Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold423
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: 617052
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 5 of 6
Found at i:478693 original size:21 final size:22
Alignment explanation
Indices: 478645--478694 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
478635 AATAAAAAAT
478645 TAATTAAAAATATAATATAATGA
1 TAATT-AAAATATAATATAATGA
*
478668 AAATTAAAATA-AATATACAT-A
1 TAATTAAAATATAATATA-ATGA
478689 TAATTA
1 TAATTA
478695 TATTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 12 0.50
22 8 0.33
23 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTAAAATATAATATAATGA
Found at i:478703 original size:32 final size:30
Alignment explanation
Indices: 478653--478756 Score: 65
Period size: 28 Copynumber: 3.4 Consensus size: 30
478643 ATTAATTAAA
*
478653 AATATAA-TATAATGAAAATTAAAATA-AATAT
1 AATATAATTAT-ATTAAAATT-AAA-ATAATAT
*
478684 ACATATAATTATATTAAAATTTAAATAATAT
1 A-ATATAATTATATTAAAATTAAAATAATAT
* * *
478715 AA-ATTATTAT-TTAAAAAT-ATATCAATAT
1 AATATAATTATATTAAAATTAAAAT-AATAT
478743 AATATGAATATATA
1 AATAT-AAT-TATA
478757 AATTGAGTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
27 3 0.05
28 14 0.24
29 9 0.15
30 4 0.07
31 12 0.20
32 14 0.24
33 3 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
AATATAATTATATTAAAATTAAAATAATAT
Found at i:478720 original size:21 final size:21
Alignment explanation
Indices: 478688--478735 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
478678 AAATATACAT
*
478688 ATAAT-TATATTAAAATTTAA
1 ATAATATAAATTAAAATTTAA
**
478708 ATAATATAAATTATTATTTAA
1 ATAATATAAATTAAAATTTAA
478729 A-AATATA
1 ATAATATA
478736 TCAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATAAATTAAAATTTAA
Found at i:479990 original size:18 final size:18
Alignment explanation
Indices: 479951--479992 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
479941 AAAATTTTTA
479951 ATTTTAATTATAATTATT
1 ATTTTAATTATAATTATT
*
479969 -TTTTAATTTTTAA-TATT
1 ATTTTAA-TTATAATTATT
479986 ATTTTAA
1 ATTTTAA
479993 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTAATTATAATTATT
Found at i:480381 original size:10 final size:12
Alignment explanation
Indices: 480348--480376 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
480338 TTAATCAATT
480348 TTTTTAATT-TA
1 TTTTTAATTATA
480359 TTTTTAATTATA
1 TTTTTAATTATA
480371 TTTTTA
1 TTTTTA
480377 TATATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTAATTATA
Found at i:480386 original size:20 final size:19
Alignment explanation
Indices: 480363--480408 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
480353 AATTTATTTT
*
480363 TAATTATATTTTTATATATA
1 TAATTATATTTGTAT-TATA
480383 TAA-TATATTTGTATTATA
1 TAATTATATTTGTATTATA
480401 T-ATTATAT
1 TAATTATAT
480409 AATATGTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 10 0.42
19 10 0.42
20 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTATATTTGTATTATA
Found at i:487171 original size:21 final size:22
Alignment explanation
Indices: 487123--487172 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
487113 AATAAAAAAT
487123 TAATTAAAAATATAATATAATGA
1 TAATT-AAAATATAATATAATGA
*
487146 AAATTAAAATA-AATATACAT-A
1 TAATTAAAATATAATATA-ATGA
487167 TAATTA
1 TAATTA
487173 TATTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 12 0.50
22 8 0.33
23 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTAAAATATAATATAATGA
Found at i:487185 original size:32 final size:30
Alignment explanation
Indices: 487132--487192 Score: 70
Period size: 32 Copynumber: 2.0 Consensus size: 30
487122 TTAATTAAAA
487132 ATATAATATAATGAAAATTAAAATAAATATAC
1 ATATAATATAATGAAAATT-AAAT-AATATAC
* *
487164 ATATAAT-TATATTAAATTTAAATAATATA
1 ATATAATATA-ATGAAAATTAAATAATATA
487193 AATTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 6 0.23
31 6 0.23
32 14 0.54
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
ATATAATATAATGAAAATTAAATAATATAC
Found at i:488173 original size:13 final size:15
Alignment explanation
Indices: 488139--488175 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
488129 TTTAAAAATT
*
488139 TTAATTATTTTTCAA
1 TTAAATATTTTTCAA
488154 TTAAATATTTTT-AA
1 TTAAATATTTTTCAA
488168 -TAAATATT
1 TTAAATATT
488176 AATTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 2 0.10
15 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAAATATTTTTCAA
Found at i:488423 original size:24 final size:23
Alignment explanation
Indices: 488396--488449 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
488386 TTAAATTAAA
488396 TTAATTTAAATAATAAAAAATTAT
1 TTAATTTAAATAAT-AAAAATTAT
* * **
488420 TTAATTTTAATTATAATTATTAT
1 TTAATTTAAATAATAAAAATTAT
488443 TTAATTT
1 TTAATTT
488450 TTAATATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTAAATAATAAAAATTAT
Found at i:488463 original size:18 final size:18
Alignment explanation
Indices: 488423--488464 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
488413 AAATTATTTA
488423 ATTTTAATTATAATTATT
1 ATTTTAATTATAATTATT
*
488441 A-TTTAATTTTTAA-TATT
1 ATTTTAA-TTATAATTATT
488458 ATTTTAA
1 ATTTTAA
488465 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAATTATAATTATT
Found at i:488746 original size:17 final size:17
Alignment explanation
Indices: 488724--488757 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
488714 TTATTTATTT
*
488724 TAAAAATTAATTAATTA
1 TAAAAAATAATTAATTA
*
488741 TAAAAAATAATTTATTA
1 TAAAAAATAATTAATTA
488758 AATATATTTG
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):
TAAAAAATAATTAATTA
Found at i:488852 original size:20 final size:19
Alignment explanation
Indices: 488840--488882 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
488830 TATTTTTAAT
488840 TATATTTTTTTATATATAA
1 TATATTTTTTTATATATAA
* *
488859 TATATTTGTATTATATATTA
1 TATATTT-TTTTATATATAA
488879 TATA
1 TATA
488883 ATATGTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATTTTTTTATATATAA
Found at i:493152 original size:193 final size:198
Alignment explanation
Indices: 492809--493196 Score: 606
Period size: 193 Copynumber: 2.0 Consensus size: 198
492799 GTTCTTTTTT
* * * **
492809 TTTTTTTTAGTTTTTCCATGTATTTGAAAAGTCTTTAAATGGTCATATTCTCGCGCCCATGTTTG
1 TTTTTTTTA-TTTTTCCAAGTATTTGAAAAGTCTTTAAAGGGTCATACTCTCGCGCCCATGTTCA
*
492874 GATATGAGTTAGAGAAGAGTGTCAGACACGGATACTACAAGAATATAACAATTAGACATGAGTCA
65 GATATGAGTCAGAG-AGAGTGTCAGACACGGATACTACAAGAATATAACAATTAGACATGAGTCA
*
492939 GACAGATTACAGATGTTACCAAGCT-CAAAGGAGGAAAAGAATATAAAAATTAGACATGCATTTC
129 GACAGATTACAGATGTTACCAAGCTCCAAAGGAGCAAAAGAATATAAAAATTAGACATGCATTTC
493003 CCCCC
194 CCCCC
** *
493008 TTTTTTTT-TTTTTCCAAGTATTTGAAGGGTCTTTAAAGGGTCATACTCTCGTGCCCATGTTCAG
1 TTTTTTTTATTTTTCCAAGTATTTGAAAAGTCTTTAAAGGGTCATACTCTCGCGCCCATGTTCAG
* * *
493072 ATATGAGTCA-AG-G-GTGTCAGACATGGGTACTACAAGAATATAACAATTAGACATGAGTCGGA
66 ATATGAGTCAGAGAGAGTGTCAGACACGGATACTACAAGAATATAACAATTAGACATGAGTCAGA
493134 CAGATTACAGATGTTACCAAGCTCCAAAGGAGCAAAAGAATATAAAAATTAGACATGCATTTC
131 CAGATTACAGATGTTACCAAGCTCCAAAGGAGCAAAAGAATATAAAAATTAGACATGCATTTC
493197 TGGACTCTTA
Statistics
Matches: 175, Mismatches: 13, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
193 69 0.39
194 39 0.22
196 2 0.01
197 57 0.33
199 8 0.05
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (198 bp):
TTTTTTTTATTTTTCCAAGTATTTGAAAAGTCTTTAAAGGGTCATACTCTCGCGCCCATGTTCAG
ATATGAGTCAGAGAGAGTGTCAGACACGGATACTACAAGAATATAACAATTAGACATGAGTCAGA
CAGATTACAGATGTTACCAAGCTCCAAAGGAGCAAAAGAATATAAAAATTAGACATGCATTTCCC
CCC
Found at i:494019 original size:2 final size:2
Alignment explanation
Indices: 494012--494046 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
494002 GATCTCTTTA
494012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
494047 AAGTGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:502621 original size:18 final size:17
Alignment explanation
Indices: 502582--502621 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
502572 CGTGTCATAA
*
502582 TAATATTTATAATATTT
1 TAATATTTATAAAATTT
502599 T-ATATTTATATAAATTT
1 TAATATTTATA-AAATTT
502616 TAATAT
1 TAATAT
502622 GTTAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 9 0.45
17 7 0.35
18 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATATTTATAAAATTT
Found at i:502629 original size:18 final size:18
Alignment explanation
Indices: 502582--502630 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
502572 CGTGTCATAA
502582 TAATATTT-ATAATATTT
1 TAATATTTAATAATATTT
502599 T-ATATTTATATAA-ATTT
1 TAATATTTA-ATAATATTT
502616 TAATATGTTAATAAT
1 TAATAT-TTAATAAT
502631 TTGTATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.22
17 6 0.22
18 12 0.44
19 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TAATATTTAATAATATTT
Found at i:503522 original size:14 final size:14
Alignment explanation
Indices: 503503--503529 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
503493 AATAATAATA
503503 ATTATTATTATTAT
1 ATTATTATTATTAT
503517 ATTATTATTATTA
1 ATTATTATTATTA
503530 AATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:503717 original size:19 final size:19
Alignment explanation
Indices: 503680--503717 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
503670 ATAATTAAAT
*
503680 TTAAATAAAAATATTTTTA
1 TTAAATAAAAATATATTTA
503699 TTAAATAAATAATA-ATTTA
1 TTAAATAAA-AATATATTTA
503718 GATTTACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAAAAATATATTTA
Found at i:506109 original size:13 final size:14
Alignment explanation
Indices: 506085--506113 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
506075 TTTGGTTTAT
506085 TATTTTATAAAAAA
1 TATTTTATAAAAAA
506099 TATTTTA-AAAAAA
1 TATTTTATAAAAAA
506112 TA
1 TA
506114 CTTGTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATTTTATAAAAAA
Found at i:506460 original size:16 final size:17
Alignment explanation
Indices: 506434--506467 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
506424 AAACTTAATT
506434 AATCTAAATTTAAAATA
1 AATCTAAATTTAAAATA
506451 AATC-AAATTTAAAATA
1 AATCTAAATTTAAAATA
506467 A
1 A
506468 TTCGAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
AATCTAAATTTAAAATA
Found at i:507954 original size:15 final size:14
Alignment explanation
Indices: 507930--507962 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
507920 TGTTCAATAT
507930 ATATTTAGACATAA
1 ATATTTAGACATAA
507944 ATATGTTAGACATAA
1 ATAT-TTAGACATAA
507959 ATAT
1 ATAT
507963 AAATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (14 bp):
ATATTTAGACATAA
Found at i:509259 original size:29 final size:30
Alignment explanation
Indices: 509220--509291 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
509210 TTTAGTACTT
* * *
509220 TATTTAGATAATTACCTAAATTTTTA-TTA
1 TATTTAAATAAATACATAAATTTTTATTTA
* * *
509249 TATTTAAATAAATATATATATTTTTATTTT
1 TATTTAAATAAATACATAAATTTTTATTTA
509279 TATTTAAATAAAT
1 TATTTAAATAAAT
509292 CTTAACCTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (30 bp):
TATTTAAATAAATACATAAATTTTTATTTA
Found at i:509461 original size:22 final size:22
Alignment explanation
Indices: 509436--509477 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
509426 AAATATTTTT
509436 TAAATTTA-ATTATAAAAATATA
1 TAAATTTATA-TATAAAAATATA
*
509458 TAAATTTTTATATAAAAATA
1 TAAATTTATATATAAAAATA
509478 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTTATATATAAAAATATA
Found at i:510031 original size:22 final size:22
Alignment explanation
Indices: 509996--510037 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
509986 TATTTTTATT
509996 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
510018 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
510038 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:510445 original size:3 final size:3
Alignment explanation
Indices: 510437--510471 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
510427 TTAGGGTTAA
510437 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
510472 AAAGTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:510529 original size:15 final size:16
Alignment explanation
Indices: 510509--510542 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
510499 TTGTTAAGAA
510509 AATTAAATT-AAAATT
1 AATTAAATTAAAAATT
510524 AATTAAATTAAAAATT
1 AATTAAATTAAAAATT
510540 AAT
1 AAT
510543 ATTTAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAATTAAAAATT
Found at i:511729 original size:17 final size:18
Alignment explanation
Indices: 511703--511738 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
511693 ACTATTATTT
511703 AAAATATATTAAA-AATA
1 AAAATATATTAAATAATA
*
511720 AAAATTTATTAAATAATA
1 AAAATATATTAAATAATA
511738 A
1 A
511739 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATATATTAAATAATA
Found at i:511855 original size:7 final size:7
Alignment explanation
Indices: 511843--511877 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
511833 ACTATCCATA
511843 TTTTCCT
1 TTTTCCT
511850 TTTTCCT
1 TTTTCCT
*
511857 TTTTCTT
1 TTTTCCT
511864 TTTTCCT
1 TTTTCCT
511871 TTGTTCC
1 TT-TTCC
511878 CATTGTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (7 bp):
TTTTCCT
Found at i:512658 original size:18 final size:19
Alignment explanation
Indices: 512637--512675 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
512627 TTATATTTTT
512637 AAATGATTT-TTTTATAAA
1 AAATGATTTATTTTATAAA
* *
512655 AAATTATTTATTTTTTAAA
1 AAATGATTTATTTTATAAA
512674 AA
1 AA
512676 TTAATCCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
AAATGATTTATTTTATAAA
Found at i:512806 original size:18 final size:18
Alignment explanation
Indices: 512785--512858 Score: 53
Period size: 17 Copynumber: 4.2 Consensus size: 18
512775 ATCATTTTAA
512785 AAATTACCAACATTTTTT
1 AAATTACCAACATTTTTT
* ** * *
512803 AAA-TATCATTATCTTTC
1 AAATTACCAACATTTTTT
* * * *
512820 AAAATA-CAAAATTTATA
1 AAATTACCAACATTTTTT
512837 AAATTACCAACATTTTTT
1 AAATTACCAACATTTTTT
512855 AAAT
1 AAAT
512859 ATCATTATCT
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
17 23 0.57
18 17 0.43
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTACCAACATTTTTT
Found at i:512840 original size:52 final size:52
Alignment explanation
Indices: 512780--512888 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
512770 TTCCCATCAT
512780 TTTA-AAAATTACCAACATTTTTTAAATATCATTATCTTTCAAAATACAAAA
1 TTTATAAAATTACCAACATTTTTTAAATATCATTATCTTTCAAAATACAAAA
512831 TTTATAAAATTACCAACATTTTTTAAATATCATTATCTTTCAAAATACAAAA
1 TTTATAAAATTACCAACATTTTTTAAATATCATTATCTTTCAAAATACAAAA
512883 TTTATA
1 TTTATA
512889 TCTAAAATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 4 0.07
52 53 0.93
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (52 bp):
TTTATAAAATTACCAACATTTTTTAAATATCATTATCTTTCAAAATACAAAA
Found at i:514076 original size:221 final size:223
Alignment explanation
Indices: 513687--514116 Score: 643
Period size: 221 Copynumber: 1.9 Consensus size: 223
513677 TATATTTAAC
* * *
513687 GTGATTATAGATATAATATATATTATAATTATTAATTACAATAATATTAACAACAGAGAAAGTTC
1 GTGATTATAGATATAATATATACTACAATAATTAATTACAATAATATTAACAACAGAGAAAGTTC
* * * *
513752 AAATGGTAAATTAGCTATCATAGCGTAATTAAAAATAAATCTTTTTAGAACTAGAGTTTAACCTA
66 AAATGGCAAATTAGCTATCATAGCATAACTAAAAATAAATCTTTTTAAAACTAGAGTTTAACCTA
* ** *
513817 GCAAATTTATTGAATTATCTTTGAAAGATATCATCTAATGGATCTGAATTCAAATATTAATATTT
131 ACAAATTTATTGAATTATCTTTGAAAGATATCATCTAATAAATCTGAATTCAAATATCAATATTT
* *
513882 ATAATTTATTTACGTATCTTAAATTATT
196 ACAATTCATTTACGTATCTTAAATTATT
513910 GTGATTATAGATATAATATATACTACAATAATTAATTACAATAAATATTAACAACAGAGAAAGTT
1 GTGATTATAGATATAATATATACTACAATAATTAATTACAAT-AATATTAACAACAGAGAAAGTT
* * * *
513975 TAAATGGCAAATTAG-T-T-ATAGCATAACTAGAAATAAATTTTTTTAAAACTCGAGTTTAACCT
65 CAAATGGCAAATTAGCTATCATAGCATAACTAAAAATAAATCTTTTTAAAACTAGAGTTTAACCT
* *
514037 AATAAATTTA-TGAAGTTATCTTTGAAAGATATTATCTAATAAATCTGAATTCAAATATCAATAT
130 AACAAATTTATTGAA-TTATCTTTGAAAGATATCATCTAATAAATCTGAATTCAAATATCAATAT
514101 TTACAATTCATTTACG
194 TTACAATTCATTTACG
514117 CATTCTAAAT
Statistics
Matches: 186, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
220 4 0.02
221 106 0.57
222 1 0.01
223 40 0.22
224 35 0.19
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (223 bp):
GTGATTATAGATATAATATATACTACAATAATTAATTACAATAATATTAACAACAGAGAAAGTTC
AAATGGCAAATTAGCTATCATAGCATAACTAAAAATAAATCTTTTTAAAACTAGAGTTTAACCTA
ACAAATTTATTGAATTATCTTTGAAAGATATCATCTAATAAATCTGAATTCAAATATCAATATTT
ACAATTCATTTACGTATCTTAAATTATT
Found at i:514420 original size:17 final size:17
Alignment explanation
Indices: 514398--514448 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
514388 TATTTAAAAT
514398 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
514415 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
514432 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
514447 AT
1 AT
514449 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 5 0.17
16 3 0.10
17 7 0.24
18 6 0.21
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:514432 original size:18 final size:18
Alignment explanation
Indices: 514386--514433 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
514376 ATATTATAAA
514386 AATATTTAA-AATATTTT
1 AATATTTAATAATATTTT
514403 -ATATTTATATAA-ATTTT
1 AATATTTA-ATAATATTTT
514420 AATATATTAATAAT
1 AATAT-TTAATAAT
514434 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 7 0.27
17 6 0.23
18 10 0.38
19 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTTAATAATATTTT
Found at i:514469 original size:33 final size:31
Alignment explanation
Indices: 514370--514476 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 31
514360 TATACTTAAT
*
514370 TTTATTATATTATAAAAATATTTAAAATA-T-
1 TTTATTATATTATATAAATA-TTAAAATATTA
* *
514400 TTTA-TAT-TTATATAAATTTTAATATATTA
1 TTTATTATATTATATAAATATTAAAATATTA
* *
514429 ATAATTTATATTATATAAATATTAAAATAATTA
1 TTTA-TTATATTATATAAATATTAAAAT-ATTA
*
514462 TTTATT-TATCATATA
1 TTTATTATATTATATA
514477 TATTTTTATA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
27 7 0.11
28 10 0.16
29 5 0.08
30 4 0.07
31 11 0.18
32 18 0.30
33 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTATTATATTATATAAATATTAAAATATTA
Found at i:515200 original size:26 final size:28
Alignment explanation
Indices: 515153--515208 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
515143 ATTACATAAA
*
515153 TTTTAAATTATATATATATTTATTTTAT
1 TTTTAAATTATATATATATTTAATTTAT
515181 TTTTATAA-TATATA-AT-TTTAATTTAT
1 TTTTA-AATTATATATATATTTAATTTAT
515207 TT
1 TT
515209 AATATTGGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 11 0.42
27 2 0.08
28 11 0.42
29 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTAAATTATATATATATTTAATTTAT
Found at i:515204 original size:22 final size:23
Alignment explanation
Indices: 515151--515213 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
515141 ATATTACATA
* *
515151 AATTTTAAATTATAT-ATATATT
1 AATTTTAATTTTTATAATATATT
*
515173 TATTTT-ATTTTTATAATATA-T
1 AATTTTAATTTTTATAATATATT
515194 AATTTTAATTTATT-TAATAT
1 AATTTTAATTT-TTATAATAT
515214 TGGCCAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 12 0.35
22 20 0.59
23 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTAATTTTTATAATATATT
Found at i:515339 original size:14 final size:14
Alignment explanation
Indices: 515314--515358 Score: 81
Period size: 14 Copynumber: 3.1 Consensus size: 14
515304 ATCAAATCAC
515314 TTTTGAATGATGTCA
1 TTTTG-ATGATGTCA
515329 TTTTGATGATGTCA
1 TTTTGATGATGTCA
515343 TTTTGATGATGTCA
1 TTTTGATGATGTCA
515357 TT
1 TT
515359 GATTGTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (14 bp):
TTTTGATGATGTCA
Found at i:515541 original size:19 final size:19
Alignment explanation
Indices: 515519--515561 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
515509 TGTTTTAATT
515519 TTAAAATATA-TATTTTATA
1 TTAAAATATATTATTTT-TA
*
515538 TTAATATATATTATTTTTA
1 TTAAAATATATTATTTTTA
515557 TTAAA
1 TTAAA
515562 TAATGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAAATATATTATTTTTA
Found at i:515907 original size:14 final size:14
Alignment explanation
Indices: 515885--515964 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 14
515875 AAAAAATTAA
515885 AATATAATATAATAT
1 AATATAA-ATAATAT
515900 AA-ATAATATAA-AT
1 AATATAA-ATAATAT
515913 ACGATATAAAT-ATAT
1 A--ATATAAATAATAT
515928 AA-ATAAATTAATAT
1 AATATAAA-TAATAT
* *
515942 ATTA-AAATTTATAT
1 AATATAAA-TAATAT
515956 AATATAAAT
1 AATATAAAT
515965 TATTAAAGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
12 5 0.09
13 5 0.09
14 28 0.52
15 12 0.22
16 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (14 bp):
AATATAAATAATAT
Found at i:515907 original size:19 final size:18
Alignment explanation
Indices: 515885--515964 Score: 69
Period size: 19 Copynumber: 4.5 Consensus size: 18
515875 AAAAAATTAA
515885 AATATAATATAATATAAAT
1 AATATAA-ATAATATAAAT
515904 AATATAAATACGATATAAAT
1 AATATAAATA--ATATAAAT
*
515924 -ATATAAATAA-ATTAAT
1 AATATAAATAATATAAAT
* * *
515940 -ATATTAA-AATTTATAT
1 AATATAAATAATATAAAT
515956 AATATAAAT
1 AATATAAAT
515965 TATTAAAGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.04
16 14 0.28
17 7 0.14
18 3 0.06
19 16 0.32
20 8 0.16
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (18 bp):
AATATAAATAATATAAAT
Found at i:515919 original size:11 final size:9
Alignment explanation
Indices: 515885--515964 Score: 69
Period size: 8 Copynumber: 9.0 Consensus size: 9
515875 AAAAAATTAA
515885 AATATAATAT
1 AATATAA-AT
515895 AATATAAAT
1 AATATAAAT
515904 AATATAAAT
1 AATATAAAT
515913 ACGATATAAAT
1 A--ATATAAAT
515924 -ATATAAAT
1 AATATAAAT
*
515932 AA-ATTAAT
1 AATATAAAT
*
515940 -ATATTAA-
1 AATATAAAT
* *
515947 AATTTATAT
1 AATATAAAT
515956 AATATAAAT
1 AATATAAAT
515965 TATTAAAGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 1 0.02
8 22 0.38
9 20 0.34
10 7 0.12
11 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (9 bp):
AATATAAAT
Found at i:515932 original size:44 final size:43
Alignment explanation
Indices: 515855--515942 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 43
515845 TCCAATTTAA
*
515855 AAATAATTTTAAATACGATAAAAAAATTAAAATATAATATAATAT
1 AAATAATTATAAATACGATAAAAAAATTAAAATA-AAT-TAATAT
* *
515900 AAATAA-TATAAATACGATATAAATA-TATAAATAAATTAATAT
1 AAATAATTATAAATACGATAAAAAAATTA-AAATAAATTAATAT
515942 A
1 A
515943 TTAAAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 7 0.18
43 5 0.13
44 21 0.54
45 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (43 bp):
AAATAATTATAAATACGATAAAAAAATTAAAATAAATTAATAT
Found at i:515960 original size:17 final size:17
Alignment explanation
Indices: 515940--515993 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
515930 ATAAATTAAT
515940 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
515957 ATA-T-AAA-TTAT-TAA
1 ATATTAAAATTTATAT-A
*
515971 AGTATTAAAATTTATAAA
1 A-TATTAAAATTTATATA
515989 ATATT
1 ATATT
515994 TTAAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
13 1 0.03
14 6 0.20
15 5 0.17
16 2 0.07
17 10 0.33
18 6 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:515967 original size:14 final size:14
Alignment explanation
Indices: 515916--515967 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
515906 TATAAATACG
515916 ATATAAA-TATATA
1 ATATAAATTATATA
515929 A-ATAAATTAATATA
1 ATATAAATT-ATATA
*
515943 TTA-AAATTTATATA
1 ATATAAA-TTATATA
515957 ATATAAATTAT
1 ATATAAATTAT
515968 TAAAGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.16
13 2 0.06
14 19 0.59
15 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAAATTATATA
Found at i:515977 original size:32 final size:33
Alignment explanation
Indices: 515917--515992 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
515907 ATAAATACGA
515917 TATAAATATATAAATAAATTAATATATTAAAATT
1 TATAAA-ATATAAATAAATTAATATATTAAAATT
* *
515951 TATATAATATAAAT-TATTAA-AGTATTAAAATT
1 TATAAAATATAAATAAATTAATA-TATTAAAATT
515983 TATAAAATAT
1 TATAAAATAT
515993 TTTAAATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 1 0.03
32 24 0.63
33 8 0.21
34 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
TATAAAATATAAATAAATTAATATATTAAAATT
Found at i:516571 original size:16 final size:17
Alignment explanation
Indices: 516531--516576 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
516521 TGATTAACTC
516531 GAACTTAAAATAATCTA
1 GAACTTAAAATAATCTA
516548 -AA-TCTAAAATAATC-A
1 GAACT-TAAAATAATCTA
516563 GAACTTAAAATAAT
1 GAACTTAAAATAAT
516577 TCAAATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.08
16 23 0.88
17 1 0.04
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (17 bp):
GAACTTAAAATAATCTA
Found at i:517089 original size:2 final size:2
Alignment explanation
Indices: 517082--517116 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
517072 AAATTTTGAA
517082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
517117 CATAGACACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:517302 original size:18 final size:18
Alignment explanation
Indices: 517270--517330 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
517260 ATTCGTATTG
517270 TATTAATATTA-ATTTTTA
1 TATT-ATATTATATTTTTA
517288 TATTATATTATA-TTTTA
1 TATTATATTATATTTTTA
* * *
517305 -ATTATTTTTTATATTTA
1 TATTATATTATATTTTTA
517322 TATTATATT
1 TATTATATT
517331 TAAAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 9 0.25
17 15 0.42
18 12 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTATATTATATTTTTA
Found at i:517324 original size:29 final size:29
Alignment explanation
Indices: 517272--517340 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
517262 TCGTATTGTA
* *
517272 TTAATATTAATTTTTATATTATATTATAT
1 TTAAAATTATTTTTTATATTATATTATAT
*
517301 TT-TAATTATTTTTTATATTTATATTATAT
1 TTAAAATTATTTTTTATA-TTATATTATAT
517330 TTAAAATTATT
1 TTAAAATTATT
517341 GCATCTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.35
29 15 0.44
30 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTAAAATTATTTTTTATATTATATTATAT
Found at i:519139 original size:2 final size:2
Alignment explanation
Indices: 519132--519163 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
519122 AATTAGAAAT
519132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519164 ATTTGACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:521511 original size:12 final size:13
Alignment explanation
Indices: 521477--521504 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
521467 TCAATTTTAT
521477 AAGCTCAAATCAA
1 AAGCTCAAATCAA
521490 AAGCTCAAATCAA
1 AAGCTCAAATCAA
521503 AA
1 AA
521505 TTCAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (13 bp):
AAGCTCAAATCAA
Found at i:521971 original size:34 final size:35
Alignment explanation
Indices: 521906--521975 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
521896 TAGATCCATG
**
521906 AAATAGACTTAAGACAAATAAAAAATTCATATTTT
1 AAATAGACTTAAGACAAATAAAAAACCCATATTTT
* * *
521941 AAATAGA-TTAAGTCAAATTAAATACCCATATTTT
1 AAATAGACTTAAGACAAATAAAAAACCCATATTTT
521975 A
1 A
521976 CAAAAATTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 23 0.77
35 7 0.23
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (35 bp):
AAATAGACTTAAGACAAATAAAAAACCCATATTTT
Found at i:522434 original size:32 final size:35
Alignment explanation
Indices: 522345--522442 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 35
522335 GATTACACAA
* * *
522345 ATATGATATAT-AAAA-TAATAAAAAAATGACATTAT
1 ATAT-ATATATCAAAATTAATATAAATAT-AAATTAT
* *
522380 ATATATATTTCAAAATTTATAT-AATATAAATTAT
1 ATATATATATCAAAATTAATATAAATATAAATTAT
522414 -TA-ATATATCAAAATTAATATAAATATAAA
1 ATATATATATCAAAATTAATATAAATATAAA
522443 ATAACTTACA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
32 16 0.30
33 10 0.19
34 11 0.21
35 12 0.23
36 4 0.08
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (35 bp):
ATATATATATCAAAATTAATATAAATATAAATTAT
Found at i:522443 original size:17 final size:16
Alignment explanation
Indices: 522391--522444 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 16
522381 TATATATTTC
522391 AAAATT-TATATAATAT
1 AAAATTATATA-AATAT
522407 -AAATTAT-TAATATAT
1 AAAATTATATAA-ATAT
522422 CAAAATTAATATAAATAT
1 -AAAATT-ATATAAATAT
522440 AAAAT
1 AAAAT
522445 AACTTACACG
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.03
15 11 0.34
16 1 0.03
17 10 0.31
18 6 0.19
19 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTATATAAATAT
Found at i:526603 original size:15 final size:15
Alignment explanation
Indices: 526583--526614 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
526573 GTTTAGACTC
526583 GATTGGATGGTCTTA
1 GATTGGATGGTCTTA
526598 GATTGGATGGTCTTA
1 GATTGGATGGTCTTA
526613 GA
1 GA
526615 AGGGTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.06, G:0.34, T:0.38
Consensus pattern (15 bp):
GATTGGATGGTCTTA
Found at i:528056 original size:15 final size:16
Alignment explanation
Indices: 528029--528058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
528019 AAGCACATAG
528029 AAAAAAACTTAAAAAA
1 AAAAAAACTTAAAAAA
528045 AAAAAAAC-TAAAAA
1 AAAAAAACTTAAAAA
528059 CACCCGTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAACTTAAAAAA
Found at i:535699 original size:3 final size:3
Alignment explanation
Indices: 535691--535719 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
535681 TTATCAATTC
535691 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
535720 AAACTATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:538259 original size:20 final size:21
Alignment explanation
Indices: 538236--538283 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
538226 TTTTATGAAG
*
538236 TATTTAATCTATT-TAA-TATT
1 TATTTAAT-TATTAAAATTATT
538256 TATTT-ATTATTAAAATTATT
1 TATTTAATTATTAAAATTATT
538276 TATTTAAT
1 TATTTAAT
538284 ATTTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 14 0.58
21 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTAATTATTAAAATTATT
Found at i:538286 original size:27 final size:27
Alignment explanation
Indices: 538274--538341 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 27
538264 ATTAAAATTA
538274 TTTATTTAATATTTAATTAAAAAATAT
1 TTTATTTAATATTTAATTAAAAAATAT
538301 TTTATTTAATTGATTCATAACTTAAAAAAT-T
1 TTTATTTAA-T-ATT--TAA-TTAAAAAATAT
538332 TTTAATTTAA
1 TTT-ATTTAA
538342 CTTTTGATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 9 0.26
28 1 0.03
29 3 0.09
31 7 0.20
32 15 0.43
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTATTTAATATTTAATTAAAAAATAT
Found at i:538656 original size:17 final size:19
Alignment explanation
Indices: 538634--538668 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
538624 GATACAAATA
538634 ATATTT-AAT-TTTTTTAT
1 ATATTTAAATATTTTTTAT
538651 ATATTTAAATATTTTTTA
1 ATATTTAAATATTTTTTA
538669 AAAGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTTAAATATTTTTTAT
Found at i:544469 original size:16 final size:18
Alignment explanation
Indices: 544448--544492 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
544438 ATTAATTAAA
544448 TTTAAA-TAAA-AATAAT
1 TTTAAATTAAATAATAAT
544464 TTTAAATTAAATAATAA-
1 TTTAAATTAAATAATAAT
*
544481 ATTAAATTAAAT
1 TTTAAATTAAAT
544493 TATTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 15 0.58
18 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAATTAAATAATAAT
Found at i:544490 original size:22 final size:20
Alignment explanation
Indices: 544441--544494 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
544431 TTAATTTATT
544441 AATTAAATTTAAATAAAAATA
1 AATTAAA-TTAAATAAAAATA
*
544462 ATTTTAAATTAAATAATAAATTA
1 A-ATTAAATTAAATAA-AAA-TA
544485 AATTAAATTA
1 AATTAAATTA
544495 TTTTAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 16 0.57
23 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAATTAAATAAAAATA
Found at i:545113 original size:11 final size:11
Alignment explanation
Indices: 545097--545170 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
545087 ATTATATGAT
545097 AATATAATATA
1 AATATAATATA
*
545108 AATATAAAATA
1 AATATAATATA
545119 AA-ATAATAATTAA
1 AATATAAT-A-T-A
*
545132 AATATAAAATA
1 AATATAATATA
* *
545143 AAAATAATATG
1 AATATAATATA
**
545154 AATATGGTATA
1 AATATAATATA
545165 AATATA
1 AATATA
545171 TAAATATTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
10 4 0.08
11 34 0.71
12 2 0.04
13 4 0.08
14 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (11 bp):
AATATAATATA
Found at i:545127 original size:19 final size:19
Alignment explanation
Indices: 545105--545149 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
545095 ATAATATAAT
545105 ATAAATATAAA-ATAAAATA
1 ATAAATA-AAATATAAAATA
*
545124 ATAATTAAAATATAAAATA
1 ATAAATAAAATATAAAATA
545143 A-AAATAA
1 ATAAATAA
545150 TATGAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAATAAAATATAAAATA
Found at i:545127 original size:24 final size:22
Alignment explanation
Indices: 545100--545158 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
545090 ATATGATAAT
545100 ATAATATAAATATAAAAT-AAA
1 ATAATATAAATATAAAATAAAA
545121 ATAATAATTAAAATATAAAATAAAA
1 ATAAT-A-T-AAATATAAAATAAAA
*
545146 ATAATATGAATAT
1 ATAATATAAATAT
545159 GGTATAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 5 0.15
22 6 0.18
23 2 0.06
24 12 0.36
25 8 0.24
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATATAAATATAAAATAAAA
Found at i:546423 original size:17 final size:16
Alignment explanation
Indices: 546397--546431 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
546387 TTCAATATAT
*
546397 ATTTAAAAATTTTTAA
1 ATTTAAAAATTATTAA
546413 ATTTAAAAAATTATTAA
1 ATTT-AAAAATTATTAA
546430 AT
1 AT
546432 ATATATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAAAAATTATTAA
Found at i:546683 original size:20 final size:20
Alignment explanation
Indices: 546660--546703 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
546650 TTGTAACTTA
546660 AATTTAAATATTTAAA-AAAT
1 AATTTAAATA-TTAAATAAAT
*
546680 AATTTTAATATTAAATAAAT
1 AATTTAAATATTAAATAAAT
546700 AATT
1 AATT
546704 AAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTAAATATTAAATAAAT
Found at i:547511 original size:17 final size:17
Alignment explanation
Indices: 547489--547544 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
547479 TAATATTTTT
547489 ATAATTA-ATTTAAATAA
1 ATAATTATATTT-AATAA
*
547506 ATAATTATAGTTAATAA
1 ATAATTATATTTAATAA
*
547523 ATAATTATAATTAATAA
1 ATAATTATATTTAATAA
547540 ATAAT
1 ATAAT
547545 AATTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 33 0.92
18 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATAATTATATTTAATAA
Found at i:547547 original size:20 final size:20
Alignment explanation
Indices: 547487--547561 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
547477 ATTAATATTT
547487 TTATAATTAATTTAAATAAATAA
1 TTATAATTAA--TAAAT-AATAA
*
547510 TTATAGTTAAT--A-AATAA
1 TTATAATTAATAAATAATAA
547527 TTATAATTAATAAATAATAA
1 TTATAATTAATAAATAATAA
*
547547 TT-TAAATTAAAAAAT
1 TTAT-AATTAATAAAT
547562 TAGCTTGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 15 0.33
19 3 0.07
20 17 0.38
21 1 0.02
23 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
TTATAATTAATAAATAATAA
Found at i:552901 original size:17 final size:17
Alignment explanation
Indices: 552879--552911 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
552869 TAATTAATTT
552879 ATATAATTATTT-TTAAA
1 ATATAA-TATTTATTAAA
552896 ATATAATATTTATTAA
1 ATATAATATTTATTAA
552912 TTTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATAATATTTATTAAA
Found at i:563937 original size:6 final size:6
Alignment explanation
Indices: 563925--563983 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
563915 AAAAAAATCA
*
563925 AAATTT AAGTTT AAATTT AAATTT AAA-TT -AATTT AATTATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AA--ATTT AAATTT
*
563973 ATTATTT AAAT
1 A-AATTT AAAT
563984 ATATTAAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 2 0.05
5 4 0.09
6 27 0.61
7 5 0.11
8 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:563952 original size:24 final size:23
Alignment explanation
Indices: 563929--563973 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
563919 AAATCAAAAT
563929 TTAAGTTTAA-ATTTAAATTTAAA
1 TTAA-TTTAATATTTAAATTTAAA
563952 TTAATTTAATTATTTAAATTTA
1 TTAATTTAA-TATTTAAATTTA
563974 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTAATATTTAAATTTAAA
Found at i:563976 original size:13 final size:13
Alignment explanation
Indices: 563954--563989 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
563944 AATTTAAATT
563954 AATTTAATTATTTA
1 AATTT-ATTATTTA
563968 AATTTATTATTTA
1 AATTTATTATTTA
*
563981 AATATATTA
1 AATTTATTA
563990 AGATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTATTATTTA
Found at i:564017 original size:14 final size:14
Alignment explanation
Indices: 564000--564031 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
563990 AGATATTAAA
*
564000 ATAATTATATTTAT
1 ATAATTAAATTTAT
564014 ATAATTAAATTTAT
1 ATAATTAAATTTAT
564028 ATAA
1 ATAA
564032 AAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTAAATTTAT
Found at i:564079 original size:15 final size:14
Alignment explanation
Indices: 564055--564101 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
564045 AATATTTTAA
564055 TAATAATTTAAATT
1 TAATAATTTAAATT
564069 TAATCAATTTAAATT
1 TAAT-AATTTAAATT
*
564084 ATAA-AAATTAATATT
1 -TAATAATTTAA-ATT
564099 TAA
1 TAA
564102 ACTTAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 13 0.45
15 13 0.45
16 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATAATTTAAATT
Found at i:564303 original size:23 final size:25
Alignment explanation
Indices: 564277--564335 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
564267 AAATAAAAAA
564277 ATATTAATTTTATTAT-TTAT-ATT
1 ATATTAATTTTATTATATTATAATT
564300 ATATTTATATATTTTATTATATTATAATT
1 ATA--T-TA-ATTTTATTATATTATAATT
564329 ATATTAA
1 ATATTAA
564336 AATATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
23 3 0.10
25 2 0.07
26 4 0.13
27 11 0.37
28 4 0.13
29 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATATTAATTTTATTATATTATAATT
Found at i:564357 original size:29 final size:29
Alignment explanation
Indices: 564283--564354 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
564273 AAAAATATTA
* *
564283 ATTTTATTAT-TTAT-ATTATATTTATAT
1 ATTTTATTATATTATAATTATATTAAAAT
564310 ATTTTATTATATTATAATTATATTAAAAT
1 ATTTTATTATATTATAATTATATTAAAAT
*
564339 ATTTTATTTTA-TATAA
1 ATTTTATTATATTATAA
564355 ATTTAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 10 0.25
28 9 0.22
29 21 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTATTATATTATAATTATATTAAAAT
Found at i:564399 original size:50 final size:45
Alignment explanation
Indices: 564290--564408 Score: 114
Period size: 47 Copynumber: 2.5 Consensus size: 45
564280 TTAATTTTAT
* * *
564290 TATTTATATTATATTTATATATTTTATTATATTATAATTATATTAAAA
1 TATTT-TATTTTA-TTA-ATATTTAAATATATTATAATTATATTAAAA
564338 TATTTTATTTTATATAA-ATTTAAATATATTAATAATTTATATTATATAA
1 TATTTTATTTTAT-TAATATTTAAATATATT-ATAA-TTATATTA-A-AA
*
564387 TTTTTTTATTTTATTAATATTT
1 -TATTTTATTTTATTAATATTT
564409 TATTTACTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
45 11 0.18
46 6 0.10
47 16 0.27
48 6 0.10
49 5 0.08
50 16 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (45 bp):
TATTTTATTTTATTAATATTTAAATATATTATAATTATATTAAAA
Found at i:564506 original size:23 final size:23
Alignment explanation
Indices: 564442--564507 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
564432 TTCAAAAAAA
* *
564442 TTTATTTTATTATTTAAA-AATAT
1 TTTATATTAATATTTAAATAA-AT
564465 TTTATATTAATATTT--ATAAAT
1 TTTATATTAATATTTAAATAAAT
564486 TTTATAATTAA-ATTTAAATAAA
1 TTTAT-ATTAATATTTAAATAAA
564508 AATAAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 12 0.32
22 7 0.19
23 18 0.49
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTATATTAATATTTAAATAAAT
Found at i:565125 original size:25 final size:23
Alignment explanation
Indices: 564999--565151 Score: 70
Period size: 23 Copynumber: 6.6 Consensus size: 23
564989 ATTTAATAAA
* *
564999 TTATATATTT-TATTATATTAAAA
1 TTATATATTTATA-TATATTATAT
* * *
565022 TTATAT-TTAAGATATTTTATAAT
1 TTATATATTTATATATATTAT-AT
*
565045 TTATATAATTT-TGATATATTAATAA
1 TTATAT-ATTTAT-ATATATT-ATAT
* * *
565070 TT-TAT-TTTATA-AAATTTTAAG
1 TTATATATTTATATATATTAT-AT
*
565091 ATATATATTTATATCATATTATGTAT
1 TTATATATTTATAT-ATATTA--TAT
565117 TTA-ATATTTAT-TATATTATAT
1 TTATATATTTATATATATTATAT
*
565138 TTATATAATTATAT
1 TTATATATTTATAT
565152 TTAAATTTAT
Statistics
Matches: 96, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
20 1 0.01
21 12 0.12
22 22 0.23
23 28 0.29
24 4 0.04
25 23 0.24
26 5 0.05
27 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (23 bp):
TTATATATTTATATATATTATAT
Found at i:565137 original size:14 final size:14
Alignment explanation
Indices: 565099--565154 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
565089 AGATATATAT
*
565099 TTATATCATA-TTA
1 TTATATTATATTTA
565112 TGTAT-TTAATATTTA
1 T-TATATT-ATATTTA
565127 TTATATTATATTTA
1 TTATATTATATTTA
565141 -TATAATTATATTTA
1 TTAT-ATTATATTTA
565155 AATTTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 5 0.14
14 26 0.70
15 6 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
TTATATTATATTTA
Found at i:565144 original size:8 final size:8
Alignment explanation
Indices: 565092--565151 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
565082 AATTTTAAGA
565092 TATATATT
1 TATATATT
565100 TATATCATAT
1 TATAT-AT-T
*
565110 TATGTATT
1 TATATATT
565118 TA-ATATT
1 TATATATT
*
565125 TAT-TATA
1 TATATATT
565132 T-TATATT
1 TATATATT
*
565139 TATATAAT
1 TATATATT
565147 TATAT
1 TATAT
565152 TTAAATTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
6 1 0.02
7 14 0.33
8 18 0.43
9 4 0.10
10 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (8 bp):
TATATATT
Found at i:565160 original size:34 final size:38
Alignment explanation
Indices: 565094--565163 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
565084 TTTTAAGATA
565094 TATATTTATATCATATTATGTATTTAATATTTATTATAT
1 TATATTTATATCATATTA-GTATTTAATATTTATTATAT
565133 TATATTTATAT-A-ATTA-TATTTAA-ATTTATTA
1 TATATTTATATCATATTAGTATTTAATATTTATTA
565164 AATCTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 8 0.26
35 7 0.23
37 4 0.13
38 1 0.03
39 11 0.35
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (38 bp):
TATATTTATATCATATTAGTATTTAATATTTATTATAT
Found at i:566003 original size:2 final size:2
Alignment explanation
Indices: 565996--566028 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
565986 CCAAAAGTAT
565996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
566029 TCTTGTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:567281 original size:42 final size:46
Alignment explanation
Indices: 567230--567313 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
567220 TATCTAATTT
*
567230 ATAAAT-AAAA-ATTTTAA-TTT-CATTAAATATA-TTTATTTGAGG
1 ATAAATAAAAAGATTTAAATTTTACATTAAAT-TACTTTATTTGAGG
567272 ATAAATAAAAAGATTTAAATTTTACATTAAATTACTTTATTT
1 ATAAATAAAAAGATTTAAATTTTACATTAAATTACTTTATTT
567314 TTTAGAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 6 0.17
43 4 0.11
44 6 0.17
45 5 0.14
46 15 0.42
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (46 bp):
ATAAATAAAAAGATTTAAATTTTACATTAAATTACTTTATTTGAGG
Found at i:567779 original size:42 final size:42
Alignment explanation
Indices: 567701--567805 Score: 174
Period size: 42 Copynumber: 2.5 Consensus size: 42
567691 AATTAAAGAG
*
567701 AATTAAATTAATAATAATAAATAATCAATTAAAAATAATTAAA
1 AATTAAATTAATAATAAT-AATAATCAATAAAAAATAATTAAA
*
567744 AATTAAATTAATAATAATAATAATCGATAAAAAATAATTAAA
1 AATTAAATTAATAATAATAATAATCAATAAAAAATAATTAAA
*
567786 AAATAAATTAATAATAATAA
1 AATTAAATTAATAATAATAA
567806 ATGATGTCTA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
42 41 0.69
43 18 0.31
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (42 bp):
AATTAAATTAATAATAATAATAATCAATAAAAAATAATTAAA
Found at i:568485 original size:14 final size:15
Alignment explanation
Indices: 568446--568485 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
568436 AATTAGATTG
568446 ATTAATATTTATATT
1 ATTAATATTTATATT
* *
568461 ATTATTTTTTAT-TT
1 ATTAATATTTATATT
568475 ATTAATATTTA
1 ATTAATATTTA
568486 ATATAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTAATATTTATATT
Found at i:568876 original size:30 final size:30
Alignment explanation
Indices: 568854--568919 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
568844 AATAATTTTT
568854 TTATATTTTT-ATAT-TATTTAAATAAATTA
1 TTAT-TTTTTAATATATATTTAAATAAATTA
*
568883 TTATTTTTTAATTTATATTTAAATAAAATT-
1 TTATTTTTTAATATATATTTAAAT-AAATTA
568913 TTATTTT
1 TTATTTT
568920 AAATAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 5 0.15
29 7 0.21
30 16 0.48
31 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATTTTTTAATATATATTTAAATAAATTA
Found at i:568917 original size:33 final size:31
Alignment explanation
Indices: 568842--568917 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
568832 TTATTTTTAA
*
568842 TAAAT-AATTTTTTTATATTTTTATATTATT
1 TAAATAAATTTTATTATATTTTTATATTATT
*
568872 TAAATAAA--TTATTAT-TTTTTAATTTATATT
1 TAAATAAATTTTATTATATTTTT-ATAT-TATT
568902 TAAATAAAATTTTATT
1 TAAAT-AAATTTTATT
568918 TTAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 5 0.13
29 9 0.24
30 14 0.37
31 5 0.13
33 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TAAATAAATTTTATTATATTTTTATATTATT
Found at i:568938 original size:9 final size:9
Alignment explanation
Indices: 568924--568950 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
568914 TATTTTAAAT
568924 AAATTATTA
1 AAATTATTA
568933 AAATTATTA
1 AAATTATTA
568942 AAATTATTA
1 AAATTATTA
568951 TATATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAATTATTA
Found at i:569315 original size:17 final size:17
Alignment explanation
Indices: 569271--569316 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
569261 AGAAGATATT
*
569271 ATTTATTTTTAAGTAAA
1 ATTTATTTTTTAGTAAA
* *
569288 TTTTATTTTTTATTAAA
1 ATTTATTTTTTAGTAAA
569305 ATTTATTTTTTA
1 ATTTATTTTTTA
569317 AATTTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTATTTTTTAGTAAA
Found at i:569556 original size:12 final size:12
Alignment explanation
Indices: 569539--569563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
569529 ATGGGGAAGA
569539 GAAGAGGAGGAG
1 GAAGAGGAGGAG
569551 GAAGAGGAGGAG
1 GAAGAGGAGGAG
569563 G
1 G
569564 CGGCGCGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
GAAGAGGAGGAG
Found at i:572514 original size:20 final size:20
Alignment explanation
Indices: 572489--572532 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
572479 AATATTATTT
572489 ATTTAAAATTATTAATAAA-A
1 ATTTAAAATT-TTAATAAATA
572509 ATTTAAAATTTTAATAAATA
1 ATTTAAAATTTTAATAAATA
572529 ATTT
1 ATTT
572533 TATAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAAATTTTAATAAATA
Found at i:572730 original size:29 final size:28
Alignment explanation
Indices: 572686--572757 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
572676 TATTAAATAT
*
572686 AAAATAA-AT-AATATAAAAAAATTTAA
1 AAAATAATATAAATATAAAAAAATATAA
* * * *
572712 AATATATTATTAAATATAACATAATATAA
1 AAAATAATA-TAAATATAAAAAAATATAA
572741 AAAATAATATAAATATA
1 AAAATAATATAAATATA
572758 CGAATATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 5 0.14
27 1 0.03
28 9 0.25
29 21 0.58
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAATAATATAAATATAAAAAAATATAA
Found at i:572857 original size:56 final size:55
Alignment explanation
Indices: 572719--572869 Score: 137
Period size: 57 Copynumber: 2.7 Consensus size: 55
572709 TAAAATATAT
* * * *
572719 TATTA-AATATAACATAATATAAAAAATAATATAAATATACGAATATTTTTAAATC
1 TATTATAATATAATA-AATATAAAAATTAATATAAATATACAAATATTTTTAAAAC
* * * *
572774 TA-TATAATATAAATTAATGTATCAAAATTTATATAAGTATA-AAATATTTTTAAACAC
1 TATTATAATAT-AA-TAA-ATATAAAAATTAATATAAATATACAAATATTTTTAAA-AC
*
572831 TATTATAATATAATAAACTATAAAAATATGATATAAATA
1 TATTATAATATAATAAA-TATAAAAAT-TAATATAAATA
572870 CATAAATAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
54 2 0.03
55 7 0.09
56 26 0.34
57 33 0.43
58 8 0.11
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (55 bp):
TATTATAATATAATAAATATAAAAATTAATATAAATATACAAATATTTTTAAAAC
Found at i:573072 original size:31 final size:30
Alignment explanation
Indices: 573035--573105 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
573025 ATTTATACAA
*
573035 ATATAAATTATTTTTAAATATAATTAT-AAT
1 ATATAAATTATTTATAAATATAA-TATGAAT
573065 ATGATAAATTA--TATAAATATAATATGAAT
1 AT-ATAAATTATTTATAAATATAATATGAAT
573094 ATATAAATTATT
1 ATATAAATTATT
573106 AAACCAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 11 0.31
29 15 0.42
30 2 0.06
31 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATATAAATTATTTATAAATATAATATGAAT
Found at i:573206 original size:19 final size:18
Alignment explanation
Indices: 573176--573227 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
573166 TAGATGTATT
573176 ATAAAA-ATAATATAAAAA
1 ATAAAATATAATAT-AAAA
573194 ATAAAATATAATATAAAA
1 ATAAAATATAATATAAAA
573212 ATAAAAATATTAATAT
1 AT-AAAATA-TAATAT
573228 CTCAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.39
19 13 0.42
20 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAATATAATATAAAA
Found at i:573209 original size:12 final size:11
Alignment explanation
Indices: 573175--573215 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
573165 TTAGATGTAT
573175 TATAAAAATAA
1 TATAAAAATAA
573186 TAT-AAAA-AA
1 TATAAAAATAA
*
573195 TA-AAATATAA
1 TATAAAAATAA
573205 TATAAAAATAA
1 TATAAAAATAA
573216 AAATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:573294 original size:16 final size:17
Alignment explanation
Indices: 573262--573294 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
573252 ATTAATTTAT
573262 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
573279 TAAAATTTAT-TAAATA
1 TAAAATTTATATAAATA
573295 CGATTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:574526 original size:2 final size:2
Alignment explanation
Indices: 574519--574545 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
574509 AACTTTTGAC
574519 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
574546 GTTTTATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:576084 original size:14 final size:14
Alignment explanation
Indices: 576065--576091 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
576055 TATTTTAAAG
576065 TAATTTTAAATGTA
1 TAATTTTAAATGTA
576079 TAATTTTAAATGT
1 TAATTTTAAATGT
576092 CAAACACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAATTTTAAATGTA
Found at i:580534 original size:9 final size:9
Alignment explanation
Indices: 580520--580563 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
580510 TAATTTGAAT
580520 TTAAAAATA
1 TTAAAAATA
580529 TTAAAAATA
1 TTAAAAATA
*
580538 ATATAAAATAA
1 TTA-AAAAT-A
*
580549 TTAAAAAAA
1 TTAAAAATA
580558 TTAAAA
1 TTAAAA
580564 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 18 0.60
10 9 0.30
11 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
TTAAAAATA
Found at i:580544 original size:20 final size:19
Alignment explanation
Indices: 580520--580563 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
580510 TAATTTGAAT
580520 TTAAAAAT-ATTAAAAATAA
1 TTAAAAATAATTAAAAA-AA
580539 -TATAAAATAATTAAAAAAA
1 TTA-AAAATAATTAAAAAAA
580558 TTAAAA
1 TTAAAA
580564 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 10 0.45
20 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAATAATTAAAAAAA
Found at i:580999 original size:16 final size:16
Alignment explanation
Indices: 580979--581016 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
580969 TTGAAATTTA
580979 AAAAATGATTAAAATT
1 AAAAATGATTAAAATT
* *
580995 TAAAATGATTTAAATT
1 AAAAATGATTAAAATT
581011 AAAAAT
1 AAAAAT
581017 AATCAAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
AAAAATGATTAAAATT
Found at i:581075 original size:22 final size:20
Alignment explanation
Indices: 581047--581096 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
581037 TTTGAAATTG
*
581047 ATTAATTTAAATATTAAATTTA
1 ATTAATTT-AATATTAAA-ATA
*
581069 ATTAATTTAATTTTAAAATA
1 ATTAATTTAATATTAAAATA
581089 ATTAATTT
1 ATTAATTT
581097 GAGTGTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 8 0.31
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTAATTTAATATTAAAATA
Found at i:581093 original size:15 final size:14
Alignment explanation
Indices: 581047--581096 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
581037 TTTGAAATTG
581047 ATTAA-TTTAAAT-
1 ATTAATTTTAAATA
* *
581059 ATTAAATTTAATTA
1 ATTAATTTTAAATA
581073 ATTTAATTTTAAAATA
1 A-TTAATTTT-AAATA
581089 ATTAATTT
1 ATTAATTT
581097 GAGTGTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 1 0.03
15 14 0.45
16 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTAATTTTAAATA
Found at i:582282 original size:18 final size:19
Alignment explanation
Indices: 582242--582285 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
582232 TTAAAATATC
* *
582242 ATTTCAAATAAATTAAATTA
1 ATTTAAAATAAA-TAAATAA
582262 ATTTAAAATAAA-AAATAA
1 ATTTAAAATAAATAAATAA
582280 ATTTAA
1 ATTTAA
582286 TTTAATCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAATAAATAAATAA
Found at i:582613 original size:2 final size:2
Alignment explanation
Indices: 582600--582644 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
582590 TCAAGCTGGA
*
582600 AT AT AC 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
582642 AT A
1 AT A
582645 ACCCTTCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:583153 original size:2 final size:2
Alignment explanation
Indices: 583146--583177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
583136 CTATTAGAAT
583146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
583178 AAGTGCAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:584288 original size:27 final size:28
Alignment explanation
Indices: 584235--584289 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
584225 ATACGTTATA
*
584235 TTTATATTATTTTTTTATCGTATCATAT
1 TTTATATTATTTTTTTATCATATCATAT
*
584263 TTTA-ATTA-TTTTTTATTATATACATAT
1 TTTATATTATTTTTTTATCATAT-CATAT
584290 CATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.46
27 9 0.38
28 4 0.17
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTATATTATTTTTTTATCATATCATAT
Found at i:587020 original size:21 final size:19
Alignment explanation
Indices: 586994--587034 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
586984 ATTATAAATA
586994 AAAATTAATAATAAAAATATT
1 AAAATT-ATAA-AAAAATATT
*
587015 AAAATTATAAAATAATATT
1 AAAATTATAAAAAAATATT
587034 A
1 A
587035 TAAAATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAAAAATATT
Found at i:587036 original size:13 final size:13
Alignment explanation
Indices: 587018--587047 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
587008 AAATATTAAA
587018 ATTATAAAATAAT
1 ATTATAAAATAAT
*
587031 ATTATAAAATCAT
1 ATTATAAAATAAT
587044 ATTA
1 ATTA
587048 CGAATGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATAAAATAAT
Found at i:589106 original size:12 final size:11
Alignment explanation
Indices: 589067--589108 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
589057 TTATTAGAAA
589067 ATTAA-TTTAT
1 ATTAATTTTAT
589077 ATTAATATTTAT
1 ATTAAT-TTTAT
589089 A-TAATTTTAT
1 ATTAATTTTAT
589099 AATTAATTTT
1 -ATTAATTTT
589109 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.36
11 5 0.18
12 13 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:590496 original size:33 final size:33
Alignment explanation
Indices: 590425--590546 Score: 99
Period size: 32 Copynumber: 3.7 Consensus size: 33
590415 TTAATTATGA
*
590425 TTATATAA-ATATAATA-AAAAATA-ATTAAAAT
1 TTATATAATATA-AATATATAAATATATTAAAAT
* *
590456 ATGATATAATATAAATATATAAATATTTTAAAAT
1 -TTATATAATATAAATATATAAATATATTAAAAT
* * * **
590490 TTATATAATATGAAT-TATTAATGTATTGTAAT
1 TTATATAATATAAATATATAAATATATTAAAAT
590522 TTATATAAATATAAAATATCATAAA
1 TTATAT-AATAT-AAATAT-ATAAA
590547 AATAATTATG
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
32 29 0.41
33 27 0.38
34 10 0.14
35 1 0.01
36 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (33 bp):
TTATATAATATAAATATATAAATATATTAAAAT
Found at i:596141 original size:27 final size:26
Alignment explanation
Indices: 596111--596177 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
596101 TCATTTTTTA
*
596111 TGTAAAAAATGGTGGTTCCTTTTTGTT
1 TGTAAAAAATAGTGGTT-CTTTTTGTT
596138 TGTAAAAAATAGTGGTTCTTTTTGTT
1 TGTAAAAAATAGTGGTTCTTTTTGTT
*
596164 TGTCAAAAATAGTG
1 TGTAAAAAATAGTG
596178 ACCTGTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (26 bp):
TGTAAAAAATAGTGGTTCTTTTTGTT
Found at i:596220 original size:24 final size:24
Alignment explanation
Indices: 596162--596227 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
596152 GTTCTTTTTG
* * *
596162 TTTGTCAAAAATAGTGACCTGTTA
1 TTTGTCAAAATTGGTGGCCTGTTA
596186 TTTGTCAAAATTGGTGGCCTGTTA
1 TTTGTCAAAATTGGTGGCCTGTTA
596210 TTTGTCAAAATTGGTGGC
1 TTTGTCAAAATTGGTGGC
596228 TAATTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCCTGTTA
Found at i:596949 original size:2 final size:2
Alignment explanation
Indices: 596944--596980 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
596934 TTTTTCAGTA
596944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
596981 AAATTTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:598193 original size:17 final size:17
Alignment explanation
Indices: 598171--598211 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
598161 GATCTGATCC
598171 AATCTAATACATGAATA
1 AATCTAATACATGAATA
* **
598188 AATCTAATATATGCGTA
1 AATCTAATACATGAATA
598205 AATCTAA
1 AATCTAA
598212 AAAATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (17 bp):
AATCTAATACATGAATA
Done.