Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 169 of 318
Found at i:53361999 original size:50 final size:47
Alignment explanation
Indices: 53361884--53362003 Score: 150
Period size: 50 Copynumber: 2.4 Consensus size: 47
53361874 TTTATCATAT
*
53361884 AACTAGAGGCCTAGCCTCTTTTAATAACTGGGGAAAAGCCCTTTTGATA
1 AACTA-AGGCATAGCC-CTTTTAATAACTGGGGAAAAGCCCTTTTGATA
* * *
53361933 AACTAGGGCAAAAGCCCTTTTAATAAACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTAAGGC-ATAGCCCTTTTAAT-AACTGGGG-AAAAGCCCTTTT-GATA
53361984 AACTAAGGCATAGCCCTTTT
1 AACTAAGGCATAGCCCTTTT
53362004 TGCACTTCCT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
48 11 0.18
49 17 0.28
50 22 0.36
51 11 0.18
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (47 bp):
AACTAAGGCATAGCCCTTTTAATAACTGGGGAAAAGCCCTTTTGATA
Found at i:53362074 original size:20 final size:20
Alignment explanation
Indices: 53362051--53362097 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
53362041 TTATGAATGC
53362051 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
53362071 ATCATGTGTATATCATACAT
1 ATCATGTGCATATCATACAT
53362091 ATCATGT
1 ATCATGT
53362098 ATATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:53369803 original size:31 final size:31
Alignment explanation
Indices: 53369765--53369828 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53369755 CCTTTTCATA
53369765 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
53369796 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
53369827 TT
1 TT
53369829 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:53370077 original size:24 final size:25
Alignment explanation
Indices: 53370037--53370144 Score: 109
Period size: 25 Copynumber: 4.4 Consensus size: 25
53370027 CTGGAGGCCT
53370037 AGCCTCTTTTAAT-AACT-GGG-ACAA
1 AGCC-CTTTTAATAAACTAGGGCA-AA
*
53370061 AGCCCTTTTGATAAACTAGGGCAAA
1 AGCCCTTTTAATAAACTAGGGCAAA
53370086 AGCCCTTTTAATAAACTAGGGCAAA
1 AGCCCTTTTAATAAACTAGGGCAAA
* * *
53370111 AG-CCTGTTTCGATAAACTGGGGC-AT
1 AGCCCT-TTT-AATAAACTAGGGCAAA
53370136 AGCCCTTTT
1 AGCCCTTTT
53370145 TGCACTTCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.10
24 11 0.15
25 40 0.55
26 15 0.21
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTAGGGCAAA
Found at i:53370133 original size:26 final size:25
Alignment explanation
Indices: 53370059--53370144 Score: 113
Period size: 25 Copynumber: 3.4 Consensus size: 25
53370049 TAACTGGGAC
53370059 AAAGCCCTTTTGATAAACTAGGGCA
1 AAAGCCCTTTTGATAAACTAGGGCA
*
53370084 AAAGCCCTTTTAATAAACTAGGGCA
1 AAAGCCCTTTTGATAAACTAGGGCA
*
53370109 AAAG-CCTGTTTCGATAAACTGGGGC-
1 AAAGCCCT-TTT-GATAAACTAGGGCA
*
53370134 ATAGCCCTTTT
1 AAAGCCCTTTT
53370145 TGCACTTCCT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
24 3 0.06
25 37 0.69
26 14 0.26
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (25 bp):
AAAGCCCTTTTGATAAACTAGGGCA
Found at i:53370142 original size:50 final size:47
Alignment explanation
Indices: 53370025--53370144 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 47
53370015 TTTATCATAT
*
53370025 AACTGGAGGCCTAGCCTCTTTTAATAACTGGGACAAAGCCCTTTTGATA
1 AACTGG-GGCATAGCC-CTTTTAATAACTGGGACAAAGCCCTTTTGATA
* *
53370074 AACTAGGGCAAAAGCCCTTTTAATAAACTAGGG-CAAAAG-CCTGTTTCGATA
1 AACTGGGGC-ATAGCCCTTTTAAT-AACT-GGGAC-AAAGCCCT-TTT-GATA
53370125 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCATAGCCCTTTT
53370145 TGCACTTCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
48 11 0.18
49 17 0.28
50 20 0.33
51 12 0.20
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (47 bp):
AACTGGGGCATAGCCCTTTTAATAACTGGGACAAAGCCCTTTTGATA
Found at i:53373275 original size:19 final size:19
Alignment explanation
Indices: 53373251--53373291 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
53373241 TGTGGTCCTT
*
53373251 ATTTCAACATCAAAATTTA
1 ATTTCAACATCAAAATTAA
**
53373270 ATTTCAATTTCAAAATTAA
1 ATTTCAACATCAAAATTAA
53373289 ATT
1 ATT
53373292 AGTATTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTCAACATCAAAATTAA
Found at i:53374886 original size:13 final size:13
Alignment explanation
Indices: 53374868--53374894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53374858 GTGATATAGG
53374868 TGATATCTAAATA
1 TGATATCTAAATA
53374881 TGATATCTAAATA
1 TGATATCTAAATA
53374894 T
1 T
53374895 TTAAGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TGATATCTAAATA
Found at i:53381815 original size:31 final size:31
Alignment explanation
Indices: 53381780--53381856 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
53381770 GCTATTAAAA
* *
53381780 TAGTCACTTTTGTTTCTCTGATATTATAGTT
1 TAGTCACTTATGTTTCTCTGATATTACAGTT
* * *
53381811 TAGTCACTAATGTTTCTCTGATGTTACATTT
1 TAGTCACTTATGTTTCTCTGATATTACAGTT
53381842 TAGTCACTTATGTTT
1 TAGTCACTTATGTTT
53381857 GAAATGTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.14, G:0.13, T:0.52
Consensus pattern (31 bp):
TAGTCACTTATGTTTCTCTGATATTACAGTT
Found at i:53383088 original size:23 final size:25
Alignment explanation
Indices: 53383060--53383107 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
53383050 AATTTTTATA
53383060 TTTTAATTTAATA-TAATA-TAATT
1 TTTTAATTTAATATTAATATTAATT
*
53383083 TTTTAATTTTATATTAATATTAATT
1 TTTTAATTTAATATTAATATTAATT
53383108 AATTCAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 5 0.23
25 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTAATTTAATATTAATATTAATT
Found at i:53387720 original size:31 final size:31
Alignment explanation
Indices: 53387682--53387823 Score: 114
Period size: 31 Copynumber: 4.6 Consensus size: 31
53387672 TAAGAAGTCA
* *
53387682 TTATTTGAGCAATTTTGAAAAGTTTTAGCCC
1 TTATTTGAACAATTTTGAAAAGGTTTAGCCC
* * * * *
53387713 TTATTTGATCACTTTCGAAAAGGTTTGGCCT
1 TTATTTGAACAATTTTGAAAAGGTTTAGCCC
**
53387744 TTATTTGAAC-ATTTTGAAAAGGTTTA-ATC
1 TTATTTGAACAATTTTGAAAAGGTTTAGCCC
* *
53387773 TTCATTTGAAC-ATTTTAATAAATG-TTAGACCC
1 TT-ATTTGAACAATTTTGA-AAAGGTTTAG-CCC
*
53387805 TTATTT-AACCATTTTGAAA
1 TTATTTGAACAATTTTGAAA
53387824 TATTTGATCT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
29 2 0.02
30 35 0.40
31 48 0.55
32 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
TTATTTGAACAATTTTGAAAAGGTTTAGCCC
Found at i:53389676 original size:26 final size:27
Alignment explanation
Indices: 53389625--53389678 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
53389615 AAAATGATTG
53389625 AAAAATTTCTCCATAAGTAGCTTTTTA
1 AAAAATTTCTCCATAAGTAGCTTTTTA
53389652 AAAAATTTCTCCATAAGTAGCTTTTTA
1 AAAAATTTCTCCATAAGTAGCTTTTTA
53389679 TCTACTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAAATTTCTCCATAAGTAGCTTTTTA
Found at i:53389913 original size:13 final size:14
Alignment explanation
Indices: 53389890--53389918 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53389880 AATAAATGAA
53389890 ATATTTAAATTTTT
1 ATATTTAAATTTTT
53389904 ATATTT-AATTTTT
1 ATATTTAAATTTTT
53389917 AT
1 AT
53389919 CTAAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTAAATTTTT
Found at i:53390746 original size:16 final size:16
Alignment explanation
Indices: 53390712--53390795 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 16
53390702 AAATGTTTTG
53390712 ATATAATT-TAATATAAA
1 ATATAATTAT-AT-TAAA
53390729 ATATAATTATATTAAA
1 ATATAATTATATTAAA
*
53390745 ATTTTATTAAATTATATT-TA
1 A---TA-T-AATTATATTAAA
53390765 ATAATAATTATATTAAA
1 AT-ATAATTATATTAAA
* *
53390782 ATATGATTAAATTA
1 ATATAATTATATTA
53390796 TTCTTAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
16 24 0.44
17 15 0.27
18 2 0.04
19 2 0.04
20 3 0.05
21 9 0.16
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
ATATAATTATATTAAA
Found at i:53390774 original size:37 final size:37
Alignment explanation
Indices: 53390731--53390822 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
53390721 AATATAAAAT
*
53390731 ATAATTATATTAAAATTTTATTAAATTATAT-TTAATA
1 ATAATTATATTAAAATTTGATTAAATTAT-TCTTAATA
*
53390768 ATAATTATATTAAAATATGATTAAATTATTCTTAATA
1 ATAATTATATTAAAATTTGATTAAATTATTCTTAATA
53390805 ATAATCT-TATTAAAATTT
1 ATAAT-TATATTAAAATTT
53390823 AATAATAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 1 0.02
37 48 0.96
38 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (37 bp):
ATAATTATATTAAAATTTGATTAAATTATTCTTAATA
Found at i:53390791 original size:26 final size:25
Alignment explanation
Indices: 53390725--53390791 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 25
53390715 TAATTTAATA
*
53390725 TAAAATATAATTATATTAAAATTTTAT
1 TAAAATAT-ATTA-ATTAAAATTATAT
*
53390752 TAAATTATATTTAA-TAATAATTATAT
1 TAAAATATA-TTAATTAA-AATTATAT
53390778 TAAAATATGATTAA
1 TAAAATAT-ATTAA
53390792 ATTATTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 3 0.09
26 20 0.59
27 11 0.32
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
TAAAATATATTAATTAAAATTATAT
Found at i:53391022 original size:15 final size:15
Alignment explanation
Indices: 53391002--53391109 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
53390992 TTTATGGAAA
53391002 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* ***
53391017 ATCAAATA-ATGTAA
1 ATCAAAGATATGGGT
53391031 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
53391047 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
53391061 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
53391077 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
53391091 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
53391107 ATC
1 ATC
53391110 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:53391039 original size:30 final size:30
Alignment explanation
Indices: 53390996--53391119 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
53390986 TCCATATTTA
* *
53390996 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
53391026 TGTAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
53391056 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
53391086 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
53391117 TGG
1 TGG
53391120 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:53395713 original size:15 final size:15
Alignment explanation
Indices: 53395693--53395770 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
53395683 TTTATGGAAA
53395693 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
53395708 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
53395722 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
53395738 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
53395752 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
53395768 ATC
1 ATC
53395771 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:53395722 original size:30 final size:30
Alignment explanation
Indices: 53395686--53395770 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
53395676 ATCCATATTT
*
53395686 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
53395716 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
53395746 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
53395771 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:53396503 original size:9 final size:9
Alignment explanation
Indices: 53396491--53396525 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
53396481 GAAAAGGAGC
53396491 AAAAAAAGAA
1 AAAAAAAG-A
53396501 AAAAAAAGA
1 AAAAAAAGA
53396510 AAAAAAAGA
1 AAAAAAAGA
53396519 AAAAAAA
1 AAAAAAA
53396526 AAGAAACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:53396504 original size:10 final size:10
Alignment explanation
Indices: 53396491--53396531 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
53396481 GAAAAGGAGC
53396491 AAAAAAAGAA
1 AAAAAAAGAA
53396501 AAAAAAAG-A
1 AAAAAAAGAA
53396510 AAAAAAAGAAA
1 AAAAAAAG-AA
53396521 AAAAAAAGAA
1 AAAAAAAGAA
53396531 A
1 A
53396532 CAGTAGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.31
10 11 0.38
11 9 0.31
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:53396504 original size:19 final size:19
Alignment explanation
Indices: 53396491--53396531 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
53396481 GAAAAGGAGC
53396491 AAAAAAAGAAAAAAAAAGA
1 AAAAAAAGAAAAAAAAAGA
53396510 AAAAAAAGAAAAAAAAAAGA
1 AAAAAAAG-AAAAAAAAAGA
53396530 AA
1 AA
53396532 CAGTAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAGA
Found at i:53396685 original size:7 final size:7
Alignment explanation
Indices: 53396668--53396698 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53396658 TTTCATTTAA
53396668 AAAAAAG
1 AAAAAAG
53396675 -AAAAAG
1 AAAAAAG
53396681 AAAAAAG
1 AAAAAAG
53396688 AAAAAAG
1 AAAAAAG
53396695 AAAA
1 AAAA
53396699 GGTGTTGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:53396686 original size:14 final size:15
Alignment explanation
Indices: 53396667--53396698 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
53396657 CTTTCATTTA
53396667 AAAAAAAG-AAAAAG
1 AAAAAAAGAAAAAAG
53396681 -AAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
53396695 AAAA
1 AAAA
53396699 GGTGTTGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.44
14 6 0.38
15 3 0.19
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:53399079 original size:27 final size:27
Alignment explanation
Indices: 53399049--53399226 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
53399039 ATATTGAGTC
* *
53399049 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
53399076 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
53399103 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
53399131 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
53399158 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
53399185 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
53399212 CGCACACATAGTGCT
1 CGCACACTTAGTGCT
53399227 GTACAATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:53414328 original size:27 final size:27
Alignment explanation
Indices: 53414298--53414475 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
53414288 ATATTGAGTC
* *
53414298 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
53414325 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
53414352 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
53414380 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
53414407 CGCACACTTAGTGC-ACCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
53414434 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
53414461 TGCACACATAGTGCT
1 CGCACACTTAGTGCT
53414476 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 101 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:53419461 original size:46 final size:46
Alignment explanation
Indices: 53419411--53419586 Score: 218
Period size: 46 Copynumber: 3.8 Consensus size: 46
53419401 TGATTGAGCA
53419411 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53419457 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53419502 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
53419550 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53419587 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 5 0.04
46 62 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53419567 original size:93 final size:93
Alignment explanation
Indices: 53419408--53419578 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
53419398 GGATGATTGA
*
53419408 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
53419473 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53419501 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
53419565 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
53419579 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53421429 original size:39 final size:39
Alignment explanation
Indices: 53421357--53421513 Score: 242
Period size: 39 Copynumber: 4.0 Consensus size: 39
53421347 AATTATATTA
* * *
53421357 CCAGCACAAAGCATGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
* *
53421396 CCTGCACGAAGCCTACGGGACTTTAGCCTGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
53421435 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
* * *
53421474 TCAGCATGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
53421513 C
1 C
53421514 GAGTATCTTG
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 107 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (39 bp):
CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
Found at i:53424031 original size:20 final size:20
Alignment explanation
Indices: 53423989--53424038 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
53423979 ATAAATTGGA
* *
53423989 ATCAAGCTCAATTAGCTAGC
1 ATCAAGCTGAATTAGCTACC
53424009 ATCAAGCTGAATTAAGCT-CC
1 ATCAAGCTGAATT-AGCTACC
*
53424029 ATCGAGCTGA
1 ATCAAGCTGA
53424039 GTCGAGCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCAAGCTGAATTAGCTACC
Found at i:53425252 original size:16 final size:14
Alignment explanation
Indices: 53425219--53425275 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 14
53425209 ATCAATATTT
*
53425219 TAAAAAATAAATAT
1 TAAAAAATAAATAA
53425233 TAAAAAATTAAATTAA
1 TAAAAAA-TAAA-TAA
*
53425249 TAAAAAGATATATACA
1 TAAAAA-ATAAATA-A
*
53425265 TATAAAATAAA
1 TAAAAAATAAA
53425276 CTTTGACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 7 0.20
15 10 0.29
16 17 0.49
17 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (14 bp):
TAAAAAATAAATAA
Found at i:53425437 original size:16 final size:16
Alignment explanation
Indices: 53425416--53425448 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53425406 GAAAAAATTT
53425416 AATAATTTATAAAAAC
1 AATAATTTATAAAAAC
*
53425432 AATAATTTATTAAAAC
1 AATAATTTATAAAAAC
53425448 A
1 A
53425449 TAAAAAATAA
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:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATTTATAAAAAC
Found at i:53427041 original size:29 final size:29
Alignment explanation
Indices: 53426998--53427054 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
53426988 TGTTTTTTGG
*
53426998 TTGGTTTGCTAACTAACCGAAAAACTTAC
1 TTGGTTTGCTAACTAACCAAAAAACTTAC
*
53427027 TTGGTTTGCTGACTAACCAAAAAACTTA
1 TTGGTTTGCTAACTAACCAAAAAACTTA
53427055 GGTAACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (29 bp):
TTGGTTTGCTAACTAACCAAAAAACTTAC
Found at i:53430463 original size:57 final size:56
Alignment explanation
Indices: 53430360--53430466 Score: 135
Period size: 57 Copynumber: 1.9 Consensus size: 56
53430350 CCTGTTTTCA
* *
53430360 ACATATGCTCACAAAAGCTTAATCAGGATTACCCGTCCGGGATAAATCCTATCTGT
1 ACATATGCTCACAAAAGCTTAATCAGGATTACCAGTCCAGGATAAATCCTATCTGT
* * * *
53430416 ACATATGCTCA-AGAGGACTTATATCAGGATTACCAGTCTAGGCTAAATCCT
1 ACATATGCTCACAAAAG-CTTA-ATCAGGATTACCAGTCCAGGATAAATCCT
53430467 TTATGTAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
55 3 0.07
56 15 0.35
57 25 0.58
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (56 bp):
ACATATGCTCACAAAAGCTTAATCAGGATTACCAGTCCAGGATAAATCCTATCTGT
Found at i:53430576 original size:18 final size:18
Alignment explanation
Indices: 53430553--53430598 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
53430543 AGGGAAATCA
53430553 CATTTA-TCTATCGATTTT
1 CATTTATTC-ATCGATTTT
53430571 CATTTATTCATCGATTTT
1 CATTTATTCATCGATTTT
53430589 CATTTATTCA
1 CATTTATTCA
53430599 AACGGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.54
Consensus pattern (18 bp):
CATTTATTCATCGATTTT
Found at i:53431005 original size:21 final size:21
Alignment explanation
Indices: 53430961--53431008 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
53430951 TATACGAGTA
*
53430961 AATTTAAAATCAATTTAATAC
1 AATTTAAAATCAATTCAATAC
* * *
53430982 AATTTAAACTCAATTCAGTCC
1 AATTTAAAATCAATTCAATAC
53431003 AATTTA
1 AATTTA
53431009 CATCTTAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTTAAAATCAATTCAATAC
Found at i:53432702 original size:40 final size:40
Alignment explanation
Indices: 53432658--53432738 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
53432648 CCGCAAGTTT
* *
53432658 TGTACTTTTTGAAAATTTAGCCCTTCATATTTACAAATTC
1 TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
53432698 TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
1 TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
53432738 T
1 T
53432739 ATCAATTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (40 bp):
TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
Found at i:53457858 original size:42 final size:42
Alignment explanation
Indices: 53457795--53457944 Score: 158
Period size: 42 Copynumber: 3.5 Consensus size: 42
53457785 TTACTAGTGT
* **
53457795 GTAAGACCATATCTGGTATATGGCATTTATATGAGACTTCGG
1 GTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCGG
* *
53457837 GTAAGACCATATTTGGGATATGGCATCAATATGAGACTTCGT
1 GTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCGG
* * * * **
53457879 GTAAGACTATAGCTGGGCTATTGGCATCGATATGAGA-TTACAT
1 GTAAGACCATATCTGGGATA-TGGCATCAATATGAGACTT-CGG
**
53457922 GTAAGATTATATCTGGGATATGG
1 GTAAGACCATATCTGGGATATGG
53457945 AATTGGTACG
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
42 58 0.63
43 34 0.37
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (42 bp):
GTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCGG
Found at i:53457925 original size:43 final size:43
Alignment explanation
Indices: 53457823--53457938 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
53457813 TATGGCATTT
** * ** *
53457823 ATATGAGACTTCGGGTAAGACCATATTTGGGATA-TGGCATCA
1 ATATGAGACTTCATGTAAGACTATAGCTGGGCTATTGGCATCA
* *
53457865 ATATGAGACTTCGTGTAAGACTATAGCTGGGCTATTGGCATCG
1 ATATGAGACTTCATGTAAGACTATAGCTGGGCTATTGGCATCA
* *
53457908 ATATGAGA-TTACATGTAAGATTATATCTGGG
1 ATATGAGACTT-CATGTAAGACTATAGCTGGG
53457939 ATATGGAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 31 0.49
43 32 0.51
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (43 bp):
ATATGAGACTTCATGTAAGACTATAGCTGGGCTATTGGCATCA
Found at i:53462312 original size:26 final size:26
Alignment explanation
Indices: 53462281--53462339 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
53462271 TGAATGGTCC
*
53462281 GTTGAATGTTAGTAAAGTTGAAAATA
1 GTTGAAGGTTAGTAAAGTTGAAAATA
53462307 GTTGAAGGTTAGTAAAGTTGAAAATA
1 GTTGAAGGTTAGTAAAGTTGAAAATA
53462333 GTTGAAG
1 GTTGAAG
53462340 TTGTTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (26 bp):
GTTGAAGGTTAGTAAAGTTGAAAATA
Found at i:53464587 original size:42 final size:42
Alignment explanation
Indices: 53464517--53464680 Score: 175
Period size: 42 Copynumber: 3.9 Consensus size: 42
53464507 TTAGGGTTAC
** * * **
53464517 TGAGATTACGTGTAAGGCCATATATGGGATATGGCATCTTTA
1 TGAGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATA
*
53464559 TGTGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATA
** * *
53464601 TGAGCCTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATTTTGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* *** *
53464644 CGAGATTACATGTAAGACTATATCTGGGATATGGCAT
1 TGAGATTTTGTGTAAGACCATATCTGGGATATGGCAT
53464681 TGGTATGGTA
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 67 0.67
43 33 0.33
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (42 bp):
TGAGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:53464658 original size:43 final size:42
Alignment explanation
Indices: 53464569--53464680 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 42
53464559 TGTGATTTTG
* * **
53464569 TGTAAGACCATATCTGGGATATGGCATCGATATGAGCCTTTG
1 TGTAAGACCATATCTGGGATATGGCATCGATACGAGCATTCA
* *
53464611 TGTAAGACCATAGCTGGGCTATTGGCATCGATACGAG-ATTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATACGAGCATT-CA
*
53464654 TGTAAGACTATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
53464681 TGGTATGGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 27 0.46
43 32 0.54
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATACGAGCATTCA
Found at i:53480926 original size:144 final size:144
Alignment explanation
Indices: 53480664--53480944 Score: 413
Period size: 144 Copynumber: 2.0 Consensus size: 144
53480654 ACTCCCAGTT
* * * * *
53480664 ATAGCTCGCGGACCGACGCTTCCAACTGATAAACTTCAACATAGCTTGTGGACCTATGTTACCAG
1 ATAGCTCGCGGAACGACGCTTCCAACTGATAAACTTCAACATAGCTAGTGGACCTACGCTACCAA
* * *
53480729 CTGATGTTTAAAGGTCAGATGAGTTATACTCATAACCTTCATTTATTTAAGTAAGCTGAGTTAAG
66 CTGATGTTTAAAGGTCAGATAAATTATACTCAGAACCTTCATTTATTTAAGTAAGCTGAGTTAAG
53480794 CTTGCTATTCTGGA
131 CTTGCTATTCTGGA
* *
53480808 ATAGCTCGC-GAACGTACGCTTCCAACTGATAAATTTCAACATAGCTAGTGGACCTACGCTCCCA
1 ATAGCTCGCGGAACG-ACGCTTCCAACTGATAAACTTCAACATAGCTAGTGGACCTACGCTACCA
* * *
53480872 ATTGATGTTTAAAGGAT-AGATAAATTATACTCAGAACCTTCTTTTATTTGAGTAAGCTGAGTTA
65 ACTGATGTTTAAAGG-TCAGATAAATTATACTCAGAACCTTCATTTATTTAAGTAAGCTGAGTTA
53480936 AGCTTGCTA
129 AGCTTGCTA
53480945 CTCCAGAACA
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
143 4 0.03
144 117 0.96
145 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (144 bp):
ATAGCTCGCGGAACGACGCTTCCAACTGATAAACTTCAACATAGCTAGTGGACCTACGCTACCAA
CTGATGTTTAAAGGTCAGATAAATTATACTCAGAACCTTCATTTATTTAAGTAAGCTGAGTTAAG
CTTGCTATTCTGGA
Found at i:53487033 original size:49 final size:49
Alignment explanation
Indices: 53486961--53487147 Score: 189
Period size: 50 Copynumber: 3.8 Consensus size: 49
53486951 GCCGAAGCTA
* *
53486961 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAACAG
* ** *
53487010 TCTGGTACACATAGTACCCTGCACTTAGTACTACACACATGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CT-AACAG
** * * * *
53487060 TCTAATACACGTAGTAGCCTGCACTTAATACTACACACGTGA-TCACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAACAG
* *
53487108 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
53487148 TGCGGCCTCA
Statistics
Matches: 112, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 37 0.33
50 38 0.34
51 34 0.30
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAACAG
Found at i:53490430 original size:30 final size:30
Alignment explanation
Indices: 53490390--53490457 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
53490380 TGCAAGTTCA
*
53490390 ACCCTATAATCATTTTCAATTACATATCAT
1 ACCCTGTAATCATTTTCAATTACATATCAT
53490420 ACCCTGTAATCATTTTCAATTACATATCAT
1 ACCCTGTAATCATTTTCAATTACATATCAT
*
53490450 ACTCTGTA
1 ACCCTGTA
53490458 CAATATGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (30 bp):
ACCCTGTAATCATTTTCAATTACATATCAT
Found at i:53497917 original size:43 final size:43
Alignment explanation
Indices: 53497844--53497938 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
53497834 GTGACATAGT
* * * *
53497844 CCAGACTGTGTGGGTATTTGAAGCAGGGACACACAGTTGTGTC
1 CCAGCCTGTGTGGGTATTCGAAGCAAGGACACACAGCTGTGTC
* **
53497887 CCAGCCTGTGTGGGTATTCGAAGTAAGGACACATGGCTGTGTC
1 CCAGCCTGTGTGGGTATTCGAAGCAAGGACACACAGCTGTGTC
53497930 CCAGCCTGT
1 CCAGCCTGT
53497939 ATGTCTATTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (43 bp):
CCAGCCTGTGTGGGTATTCGAAGCAAGGACACACAGCTGTGTC
Found at i:53499232 original size:29 final size:29
Alignment explanation
Indices: 53499200--53499279 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
53499190 TTCAGATACT
* * *
53499200 TGTATCTGGCCCACTAGGCCCAAATCACC
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
53499229 TGTATATGGCCCATTAGACCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
53499258 TTTATATGGCCCGTTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
53499280 GTCACATTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:53501189 original size:46 final size:46
Alignment explanation
Indices: 53501129--53501540 Score: 664
Period size: 46 Copynumber: 9.0 Consensus size: 46
53501119 TTTGACATGA
* * * * *
53501129 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
53501175 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
53501221 TGCCATGGTATATTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
53501267 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
53501313 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * **
53501359 TGCCATGGTGTCTTTCAACCATGGGCTTACATGTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
53501405 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCTGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
53501451 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
53501497 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
53501541 AGAGCACACT
Statistics
Matches: 340, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
45 4 0.01
46 336 0.99
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:53504036 original size:30 final size:30
Alignment explanation
Indices: 53503969--53504036 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
53503959 CACCCTTAAA
* * *
53503969 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
53503999 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
53504028 AGTATTTAC
1 A-TATTTAC
53504037 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:53510689 original size:5 final size:5
Alignment explanation
Indices: 53510679--53510711 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
53510669 CTGTGTGTTC
53510679 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
53510712 CACAGATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:53518756 original size:46 final size:48
Alignment explanation
Indices: 53518684--53518788 Score: 142
Period size: 46 Copynumber: 2.2 Consensus size: 48
53518674 GACAGGATAG
* * *
53518684 GACAGAAATGAGCCATGTAAGTCCATATCAG-T-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCAGATATATATGGCATTGGA
*
53518730 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCAG--ATATATATGGCATTGGA
53518780 GACAGGAAT
1 GACAGGAAT
53518789 AATTCATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 28 0.55
49 1 0.02
50 22 0.43
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCAGATATATATGGCATTGGA
Found at i:53536994 original size:29 final size:29
Alignment explanation
Indices: 53536886--53537004 Score: 107
Period size: 29 Copynumber: 4.2 Consensus size: 29
53536876 CATATACCTG
* * *
53536886 TATATGGCCCACTAGACCCAACT-ATATT
1 TATATGGCCCACTAGGCCCAAATCACATT
* * ** *
53536914 CACATGGCCCGTTAGGCCCAAACCACATT
1 TATATGGCCCACTAGGCCCAAATCACATT
** *
53536943 TATATGGCCCTTTAGACCCAAATCACATT
1 TATATGGCCCACTAGGCCCAAATCACATT
* *
53536972 TATGTGGCCCACTAGGCCCAAATCGCA-T
1 TATATGGCCCACTAGGCCCAAATCACATT
53537000 TATAT
1 TATAT
53537005 TCATGCTCAC
Statistics
Matches: 71, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
28 21 0.30
29 50 0.70
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
TATATGGCCCACTAGGCCCAAATCACATT
Found at i:53537229 original size:8 final size:8
Alignment explanation
Indices: 53537216--53537258 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
53537206 GTAGCCAAAC
53537216 TTTCGGCT
1 TTTCGGCT
*
53537224 TTTCGGCA
1 TTTCGGCT
*
53537232 TTTCAGCT
1 TTTCGGCT
* *
53537240 TTTTGGCA
1 TTTCGGCT
53537248 TTTCGGCT
1 TTTCGGCT
53537256 TTT
1 TTT
53537259 GCTGATCTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.07, C:0.21, G:0.21, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:53537240 original size:16 final size:16
Alignment explanation
Indices: 53537216--53537258 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
53537206 GTAGCCAAAC
53537216 TTTCGGCTTTTCGGCA
1 TTTCGGCTTTTCGGCA
* *
53537232 TTTCAGCTTTTTGGCA
1 TTTCGGCTTTTCGGCA
53537248 TTTCGGCTTTT
1 TTTCGGCTTTT
53537259 GCTGATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.21, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:53540594 original size:27 final size:27
Alignment explanation
Indices: 53540562--53540613 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
53540552 ATTACTTATT
53540562 ACTTGAACGGTTTTCTAAAAGCAACAC
1 ACTTGAACGGTTTTCTAAAAGCAACAC
53540589 ACTTGAACGGTTTTCTAAAAGCAAC
1 ACTTGAACGGTTTTCTAAAAGCAAC
53540614 GTTTTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (27 bp):
ACTTGAACGGTTTTCTAAAAGCAACAC
Found at i:53547242 original size:27 final size:27
Alignment explanation
Indices: 53547212--53547270 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
53547202 AATATACATC
53547212 TTACCCTACAGGGGTATTTCGATCATT
1 TTACCCTACAGGGGTATTTCGATCATT
53547239 TTACCCTACAGGGGTATTTCGATCATT
1 TTACCCTACAGGGGTATTTCGATCATT
53547266 TTACC
1 TTACC
53547271 TATTTTAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (27 bp):
TTACCCTACAGGGGTATTTCGATCATT
Found at i:53548702 original size:20 final size:20
Alignment explanation
Indices: 53548677--53548721 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
53548667 ATTCCTCCAA
53548677 CAACTCCTCCATGACCATTT
1 CAACTCCTCCATGACCATTT
53548697 CAACTCCTCCATGACCATTT
1 CAACTCCTCCATGACCATTT
53548717 CAACT
1 CAACT
53548722 TAGAGTCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.40, G:0.04, T:0.29
Consensus pattern (20 bp):
CAACTCCTCCATGACCATTT
Found at i:53549911 original size:49 final size:49
Alignment explanation
Indices: 53549839--53549938 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
53549829 CTACATCCGA
53549839 ACTACGTTTTTCTTGATCCATAATGTCAAATTTAACTTATTAAATCATC
1 ACTACGTTTTTCTTGATCCATAATGTCAAATTTAACTTATTAAATCATC
53549888 ACTACGTTTTTCTTGATCCATAATGTCAAATTTAACTTATTAAATCATC
1 ACTACGTTTTTCTTGATCCATAATGTCAAATTTAACTTATTAAATCATC
53549937 AC
1 AC
53549939 ATTATTCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (49 bp):
ACTACGTTTTTCTTGATCCATAATGTCAAATTTAACTTATTAAATCATC
Found at i:53553525 original size:22 final size:23
Alignment explanation
Indices: 53553497--53553540 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
53553487 AGAAGATAAC
* *
53553497 TTCTTTATTTTATTA-TTATTAT
1 TTCTTTAATTTATGAGTTATTAT
53553519 TTCTTTAATTTATGAGTTATTA
1 TTCTTTAATTTATGAGTTATTA
53553541 ACATAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (23 bp):
TTCTTTAATTTATGAGTTATTAT
Found at i:53556976 original size:40 final size:40
Alignment explanation
Indices: 53556902--53557043 Score: 225
Period size: 40 Copynumber: 3.6 Consensus size: 40
53556892 AACCCAAGTA
* *
53556902 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
53556941 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
53556981 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
53557021 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
53557044 CATCTGAATA
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 12 0.12
40 83 0.86
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:53560420 original size:40 final size:39
Alignment explanation
Indices: 53560351--53560444 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 39
53560341 CCAACTCCGT
* * *
53560351 CCAA-CCTATCACACC-ATATGGGGATAAAATCGACCTAC
1 CCAACCCTA-CACACCAATATGGAGAAAAAATCGACCCAC
* * *
53560389 CCATCCCTACACACCAATTATGGAGAAAAAATTGACCCAT
1 CCAACCCTACACACCAA-TATGGAGAAAAAATCGACCCAC
*
53560429 TCAACCCTACACACCA
1 CCAACCCTACACACCA
53560445 TAAGGTACTG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
38 9 0.20
39 5 0.11
40 31 0.69
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (39 bp):
CCAACCCTACACACCAATATGGAGAAAAAATCGACCCAC
Found at i:53564971 original size:43 final size:43
Alignment explanation
Indices: 53564882--53564988 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 43
53564872 TGTGATTACA
* * * *
53564882 TGTAAGACCATGTCTAAGACATTGGCATTGTATTGTGATTATG
1 TGTAAGACCATGTCTAGGACATTGACATTGTAATGCGATTATG
53564925 TGTAAGACCATGTCTAGGACATTGACATCAT-TAAT-CGATT-TCG
1 TGTAAGACCATGTCTAGGACATTGACAT--TGTAATGCGATTAT-G
* *
53564968 TGTAAGACCCTTTCTAGGACA
1 TGTAAGACCATGTCTAGGACA
53564989 GCGGGATCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 50 0.91
44 3 0.05
45 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGACATTGTAATGCGATTATG
Found at i:53566902 original size:18 final size:17
Alignment explanation
Indices: 53566870--53566911 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
53566860 GACTAAGTGA
*
53566870 TTATGT-TTGATGGATGT
1 TTATGTGTTAATGGAT-T
53566887 TTATGTGTTAATGGATT
1 TTATGTGTTAATGGATT
53566904 TTCATGTG
1 TT-ATGTG
53566912 AGAAATGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.52
Consensus pattern (17 bp):
TTATGTGTTAATGGATT
Found at i:53569191 original size:42 final size:43
Alignment explanation
Indices: 53569122--53569242 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 43
53569112 GTAATTCAGT
* * *
53569122 ATCGATGCCTCTGTCCCAGACAGGGTCTTACACGAAAT-T-AG
1 ATCGATGCCTATGTCCCAGACAAGGTCTTACACGAAATCTCAA
* * *
53569163 ATACGATGCCTATGTCCCAAACATGGTCTTACTCGTAAATCTCAA
1 AT-CGATGCCTATGTCCCAGACAAGGTCTTACACG-AAATCTCAA
* *
53569208 ATCGAGGCCTATGTCCCAGACAAGGTGTTACACGA
1 ATCGATGCCTATGTCCCAGACAAGGTCTTACACGA
53569243 TATTTCAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
41 2 0.03
42 28 0.42
43 5 0.08
44 28 0.42
45 3 0.05
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
ATCGATGCCTATGTCCCAGACAAGGTCTTACACGAAATCTCAA
Found at i:53574798 original size:42 final size:43
Alignment explanation
Indices: 53574738--53574865 Score: 152
Period size: 44 Copynumber: 3.0 Consensus size: 43
53574728 GTAATTCAGT
* * *
53574738 ATCGATGCCTCTATCCCAGATAAGGTCTTACACGAAATCT--A
1 ATCGATGCCTATGTCCCAGACAAGGTCTTACACGAAATCTCAA
*
53574779 ATACGATGCCTATGTCCCAGACATGGTCTTACACGTAAATCTCAA
1 AT-CGATGCCTATGTCCCAGACAAGGTCTTACACG-AAATCTCAA
* * * *
53574824 ATCGAGGCCTATGTGCCAGACACGGTCTTACACGATATCTCA
1 ATCGATGCCTATGTCCCAGACAAGGTCTTACACGAAATCTCA
53574866 TATCAATGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 2 0.03
42 28 0.37
43 13 0.17
44 29 0.39
45 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
ATCGATGCCTATGTCCCAGACAAGGTCTTACACGAAATCTCAA
Found at i:53576858 original size:40 final size:40
Alignment explanation
Indices: 53576803--53576934 Score: 239
Period size: 40 Copynumber: 3.3 Consensus size: 40
53576793 CGGATGATAA
53576803 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53576843 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53576883 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53576923 CCGGGCT-AGTCC
1 CCGGGCTAAGTCC
53576935 GAGCATGTGC
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 5 0.06
40 83 0.94
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53584822 original size:40 final size:40
Alignment explanation
Indices: 53584767--53584973 Score: 328
Period size: 40 Copynumber: 5.2 Consensus size: 40
53584757 GGATGATAAT
53584767 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
53584807 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
53584847 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
53584887 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* * *
53584927 CGGGCTAAGTCCCGAAGACATTTGAGCGAG-TAGCTATGTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
53584967 C-GGCTAA
1 CGGGCTAA
53584974 ATTCCAAAGG
Statistics
Matches: 155, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 7 0.05
40 148 0.95
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:53608939 original size:47 final size:47
Alignment explanation
Indices: 53608885--53608980 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
53608875 GTTGAATTTA
*
53608885 AAGCTTGTTAAATTTGCTCTTAATACTTCCAGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATACTTCCAGATAAGTTACTTAGTT
* * *
53608932 AAGCTTGTTAAATTTTCCCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATACTTCCAGATAAGTTACTTAGTT
53608979 AA
1 AA
53608981 AGAAAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCCCTTAATACTTCCAGATAAGTTACTTAGTT
Found at i:53610303 original size:31 final size:31
Alignment explanation
Indices: 53610252--53610335 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
53610242 TTAGTCTTGA
* *
53610252 CATAT-ACTGGGCCAAAGCCTTTCCATAAAT
1 CATATCACTAGGCCGAAGCCTTTCCATAAAT
* *
53610282 CATATCAGTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTCCATAAAT
*
53610313 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTAGGCCGAAGCCTTT
53610336 ACTATAAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.11
31 42 0.89
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTCCATAAAT
Found at i:53610418 original size:42 final size:42
Alignment explanation
Indices: 53610359--53610450 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
53610349 TGGCCCTTAG
*
53610359 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
53610401 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
53610443 GCCCATTT
1 GCCCATTT
53610451 GGGGAGACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:53610612 original size:24 final size:24
Alignment explanation
Indices: 53610585--53610666 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 24
53610575 GTGGAGGCCT
*
53610585 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTAATAAACTAGGGCAA
*
53610609 AGCCCTTTCTGATAAACTAGGGCAA
1 AGCCCTTT-TAATAAACTAGGGCAA
* ** * *
53610634 AACCCTTTTCGGTAAACTGGGGCAG
1 AGCCCTTTT-AATAAACTAGGGCAA
53610659 AGCCCTTT
1 AGCCCTTT
53610667 CAGCACTTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 4 0.08
24 8 0.17
25 36 0.75
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTAGGGCAA
Found at i:53610631 original size:25 final size:26
Alignment explanation
Indices: 53610598--53610667 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
53610588 CTCTTTTAAT
53610598 AACTGGGGCAAAGCCCTTTCT-GATA
1 AACTGGGGCAAAGCCCTTTCTCGATA
* * *
53610623 AACTAGGGCAAAACCCTTT-TCGGTA
1 AACTGGGGCAAAGCCCTTTCTCGATA
*
53610648 AACTGGGGCAGAGCCCTTTC
1 AACTGGGGCAAAGCCCTTTC
53610668 AGCACTTCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTCTCGATA
Found at i:53614422 original size:23 final size:22
Alignment explanation
Indices: 53614371--53614422 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53614361 CCTCGTCTTT
*
53614371 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53614393 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53614416 TTCTTTT
1 TTCTTTT
53614423 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53617917 original size:45 final size:45
Alignment explanation
Indices: 53617853--53618056 Score: 288
Period size: 45 Copynumber: 4.6 Consensus size: 45
53617843 CGCACAGTAT
* *
53617853 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAC
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
53617898 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCAGGTAAGATAC
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
53617943 TATTTGGGCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * * *
53617988 TATTCGGGCTTTCGAGCCTAGTAGGCTATGATGCCGGTGAAATGA-
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
53618033 TA-TCGGGC-TTTGAGCCTAGCAGGC
1 TATTCGGGCTTTTGAGCCTAGCAGGC
53618057 GAAATGCTCG
Statistics
Matches: 144, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 14 0.10
44 6 0.04
45 123 0.85
46 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:53631150 original size:68 final size:67
Alignment explanation
Indices: 53631078--53631227 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
53631068 CATCATGTGT
* * * *
53631078 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
53631140 ATGTAG
62 ATGTAG
** * *
53631146 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
53631211 AG
66 AG
53631213 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
53631228 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:53631183 original size:64 final size:64
Alignment explanation
Indices: 53631102--53631285 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
53631092 AGACATTATG
* *
53631102 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
53631166 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53631231 AA
63 AA
* * * *
53631233 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53631286 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53634912 original size:27 final size:27
Alignment explanation
Indices: 53634878--53635077 Score: 274
Period size: 27 Copynumber: 7.4 Consensus size: 27
53634868 TGGATAAGTT
* *
53634878 GTAGAATTAACGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
53634905 GTAAAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
53634932 GTAGAATTATTGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
53634959 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
53634986 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
53635013 GTAGAAATACCAAAATACCCCTATAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
53635040 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
53635067 GTAAAATTACC
1 GTAGAATTACC
53635078 ATTTTGCCCC
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:53635768 original size:27 final size:26
Alignment explanation
Indices: 53635724--53635775 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53635714 CTCGCTGCAA
*
53635724 TCTGGTGGCCTTGGCACATATATCTGT
1 TCTGGTGACCTTGGCACA-ATATCTGT
* *
53635751 TCTGGTGACTTTGTCACAATATCTG
1 TCTGGTGACCTTGGCACAATATCTG
53635776 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (26 bp):
TCTGGTGACCTTGGCACAATATCTGT
Found at i:53636867 original size:17 final size:17
Alignment explanation
Indices: 53636847--53636898 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 17
53636837 ATCTTTTCCA
53636847 TCTATCTTATTTATTGT
1 TCTATCTTATTTATTGT
53636864 TCTAACTCTTTAATTTATTGT
1 TCT-A-TC-TT-ATTTATTGT
*
53636885 TCTATTTTATTTAT
1 TCTATCTTATTTAT
53636899 ATTAGTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 9 0.30
18 3 0.10
19 3 0.10
20 3 0.10
21 12 0.40
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.63
Consensus pattern (17 bp):
TCTATCTTATTTATTGT
Found at i:53638248 original size:47 final size:47
Alignment explanation
Indices: 53638181--53638300 Score: 120
Period size: 47 Copynumber: 2.6 Consensus size: 47
53638171 GTGAGCCAGT
* * * *
53638181 GTAAAACATGTTTGGGACATGCATCAGCCACAT-TG-CGAGAGCTACT
1 GTAAGACATGTCTGGGACATGCATCAGCCA-ATGAGACGAGAGCTACA
* * *
53638227 GTAAGACCATGTCTGGGACATGGCATC-GGCAGTGAGACGAGAGCTAGA
1 GTAAGA-CATGTCTGGGACAT-GCATCAGCCAATGAGACGAGAGCTACA
*
53638275 GTAAGACATGTCTGAGACATGCATCA
1 GTAAGACATGTCTGGGACATGCATCA
53638301 ACCTCGAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
46 11 0.18
47 30 0.49
48 20 0.33
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (47 bp):
GTAAGACATGTCTGGGACATGCATCAGCCAATGAGACGAGAGCTACA
Found at i:53638328 original size:46 final size:44
Alignment explanation
Indices: 53638275--53638391 Score: 121
Period size: 46 Copynumber: 2.6 Consensus size: 44
53638265 GAGAGCTAGA
53638275 GTAAGACATGTCTGAGACATGCATCAACCT-CGAGATGTAAGCCAGT
1 GTAAGACATGTCTGAGACATGCATC-ACCTACGAG-T-TAAGCCAGT
* ** *
53638321 GTAAGACATGTCT-AGGACATGTATCGGCTACGAGTTAAGCTAGT
1 GTAAGACATGTCTGA-GACATGCATCACCTACGAGTTAAGCCAGT
*
53638365 GTAAGACCATGTCTGGGACATGGCATC
1 GTAAGA-CATGTCTGAGACAT-GCATC
53638392 GGTATCCTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
44 14 0.23
45 16 0.27
46 30 0.50
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
GTAAGACATGTCTGAGACATGCATCACCTACGAGTTAAGCCAGT
Found at i:53639294 original size:6 final size:6
Alignment explanation
Indices: 53639258--53639287 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53639248 TTATTATTAA
53639258 TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT
53639288 AGTTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:53642616 original size:11 final size:11
Alignment explanation
Indices: 53642600--53642631 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
53642590 TTTTATATGA
53642600 TATTTTATTAT
1 TATTTTATTAT
53642611 TATTTTATTAT
1 TATTTTATTAT
53642622 TATTTTATTA
1 TATTTTATTA
53642632 GTATATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:53644231 original size:16 final size:16
Alignment explanation
Indices: 53644210--53644247 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
53644200 GCATATAGAA
53644210 TTTGATTTATGTTAAG
1 TTTGATTTATGTTAAG
53644226 TTTGATTTATGTTAAG
1 TTTGATTTATGTTAAG
53644242 TTTGAT
1 TTTGAT
53644248 ATGAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTGATTTATGTTAAG
Found at i:53647179 original size:20 final size:20
Alignment explanation
Indices: 53647154--53647191 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53647144 AAAAGCATAC
*
53647154 AAAATTTTAAAAATATATTA
1 AAAATTATAAAAATATATTA
*
53647174 AAAATTATAAAATTATAT
1 AAAATTATAAAAATATAT
53647192 AGAATTACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTATAAAAATATATTA
Found at i:53647621 original size:18 final size:18
Alignment explanation
Indices: 53647580--53647621 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
53647570 GAGATTATTA
53647580 TATTATAAATTTTATATG
1 TATTATAAATTTTATATG
* *
53647598 TCTTATAATTTTTATGAT-
1 TATTATAAATTTTAT-ATG
53647616 TATTAT
1 TATTAT
53647622 GTTTATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TATTATAAATTTTATATG
Found at i:53647691 original size:18 final size:18
Alignment explanation
Indices: 53647668--53647803 Score: 86
Period size: 18 Copynumber: 7.6 Consensus size: 18
53647658 ACCATTTCCT
53647668 ATATTTTTATATTTTATA
1 ATATTTTTATATTTTATA
*
53647686 ATATTTTTAGATTTTTTTATA
1 ATATTTTT--A-TATTTTATA
** *
53647707 A-ATTTAAAATACTTTT-TT
1 ATATTT-TTATA-TTTTATA
*
53647725 ATATTTTTACATTTTATA
1 ATATTTTTATATTTTATA
** *
53647743 ATAAATTT-TCTTTTATA
1 ATATTTTTATATTTTATA
* *
53647760 A-ATTTTTGTATTTCA-A
1 ATATTTTTATATTTTATA
53647776 ATATTTTTATAATTTT-TA
1 ATATTTTTAT-ATTTTATA
53647794 ATATTTTTAT
1 ATATTTTTAT
53647804 TGATTAAAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
16 6 0.07
17 24 0.27
18 35 0.40
19 9 0.10
20 5 0.06
21 9 0.10
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
ATATTTTTATATTTTATA
Found at i:53647801 original size:10 final size:9
Alignment explanation
Indices: 53647668--53647802 Score: 50
Period size: 9 Copynumber: 15.0 Consensus size: 9
53647658 ACCATTTCCT
53647668 ATATTTTT-
1 ATATTTTTA
53647676 ATATTTTATA
1 ATATTTT-TA
53647686 ATATTTTTA
1 ATATTTTTA
*
53647695 GATTTTTTTA
1 -ATATTTTTA
* **
53647705 TAAATTTAAA
1 -ATATTTTTA
*
53647715 ATACTTTTTT
1 ATA-TTTTTA
53647725 ATATTTTTA
1 ATATTTTTA
*
53647734 CAT-TTTATA
1 -ATATTTTTA
*
53647743 ATAAATTTT-
1 AT-ATTTTTA
* *
53647752 CT-TTTATA
1 ATATTTTTA
53647760 A-ATTTTT-
1 ATATTTTTA
* **
53647767 GTATTTCAA
1 ATATTTTTA
53647776 ATATTTTT-
1 ATATTTTTA
53647784 ATAATTTTTA
1 AT-ATTTTTA
53647794 ATATTTTTA
1 ATATTTTTA
53647803 TTGATTAAAA
Statistics
Matches: 89, Mismatches: 25, Indels: 25
0.64 0.18 0.18
Matches are distributed among these distances:
7 3 0.03
8 19 0.21
9 34 0.38
10 33 0.37
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
ATATTTTTA
Found at i:53649081 original size:20 final size:20
Alignment explanation
Indices: 53649049--53649094 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
53649039 ATTCTTCAGC
*
53649049 AATTTTGTTAAAAAAATTTA
1 AATTTTGTTAAAAAAATATA
53649069 TAATTTT-TTAAAAAAATATA
1 -AATTTTGTTAAAAAAATATA
53649089 AATTTT
1 AATTTT
53649095 AGAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 12 0.50
21 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTTTGTTAAAAAAATATA
Found at i:53649155 original size:20 final size:20
Alignment explanation
Indices: 53649090--53649156 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
53649080 AAAAATATAA
*
53649090 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAGAAATT
*
53649110 ATTTT-AAGTTTTAGAAATT
1 ATTTTGAATTTTTAGAAATT
53649129 ATTTTTGAATTTTT-GAAAATT
1 A-TTTTGAATTTTTAG-AAATT
53649150 ATTTTGA
1 ATTTTGA
53649157 TTCTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 10 0.25
19 2 0.05
20 16 0.40
21 12 0.30
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
ATTTTGAATTTTTAGAAATT
Found at i:53649303 original size:118 final size:118
Alignment explanation
Indices: 53649178--53649415 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
53649168 GTAATATTTA
53649178 TTGAGAGAGACCAATTTACTCATTTTCAAAATTGATAGGGACCAAAGGAGTATTTACACTAATTT
1 TTGAGAGAGACCAATTTACTCATTTTCAAAATTGATAGGGACCAAAGGAGTATTTACACTAATTT
53649243 GTTATTTGAATTATCCGAGTTATTCGAATTGTAAAATTTAACTCGACTCAAAC
66 GTTATTTGAATTATCCGAGTTATTCGAATTGTAAAATTTAACTCGACTCAAAC
53649296 TTGAGAGAGACCAATTTACTCATTTTCAAAATTGATAGGGACCAAAGGAGTATTTACACTAATTT
1 TTGAGAGAGACCAATTTACTCATTTTCAAAATTGATAGGGACCAAAGGAGTATTTACACTAATTT
53649361 GTTATTTGAATTATCCGAGTTATTCGAATTGTAAAATTTAACTCGACTCAAAC
66 GTTATTTGAATTATCCGAGTTATTCGAATTGTAAAATTTAACTCGACTCAAAC
53649414 TT
1 TT
53649416 AAAACTAGAA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (118 bp):
TTGAGAGAGACCAATTTACTCATTTTCAAAATTGATAGGGACCAAAGGAGTATTTACACTAATTT
GTTATTTGAATTATCCGAGTTATTCGAATTGTAAAATTTAACTCGACTCAAAC
Found at i:53651744 original size:2 final size:2
Alignment explanation
Indices: 53651703--53651729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53651693 GGGTTATTTA
53651703 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 A
53651730 AGATTTTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53652430 original size:3 final size:3
Alignment explanation
Indices: 53652424--53652450 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53652414 TGACAAAAAC
53652424 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
53652451 AAGGTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:53656033 original size:101 final size:99
Alignment explanation
Indices: 53655900--53656131 Score: 297
Period size: 101 Copynumber: 2.3 Consensus size: 99
53655890 CGGTTTTGGG
*
53655900 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTG-TAGTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGT--CATGTGATAGTA
* * *
53655964 CTAAGTGCAGGCTACTATGCGTACTC-GATAGCTTCGA
64 CTAAGTGCAAGCTACTACGCGTAC-CAGATAG-TTAGA
* * *
53656001 TCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTATCTGATGGTTAGGTCATGTGTATAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCATGTG-ATAGTAC
* * *
53656066 TAAGTGCAAGCTACTACGTGTACCAGATTGTTAGG
65 TAAGTGCAAGCTACTACGCGTACCAGATAGTTAGA
* *
53656101 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
53656132 TTCGTACCAG
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
99 6 0.05
100 32 0.28
101 77 0.67
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (99 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCATGTGATAGTACT
AAGTGCAAGCTACTACGCGTACCAGATAGTTAGA
Found at i:53656142 original size:50 final size:50
Alignment explanation
Indices: 53655905--53656131 Score: 289
Period size: 50 Copynumber: 4.5 Consensus size: 50
53655895 TTGGGTCACG
53655905 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCA
* * * * * * *
53655955 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-GATAGCTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTG-TTAGGTCGCA
* * * *
53656006 TGTGTAGTACTAAGTGCAGACTACTACGTGTATCTGATGGTTAGGT--CA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCA
*
53656054 TGTGTATAGTACTAAGTGCAAGCTACTACGTGTACCAGATTGTTAGGTCGCA
1 TGTG--TAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCA
53656106 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
53656132 TTCGTACCAG
Statistics
Matches: 149, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
48 5 0.03
50 98 0.66
51 40 0.27
52 6 0.04
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCA
Found at i:53661834 original size:14 final size:15
Alignment explanation
Indices: 53661794--53661834 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
53661784 TATTTAAAAA
53661794 TTATTTTCTGTG--T
1 TTATTTTCTGTGAAT
*
53661807 TTATTTTGTGTGAAT
1 TTATTTTCTGTGAAT
53661822 TTA-TTTCTGTGAA
1 TTATTTTCTGTGAA
53661835 ATTTTCGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.46
14 9 0.38
15 4 0.17
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.61
Consensus pattern (15 bp):
TTATTTTCTGTGAAT
Found at i:53662374 original size:350 final size:350
Alignment explanation
Indices: 53661733--53662425 Score: 1180
Period size: 350 Copynumber: 2.0 Consensus size: 350
53661723 AGCCTGATCC
* * *
53661733 AGACCCTAATCGGAACGGTGATTTTGAGACCACGAATCTGAGTTAGAAAAATATTTAAAAATTAT
1 AGACCCTAATCAGAACGGTGATTTAGAGACCACGAATCTGAGTCAGAAAAATATTTAAAAATTAT
53661798 TTTCTGTGTTTATTTTGTGTGAATTTATTTCTGTGAAATTTTCGTGATTTAATTTTGTCGTTTAG
66 TTTCTGTGTTTATTTTGTGTGAATTTATTTCTGTGAAATTTTCGTGATTTAATTTTGTCGTTTAG
**
53661863 GTGTTCGATTAAATAAAAGGACTTAATCGTGTAAAATGAAAATTCTGTGGTTTTTCTAAAAAGGG
131 GTGTTCGATTAAATAAAAGGACTTAATCGCATAAAATGAAAATTCTGTGGTTTTTCTAAAAAGGG
*
53661928 CTGAATTGTACTGGGCTTTTTAAATGGAAGCCTTAAAGTTGCAATTAACCCATTAAGAGAATAAG
196 CTAAATTGTACTGGGCTTTTTAAATGGAAGCCTTAAAGTTGCAATTAACCCATTAAGAGAATAAG
53661993 TGGACAGTACTAGGCATATGTTATATGGCTTTGTTATAATATTATTAAGGTTAAATAAGTAATTA
261 TGGACAGTACTAGGCATATGTTATATGGCTTTGTTATAATATTATTAAGGTTAAATAAGTAATTA
53662058 GATAAAATGTTATTATATTTGATTT
326 GATAAAATGTTATTATATTTGATTT
* * * * *
53662083 AGACCCTAATTAGAACGGTGGTTTCAG-GACCACTAATC-GAGTCAGAAAAATATTTAAAATTTT
1 AGACCCTAATCAGAACGGTGATTT-AGAGACCACGAATCTGAGTCAGAAAAATATTTAAAAATTA
*
53662146 TTTTCTGTGTTTATTTTGTGTGAATTTATATT-TGTGAAATTTTTGTGATTTAATTTTGTCGTTT
65 TTTTCTGTGTTTATTTTGTGTGAATTTAT-TTCTGTGAAATTTTCGTGATTTAATTTTGTCGTTT
53662210 AGGTGTTCGATTAAATAAAAGGACTTAATCGCATAAAATGAAAATT-TAGTGGTTTTTTCTAAAA
129 AGGTGTTCGATTAAATAAAAGGACTTAATCGCATAAAATGAAAATTCT-GTGG-TTTTTCTAAAA
*
53662274 AGGGCTAAATTGTACTTGGCTTTTTAAATGGAAGCCTTAAAGTTGCAATTAACCCATTAAGAGAA
192 AGGGCTAAATTGTACTGGGCTTTTTAAATGGAAGCCTTAAAGTTGCAATTAACCCATTAAGAGAA
*
53662339 TAAGTGGA-TGCTACTAGGCATATGTTATATGGCTTTGTTATAATATTATTAAGGTTAAATAAGT
257 TAAGTGGACAG-TACTAGGCATATGTTATATGGCTTTGTTATAATATTATTAAGGTTAAATAAGT
53662403 AATTAGATAAAATGTTATTATAT
321 AATTAGATAAAATGTTATTATAT
53662426 GTTATAATTT
Statistics
Matches: 324, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
348 1 0.00
349 131 0.40
350 191 0.59
351 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (350 bp):
AGACCCTAATCAGAACGGTGATTTAGAGACCACGAATCTGAGTCAGAAAAATATTTAAAAATTAT
TTTCTGTGTTTATTTTGTGTGAATTTATTTCTGTGAAATTTTCGTGATTTAATTTTGTCGTTTAG
GTGTTCGATTAAATAAAAGGACTTAATCGCATAAAATGAAAATTCTGTGGTTTTTCTAAAAAGGG
CTAAATTGTACTGGGCTTTTTAAATGGAAGCCTTAAAGTTGCAATTAACCCATTAAGAGAATAAG
TGGACAGTACTAGGCATATGTTATATGGCTTTGTTATAATATTATTAAGGTTAAATAAGTAATTA
GATAAAATGTTATTATATTTGATTT
Found at i:53667016 original size:14 final size:15
Alignment explanation
Indices: 53666988--53667016 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53666978 CTCTTTCTTG
53666988 GACAAGAATAATCCA
1 GACAAGAATAATCCA
53667003 GACAAGAA-AATCCA
1 GACAAGAATAATCCA
53667017 TATGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (15 bp):
GACAAGAATAATCCA
Found at i:53667710 original size:15 final size:15
Alignment explanation
Indices: 53667687--53667735 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
53667677 ACGGAGAAGC
*
53667687 CCAAAATAAAGAAAT
1 CCAAGATAAAGAAAT
*
53667702 CTAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
* *
53667717 CCATGATAACGAAAT
1 CCAAGATAAAGAAAT
53667732 CCAA
1 CCAA
53667736 TTTACAACAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.57, C:0.16, G:0.10, T:0.16
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:53670789 original size:96 final size:96
Alignment explanation
Indices: 53670625--53670804 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 96
53670615 TAAATTTCCA
* * * * *
53670625 ATGCCATGTCCCAGATATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAAACATAGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCCCAAACA
*
53670690 TGGTCTTACTCTAGCTCTCGTAACATTGCCG
66 TGGTCTTACACTAGCTCTCGTAACATTGCCG
* * *
53670721 ATGCCATGTTCCAAACATAGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCCATGTCCCAAAC
1 ATGCCATGTCCCAAACATAGTCTTACACTGGCTCACAT-ATCGAGGCTGATGCCATGTCCCAAAC
*
53670785 ATGGTCTTACACTGGCTCTC
65 ATGGTCTTACACTAGCTCTC
53670805 ATAATGTGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 72 0.99
97 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (96 bp):
ATGCCATGTCCCAAACATAGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCCCAAACA
TGGTCTTACACTAGCTCTCGTAACATTGCCG
Found at i:53670808 original size:48 final size:48
Alignment explanation
Indices: 53670625--53670812 Score: 225
Period size: 48 Copynumber: 3.9 Consensus size: 48
53670615 TAAATTTCCA
* * * * *
53670625 ATGCCATGTCCCAGATATGGTCTTACACTGGCTCACAT-GTCGAGGCTG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCTG
* * * * ** * *
53670673 ATGCCATGTCCCAGACATGGTCTTACTCTAGCTCTCGTAACATTGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCTG
* *
53670721 ATGCCATGTTCCAAACATAGTCTTACACTGGCTCTCATAATGTGGCTG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCTG
53670769 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTG
53670813 ATCTTACATT
Statistics
Matches: 116, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
48 116 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCTG
Found at i:53670829 original size:25 final size:25
Alignment explanation
Indices: 53670789--53670837 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
53670779 CCAAACATGG
53670789 TCTTACACTGGCTCTCATAATGTGA
1 TCTTACACTGGCTCTCATAATGTGA
* *
53670814 TCTTACATTGGTTCTCATAATGTG
1 TCTTACACTGGCTCTCATAATGTG
53670838 GCCGATGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.41
Consensus pattern (25 bp):
TCTTACACTGGCTCTCATAATGTGA
Found at i:53681808 original size:32 final size:32
Alignment explanation
Indices: 53681767--53681883 Score: 180
Period size: 32 Copynumber: 3.7 Consensus size: 32
53681757 TGATATTGAA
53681767 ATGGGCTAGGCCCAACTGATATTGGTTCTGAT
1 ATGGGCTAGGCCCAACTGATATTGGTTCTGAT
53681799 ATGGGCTAGGCCCAACTGATATTGGTTCTGAT
1 ATGGGCTAGGCCCAACTGATATTGGTTCTGAT
* * * * *
53681831 ATAGGCTAAGCCCAACTGATATTGATTTTGAG
1 ATGGGCTAGGCCCAACTGATATTGGTTCTGAT
*
53681863 ATGGGCTAGGCCCAATTGATA
1 ATGGGCTAGGCCCAACTGATA
53681884 CTGTGATGGG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (32 bp):
ATGGGCTAGGCCCAACTGATATTGGTTCTGAT
Found at i:53689836 original size:47 final size:47
Alignment explanation
Indices: 53689775--53690248 Score: 831
Period size: 47 Copynumber: 10.1 Consensus size: 47
53689765 CAGCCAAGAC
*
53689775 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53689822 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53689869 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53689916 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53689963 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53690010 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53690057 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53690104 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53690151 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * * *
53690198 AGTGTATATATGTGACAGGGCCGAGTGACCAACGTGATGGATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53690245 AGTG
1 AGTG
53690249 CATAAATGTG
Statistics
Matches: 413, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 413 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:53690432 original size:37 final size:37
Alignment explanation
Indices: 53690382--53690460 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
53690372 CCGAGCTCTA
*
53690382 AAGACCCGATAACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
53690419 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53690456 AAGAC
1 AAGAC
53690461 TTCGTAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 38 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53692374 original size:43 final size:43
Alignment explanation
Indices: 53692326--53692428 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
53692316 TTGGTTTTCA
53692326 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
53692369 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
53692412 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
53692429 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:53692445 original size:29 final size:29
Alignment explanation
Indices: 53692410--53692483 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
53692400 GTTGTGAGAT
* *
53692410 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
53692439 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
53692468 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
53692484 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:53692919 original size:40 final size:40
Alignment explanation
Indices: 53692796--53692991 Score: 184
Period size: 40 Copynumber: 4.9 Consensus size: 40
53692786 TCGAATGATG
** *
53692796 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
53692836 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
53692876 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
53692916 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * *
53692956 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
53692992 CGTGTATTCG
Statistics
Matches: 130, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 110 0.85
41 19 0.15
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:53692959 original size:80 final size:81
Alignment explanation
Indices: 53692796--53692992 Score: 206
Period size: 80 Copynumber: 2.5 Consensus size: 81
53692786 TCGAATGATG
** *
53692796 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGACCATATCCGGACTAAGATCCAAAGGCAT
* *
53692859 TGGTGCGAGTTACTAAA
65 TCGTGCGAGTGACTAAA
** *
53692876 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAG-TCCCAAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGAT-CCAAAG-GCA
* *
53692939 TTCGTGCTAGTGA-TATA
64 TTCGTGCGAGTGACTAAA
* * * *
53692956 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAC
53692993 GTGTATTCGG
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 71 0.72
81 20 0.20
82 6 0.06
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCAAAGGCATT
CGTGCGAGTGACTAAA
Found at i:53695717 original size:47 final size:47
Alignment explanation
Indices: 53695656--53696144 Score: 825
Period size: 47 Copynumber: 10.4 Consensus size: 47
53695646 CAGCCAAGAC
53695656 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53695703 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53695750 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53695797 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53695844 AGTGTATATATGTGATAAGGCCTAATTGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53695891 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53695938 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53695985 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53696032 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
53696079 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53696126 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
53696145 TCCCGAAGGG
Statistics
Matches: 419, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 419 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:53696319 original size:37 final size:37
Alignment explanation
Indices: 53696265--53696341 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
53696255 GAGCTCTAAG
*
53696265 GACCCGATAACTACGTGTGG-GAATTTTGTCCGGGTAA
1 GACCCGATAACTACGTGTGGAG-ATTATGTCCGGGTAA
*
53696302 GACCCGATAACTTCGTGTGGAGATTATGTCCGGGTAA
1 GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
53696339 GAC
1 GAC
53696342 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
Found at i:53698422 original size:40 final size:40
Alignment explanation
Indices: 53698378--53698565 Score: 308
Period size: 40 Copynumber: 4.7 Consensus size: 40
53698368 GCTACTAGCT
53698378 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
53698418 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
53698458 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
53698498 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
53698537 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
53698566 CAATCCGAAT
Statistics
Matches: 137, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
38 1 0.01
39 34 0.25
40 101 0.74
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:53698564 original size:79 final size:80
Alignment explanation
Indices: 53698355--53698565 Score: 331
Period size: 80 Copynumber: 2.7 Consensus size: 80
53698345 CCTTCTGAGT
* *
53698355 TTAG-CCGAATATAGCT-ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 TTAGCCCGGATATAG-TAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
53698418 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* *
53698434 TTAGCCCGGATATAGTAACTCGGACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
53698499 AAATGCCTTCGGG-C
66 AAATGCCTTCGGGAC
*
53698513 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 TTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
53698566 CAATCCGAAT
Statistics
Matches: 122, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
78 1 0.01
79 54 0.44
80 67 0.55
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
AAATGCCTTCGGGAC
Found at i:53714465 original size:40 final size:40
Alignment explanation
Indices: 53714421--53714648 Score: 370
Period size: 40 Copynumber: 5.7 Consensus size: 40
53714411 GCTACTAGCT
**
53714421 CAAATGCCTTCGAAACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
53714461 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
53714501 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
53714541 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
53714581 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
53714620 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
53714649 CAATCCGAAT
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 33 0.19
40 140 0.80
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:53719514 original size:43 final size:43
Alignment explanation
Indices: 53719448--53719590 Score: 178
Period size: 43 Copynumber: 3.3 Consensus size: 43
53719438 CTTTGCTCGA
** * * *
53719448 ATCACCGGCATTAAACCTGCTAGGCACGAAGACCCAAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* *
53719491 ATCACCGGCACGAAGCCTACTAGGAACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* * * * *
53719534 ATCACCAGCACAAAGCCTGCTAGGCATGAAGGCCTGATTACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
53719577 ATCACCGGCACGAA
1 ATCACCGGCACGAA
53719591 CGCCCTTCAG
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.35, C:0.32, G:0.20, T:0.13
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:53719644 original size:40 final size:40
Alignment explanation
Indices: 53719579--53719699 Score: 188
Period size: 40 Copynumber: 3.0 Consensus size: 40
53719569 GATTACACAT
* * * * * *
53719579 CACCGGCACGAACGCCCTTCAGGACTTAGCCCAGATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
53719619 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
53719659 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
53719699 C
1 C
53719700 TCTCAATTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.18
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:53722734 original size:37 final size:37
Alignment explanation
Indices: 53722684--53722762 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53722674 TTATTACGAA
* * *
53722684 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
53722721 GTCTTACCCGGACAAAATCCCCACACGTAGTCATTGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
53722758 GTCTT
1 GTCTT
53722763 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:53722990 original size:22 final size:22
Alignment explanation
Indices: 53722965--53723011 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
53722955 TTAGGCCTTA
53722965 TCACATATATACACTTTCACAT
1 TCACATATATACACTTTCACAT
53722987 TCACATATATACACTTTCACAT
1 TCACATATATACACTTTCACAT
53723009 TCA
1 TCA
53723012 TCACATCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (22 bp):
TCACATATATACACTTTCACAT
Found at i:53723008 original size:69 final size:69
Alignment explanation
Indices: 53722922--53723125 Score: 342
Period size: 67 Copynumber: 3.0 Consensus size: 69
53722912 CCTATCACAT
53722922 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
53722987 TCAC
66 TCAC
** *
53722991 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT--ACTGGCA-TT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
53723053 ATCAC
66 -TCAC
*
53723058 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
53723123 TCA
66 TCA
53723126 TCACATCGGC
Statistics
Matches: 124, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
66 1 0.01
67 61 0.49
69 61 0.49
70 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.33
Consensus pattern (69 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCAC
Done.