Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 14 of 187
Found at i:5087611 original size:18 final size:18
Alignment explanation
Indices: 5087588--5087622 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5087578 TTATATTTAT
5087588 TTAATGTTAATGTTAATG
1 TTAATGTTAATGTTAATG
5087606 TTAATGTTAATGTTAAT
1 TTAATGTTAATGTTAAT
5087623 ATAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
TTAATGTTAATGTTAATG
Found at i:5087694 original size:59 final size:59
Alignment explanation
Indices: 5087629--5087753 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 59
5087619 TAATATAATA
* * *
5087629 TAAATTTTAAAT-TTATTATTATATTTTTTTGAAAAATATTTTTCT-TATTTATATATTTT
1 TAAATTTTAAATATTATTATTAT-TTCTTGTCAAAAATATTTTT-TATATTTATATATTTT
* * *
5087688 TAAATTTTATATATTATTATTATTTCTTGTCAACAATATTTTTTATTTTTATATATTTT
1 TAAATTTTAAATATTATTATTATTTCTTGTCAAAAATATTTTTTATATTTATATATTTT
5087747 TAAATTT
1 TAAATTT
5087754 ATTTTTTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.02
59 47 0.81
60 10 0.17
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (59 bp):
TAAATTTTAAATATTATTATTATTTCTTGTCAAAAATATTTTTTATATTTATATATTTT
Found at i:5088598 original size:9 final size:9
Alignment explanation
Indices: 5088584--5088709 Score: 64
Period size: 9 Copynumber: 13.8 Consensus size: 9
5088574 TTTTCCCATA
5088584 AAAAATTAT
1 AAAAATTAT
*
5088593 AAAAATTCAG
1 AAAAATT-AT
5088603 AAAAATTAT
1 AAAAATTAT
*
5088612 AAAAATATTT
1 AAAAAT-TAT
*
5088622 TAAAATTCAT
1 AAAAATT-AT
*
5088632 TAAAA-T-T
1 AAAAATTAT
*
5088639 AATAATTAAT
1 AAAAATT-AT
*
5088649 AAAACTTAT
1 AAAAATTAT
*
5088658 AAATATTAT
1 AAAAATTAT
5088667 -AAAA-TAT
1 AAAAATTAT
*
5088674 AATAAA-TCT
1 AA-AAATTAT
* *
5088683 AATAATTTT
1 AAAAATTAT
5088692 CAATAAATTAT
1 -AA-AAATTAT
5088703 AAAAATT
1 AAAAATT
5088710 TTATAAGATT
Statistics
Matches: 89, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 39 0.44
10 31 0.35
11 5 0.06
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.37
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5088626 original size:29 final size:29
Alignment explanation
Indices: 5088581--5088639 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5088571 TTATTTTCCC
5088581 ATAAAAAATTATAAAAATTCAGAAAAATT
1 ATAAAAAATTATAAAAATTCAGAAAAATT
* **
5088610 ATAAAAATATT-TTAAAATTCATTAAAATT
1 ATAAAAA-ATTATAAAAATTCAGAAAAATT
5088639 A
1 A
5088640 ATAATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAAAAAATTATAAAAATTCAGAAAAATT
Found at i:5088687 original size:19 final size:17
Alignment explanation
Indices: 5088632--5088706 Score: 57
Period size: 19 Copynumber: 4.3 Consensus size: 17
5088622 TAAAATTCAT
5088632 TAAAATTAAT-AATTAA
1 TAAAATTAATAAATTAA
*
5088648 TAAAACTT-ATAAATATTA
1 TAAAA-TTAATAAAT-TAA
5088666 TAAAATATAATAAATCTAA
1 TAAAAT-TAATAAAT-TAA
**
5088685 TAATTTTCAATAAATT-A
1 TAAAATT-AATAAATTAA
5088702 TAAAA
1 TAAAA
5088707 ATTTTATAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.15
17 10 0.22
18 10 0.22
19 19 0.41
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATTAATAAATTAA
Found at i:5093506 original size:19 final size:19
Alignment explanation
Indices: 5093482--5093518 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5093472 AAAGTTGTAG
5093482 ATTTAATTTATATATTTTA
1 ATTTAATTTATATATTTTA
*
5093501 ATTTAATTTATGTATTTT
1 ATTTAATTTATATATTTT
5093519 GTGAAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTAATTTATATATTTTA
Found at i:5093560 original size:50 final size:50
Alignment explanation
Indices: 5093461--5093566 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
5093451 TATTAGTCTT
*
5093461 TGTATTTTGTGAAAGTTGTAGATTTAATTTATATATTTTAATTTAATTTA
1 TGTATTTTGTGAAAGTTGTAGATTTAATTTATATATTATAATTTAATTTA
* * * *
5093511 TGTATTTTGTGAAAGTTGTGGATTTAATTTATGTATTAT-CTTTGTATTTA
1 TGTATTTTGTGAAAGTTGTAGATTTAATTTATATATTATAATTT-AATTTA
5093561 TGTATT
1 TGTATT
5093567 AATCTTAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 3 0.06
50 47 0.94
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (50 bp):
TGTATTTTGTGAAAGTTGTAGATTTAATTTATATATTATAATTTAATTTA
Found at i:5099799 original size:23 final size:23
Alignment explanation
Indices: 5099743--5099793 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5099733 ATTTTATTAG
**
5099743 ATAATAATTTTAAATATTAAGTT
1 ATAATAATAATAAATATTAAGTT
* *
5099766 ATTATAATAATAAATATTATGTT
1 ATAATAATAATAAATATTAAGTT
5099789 ATAAT
1 ATAAT
5099794 TTTAATTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATAATAATAATAAATATTAAGTT
Found at i:5100004 original size:16 final size:16
Alignment explanation
Indices: 5099983--5100015 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5099973 ATCCTTTACA
*
5099983 TTTTTTTAAGATAAAT
1 TTTTTTTAACATAAAT
5099999 TTTTTTTAACATAAAT
1 TTTTTTTAACATAAAT
5100015 T
1 T
5100016 ATAATTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTTTTTAACATAAAT
Found at i:5106830 original size:4 final size:4
Alignment explanation
Indices: 5106823--5106849 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5106813 CATAAACATT
5106823 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
5106850 GAGATGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:5107150 original size:24 final size:23
Alignment explanation
Indices: 5107091--5107150 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
5107081 CAGTTCTTGT
* *
5107091 ACTCTTCCAATTTTTAAAATTTA
1 ACTCTTCCACTTTTCAAAATTTA
**
5107114 ATCTCTTAGACTTTTCAAATATTTA
1 A-CTCTTCCACTTTTCAAA-ATTTA
*
5107139 ACTCTTCTACTT
1 ACTCTTCCACTT
5107151 ATTTGATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.03
24 22 0.76
25 6 0.21
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (23 bp):
ACTCTTCCACTTTTCAAAATTTA
Found at i:5116962 original size:50 final size:50
Alignment explanation
Indices: 5116840--5117138 Score: 409
Period size: 50 Copynumber: 5.8 Consensus size: 50
5116830 GATCATAACA
* * ** * *
5116840 TGCCAAAGCTATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
5116891 TGCCCATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
5116941 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5116991 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5117041 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * * *
5117096 ATGCCAATGCCATGTCCCAGACATGGCCTTACATAGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5117139 TTACCCAAAT
Statistics
Matches: 225, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
50 147 0.65
51 34 0.15
53 5 0.02
55 2 0.01
56 37 0.16
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5118391 original size:26 final size:26
Alignment explanation
Indices: 5118355--5118418 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
5118345 TCGTATTTTT
5118355 CCTTATCCTTCTCTTTATGTTTCTCC
1 CCTTATCCTTCTCTTTATGTTTCTCC
5118381 CCTTATCCTTCTCTTTATGTTTCTCC
1 CCTTATCCTTCTCTTTATGTTTCTCC
* *
5118407 CTTTATCATTCT
1 CCTTATCCTTCT
5118419 TATGCTTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.09, C:0.33, G:0.03, T:0.55
Consensus pattern (26 bp):
CCTTATCCTTCTCTTTATGTTTCTCC
Found at i:5118410 original size:14 final size:14
Alignment explanation
Indices: 5118367--5118412 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5118357 TTATCCTTCT
5118367 CTTTATGTTTCTCC
1 CTTTATGTTTCTCC
* **
5118381 CCTTATCCTTCT--
1 CTTTATGTTTCTCC
5118393 CTTTATGTTTCTCC
1 CTTTATGTTTCTCC
5118407 CTTTAT
1 CTTTAT
5118413 CATTCTTATG
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
12 9 0.38
14 15 0.62
ACGTcount: A:0.09, C:0.30, G:0.04, T:0.57
Consensus pattern (14 bp):
CTTTATGTTTCTCC
Found at i:5121773 original size:29 final size:29
Alignment explanation
Indices: 5121739--5121811 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
5121729 ATGTATTAGT
* *
5121739 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
5121768 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
5121797 TTAGGACATATTTAA
1 TTAGGACATATTTAA
5121812 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:5127173 original size:12 final size:11
Alignment explanation
Indices: 5127150--5127212 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
5127140 CCGTATACAA
5127150 TTTTTTTC--T
1 TTTTTTTCAAT
5127159 TTTTTTTCAAT
1 TTTTTTTCAAT
* *
5127170 TTTTTTTGATT
1 TTTTTTTCAAT
**
5127181 TTTTTTTTGAT
1 TTTTTTTCAAT
5127192 TTTTTTTCAAAT
1 TTTTTTTC-AAT
5127204 TTTTTTTCA
1 TTTTTTTCA
5127213 CGAGTCTACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 8 0.18
11 26 0.59
12 10 0.23
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:5127182 original size:19 final size:19
Alignment explanation
Indices: 5127147--5127184 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5127137 AGACCGTATA
*
5127147 CAATTTTTTTCTTTTTTTT
1 CAATTTTTTTCTATTTTTT
5127166 CAATTTTTTT-TGATTTTTT
1 CAATTTTTTTCT-ATTTTTT
5127185 TTTTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (19 bp):
CAATTTTTTTCTATTTTTT
Found at i:5128430 original size:29 final size:29
Alignment explanation
Indices: 5128396--5128468 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
5128386 ATGTATTAGT
* *
5128396 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
5128425 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
5128454 TTAAGACATATTTAA
1 TTAGGACATATTTAA
5128469 TAATATCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:5129019 original size:11 final size:11
Alignment explanation
Indices: 5128987--5129011 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5128977 TGTTATCATT
5128987 TTGCTATTATA
1 TTGCTATTATA
5128998 TTGCTATTATA
1 TTGCTATTATA
5129009 TTG
1 TTG
5129012 TTGTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (11 bp):
TTGCTATTATA
Found at i:5129664 original size:20 final size:20
Alignment explanation
Indices: 5129639--5129681 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5129629 AAAATAAACT
5129639 ATAATAATAATTT-GAAAAAA
1 ATAATAA-AATTTAGAAAAAA
*
5129659 ATAATAAAATTTAGTAAAAA
1 ATAATAAAATTTAGAAAAAA
5129679 ATA
1 ATA
5129682 GTTTATGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
ATAATAAAATTTAGAAAAAA
Found at i:5129987 original size:2 final size:2
Alignment explanation
Indices: 5129980--5130015 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5129970 CTTCATTCTT
5129980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5130016 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5135570 original size:33 final size:34
Alignment explanation
Indices: 5135532--5135596 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
5135522 GAACAAAACA
*
5135532 TAATATTATTAAT-TAATAGTA-AATATTCAATTT
1 TAATATTAAT-ATGTAATAGTATAATATTCAATTT
*
5135565 TAATATTAATATGTAATATTATAATATTCAAT
1 TAATATTAATATGTAATAGTATAATATTCAAT
5135597 AATATTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 2 0.07
33 16 0.57
34 10 0.36
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (34 bp):
TAATATTAATATGTAATAGTATAATATTCAATTT
Found at i:5135661 original size:21 final size:22
Alignment explanation
Indices: 5135621--5135662 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5135611 ATATTTAATT
5135621 ATTTATATTGAATAATACAATA
1 ATTTATATTGAATAATACAATA
5135643 ATTTATATTGAAT-ATACAAT
1 ATTTATATTGAATAATACAAT
5135663 TTTATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (22 bp):
ATTTATATTGAATAATACAATA
Found at i:5135792 original size:23 final size:23
Alignment explanation
Indices: 5135766--5135833 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
5135756 ATAATCTATC
**
5135766 TATATTATAATTTATAAATATTT
1 TATATTATAAAATATAAATATTT
*
5135789 TATAGTATAAAATATAAATATTT
1 TATATTATAAAATATAAATATTT
* *
5135812 TA-ATTACATAAATATAAGTATT
1 TATATTATA-AAATATAAATATT
5135834 GGTTTAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 34 0.89
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (23 bp):
TATATTATAAAATATAAATATTT
Found at i:5135995 original size:14 final size:15
Alignment explanation
Indices: 5135967--5136007 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
5135957 TATTATGTTT
*
5135967 ATTTTATAAAGAATA
1 ATTTTATAAAAAATA
5135982 ATTTT-TAAAAAATA
1 ATTTTATAAAAAATA
*
5135996 ATTTTAGAAAAA
1 ATTTTATAAAAA
5136008 TTTGTCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (15 bp):
ATTTTATAAAAAATA
Found at i:5136028 original size:33 final size:34
Alignment explanation
Indices: 5135990--5136061 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
5135980 TAATTTTTAA
* *
5135990 AAAATAATTTTAGA-AAAAT-TTGTCAAACAACAG
1 AAAATAATTTTACAGAAAATCAT-TCAAACAACAG
*
5136023 AAAAT-ATTTTACAGAAAATCATTCAAACATCAG
1 AAAATAATTTTACAGAAAATCATTCAAACAACAG
5136056 AAAATA
1 AAAATA
5136062 TCAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
32 7 0.21
33 25 0.76
34 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (34 bp):
AAAATAATTTTACAGAAAATCATTCAAACAACAG
Found at i:5136089 original size:22 final size:20
Alignment explanation
Indices: 5136054--5136101 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5136044 TTCAAACATC
5136054 AGAAAAT-ATCAATTTTTTTA
1 AGAAAATCATCAA-TTTTTTA
5136074 AGAAAATCAATCAATTTTTTA
1 AGAAAATC-ATCAATTTTTTA
5136095 A-AAAATC
1 AGAAAATC
5136102 CTTTTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.50
21 8 0.31
22 5 0.19
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (20 bp):
AGAAAATCATCAATTTTTTA
Found at i:5136858 original size:25 final size:25
Alignment explanation
Indices: 5136824--5136873 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
5136814 CAGGTAAGGC
5136824 TCATTCTTCTTCTTCCGTTCTTCAT
1 TCATTCTTCTTCTTCCGTTCTTCAT
* *
5136849 TCATTTTTCTTCTTCTGTTCTTCAT
1 TCATTCTTCTTCTTCCGTTCTTCAT
5136874 CTTCTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.08, C:0.28, G:0.04, T:0.60
Consensus pattern (25 bp):
TCATTCTTCTTCTTCCGTTCTTCAT
Found at i:5139544 original size:22 final size:20
Alignment explanation
Indices: 5139501--5139539 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5139491 TAATTTAAAA
5139501 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
5139521 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
5139540 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:5139596 original size:32 final size:33
Alignment explanation
Indices: 5139560--5139646 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 33
5139550 AACTTTTCCG
**
5139560 GAAAATATTTT-CAGAAAATCTGTCAAACAGCA
1 GAAAATATTTTACAGAAAATCAATCAAACAGCA
* * * *
5139592 GAAAATATTTTACACAGATTCAATCAAACATCA
1 GAAAATATTTTACAGAAAATCAATCAAACAGCA
* *
5139625 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTACAGAAAATCA
5139647 TTTTACAGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 11 0.26
33 32 0.74
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (33 bp):
GAAAATATTTTACAGAAAATCAATCAAACAGCA
Found at i:5139682 original size:34 final size:34
Alignment explanation
Indices: 5139626--5139691 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
5139616 CAAACATCAG
* *
5139626 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTAC-GAAAAGT
5139661 AAAACATTTTCCA-AAAATCATTTTACGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACGAAAA
5139692 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGAAAATCATTTTACGAAAAGT
Found at i:5139693 original size:15 final size:15
Alignment explanation
Indices: 5139661--5139700 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
5139651 ACAGAAAAGT
5139661 AAAA-CATTTT-CCA
1 AAAATCATTTTACCA
*
5139674 AAAATCATTTTACGA
1 AAAATCATTTTACCA
5139689 AAAAT-ATTTTAC
1 AAAATCATTTTAC
5139701 TGCCAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (15 bp):
AAAATCATTTTACCA
Found at i:5144195 original size:12 final size:12
Alignment explanation
Indices: 5144178--5144202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5144168 TTTTTTTTTT
5144178 AAGTTTCCATTA
1 AAGTTTCCATTA
5144190 AAGTTTCCATTA
1 AAGTTTCCATTA
5144202 A
1 A
5144203 TTATTTTTGG
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AAGTTTCCATTA
Found at i:5144716 original size:93 final size:93
Alignment explanation
Indices: 5144557--5144734 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 93
5144547 GGTGTTACAC
* ** * * * *
5144557 GAAAAGTATAATAACTAGTCATTCTTTAATTAATTATCAAGTCAGGATTTGAAACTGAGATGATA
1 GAAAAGTACAATAACTAAACATTCTTTAATTAATCATCAAGTCAGGAGTTGAAACTGAAATAATA
*
5144622 AAATGAATCAAAATTCGAAATGTCATTT
66 AAATGAATCAAAACTCGAAATGTCATTT
* * *
5144650 GAAAAGTACAATAACTAAACATT-TTCTCATTAATCATCAAGT-TGAGAGTTGAACCTGAAATAA
1 GAAAAGTACAATAACTAAACATTCTT-TAATTAATCATCAAGTCAG-GAGTTGAAACTGAAATAA
5144713 TAAAATGAATCAAAACTCGAAA
64 TAAAATGAATCAAAACTCGAAA
5144735 GTTGGGAATT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (93 bp):
GAAAAGTACAATAACTAAACATTCTTTAATTAATCATCAAGTCAGGAGTTGAAACTGAAATAATA
AAATGAATCAAAACTCGAAATGTCATTT
Found at i:5144747 original size:45 final size:45
Alignment explanation
Indices: 5144688--5144775 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
5144678 ATTAATCATC
* *
5144688 AAGTTGAGAGTTGAACCTGAAATAATAAAATGAATCAAAACTCGA
1 AAGTTGAGAATTGAACCAGAAATAATAAAATGAATCAAAACTCGA
* ** * *
5144733 AAGTTGGGAATTGAACCAGTGATAATAAGATGATTCAAAACTC
1 AAGTTGAGAATTGAACCAGAAATAATAAAATGAATCAAAACTC
5144776 AAACTGTCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.24
Consensus pattern (45 bp):
AAGTTGAGAATTGAACCAGAAATAATAAAATGAATCAAAACTCGA
Found at i:5148907 original size:30 final size:30
Alignment explanation
Indices: 5148851--5148907 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5148841 TTACATTATA
* * *
5148851 GTATTACATATTGCTATAGATTTAAAATGT
1 GTATTACAAATTGATATAGATGTAAAATGT
5148881 GTATTACAAATT-ATATAAGATGTAAAA
1 GTATTACAAATTGATAT-AGATGTAAAA
5148908 ATAACATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (30 bp):
GTATTACAAATTGATATAGATGTAAAATGT
Found at i:5151202 original size:30 final size:30
Alignment explanation
Indices: 5151168--5151224 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5151158 TTTGATTCCC
* *
5151168 AAAAATGATAAAAATTTGATTTAATAATTT
1 AAAAATGATAAAAATTTAAATTAATAATTT
* *
5151198 AAAAATTATAAAGATTTAAATTAATAA
1 AAAAATGATAAAAATTTAAATTAATAA
5151225 AATAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAAATGATAAAAATTTAAATTAATAATTT
Found at i:5158908 original size:11 final size:11
Alignment explanation
Indices: 5158892--5158918 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5158882 CATATCAACC
5158892 TTTTTTTAATG
1 TTTTTTTAATG
5158903 TTTTTTTAATG
1 TTTTTTTAATG
5158914 TTTTT
1 TTTTT
5158919 AAGTTGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTAATG
Found at i:5159832 original size:15 final size:16
Alignment explanation
Indices: 5159803--5159832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5159793 TTAATTAAAA
5159803 ATTTAAAAGTTTTCAT
1 ATTTAAAAGTTTTCAT
5159819 ATTTAAAA-TTTTCA
1 ATTTAAAAGTTTTCA
5159833 GTACAAGTAT
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:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTAAAAGTTTTCAT
Found at i:5166967 original size:11 final size:11
Alignment explanation
Indices: 5166951--5166990 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5166941 GATTGATACT
5166951 TGAGTTAAACA
1 TGAGTTAAACA
* *
5166962 TGAGTTAATGCT
1 TGAGTTAA-ACA
5166974 TGAGTTAAACA
1 TGAGTTAAACA
5166985 TGAGTT
1 TGAGTT
5166991 GTGATTGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (11 bp):
TGAGTTAAACA
Found at i:5167525 original size:10 final size:10
Alignment explanation
Indices: 5167510--5167541 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
5167500 AATTTTCTGA
5167510 TTTTTCTTTT
1 TTTTTCTTTT
5167520 TTTTTCTTTTT
1 TTTTTC-TTTT
5167531 TTTTTCTTTT
1 TTTTTCTTTT
5167541 T
1 T
5167542 CTTGGGGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5167530 original size:11 final size:11
Alignment explanation
Indices: 5167510--5167541 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5167500 AATTTTCTGA
5167510 TTTTTC-TTTT
1 TTTTTCTTTTT
5167520 TTTTTCTTTTT
1 TTTTTCTTTTT
5167531 TTTTTCTTTTT
1 TTTTTCTTTTT
5167542 CTTGGGGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:5168257 original size:99 final size:99
Alignment explanation
Indices: 5168082--5168279 Score: 297
Period size: 99 Copynumber: 2.0 Consensus size: 99
5168072 TAATTACCGA
* * * * *
5168082 TAAAATTAAAAATTTTAAGTGTGAACTTGAGATAGATATCATTATTATACGTTAACTTTGGACCA
1 TAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACCA
* *
5168147 ATGTGCGCTACATGAATTTTAATCTTGTGCGATT
66 ATGTGCACTACATGAACTTTAATCTTGTGCGATT
* *
5168181 TAAAACTACAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATATATTAACTTTGGACCA
1 TAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACCA
* *
5168246 ATGTGCACTACATGAGCTTTAATCTTGTGGGATT
66 ATGTGCACTACATGAACTTTAATCTTGTGCGATT
5168280 AAATTAGAGG
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (99 bp):
TAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACCA
ATGTGCACTACATGAACTTTAATCTTGTGCGATT
Found at i:5169056 original size:30 final size:30
Alignment explanation
Indices: 5169022--5169079 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5169012 ATGAGATGTG
* *
5169022 TACAACTGAATTAAAATCAAAGTTTCATAA
1 TACAACTAAATCAAAATCAAAGTTTCATAA
* *
5169052 TACAATTAAATCATAATCAAAGTTTCAT
1 TACAACTAAATCAAAATCAAAGTTTCAT
5169080 GCCTATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (30 bp):
TACAACTAAATCAAAATCAAAGTTTCATAA
Found at i:5178252 original size:26 final size:25
Alignment explanation
Indices: 5178213--5178268 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
5178203 ATCTGACTCG
*
5178213 AAAACTCAACTAACACAA-AATAATTC
1 AAAACTCAAATAAC-CAACAA-AATTC
* *
5178239 AAAACTGAAATAACCAACAAATTTC
1 AAAACTCAAATAACCAACAAAATTC
5178264 AAAAC
1 AAAAC
5178269 CTTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.59, C:0.21, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAACTCAAATAACCAACAAAATTC
Found at i:5178713 original size:2 final size:2
Alignment explanation
Indices: 5178708--5178754 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5178698 GCTCTCTGTA
*
5178708 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5178750 TC TC T
1 TC TC T
5178755 GTAAGCAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5192417 original size:25 final size:27
Alignment explanation
Indices: 5192367--5192419 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5192357 TTTAAAATAC
* *
5192367 TTTTAAAATATATTTTTATTTTTTTAT
1 TTTTAAAATATATTTTTATGTATTTAT
5192394 TTTTAAAATAT-TTTTT-TGTATTTAT
1 TTTTAAAATATATTTTTATGTATTTAT
5192419 T
1 T
5192420 AAAAATCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 11 0.46
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTTAAAATATATTTTTATGTATTTAT
Found at i:5193353 original size:48 final size:48
Alignment explanation
Indices: 5193301--5193395 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
5193291 CAGCTAAATG
5193301 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTT
1 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTT
5193349 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTT
1 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTT
5193396 CTAACCTACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (48 bp):
TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTT
Found at i:5193428 original size:91 final size:90
Alignment explanation
Indices: 5193349--5193734 Score: 434
Period size: 91 Copynumber: 4.2 Consensus size: 90
5193339 TGGCTACTTT
* * **
5193349 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTCTAACCTACCGCTACGAA
1 TTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTCGGCTACTTCTAACCTACCAATACGAA
5193414 ATATATCTCAATGAGTCAGCTAAATG
66 ATA-ATCTCAATGAGTCAGCTAAATG
* * *
5193440 TTCATTTCTTTGAGCT-AAAAGATGAAGCAAATATGAGTCGGCTACTTCTAAGCTACCAATACGA
1 TTCATTTCTTTGAGCTGAAAA-TTGAAACAAATATGAGTCGGCTACTTCTAACCTACCAATACGA
*
5193504 AATGAATCTCAACGACG-CAGCTAAATG
65 AAT-AATCTCAATGA-GTCAGCTAAATG
* * *
5193531 TTCATTTCTTTGAGCTGAAAATGGAAGCAAATATGAGTCGGCTACTTCTAAGCTACCAATACGAA
1 TTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTCGGCTACTTCTAACCTACCAATACGAA
* * * * *
5193596 ATGGACCTCAATGAGGCAGCTACATA
66 AT-AATCTCAATGAGTCAGCTAAATG
* * * * * ***
5193622 TTCAATTCTGTGAGCTGAAAATTGAAACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAA
1 TTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTCGGCTACTTCTAACCTACCAATACGAA
* * ** * *
5193687 ACTGACCTTGATGTGGCAGCTAAATG
66 A-TAATCTCAATGAGTCAGCTAAATG
5193713 TTCATTTCTTTGAGCTGAAAAT
1 TTCATTTCTTTGAGCTGAAAAT
5193735 CGAGAGTGAA
Statistics
Matches: 256, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
90 5 0.02
91 244 0.95
92 7 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (90 bp):
TTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTCGGCTACTTCTAACCTACCAATACGAA
ATAATCTCAATGAGTCAGCTAAATG
Found at i:5193471 original size:139 final size:139
Alignment explanation
Indices: 5193210--5193486 Score: 439
Period size: 139 Copynumber: 2.0 Consensus size: 139
5193200 CAGCTAAATG
*
5193210 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTCTAACCTACTGATACGAA
1 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTCTAACCTACCGATACGAA
* * * *
5193275 ATGGACCTGAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTT
66 ATAGACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAAAAATGAAACAAATATGAGTC
5193340 GGCTACTTT
131 GGCTACTTT
*
5193349 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTCTAACCTACCGCTACGAA
1 TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTCTAACCTACCGATACGAA
* * * * *
5193414 ATATATCTCAATGAGTCAGCTAAATGTTCATTTCTTTGAGCT-AAAAGATGAAGCAAATATGAGT
66 ATAGACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAAAA-ATGAAACAAATATGAGT
5193478 CGGCTACTT
130 CGGCTACTT
5193487 CTAAGCTACC
Statistics
Matches: 126, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 4 0.03
139 122 0.97
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (139 bp):
TTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTACTTCTAACCTACCGATACGAA
ATAGACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAAAAATGAAACAAATATGAGTC
GGCTACTTT
Found at i:5193922 original size:122 final size:122
Alignment explanation
Indices: 5193647--5194979 Score: 1757
Period size: 122 Copynumber: 10.9 Consensus size: 122
5193637 TGAAAATTGA
* * * * * * ** *
5193647 AACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACT-GACCTTGATGTGGCAGCTAAA
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATAC-AAAATGGACCTCAATGAGGCAGCTAAA
* *
5193711 TGTTCATTTCTTTGAGCTGAAAATCGAGAGTGAATAGGTTTTTATGTTTCTGTAGCTCTG
65 TGTTCATTTCTGTGAGCTGAAAATC-AAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * * *
5193771 AACAAATATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* *
5193836 GTTCGTTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * *
5193893 AACAAATATGAATTGGCTAGTTCTAACCTACCAATACAAAATGGACCTCAAAGAGACAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* *
5193958 GTTCGTTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* *
5194015 AACAAATATGAATTGCCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGTCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
** * * * *
5194080 GTTCATTTCCATGAGCTGAAAATCAAAGTGAATAGATTTTATGTTTCCGTAACCCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * *
5194137 AACAAATATGAATTGGCTACTTCTGACCTATCGATACGAAATGTACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
*
5194202 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGGAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
*
5194260 AACAAATATGAATTGCCTACTTCTAA-C--CCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* ** * * * * *
5194322 GTTCACTTCCATGAGCTGAAAA-CCAA---AATAGATTTTATGTTTCAGTAACCCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * * * *
5194375 AACAAATATGTATTGGCTACTTCTGACCTACCGATACGAAATGTACCTCAATGAAGCGGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
5194440 GTTCATTTCTGTGAGCTGAAAATCAAATGTGAATAGGTTTTTATGTTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAA-GTGAATAGG-TTTTATG-TTTCTGTAGCTCTG
* * ** * * *
5194500 AACTAATAATGAATTGGCTACTTCTAACCAACCGATATGAAATAGACCTAAATGAGGCAGCAAAA
1 AACAAAT-ATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAA
* * *
5194565 TGTTCATTTCTGTGAGATGAAAATCGAAGTGAATAGGTTTTATGTTTCTGTAGCTCTC
65 TGTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
** * * * *
5194623 AACAAATATGAATTTCCTACTTCTAACCTACCAATACAAAACGGCCCTCAATGAGCCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * *
5194688 GTTCATTTCTATGAGCTAAAAATCAAAGTGAATAGGTTTTTAGGTTTCTGCAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * * *
5194746 GACAAATATGAATTGGCTACTTCTAAGCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
*
5194811 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGGTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * *
5194868 AACTAATATGAATTGGCTACCTCTAACCTACCCATACAAAATGGAACTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * * *
5194933 GTTAATTTCTATGAGCTG-AAATCGAAGTAAATAGGTCTTATGTTTCT
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCT
5194980 ATAATCCAAA
Statistics
Matches: 1058, Mismatches: 137, Indels: 31
0.86 0.11 0.03
Matches are distributed among these distances:
115 40 0.04
116 6 0.01
118 50 0.05
119 6 0.01
120 51 0.05
121 25 0.02
122 512 0.48
123 186 0.18
124 83 0.08
125 26 0.02
126 73 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (122 bp):
AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
Found at i:5194568 original size:486 final size:484
Alignment explanation
Indices: 5193647--5194977 Score: 1747
Period size: 486 Copynumber: 2.7 Consensus size: 484
5193637 TGAAAATTGA
* * * ** *
5193647 AACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACTGACCTTGATGTGGCAGCTAAAT
1 AACAAATATGAATTGACTACTTCTAACCTAC-GATACGAAA-TGACCTCAATGAGGCAGCTAAAT
* * *
5193712 GTTCATTTCTTTGAGCTGAAAATCGAGAGTGAATAGGTTTTTATGTTTCTGTAGCTCTGAACAAA
64 GTTCATTTCTATGAGCTGAAAATC-AAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAA
* * * *
5193777 TATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAGAGGCAGCTAAATGTTCGT
128 TATGAATTGGCTACTTCTAACC-ACCGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCAT
5193842 TTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATT
192 TTCTGTGAGCTGAAAACC-AA--GAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATT
* * *
5193907 GGCTAGTTCTAACCTACCAATACAAAATGGACCTCAAAG-AGACAGCTAAATGTTCGTTTCTGTG
254 GGCTACTTCTAACCTACCAATACAAAATGGACCTCAATGAAG-CAGCTAAATGTTCATTTCTGTG
*
5193971 AGCTGAAAACCAAAGTGAATAGGTTTTATG-TTTCTGTAGCTCTGAACAAATATGAATTGCCTAC
318 AGCTGAAAATCAAAGTGAATAGGTTTTATGTTTTCTGTAGCTCTGAACAAATATGAATTGCCTAC
* * * * * *
5194035 TTCTAACCTACCGATACAAAATGGACCTCAATGAGTCAGCTAAATGTTCATTTCCATGAGCTGAA
383 TTCTAACCAACCGATACAAAATAGACCTAAATGAGGCAGCAAAATGTTCATTTCCATGAGATGAA
*
5194100 AATCAAAGTGAATAGATTTTATGTTTCCGTAACCCTG
448 AATCAAAGTGAATAGATTTTATGTTTCCGTAACCCTC
* *
5194137 AACAAATATGAATTGGCTACTTCTGACCTATCGATACGAAATGTACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGACTACTTCTAACCTA-CGATACGAAATG-ACCTCAATGAGGCAGCTAAAT
* *
5194202 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGGAGCTCTGAACAAAT
64 GTTCATTTCTATGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAAT
* * *
5194267 ATGAATTGCCTACTTCTAA-C-CCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCACTT
129 ATGAATTGGCTACTTCTAACCACCGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTT
** * * * * *
5194330 CCATGAGCTGAAAACCAA-AATAGATTTTATGTTTCAGTAACCCTGAACAAATATGTATTGGCTA
194 CTGTGAGCTGAAAACCAAGAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGGCTA
* * * * *
5194394 CTTCTGACCTACCGATACGAAATGTACCTCAATGAAGCGGCTAAATGTTCATTTCTGTGAGCTGA
259 CTTCTAACCTACCAATACAAAATGGACCTCAATGAAGCAGCTAAATGTTCATTTCTGTGAGCTGA
* *
5194459 AAATCAAATGTGAATAGGTTTTTATGTTTTCTGTAGCTCTGAACTAATAATGAATTGGCTACTTC
324 AAATCAAA-GTGAATAGG-TTTTATGTTTTCTGTAGCTCTGAACAAAT-ATGAATTGCCTACTTC
** **
5194524 TAACCAACCGATATGAAATAGACCTAAATGAGGCAGCAAAATGTTCATTTCTGTGAGATGAAAAT
386 TAACCAACCGATACAAAATAGACCTAAATGAGGCAGCAAAATGTTCATTTCCATGAGATGAAAAT
* * * * *
5194589 CGAAGTGAATAGGTTTTATGTTTCTGTAGCTCTC
451 CAAAGTGAATAGATTTTATGTTTCCGTAACCCTC
** * * * * *
5194623 AACAAATATGAATTTCCTACTTCTAACCTACCAATACAAAACGGCCCTCAATGAGCCAGCTAAAT
1 AACAAATATGAATTGACTACTTCTAACCTA-CGATACGAAA-TGACCTCAATGAGGCAGCTAAAT
* * *
5194688 GTTCATTTCTATGAGCTAAAAATCAAAGTGAATAGGTTTTTAGGTTTCTGCAGCTCTGGACAAAT
64 GTTCATTTCTATGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAAT
* *
5194753 ATGAATTGGCTACTTCTAAGCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATT
129 ATGAATTGGCTACTTCTAA-CCACCGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATT
* * *
5194818 TCTGTGAGCTGAAAATCAAAGTGAATAGGGTTTATGTTTCTGTAGCTCTGAACTAATATGAATTG
193 TCTGTGAGCTGAAAA-CCAA--GAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTG
* * * * * *
5194883 GCTACCTCTAACCTACCCATACAAAATGGAACTCAATGAGGCAGCTAAATGTTAATTTCTATGAG
255 GCTACTTCTAACCTACCAATACAAAATGGACCTCAATGAAGCAGCTAAATGTTCATTTCTGTGAG
* * *
5194948 CTG-AAATCGAAGTAAATAGGTCTTATGTTT
320 CTGAAAATCAAAGTGAATAGGTTTTATGTTT
5194978 CTATAATCCA
Statistics
Matches: 732, Mismatches: 94, Indels: 30
0.86 0.11 0.04
Matches are distributed among these distances:
482 102 0.14
483 11 0.02
484 7 0.01
485 22 0.03
486 282 0.39
487 1 0.00
488 1 0.00
489 110 0.15
490 87 0.12
491 9 0.01
492 7 0.01
493 93 0.13
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (484 bp):
AACAAATATGAATTGACTACTTCTAACCTACGATACGAAATGACCTCAATGAGGCAGCTAAATGT
TCATTTCTATGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAATAT
GAATTGGCTACTTCTAACCACCGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCT
GTGAGCTGAAAACCAAGAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGGCTACT
TCTAACCTACCAATACAAAATGGACCTCAATGAAGCAGCTAAATGTTCATTTCTGTGAGCTGAAA
ATCAAAGTGAATAGGTTTTATGTTTTCTGTAGCTCTGAACAAATATGAATTGCCTACTTCTAACC
AACCGATACAAAATAGACCTAAATGAGGCAGCAAAATGTTCATTTCCATGAGATGAAAATCAAAG
TGAATAGATTTTATGTTTCCGTAACCCTC
Found at i:5197250 original size:21 final size:21
Alignment explanation
Indices: 5197211--5197251 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5197201 ATTTTCGCCA
5197211 TTTTAAATATAAAATATTTAT
1 TTTTAAATATAAAATATTTAT
*
5197232 TTTTATATCATAAAA-ATTTA
1 TTTTAAAT-ATAAAATATTTA
5197252 AAATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAATATAAAATATTTAT
Found at i:5199522 original size:126 final size:124
Alignment explanation
Indices: 5199274--5199525 Score: 414
Period size: 126 Copynumber: 2.0 Consensus size: 124
5199264 CTTCTAATTC
* * *
5199274 CCAATCAACAAAGCACAGTTCATTGCAATTGAATCTGAGAAATGGATAAAATTTCATTCATTTGT
1 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGGATAAAATTTCATTCATTTGT
* * *
5199339 TGAAGTAAACACTTAAATTGGATCATTCAATAAGCATTCATTACTTAAGATTCAATTAT
66 TGAAATAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAAATTCAATTAT
*
5199398 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGTATAAAATTTTCATTCATTTG
1 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGGATAAAA-TTTCATTCATTTG
*
5199463 TTGAAATAAAACACTTAAATCGGATCATTCACTAAGCATTCATTACTTAAAATTCAATTAT
65 TTGAAAT-AAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAAATTCAATTAT
5199524 CC
1 CC
5199526 CAACAATAAT
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
124 47 0.40
125 19 0.16
126 52 0.44
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (124 bp):
CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGGATAAAATTTCATTCATTTGT
TGAAATAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAAATTCAATTAT
Found at i:5200766 original size:19 final size:20
Alignment explanation
Indices: 5200727--5200776 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
5200717 TTATCCATAA
5200727 TTTAATAATTAATTATATAG
1 TTTAATAATTAATTATATAG
5200747 TTTAATAACTT-ATT-TATAG
1 TTTAATAA-TTAATTATATAG
*
5200766 TTTAGTAATTA
1 TTTAATAATTA
5200777 GGAAGTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 12 0.44
20 11 0.41
21 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTAATAATTAATTATATAG
Found at i:5210077 original size:18 final size:19
Alignment explanation
Indices: 5210054--5210094 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5210044 TGAAAATAGA
* *
5210054 TAAATGTATTTA-TTAATT
1 TAAATGTATATAGTTAAAT
5210072 TAAATGTATATAGTTAAAT
1 TAAATGTATATAGTTAAAT
5210091 TAAA
1 TAAA
5210095 ATTAATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (19 bp):
TAAATGTATATAGTTAAAT
Found at i:5210747 original size:155 final size:151
Alignment explanation
Indices: 5210469--5211047 Score: 749
Period size: 155 Copynumber: 3.8 Consensus size: 151
5210459 TTTTTTATTG
* ** * * *
5210469 AAAGTAATAAAATCCGATAAAAAAATACTAACAAAGGGCTGAAATAAGGTTTTTTTTAATTTATT
1 AAAGTAATAAAATCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAATTTATT
* *
5210534 TAAAACACACACTAAATGAATACATTTCAAACATGATGTACTAAAATAATGTAAAATAATAAAAT
66 TAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
*
5210599 TAGAAAATATTATATTTTTAA
131 TAGAAAATAATATATTTTTAA
5210620 AAAGTAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAATGGTTTTTTTAAAAATT
1 AAAGTAATAAAA-TCGGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTTTT--AAATT
* * *
5210685 TATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATA
62 TATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
5210750 AAA-TACAAAAATAATATATTTTTATTG
127 AAATTA-GAAAATAATATATTTTTA--A
* * * ** *
5210777 AAAGTAATAAAATC--CGAAAAAAATACAAATAAAAAGCCAAAATAAGGATTTTTTTTAAAATTT
1 AAAGTAATAAAATCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGG--TTTTTTT-AAATTT
*
5210840 ATTT-AAAAACACACTAAATGAATACATTTCAAACATGATGTACTAAAATAATGTAAAATAATAA
63 ATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
* * *
5210904 AATTAGAAAATAGTGTATTTTT-T
128 AATTAGAAAATAATATATTTTTAA
* * *
5210927 AAAGTAATAAAATACGGGG-AAAAAATACGAACAAATGGCCTAAATAAGGGTTTTTT-AATTTAT
1 AAAGTAATAAAAT-CGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAATTTAT
* *
5210990 TTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
65 TTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
5211048 TAGAAAATAG
Statistics
Matches: 376, Mismatches: 38, Indels: 30
0.85 0.09 0.07
Matches are distributed among these distances:
148 9 0.02
149 52 0.14
150 19 0.05
151 13 0.03
152 55 0.15
153 84 0.22
154 40 0.11
155 90 0.24
156 2 0.01
157 12 0.03
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.30
Consensus pattern (151 bp):
AAAGTAATAAAATCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAATTTATT
TAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
TAGAAAATAATATATTTTTAA
Found at i:5210749 original size:13 final size:13
Alignment explanation
Indices: 5210716--5210767 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
5210706 TAATACATTT
* *
5210716 CAAACATAATGTA
1 CAAAAATAATATA
*
5210729 CTAAAATAATATA
1 CAAAAATAATATA
*
5210742 -AAATAATAAAATA
1 CAAA-AATAATATA
5210755 CAAAAATAATATA
1 CAAAAATAATATA
5210768 TTTTTATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 2 0.06
13 26 0.84
14 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (13 bp):
CAAAAATAATATA
Found at i:5210897 original size:153 final size:152
Alignment explanation
Indices: 5210460--5211047 Score: 755
Period size: 153 Copynumber: 3.9 Consensus size: 152
5210450 TTTAGTGTGT
* *
5210460 TTTTTATTGAAAGTAATAAAATC-CGATAAAAAAATACTAACAAAGGGCTGAAATAAGGTTTTTT
1 TTTTTATTGAAAGTAATAAAATCGCG--AAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTT
* *
5210524 TTAATTTATTTAAAACACACACTAAATGAATACATTTCAAACATGATGTACTAAAATAATGTAAA
64 TTAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
*
5210589 ATAATAAAATTAGAAAATATTATA
129 ATAATAAAATTAGAAAATAATATA
* *
5210613 TTTTTA--AAAAGTAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAATGGTTTTT
1 TTTTTATTGAAAGTAATAAAA-TC-GCGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTT
* * * *
5210676 TTAAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATAT
63 TT--TAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGT
*
5210741 AAAATAATAAAA-TACAAAAATAATATA
126 AAAATAATAAAATTA-GAAAATAATATA
* * ** *
5210768 TTTTTATTGAAAGTAATAAAATC-CGAAAAAAATACAAATAAAAAGCCAAAATAAGGATTTTTTT
1 TTTTTATTGAAAGTAATAAAATCGCGAAAAAAATACGAACAAAGGGCCGAAATAAGG-TTTTTTT
*
5210832 TAAAATTTATTT-AAAAACACACTAAATGAATACATTTCAAACATGATGTACTAAAATAATGTAA
65 T--AATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
* *
5210896 AATAATAAAATTAGAAAATAGTGTA
128 AATAATAAAATTAGAAAATAATATA
* * * * *
5210921 -TTTT-TT-AAAGTAATAAAATACGGGGAAAAAATACGAACAAATGGCCTAAATAAGG-GTTTTT
1 TTTTTATTGAAAGTAATAAAAT-CGCGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTT
* *
5210982 TAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
65 TAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
5211047 T
130 T
5211048 TAGAAAATAG
Statistics
Matches: 381, Mismatches: 38, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
148 9 0.02
149 52 0.14
150 19 0.05
151 15 0.04
152 59 0.15
153 84 0.22
154 46 0.12
155 83 0.22
156 2 0.01
157 12 0.03
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (152 bp):
TTTTTATTGAAAGTAATAAAATCGCGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTT
AATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
AATAAAATTAGAAAATAATATA
Found at i:5211154 original size:17 final size:17
Alignment explanation
Indices: 5211102--5211154 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
5211092 TATGGAAACA
* *
5211102 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
5211119 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
5211138 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
5211155 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:5211154 original size:22 final size:23
Alignment explanation
Indices: 5211126--5211170 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5211116 ATGCAATCTT
5211126 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
5211148 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
5211171 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:5211180 original size:22 final size:23
Alignment explanation
Indices: 5211136--5211180 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5211126 AGATATGATA
*
5211136 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
5211159 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
5211181 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:5211603 original size:3 final size:3
Alignment explanation
Indices: 5211595--5211634 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
5211585 ATTAATTTTG
*
5211595 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
5211635 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5211603 original size:15 final size:15
Alignment explanation
Indices: 5211579--5211633 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5211569 GTTTTTAGTC
5211579 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
5211593 TGTTATTATTATTTT
1 TATTATTATTAATTT
5211608 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
5211622 ATATTATTATTA
1 -TATTATTATTA
5211634 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:5211610 original size:12 final size:12
Alignment explanation
Indices: 5211581--5211632 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
5211571 TTTTAGTCTA
5211581 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
5211593 TGTTATTATTAT
1 TTTTATTATTAT
5211605 TTTTATTATTAT
1 TTTTATTATTAT
5211617 ATTATATATTATTAT
1 -TT-T-TATTATTAT
5211632 T
1 T
5211633 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:5212000 original size:51 final size:52
Alignment explanation
Indices: 5211903--5212002 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
5211893 GTTTTTATAT
**
5211903 TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATATTTTATATGTA
1 TATACTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTATATGTA
* * *
5211955 TATATTTATAT-TTTCATTGTTTTCATAAATGCAT-TATGTATTTTATAT
1 TATACTTATATATTTCATT-TTTTCATAAATGCATGAATATATTTTATAT
5212003 ATAAGTTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 19 0.45
52 23 0.55
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (52 bp):
TATACTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTATATGTA
Found at i:5213261 original size:154 final size:152
Alignment explanation
Indices: 5212994--5213359 Score: 542
Period size: 153 Copynumber: 2.4 Consensus size: 152
5212984 TGGTTTTGAC
* *
5212994 AATATATTTTTTTAAAGTAATAAAATCCAGGAAAAAAAATAGGAACAAAGGGCCGAAATAAGGGT
1 AATATATTTTTTTAAAGTAATAAAATCC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
** * * *
5213059 TTTTTTTAATTTATTTAAAAAACATAGTAAATTAATACATTTCAAACATAATGTACTAAAATAAT
65 TTTTTTTAATTTAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAAT
5213124 GA-AAAATAATAAAA-TACAAAAAT
130 -ATAAAATAATAAAACTA-AAAAAT
5213147 AATATATTTTTATTGAAAGTAATAAAATCC-GGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
1 AATATATTTTT-TT-AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
5213211 TTTTTTTTAAATTTAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATA
64 TTTTTTTT-AATTTAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATA
*
5213276 ATATAAAATAATAAAACTAGAAAAT
128 ATATAAAATAATAAAACTAAAAAAT
* * *
5213301 AGTATA-TTTTTTAAAGTAATAAAATCCGGGGAAAAAATTACGAACAAAGGGCTGAAATA
1 AATATATTTTTTTAAAGTAATAAAATCC-GGGAAAAAAATACGAACAAAGGGCCGAAATA
5213360 CGAACATGTT
Statistics
Matches: 195, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
151 15 0.08
152 2 0.01
153 84 0.43
154 77 0.39
155 17 0.09
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (152 bp):
AATATATTTTTTTAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTT
TTTTTTAATTTAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATA
TAAAATAATAAAACTAAAAAAT
Found at i:5213551 original size:60 final size:61
Alignment explanation
Indices: 5213432--5213551 Score: 136
Period size: 61 Copynumber: 2.0 Consensus size: 61
5213422 TTCAGCCGTT
* ** * * * *
5213432 TTTTTTTTGTATTATTTTGGTAAATAATCTTTTTTGTATATTATTTTGGTATTTTTTATTA
1 TTTTTTTTGTAATATTTTGGTAAATAATCTCATTAGTAGATTATTTTGGTAGTTCTTATTA
* *
5213493 TTTTTTTTGTAATATTTTGGTAAA-AATCTCATTAGTGGATTATGTTT-TTAGTTCTTATT
1 TTTTTTTTGTAATATTTTGGTAAATAATCTCATTAGTAGATTAT-TTTGGTAGTTCTTATT
5213552 TATCATCTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
60 23 0.47
61 26 0.53
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (61 bp):
TTTTTTTTGTAATATTTTGGTAAATAATCTCATTAGTAGATTATTTTGGTAGTTCTTATTA
Found at i:5221649 original size:19 final size:20
Alignment explanation
Indices: 5221625--5221663 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5221615 TGGGTAATAA
5221625 AAATT-ATAAAAAAATATAT
1 AAATTAATAAAAAAATATAT
*
5221644 AAATTACATATAAAAATATA
1 AAATTA-ATAAAAAAATATA
5221664 ATTGCTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAATAAAAAAATATAT
Found at i:5225022 original size:2 final size:2
Alignment explanation
Indices: 5225015--5225063 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5225005 TGTTCAAAAG
5225015 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
5225057 AT AT AT A
1 AT AT AT A
5225064 AGTCTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5228682 original size:26 final size:27
Alignment explanation
Indices: 5228629--5228683 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
5228619 ATACTTAACA
**
5228629 TATTCAAATATCTAAAAATAATTTATT
1 TATTCAAATATCTAAAAATAATACATT
* *
5228656 TATTTAAATAT-TTAAAATAATACATT
1 TATTCAAATATCTAAAAATAATACATT
5228682 TA
1 TA
5228684 ATATGTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTCAAATATCTAAAAATAATACATT
Found at i:5242199 original size:21 final size:21
Alignment explanation
Indices: 5242175--5242216 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5242165 AAATTAGAAT
* *
5242175 AAAATTAACATTTATTGTTTA
1 AAAAATAACATCTATTGTTTA
*
5242196 AAAAATAGCATCTATTGTTTA
1 AAAAATAACATCTATTGTTTA
5242217 GCAAAATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
AAAAATAACATCTATTGTTTA
Found at i:5247881 original size:20 final size:19
Alignment explanation
Indices: 5247856--5247896 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5247846 CTTATAACAT
* *
5247856 TATTTTGAATATATAAACTA
1 TATTTTAAATAT-TAAAATA
5247876 TATTTTAAATATTAAAATA
1 TATTTTAAATATTAAAATA
5247895 TA
1 TA
5247897 ATAATTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TATTTTAAATATTAAAATA
Found at i:5261738 original size:20 final size:21
Alignment explanation
Indices: 5261713--5261764 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
5261703 AACAGACTTA
5261713 ATTTAATATATATTT-TAATT
1 ATTTAATATATATTTATAATT
*
5261733 ATTTAAAATATATTTATAATT
1 ATTTAATATATATTTATAATT
*
5261754 -TATAATATATA
1 ATTTAATATATA
5261765 AAATAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATATATATTTATAATT
Found at i:5261754 original size:18 final size:19
Alignment explanation
Indices: 5261711--5261763 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
5261701 AAAACAGACT
*
5261711 TAATTTAATATATATTTTAA
1 TAATTTAAAATATA-TTTAA
*
5261731 TTATTTAAAATATATTT-A
1 TAATTTAAAATATATTTAA
*
5261749 TAATTTATAATATAT
1 TAATTTAAAATATAT
5261764 AAAATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 3 0.10
20 12 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATTTAAAATATATTTAA
Found at i:5264622 original size:68 final size:68
Alignment explanation
Indices: 5264513--5264681 Score: 266
Period size: 68 Copynumber: 2.5 Consensus size: 68
5264503 CTTAGAATCG
* * *
5264513 GAAGTCCGTCAGGACAATAAACATGAGATTATACTGTGTAAGACCATAGCTAGGCTATGGCAACA
1 GAAGTCTGCCAGGACAATAAACATGAGATTATACTGTGTAAGACCATAGCTAGGCTATGACAACA
5264578 AAT
66 AAT
** *
5264581 GAAGTCTGGTAGGACAATAAACATGAGATTATATTGTGTAAGACCATAGCTAGGCTATGACAACA
1 GAAGTCTGCCAGGACAATAAACATGAGATTATACTGTGTAAGACCATAGCTAGGCTATGACAACA
5264646 AAT
66 AAT
* *
5264649 GAAGTCTGCCAAGACAATAAATATGAGATTATA
1 GAAGTCTGCCAGGACAATAAACATGAGATTATA
5264682 AGATGTAATT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 92 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (68 bp):
GAAGTCTGCCAGGACAATAAACATGAGATTATACTGTGTAAGACCATAGCTAGGCTATGACAACA
AAT
Found at i:5270149 original size:38 final size:40
Alignment explanation
Indices: 5270101--5270221 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 40
5270091 GGCCCGGCCC
*
5270101 ATATTTGATTAAAAATAAAAA-ATATATATTTAATATA-T
1 ATATTCGATTAAAAATAAAAATATATATATTTAATATAGT
* *
5270139 A-ATTCGGATTAAAAGTCCAAAAAATATATATATTTAATAAAAAGT
1 ATATTC-GATTAAAAAT---AAAAATATATATATTTAAT--ATAGT
* *
5270184 ATATTCGATTAAAAATAAAAATAAAAATATTTAATATA
1 ATATTCGATTAAAAATAAAAATATATATATTTAATATA
5270222 ATTCGGGCCG
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
37 3 0.04
38 10 0.15
40 2 0.03
41 5 0.07
42 30 0.45
44 2 0.03
45 11 0.16
46 4 0.06
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (40 bp):
ATATTCGATTAAAAATAAAAATATATATATTTAATATAGT
Found at i:5271921 original size:19 final size:19
Alignment explanation
Indices: 5271897--5271951 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
5271887 CAACACATAT
5271897 CTGGCACACGAAGTGCATC
1 CTGGCACACGAAGTGCATC
* *
5271916 CTGGCACACGAGGTACATC
1 CTGGCACACGAAGTGCATC
* *
5271935 TTGGCACA-GAAGCGCAT
1 CTGGCACACGAAGTGCAT
5271952 AATCCCGTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (19 bp):
CTGGCACACGAAGTGCATC
Found at i:5272420 original size:11 final size:11
Alignment explanation
Indices: 5272404--5272430 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5272394 TATATACATT
5272404 ATTTAATCTTG
1 ATTTAATCTTG
5272415 ATTTAATCTTG
1 ATTTAATCTTG
5272426 ATTTA
1 ATTTA
5272431 CATTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
ATTTAATCTTG
Found at i:5274792 original size:27 final size:27
Alignment explanation
Indices: 5274728--5274792 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
5274718 GGTCGAGGGT
*
5274728 CTGCCACAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCAGCACCAAAGGTGCCA
* * *
5274755 GTGGCAGAGGCAGCACCAAAGGTGCCA
1 CTGCCACAGGCAGCACCAAAGGTGCCA
5274782 CTGCCACAGGC
1 CTGCCACAGGC
5274793 GACACCTGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.34, G:0.32, T:0.08
Consensus pattern (27 bp):
CTGCCACAGGCAGCACCAAAGGTGCCA
Found at i:5274877 original size:6 final size:6
Alignment explanation
Indices: 5274868--5274958 Score: 57
Period size: 6 Copynumber: 15.3 Consensus size: 6
5274858 TCAGCTGCAC
* * * *
5274868 GAAGGA GAA-GA -AA-GA AAAGGA -AAGGA GAAGAA GAAGAA GAAGAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
* *
5274912 GAAGGAA GAAGGAA GAAGGAA GTAGGA GGAA-GA GGAGGA GAAGGA GA
1 GAAGG-A GAAGG-A GAAGG-A GAAGGA -GAAGGA GAAGGA GAAGGA GA
5274959 GGGCAGTGCC
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.05
5 11 0.15
6 37 0.51
7 21 0.29
ACGTcount: A:0.56, C:0.00, G:0.43, T:0.01
Consensus pattern (6 bp):
GAAGGA
Found at i:5274901 original size:3 final size:3
Alignment explanation
Indices: 5274893--5274929 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
5274883 AAAGGAAAGG
5274893 AGA AGA AGA AGA AGA AGA AGA AGGA AGA AGGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA A-GA AGA A-GA AGA AG
5274930 GAAGTAGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5274921 original size:7 final size:7
Alignment explanation
Indices: 5274889--5274943 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
5274879 AAGAAAAGGA
5274889 AAGG-AG
1 AAGGAAG
5274895 AA-GAAG
1 AAGGAAG
5274901 AA-GAAG
1 AAGGAAG
5274907 AA-GAAG
1 AAGGAAG
5274913 AAGGAAG
1 AAGGAAG
5274920 AAGGAAG
1 AAGGAAG
5274927 AAGGAAG
1 AAGGAAG
* *
5274934 TAGGAGG
1 AAGGAAG
5274941 AAG
1 AAG
5274944 AGGAGGAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
5 1 0.02
6 18 0.41
7 25 0.57
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (7 bp):
AAGGAAG
Found at i:5274926 original size:29 final size:29
Alignment explanation
Indices: 5274868--5274929 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
5274858 TCAGCTGCAC
* *
5274868 GAAGGAGAAGAAAGAAAAGGAAAGGAGAA
1 GAAGAAGAAGAAAGAAAAGGAAAAGAGAA
5274897 GAAGAAGAAG-AAGAAGAAGGAAGAAG-GAA
1 GAAGAAGAAGAAAGAA-AAGGAA-AAGAGAA
5274926 GAAG
1 GAAG
5274930 GAAGTAGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 22 0.76
30 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (29 bp):
GAAGAAGAAGAAAGAAAAGGAAAAGAGAA
Found at i:5275226 original size:36 final size:38
Alignment explanation
Indices: 5275181--5275258 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
5275171 TTTTTAGGGT
*
5275181 TTAGTTATTAATAATTA-T-TGTTACTTAGTATTATTG
1 TTAGTTATTAATAATTATTATGTTACTTAGTATGATTG
* *
5275217 TTAGTTATTAATAATTATTATTTTAGTTAGTATGATTG
1 TTAGTTATTAATAATTATTATGTTACTTAGTATGATTG
5275255 TTAG
1 TTAG
5275259 ATTTTACACT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 17 0.46
37 1 0.03
38 19 0.51
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (38 bp):
TTAGTTATTAATAATTATTATGTTACTTAGTATGATTG
Found at i:5276979 original size:25 final size:25
Alignment explanation
Indices: 5276929--5276987 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
5276919 TAATTAAATT
**
5276929 TATACAAAAAATTACAAACTTTGTAA
1 TATA-AAAAAATTACAAACTGAGTAA
5276955 TATAAAAAAA-TACAAACTAGAGTAA
1 TATAAAAAAATTACAAACT-GAGTAA
*
5276980 TATCAAAA
1 TATAAAAA
5276988 CCGCAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.28
25 17 0.59
26 4 0.14
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.25
Consensus pattern (25 bp):
TATAAAAAAATTACAAACTGAGTAA
Found at i:5279578 original size:160 final size:159
Alignment explanation
Indices: 5279063--5279751 Score: 1100
Period size: 160 Copynumber: 4.3 Consensus size: 159
5279053 TAATTTCAAT
* *
5279063 GTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
5279128 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTG-TTTTTTATATAAATTTAG
*
5279193 --CAAAAACCCTTATTTTGGCCATTTGTTC
130 TAAAAAAACCCTTATTTTGGCCATTTGTTC
* * *
5279221 GTA-TTTTCTTATTTTCGGATTTTATTACTTTAAAAAAATATAGTATTTTTGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
**
5279285 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTGGGGTTTATATAAATTTA
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGT--TTTTTATATAAATTTA
* * *
5279350 GTAAAAAAAAGCGTTATTTTGGCCCTTTGTTC
129 GT-AAAAAAACCCTTATTTTGGCCATTTGTTC
*
5279382 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATAGTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5279447 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGCTTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGT
5279512 AAAAAAAACCCTTATTTTGGTCC-TTTGTTC
131 -AAAAAAACCCTTATTTTGG-CCATTTGTTC
* * *
5279542 ATATTTTTCTTATTTTCGGATTTAATTACTTTCAAAATATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5279607 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTTATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGT
5279672 AAAAAAACCCTTATTTTGGCCATTTGTTC
131 AAAAAAACCCTTATTTTGGCCATTTGTTC
*
5279701 GTATTTTTCTT-TCTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTC
1 GTATTTTTCTTAT-TTTCGGATTTTATTACTTTCAAAAAATATACTATTTTC
5279752 ATTTTTTTTT
Statistics
Matches: 493, Mismatches: 29, Indels: 17
0.91 0.05 0.03
Matches are distributed among these distances:
156 1 0.00
157 101 0.20
158 21 0.04
159 71 0.14
160 165 0.33
161 29 0.06
162 105 0.21
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (159 bp):
GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGT
AAAAAAACCCTTATTTTGGCCATTTGTTC
Found at i:5279678 original size:319 final size:318
Alignment explanation
Indices: 5279063--5279751 Score: 1109
Period size: 319 Copynumber: 2.2 Consensus size: 318
5279053 TAATTTCAAT
*
5279063 GTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5279128 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTCTTTTTATATAAATTTAG
* * *
5279193 CAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTCTTATTTTCGGATTTTATTACTTTAAAAAA
131 AAAAAACCCTTATTTTGGCCATTTGTTCATATTTTCTTATTTTCGGATTTAATTACTTTAAAAAA
* *
5279258 ATATAGTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATT
196 ATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATT
* * *
5279323 TTAGTGTGTGGGGTTTATATAAATTTAGTAAAAAAAAGCGTTATTTTGGCCCTTTGTTC
261 TTAGTGTGT-GGGTTTATATAAATTTAGTAAAAAAAACCCTTATTTTGGCCATTTGTTC
* *
5279382 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATAGTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
5279447 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTG-CTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTCTTTTTATATAAATTTAG
*
5279511 TAAAAAAAACCCTTATTTTGGTCC-TTTGTTCATATTTTTCTTATTTTCGGATTTAATTACTTTC
131 ---AAAAAACCCTTATTTTGG-CCATTTGTTCATA-TTTTCTTATTTTCGGATTTAATTACTTTA
*
5279575 AAAATATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTA
191 AAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTA
** *
5279640 TTATTTTAGTGTGT-TTTTTTTATAAATTTAGT-AAAAAAACCCTTATTTTGGCCATTTGTTC
256 TTATTTTAGTGTGTGGGTTTATATAAATTTAGTAAAAAAAACCCTTATTTTGGCCATTTGTTC
5279701 GTATTTTTCTT-TCTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTC
1 GTATTTTTCTTAT-TTTCGAATTTTATTACTTTCAAAAAATATACTATTTTC
5279752 ATTTTTTTTT
Statistics
Matches: 344, Mismatches: 20, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
318 18 0.05
319 180 0.52
320 15 0.04
321 26 0.08
322 105 0.31
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (318 bp):
GTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTCTTTTTATATAAATTTAG
AAAAAACCCTTATTTTGGCCATTTGTTCATATTTTCTTATTTTCGGATTTAATTACTTTAAAAAA
ATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATT
TTAGTGTGTGGGTTTATATAAATTTAGTAAAAAAAACCCTTATTTTGGCCATTTGTTC
Found at i:5279781 original size:15 final size:15
Alignment explanation
Indices: 5279763--5279810 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
5279753 TTTTTTTTTC
5279763 TTTTCGTATTTTATT
1 TTTTCGTATTTTATT
* **
5279778 TTTTCATA-CATATT
1 TTTTCGTATTTTATT
5279792 TTTTCGGTATTTTATT
1 TTTTC-GTATTTTATT
5279808 TTT
1 TTT
5279811 AATACTATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 9 0.36
15 9 0.36
16 7 0.28
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTCGTATTTTATT
Found at i:5279946 original size:30 final size:30
Alignment explanation
Indices: 5279912--5280022 Score: 139
Period size: 30 Copynumber: 4.0 Consensus size: 30
5279902 AAATAAAATA
*
5279912 AAATAATAAAACATAGAATGTACTTAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
5279942 AAATAATAAAACATA-AA--TA-AT---A-
1 AAATAATAAAACATAGAATGTACATAACAT
* *
5279964 AAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
5279994 AAATAATAAAACATAGAATGTACATAACA
1 AAATAATAAAACATAGAATGTACATAACA
5280023 CAAAAATTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
22 14 0.21
23 2 0.03
25 2 0.03
26 3 0.04
27 2 0.03
29 3 0.04
30 42 0.62
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:5279956 original size:14 final size:14
Alignment explanation
Indices: 5279898--5279966 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
5279888 CACACTTAAC
*
5279898 AAATAAATAAAATA-
1 AAAT-AATAAAACAT
5279912 AAATAATAAAACAT
1 AAATAATAAAACAT
* *
5279926 AGAAT-GTACTTAACAT
1 A-AATAATA--AAACAT
5279942 AAATAATAAAACAT
1 AAATAATAAAACAT
5279956 AAATAATAAAA
1 AAATAATAAAA
5279967 TAATAAGACA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.18
14 23 0.51
15 6 0.13
16 8 0.18
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (14 bp):
AAATAATAAAACAT
Found at i:5279978 original size:52 final size:52
Alignment explanation
Indices: 5279908--5280008 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
5279898 AAATAAATAA
*
5279908 AATAAAATAATAAAACATAGAATGTACTTAACATAAATAATAAAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
* *
5279960 AATAAAATAATAAGACATAGTATGTACATAACATAAATAATAAAACATA
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATA
5280009 GAATGTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (52 bp):
AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
Found at i:5280034 original size:30 final size:30
Alignment explanation
Indices: 5279964--5280034 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
5279954 ATAAATAATA
* * *
5279964 AAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAC
5279994 AAATAATAAAACATAGAATGTACATAACAC
1 AAATAATAAAACATAGAATGTACATAACAC
5280024 AAA-AATTAAAA
1 AAATAA-TAAAA
5280035 TTAAATTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.23
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAC
Found at i:5280075 original size:82 final size:81
Alignment explanation
Indices: 5279900--5280076 Score: 175
Period size: 82 Copynumber: 2.2 Consensus size: 81
5279890 CACTTAACAA
* * *
5279900 ATAAATAAAATA-AAATAATAAAACATAGAATGTACTTAACATAAATAATAAAACATAAATAATA
1 ATAAATAAAACATAAATAATAAAACATAGAATGTACATAACACAAATAATAAAACATAAATAATA
*
5279964 AAATAATAAGACATAG
66 AAATAATAAAACATAG
** * *
5279980 -TATGTACATAACATAAATAATAAAACATAGAATGTACATAACACAAA-AATTAAAA-TTAAATT
1 ATAAATA-A-AACATAAATAATAAAACATAGAATGTACATAACACAAATAA-TAAAACATAAATA
* *
5280042 AT-GAATGAATGAAAATATAG
63 ATAAAAT-AAT-AAAACATAG
5280062 ATAAATATAAACATA
1 ATAAATA-AAACATA
5280077 CCTTAATATC
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
79 4 0.05
80 4 0.05
81 15 0.19
82 49 0.64
83 5 0.06
ACGTcount: A:0.62, C:0.07, G:0.06, T:0.25
Consensus pattern (81 bp):
ATAAATAAAACATAAATAATAAAACATAGAATGTACATAACACAAATAATAAAACATAAATAATA
AAATAATAAAACATAG
Found at i:5280276 original size:3 final size:3
Alignment explanation
Indices: 5280268--5280380 Score: 76
Period size: 3 Copynumber: 39.0 Consensus size: 3
5280258 CTTCCCTCCC
* * * *
5280268 TCT TCT TCT TCT TCT TCT CCT TC- TCT TTT TCT TTT TCCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT
* * * * * *
5280313 TCCT TCT GCG CCT CCT TCC CCT TCT TCT TCT TC- TCT TC- TCT TC-
1 T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5280356 TCT TC- TCT TCT TCT T-T TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
5280381 CTCATTCTTT
Statistics
Matches: 85, Mismatches: 17, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
2 12 0.14
3 68 0.80
4 5 0.06
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:5280351 original size:5 final size:5
Alignment explanation
Indices: 5280335--5280377 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
5280325 TCCTTCCCCT
*
5280335 TCTTC TTCTTC TCTTC TCTTC TCTTC TCTTC TTCTTT TCTTC T
1 TCTTC -TCTTC TCTTC TCTTC TCTTC TCTTC -TCTTC TCTTC T
5280378 TCTCTCATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (5 bp):
TCTTC
Found at i:5281160 original size:2 final size:2
Alignment explanation
Indices: 5281153--5281180 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5281143 ATTCAAATTT
5281153 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
5281181 ATGCCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5281421 original size:21 final size:22
Alignment explanation
Indices: 5281397--5281437 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5281387 ATGACGCGCT
*
5281397 AAAAATAATTTA-AAAATATTC
1 AAAAATAAATTATAAAATATTC
5281418 AAAAATAAATTATAAAATAT
1 AAAAATAAATTATAAAATAT
5281438 AAAAAGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAATAAATTATAAAATATTC
Found at i:5281442 original size:21 final size:21
Alignment explanation
Indices: 5281397--5281442 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5281387 ATGACGCGCT
* *
5281397 AAAAATAATTTAAAAATATTC
1 AAAAATAAATTAAAAATATTA
5281418 AAAAATAAATTATAAAATA-TA
1 AAAAATAAATTA-AAAATATTA
5281439 AAAA
1 AAAA
5281443 GTTCATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATAAATTAAAAATATTA
Found at i:5289926 original size:25 final size:29
Alignment explanation
Indices: 5289892--5289956 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
5289882 ATAAAAAATA
5289892 ACCAAAATATTAT-A-A-TTTT-TTATTT
1 ACCAAAATATTATAATATTTTTATTATTT
5289917 ACCAAAATATTATAATTATTTTTATTATTT
1 ACCAAAATATTATAA-TATTTTTATTATTT
5289947 ACCAAAATAT
1 ACCAAAATAT
5289957 ATCAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.37
26 1 0.03
28 1 0.03
29 4 0.11
30 16 0.46
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (29 bp):
ACCAAAATATTATAATATTTTTATTATTT
Found at i:5290054 original size:27 final size:27
Alignment explanation
Indices: 5290024--5290115 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
5290014 GGCCAATGGT
5290024 ATTGGCGGCACCAAAGGTGCCAAAGCC
1 ATTGGCGGCACCAAAGGTGCCAAAGCC
* *
5290051 ATTGGCGGCACCAAATGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAGCC
* *
5290078 ATTGGCGGCACCAATGGTGCCAAAGGC
1 ATTGGCGGCACCAAAGGTGCCAAAGCC
*
5290105 ATTGGTGGCAC
1 ATTGGCGGCAC
5290116 TACTCGTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGCC
Found at i:5290212 original size:11 final size:11
Alignment explanation
Indices: 5290196--5290233 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5290186 GGTGTTGTGG
5290196 AAAAGAAGAGA
1 AAAAGAAGAGA
5290207 AAAAG-AGAGA
1 AAAAGAAGAGA
*
5290217 AAGAGAAGAGA
1 AAAAGAAGAGA
5290228 AAAAGA
1 AAAAGA
5290234 TGTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:5290225 original size:21 final size:20
Alignment explanation
Indices: 5290195--5290233 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5290185 AGGTGTTGTG
5290195 GAAAAGAAGAGAAAAAGAGA
1 GAAAAGAAGAGAAAAAGAGA
5290215 GAAAGAGAAGAGAAAAAGA
1 GAAA-AGAAGAGAAAAAGA
5290234 TGTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
GAAAAGAAGAGAAAAAGAGA
Found at i:5290367 original size:3 final size:3
Alignment explanation
Indices: 5290359--5290393 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5290349 TTTAGTTAGT
5290359 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5290394 GTTGTTGTTG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5290398 original size:3 final size:3
Alignment explanation
Indices: 5290392--5290426 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5290382 ATTATTATTA
5290392 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5290427 AGTATTAAGA
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5292826 original size:52 final size:52
Alignment explanation
Indices: 5292766--5292933 Score: 147
Period size: 51 Copynumber: 3.3 Consensus size: 52
5292756 AAAAAAATTA
*
5292766 CCTT-TTT-TTTCTTTTTTTTTCCTTCCTTGCTTCCCTCTTCTCCTTTCCTTT
1 CCTTCTTTCTTTCTTTTTTTTTCCTTCCTTCCTTCCCTCTTCTCCTTT-CTTT
* *
5292817 CCTTC-TT-TTTCTTTCTTTTTT-CTT-C-TCCTTTCCTCTTCTTC-TTCTTT
1 CCTTCTTTCTTTCTTT-TTTTTTCCTTCCTTCCTTCCCTCTTCTCCTTTCTTT
* * * * *
5292864 CCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTCCT-TCCTTTCTTT
1 CC--TTCTTTCTTTCTTTTTTTTTCCTTCCT-TCCTTCCCTCTTCTCCTTTCTTT
*
5292918 CTTTCTTTCTTTCTTT
1 CCTTCTTTCTTTCTTT
5292934 CAATTTCAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
47 6 0.06
48 2 0.02
49 16 0.17
50 8 0.09
51 24 0.26
52 20 0.21
53 2 0.02
54 16 0.17
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (52 bp):
CCTTCTTTCTTTCTTTTTTTTTCCTTCCTTCCTTCCCTCTTCTCCTTTCTTT
Found at i:5292827 original size:10 final size:10
Alignment explanation
Indices: 5292814--5292891 Score: 58
Period size: 10 Copynumber: 8.1 Consensus size: 10
5292804 TCTCCTTTCC
5292814 TTTCCTTCTT
1 TTTCCTTCTT
*
5292824 TTTCTTTCTT
1 TTTCCTTCTT
* *
5292834 TTTTCTTCTCC
1 TTTCCTTCT-T
5292845 TTTCC-TCTT
1 TTTCCTTCTT
*
5292854 CTT-CTTC--
1 TTTCCTTCTT
5292861 TTTCCTT-TT
1 TTTCCTTCTT
5292870 CTTTCCTTCTT
1 -TTTCCTTCTT
*
5292881 TTTCTTTCTT
1 TTTCCTTCTT
5292891 T
1 T
5292892 CCTCTCCTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 4 0.08
10 36 0.69
11 6 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTCCTTCTT
Found at i:5292833 original size:4 final size:4
Alignment explanation
Indices: 5292824--5292934 Score: 70
Period size: 4 Copynumber: 27.0 Consensus size: 4
5292814 TTTCCTTCTT
5292824 TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC -TTC -TTC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC TTTC TTTC TTT-C -TTTC
* * * * *
5292871 TTTC CTTC -TT- TTTC TTTC TTTCC TCTCC TTCC TTCC TTCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC
5292919 TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC
5292935 AATTTCAATA
Statistics
Matches: 93, Mismatches: 3, Indels: 22
0.79 0.03 0.19
Matches are distributed among these distances:
3 13 0.14
4 59 0.63
5 12 0.13
6 9 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:5292848 original size:36 final size:39
Alignment explanation
Indices: 5292801--5292873 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 39
5292791 CTTGCTTCCC
5292801 TCTTCTCCTTTCCT-TTCCTTCTT-TTT-C-TTTCTTTTT
1 TCTTCTCCTTTCCTCTT-CTTCTTCTTTCCTTTTCTTTTT
5292837 TCTTCTCCTTTCCTCTTCTTCTTCTTTCCTTTTCTTT
1 TCTTCTCCTTTCCTCTTCTTCTTCTTTCCTTTTCTTT
5292874 CCTTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 20 0.61
37 5 0.15
38 1 0.03
39 7 0.21
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (39 bp):
TCTTCTCCTTTCCTCTTCTTCTTCTTTCCTTTTCTTTTT
Found at i:5292869 original size:44 final size:43
Alignment explanation
Indices: 5292804--5292934 Score: 137
Period size: 44 Copynumber: 3.0 Consensus size: 43
5292794 GCTTCCCTCT
5292804 TCTCCTTTCCTTTCCTT-CTTTTTCTTTCTTTTTTCTTCTCCTTTCC
1 TCTCC-TTCC-TTCCTTCCTTTTTCTTTCTTTTTTCTT-T-CTTTCC
* *
5292850 TCTTCTT-CTTCTTTCC-TTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TCTCCTTCCTTCCTTCCTTTTTCTTT-C-T-TTTTTCTTTCTTTCC
5292894 TCTCCTTCCTTCCTTCC--TTTCTTTCTTTCTTTCTTTCTTTC
1 TCTCCTTCCTTCCTTCCTTTTTCTTTCTTT-TTTCTTTCTTTC
5292935 AATTTCAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
41 2 0.03
42 13 0.17
43 14 0.19
44 22 0.29
45 12 0.16
46 12 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (43 bp):
TCTCCTTCCTTCCTTCCTTTTTCTTTCTTTTTTCTTTCTTTCC
Found at i:5292876 original size:57 final size:55
Alignment explanation
Indices: 5292767--5292891 Score: 166
Period size: 57 Copynumber: 2.3 Consensus size: 55
5292757 AAAAAATTAC
5292767 CTTTTT-TTTCTTTTTTTTTCCTTCCTTGCTTCCCTCTTCTCCTTTCCTTTCCTT
1 CTTTTTCTTTCTTTTTTTTTCCTTCCTTGCTTCCCTCTTCTCCTTTCCTTTCCTT
* * *
5292821 CTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTT-CTTCTT-TCCTTTTCTTTCCTT
1 CTTTTTCTTTCTTTTTT-TT-TCC-TTCCT-TGCTTCCCTCTTCTCCTTTCCTTTCCTT
5292878 CTTTTTCTTTCTTT
1 CTTTTTCTTTCTTT
5292892 CCTCTCCTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
54 6 0.10
55 10 0.16
56 2 0.03
57 31 0.49
58 10 0.16
59 4 0.06
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (55 bp):
CTTTTTCTTTCTTTTTTTTTCCTTCCTTGCTTCCCTCTTCTCCTTTCCTTTCCTT
Found at i:5292916 original size:57 final size:57
Alignment explanation
Indices: 5292784--5292930 Score: 158
Period size: 57 Copynumber: 2.6 Consensus size: 57
5292774 TTCTTTTTTT
* * * * ** *
5292784 TTCCTTCCTTGCTTCCCTCTTCTCCTTTCCTTTCCTTCTTTTTCTTTCTTTTTTCTTC
1 TTCCTTCCTTCCTTTCTTCTT-TCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
*
5292842 -TCCTTTCC-TCTTCTTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
1 TTCC-TTCCTTCCT-TTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
5292899 TTCCTTCCTTCCTTTCTTTCTTT-C-TTTCTTTC
1 TTCCTTCCTTCCTTTC-TTCTTTCCTTTTCTTTC
5292931 TTTCAATTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
56 8 0.11
57 45 0.60
58 22 0.29
ACGTcount: A:0.00, C:0.36, G:0.01, T:0.63
Consensus pattern (57 bp):
TTCCTTCCTTCCTTTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
Found at i:5293213 original size:16 final size:16
Alignment explanation
Indices: 5293192--5293248 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
5293182 TTTGGTTCGC
*
5293192 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
5293208 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
5293224 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
5293240 TGTAATGGA
1 TGTAATGGA
5293249 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:5293615 original size:14 final size:15
Alignment explanation
Indices: 5293483--5293617 Score: 61
Period size: 15 Copynumber: 8.9 Consensus size: 15
5293473 TTTAAACATA
*
5293483 ATTATTATTAAATAT
1 ATTATAATTAAATAT
*
5293498 ATTTTAATTAAA-AT
1 ATTATAATTAAATAT
*
5293512 A-TATAATTTAATAT
1 ATTATAATTAAATAT
*
5293526 GAATTTACTCAAATCATAATAT
1 --A-TTA-T--AATTA-AATAT
* *
5293548 ATGATACTGTAAA-AT
1 ATTATAAT-TAAATAT
5293563 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
5293576 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5293591 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5293605 A-TATAATTTAATA
1 ATTATAATTAAATA
5293618 AAATTCTTAA
Statistics
Matches: 90, Mismatches: 14, Indels: 33
0.66 0.10 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 16 0.18
15 29 0.32
16 5 0.06
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
21 3 0.03
22 5 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5293632 original size:44 final size:43
Alignment explanation
Indices: 5293543--5293633 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
5293533 CTCAAATCAT
* * *
5293543 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
5293586 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
5293630 AATA
1 AATA
5293634 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:5293722 original size:15 final size:16
Alignment explanation
Indices: 5293702--5293737 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
5293692 AATAATTAAT
5293702 ATTAA-ATATGATTTA
1 ATTAATATATGATTTA
5293717 ATTAAATATATGATTTA
1 ATT-AATATATGATTTA
5293734 ATTA
1 ATTA
5293738 TAACTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 3 0.16
17 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTAATATATGATTTA
Found at i:5293727 original size:17 final size:20
Alignment explanation
Indices: 5293706--5293751 Score: 71
Period size: 17 Copynumber: 2.5 Consensus size: 20
5293696 ATTAATATTA
5293706 AATATGATTTAATTA-AA-T
1 AATATGATTTAATTATAACT
5293724 -ATATGATTTAATTATAACT
1 AATATGATTTAATTATAACT
5293743 AATATGATT
1 AATATGATT
5293752 ATAGTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 1 0.04
20 8 0.32
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (20 bp):
AATATGATTTAATTATAACT
Found at i:5293868 original size:93 final size:91
Alignment explanation
Indices: 5293758--5293951 Score: 282
Period size: 93 Copynumber: 2.1 Consensus size: 91
5293748 GATTATAGTT
* * *
5293758 TATGAATTTGTATAATTTAAAATAATAAATATTACATATAATT-TAATAATAATATATAATTTCA
1 TATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTAT-ATAATAATATATAATTTCA
* *
5293822 TAAAATTCTTGATAATAAAAATTTTCTTA
65 TAAAATTCTTAATAAT-AAAATGTTC-TA
* * *
5293851 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTATATAATAATATATAATTTCAT
5293916 AAAATTCTTAATAATAAAATGTTCTA
66 AAAATTCTTAATAATAAAATGTTCTA
5293942 TATGAATTTA
1 TATGAATTTA
5293952 CTAAAATCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
91 12 0.13
92 8 0.09
93 71 0.77
94 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTA
Found at i:5293944 original size:47 final size:47
Alignment explanation
Indices: 5293808--5293944 Score: 122
Period size: 47 Copynumber: 2.9 Consensus size: 47
5293798 ATTTAATAAT
* *
5293808 AATATATAATTTCATAAAATTCTTGATAATAAAAATTTTCT-TATATG
1 AATATATAATTTCATAAAATTCTTAATAAT-AAAATATTCTATATATG
* * ** * *
5293855 AATTTATACAATT--TAAAATAATTAATATTAAATATAAT-TATATAGTG
1 AATATATA-ATTTCATAAAATTCTTAATAATAAA-ATATTCTATATA-TG
*
5293902 -ATATATAATTTCATAAAATTCTTAATAATAAAATGTTCTATAT
1 AATATATAATTTCATAAAATTCTTAATAATAAAATATTCTATAT
5293945 GAATTTACTA
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
45 7 0.10
46 28 0.41
47 30 0.44
48 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (47 bp):
AATATATAATTTCATAAAATTCTTAATAATAAAATATTCTATATATG
Found at i:5301472 original size:77 final size:77
Alignment explanation
Indices: 5301371--5301547 Score: 257
Period size: 77 Copynumber: 2.3 Consensus size: 77
5301361 TTTGGTTTAT
* * * *
5301371 TGAAATATATGATAAGTTGGTTTTATGTAGTGTATGCATATATAAATGTAAGGTTAAGAAAGGAA
1 TGAAATATATGATAAGTTGCTTTTATGCAGTGTATGCATATATAAATGTAAGGTGAAGAAAAGAA
5301436 CATC-GACATTAC
66 CATCAG-CATTAC
* * *
5301448 TGAAATATACGATAAGTTGCTTTTATGCAGTGTATGCATCTCTAAATGTAAGGTGAAGAAAAGAA
1 TGAAATATATGATAAGTTGCTTTTATGCAGTGTATGCATATATAAATGTAAGGTGAAGAAAAGAA
*
5301513 CATCAGCATTAG
66 CATCAGCATTAC
5301525 TGAAAATATATGATAAGTTGCTT
1 TG-AAATATATGATAAGTTGCTT
5301548 CTATATAGAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
77 69 0.78
78 20 0.22
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (77 bp):
TGAAATATATGATAAGTTGCTTTTATGCAGTGTATGCATATATAAATGTAAGGTGAAGAAAAGAA
CATCAGCATTAC
Done.