACATAACTTACAT
12171699 AAGTTTCATA
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
41 29 0.31
42 3 0.03
43 1 0.01
44 1 0.01
45 4 0.04
46 1 0.01
47 1 0.01
48 3 0.03
49 50 0.54
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (49 bp):
CTTACATAAGACATAACTTACATGTGTAAATAATACATAAATTACATAA
Found at i:12171603 original size:16 final size:16
Alignment explanation
Indices: 12171584--12171622 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12171574 TAAATTACAT
12171584 AACTTACATAAGACAA
1 AACTTACATAAGACAA
* * *
12171600 AACTTTCATAATACAC
1 AACTTACATAAGACAA
12171616 AACTTAC
1 AACTTAC
12171623 GCAACTTACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (16 bp):
AACTTACATAAGACAA
Found at i:12171614 original size:41 final size:41
Alignment explanation
Indices: 12171566--12171645 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
12171556 ACATGTGTAA
* *
12171566 ATAATACATAAATTACATAACTTACATAAGACAAAACTTTC
1 ATAATACACAAATTACACAACTTACATAAGACAAAACTTTC
* * *
12171607 ATAATACACAACTTACGCAACTTACATAAGACATAACTT
1 ATAATACACAAATTACACAACTTACATAAGACAAAACTT
12171646 ACATGTGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.28
Consensus pattern (41 bp):
ATAATACACAAATTACACAACTTACATAAGACAAAACTTTC
Found at i:12171646 original size:16 final size:16
Alignment explanation
Indices: 12171625--12171701 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
12171615 CAACTTACGC
12171625 AACTTACATAAGACAT
1 AACTTACATAAGACAT
** *
12171641 AACTTACATGTGTAAAT
1 AACTTACATAAG-ACAT
**
12171658 AA--TACATATTTTACAT
1 AACTTACATA--AGACAT
*
12171674 AACTTACATAAGACGT
1 AACTTACATAAGACAT
12171690 AACTTACATAAG
1 AACTTACATAAG
12171702 TTTCATAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
15 5 0.11
16 30 0.64
17 6 0.13
18 6 0.13
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (16 bp):
AACTTACATAAGACAT
Found at i:12171694 original size:90 final size:90
Alignment explanation
Indices: 12171512--12171700 Score: 301
Period size: 90 Copynumber: 2.1 Consensus size: 90
12171502 CAACTTACGC
*
12171512 AACTTACAT-A-ACACAACTTACGCATCTTACATAAGACACAACTTACATGTGTAAATAATACAT
1 AACTTACATAATACACAACTTACGCAACTTACATAAGACACAACTTACATGTGTAAATAATACAT
12171575 AAATTACATAACTTACATAAGACAA
66 AAATTACATAACTTACATAAGACAA
* *
12171600 AACTTTCATAATACACAACTTACGCAACTTACATAAGACATAACTTACATGTGTAAATAATACAT
1 AACTTACATAATACACAACTTACGCAACTTACATAAGACACAACTTACATGTGTAAATAATACAT
** **
12171665 ATTTTACATAACTTACATAAGACGT
66 AAATTACATAACTTACATAAGACAA
12171690 AACTTACATAA
1 AACTTACATAA
12171701 GTTTCATAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 8 0.09
89 1 0.01
90 82 0.90
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (90 bp):
AACTTACATAATACACAACTTACGCAACTTACATAAGACACAACTTACATGTGTAAATAATACAT
AAATTACATAACTTACATAAGACAA
Found at i:12171720 original size:25 final size:25
Alignment explanation
Indices: 12171600--12171771 Score: 96
Period size: 25 Copynumber: 6.8 Consensus size: 25
12171590 CATAAGACAA
* * * **
12171600 AACTTTCATAATACACAACTTACGC
1 AACTTACATAATACATATCTTACAT
* *
12171625 AACTTACATAAGACATAACTTACAT
1 AACTTACATAATACATATCTTACAT
* * *
12171650 --GTGTAAATAATACATATTTTACAT
1 AACT-TACATAATACATATCTTACAT
* * *
12171674 AACTTACATAAGACGTAACTTACAT
1 AACTTACATAATACATATCTTACAT
* * * **
12171699 AAGTTTCATAATACACATCTTACGC
1 AACTTACATAATACATATCTTACAT
* * *
12171724 AACTTACACAACTTACACAACTTACAT
1 AACTTACATAA--TACATATCTTACAT
**
12171751 AACTTACATAATGTATATCTT
1 AACTTACATAATACATATCTT
12171772 GTTGTCAAAT
Statistics
Matches: 107, Mismatches: 35, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
23 1 0.01
24 17 0.16
25 67 0.63
26 1 0.01
27 21 0.20
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATATCTTACAT
Found at i:12173751 original size:42 final size:42
Alignment explanation
Indices: 12173692--12173779 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
12173682 TGTTGCTAGA
* *
12173692 GGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGCTTAGAAAAAAACGCCGCTAAAGAACATGGTCTTCAGC
*
12173734 GGCGCTTATG-AAAAAACGCCGCTGAAGAACATGGTCTTCAGC
1 GGCGCTTA-GAAAAAAACGCCGCTAAAGAACATGGTCTTCAGC
12173776 GGCG
1 GGCG
12173780 TTTTTGTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (42 bp):
GGCGCTTAGAAAAAAACGCCGCTAAAGAACATGGTCTTCAGC
Found at i:12180343 original size:31 final size:31
Alignment explanation
Indices: 12180308--12180371 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
12180298 TATAATTAAT
*
12180308 TATATCAACAATTTTATTTA-AAATCAATCAC
1 TATATCAACAATTTTA-ATAGAAATCAATCAC
* *
12180339 TATATCAATAATTTTAATAGGAATCAATCAC
1 TATATCAACAATTTTAATAGAAATCAATCAC
12180370 TA
1 TA
12180372 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (31 bp):
TATATCAACAATTTTAATAGAAATCAATCAC
Found at i:12183889 original size:24 final size:26
Alignment explanation
Indices: 12183819--12183920 Score: 90
Period size: 24 Copynumber: 4.1 Consensus size: 26
12183809 GTTGTATAAT
* *
12183819 GGAAGCTCA-AAAGAGCCA-TAATCC
1 GGAAGCTCACGAAGAGCCATTAATCG
* * * *
12183843 GGAAGCTCATG-CGAGTCAATAAT-G
1 GGAAGCTCACGAAGAGCCATTAATCG
*
12183867 GGTAGCTC-CGAAGAGCCATTAATCG
1 GGAAGCTCACGAAGAGCCATTAATCG
12183892 GGAAGCTCACGAAGAGCCATATAA-CG
1 GGAAGCTCACGAAGAGCCAT-TAATCG
12183918 GGA
1 GGA
12183921 TGTTCATAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 30 0.48
25 12 0.19
26 16 0.26
27 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCG
Found at i:12186500 original size:25 final size:26
Alignment explanation
Indices: 12186472--12186528 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
12186462 CATGCTATTC
12186472 TTTTAATTTTATAA-ACTTTTT-AAA-T
1 TTTTAATTTT-TAATA-TTTTTAAAAGT
*
12186497 TTTTTATTTTTAATATTTTTAAAAGT
1 TTTTAATTTTTAATATTTTTAAAAGT
12186523 TTTTAA
1 TTTTAA
12186529 ATTATTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.30
25 13 0.48
26 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTAATTTTTAATATTTTTAAAAGT
Found at i:12194616 original size:25 final size:25
Alignment explanation
Indices: 12194588--12194646 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
12194578 AAATATATTG
*
12194588 TATATTAT-TGTATATATTTTAAGAA
1 TATATTATATGAATATA-TTTAAGAA
*
12194613 TATATT-TATGAATATATTTAGGAA
1 TATATTATATGAATATATTTAAGAA
*
12194637 TATTTTATAT
1 TATATTATAT
12194647 ACCTTTCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
TATATTATATGAATATATTTAAGAA
Found at i:12194620 original size:12 final size:12
Alignment explanation
Indices: 12194599--12194643 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
12194589 ATATTATTGT
12194599 ATATATTTTAAGA
1 ATATA-TTTAAGA
*
12194612 ATATATTTATGA
1 ATATATTTAAGA
*
12194624 ATATATTTAGGA
1 ATATATTTAAGA
12194636 ATAT-TTTA
1 ATATATTTA
12194644 TATACCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 4 0.13
12 21 0.70
13 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (12 bp):
ATATATTTAAGA
Found at i:12194643 original size:23 final size:25
Alignment explanation
Indices: 12194599--12194644 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
12194589 ATATTATTGT
12194599 ATATATTTTAAGAATATATTTATGA
1 ATATATTTTAAGAATATATTTATGA
*
12194624 ATATA-TTTAGGAATAT-TTTAT
1 ATATATTTTAAGAATATATTTAT
12194645 ATACCTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (25 bp):
ATATATTTTAAGAATATATTTATGA
Found at i:12196101 original size:2 final size:2
Alignment explanation
Indices: 12196094--12196127 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12196084 GACCATCTCA
12196094 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
12196128 CAAAGAGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12201861 original size:60 final size:60
Alignment explanation
Indices: 12201767--12201881 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
12201757 AGTTTACCCT
* *
12201767 AAAATATAAGAAAAATTATGATAAATTATGATTATAATTTAATTTAAATATTATTAATTGG
1 AAAATATAAGAAAAATTATGATAAAATATAATTATAATTTAATTTAAA-ATTATTAATTGG
*
12201828 AAAATATAA-AAAATTTATGATAAAATATAATTATAATTTAATTTAAAATTATTA
1 AAAATATAAGAAAAATTATGATAAAATATAATTATAATTTAATTTAAAATTATTA
12201882 GTTAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 7 0.14
60 35 0.69
61 9 0.18
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (60 bp):
AAAATATAAGAAAAATTATGATAAAATATAATTATAATTTAATTTAAAATTATTAATTGG
Found at i:12202079 original size:22 final size:23
Alignment explanation
Indices: 12202049--12202094 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
12202039 ATAAAAATAA
*
12202049 ATCCCTACAAATCAA-TTCTATG
1 ATCCCTACAAATCAACTCCTATG
*
12202071 ATCCTTACAAATCAACTCCTATG
1 ATCCCTACAAATCAACTCCTATG
12202094 A
1 A
12202095 ATCAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.30
Consensus pattern (23 bp):
ATCCCTACAAATCAACTCCTATG
Found at i:12202922 original size:354 final size:347
Alignment explanation
Indices: 12202247--12202945 Score: 1049
Period size: 354 Copynumber: 2.0 Consensus size: 347
12202237 TCAATCTAAG
*
12202247 GAAGTCTTCCTTCTTAAGTGCTTTAGTGAACATATCAACAATTTGTTCTCTTGATGGGGTAAAAA
1 GAAGTCTTCCTTCTTAAGTGCTTTAGTGAACATATCAACAATTTGTTCTCTTGAAGGGGTAAAAA
* *
12202312 GAGTGCAAATCTTCTTATTAGTAATTGCACTTCTCACAAAATGGCAATCGACTTTGATGTGCTTT
66 GAGTGCAAATCTTCTTATTAGTAATTGCACTTCTCACAAAATGACAATAGACTTTGATGTGCTTT
* * **
12202377 GTCCGTTACGAAAACAAGATTGTTTATGAATTGTCGTATGATTATCACAATGCACATGCATATTA
131 GTCCGTTACGAAAACAAGATTGTTTATGAATTGTCG-ATGATTATCACAATGCACAGGAATAGGA
* * * *
12202442 TTTTAATAGATGATACTGAAATCCTTGAGTAAAGCTTTTAACCAAATCAACTCACATGTCATGTG
195 TCTGAATAGATGATACTAAAATCCTTGAGTAAAGCTTTCAACCAAATCAACTCACATGTCATGTG
* *** *
12202507 AGCCATGTCATGGTATTCTGCTTCAGCACTAGATCTCGATACAACTGTTTGTTTCTTACTCTTCC
260 AGCCATGGCACAATATTCCGCTTCAGCACTAGATCTCGATACAACTGTTTGTTTCTTACTCTTCC
*
12202572 AAGTTACTAGATTCTGACCTGAA
325 AAGTTACTAGATTCCGACCTGAA
* *
12202595 GAAGTCTTCCTTCTTAAGTGCTTTAGTGAGCATATCAACAATTTGTTCTCTTGAAGGGGTAAAAG
1 GAAGTCTTCCTTCTTAAGTGCTTTAGTGAACATATCAACAATTTGTTCTCTTGAAGGGGTAAAAA
* *
12202660 GAGTGTAAATCTTCTTATTAGTAATTGCATTTCTCACAAAATGACAATAGACTTTGATGTGCTTT
66 GAGTGCAAATCTTCTTATTAGTAATTGCACTTCTCACAAAATGACAATAGACTTTGATGTGCTTT
* * * * *
12202725 GTCCGTTAATGAAAATACGATTGCTTGCAATATGAATTGCTAC-ATGATTATCACAGTGCATAGG
131 GTCCGTT-ACGAAAACAAGATTG-TT----TATGAATTG-T-CGATGATTATCACAATGCACAGG
*
12202789 AATAGGATCTGAATAGATGATACTAAAATTCTTGAGTAAAGCTTTCAACCAAATCAACTCACATG
188 AATAGGATCTGAATAGATGATACTAAAATCCTTGAGTAAAGCTTTCAACCAAATCAACTCACATG
*
12202854 TCATGTGAGCCATGGCACAATATTCCGCTTCAGCACTAGATCTCGATACAACTGTTTGTTTTTTA
253 TCATGTGAGCCATGGCACAATATTCCGCTTCAGCACTAGATCTCGATACAACTGTTTGTTTCTTA
*
12202919 CTCTTCCAAGTTATTAGATTCCGACCT
318 CTCTTCCAAGTTACTAGATTCCGACCT
12202946 ACAAAGGTAC
Statistics
Matches: 314, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
348 130 0.41
349 12 0.04
350 2 0.01
354 168 0.54
355 1 0.00
356 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (347 bp):
GAAGTCTTCCTTCTTAAGTGCTTTAGTGAACATATCAACAATTTGTTCTCTTGAAGGGGTAAAAA
GAGTGCAAATCTTCTTATTAGTAATTGCACTTCTCACAAAATGACAATAGACTTTGATGTGCTTT
GTCCGTTACGAAAACAAGATTGTTTATGAATTGTCGATGATTATCACAATGCACAGGAATAGGAT
CTGAATAGATGATACTAAAATCCTTGAGTAAAGCTTTCAACCAAATCAACTCACATGTCATGTGA
GCCATGGCACAATATTCCGCTTCAGCACTAGATCTCGATACAACTGTTTGTTTCTTACTCTTCCA
AGTTACTAGATTCCGACCTGAA
Found at i:12205197 original size:22 final size:22
Alignment explanation
Indices: 12205169--12205213 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12205159 TAAAAAATAA
*
12205169 ATCCCTACAAACCAGTTCTATG
1 ATCCCTACAAACCAGCTCTATG
*
12205191 ATCCCTACAAATCAGCTCTATG
1 ATCCCTACAAACCAGCTCTATG
12205213 A
1 A
12205214 ATCAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (22 bp):
ATCCCTACAAACCAGCTCTATG
Found at i:12206512 original size:18 final size:18
Alignment explanation
Indices: 12206489--12206527 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12206479 GTAATAAAGT
12206489 ATGCATAATATAATTAAA
1 ATGCATAATATAATTAAA
12206507 ATGCATAATATAATTAAA
1 ATGCATAATATAATTAAA
12206525 ATG
1 ATG
12206528 TAAATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (18 bp):
ATGCATAATATAATTAAA
Found at i:12208386 original size:18 final size:18
Alignment explanation
Indices: 12208363--12208400 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12208353 TTAATCATAA
*
12208363 TTTAAAAAAACATTGAAT
1 TTTAAAAAAAAATTGAAT
*
12208381 TTTAAAAAAAAATTGTAT
1 TTTAAAAAAAAATTGAAT
12208399 TT
1 TT
12208401 AATTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
TTTAAAAAAAAATTGAAT
Found at i:12209948 original size:50 final size:50
Alignment explanation
Indices: 12209894--12210052 Score: 160
Period size: 50 Copynumber: 3.2 Consensus size: 50
12209884 ACCATTTTGG
* * *
12209894 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGCCGTTGTGA
1 CTTTAATCTCTTTAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGA
* ** * * * * *
12209944 CTTTAATCTGTTCCACTGC-ATCGCCTGGGAAGTAAGATTTGCTGTTGT-A
1 CTTTAATCTCTTTAACTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGA
* * *
12209993 GCTTTAATCTCTTTAACTGCAATATCAGGGAAGCAAGATTCACCGTTGTGG
1 -CTTTAATCTCTTTAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGA
12210044 CTTTAATCT
1 CTTTAATCT
12210053 GTTCCACGGT
Statistics
Matches: 85, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
49 3 0.04
50 80 0.94
51 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (50 bp):
CTTTAATCTCTTTAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGA
Found at i:12210048 original size:100 final size:100
Alignment explanation
Indices: 12209893--12210081 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 100
12209883 CACCATTTTG
* * * * *
12209893 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGCCGTTGTGACTTTAATCTGTTCC
1 GCTTTAATCTCTTTAACTGCAATATCAGGGAAGCAAGATTCACCGTTGTGACTTTAATCTGTTCC
* *
12209958 ACTGCATCGCCTGGGAAGTAAGATTTGCTGTTGTA
66 ACGGCATCGCCTGAGAAGTAAGATTTGCTGTTGTA
*
12209993 GCTTTAATCTCTTTAACTGCAATATCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTCTTTAACTGCAATATCAGGGAAGCAAGATTCACCGTTGTGACTTTAATCTGTTCC
* *
12210058 ACGGTATCGCCTGAGAGGTAAGAT
66 ACGGCATCGCCTGAGAAGTAAGAT
12210082 CTATAATTCT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (100 bp):
GCTTTAATCTCTTTAACTGCAATATCAGGGAAGCAAGATTCACCGTTGTGACTTTAATCTGTTCC
ACGGCATCGCCTGAGAAGTAAGATTTGCTGTTGTA
Found at i:12210208 original size:44 final size:44
Alignment explanation
Indices: 12210179--12210540 Score: 174
Period size: 44 Copynumber: 7.8 Consensus size: 44
12210169 CATTTATTTT
* *
12210179 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTC
* * ** *
12210223 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTC
* ** * *
12210267 AATCTGAAGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATTCTTTA-TTTT
1 AATC-----CG--CT-C-C-ACTGTAATC-TCAGGGAGATAAGA-TCACTAGCTTC
* * * *
12210321 AATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTT
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTC
* * * ** *
12210365 AATCTGCTTCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTC
** ** * *
12210409 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAAAGATAAGATTCTTTA-TTTT
1 AATC-----CG--CT-C-C-ACTGTAATC-TCAGGGAGATAAGA-TCACTAGCTTC
* * * *
12210463 AATCTGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTC
* *
12210507 AATCTGCTCCACTGTAATCTCAGAGAGATAAGAT
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGAT
12210541 ATGTAATTTC
Statistics
Matches: 243, Mismatches: 47, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
43 6 0.02
44 158 0.65
45 4 0.02
46 2 0.01
47 4 0.02
49 5 0.02
51 4 0.02
52 1 0.00
53 4 0.02
54 49 0.20
55 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
AATCCGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTC
Found at i:12210389 original size:142 final size:142
Alignment explanation
Indices: 12210128--12210540 Score: 720
Period size: 142 Copynumber: 2.9 Consensus size: 142
12210118 GAGATAAGAC
*
12210128 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAATA-TCATTTATTTTAATCCGCTCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATTC-TTTATTTTAATCCGCTCCACT
12210192 GTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
65 GTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
12210257 TTCTGGCTTCAAT
130 TTCTGGCTTCAAT
* * *
12210270 CTGAAGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATTCTTTATTTTAATCCGCTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATTCTTTATTTTAATCCGCTCCACTG
* *
12210335 TAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTTCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
12210400 TCTGGCTTCAAT
131 TCTGGCTTCAAT
*
12210412 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATTCTTTATTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATTCTTTATTTTAATCCGCTCCACTG
* * *
12210477 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGAGAGATAAGAT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
12210541 ATGTAATTTC
Statistics
Matches: 255, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
142 253 0.99
143 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATTCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:12210722 original size:131 final size:130
Alignment explanation
Indices: 12210531--12210982 Score: 652
Period size: 131 Copynumber: 3.5 Consensus size: 130
12210521 TAATCTCAGA
* * * * **
12210531 GAGATAAGATATGTAATTTCCAACCTATTCCTCTGCTGGTCAGGGACATAGGACTTGTGGCTTAA
1 GAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
* * * *
12210596 ATCTGTTTCCCTACTCCTGGGAAAGATAAGATTCGCCGTATTGGATCTACTCCGCTACTGCTTAG
66 ATCTGTTTCCCTACTCCTGGG-AAGGTAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAG
12210661 G
130 G
* ** ** *
12210662 GAGATAAGATCTGCAATTTCTGACCTATTCCACTGCTGGTCAGGGACATAAGACTTGTGGCTTAA
1 GAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
*
12210727 ATCTGTTTCCCTACTCCTAGGGAAGGTAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTCG
66 ATCTGTTTCCCTACTCCT-GGGAAGGTAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAG
12210792 G
130 G
* * *
12210793 GAGACAAGATCTGCAATTTCCAACCAACTCCACTGCTGACCAGGGACATAGGACGTGTGGCTTAA
1 GAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
* *
12210858 ATCTGTTTCCCTACTCTTGGGGAAGGTAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTCAG
66 ATCTGTTTCCCTACTCCT-GGGAAGGTAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAG
12210923 G
130 G
* * *
12210924 GAAACAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGGGACATAGGACTTGTG
1 GAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTG
12210983 ATTTCACCGA
Statistics
Matches: 290, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
131 287 0.99
132 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (130 bp):
GAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
ATCTGTTTCCCTACTCCTGGGAAGGTAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
Found at i:12212228 original size:6 final size:6
Alignment explanation
Indices: 12212217--12212266 Score: 64
Period size: 6 Copynumber: 7.8 Consensus size: 6
12212207 TAACCTCTCT
*
12212217 ATTTTC ATTTTC ATTTTC ATTTTTC ATTCTC ATTTTTC ATTTTTC ATTTT
1 ATTTTC ATTTTC ATTTTC A-TTTTC ATTTTC A-TTTTC A-TTTTC ATTTT
12212267 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 22 0.55
7 18 0.45
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTC
Found at i:12212242 original size:7 final size:7
Alignment explanation
Indices: 12212218--12212267 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
12212208 AACCTCTCTA
12212218 TTTTCA-
1 TTTTCAT
12212224 TTTTCA-
1 TTTTCAT
12212230 TTTTCAT
1 TTTTCAT
12212237 TTTTCA-
1 TTTTCAT
*
12212243 TTCTCAT
1 TTTTCAT
12212250 TTTTCAT
1 TTTTCAT
12212257 TTTTCAT
1 TTTTCAT
12212264 TTTT
1 TTTT
12212268 TTTATTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
6 17 0.43
7 23 0.57
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCAT
Found at i:12212242 original size:13 final size:13
Alignment explanation
Indices: 12212217--12212267 Score: 77
Period size: 13 Copynumber: 3.9 Consensus size: 13
12212207 TAACCTCTCT
12212217 ATTTTCA-TTTTC
1 ATTTTCATTTTTC
12212229 ATTTTCATTTTTC
1 ATTTTCATTTTTC
*
12212242 ATTCTCATTTTTC
1 ATTTTCATTTTTC
12212255 ATTTTTCATTTTT
1 A-TTTTCATTTTT
12212268 TTTATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.20
13 18 0.51
14 10 0.29
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTCATTTTTC
Found at i:12217979 original size:18 final size:18
Alignment explanation
Indices: 12217956--12217993 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12217946 TTAATCATAA
*
12217956 TTTAAAAAAACATTGAAT
1 TTTAAAAAAAAATTGAAT
*
12217974 TTTAAAAAAAAATTGTAT
1 TTTAAAAAAAAATTGAAT
12217992 TT
1 TT
12217994 AATTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
TTTAAAAAAAAATTGAAT
Found at i:12224681 original size:10 final size:10
Alignment explanation
Indices: 12224666--12224699 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
12224656 TTAAAAATTT
12224666 AAAATTAAAA
1 AAAATTAAAA
12224676 AAAATTAAAA
1 AAAATTAAAA
*
12224686 AATA-TAAAA
1 AAAATTAAAA
12224695 AAAAT
1 AAAAT
12224700 ATGTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:12228093 original size:27 final size:27
Alignment explanation
Indices: 12228037--12228108 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
12228027 AATCTAATCA
* * *
12228037 TTATAATATGGCCGGTGGAATCTGATTG
1 TTATAATATGG-TGTTGGAATCTGACTG
12228065 TTATAATATGGTGTTGGAATCTGACTG
1 TTATAATATGGTGTTGGAATCTGACTG
**
12228092 TTCCAATATGGTCGTTG
1 TTATAATATGGT-GTTG
12228109 AATTTTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (27 bp):
TTATAATATGGTGTTGGAATCTGACTG
Found at i:12233502 original size:30 final size:30
Alignment explanation
Indices: 12233466--12233526 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
12233456 ACAAAATTAA
*
12233466 GTTATCTGCGAAGAGATGAGACAATGTTGG
1 GTTATCTGCGAAGAGATGAGACAACGTTGG
12233496 GTTATCTGCGAAGAGATGAGACAACGTTGG
1 GTTATCTGCGAAGAGATGAGACAACGTTGG
12233526 G
1 G
12233527 CCATTCCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (30 bp):
GTTATCTGCGAAGAGATGAGACAACGTTGG
Found at i:12245386 original size:27 final size:26
Alignment explanation
Indices: 12245355--12245417 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
12245345 AAATTTACTA
12245355 GGGGTAAAATGGTCAAAAATTTTATTG
1 GGGGTAAAATGGTC-AAAATTTTATTG
12245382 GGGGTAAAATGGTCAAAATTTTATTG
1 GGGGTAAAATGGTCAAAATTTTATTG
12245408 GGGGTAAAAT
1 GGGGTAAAAT
12245418 AGGAATGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.32
Consensus pattern (26 bp):
GGGGTAAAATGGTCAAAATTTTATTG
Found at i:12256784 original size:30 final size:30
Alignment explanation
Indices: 12256748--12256815 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
12256738 ATATAAAATG
12256748 ATAAAAAATTGAAATTATTTTTAAAAATAT
1 ATAAAAAATTGAAATTATTTTTAAAAATAT
12256778 ATAAAAAATTGAAATTATTTTTAAAAATAT
1 ATAAAAAATTGAAATTATTTTTAAAAATAT
12256808 ATAAAAAA
1 ATAAAAAA
12256816 ACTATATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
ATAAAAAATTGAAATTATTTTTAAAAATAT
Found at i:12258826 original size:14 final size:13
Alignment explanation
Indices: 12258809--12258863 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
12258799 TCATGTGGGT
12258809 TCACACTTTAGGGG
1 TCACAC-TTAGGGG
*
12258823 TCACACCTAGGGG
1 TCACACTTAGGGG
* *
12258836 TTCACTCATTAGGGA
1 -TCACAC-TTAGGGG
12258851 TCACACTTAGGGG
1 TCACACTTAGGGG
12258864 GTTTGTACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 12 0.36
14 16 0.48
15 5 0.15
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (13 bp):
TCACACTTAGGGG
Found at i:12258836 original size:28 final size:28
Alignment explanation
Indices: 12258805--12258863 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
12258795 TTGCTCATGT
* *
12258805 GGGTTCACACTTTAGGGGTCACACCTAG
1 GGGTTCACACATTAGGGATCACACCTAG
* *
12258833 GGGTTCACTCATTAGGGATCACACTTAG
1 GGGTTCACACATTAGGGATCACACCTAG
12258861 GGG
1 GGG
12258864 GTTTGTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (28 bp):
GGGTTCACACATTAGGGATCACACCTAG
Found at i:12259199 original size:181 final size:181
Alignment explanation
Indices: 12258895--12259262 Score: 709
Period size: 181 Copynumber: 2.0 Consensus size: 181
12258885 CACAGGCTCA
*
12258895 CACATAGGGCTCACAGATTGGGTTTCGCACATAGGCTCGCTCATACGGGCTCGCACATACAGTTT
1 CACATAGGGCTCACAGATTGGGTTTCGCACATAGGCTCGCTCATAAGGGCTCGCACATACAGTTT
12258960 GCATAATTAAACATGTACGATCTGCATACTATATCGGGTTCGCTCGTCCTATGTAGCATGTGCCT
66 GCATAATTAAACATGTACGATCTGCATACTATATCGGGTTCGCTCGTCCTATGTAGCATGTGCCT
12259025 AGGGTTCACATATTTTATCATATAGGGTTCGCATAATAAACAAGTATGTTT
131 AGGGTTCACATATTTTATCATATAGGGTTCGCATAATAAACAAGTATGTTT
*
12259076 CACATAGGGCTCACAGATTGGGTTTCGCACATAGGCTTGCTCATAAGGGCTCGCACATACAGTTT
1 CACATAGGGCTCACAGATTGGGTTTCGCACATAGGCTCGCTCATAAGGGCTCGCACATACAGTTT
12259141 GCATAATTAAACATGTACGATCTGCATACTATATCGGGTTCGCTCGTCCTATGTAGCATGTGCCT
66 GCATAATTAAACATGTACGATCTGCATACTATATCGGGTTCGCTCGTCCTATGTAGCATGTGCCT
*
12259206 AGGGTTCACATATTTTATCATGTAGGGTTCGCATAATAAACAAGTATGTTT
131 AGGGTTCACATATTTTATCATATAGGGTTCGCATAATAAACAAGTATGTTT
12259257 CACATA
1 CACATA
12259263 ACTAAACATG
Statistics
Matches: 184, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 184 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (181 bp):
CACATAGGGCTCACAGATTGGGTTTCGCACATAGGCTCGCTCATAAGGGCTCGCACATACAGTTT
GCATAATTAAACATGTACGATCTGCATACTATATCGGGTTCGCTCGTCCTATGTAGCATGTGCCT
AGGGTTCACATATTTTATCATATAGGGTTCGCATAATAAACAAGTATGTTT
Found at i:12259269 original size:23 final size:22
Alignment explanation
Indices: 12259231--12259285 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
12259221 TATCATGTAG
* *
12259231 GGTTCGCATAATAAACAAGTAT
1 GGTTCACATAATAAACAAGTAC
* *
12259253 GTTTCACATAACTAAACATGTAC
1 GGTTCACATAA-TAAACAAGTAC
12259276 GGTTCACATA
1 GGTTCACATA
12259286 CTATACAGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (22 bp):
GGTTCACATAATAAACAAGTAC
Found at i:12259484 original size:18 final size:20
Alignment explanation
Indices: 12259441--12259488 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
12259431 ATAATAATTT
12259441 TAAAAATAAATATTAATTAAA
1 TAAAAAT-AATATTAATTAAA
*
12259462 GAAAAATAAT-TTAA-TAAA
1 TAAAAATAATATTAATTAAA
12259480 TAAAAATAA
1 TAAAAATAA
12259489 GCTAGAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 4 0.16
20 3 0.12
21 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAAATAATATTAATTAAA
Found at i:12263884 original size:31 final size:32
Alignment explanation
Indices: 12263849--12263912 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
12263839 TTACATAATC
*
12263849 AAAGTACAAGGGCCAAATTAATA-ACAAAAAT
1 AAAGTACAAGGGCCAAATTAATAGAAAAAAAT
* *
12263880 AAAGTATAAGGGCCAAATTGATAGAAAAAAAT
1 AAAGTACAAGGGCCAAATTAATAGAAAAAAAT
12263912 A
1 A
12263913 GTATAGGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.17
Consensus pattern (32 bp):
AAAGTACAAGGGCCAAATTAATAGAAAAAAAT
Found at i:12266568 original size:22 final size:24
Alignment explanation
Indices: 12266542--12266596 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
12266532 AAATTTTTAA
*
12266542 AATTTAATTTATAAT-GAAATTAT
1 AATTTAATTTATAATAAAAATTAT
* *
12266565 -ATTT-TTTTATCATAAAAATTAT
1 AATTTAATTTATAATAAAAATTAT
12266587 AATTTAATTT
1 AATTTAATTT
12266597 CGATTTCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
21 7 0.28
22 11 0.44
23 4 0.16
24 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTTAATTTATAATAAAAATTAT
Found at i:12267558 original size:26 final size:26
Alignment explanation
Indices: 12267509--12267559 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12267499 TATTTGTTTA
*
12267509 TTTTAAAATTTTATTAAATAATATAT
1 TTTTAAAATTTTATAAAATAATATAT
*
12267535 TTTTATAATTTTA-AAAATATATATA
1 TTTTAAAATTTTATAAAATA-ATATA
12267560 CATATTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTAAAATTTTATAAAATAATATAT
Found at i:12269100 original size:18 final size:18
Alignment explanation
Indices: 12269063--12269105 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12269053 AATTATTATC
*
12269063 ATATTTA-ATATAAAACT
1 ATATTTATATAAAAAACT
*
12269080 ATATTTATATAAAAAATT
1 ATATTTATATAAAAAACT
12269098 ATATTTAT
1 ATATTTAT
12269106 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTATATAAAAAACT
Found at i:12269466 original size:18 final size:18
Alignment explanation
Indices: 12269424--12269485 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
12269414 ATAGATAGAA
12269424 TTTATATATTTTTAAGTTTAAT
1 TTTATATATTTTTAA----AAT
12269446 TTTATATATTTTTAAAAT
1 TTTATATATTTTTAAAAT
**
12269464 TTTA-ATGAAATTTAAAAT
1 TTTATAT-ATTTTTAAAAT
12269482 TTTA
1 TTTA
12269486 CTTTTTATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 2 0.05
18 20 0.54
22 15 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTATATATTTTTAAAAT
Found at i:12276726 original size:6 final size:6
Alignment explanation
Indices: 12276715--12276751 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
12276705 AAAGAATATT
*
12276715 AAAAAG AAAAAG AAAAAG -AAAAG -AAAAG AAAAGG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
12276752 GGCAGGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12276736 original size:11 final size:11
Alignment explanation
Indices: 12276715--12276747 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
12276705 AAAGAATATT
12276715 AAAAAGAAAAAG
1 AAAAAG-AAAAG
12276727 AAAAAGAAAAG
1 AAAAAGAAAAG
12276738 -AAAAGAAAAG
1 AAAAAGAAAAG
12276748 GAAAGGCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 5 0.24
12 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:12277624 original size:17 final size:17
Alignment explanation
Indices: 12277604--12277637 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12277594 ATTTTTAAAT
12277604 TTAAAATAAAAATATTA
1 TTAAAATAAAAATATTA
* *
12277621 TTAATATAATAATATTA
1 TTAAAATAAAAATATTA
12277638 GACTTTATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAATAAAAATATTA
Found at i:12277634 original size:23 final size:23
Alignment explanation
Indices: 12277591--12277634 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12277581 GTTTGATGTT
* *
12277591 AATATTTTTAAATTTAAAATAAA
1 AATATTATTAAATATAAAATAAA
12277614 AATATTATT-AATATAATAATA
1 AATATTATTAAATATAA-AATA
12277635 TTAGACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATTATTAAATATAAAATAAA
Found at i:12281068 original size:28 final size:28
Alignment explanation
Indices: 12281032--12281090 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
12281022 TATCATACTT
*
12281032 AGGCACGACACAAATTATAGGACTAGAA
1 AGGCACGACACAAATTAGAGGACTAGAA
*
12281060 AGGCCCGACACAAATTAGAGGACTAGAA
1 AGGCACGACACAAATTAGAGGACTAGAA
12281088 AGG
1 AGG
12281091 TTGGTATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (28 bp):
AGGCACGACACAAATTAGAGGACTAGAA
Found at i:12286997 original size:9 final size:9
Alignment explanation
Indices: 12286983--12287014 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12286973 GTATGAATAA
12286983 AATAATTAT
1 AATAATTAT
12286992 AATAATTAT
1 AATAATTAT
*
12287001 AATAATAAT
1 AATAATTAT
12287010 AATAA
1 AATAA
12287015 AACCATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATAATTAT
Found at i:12288704 original size:44 final size:44
Alignment explanation
Indices: 12288633--12288828 Score: 259
Period size: 44 Copynumber: 4.5 Consensus size: 44
12288623 TCAGGGGGAT
*
12288633 AAGATTTG-TATCTTCGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
* *
12288676 AAAATCTGCTATCTTCGATCTACTTCACGCCAATAAATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
* * * * * * * *
12288720 AAGATCTTCTTTCTTCGATCTACCTCGCCACCAGTATAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGAC
*
12288765 AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
*
12288809 AAGATCTGCTTTCTTCGATC
1 AAGATCTGCTATCTTCGATC
12288829 GATTCCACTG
Statistics
Matches: 128, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
43 6 0.05
44 87 0.68
45 35 0.27
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
Found at i:12292433 original size:14 final size:14
Alignment explanation
Indices: 12292413--12292556 Score: 62
Period size: 14 Copynumber: 10.0 Consensus size: 14
12292403 TAAAAGGATG
12292413 TATATATATA-AAA
1 TATATATATATAAA
12292426 TAATATATATATAAA
1 T-ATATATATATAAA
*
12292441 TATATAGGTACGTATACA
1 TATATA--TA--TATAAA
* *
12292459 TATATTGTGAGATAAA
1 TATA-TAT-ATATAAA
* * *
12292475 GATATAAATATAGA
1 TATATATATATAAA
* *
12292489 TATATGTATATAAG
1 TATATATATATAAA
*
12292503 T-TATAAAATATAAA
1 TATAT-ATATATAAA
*
12292517 -A-ATATATATAAG
1 TATATATATATAAA
* * *
12292529 TATGTATGTATATA
1 TATATATATATAAA
*
12292543 TATATGTATATAAA
1 TATATATATATAAA
12292557 AAAATTTGAG
Statistics
Matches: 92, Mismatches: 27, Indels: 23
0.65 0.19 0.16
Matches are distributed among these distances:
12 7 0.08
13 7 0.08
14 52 0.57
15 5 0.05
16 9 0.10
17 1 0.01
18 10 0.11
19 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (14 bp):
TATATATATATAAA
Found at i:12292609 original size:13 final size:13
Alignment explanation
Indices: 12292591--12292615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12292581 AAAATGTGTA
12292591 AATAATAATAATC
1 AATAATAATAATC
12292604 AATAATAATAAT
1 AATAATAATAAT
12292616 ACAAGATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAATAATAATC
Found at i:12292692 original size:17 final size:17
Alignment explanation
Indices: 12292661--12292693 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12292651 ATAAAATAGA
12292661 AATACAATAACAATAAT
1 AATACAATAACAATAAT
12292678 AATACAA-AACTAATAA
1 AATACAATAAC-AATAA
12292694 CATAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AATACAATAACAATAAT
Found at i:12294291 original size:132 final size:132
Alignment explanation
Indices: 12294144--12294615 Score: 811
Period size: 132 Copynumber: 3.6 Consensus size: 132
12294134 CCCTACTATC
* *
12294144 TTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAT-ACAGAATCTACA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG-TGACAGAATCTGCA
* * * **
12294208 ATCTTTGACATATTCCACTACTATTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
65 ATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
12294273 GTA
130 GTA
*
12294276 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
12294341 TCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
12294406 TA
131 TA
12294408 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * *
12294473 TCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATAGCTTAAATCTGCTTCTCCACTG
66 TCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
12294538 TA
131 TA
*
12294540 TTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
*
12294605 TCTTCAACCTA
66 TCTTCGACCTA
12294616 GTTTAAATCT
Statistics
Matches: 326, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
131 1 0.00
132 325 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
TCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
TA
Found at i:12294346 original size:44 final size:44
Alignment explanation
Indices: 12294296--12294609 Score: 164
Period size: 44 Copynumber: 7.1 Consensus size: 44
12294286 AAGATTCACC
*
12294296 ATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
12294340 ATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * * * * *
12294381 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCA
12294428 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * *
12294472 ATCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * * * *
12294513 ATAGCTTAAATCTGCTTCTCCACTGTATTGAGAAGAT-A-AGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTG-CTT-AG--GGTGACAGAATCTGCA
12294560 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
12294604 ATCTTC
1 ATCTTC
12294610 AACCTAGTTT
Statistics
Matches: 191, Mismatches: 57, Indels: 44
0.65 0.20 0.15
Matches are distributed among these distances:
41 8 0.04
42 2 0.01
43 48 0.25
44 81 0.42
45 42 0.22
46 4 0.02
47 6 0.03
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:12294691 original size:100 final size:100
Alignment explanation
Indices: 12294518--12294715 Score: 387
Period size: 100 Copynumber: 2.0 Consensus size: 100
12294508 GACTAATAGC
12294518 TTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
12294583 CTTAGGGTGACAGAATCTGCAATCTTCAACCTAGT
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTAGT
*
12294618 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
12294683 CTTAGGGTGACAGAATCTGCAATCTTCAACCTA
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTA
12294716 CTCCACTACT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (100 bp):
TTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
CTTAGGGTGACAGAATCTGCAATCTTCAACCTAGT
Found at i:12294792 original size:232 final size:232
Alignment explanation
Indices: 12294386--12294847 Score: 825
Period size: 232 Copynumber: 2.0 Consensus size: 232
12294376 GACTAATGGC
12294386 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
* *
12294451 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATA
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATA
* * *
12294516 GCTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTAC
131 GCTTAAATCTGCTTCCCCACTGTACTGAGAAGATAAGATTCACCATCTTCGATCTACTCCACTAC
* *
12294581 TGCTTAGGGTGACAGAATCTGCAATCTTCAACCTAGT
196 TGCATAGGGTGACAGAATATGCAATCTTCAACCTAGT
12294618 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
*
12294683 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATA
* *
12294748 GCTTAAATCTGCTTCCCCACTGTACTGGGAAGATAAGATTCACCATCTTTGATCTACTCCACTAC
131 GCTTAAATCTGCTTCCCCACTGTACTGAGAAGATAAGATTCACCATCTTCGATCTACTCCACTAC
*
12294813 TGCATAGGGTGACAGAATATGCAATCTTTAACCTA
196 TGCATAGGGTGACAGAATATGCAATCTTCAACCTA
12294848 CTCCACTAAA
Statistics
Matches: 219, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
232 219 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (232 bp):
TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATA
GCTTAAATCTGCTTCCCCACTGTACTGAGAAGATAAGATTCACCATCTTCGATCTACTCCACTAC
TGCATAGGGTGACAGAATATGCAATCTTCAACCTAGT
Found at i:12294855 original size:132 final size:132
Alignment explanation
Indices: 12294618--12294855 Score: 413
Period size: 132 Copynumber: 1.8 Consensus size: 132
12294608 TCAACCTAGT
* * *
12294618 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG
1 TTAAATCTGCTTCCCCACTGTACTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
* *
12294683 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATG
66 CATAGGGTGACAGAATATGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATG
12294748 GC
131 GC
*
12294750 TTAAATCTGCTTCCCCACTGTACTGGGAAGATAAGATTCACCATCTTTGATCTACTCCACTACTG
1 TTAAATCTGCTTCCCCACTGTACTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
*
12294815 CATAGGGTGACAGAATATGCAATCTTTAACCTACTCCACTA
66 CATAGGGTGACAGAATATGCAATCTTCAACCTACTCCACTA
12294856 AAACAGAGAG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 99 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (132 bp):
TTAAATCTGCTTCCCCACTGTACTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
CATAGGGTGACAGAATATGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATG
GC
Found at i:12296466 original size:88 final size:88
Alignment explanation
Indices: 12296312--12296897 Score: 987
Period size: 88 Copynumber: 6.7 Consensus size: 88
12296302 NNNNNNNNNN
* *
12296312 AGAG-GGCAAGGGTTTGTGTCTTCGA-CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGT
1 AGAGAGGCAA-GGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGT
12296375 CTTCAACCAGCTCCATCACAACCG
65 CTTCAACCAGCTCCATCACAACCG
* *
12296399 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAAATCTTTTATC
1 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGTC
12296464 TTCAACCAGCTCCATCACAACCG
66 TTCAACCAGCTCCATCACAACCG
* * *
12296487 AGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATACAGAAAGGTAAGATCTTTTATC
1 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGTC
12296552 TTCAACCAGCTCCATCACAACCG
66 TTCAACCAGCTCCATCACAACCG
* *
12296575 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTC
1 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGTC
12296640 TTCAACCAGCTCCATCACAACCG
66 TTCAACCAGCTCCATCACAACCG
* *
12296663 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGTAAGATTTTTTGTC
1 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGTC
*
12296728 TTCAACCAGCTCCATCACAATCG
66 TTCAACCAGCTCCATCACAACCG
*
12296751 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTTAATACAGAAAGGCAAGATCTTTTGTC
1 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGTC
* * *
12296816 TTCAACCAACTCCGTCACAATCG
66 TTCAACCAGCTCCATCACAACCG
* *
12296839 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAAATCT
1 AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCT
12296898 GCAACTTCAT
Statistics
Matches: 472, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
87 19 0.04
88 453 0.96
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
AGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATCTTTTGTC
TTCAACCAGCTCCATCACAACCG
Found at i:12298162 original size:23 final size:21
Alignment explanation
Indices: 12298124--12298167 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12298114 TTAGCCTCTC
12298124 CATTTTTACTTTTTCATTTTT
1 CATTTTTACTTTTTCATTTTT
*
12298145 CATTTTTTCTTTCATTCATTTTT
1 CATTTTTACTTT--TTCATTTTT
12298168 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
CATTTTTACTTTTTCATTTTT
Found at i:12298985 original size:1 final size:1
Alignment explanation
Indices: 12298979--12299050 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
12298969 GACCTCTACC
* * * * * * * * *
12298979 TTTTTTTTTTCTTTCTTTCTTTTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12299044 TTTTTTT
1 TTTTTTT
12299051 AGTCTGAACT
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:12299019 original size:18 final size:17
Alignment explanation
Indices: 12298979--12299050 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 17
12298969 GACCTCTACC
*
12298979 TTTTTTTTTTCTTTCTTTC
1 TTTTTTTTTT-TTT-TTTG
12298998 TTTTTTTTTTTGTTTTTG
1 TTTTTTTTTTT-TTTTTG
*
12299016 TTTTTGTTTTTGTTTTTG
1 TTTTT-TTTTTTTTTTTG
12299034 TTTTTGTTTTTTTTTTT
1 TTTTT-TTTTTTTTTTT
12299051 AGTCTGAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 31 0.65
19 17 0.35
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTTG
Found at i:12299050 original size:6 final size:6
Alignment explanation
Indices: 12298998--12299049 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
12298988 TCTTTCTTTC
*
12298998 TTTTTT TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
12299045 TTTTT
1 TTTTT
12299050 TAGTCTGAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:12299050 original size:12 final size:12
Alignment explanation
Indices: 12298979--12299050 Score: 83
Period size: 12 Copynumber: 5.8 Consensus size: 12
12298969 GACCTCTACC
*
12298979 TTTTTTTTTTCT
1 TTTTTTTTTTGT
12298991 TTCTTTCTTTTT-T
1 TT-TTT-TTTTTGT
12299004 TTTTTGTTTTTGT
1 TTTTT-TTTTTGT
*
12299017 TTTTGTTTTTGT
1 TTTTTTTTTTGT
*
12299029 TTTTGTTTTTGT
1 TTTTTTTTTTGT
12299041 TTTTTTTTTT
1 TTTTTTTTTT
12299051 AGTCTGAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
12 38 0.70
13 11 0.20
14 5 0.09
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:12303231 original size:16 final size:15
Alignment explanation
Indices: 12303210--12303247 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12303200 TAAAAGGATG
12303210 TATATATATAAAATAA
1 TATATATAT-AAATAA
*
12303226 TATATATATATATAA
1 TATATATATAAATAA
12303241 -ATATATA
1 TATATATA
12303248 GGTACGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 5 0.24
16 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATATATAAATAA
Found at i:12303413 original size:13 final size:13
Alignment explanation
Indices: 12303395--12303419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12303385 AAAATGAGTA
12303395 AATAATAATAATC
1 AATAATAATAATC
12303408 AATAATAATAAT
1 AATAATAATAAT
12303420 ACAAGATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAATAATAATC
Found at i:12314354 original size:3 final size:3
Alignment explanation
Indices: 12314325--12314373 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
12314315 AGCATGTATG
* * *
12314325 AAT AA- AAT AAT TAT AAT AGT TAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12314372 AA
1 AA
12314374 AACCATAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:12315329 original size:20 final size:21
Alignment explanation
Indices: 12315293--12315335 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
12315283 CTGGAGGCGT
12315293 TGGGTGCGACGTGGGGC-TGC
1 TGGGTGCGACGTGGGGCTTGC
*
12315313 TGGGTGCG-CTTGAGGGCTTGC
1 TGGGTGCGACGTG-GGGCTTGC
12315334 TG
1 TG
12315336 TGGCGCTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 12 0.60
21 5 0.25
ACGTcount: A:0.05, C:0.19, G:0.51, T:0.26
Consensus pattern (21 bp):
TGGGTGCGACGTGGGGCTTGC
Found at i:12320554 original size:76 final size:76
Alignment explanation
Indices: 12320461--12320610 Score: 221
Period size: 76 Copynumber: 2.0 Consensus size: 76
12320451 TTAGAAATGT
* ** * *
12320461 AAATATTAAAATTATATTAGGTTATATTTTAAAATAAAAAATCGGCAAGGACACTTGT-GTTCAT
1 AAATATTAAAAATATATTAAATTATATTGTAAAATAAAAAATCGACAAGGACACTTGTGGTT-AT
12320525 ACAAAAAAATTA
65 ACAAAAAAATTA
* *
12320537 AAATATTAAAAATATATTAAATTATATTGTAAAATAAAAAATCTATAAGGACACTTGTGGTTATA
1 AAATATTAAAAATATATTAAATTATATTGTAAAATAAAAAATCGACAAGGACACTTGTGGTTATA
12320602 CAAAAAAAT
66 CAAAAAAAT
12320611 GTATTAAGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 63 0.95
77 3 0.05
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (76 bp):
AAATATTAAAAATATATTAAATTATATTGTAAAATAAAAAATCGACAAGGACACTTGTGGTTATA
CAAAAAAATTA
Found at i:12321968 original size:3 final size:3
Alignment explanation
Indices: 12321960--12322008 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
12321950 TGAAGAGATA
*
12321960 GAT GAT GAT GGT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
12322008 G
1 G
12322009 GTGAAAATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:12325402 original size:43 final size:42
Alignment explanation
Indices: 12325354--12325468 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 42
12325344 GGTATAATTT
* *
12325354 CGTGTAAGACCATGTCTGGGACATTGGCATCAATATGAGATTA
1 CGTGTAAGACCATGTCTGGGACA-TGGCATCAAGATGAGATAA
* * * * *
12325397 CGTGTAAGACCCTGTTTGGGACAGTGGTATCGAGATGTGATAA
1 CGTGTAAGACCATGTCTGGGACA-TGGCATCAAGATGAGATAA
* * * *
12325440 CATGAAAGACCATATCTGGGATATGGCAT
1 CGTGTAAGACCATGTCTGGGACATGGCAT
12325469 TGAATGTGAT
Statistics
Matches: 57, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
42 5 0.09
43 52 0.91
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATGGCATCAAGATGAGATAA
Found at i:12326388 original size:69 final size:69
Alignment explanation
Indices: 12326277--12326436 Score: 230
Period size: 69 Copynumber: 2.3 Consensus size: 69
12326267 CTATTTTTAC
* * * *
12326277 ATGTTATTAATGCTGTCCAACTTAGTGCTTAAATGTTGTCCATTTTTGGTACAAATCAATGCTAT
1 ATGTTATTAATGCTGTCCAAATTAATGCTTAAATGCTGTCCATGTTTGGTACAAATCAATGCTAT
*
12326342 CCGA
66 CCAA
* *
12326346 ATGTTATTAATGCTGTCCAAATTAATGCTTAAATGCTGTCCATGTTTGGTACAAGTCAATGCTGT
1 ATGTTATTAATGCTGTCCAAATTAATGCTTAAATGCTGTCCATGTTTGGTACAAATCAATGCTAT
12326411 CCAA
66 CCAA
* * *
12326415 ATGTTTTTACTGCTATCCAAAT
1 ATGTTATTAATGCTGTCCAAAT
12326437 ATTTGTGAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (69 bp):
ATGTTATTAATGCTGTCCAAATTAATGCTTAAATGCTGTCCATGTTTGGTACAAATCAATGCTAT
CCAA
Found at i:12328601 original size:9 final size:9
Alignment explanation
Indices: 12328584--12328620 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12328574 TGAGTTTTCA
12328584 AATTCGAAT
1 AATTCGAAT
*
12328593 AACTCGAAT
1 AATTCGAAT
12328602 AATTCGAAT
1 AATTCGAAT
12328611 AATTCGAAT
1 AATTCGAAT
12328620 A
1 A
12328621 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12328871 original size:29 final size:31
Alignment explanation
Indices: 12328834--12328892 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
12328824 AAACATTTTA
*
12328834 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
12328864 TTTT-CCCCTAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
12328893 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:12329658 original size:5 final size:5
Alignment explanation
Indices: 12329648--12329673 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12329638 CTCGAAAATT
12329648 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
12329674 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12331533 original size:101 final size:101
Alignment explanation
Indices: 12331357--12332274 Score: 1390
Period size: 101 Copynumber: 9.1 Consensus size: 101
12331347 TTTTTGGCTG
* * * *
12331357 CAATCTGTTTTGCTGCACCGTCTGAGAAGTAGGATTCACCGTTGTGGCTTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
* * *
12331422 CAAGGACAGGGAAAACGAGATTCGCCGTTGTAGCTT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
*
12331458 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCACCGTTGTGGCTTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
*
12331523 CAATGTCAGGGAAAACGAGATTTGCCATTGTAGCTT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
* * *
12331559 CAATCTGTTTCGCTACACCGTCTGAGAAGTAAGATTTGCCGTTGTGGCTTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
* * *
12331624 CAATGTCAGGGAAAACAAGATTCGTCATTGTAGCCT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
12331660 CAATCTG-TTCTGCTGCACCGCCTGAGAAAG-AAGATTCGCCGTTGTGGCTTCAATCCTTTAAAT
1 CAATCTGTTTC-GCTGCACCGCCTGAG-AAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAAT
*
12331723 TGCAATGTCAGGGAAAACGAGATTCGTCATTGTAGCTT
64 TGCAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
* *
12331761 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCACCGTTGTGGCGTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
*
12331826 CAATGTCAGGGAAAACGAGATTCGCCATTGTAACTT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
* * * **
12331862 TAATCTGTTCCGCTGCACCGCCTGAGAAGTAAAATTCGCCGTTGTGGCTTCAATATTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
* * *
12331927 TAATGTCAGGGAAAACGAGATTCACCGTTGTAGCTT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
* ** *
12331963 CAATCTATTTCGCTGCACTACCTGAGAAGTAAGATTCGCCGTTATGGCTTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
12332028 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
* * * * *
12332064 CAATCTGTTTCGCTACACCGTCTAAGAAATAAGATTTGCCGTTGTGGCTTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
* *
12332129 CAATGTCAGGGAAAACGAGATTCGTCGTTGTAGCTT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
* * * *
12332165 CAATCTATTCCGCTCCACCGCCTGAGAAGTAAGATTCACCGTTGTGGCTTCAATCCTTTAAATTG
1 CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
* * *
12332230 TAATGTCAAGGAAAACGAGATTCGCCATTGTAGATT
66 CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
*
12332266 CAATTTGTT
1 CAATCTGTT
12332275 CCACTGTACT
Statistics
Matches: 740, Mismatches: 73, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
100 6 0.01
101 728 0.98
102 6 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (101 bp):
CAATCTGTTTCGCTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTG
CAATGTCAGGGAAAACGAGATTCGCCATTGTAGCTT
Found at i:12332362 original size:44 final size:44
Alignment explanation
Indices: 12332314--12332492 Score: 120
Period size: 44 Copynumber: 4.1 Consensus size: 44
12332304 ACTGTCTTCG
*
12332314 ATCTGCTTCACTACTGCTTAGGGAGACAGGATCTAATGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAATGGCTTAA
* * * ** **
12332358 ATCTGTTTCTCCACTA-T-CTT-GGGAAGATAAGAT-TCACTATCTTCG
1 ATCTG---CTCCACTACTGCTTAGGG-AGACAGGATCT-AATGGCTTAA
* *
12332403 ATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAAT--CTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGACAGGATC--TAATGGCTTAA
* * * *
12332447 ACCTACTCCACTACTGCTTAGGGTGATAGGA-CTAATGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAATGGCTTAA
12332490 ATC
1 ATC
12332493 CACTTCTCCA
Statistics
Matches: 102, Mismatches: 20, Indels: 27
0.68 0.13 0.18
Matches are distributed among these distances:
41 4 0.04
42 8 0.08
43 8 0.08
44 48 0.47
45 23 0.23
46 3 0.03
47 8 0.08
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAATGGCTTAA
Found at i:12332592 original size:46 final size:46
Alignment explanation
Indices: 12332531--12332848 Score: 438
Period size: 46 Copynumber: 6.9 Consensus size: 46
12332521 ATTCACCATT
* * * * *
12332531 TTCGATCTACTCCGCTGCTAAATATAGGAAAACATGATCTGCTATC
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
** * *
12332577 TTTAATCTTCTCCGCTGCCAAATATAGGAAGACAAGATCTGCTATC
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
* * ** * *
12332623 TTTGATCTCTTTTGCTGCCAAATACAGAAAGATAAGATCTGCTATC
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
12332669 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
* * *
12332715 TTCAATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTACTATA
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
* **
12332761 TTCGATCTCCTCCGCTGCCAAGTACAGGAAGACAAGATCTATTATC
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
*
12332807 TTCGATCTCCTCCGCTGCCAAATACAGGAAGAAAAGATCTGC
1 TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGC
12332849 AACTTCATTG
Statistics
Matches: 241, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 241 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (46 bp):
TTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC
Found at i:12334033 original size:43 final size:43
Alignment explanation
Indices: 12333965--12334066 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 43
12333955 TGCCCTGATC
* * * * **
12333965 TGAT-CAAAATTTGAGCTTCTTTGATCGCCTCATGCCCCAATT
1 TGATCCAAAATTTGAGCTGCTCTGATCACCTAATGCCCCAACA
* *
12334007 TGATCCAAAATTTGAG-TCGCTCTGATCACCTAATGTCCCACCA
1 TGATCCAAAATTTGAGCT-GCTCTGATCACCTAATGCCCCAACA
*
12334050 TGATCAAAAATTTGAGC
1 TGATCCAAAATTTGAGC
12334067 AGACATTTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
42 5 0.10
43 43 0.90
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (43 bp):
TGATCCAAAATTTGAGCTGCTCTGATCACCTAATGCCCCAACA
Found at i:12334186 original size:9 final size:8
Alignment explanation
Indices: 12334150--12334185 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
12334140 CCATTTTTAC
12334150 TTTTCATT
1 TTTTCATT
12334158 TTTTCA-T
1 TTTTCATT
12334165 TTTTCATTT
1 TTTTCA-TT
12334174 TTTTCATT
1 TTTTCATT
12334182 TTTT
1 TTTT
12334186 TTGTTCGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
8 12 0.46
9 7 0.27
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:12334187 original size:10 final size:9
Alignment explanation
Indices: 12334150--12334186 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12334140 CCATTTTTAC
12334150 TTTTCA-TT
1 TTTTCATTT
12334158 TTTTCA--T
1 TTTTCATTT
12334165 TTTTCATTT
1 TTTTCATTT
12334174 TTTTCATTT
1 TTTTCATTT
12334183 TTTT
1 TTTT
12334187 TGTTCGACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.26
8 6 0.22
9 14 0.52
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCATTT
Found at i:12335000 original size:1 final size:1
Alignment explanation
Indices: 12334996--12335039 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
12334986 TCCTTTTTCA
* * * *
12334996 TTTTTTTTCTTTTTTTTCTTTTTTTTCTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12335040 ATTGTTTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:12335047 original size:9 final size:9
Alignment explanation
Indices: 12334989--12335039 Score: 93
Period size: 9 Copynumber: 5.6 Consensus size: 9
12334979 TGGCCTCTCC
12334989 TTTTTCATTT
1 TTTTTC-TTT
12334999 TTTTTCTTT
1 TTTTTCTTT
12335008 TTTTTCTTT
1 TTTTTCTTT
12335017 TTTTTCTTT
1 TTTTTCTTT
12335026 TTTTTCTTT
1 TTTTTCTTT
12335035 TTTTT
1 TTTTT
12335040 ATTGTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
9 35 0.85
10 6 0.15
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:12335047 original size:27 final size:28
Alignment explanation
Indices: 12334989--12335047 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
12334979 TGGCCTCTCC
* *
12334989 TTTTTCATTTTTTTTCTTTTTTTTCTTT
1 TTTTTCATTTTTTTTCTTTTTTTTATTG
12335017 TTTTTC-TTTTTTTTCTTTTTTTTATTG
1 TTTTTCATTTTTTTTCTTTTTTTTATTG
12335044 TTTT
1 TTTT
12335048 ATTTCTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.03, C:0.08, G:0.02, T:0.86
Consensus pattern (28 bp):
TTTTTCATTTTTTTTCTTTTTTTTATTG
Found at i:12339761 original size:3 final size:3
Alignment explanation
Indices: 12339749--12339831 Score: 55
Period size: 3 Copynumber: 28.0 Consensus size: 3
12339739 GCAATTATAT
* * * ***
12339749 TAA T-A TAA TAA TAG TAA TAA TAA TAA TAA TAA TGA CAA CGC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
12339796 TAA TAA TAA CAT TAA -AA TAA TTAA CTAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA
12339832 AAGTGCTAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
2 6 0.10
3 49 0.80
4 6 0.10
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:12342365 original size:85 final size:85
Alignment explanation
Indices: 12342222--12342385 Score: 310
Period size: 85 Copynumber: 1.9 Consensus size: 85
12342212 AAGTAAGAAA
12342222 ATTATTTTTAGTTTTATGTTTGGTTCGTAATTGTTCGAGCCCACACTTGAAGCAGTTTGTAGTAC
1 ATTATTTTTAGTTTTATGTTTGGTTCGTAATTGTTCGAGCCCACACTTGAAGCAGTTTGTAGTAC
12342287 AAGAATAACGGAGAGAAGAC
66 AAGAATAACGGAGAGAAGAC
* *
12342307 ATTATTTTTGGTTTTATGTTTGGTTCGTAATTGTTCGAGCCCACACTTGAAGCGGTTTGTAGTAC
1 ATTATTTTTAGTTTTATGTTTGGTTCGTAATTGTTCGAGCCCACACTTGAAGCAGTTTGTAGTAC
12342372 AAGAATAACGGAGA
66 AAGAATAACGGAGA
12342386 AGACCGTTCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (85 bp):
ATTATTTTTAGTTTTATGTTTGGTTCGTAATTGTTCGAGCCCACACTTGAAGCAGTTTGTAGTAC
AAGAATAACGGAGAGAAGAC
Found at i:12358670 original size:2 final size:2
Alignment explanation
Indices: 12358663--12358692 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12358653 TCAGTTAATG
12358663 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
12358693 GAAATATCAA
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:12366520 original size:2 final size:2
Alignment explanation
Indices: 12366513--12366584 Score: 110
Period size: 2 Copynumber: 36.5 Consensus size: 2
12366503 TGCTTCCAAA
12366513 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
* * *
12366555 AT AT AT AT AT GT CT -T CT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12366585 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12369649 original size:13 final size:14
Alignment explanation
Indices: 12369628--12369664 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
12369618 TCCAAGTCAG
12369628 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
12369642 AT-AAATAACTAAA
1 ATAAAATAATTAAA
12369655 ATAAAATAAT
1 ATAAAATAAT
12369665 AAATCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:12371906 original size:27 final size:26
Alignment explanation
Indices: 12371876--12371946 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
12371866 AGGAATAACT
12371876 TTGTGGTACAATATGAATGGAATGCCC
1 TTGTGGTACAATATGAA-GGAATGCCC
* *
12371903 TTGTGGTGCAATATGGAAGGAATGCCT
1 TTGTGGTACAATAT-GAAGGAATGCCC
* *
12371930 TTGTGGCAAAATATGAA
1 TTGTGGTACAATATGAA
12371947 ATGACTGTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 3 0.08
27 32 0.84
28 3 0.08
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (26 bp):
TTGTGGTACAATATGAAGGAATGCCC
Found at i:12374468 original size:19 final size:20
Alignment explanation
Indices: 12374428--12374466 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12374418 TTATCTCAAA
*
12374428 CCCCCAAACCTTTTTACTTT
1 CCCCCAAACATTTTTACTTT
*
12374448 CCCCCAAATATTTTTACTT
1 CCCCCAAACATTTTTACTT
12374467 CCTCCCACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (20 bp):
CCCCCAAACATTTTTACTTT
Found at i:12383033 original size:99 final size:98
Alignment explanation
Indices: 12382863--12383061 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 98
12382853 TTAATTAAAA
*
12382863 ATGAAAATAAAAAAGTATTAAATTAAAAGTCTCAAACATGAATTTCTTGGATCTTCAAAATGAAG
1 ATGAAAATAAAAAAGTATTAAATTAAAAGTCTCAAACAGGAATTTCTTGGATCTTCAAAATGAAG
*
12382928 ACTTTGTAAATTTCTATATGAGTAATCATATGT
66 ACTTTGTAAATTTCCATATGAGTAATCATATGT
12382961 ATGAAAATAAAAAAAGTATTAAATTAAAAGTCTCAAACAGGAATTTCTTGGATCTTCAAAATGAA
1 ATGAAAAT-AAAAAAGTATTAAATTAAAAGTCTCAAACAGGAATTTCTTGGATCTTCAAAATGAA
12383026 GACTTTGTAAATTTCCATATGAGTAATCATATGT
65 GACTTTGTAAATTTCCATATGAGTAATCATATGT
12383060 AT
1 AT
12383062 TATGAATAAT
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 8 0.08
99 90 0.92
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (98 bp):
ATGAAAATAAAAAAGTATTAAATTAAAAGTCTCAAACAGGAATTTCTTGGATCTTCAAAATGAAG
ACTTTGTAAATTTCCATATGAGTAATCATATGT
Found at i:12383842 original size:19 final size:19
Alignment explanation
Indices: 12383799--12383835 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12383789 AAAAAAATAA
*
12383799 ATTTTCTTTTTGTATGTAT
1 ATTTTCTTTTTGTAAGTAT
12383818 ATTTTCTTTTT-TAAGTAT
1 ATTTTCTTTTTGTAAGTAT
12383836 TTGTTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (19 bp):
ATTTTCTTTTTGTAAGTAT
Found at i:12385185 original size:2 final size:2
Alignment explanation
Indices: 12385173--12385218 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
12385163 GGATCTTGTA
12385173 AT AT A- 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
12385214 GAT AT
1 -AT AT
12385219 TTTTTTTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12385677 original size:19 final size:19
Alignment explanation
Indices: 12385655--12385698 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12385645 ATTTTTTGAA
12385655 TTTTTATGAAACTTTTA-AT
1 TTTTTATGAAA-TTTTATAT
* *
12385674 TTTTTTTTAAATTTTATAT
1 TTTTTATGAAATTTTATAT
12385693 TTTTTA
1 TTTTTA
12385699 AATTATTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTATGAAATTTTATAT
Found at i:12386201 original size:18 final size:19
Alignment explanation
Indices: 12386165--12386203 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12386155 AAATTTACAT
12386165 AATAAACCACTATAAACTA
1 AATAAACCACTATAAACTA
*
12386184 AATAAACCATTA-AAACTA
1 AATAAACCACTATAAACTA
12386202 AA
1 AA
12386204 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAAACCACTATAAACTA
Found at i:12394533 original size:90 final size:91
Alignment explanation
Indices: 12394428--12394597 Score: 238
Period size: 92 Copynumber: 1.9 Consensus size: 91
12394418 GCTCTCTATT
* * ** *
12394428 TTTTTTCAAAAAAAGCAATTAAG--TCTGCATTTTTTTT-TTGCACTCAATTGGATGCTTTAACT
1 TTTTTTCAAAAAAAGCAATTAAGCCCCTAC-TTTTTTTTCTTGCACTCAATTGGACACTTGAACT
*
12394490 TTCAAAATACATCAAAAGGGCCTTCAAA
65 ATCAAAATACAT-AAAAGGGCCTTCAAA
*
12394518 TTTTTTCGAAAAAAGCAATTAAGCCCCTACTTTTTTTTCTTGCACTCAATTGGACACTTGAACTA
1 TTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCTTGCACTCAATTGGACACTTGAACTA
12394583 TCAAAATACATAAAA
66 TCAAAATACATAAAA
12394598 CAGGTCATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
90 22 0.31
91 12 0.17
92 36 0.51
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (91 bp):
TTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCTTGCACTCAATTGGACACTTGAACTA
TCAAAATACATAAAAGGGCCTTCAAA
Found at i:12394740 original size:19 final size:17
Alignment explanation
Indices: 12394709--12394752 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
12394699 TAGCAAAAAA
12394709 AAAAATTAAAATTTTAAT
1 AAAAATTAAAA-TTTAAT
* *
12394727 AAAAATATATAATTTATT
1 AAAAAT-TAAAATTTAAT
12394745 AAAAATTA
1 AAAAATTA
12394753 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATTAAAATTTAAT
Found at i:12395126 original size:89 final size:89
Alignment explanation
Indices: 12394924--12395182 Score: 269
Period size: 89 Copynumber: 2.9 Consensus size: 89
12394914 CACGCCGTGA
** *
12394924 TTGATGCATTTTGGTAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAATAGGGGCTTAATT--T
1 TTGATGCATTTTGAAAGTTCAAATACCCAATTGAGTGC-AAAAAAAAAA-AGGGACTTAATTGCT
* * * *
12394987 TTTTTT--TAA-GTTTGAGGGCCTTT
64 TTTTTTGAAAATTTTTAAGAGCCTTT
* *
12395010 TTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAAGGGACTTAATTGCTTT
1 TTGATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAGGGACTTAATTGCTTT
12395075 TTTTGAAAATTTTTAAGAGCCTTT
66 TTTTGAAAATTTTTAAGAGCCTTT
* * * * * ** * *
12395099 TTTATGCATTTT-AAACTTTCAATTACCCAATTAAGTGCCAAAAAAAGTAGAGACTTAATAGCTT
1 TTGATGCATTTTGAAA-GTTCAAATACCCAATTGAGTGCAAAAAAAAAAAGGGACTTAATTGCTT
*
12395163 TTTTTGGAAAATTTTGAAGA
65 TTTTT-GAAAATTTTTAAGA
12395183 CTTTTTACAT
Statistics
Matches: 146, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
84 11 0.08
85 10 0.07
86 41 0.28
88 5 0.03
89 66 0.45
90 13 0.09
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (89 bp):
TTGATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAGGGACTTAATTGCTTT
TTTTGAAAATTTTTAAGAGCCTTT
Found at i:12395885 original size:5 final size:5
Alignment explanation
Indices: 12395875--12395908 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
12395865 TCTAATTTTC
12395875 TATTA TATTA TATTA TATTA TATT- TA-TA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA T
12395909 GTATTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 1 0.04
4 4 0.15
5 22 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:12407475 original size:26 final size:25
Alignment explanation
Indices: 12407445--12407502 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
12407435 ACTCCCAGTA
*
12407445 AAATTTTAATGATTTTACCCCTGGT
1 AAATTTTAACGATTTTACCCCTGGT
* * *
12407470 ATAATTTTGACGATTTTGCCTCTGGT
1 A-AATTTTAACGATTTTACCCCTGGT
12407496 AAATTTT
1 AAATTTT
12407503 CAAGAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (25 bp):
AAATTTTAACGATTTTACCCCTGGT
Found at i:12412180 original size:74 final size:73
Alignment explanation
Indices: 12411999--12412193 Score: 302
Period size: 74 Copynumber: 2.6 Consensus size: 73
12411989 TTTTTTCATT
* *
12411999 TTTTCATTTTTGGGTAAATTGTAAATAATTATATTATTGATGT-AAAATACAATAGAATACAGTA
1 TTTTCATTTTTGGGTAAATTGTAAATAA-TATATTATTGATGTAAAAATACAATAAAATACAATA
12412063 CAAACAATA
65 CAAACAATA
*
12412072 TTTTCATTTTTGGGTAAATTGTAACTAAATATATTATTGATGTAAAAATACAATAAAATACAATA
1 TTTTCATTTTTGGGTAAATTGTAAAT-AATATATTATTGATGTAAAAATACAATAAAATACAATA
12412137 CAAACAATA
65 CAAACAATA
** *
12412146 TTTTCATTTTTTTTGTAAATTGTAAATAAGATATTATTGATGTAAAAA
1 TTTTCA-TTTTTGGGTAAATTGTAAATAATATATTATTGATGTAAAAA
12412194 ATAAAAAAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
73 39 0.35
74 56 0.50
75 17 0.15
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (73 bp):
TTTTCATTTTTGGGTAAATTGTAAATAATATATTATTGATGTAAAAATACAATAAAATACAATAC
AAACAATA
Found at i:12417891 original size:2 final size:2
Alignment explanation
Indices: 12417884--12417952 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
12417874 AGCTTGTGAG
*
12417884 AT AT AT AT AT AT AT AT AT AT AT AA 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
* *
12417926 AT CT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12417953 AATTTTATGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12427097 original size:16 final size:15
Alignment explanation
Indices: 12427063--12427100 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12427053 CAGATTCCAT
*
12427063 AAAAA-AAGGCAAAA
1 AAAAAGAAGGAAAAA
12427077 AAAAAGAAGGAAAAGA
1 AAAAAGAAGGAAAA-A
12427093 AAAAAGAA
1 AAAAAGAA
12427101 AAAAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 7 0.33
16 9 0.43
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGGAAAAA
Found at i:12427106 original size:16 final size:15
Alignment explanation
Indices: 12427073--12427165 Score: 69
Period size: 16 Copynumber: 6.0 Consensus size: 15
12427063 AAAAAAAGGC
*
12427073 AAAAAAAAAGAAGGAA
1 AAAAAAAAAGAA-AAA
*
12427089 AAGAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
* ** *
12427104 AAATCAAAATCAAAAG
1 AAA-AAAAAAGAAAAA
* *
12427120 CAGAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
**
12427135 AATCAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
12427150 AAAAGAAAAAGAAAAA
1 AAAA-AAAAAGAAAAA
12427166 GGAGAGGTCA
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 26 0.46
16 31 0.54
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAAA
Found at i:12427124 original size:24 final size:21
Alignment explanation
Indices: 12427093--12427158 Score: 78
Period size: 24 Copynumber: 2.9 Consensus size: 21
12427083 AAGGAAAAGA
*
12427093 AAAAAGAAAAAAAATCAAAATC
1 AAAAAGAAAAAAAA-AAAAATC
12427115 AAAAGCAGAAAAAAGAAAAAAATC
1 AAAA--AGAAAAAA-AAAAAAATC
12427139 AAAAAGAAAAAAAAAGAAAA
1 AAAAAGAAAAAAAAA-AAAA
12427159 AGAAAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
21 3 0.08
22 16 0.41
24 18 0.46
25 2 0.05
ACGTcount: A:0.80, C:0.06, G:0.09, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAAAAAAAAAAATC
Found at i:12427154 original size:25 final size:24
Alignment explanation
Indices: 12427109--12427159 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
12427099 AAAAAAAATC
* *
12427109 AAAATCAAAAGCAGAAAAAAGAAA
1 AAAATCAAAAGAAAAAAAAAGAAA
12427133 AAAATCAAAAAGAAAAAAAAAGAAA
1 AAAATC-AAAAGAAAAAAAAAGAAA
12427158 AA
1 AA
12427160 GAAAAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.80, C:0.06, G:0.10, T:0.04
Consensus pattern (24 bp):
AAAATCAAAAGAAAAAAAAAGAAA
Found at i:12427159 original size:24 final size:24
Alignment explanation
Indices: 12427073--12427159 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 24
12427063 AAAAAAAGGC
**
12427073 AAAAAAAAAGAAGGAAAAGAAAAAAG
1 AAAAAAAAAGAA--AAAATCAAAAAG
**
12427099 -AAAAAAAA-TCAAAATC-AAAAG
1 AAAAAAAAAGAAAAAATCAAAAAG
* *
12427120 CAGAAAAAAGAAAAAAATCAAAAAG
1 AAAAAAAAAG-AAAAAATCAAAAAG
12427145 AAAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
12427160 GAAAAAGGAG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
21 5 0.10
22 11 0.23
24 11 0.23
25 21 0.44
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAGAAAAAATCAAAAAG
Found at i:12427159 original size:31 final size:31
Alignment explanation
Indices: 12427087--12427165 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
12427077 AAAAAGAAGG
* *
12427087 AAAAGAAAAAAGAAAAAAAATCAAAATCAAAAG
1 AAAAG-AAAAAG-AAAAAAATCAAAAACAAAAA
* * *
12427120 CAGA-AAAAAGAAAAAAATCAAAAAGAAAAA
1 AAAAGAAAAAGAAAAAAATCAAAAACAAAAA
12427150 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
12427166 GGAGAGGTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 19 0.50
31 17 0.45
33 2 0.05
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.04
Consensus pattern (31 bp):
AAAAGAAAAAGAAAAAAATCAAAAACAAAAA
Done.