Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 198 of 210
Found at i:58086318 original size:24 final size:24
Alignment explanation
Indices: 58086286--58086331 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
58086276 ACTGCATATA
58086286 ATATTATATGTACGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
**
58086310 ATATTATATGTGTGTAATATGT
1 ATATTATATGTACGTAATATGT
58086332 GTTATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (24 bp):
ATATTATATGTACGTAATATGTAT
Found at i:58089682 original size:31 final size:31
Alignment explanation
Indices: 58089644--58089713 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
58089634 ATAGATTTAA
58089644 AAAGGAAAGAAAAAATAACTTTCATCATTAT
1 AAAGGAAAGAAAAAATAACTTTCATCATTAT
58089675 AAAGGAAAGAAAAAATAACTTTCATCATTAT
1 AAAGGAAAGAAAAAATAACTTTCATCATTAT
58089706 AAAGGAAA
1 AAAGGAAA
58089714 AGTGAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (31 bp):
AAAGGAAAGAAAAAATAACTTTCATCATTAT
Found at i:58090690 original size:11 final size:11
Alignment explanation
Indices: 58090674--58090716 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
58090664 ATATAATATT
*
58090674 ATATGTACGTA
1 ATATGTATGTA
*
58090685 ATATGTATATA
1 ATATGTATGTA
58090696 TTATATGTATGTA
1 --ATATGTATGTA
58090709 ATATGTAT
1 ATATGTAT
58090717 TATACATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (11 bp):
ATATGTATGTA
Found at i:58090701 original size:24 final size:24
Alignment explanation
Indices: 58090669--58090716 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
58090659 ACTGCATATA
58090669 ATATTATATGTACGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
*
58090693 ATATTATATGTATGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
58090717 TATACATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (24 bp):
ATATTATATGTACGTAATATGTAT
Found at i:58090719 original size:20 final size:21
Alignment explanation
Indices: 58090664--58090720 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
58090654 ATGTAACTGC
*
58090664 ATATAATATTATATGTACGTA
1 ATATGATATTATATGTACGTA
*
58090685 ATATGTATATATTATATGTATGTA
1 ATATG---ATATTATATGTACGTA
58090709 ATATG-TATTATA
1 ATATGATATTATA
58090721 CATTATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
24 20 0.65
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
ATATGATATTATATGTACGTA
Found at i:58092103 original size:77 final size:76
Alignment explanation
Indices: 58091967--58092124 Score: 289
Period size: 77 Copynumber: 2.1 Consensus size: 76
58091957 AATTAAAGAC
* *
58091967 TGGTATGGTCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
1 TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
58092032 TATGTTTGGTAG
66 TAT-TTTGGTAG
58092044 TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
1 TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
58092109 TATTTTGGTAG
66 TATTTTGGTAG
58092120 TGGTG
1 TGGTG
58092125 AAGGTTAAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
76 13 0.16
77 66 0.84
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (76 bp):
TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
TATTTTGGTAG
Found at i:58097059 original size:21 final size:23
Alignment explanation
Indices: 58097034--58097082 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
58097024 TTCAACTATT
58097034 TAATTAT-AACAAATT-AATTAA
1 TAATTATAAACAAATTAAATTAA
*
58097055 TAATT-TAAATAAATTAAATTAA
1 TAATTATAAACAAATTAAATTAA
*
58097077 TCATTA
1 TAATTA
58097083 AGTTATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATTATAAACAAATTAAATTAA
Found at i:58098540 original size:15 final size:15
Alignment explanation
Indices: 58098520--58098551 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58098510 ATGTATAAAA
58098520 AAAATGGAAGAATTT
1 AAAATGGAAGAATTT
58098535 AAAATGGAAGAATTT
1 AAAATGGAAGAATTT
58098550 AA
1 AA
58098552 TTCAATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (15 bp):
AAAATGGAAGAATTT
Found at i:58100881 original size:6 final size:6
Alignment explanation
Indices: 58100870--58100905 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
58100860 GGGAAGTTAC
58100870 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
58100906 TATAAGTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:58102434 original size:99 final size:99
Alignment explanation
Indices: 58102250--58102444 Score: 230
Period size: 99 Copynumber: 2.0 Consensus size: 99
58102240 ATGCTCCTAC
* * *
58102250 AAGATGGAGTTTATACAACTCAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTGAAACAAAT
1 AAGATGGAGTTTATACAACTAAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTCAAAAAAAT
* *
58102315 CAATTTAACAGACATATTGGAAGTAGCCTCCCAG
66 CAACTCAACAGACATATTGGAAGTAGCCTCCCAG
* *** * * *
58102349 AAGATGGAGTTTATACAGCTAAACCAGTTTACTTGGAGTGTAGGGTTAACTCACTTCAAAAAAAT
1 AAGATGGAGTTTATACAACTAAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTCAAAAAAAT
** * *
58102414 -ACACTCAATGGTCATGTTGGAAGTAGCCTCC
66 CA-ACTCAACAGACATATTGGAAGTAGCCTCC
58102445 AAGATGAGCT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
98 1 0.01
99 78 0.99
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (99 bp):
AAGATGGAGTTTATACAACTAAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTCAAAAAAAT
CAACTCAACAGACATATTGGAAGTAGCCTCCCAG
Found at i:58104684 original size:30 final size:30
Alignment explanation
Indices: 58104648--58104706 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
58104638 CATCAATCAT
*
58104648 AGAGAGAACCATCCACATTGCCAATGCCAC
1 AGAGAGAACCATCCACAATGCCAATGCCAC
* *
58104678 AGAGAGATCCATCCACAATGTCAATGCCA
1 AGAGAGAACCATCCACAATGCCAATGCCA
58104707 ACGCCAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.15
Consensus pattern (30 bp):
AGAGAGAACCATCCACAATGCCAATGCCAC
Found at i:58109623 original size:20 final size:21
Alignment explanation
Indices: 58109580--58109636 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
58109570 ATATATGAAC
*
58109580 ATTTTGGAATTTTTGAAAAAT
1 ATTTTGGAATTTTTTAAAAAT
**
58109601 ATTTT-GAATTTTTTAAATTT
1 ATTTTGGAATTTTTTAAAAAT
58109621 ATTTTGGAATTGTTTT
1 ATTTTGGAATT-TTTT
58109637 GTATTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (21 bp):
ATTTTGGAATTTTTTAAAAAT
Found at i:58112550 original size:15 final size:14
Alignment explanation
Indices: 58112520--58112553 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
58112510 AGGCGCCATG
*
58112520 AGTAAATAATTAAT
1 AGTAAATAAGTAAT
58112534 AGTAAAGTAAGTAAT
1 AGTAAA-TAAGTAAT
58112549 AGTAA
1 AGTAA
58112554 TAAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (14 bp):
AGTAAATAAGTAAT
Found at i:58114354 original size:87 final size:86
Alignment explanation
Indices: 58114175--58114813 Score: 508
Period size: 87 Copynumber: 7.3 Consensus size: 86
58114165 ACTGGATGCG
* * * * * * * * *
58114175 ATCTGCTCTACTATTGCTTAGAGAGATAAGATATACAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGCCATCTTCGACCTGCTCCACTACTGCTTAG
* ** **
58114240 GGAGATAGGATTGGTTTCTTTT
65 GGAGATAGGACTGGTGGCTTAA
* * * *
58114262 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGACCTGCTCCACTACTGCTTAG
58114327 GGAGATAGGACTGGTGGCTTAA
65 GGAGATAGGACTGGTGGCTTAA
* * * * * *
58114349 ATCTGCTTCACTACTGTTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGACCTGCTCCACTACTGCTTAG
***** **
58114414 GGAGATAGGATCTACCATCTTTG
65 GGAGATAGGA-CTGGTGGCTTAA
* * * * ** ** * *
58114437 A-CTTGTTCCTCTACTGCTTAGGGAGATAGGACTCGTGA-CTTAAATCTGCTTCACTACTGCTTA
1 ATC-TGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGACCTGCTCCACTACTGCTTA
* * * ** * **
58114500 GGAAGATAAGATTCGCCGTCTTTG
64 GGGAGATAGGACT-GGTGGCTTAA
* * ** * *
58114524 ACCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCGCTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGCCATCTTCGACCTGCTCCACTACTGCTTAG
*
58114589 GGAGATAGGACTAGTGGCTTAA
65 GGAGATAGGACTGGTGGCTTAA
* * * *
58114611 ATCTGCTCCGCTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATT-GCCATCTTCGACCTGCTCCACTACTGCTTAG
58114676 GGAGATAGGACTGGTGGCTTAA
65 GGAGATAGGACTGGTGGCTTAA
* * * * *
58114698 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATT-GCCATCTTCGACCTGCTCCACTACTGCTTAG
***** **
58114763 GGAGATAGGATCTAACATCTTTG
65 GGAGATAGGA-CTGGTGGCTTAA
*
58114786 ACCTGCTCCACTACTGCTTAGGGAGATA
1 ATCTGCTCCACTACTGCTTAGGGAGATA
58114814 GGACTGGTGG
Statistics
Matches: 444, Mismatches: 99, Indels: 17
0.79 0.18 0.03
Matches are distributed among these distances:
86 3 0.01
87 350 0.79
88 91 0.20
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (86 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATTGCCATCTTCGACCTGCTCCACTACTGCTTAGG
GAGATAGGACTGGTGGCTTAA
Found at i:58114399 original size:131 final size:130
Alignment explanation
Indices: 58114264--58114818 Score: 648
Period size: 131 Copynumber: 4.2 Consensus size: 130
58114254 TTTCTTTTGT
* * *
58114264 CTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTTAC-ATCTTTGACCTGCTCCACTACTGCTTAGGG
* * * *
58114329 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGTTTAGGAAGATAAGATTTGCCGTCTTCGA
65 AGATAGGACTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGA
*
58114394 T
130 C
* * * *
58114395 CTGCTCCACTACTGCTTAAGGAGATAGGA-TCTACCATCTTTGACTTGTTCCTCTACTGCTTAGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGACT-TA-CATCTTTGACCTGCTCCACTACTGCTTAGG
* *
58114459 GAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTTG
64 GAGATAGGACTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTTG
58114524 AC
129 AC
* *
58114526 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCGCTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTTACATCTTTGACCTGCTCCACTACTGCTTAGGG
* *
58114591 AGATAGGACTAGTGGCTTAAATCTGCTCCGCTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGA
65 AGATAGGACTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGA
58114656 C
130 C
***** ** * * *
58114657 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTTACATCTTTGACCTGCTCCACTACTGCTTAGGGA
* * *** ** * * * * ** *
58114722 GAT-GAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGA-TCTAACATCTTT
66 GATAG-GACTAG-TGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTC-GCCGTCTTT
58114785 GAC
128 GAC
58114788 CTGCTCCACTACTGCTTAGGGAGATAGGACT
1 CTGCTCCACTACTGCTTAGGGAGATAGGACT
58114819 GGTGGCTTAA
Statistics
Matches: 370, Mismatches: 47, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
129 1 0.00
130 35 0.09
131 331 0.89
132 2 0.01
133 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (130 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTTACATCTTTGACCTGCTCCACTACTGCTTAGGGA
GATAGGACTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGAC
Found at i:58114551 original size:218 final size:218
Alignment explanation
Indices: 58114175--58114903 Score: 768
Period size: 218 Copynumber: 3.3 Consensus size: 218
58114165 ACTGGATGCG
* * * ** * * *
58114175 ATCTGCTCTACTATTGCTTA-GAGAGATAAGATAT-ACAATCTTCAACCTACTCCACTGCTGCTC
1 ATCTGCTCCACTACTGCTTAGGA-AGATAAGAT-TCACCATCTTTGACCTGCTCCACTACTGCTT
* * ** *** * * * * *
58114238 AGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTT-ACAATC
64 AGGGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGA-TTCGCCATC
**** * * *
58114302 TTCGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGT
128 TTCGACCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACAGCTTAAACCTGCTCCACTACTGC
* * * **
58114366 TTAGGAAGATAAGATTTGCCGTCTTCG
193 TTAGGAAGATAAGACTAG-CGGCTTAA
* * * *
58114393 ATCTGCTCCACTACTGCTTAAGG-AGATAGGA-TCTACCATCTTTGACTTGTTCCTCTACTGCTT
1 ATCTGCTCCACTACTGCTT-AGGAAGATAAGATTC-ACCATCTTTGACCTGCTCCACTACTGCTT
*
58114456 AGGGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
64 AGGGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATCT
* * ** *
58114521 TTGACCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCGCTACTGCT
129 TCGACCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACAGCTTAAACCTGCTCCACTACTGCT
* * *
58114586 TAGGGAGATAGGACTAGTGGCTTAA
194 TAGGAAGATAAGACTAGCGGCTTAA
* * *
58114611 ATCTGCTCCGCTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATTCACCATCTTTGACCTGCTCCACTACTGCTTAG
* * *
58114676 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCATCTTC
66 GGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATCTTC
* * * **
58114741 GATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTA
131 GACCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACAGCTTAAACCTGCTCCACTACTGCTTA
* * * *
58114806 GGGAGATAGGACTGGTGGCTTAA
196 GGAAGATAAGACTAGCGGCTTAA
** * * * *
58114829 ATCTGCTTGACTACTGCTTAGGAAGATGAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATTCACCATCTTTGACCTGCTCCACTACTGCTTAG
58114894 GGAGATAGGA
66 GGAGATAGGA
58114904 TCTAACATCT
Statistics
Matches: 435, Mismatches: 68, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
216 1 0.00
217 5 0.01
218 393 0.90
219 35 0.08
220 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (218 bp):
ATCTGCTCCACTACTGCTTAGGAAGATAAGATTCACCATCTTTGACCTGCTCCACTACTGCTTAG
GGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATCTTC
GACCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACAGCTTAAACCTGCTCCACTACTGCTTA
GGAAGATAAGACTAGCGGCTTAA
Found at i:58114842 original size:87 final size:87
Alignment explanation
Indices: 58114264--58114903 Score: 443
Period size: 87 Copynumber: 7.3 Consensus size: 87
58114254 TTTCTTTTGT
* * * ** * *
58114264 CTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGAC-TGCCGTCTTAGATCTGCTCCACTACTGCTTAGGG
***** ** *
58114329 AGATAGGA-CTGGTGGCTTAAAT
65 AGATAGGATCTACCATCTTTGAC
* * * * * * *
58114351 CTGCTTCACTACTGTTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAAGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTGCCGTCTTAGATCTGCTCCACTACTGCTTAGGG
58114416 AGATAGGATCTACCATCTTTGAC
65 AGATAGGATCTACCATCTTTGAC
* * * * *
58114439 TTGTTCCTCTACTGCTTAGGGAGATAGGACT--CGTGACTTAAATCTGCTTCACTACTGCTTAGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGCCGT--CTTAGATCTGCTCCACTACTGCTTAGG
* * * *
58114502 AAGATAAGAT-TCGCCGTCTTTGAC
64 GAGATAGGATCT-ACCATCTTTGAC
** * * * *
58114526 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCGCTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTGCCGTCTTAGATCTGCTCCACTACTGCTTAGGG
**** ** *
58114591 AGATAGGA-CTAGTGGCTTAAAT
65 AGATAGGATCTACCATCTTTGAC
* * * * * *
58114613 CTGCTCCGCTACTGCTTAGGAAGATAAGATTCGCCGTCTTTGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGACT-GCCGTCTTAGATCTGCTCCACTACTGCTTAGGG
***** ** *
58114678 AGATAGGA-CTGGTGGCTTAAAT
65 AGATAGGATCTACCATCTTTGAC
* * * * * *
58114700 CTGCTTCACTACTGCTTAGGAAGAT-GAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGG
1 CTGCTCCACTACTGCTTAGGGAGATAG-GACT-GCCGTCTTAGATCTGCTCCACTACTGCTTAGG
*
58114764 GAGATAGGATCTAACATCTTTGAC
64 GAGATAGGATCTACCATCTTTGAC
** * * ** *
58114788 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTGACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGCCGTCTTAGATCTGCTCCACTACTGCTTAGGGA
* * *
58114853 GAT-GAGAT-TCGCCATCTTCGAT
66 GATAG-GATCT-ACCATCTTTGAC
58114875 CTGCTCCACTACTGCTTAGGGAGATAGGA
1 CTGCTCCACTACTGCTTAGGGAGATAGGA
58114904 TCTAACATCT
Statistics
Matches: 445, Mismatches: 93, Indels: 30
0.78 0.16 0.05
Matches are distributed among these distances:
85 3 0.01
86 4 0.01
87 343 0.77
88 92 0.21
89 1 0.00
90 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (87 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTGCCGTCTTAGATCTGCTCCACTACTGCTTAGGGA
GATAGGATCTACCATCTTTGAC
Found at i:58114855 original size:131 final size:131
Alignment explanation
Indices: 58114649--58114917 Score: 520
Period size: 131 Copynumber: 2.1 Consensus size: 131
58114639 AGATTCGCCG
58114649 TCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTG
1 TCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTG
58114714 CTTAGGAAGATGAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAAC
66 CTTAGGAAGATGAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAAC
58114779 A
131 A
*
58114780 TCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTGACTACTG
1 TCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTG
*
58114845 CTTAGGAAGATGAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAAC
66 CTTAGGAAGATGAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAAC
58114910 A
131 A
58114911 TCTTTGA
1 TCTTTGA
58114918 TCTATTCTCT
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 136 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (131 bp):
TCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTG
CTTAGGAAGATGAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAAC
A
Found at i:58117024 original size:6 final size:6
Alignment explanation
Indices: 58117013--58117047 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
58117003 TGGCCTCTCC
58117013 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
58117048 ATCCTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:58117143 original size:7 final size:7
Alignment explanation
Indices: 58117133--58117171 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
58117123 TTGATTTTGA
58117133 TTTTTCT
1 TTTTTCT
58117140 TTTTTCT
1 TTTTTCT
58117147 TTTTTCT
1 TTTTTCT
58117154 TTTTGT-T
1 TTTT-TCT
*
58117161 TTTTTAT
1 TTTTTCT
58117168 TTTT
1 TTTT
58117172 ATTTTTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (7 bp):
TTTTTCT
Found at i:58117150 original size:14 final size:14
Alignment explanation
Indices: 58117133--58117178 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
58117123 TTGATTTTGA
58117133 TTTTTCTTTTT-TCT
1 TTTTTCTTTTTGT-T
58117147 TTTTTCTTTTTGTT
1 TTTTTCTTTTTGTT
* *
58117161 TTTTTATTTTTATT
1 TTTTTCTTTTTGTT
58117175 TTTT
1 TTTT
58117179 GATTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 28 0.97
15 1 0.03
ACGTcount: A:0.04, C:0.07, G:0.02, T:0.87
Consensus pattern (14 bp):
TTTTTCTTTTTGTT
Found at i:58117183 original size:14 final size:13
Alignment explanation
Indices: 58117126--58117185 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
58117116 TTTGATCTTG
*
58117126 ATTTTGATTTTTCT
1 ATTTTTATTTTT-T
*
58117140 -TTTTTCTTTTTT
1 ATTTTTATTTTTT
* *
58117152 CTTTTTGTTTTTTT
1 ATTTTT-ATTTTTT
58117166 ATTTTTATTTTTT
1 ATTTTTATTTTTT
58117179 GATTTTT
1 -ATTTTT
58117186 TTCATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 20 0.53
14 17 0.45
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:58125187 original size:131 final size:131
Alignment explanation
Indices: 58124911--58125351 Score: 580
Period size: 131 Copynumber: 3.4 Consensus size: 131
58124901 AGACTGGATG
* * * * * ** * *
58124911 CGATCTGCTCTACTATTGCTTAGAGAGATAAGATAT-ACAATCTTCAACCTACTCCACTGCTGCT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAAC-ATCTTTGACCTGCTCCACTACTGCT
* * ** *** * * ** *
58124975 CAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGAAAGATAAGATTTACAAT
65 TAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGG-AAGATGAGATTCGCCAT
58125040 CTT
129 CTT
* **
58125043 CGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGCATCTTTGACCTGCTCCACTACTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTT
58125107 AGAGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCATC
66 AG-GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCATC
58125172 TT
130 TT
58125174 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTT
* * * *
58125239 AGGGAGATAAGACTGGTGGCTTAAATCTGCTTGACTACTGCTTAGGAAGTTGATATTCGCCATCT
66 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCATCT
58125304 T
131 T
*
58125305 CGATTTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
58125352 TCTATTCTTT
Statistics
Matches: 275, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
131 178 0.65
132 97 0.35
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (131 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTT
AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCATCT
T
Found at i:58125204 original size:87 final size:87
Alignment explanation
Indices: 58125047--58125206 Score: 234
Period size: 87 Copynumber: 1.8 Consensus size: 87
58125037 AATCTTCGAC
* * *
58125047 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGCATCTTTGACCTGCTCCACTACTGCTTAGAGG
1 CTGCTCCACTACTGCTTAGGAAGATAGGACTGCCATCTTCGACCTGCTCCACTACTGCTTAGAGG
58125112 AGATAGGACTGGTGGCTTAAAT
66 AGATAGGACTGGTGGCTTAAAT
* * *
58125134 CTGCTTCACTACTGCTTAGGAAGAT-GAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAG-
1 CTGCTCCACTACTGCTTAGGAAGATAG-GACT-GCCATCTTCGACCTGCTCCACTACTGCTTAGA
58125197 GGAGATAGGA
64 GGAGATAGGA
58125207 TCTAACATCT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
86 1 0.02
87 36 0.55
88 28 0.43
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (87 bp):
CTGCTCCACTACTGCTTAGGAAGATAGGACTGCCATCTTCGACCTGCTCCACTACTGCTTAGAGG
AGATAGGACTGGTGGCTTAAAT
Found at i:58125347 original size:44 final size:44
Alignment explanation
Indices: 58124911--58125354 Score: 289
Period size: 44 Copynumber: 10.1 Consensus size: 44
58124901 AGACTGGATG
* * * * *
58124911 CGATCTGCTCTACTATTGCTTAGAGAGATAAGATAT-ACAATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGAC-ATCTT
* * * * * ***
58124955 CAACCTACTCCACTGCTGCTCAGGGAGATAGGAT-TGGTTTCTTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGACATC-TT
* * * *
58124999 TG-TCTGCTCCACTACTGCTTAGGAAAGATAAGAT-TTACAATCTT
1 CGATCTGCTCCACTACTGCTTAGG-GAGATAGGATCTGAC-ATCTT
* *
58125043 CGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGCATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGACATCTT
* * ****
58125086 TGACCTGCTCCACTACTGCTTAGAGGAGATAGGA-CTGGTGGCTT
1 CGATCTGCTCCACTACTGCTTAG-GGAGATAGGATCTGACATCTT
** * * *
58125130 AAATCTGCTTCACTACTGCTTAGGAAGAT-GAGAT-TCGCCATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-GACATCTT
*
58125174 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGACATCTT
* * * ****
58125218 TGACCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGGTGGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGACATCTT
** ** * * * *
58125261 AAATCTGCTTGACTACTGCTTAGGAAG-T-TGATATTCGCCATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGAT-CT-GACATCTT
* *
58125305 CGATTTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGACATCTT
*
58125349 TGATCT
1 CGATCT
58125355 ATTCTTTGGG
Statistics
Matches: 302, Mismatches: 81, Indels: 34
0.72 0.19 0.08
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
43 82 0.27
44 187 0.62
45 26 0.09
46 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGACATCTT
Found at i:58132270 original size:20 final size:20
Alignment explanation
Indices: 58132245--58132282 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58132235 AAATTTTGAG
58132245 ATTTTTGAAATATATTTTTA
1 ATTTTTGAAATATATTTTTA
*
58132265 ATTTTTGAAATTTATTTT
1 ATTTTTGAAATATATTTT
58132283 GAACTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTTGAAATATATTTTTA
Found at i:58139327 original size:103 final size:104
Alignment explanation
Indices: 58139167--58139354 Score: 290
Period size: 103 Copynumber: 1.8 Consensus size: 104
58139157 TTTAAGAATG
* * *
58139167 TGTTGGGCTAAGTAACCAGGATGGGGTGTTTGGTTATCATCTTTCTTTGCGTCAAAAGGTTCAAT
1 TGTTGGGCTAAGTAACCAGGATGGGGTGCTTGGTTATCATCTCTCTTCGCGTCAAAAGGTTCAAT
58139232 ATATTATTAAGAAAAGAAAACATATATAAATTAGAAGTA
66 ATATTATTAAGAAAAGAAAACATATATAAATTAGAAGTA
* * *
58139271 TGTTGGGCTGAGTAACCAGGGT-GGGTGCTTGGTTGTCATCTCTCTTCGCG-CGAAAAGGTTCAA
1 TGTTGGGCTAAGTAACCAGGATGGGGTGCTTGGTTATCATCTCTCTTCGCGTC-AAAAGGTTCAA
*
58139334 TATATTCTTAAGAAAAGAAAA
65 TATATTATTAAGAAAAGAAAA
58139355 AAAAAGAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
102 1 0.01
103 55 0.72
104 20 0.26
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (104 bp):
TGTTGGGCTAAGTAACCAGGATGGGGTGCTTGGTTATCATCTCTCTTCGCGTCAAAAGGTTCAAT
ATATTATTAAGAAAAGAAAACATATATAAATTAGAAGTA
Found at i:58139391 original size:26 final size:25
Alignment explanation
Indices: 58139343--58139393 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
58139333 ATATATTCTT
58139343 AAGAAAAGAAAAAAAAAGAAAAAAG
1 AAGAAAAGAAAAAAAAAGAAAAAAG
* *
58139368 AAGAAGAAGGAAAAACAAGTAAAAAA
1 AAGAA-AAGAAAAAAAAAG-AAAAAA
58139394 TAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (25 bp):
AAGAAAAGAAAAAAAAAGAAAAAAG
Found at i:58144543 original size:12 final size:12
Alignment explanation
Indices: 58144526--58144550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58144516 TGATATTAAG
58144526 AACTATCATATA
1 AACTATCATATA
58144538 AACTATCATATA
1 AACTATCATATA
58144550 A
1 A
58144551 TTACACTTTA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AACTATCATATA
Found at i:58147783 original size:15 final size:16
Alignment explanation
Indices: 58147763--58147796 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
58147753 TCAATTTTTT
58147763 TTCTTTCTT-TCTTTC
1 TTCTTTCTTATCTTTC
*
58147778 TTCTTTCTTATGTTTC
1 TTCTTTCTTATCTTTC
58147794 TTC
1 TTC
58147797 CGCCATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (16 bp):
TTCTTTCTTATCTTTC
Found at i:58167326 original size:31 final size:30
Alignment explanation
Indices: 58167271--58167346 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
58167261 ACGTGAAAGG
* **
58167271 CTTAATTGATTTATT-ATTATTTTAGGAGGT
1 CTTAATTGATTT-TTAAGTATTTTAGGAGAA
58167301 CTTAATTGACTTTTTAAGTATTTTAGGAGAA
1 CTTAATTGA-TTTTTAAGTATTTTAGGAGAA
58167332 CTTAATTGATTTTTA
1 CTTAATTGATTTTTA
58167347 GGGACTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
CTTAATTGATTTTTAAGTATTTTAGGAGAA
Found at i:58167978 original size:28 final size:27
Alignment explanation
Indices: 58167947--58168016 Score: 63
Period size: 29 Copynumber: 2.4 Consensus size: 27
58167937 ATCAATAAAA
58167947 TTTTATAACATTTA-GCAATATTT-ATAAT
1 TTTTATAA-ATTTATG--ATATTTAATAAT
*
58167975 TTTTTTAAAATTTTATGATATTTAATAAT
1 TTTTAT-AAA-TTTATGATATTTAATAAT
58168004 TTTCTATAAATTT
1 TTT-TATAAATTT
58168017 TATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
28 15 0.43
29 17 0.49
30 3 0.09
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (27 bp):
TTTTATAAATTTATGATATTTAATAAT
Found at i:58168017 original size:29 final size:30
Alignment explanation
Indices: 58167963--58168037 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
58167953 AACATTTAGC
*
58167963 AATATTT-ATAATTTT-TTTAAAATTTTAT
1 AATATTTAATAATTTTCTATAAAATTTTAT
*
58167991 GATATTTAATAATTTTCTAT-AAATTTTAT
1 AATATTTAATAATTTTCTATAAAATTTTAT
58168020 AATAAATTTAAT-ATTTTC
1 AAT--ATTTAATAATTTTC
58168038 AATTTAGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.15
29 19 0.47
30 8 0.20
31 7 0.17
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (30 bp):
AATATTTAATAATTTTCTATAAAATTTTAT
Found at i:58168426 original size:36 final size:36
Alignment explanation
Indices: 58168386--58168469 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 36
58168376 ATTTTGTCCA
58168386 GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
1 GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
*
58168422 GGCCCGGCCCGGAAAAAATTTCTTAGGCCCGAGCCC
1 GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
58168458 GGCCCGGCCCGA
1 GGCCCGGCCCGA
58168470 TCCGTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (36 bp):
GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
Found at i:58175916 original size:21 final size:20
Alignment explanation
Indices: 58175884--58175924 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
58175874 TGGCAGATAC
*
58175884 AAATTTCAAAAATTTATAAA
1 AAATTTCAAAAATATATAAA
58175904 AAATTTACAAAAATATATAAA
1 AAATTT-CAAAAATATATAAA
58175925 TTAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTTCAAAAATATATAAA
Found at i:58183130 original size:2 final size:2
Alignment explanation
Indices: 58183119--58183148 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58183109 TAGAATCATA
58183119 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58183149 ACTTAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58187622 original size:17 final size:18
Alignment explanation
Indices: 58187600--58187634 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
58187590 TGTAAGTAAT
58187600 TTAAAATT-TTCAATTAA
1 TTAAAATTATTCAATTAA
*
58187617 TTAAAATTATTTAATTAA
1 TTAAAATTATTCAATTAA
58187635 AAACCTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAATTATTCAATTAA
Found at i:58189177 original size:17 final size:17
Alignment explanation
Indices: 58189157--58189193 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
58189147 GTATTTTAAT
*
58189157 TTAAAAATTTAACAATA
1 TTAAAAATTTAAAAATA
*
58189174 TTAAATATTTAAAAATA
1 TTAAAAATTTAAAAATA
58189191 TTA
1 TTA
58189194 TGAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATTTAAAAATA
Found at i:58189709 original size:24 final size:24
Alignment explanation
Indices: 58189654--58189702 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
58189644 TGCCGGGGAT
*
58189654 TATGTTGTCCCTCCACCAGTACCA
1 TATGTTGACCCTCCACCAGTACCA
58189678 TATGTTGACCCTCCACCAGTACCA
1 TATGTTGACCCTCCACCAGTACCA
58189702 T
1 T
58189703 TGATTGATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.12, T:0.29
Consensus pattern (24 bp):
TATGTTGACCCTCCACCAGTACCA
Found at i:58191595 original size:61 final size:61
Alignment explanation
Indices: 58191424--58191613 Score: 299
Period size: 61 Copynumber: 3.0 Consensus size: 61
58191414 GAACCCTCCA
58191424 AAAAAACACATATATATAAATTGTGAAAATAATGTGGGAATTTGCTTGTTATGATTTGTGT
1 AAAAAACACATATATATAAATTGTGAAAATAATGTGGGAATTTGCTTGTTATGATTTGTGT
* *
58191485 AAAAAACACATATATATATATATAAATTGTGAAAATATTGTGGGGATTTGCTTGTTATGATTTGT
1 AAAAAACAC------ATATATATAAATTGTGAAAATAATGTGGGAATTTGCTTGTTATGATTTGT
58191550 GT
60 GT
*
58191552 AAAAAACACATATATATAAATTGTGAAAATAATGTGGGAATTTGGTTGTTATGATTTGTGT
1 AAAAAACACATATATATAAATTGTGAAAATAATGTGGGAATTTGCTTGTTATGATTTGTGT
58191613 A
1 A
58191614 TGTTTAACTG
Statistics
Matches: 118, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
61 59 0.50
67 59 0.50
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.38
Consensus pattern (61 bp):
AAAAAACACATATATATAAATTGTGAAAATAATGTGGGAATTTGCTTGTTATGATTTGTGT
Found at i:58194043 original size:7 final size:7
Alignment explanation
Indices: 58194031--58194058 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
58194021 AGACGCATCA
58194031 TAAGAAG
1 TAAGAAG
58194038 TAAGAAG
1 TAAGAAG
58194045 TAAGAAG
1 TAAGAAG
58194052 TAAGAAG
1 TAAGAAG
58194059 AAAAGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
TAAGAAG
Found at i:58197396 original size:11 final size:11
Alignment explanation
Indices: 58197363--58197397 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
58197353 TGCATGATAT
*
58197363 TGAACATTATA
1 TGAAAATTATA
58197374 TGAAAATGTATA
1 TGAAAAT-TATA
58197386 TGAAAATTATA
1 TGAAAATTATA
58197397 T
1 T
58197398 ATCTTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (11 bp):
TGAAAATTATA
Found at i:58199853 original size:32 final size:32
Alignment explanation
Indices: 58199807--58199888 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
58199797 TGTCAATTAT
*
58199807 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAACTTAAAACATAATAAA
* * * *
58199839 TTCAATATCTAACAAATTTAAGACATAATAAT
1 TTCAATATCCAACAAACTTAAAACATAATAAA
*
58199871 TTCAAAATCCAACAAACT
1 TTCAATATCCAACAAACT
58199889 AATTTCTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAACTTAAAACATAATAAA
Found at i:58208719 original size:2 final size:2
Alignment explanation
Indices: 58208714--58208756 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
58208704 AAATGAGTTG
58208714 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
58208756 A
1 A
58208757 AACACTTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58214616 original size:9 final size:9
Alignment explanation
Indices: 58214583--58214621 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
58214573 AGTAAATTTG
58214583 ATTTTTAAA
1 ATTTTTAAA
58214592 A-TTTTAAA
1 ATTTTTAAA
*
58214600 ATTGTTAAA
1 ATTTTTAAA
58214609 ATTTTTAATA
1 ATTTTTAA-A
58214619 ATT
1 ATT
58214622 AAAAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 8 0.31
9 14 0.54
10 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:58214692 original size:29 final size:30
Alignment explanation
Indices: 58214650--58214707 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
58214640 ATCTTTTCTA
*
58214650 TTTTAGTAATTTTTAATTTTAAATAATTTT
1 TTTTAGTAATTTTTAATTTTAAAAAATTTT
* *
58214680 TTTTA-TATTTTTTCATTTTAAAAAATTT
1 TTTTAGTAATTTTTAATTTTAAAAAATTT
58214708 AGGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTAGTAATTTTTAATTTTAAAAAATTTT
Found at i:58227656 original size:20 final size:21
Alignment explanation
Indices: 58227623--58227665 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
58227613 GATATTCTTT
*
58227623 TCTTCTTCCTTTTTTCTTCTC
1 TCTTCTTCCCTTTTTCTTCTC
*
58227644 TCTT-TTCCCTTTTTCTTTTC
1 TCTTCTTCCCTTTTTCTTCTC
58227664 TC
1 TC
58227666 AATTTCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TCTTCTTCCCTTTTTCTTCTC
Found at i:58232626 original size:21 final size:22
Alignment explanation
Indices: 58232600--58232646 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
58232590 CTCTGCTCAA
*
58232600 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
58232621 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
58232643 ACTC
1 ACTC
58232647 ACTCATTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:58240023 original size:23 final size:23
Alignment explanation
Indices: 58239995--58240048 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
58239985 TCTCCTTATG
* * *
58239995 CTTCTTTTCTTATTTTTTTTCTT
1 CTTCTTTTCTTATTTCTCTTCAT
* *
58240018 CTTCTTCTCTTCTTTCTCTTCAT
1 CTTCTTTTCTTATTTCTCTTCAT
58240041 CTTCTTTT
1 CTTCTTTT
58240049 ACCACCTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (23 bp):
CTTCTTTTCTTATTTCTCTTCAT
Found at i:58252806 original size:18 final size:18
Alignment explanation
Indices: 58252785--58252822 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
58252775 CCAAAAGGAT
58252785 CTGTGAGTGTCGAAGCAC
1 CTGTGAGTGTCGAAGCAC
*
58252803 CTGTGAGTGTTGAAGCAC
1 CTGTGAGTGTCGAAGCAC
58252821 CT
1 CT
58252823 ACAGTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (18 bp):
CTGTGAGTGTCGAAGCAC
Found at i:58253000 original size:18 final size:18
Alignment explanation
Indices: 58252986--58253020 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58252976 CCAAAAGGAG
58252986 CTGCGAGTGTCAAAGCAA
1 CTGCGAGTGTCAAAGCAA
* *
58253004 CTGTGAGTGTCGAAGCA
1 CTGCGAGTGTCAAAGCA
58253021 CCTACAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (18 bp):
CTGCGAGTGTCAAAGCAA
Found at i:58253010 original size:201 final size:198
Alignment explanation
Indices: 58252664--58253178 Score: 746
Period size: 201 Copynumber: 2.6 Consensus size: 198
58252654 GAGTGTTGAG
58252664 GCACCTACGGTTAATGAAGTTGATGATGGTGGCTCAAGCGTTACCAGTGGTAAGTTGAGGAGAAG
1 GCACCTACGGTTAATGAAGTTGAT-A-GGTGGCTCAAGCGTTA-CAGTGGTAAGTTGAGGAGAAG
* * *
58252729 GACATGCTATGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGATCTGTGAGTG
63 GACATGCTACGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGAGCTGCGAGTG
* * * * * *
58252794 TCGAAGCACCTGTGAGTGTTGAAGCACCTACAGTTAATGAAGTTGGTAACAGTGGTTCGATGGTT
128 TCAAAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTT
58252859 AATGAA
193 AATGAA
* * *
58252865 GCACCTACAGCTAATGAAGTTGATAACGGTGGCTCAAGCATTACTAGTGGTAAGTTGAGGAGAAG
1 GCACCTACGGTTAATGAAGTTGAT-A-GGTGGCTCAAGCGTTAC-AGTGGTAAGTTGAGGAGAAG
* *
58252930 GACATGCTACGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGTCCAAAAGGAGCTGCGAGTG
63 GACATGCTACGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGAGCTGCGAGTG
58252995 TCAAAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTT
128 TCAAAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTT
58253060 AATGAA
193 AATGAA
* * * * * *
58253066 GCACCTACGGTTAACGAAGTTGCT-GATGGCTC-GGCTGTTAGCAGTGGGAAATTGAGGAGAAGG
1 GCACCTACGGTTAATGAAGTTGATAGGTGGCTCAAGC-GTTA-CAGTGGTAAGTTGAGGAGAAGG
* *
58253129 ACATGCTACGAGTGCGGACAAAAGGGTCATATCTCTTCTGCTTGCCCAAA
64 ACATGCTACGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAA
58253179 TAAGAAATCT
Statistics
Matches: 282, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
197 2 0.01
198 75 0.27
199 1 0.00
200 1 0.00
201 203 0.72
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (198 bp):
GCACCTACGGTTAATGAAGTTGATAGGTGGCTCAAGCGTTACAGTGGTAAGTTGAGGAGAAGGAC
ATGCTACGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGAGCTGCGAGTGTCA
AAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTTAAT
GAA
Found at i:58254073 original size:20 final size:20
Alignment explanation
Indices: 58254050--58254093 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
58254040 AATTTTAGTT
58254050 TTTTAGAGGAAAA-CTTGGAA
1 TTTTAGAGGAAAAGCTT-GAA
58254070 TTTTAGAGGAAAAGCTTGAA
1 TTTTAGAGGAAAAGCTTGAA
58254090 TTTT
1 TTTT
58254094 TATTGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTTAGAGGAAAAGCTTGAA
Found at i:58259036 original size:15 final size:15
Alignment explanation
Indices: 58259016--58259045 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58259006 TTCCGAAGAA
*
58259016 GGAAAGAGGCTAAAC
1 GGAAAGAAGCTAAAC
58259031 GGAAAGAAGCTAAAC
1 GGAAAGAAGCTAAAC
58259046 ATTTCAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.30, T:0.07
Consensus pattern (15 bp):
GGAAAGAAGCTAAAC
Found at i:58260116 original size:36 final size:36
Alignment explanation
Indices: 58260076--58260206 Score: 147
Period size: 36 Copynumber: 3.6 Consensus size: 36
58260066 AATAGAAGTG
*
58260076 ATAATTACAAATTTAAAAATAAATAGAATTTAAATT
1 ATAATTATAAATTTAAAAATAAATAGAATTTAAATT
* * * * *
58260112 ATAATTATTAA-TTAAAAATTTGAAATAAAATTGAAGTG
1 ATAATTATAAATTTAAAAA--T-AAATAGAATTTAAATT
*
58260150 ATAATTATAGATTTAAAAATAAATAGAATTTAAATT
1 ATAATTATAAATTTAAAAATAAATAGAATTTAAATT
* *
58260186 ATAATTATTAATTAAAAAATA
1 ATAATTATAAATTTAAAAATA
58260207 CATGTTAATT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
35 7 0.09
36 39 0.51
37 2 0.03
38 21 0.28
39 7 0.09
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (36 bp):
ATAATTATAAATTTAAAAATAAATAGAATTTAAATT
Found at i:58260138 original size:74 final size:74
Alignment explanation
Indices: 58260010--58260203 Score: 289
Period size: 74 Copynumber: 2.6 Consensus size: 74
58260000 TTAAATTCAC
* * * *
58260010 ATTTAAAAATAATTATAATGTTTAATTTAGAATTATTAATTAAAAAGTTAAAATAAAATAGAAGT
1 ATTTAAAAATAAATAGAA--TTTAAATTATAATTATTAATTAAAAAGTTAAAATAAAATAGAAGT
58260075 GATAATTACAA
64 GATAATTACAA
* * *
58260086 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAATTTGAAATAAAATTGAAGTGA
1 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAAGTTAAAATAAAATAGAAGTGA
* *
58260151 TAATTATAG
66 TAATTACAA
58260160 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAA
1 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAA
58260204 ATACATGTTA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
74 93 0.85
76 16 0.15
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (74 bp):
ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAAGTTAAAATAAAATAGAAGTGA
TAATTACAA
Found at i:58265414 original size:28 final size:28
Alignment explanation
Indices: 58265372--58265446 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
58265362 GAAAAAATTT
* **
58265372 TAAAAAATTTAAGAATTGAGAATTTTGAA
1 TAAAAAA-TAAAGAATTGAGAATTGAGAA
*
58265401 TAAAAAATAAAGAATTGACAATTGAGAA
1 TAAAAAATAAAGAATTGAGAATTGAGAA
58265429 T-AAAAA-AAA-AATTGAGAA
1 TAAAAAATAAAGAATTGAGAA
58265447 CTAAAATGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 8 0.20
26 3 0.07
27 5 0.12
28 18 0.44
29 7 0.17
ACGTcount: A:0.60, C:0.01, G:0.13, T:0.25
Consensus pattern (28 bp):
TAAAAAATAAAGAATTGAGAATTGAGAA
Found at i:58280381 original size:23 final size:22
Alignment explanation
Indices: 58280341--58280384 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
58280331 TAAAAAATAT
58280341 ATATTTATATTATATTATTTTA
1 ATATTTATATTATATTATTTTA
* *
58280363 ATATTTAATATTTTTTTATTTT
1 ATATTT-ATATTATATTATTTT
58280385 TTGAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
ATATTTATATTATATTATTTTA
Found at i:58294562 original size:31 final size:30
Alignment explanation
Indices: 58294495--58294563 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
58294485 GCGACAACGT
**
58294495 AAGTGACTAAAATGTAACATTTCAAACATA
1 AAGTGACTAAAATGTAACATAGCAAACATA
*
58294525 AA-TGACTAAAATGTAACCTGAAGCAAACA-A
1 AAGTGACTAAAATGTAACAT--AGCAAACATA
58294555 AAGTGACTA
1 AAGTGACTA
58294564 TTTTTGTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 16 0.48
30 5 0.15
31 12 0.36
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (30 bp):
AAGTGACTAAAATGTAACATAGCAAACATA
Found at i:58299607 original size:5 final size:5
Alignment explanation
Indices: 58299597--58299630 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
58299587 GCATGCTTGG
58299597 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
58299631 CCCAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:58301190 original size:16 final size:16
Alignment explanation
Indices: 58301171--58301201 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58301161 TATTTTAGAG
58301171 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
58301187 CATATATATTTGAAA
1 CATATAAATTTGAAA
58301202 ACTCTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:58303746 original size:19 final size:19
Alignment explanation
Indices: 58303724--58303762 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
58303714 GAAGCTCATC
*
58303724 TTTCGAATTAAACCAAGTT
1 TTTCGAAATAAACCAAGTT
*
58303743 TTTCGAAATAAACCGAGTT
1 TTTCGAAATAAACCAAGTT
58303762 T
1 T
58303763 AGACAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
TTTCGAAATAAACCAAGTT
Found at i:58307182 original size:14 final size:15
Alignment explanation
Indices: 58307157--58307185 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58307147 GCAAAATTAA
58307157 TAACACAATTTAACT
1 TAACACAATTTAACT
58307172 TAACA-AATTTAACT
1 TAACACAATTTAACT
58307186 ATTACCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (15 bp):
TAACACAATTTAACT
Found at i:58309868 original size:33 final size:33
Alignment explanation
Indices: 58309841--58309920 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
58309831 TCCTCTTCAT
* *
58309841 TAGAGTCTCCTTCTTCCACTGGATCCTCCCTAC
1 TAGAGTCTCCTTCTTCCACTGAATCCTCTCTAC
* * *
58309874 TAGAGTCTCATTCTTTCATTGAATCCTCTCTAC
1 TAGAGTCTCCTTCTTCCACTGAATCCTCTCTAC
58309907 TAGAGTCTCCTTCT
1 TAGAGTCTCCTTCT
58309921 AGCATAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (33 bp):
TAGAGTCTCCTTCTTCCACTGAATCCTCTCTAC
Found at i:58322440 original size:37 final size:36
Alignment explanation
Indices: 58322378--58322455 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
58322368 TATTCTGATT
*
58322378 ATATTTAAAAAATAATTTAAATATTTAATA-TAGTAA
1 ATATTTAAAAAATAACTTAAATATTTAATAGT-GTAA
*
58322414 ATATTTAAAATATGAACTTAAATATTTAATAGTGTAA
1 ATATTTAAAAAAT-AACTTAAATATTTAATAGTGTAA
58322451 ATATT
1 ATATT
58322456 AAGAGAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 12 0.32
37 25 0.66
38 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (36 bp):
ATATTTAAAAAATAACTTAAATATTTAATAGTGTAA
Found at i:58328207 original size:19 final size:19
Alignment explanation
Indices: 58328164--58328247 Score: 80
Period size: 19 Copynumber: 4.1 Consensus size: 19
58328154 ATTACAAAAC
58328164 AATTCAAAATAATTTTTCAAA
1 AATTCAAAATAATTTTT--AA
*
58328185 AATTTAAAATAATTTTTAA
1 AATTCAAAATAATTTTTAA
*
58328204 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TTAA
58328223 AATTCCAAAACTTATATTTTTAA
1 AATT-CAAAA--TA-ATTTTTAA
58328246 AA
1 AA
58328248 AATTATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.08
19 18 0.34
20 5 0.09
21 16 0.30
22 1 0.02
23 5 0.09
24 4 0.08
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTCAAAATAATTTTTAA
Found at i:58334322 original size:57 final size:57
Alignment explanation
Indices: 58334232--58334345 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
58334222 AGAAGAGAAC
58334232 AGAGAGCACAGAACAATGAAGCAAGATGCAAGAAATATTTTTACTTGCTCACAAATG
1 AGAGAGCACAGAACAATGAAGCAAGATGCAAGAAATATTTTTACTTGCTCACAAATG
*
58334289 AGAGAGCACAGAACAATGAAGCAAGATGTAAGAAATATTTTTACTTGCTCACAAATG
1 AGAGAGCACAGAACAATGAAGCAAGATGCAAGAAATATTTTTACTTGCTCACAAATG
58334346 TGCAGCAAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (57 bp):
AGAGAGCACAGAACAATGAAGCAAGATGCAAGAAATATTTTTACTTGCTCACAAATG
Found at i:58335083 original size:16 final size:16
Alignment explanation
Indices: 58335064--58335096 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58335054 CTTGCAGTTC
58335064 GACAGGCTCACACTTT
1 GACAGGCTCACACTTT
58335080 GACAGGCTCACACTTT
1 GACAGGCTCACACTTT
58335096 G
1 G
58335097 CTTATTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (16 bp):
GACAGGCTCACACTTT
Found at i:58341359 original size:121 final size:121
Alignment explanation
Indices: 58341145--58341375 Score: 453
Period size: 121 Copynumber: 1.9 Consensus size: 121
58341135 CAACTCAACC
*
58341145 CTTTGATTTAATAACCCTTCGTAGGCTGCATTCTTCACACCAATCACTCCATCCTCAATCAAAGT
1 CTTTGATTTAATAACCCTTCGTAGGCTACATTCTTCACACCAATCACTCCATCCTCAATCAAAGT
58341210 GCTCATAATCAATAACACCCCTTCACCTCCTTGACCAATCAAAGTGCTCATAATCA
66 GCTCATAATCAATAACACCCCTTCACCTCCTTGACCAATCAAAGTGCTCATAATCA
58341266 CTTTGATTTAATAACCCTTCGTAGGCTACATTCTTCACACCAATCACTCCATCCTCAATCAAAGT
1 CTTTGATTTAATAACCCTTCGTAGGCTACATTCTTCACACCAATCACTCCATCCTCAATCAAAGT
58341331 GCTCATAATCAATAACACCCCTTCACCTCCTTGACCAATCAAAGT
66 GCTCATAATCAATAACACCCCTTCACCTCCTTGACCAATCAAAGT
58341376 CTTCATGGCT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.29
Consensus pattern (121 bp):
CTTTGATTTAATAACCCTTCGTAGGCTACATTCTTCACACCAATCACTCCATCCTCAATCAAAGT
GCTCATAATCAATAACACCCCTTCACCTCCTTGACCAATCAAAGTGCTCATAATCA
Found at i:58346740 original size:15 final size:15
Alignment explanation
Indices: 58346720--58346750 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58346710 TCTGGTCACC
*
58346720 TGTTTGAAAATTTGT
1 TGTTTGAAAACTTGT
58346735 TGTTTGAAAACTTGT
1 TGTTTGAAAACTTGT
58346750 T
1 T
58346751 TGAAGACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (15 bp):
TGTTTGAAAACTTGT
Found at i:58357704 original size:3 final size:3
Alignment explanation
Indices: 58357696--58357745 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
58357686 GAAAGAAAGA
58357696 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58357744 AA
1 AA
58357746 CGTGAACTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58358302 original size:3 final size:3
Alignment explanation
Indices: 58358277--58358342 Score: 105
Period size: 3 Copynumber: 21.3 Consensus size: 3
58358267 AATTTACAAG
*
58358277 ATT ATGT ATT ATGT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58358324 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
58358343 CGTGTCACTC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:58359099 original size:36 final size:36
Alignment explanation
Indices: 58359052--58359122 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
58359042 ACATAGACAA
*
58359052 AAGCGTTAGTCCCGTAATGCGGAGAAACGATGAATT
1 AAGCGTCAGTCCCGTAATGCGGAGAAACGATGAATT
58359088 AAGCGTCAGTCCCGTAATGCGGAGAAACGATGAAT
1 AAGCGTCAGTCCCGTAATGCGGAGAAACGATGAAT
58359123 ACTCACTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (36 bp):
AAGCGTCAGTCCCGTAATGCGGAGAAACGATGAATT
Found at i:58366223 original size:18 final size:18
Alignment explanation
Indices: 58366186--58366228 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
58366176 GAAAACATCA
* *
58366186 TTCAACCCAAACAATGAT
1 TTCAAACCAAACAATAAT
*
58366204 TTCAAACCAAACATTAAT
1 TTCAAACCAAACAATAAT
*
58366222 TTTAAAC
1 TTCAAAC
58366229 TAGGATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (18 bp):
TTCAAACCAAACAATAAT
Found at i:58367388 original size:3 final size:3
Alignment explanation
Indices: 58367380--58367411 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58367370 ATAAAGAAAG
58367380 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58367412 GAGAATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58371646 original size:15 final size:16
Alignment explanation
Indices: 58371626--58371658 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
58371616 GCAACCCAAA
*
58371626 TTTATTTTGTTT-TAT
1 TTTATTTTATTTATAT
58371641 TTTATTTTATTTATAT
1 TTTATTTTATTTATAT
58371657 TT
1 TT
58371659 ATAGTTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTATTTTATTTATAT
Found at i:58373650 original size:3 final size:3
Alignment explanation
Indices: 58373642--58373727 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
58373632 CAATATGTCA
58373642 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58373690 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
58373728 ACTTTACATT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:58375905 original size:3 final size:3
Alignment explanation
Indices: 58375897--58375922 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58375887 AGAAAGAAAG
58375897 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
58375923 ATAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58377797 original size:2 final size:2
Alignment explanation
Indices: 58377790--58377852 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
58377780 CAACTCTAAT
58377790 TA TA TA 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 TA TA TA
58377832 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
58377853 GTCANNNNNN
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58379135 original size:21 final size:21
Alignment explanation
Indices: 58379111--58379153 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58379101 GTTGATGTTC
* *
58379111 TATTTTAATTTTTAATTTTTT
1 TATTTTAATTATTAAATTTTT
*
58379132 TATTTTAGTTATTAAATTTTT
1 TATTTTAATTATTAAATTTTT
58379153 T
1 T
58379154 GAAATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TATTTTAATTATTAAATTTTT
Found at i:58379152 original size:15 final size:15
Alignment explanation
Indices: 58379134--58379178 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
58379124 AATTTTTTTA
*
58379134 TTTTAGTTATTAAAT
1 TTTTTGTTATTAAAT
**
58379149 TTTTTGAAATTAAAT
1 TTTTTGTTATTAAAT
*
58379164 TTTTTGTTATCAAAT
1 TTTTTGTTATTAAAT
58379179 GTTAACAGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (15 bp):
TTTTTGTTATTAAAT
Found at i:58380810 original size:18 final size:19
Alignment explanation
Indices: 58380787--58380824 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
58380777 CATATGGATT
58380787 TAAAATAAAA-TTTAAAAA
1 TAAAATAAAATTTTAAAAA
58380805 TAAAATAAAATTTTAAAAA
1 TAAAATAAAATTTTAAAAA
58380824 T
1 T
58380825 CCAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATAAAATTTTAAAAA
Found at i:58380927 original size:16 final size:16
Alignment explanation
Indices: 58380896--58380933 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
58380886 ATTTAAAGGA
58380896 TATTTTTCTATTAA-T
1 TATTTTTCTATTAATT
58380911 TATTTTTCTATTAAATT
1 TATTTTTCTATT-AATT
58380928 TATTTT
1 TATTTT
58380934 ACTTTATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTCTATTAATT
Found at i:58384087 original size:2 final size:2
Alignment explanation
Indices: 58384080--58384118 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
58384070 TCTATCTTAA
58384080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58384119 ACCTATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58393681 original size:13 final size:13
Alignment explanation
Indices: 58393663--58393699 Score: 67
Period size: 12 Copynumber: 2.9 Consensus size: 13
58393653 CTATTTAGAA
58393663 TCAATTAAAATAT
1 TCAATTAAAATAT
58393676 TCAATT-AAATAT
1 TCAATTAAAATAT
58393688 TCAATTAAAATA
1 TCAATTAAAATA
58393700 AATTAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TCAATTAAAATAT
Found at i:58396412 original size:3 final size:3
Alignment explanation
Indices: 58396404--58396439 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
58396394 TGTCATTCTC
58396404 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58396440 GTGGATAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:58398300 original size:18 final size:19
Alignment explanation
Indices: 58398277--58398314 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
58398267 CTGATGGATT
58398277 TAAAATAAAA-TTTAAAAA
1 TAAAATAAAATTTTAAAAA
58398295 TAAAATAAAATTTTAAAAA
1 TAAAATAAAATTTTAAAAA
58398314 T
1 T
58398315 CCAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATAAAATTTTAAAAA
Found at i:58398527 original size:4 final size:4
Alignment explanation
Indices: 58398518--58398551 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
58398508 TAAAAATATA
58398518 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
58398552 GAGACCCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:58400792 original size:19 final size:19
Alignment explanation
Indices: 58400768--58400804 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58400758 TATCATTAAT
*
58400768 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
58400787 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
58400805 TTAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:58405747 original size:14 final size:14
Alignment explanation
Indices: 58405728--58405762 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
58405718 CTACAGAATA
*
58405728 AAACTAGTGAACTC
1 AAACTACTGAACTC
58405742 AAACTACTGAACTC
1 AAACTACTGAACTC
58405756 AAACTAC
1 AAACTAC
58405763 GCTAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.20
Consensus pattern (14 bp):
AAACTACTGAACTC
Found at i:58406042 original size:25 final size:24
Alignment explanation
Indices: 58405986--58406042 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
58405976 TATTGAATAT
*
58405986 TATTTTA-TTTAATAAAATATAAT
1 TATTTTATTTTAATAAAATATAAA
* * *
58406009 TACTATATTTTATATAAAATTTAAA
1 TATTTTATTTTA-ATAAAATATAAA
58406034 TATTTTATT
1 TATTTTATT
58406043 GTTTGTTAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 5 0.19
24 4 0.15
25 17 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTTATTTTAATAAAATATAAA
Found at i:58409142 original size:25 final size:24
Alignment explanation
Indices: 58409088--58409142 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
58409078 GTAATATTAT
*
58409088 TTTTA-TTTAATAAAATATAATTA
1 TTTTATTTTAATAAAATATAAATA
* * *
58409111 ATATATTTTATATAAAATTTAAATA
1 TTTTATTTTA-ATAAAATATAAATA
58409136 TTTTATT
1 TTTTATT
58409143 GAAATATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.12
24 4 0.17
25 17 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATTTTAATAAAATATAAATA
Found at i:58412077 original size:13 final size:14
Alignment explanation
Indices: 58412051--58412082 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
58412041 TAAAAGAACA
58412051 AAATATATATATAT
1 AAATATATATATAT
58412065 AAATATA-ATATAT
1 AAATATATATATAT
58412078 AAATA
1 AAATA
58412083 AACTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:58412222 original size:2 final size:2
Alignment explanation
Indices: 58412215--58412261 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
58412205 AAAGCTTAGA
58412215 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
58412257 AT AT A
1 AT AT A
58412262 ACTACTACTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58412745 original size:2 final size:2
Alignment explanation
Indices: 58412659--58412731 Score: 101
Period size: 2 Copynumber: 34.0 Consensus size: 2
58412649 NNNNNNNNAC
58412659 TA TA TA TA TA TA TA CTA CTA CTA TA CTA GTA 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 TA TA
58412704 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
58412732 AACATGCCTA
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
2 56 0.82
3 12 0.18
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58413699 original size:16 final size:17
Alignment explanation
Indices: 58413678--58413713 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
58413668 TTTTTTGTTT
58413678 TTTGGGC-TAGGTTTAG
1 TTTGGGCTTAGGTTTAG
58413694 TTTGGGCTTAGGTTTAG
1 TTTGGGCTTAGGTTTAG
58413711 TTT
1 TTT
58413714 ATTGGGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.11, C:0.06, G:0.33, T:0.50
Consensus pattern (17 bp):
TTTGGGCTTAGGTTTAG
Found at i:58413947 original size:24 final size:23
Alignment explanation
Indices: 58413920--58413969 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
58413910 ACATATCGAA
58413920 GGTCTGCTACTCTAGCACGTCTTT
1 GGTCTGCTACTCTAGCACGT-TTT
* *
58413944 GGTCTGCTGCTCTAGCATGTTTT
1 GGTCTGCTACTCTAGCACGTTTT
58413967 GGT
1 GGT
58413970 TTTTTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.10, C:0.24, G:0.26, T:0.40
Consensus pattern (23 bp):
GGTCTGCTACTCTAGCACGTTTT
Found at i:58416716 original size:18 final size:18
Alignment explanation
Indices: 58416674--58416716 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
58416664 AAAAGTATCA
58416674 TTAAACCCAAACAATTATT
1 TTAAA-CCAAACAATTATT
*
58416693 TCAAACCAAAC-ATTAATT
1 TTAAACCAAACAATT-ATT
58416711 TTAAAC
1 TTAAAC
58416717 TAGGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 14 0.67
19 4 0.19
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAACCAAACAATTATT
Found at i:58417814 original size:56 final size:56
Alignment explanation
Indices: 58417728--58417856 Score: 240
Period size: 56 Copynumber: 2.3 Consensus size: 56
58417718 ACTTATTCAC
*
58417728 GGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTCT
1 GGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTCCT
58417784 GGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTCCT
1 GGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTCCT
*
58417840 GGCACAAGCAACTTATG
1 GGCACAAGGAACTTATG
58417857 GGATTCGTCC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (56 bp):
GGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTCCT
Found at i:58418195 original size:65 final size:65
Alignment explanation
Indices: 58418117--58418247 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
58418107 TTTAAGATAG
58418117 TACCGGTAATGTGTCAAGTGATATCAATTTAAATTTTTAAAAAAAGTTGTTTGAATTAATTTGAT
1 TACCGGTAATGTGTCAAGTGATATCAATTTAAATTTTTAAAAAAAGTTGTTTGAATTAATTTGAT
58418182 TACCGGTAATGTGTCAAGTGATATCAATTTAAATTTTTAAAAAAAGTTGTTTGAATTAATTTGAT
1 TACCGGTAATGTGTCAAGTGATATCAATTTAAATTTTTAAAAAAAGTTGTTTGAATTAATTTGAT
58418247 T
1 T
58418248 TCGTTCGGTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (65 bp):
TACCGGTAATGTGTCAAGTGATATCAATTTAAATTTTTAAAAAAAGTTGTTTGAATTAATTTGAT
Found at i:58419799 original size:29 final size:30
Alignment explanation
Indices: 58419756--58419814 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
58419746 GAATTGGATC
* *
58419756 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
*
58419786 AAATC-AAAGTTCATGTATACAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
58419815 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:58419833 original size:31 final size:29
Alignment explanation
Indices: 58419766--58419835 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
58419756 AAATCAAAAT
* *
58419766 TTCATGTATAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTACACAAAACCAAAG
*
58419795 TTCATGTATACAATTACACATTAAACCATAA-
1 TTCATGTATAAAATTACACA--AAACCA-AAG
58419826 TTCATGTATA
1 TTCATGTATA
58419836 GTTTTAGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.51
31 15 0.43
32 2 0.06
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (29 bp):
TTCATGTATAAAATTACACAAAACCAAAG
Found at i:58420442 original size:14 final size:13
Alignment explanation
Indices: 58420412--58420438 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58420402 ATGTGAAGAA
58420412 TATTTTTTAAAAT
1 TATTTTTTAAAAT
58420425 TATTTTTTAAAAT
1 TATTTTTTAAAAT
58420438 T
1 T
58420439 TATTATTAAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTTAAAAT
Found at i:58422923 original size:24 final size:26
Alignment explanation
Indices: 58422885--58422934 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
58422875 TATCAAAGAA
58422885 AAATTTAGAAAAAAAAA-GA-ATTTG
1 AAATTTAGAAAAAAAAATGAGATTTG
58422909 AAATTTA-AAATAAAAAATGAGATTTG
1 AAATTTAGAAA-AAAAAATGAGATTTG
58422935 TGATAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.13
24 13 0.57
25 2 0.09
26 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (26 bp):
AAATTTAGAAAAAAAAATGAGATTTG
Found at i:58423087 original size:25 final size:24
Alignment explanation
Indices: 58423033--58423087 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
58423023 CCAATATTAT
*
58423033 TTTTA-TTTAATAAAATATAATTA
1 TTTTATTTTAATAAAATATAAATA
* * *
58423056 ATATATTTTATATAAAATTTAAATA
1 TTTTATTTTA-ATAAAATATAAATA
58423081 TTTTATT
1 TTTTATT
58423088 GAAATATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.12
24 4 0.17
25 17 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATTTTAATAAAATATAAATA
Found at i:58428470 original size:21 final size:20
Alignment explanation
Indices: 58428432--58428472 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
58428422 TAACAATGAG
58428432 AATACCAATTTTATAATAAT
1 AATACCAATTTTATAATAAT
*
58428452 AATATCAATTTTGATAATAAT
1 AATACCAATTTT-ATAATAAT
58428473 GGTACTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
AATACCAATTTTATAATAAT
Found at i:58428822 original size:8 final size:7
Alignment explanation
Indices: 58428805--58428842 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 7
58428795 GCAAGGCAAT
58428805 AATAATA
1 AATAATA
58428812 AATAGATA
1 AATA-ATA
58428820 AATAAGTA
1 AATAA-TA
58428828 AATAAT-
1 AATAATA
58428834 AATAATA
1 AATAATA
58428841 AA
1 AA
58428843 ATTTAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.21
7 8 0.29
8 14 0.50
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:58429511 original size:13 final size:13
Alignment explanation
Indices: 58429493--58429518 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58429483 ATGATGAAAT
58429493 TTGCATAAAATAA
1 TTGCATAAAATAA
58429506 TTGCATAAAATAA
1 TTGCATAAAATAA
58429519 GCAGTAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TTGCATAAAATAA
Found at i:58437968 original size:6 final size:6
Alignment explanation
Indices: 58437959--58437987 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
58437949 TAATATAAAA
58437959 TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTAT
58437988 ATATTTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:58438550 original size:41 final size:39
Alignment explanation
Indices: 58438505--58438597 Score: 96
Period size: 41 Copynumber: 2.3 Consensus size: 39
58438495 AGCGGCGTTT
* * *
58438505 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAACTCGAGCA
1 TTAGCGGCGTTTCGA-AAAAAACGCCACTAAAAC-CAAGAA
** * *
58438546 TTAGCGGCGCTACCTAAAAAAACGCCGCTAAAACCAAGAA
1 TTAGCGGCG-TTTCGAAAAAAACGCCACTAAAACCAAGAA
58438586 TTAGCGGCGTTT
1 TTAGCGGCGTTT
58438598 TACACAAAGC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
39 1 0.02
40 13 0.31
41 26 0.62
42 2 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (39 bp):
TTAGCGGCGTTTCGAAAAAAACGCCACTAAAACCAAGAA
Found at i:58438768 original size:44 final size:41
Alignment explanation
Indices: 58438693--58438816 Score: 117
Period size: 41 Copynumber: 3.0 Consensus size: 41
58438683 CGCTAATACT
* * *
58438693 CCGT-TCTTCAGCGGCGTTTTTATCTAAGCGCCGCGAAA-GG
1 CCGTATCTTTAGCGGCGTTTTTGTCTATGCGCCGC-AAATGG
* * *
58438733 ACCAGTATTTTTTAGCGGTGTTTTTGTGTATGCGCCGCAAATGG
1 -CC-GTA-TCTTTAGCGGCGTTTTTGTCTATGCGCCGCAAATGG
* * *
58438777 TCTTATCTTTAGCGGCGTTTTTGTTTATGCGCCGCAAATG
1 CCGTATCTTTAGCGGCGTTTTTGTCTATGCGCCGCAAATG
58438817 CTCCGGTCTA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
41 34 0.50
42 4 0.06
43 4 0.06
44 26 0.38
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (41 bp):
CCGTATCTTTAGCGGCGTTTTTGTCTATGCGCCGCAAATGG
Found at i:58438833 original size:41 final size:41
Alignment explanation
Indices: 58438745--58439061 Score: 271
Period size: 41 Copynumber: 7.7 Consensus size: 41
58438735 CAGTATTTTT
* * * * * *** *
58438745 TAGCGGTGTTTTTGTGTATGCGCCGCAAATGGTCTTATCTT
1 TAGCGGCGTTTTTGTATAAGCGCCGCTAATGCTCCGGTCTA
* * *
58438786 TAGCGGCGTTTTTGTTTATGCGCCGCAAATGCTCCGGTCTA
1 TAGCGGCGTTTTTGTATAAGCGCCGCTAATGCTCCGGTCTA
* * * *
58438827 TTGCGGCGTTTTAG-ATAAAGCGCCGCTAATGGTCCGGCCTA
1 TAGCGGCGTTTTTGTAT-AAGCGCCGCTAATGCTCCGGTCTA
*** *
58438868 TAGCGGCGTTTTT-TATTAAGCGCCGCTGCGGTTCCGGTCTA
1 TAGCGGCGTTTTTGTA-TAAGCGCCGCTAATGCTCCGGTCTA
* * **
58438909 TAGCGGCGTTTTTGAAAAAGCGCCGCTGTTGCTCCGGTCTA
1 TAGCGGCGTTTTTGTATAAGCGCCGCTAATGCTCCGGTCTA
* * * **
58438950 TAGCGGCGTTTCTG-AAAATTCGCCGCTAATGCTCTTGTCTA
1 TAGCGGCGTTTTTGTATAA-GCGCCGCTAATGCTCCGGTCTA
* * * * *
58438991 TTGCGGCGTTTGTGGATAAGCGCTGCTAATGTTCCGGTCTA
1 TAGCGGCGTTTTTGTATAAGCGCCGCTAATGCTCCGGTCTA
*
58439032 TAGCGGCGTTTTTGTAAAAGCGCCGCTAAT
1 TAGCGGCGTTTTTGTATAAGCGCCGCTAAT
58439062 TAGAAAATCT
Statistics
Matches: 225, Mismatches: 45, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
40 5 0.02
41 215 0.96
42 5 0.02
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (41 bp):
TAGCGGCGTTTTTGTATAAGCGCCGCTAATGCTCCGGTCTA
Found at i:58439058 original size:123 final size:123
Alignment explanation
Indices: 58438786--58439061 Score: 324
Period size: 123 Copynumber: 2.2 Consensus size: 123
58438776 GTCTTATCTT
** * * *
58438786 TAGCGGCGTTTTTGTTTATGCGCCGCAAATGCTCCGGTCTATTGCGGCGTTTTAGATAAAGCGCC
1 TAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCCGGTCTATAGCGGCGTTTTAGATAAAGCGCC
* ** **
58438851 GCTAATGGTCCGGCCTATAGCGGCGTTTTTTATTAAGCGCCGCTGCGGTTCCGGTCTA
66 GCTAATGCTCCGGCCTATAGCGGCGTTTTGGATTAAGCGCCGCTAAGGTTCCGGTCTA
* ** *
58438909 TAGCGGCGTTTTTGAAAAAGCGCCGCTGTTGCTCCGGTCTATAGCGGCGTTTCT-GA-AAATTCG
1 TAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCCGGTCTATAGCGGCGTTT-TAGATAAA-GCG
** * * * *
58438972 CCGCTAATGCTCTTGTCTATTGCGGCGTTTGTGGA-TAAGCGCTGCTAATGTTCCGGTCTA
64 CCGCTAATGCTCCGGCCTATAGCGGCGTTT-TGGATTAAGCGCCGCTAAGGTTCCGGTCTA
58439032 TAGCGGCGTTTTTGTAAAAGCGCCGCTAAT
1 TAGCGGCGTTTTTGTAAAAGCGCCGCTAAT
58439062 TAGAAAATCT
Statistics
Matches: 127, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
122 3 0.02
123 121 0.95
124 3 0.02
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (123 bp):
TAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCCGGTCTATAGCGGCGTTTTAGATAAAGCGCC
GCTAATGCTCCGGCCTATAGCGGCGTTTTGGATTAAGCGCCGCTAAGGTTCCGGTCTA
Found at i:58440375 original size:78 final size:78
Alignment explanation
Indices: 58440246--58440403 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 78
58440236 CGTTTTTTGT
*
58440246 AAAAACGCTGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTATAAATTTTAATG
1 AAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTATAAATTTTAATG
58440311 TTGTTAATATTTA
66 TTGTTAATATTTA
58440324 AAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTATAAATTTTAATG
1 AAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTATAAATTTTAATG
58440389 TTGTTAATATTTA
66 TTGTTAATATTTA
58440402 AA
1 AA
58440404 TTAATCCTAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.41
Consensus pattern (78 bp):
AAAAACGCCGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTATAAATTTTAATG
TTGTTAATATTTA
Found at i:58443277 original size:31 final size:31
Alignment explanation
Indices: 58443239--58443300 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
58443229 AAGATAAAAA
58443239 GGCGGAGTACGAAGCGATTGCTTCCAGTGAT
1 GGCGGAGTACGAAGCGATTGCTTCCAGTGAT
58443270 GGCGGAGTACGAAGCGATTGCTTCCAGTGAT
1 GGCGGAGTACGAAGCGATTGCTTCCAGTGAT
58443301 AGTTCTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (31 bp):
GGCGGAGTACGAAGCGATTGCTTCCAGTGAT
Found at i:58443633 original size:66 final size:65
Alignment explanation
Indices: 58443524--58443694 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
58443514 GAGCAAATTA
* * * * * *
58443524 CACAACTTAAAGCGGAGGCAACATCGAGAGAAACTGAGGTTCAA-AAAAGATATGAAGAACTCTA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
58443588 G
65 G
* *
58443589 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGTTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
58443654 G
65 G
* * *
58443655 CAGCAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
58443695 CTGCAGCGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:58443690 original size:21 final size:21
Alignment explanation
Indices: 58443665--58443734 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
58443655 CAGCAGCTTA
* * *
58443665 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
58443686 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
58443707 AAGTAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
58443728 AAGCAGA
1 AAGCAGA
58443735 ACAGCTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.33, C:0.17, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:58444180 original size:43 final size:43
Alignment explanation
Indices: 58444095--58444427 Score: 472
Period size: 43 Copynumber: 7.7 Consensus size: 43
58444085 TGGTGCAAGT
* * * ***
58444095 GCCGCTAAAGGTCATGGTATTTTAGCGGCGTTTTCGGGGTAAGC
1 GCCGCTAAAGATCATGGT-CTATAGCGGCGTTTTATTGGTAAGC
* * * *
58444139 GCCGCTAAAGTTCATTGTCTTTAGCGGCGTTTCA-TGTGTAAGC
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTG-GTAAGC
*
58444182 GCCGCTAAATATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
* * *
58444225 GCCGCTAAAGATCATGGTCTATGGCGGCGTTTTATTGGAAAGT
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
*
58444268 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTGATTGGTAAGC
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
58444311 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
*
58444354 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTGATTGGTAAGC
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
* *
58444397 GCCGCTAAAG-TCTTGGTCTTTAGCGGCGTTT
1 GCCGCTAAAGATCATGGTCTATAGCGGCGTTT
58444428 ATTAAAAAAA
Statistics
Matches: 264, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
42 20 0.08
43 226 0.86
44 18 0.07
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (43 bp):
GCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGTAAGC
Found at i:58444336 original size:25 final size:25
Alignment explanation
Indices: 58444308--58444379 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 25
58444298 TTGATTGGTA
58444308 AGCGCCGCTAAAGATCATGGTCTAT
1 AGCGCCGCTAAAGATCATGGTCTAT
* ***
58444333 AGCGGCG-T-TTTAT--TGG--TA-
1 AGCGCCGCTAAAGATCATGGTCTAT
58444351 AGCGCCGCTAAAGATCATGGTCTAT
1 AGCGCCGCTAAAGATCATGGTCTAT
58444376 AGCG
1 AGCG
58444380 GCGTTTGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 14
0.59 0.15 0.26
Matches are distributed among these distances:
18 6 0.19
19 3 0.09
20 2 0.06
21 3 0.09
22 3 0.09
23 2 0.06
24 3 0.09
25 10 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (25 bp):
AGCGCCGCTAAAGATCATGGTCTAT
Found at i:58444448 original size:43 final size:42
Alignment explanation
Indices: 58444048--58444430 Score: 450
Period size: 43 Copynumber: 8.9 Consensus size: 42
58444038 GTTTTTCTAA
* * ** * *
58444048 AAGCGCCGCTAAAGACCGTGACCTTTAGCGGCGTTT-GTGGT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTTATTGGT
* * * * *
58444089 GCAAGTGCCGCTAAAGGTCATGGTATTTTAGCGGCGTTT-TCGGGGT
1 --AAGCGCCGCTAAAGATCATGGT-CTATAGCGGCGTTTAT--TGGT
* * *
58444135 AAGCGCCGCTAAAGTTCATTGTCTTTAGCGGCGTTTCA-TGTGT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTT-ATTG-GT
*
58444178 AAGCGCCGCTAAATATCATGGTCTATAGCGGCGTTTTATTGGT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCG-TTTATTGGT
* *
58444221 AAGCGCCGCTAAAGATCATGGTCTATGGCGGCGTTTTATTGGA
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCG-TTTATTGGT
*
58444264 AAGTGCCGCTAAAGATCATGGTCTATAGCGGCGTTTGATTGGT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTT-ATTGGT
58444307 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTTTATTGGT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCG-TTTATTGGT
58444350 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTTGATTGGT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTT-ATTGGT
* *
58444393 AAGCGCCGCTAAAG-TCTTGGTCTTTAGCGGCGTTTATT
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTTATT
58444431 AAAAAAAGCG
Statistics
Matches: 302, Mismatches: 27, Indels: 24
0.86 0.08 0.07
Matches are distributed among these distances:
41 3 0.01
42 26 0.09
43 230 0.76
44 40 0.13
46 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTTATTGGT
Done.