Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 195 of 292
Found at i:58210505 original size:18 final size:19
Alignment explanation
Indices: 58210477--58210521 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
58210467 TGAATTTGTG
58210477 TAAAAAAATAA-ATA-AAA
1 TAAAAAAATAACATAGAAA
*
58210494 TATAAAATATAACATAGAAA
1 TA-AAAAAATAACATAGAAA
58210514 TAAAAAAA
1 TAAAAAAA
58210522 AGGTAATGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 8 0.35
19 8 0.35
20 5 0.22
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAAAAAATAACATAGAAA
Found at i:58212222 original size:33 final size:33
Alignment explanation
Indices: 58212185--58212251 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
58212175 TTAAATTGGT
58212185 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
1 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
58212218 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
1 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
58212251 A
1 A
58212252 CATAATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (33 bp):
AAACATCTATGTTTTGGTTGTGAATTGATAGAC
Found at i:58214461 original size:40 final size:40
Alignment explanation
Indices: 58214414--58214597 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
58214404 CTCGGACAAG
* * *
58214414 GCCTTCGGGTTTTAGCCCGGATATGGTC-ACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTAGCACAAAT
*
58214454 GCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAAT
* * * *
58214494 GCCTTCGGATCTTAGTCCGGATATAGCAACTCGTACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAAT
* * ** * *
58214534 GCCTTTGGATCTTAGTTCGGATATAGTC-ACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTAGCACAAAT
*
58214574 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
58214598 CATTCGGATA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 122 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAAT
Found at i:58214515 original size:80 final size:78
Alignment explanation
Indices: 58214378--58214597 Score: 196
Period size: 80 Copynumber: 2.8 Consensus size: 78
58214368 ACCCAAGTAT
* * * * * *
58214378 CTTCGGGAT-TTAGCCGGATATAACTACTCGGAC-AAGGCCTTCGGGTTTTAGCCCGGATATGGT
1 CTTCGGG-TCTTAGCCGGATATAGC-ACTCGCACAAAAGCCTTCGGATCTTAGCCCGGATATAG-
*
58214441 C-ACTAGCATAAATGC
63 CAACTAGCACAAATGC
* *
58214456 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGC
1 CTTCGGGTCTTAG-CCGGATATAGC-ACTCGCACAAAAGCCTTCGGATCTTAGCCCGGATATAGC
* *
58214521 AACTCGTACAAATGC
64 AACTAGCACAAATGC
* * * * *
58214536 CTTTGGATCTTAGTTCGGATATAGTCACTAGCATAAAAGCCTTCGGGA-CTTAGCCCGGATAT
1 CTTCGGGTCTTAG-CCGGATATAG-CACTCGCACAAAAGCCTTC-GGATCTTAGCCCGGATAT
58214598 CATTCGGATA
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
77 1 0.01
78 11 0.09
79 18 0.15
80 83 0.71
81 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (78 bp):
CTTCGGGTCTTAGCCGGATATAGCACTCGCACAAAAGCCTTCGGATCTTAGCCCGGATATAGCAA
CTAGCACAAATGC
Found at i:58219882 original size:22 final size:22
Alignment explanation
Indices: 58219857--58219906 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
58219847 TTCCCAAACT
58219857 CACACGGGCGTGTCCCCTAGGG
1 CACACGGGCGTGTCCCCTAGGG
*
58219879 CACACGGGCGTGTGCCCTAGGG
1 CACACGGGCGTGTCCCCTAGGG
*
58219901 GACACG
1 CACACG
58219907 CCCGTGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.34, G:0.38, T:0.12
Consensus pattern (22 bp):
CACACGGGCGTGTCCCCTAGGG
Found at i:58219912 original size:22 final size:22
Alignment explanation
Indices: 58219865--58219914 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
58219855 CTCACACGGG
* **
58219865 CGTGTCCCCTAGGGCACACGGG
1 CGTGTGCCCTAGGGCACACGCC
*
58219887 CGTGTGCCCTAGGGGACACGCC
1 CGTGTGCCCTAGGGCACACGCC
58219909 CGTGTG
1 CGTGTG
58219915 GTTTCCGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.12, C:0.34, G:0.38, T:0.16
Consensus pattern (22 bp):
CGTGTGCCCTAGGGCACACGCC
Found at i:58228922 original size:21 final size:22
Alignment explanation
Indices: 58228898--58228941 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
58228888 TTTTATTTTT
58228898 TAAAATATT-TAAATATT-AATA
1 TAAAATATTAT-AATATTCAATA
58228919 TAAAATATTATAATATTCAATA
1 TAAAATATTATAATATTCAATA
58228941 T
1 T
58228942 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATATTATAATATTCAATA
Found at i:58228934 original size:15 final size:16
Alignment explanation
Indices: 58228911--58228956 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
58228901 AATATTTAAA
58228911 TATTAATATAAAATAT
1 TATTAATATAAAATAT
**
58228927 TA-TAATATTCAATAT
1 TATTAATATAAAATAT
58228942 TATTAA-A-AAAATAT
1 TATTAATATAAAATAT
58228956 T
1 T
58228957 TAGTTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAATATAAAATAT
Found at i:58232124 original size:36 final size:36
Alignment explanation
Indices: 58232084--58232163 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
58232074 ATTCCAACCA
* *
58232084 AAACACA-TCAGATGCTCATAAAAGCTAATCCATTTG
1 AAACACACT-AGATGCTCATAAAAGATAATCCATTCG
* *
58232120 AAACACACTAGATGCTCATAACAGATAATTCATTCG
1 AAACACACTAGATGCTCATAAAAGATAATCCATTCG
58232156 AAACACAC
1 AAACACAC
58232164 CAATAGTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 38 0.97
37 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (36 bp):
AAACACACTAGATGCTCATAAAAGATAATCCATTCG
Found at i:58237144 original size:12 final size:13
Alignment explanation
Indices: 58237122--58237150 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
58237112 AGTGAGTAGT
58237122 TTTTGAATTTTAA
1 TTTTGAATTTTAA
58237135 TTTT-AATTTTAA
1 TTTTGAATTTTAA
58237147 TTTT
1 TTTT
58237151 TGTTAGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:58241567 original size:21 final size:22
Alignment explanation
Indices: 58241543--58241586 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
58241533 TTTTATTTTT
58241543 TAAAATATT-TAAATATT-AATA
1 TAAAATATTAT-AATATTCAATA
58241564 TAAAATATTATAATATTCAATA
1 TAAAATATTATAATATTCAATA
58241586 T
1 T
58241587 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATATTATAATATTCAATA
Found at i:58241579 original size:15 final size:16
Alignment explanation
Indices: 58241556--58241601 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
58241546 AATATTTAAA
58241556 TATTAATATAAAATAT
1 TATTAATATAAAATAT
**
58241572 TA-TAATATTCAATAT
1 TATTAATATAAAATAT
58241587 TATTAA-A-AAAATAT
1 TATTAATATAAAATAT
58241601 T
1 T
58241602 TAGTTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAATATAAAATAT
Found at i:58244768 original size:36 final size:35
Alignment explanation
Indices: 58244728--58244843 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 35
58244718 ATTCCAACCA
58244728 AAACACATCAGATGCTCATAAAAGCTAATCCATTTG
1 AAACACA-CAGATGCTCATAAAAGCTAATCCATTTG
* * * *
58244764 AAACACACTAGATGCTCATAACAGATAATTCATTCG
1 AAACACAC-AGATGCTCATAAAAGCTAATCCATTTG
* * * **
58244800 AAACACACCA-ATAGCTCAGAAGAGCTAGTCCAACTG
1 AAACACA-CAGAT-GCTCATAAAAGCTAATCCATTTG
58244836 AAACACAC
1 AAACACAC
58244844 CAAAATAGGG
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
35 4 0.06
36 60 0.92
37 1 0.02
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (35 bp):
AAACACACAGATGCTCATAAAAGCTAATCCATTTG
Found at i:58248657 original size:24 final size:24
Alignment explanation
Indices: 58248625--58248683 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
58248615 ATGTACGCTT
* * *
58248625 ACACGAGCTGTTATTAAAATGCTC
1 ACACGAGCTATAATCAAAATGCTC
*
58248649 ACACGAGCTATAATCAGAATGCTC
1 ACACGAGCTATAATCAAAATGCTC
58248673 ACACGAGCTAT
1 ACACGAGCTAT
58248684 GAAAATGGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (24 bp):
ACACGAGCTATAATCAAAATGCTC
Found at i:58252465 original size:21 final size:19
Alignment explanation
Indices: 58252425--58252472 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
58252415 TGTTATCTAA
**
58252425 TTTTTTTAATTTTTTTTCT
1 TTTTTTTAATTTTTCCTCT
58252444 TTTTTTTCAAATTTTTCCTCT
1 TTTTTTT--AATTTTTCCTCT
58252465 TTGTTTTT
1 TT-TTTTT
58252473 GACGTATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
21 12 0.50
22 5 0.21
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTTTTAATTTTTCCTCT
Found at i:58253930 original size:13 final size:13
Alignment explanation
Indices: 58253896--58253939 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
58253886 GGGTTAGGAT
58253896 TCTGTATATCTGT-
1 TCTGT-TATCTGTA
*
58253909 TCTGCTTATTTGTA
1 TCTG-TTATCTGTA
58253923 TCTGTTATCTGTA
1 TCTGTTATCTGTA
58253936 TCTG
1 TCTG
58253940 AAATTATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.55
Consensus pattern (13 bp):
TCTGTTATCTGTA
Found at i:58256240 original size:38 final size:37
Alignment explanation
Indices: 58256179--58256326 Score: 163
Period size: 38 Copynumber: 3.9 Consensus size: 37
58256169 ATTTGATGTG
* *
58256179 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAACTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGAAA-TA
*
58256219 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCT-GAAATA
* * *
58256257 TATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCT-GAAATA
* *
58256295 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTG
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTG
58256327 GTATTATATC
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
37 2 0.02
38 80 0.82
39 8 0.08
40 8 0.08
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (37 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGAAATA
Found at i:58256327 original size:38 final size:38
Alignment explanation
Indices: 58256217--58256368 Score: 214
Period size: 38 Copynumber: 3.9 Consensus size: 38
58256207 ATGCTGAAAC
*
58256217 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
58256255 TATATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
58256293 TATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * * *
58256331 TATATCTGAGCTTAAAGTCCCGCAGGTTTTGTGCTGGT
1 TATATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGT
58256369 GACTAGATTT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 78 0.76
39 6 0.06
40 18 0.18
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:58258146 original size:94 final size:94
Alignment explanation
Indices: 58257985--58258176 Score: 339
Period size: 94 Copynumber: 2.0 Consensus size: 94
58257975 GTAAAGTTAC
*
58257985 CAGTCTAGCTAAACTTTTAAAATGACAACGAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
1 CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
* *
58258050 TATCTGAGTCCACAACAAATGCTGGAGCT
66 TATCTGAATCCACAACAAATGCTAGAGCT
* *
58258079 CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAGGCTAAATCCGTGTCACATGTA
1 CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
58258144 TATCTGAATCCACAACAAATGCTAGAGCT
66 TATCTGAATCCACAACAAATGCTAGAGCT
58258173 CAGT
1 CAGT
58258177 TTAGAATGGG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (94 bp):
CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
TATCTGAATCCACAACAAATGCTAGAGCT
Found at i:58260067 original size:25 final size:25
Alignment explanation
Indices: 58260039--58260093 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
58260029 AATATAACTT
*
58260039 ATAATTAT-TTTTAAATGTCAATTTA
1 ATAATTATATTTGAAATGTCAA-TTA
*
58260064 ATAA-TATGATTTGAAATGTTAATTA
1 ATAATTAT-ATTTGAAATGTCAATTA
58260089 ATAAT
1 ATAAT
58260094 ATGATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 3 0.12
25 11 0.44
26 11 0.44
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (25 bp):
ATAATTATATTTGAAATGTCAATTA
Found at i:58260360 original size:21 final size:22
Alignment explanation
Indices: 58260336--58260376 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
58260326 AACAAGAGTC
*
58260336 AAATTTAATTA-AATTTTTTTT
1 AAATCTAATTATAATTTTTTTT
*
58260357 AAATCTAATTATTATTTTTT
1 AAATCTAATTATAATTTTTT
58260377 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATCTAATTATAATTTTTTTT
Found at i:58267798 original size:55 final size:55
Alignment explanation
Indices: 58267733--58267842 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
58267723 GAGTTCACCA
58267733 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
1 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
* *
58267788 ACACCCTTTTACAATAATCCTATAGCAATTTATTTGAGTGGACCTTTATAAATAT
1 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
58267843 GTAATCCAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (55 bp):
ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
Found at i:58268887 original size:2 final size:2
Alignment explanation
Indices: 58268880--58268923 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
58268870 CTAATCTCCT
58268880 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
58268922 TA
1 TA
58268924 GGAGCATACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58271485 original size:6 final size:6
Alignment explanation
Indices: 58271474--58271500 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58271464 GTGAGCAGTT
58271474 TTTGAA TTTGAA TTTGAA TTTGAA TTT
1 TTTGAA TTTGAA TTTGAA TTTGAA TTT
58271501 TGTTAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTGAA
Found at i:58273740 original size:14 final size:14
Alignment explanation
Indices: 58273721--58273748 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58273711 TATACCTCTA
58273721 TTTAATTGCTTAAC
1 TTTAATTGCTTAAC
58273735 TTTAATTGCTTAAC
1 TTTAATTGCTTAAC
58273749 CATTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTAATTGCTTAAC
Found at i:58275569 original size:28 final size:30
Alignment explanation
Indices: 58275538--58275601 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
58275528 AATGTGCAAG
* *
58275538 TTATACAT-AAACTTTGATTT-GTTCAATT
1 TTATACATGAAACTTTCATTTAATTCAATT
* *
58275566 TTATATATGAAATTTTCATTTAATTCAATT
1 TTATACATGAAACTTTCATTTAATTCAATT
58275596 TT-TACA
1 TTATACA
58275602 AATCACTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.24
29 13 0.45
30 9 0.31
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATACATGAAACTTTCATTTAATTCAATT
Found at i:58275806 original size:29 final size:30
Alignment explanation
Indices: 58275774--58275831 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
58275764 TCACATCTAT
*
58275774 AATTACACG-AAATCAAAGTTCATATATTA
1 AATTAAACGTAAATCAAAGTTCATATATTA
* *
58275803 AATTAAACGTTGAATCAAATTTCATATAT
1 AATTAAACG-TAAATCAAAGTTCATATAT
58275832 AGTTTTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
31 16 0.67
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (30 bp):
AATTAAACGTAAATCAAAGTTCATATATTA
Found at i:58276023 original size:2 final size:2
Alignment explanation
Indices: 58276016--58276054 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
58276006 TAAACTGACA
58276016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58276055 TTTTTTAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:58276185 original size:31 final size:31
Alignment explanation
Indices: 58276118--58276186 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
58276108 TTGGTCATTA
** *
58276118 AACTATTCAAAAGTTTTCATTTAAGTCACTG
1 AACTATTTGAAAGTTTTCATTTAAGCCACTG
* *
58276149 AACTATTTGAAAGTTTTTATTTAAGCCATTG
1 AACTATTTGAAAGTTTTCATTTAAGCCACTG
*
58276180 GACTATT
1 AACTATT
58276187 AAGTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (31 bp):
AACTATTTGAAAGTTTTCATTTAAGCCACTG
Found at i:58277326 original size:24 final size:24
Alignment explanation
Indices: 58277288--58277340 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
58277278 ATTTCTAGAT
* *
58277288 ATTTTT-AAACTTTTAGAAAGCTCA
1 ATTTTTAAAAATTTAAGAAA-CTCA
*
58277312 ATTTTTAAAAATTTAAGAAACTTA
1 ATTTTTAAAAATTTAAGAAACTCA
58277336 ATTTT
1 ATTTT
58277341 GAAAGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTTTTAAAAATTTAAGAAACTCA
Found at i:58279455 original size:9 final size:8
Alignment explanation
Indices: 58279438--58279462 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58279428 TAAAATCACA
58279438 TTATTTTT
1 TTATTTTT
58279446 TTATTTTT
1 TTATTTTT
58279454 TTATTTTT
1 TTATTTTT
58279462 T
1 T
58279463 ATATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:58280589 original size:23 final size:22
Alignment explanation
Indices: 58280525--58280592 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
58280515 AATCAAATAC
*
58280525 TAAATTGAAAATATAA-ATTAAAA
1 TAAATTGAAAA-A-AACATAAAAA
*
58280548 TAAATTGAATAAAACATAAAAA
1 TAAATTGAAAAAAACATAAAAA
* *
58280570 TAAATCTTAAAAAAATATAAAAA
1 TAAAT-TGAAAAAAACATAAAAA
58280593 GTTTAAACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 24 0.63
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (22 bp):
TAAATTGAAAAAAACATAAAAA
Found at i:58281362 original size:29 final size:29
Alignment explanation
Indices: 58281312--58281372 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
58281302 TTTCAATGAA
58281312 TTTATTTTAATTATTGTATTTTTCATAAAT
1 TTTATTTTAATTATTGTATTTTTC-TAAAT
* *
58281342 TTTATTTTTA-TATATGT-TTTTTCTGAAT
1 TTTATTTTAATTAT-TGTATTTTTCTAAAT
58281370 TTT
1 TTT
58281373 TTATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 9 0.32
30 12 0.43
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTATTTTAATTATTGTATTTTTCTAAAT
Found at i:58281394 original size:21 final size:22
Alignment explanation
Indices: 58281346--58281404 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
58281336 ATAAATTTTA
*
58281346 TTTTTATATATGTTTTTTCTGAAT
1 TTTTTATATAT-TTATTTCT-AAT
58281370 TTTTTATATATTTATTTCT-AT
1 TTTTTATATATTTATTTCTAAT
* *
58281391 TTTTCATATTTTTA
1 TTTTTATATATTTA
58281405 ATGTACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.44
23 7 0.22
24 11 0.34
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTTTATATATTTATTTCTAAT
Found at i:58282103 original size:11 final size:11
Alignment explanation
Indices: 58282089--58282125 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
58282079 TCCAAAATAG
58282089 ATAAAAAATTT
1 ATAAAAAATTT
*
58282100 AT-AAATATTT
1 ATAAAAAATTT
58282110 ATAAAAAATTT
1 ATAAAAAATTT
58282121 A-AAAA
1 ATAAAA
58282126 GACGAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAAAAATTT
Found at i:58287315 original size:3 final size:3
Alignment explanation
Indices: 58287307--58287351 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
58287297 TTCTTGATCC
*
58287307 ATT ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58287352 CTACCTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:58288036 original size:26 final size:26
Alignment explanation
Indices: 58288002--58288060 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
58287992 TAATTTAGCC
*
58288002 AAAATTCCTTAACCCTATTAGTTAAG
1 AAAACTCCTTAACCCTATTAGTTAAG
58288028 AAAACTCCTTAACCCTATTAGTTAAG
1 AAAACTCCTTAACCCTATTAGTTAAG
58288054 AAAACTC
1 AAAACTC
58288061 ACAGTAATTT
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:0.22, G:0.07, T:0.31
Consensus pattern (26 bp):
AAAACTCCTTAACCCTATTAGTTAAG
Found at i:58290533 original size:21 final size:21
Alignment explanation
Indices: 58290509--58290548 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58290499 GATTATATTT
*
58290509 ATATATTTTAAATATTATAAA
1 ATATATTTAAAATATTATAAA
58290530 ATATATTTAAAATATTATA
1 ATATATTTAAAATATTATA
58290549 GATCTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATTTAAAATATTATAAA
Found at i:58294709 original size:20 final size:20
Alignment explanation
Indices: 58294644--58294711 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
58294634 CCACATTTAC
*
58294644 TAAATTTTATTTTTTATTTGT
1 TAAATTTT-CTTTTTATTTGT
* * *
58294665 TTAATTTCCTTTTTCTTT-T
1 TAAATTTTCTTTTTATTTGT
58294684 TAAATTTTCTTTATT-TTTGT
1 TAAATTTTCTTT-TTATTTGT
*
58294704 TGAATTTT
1 TAAATTTT
58294712 TTTCACCACA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 14 0.37
20 18 0.47
21 6 0.16
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (20 bp):
TAAATTTTCTTTTTATTTGT
Found at i:58299460 original size:21 final size:21
Alignment explanation
Indices: 58299431--58299470 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58299421 TGACTACAAA
58299431 TCAGATTTTTCCTCCTGATTT
1 TCAGATTTTTCCTCCTGATTT
*
58299452 TCAGCTTTTTCCTCCTGAT
1 TCAGATTTTTCCTCCTGAT
58299471 AAAATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.10, T:0.50
Consensus pattern (21 bp):
TCAGATTTTTCCTCCTGATTT
Found at i:58303614 original size:39 final size:39
Alignment explanation
Indices: 58303571--58303650 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
58303561 TGTAATCGTA
58303571 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
1 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
** *
58303610 AATCAATGAGCTGTTTGGAGTTGCGATTGTAAATCAACT
1 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
58303649 AA
1 AA
58303651 CTTAGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
Found at i:58303773 original size:94 final size:94
Alignment explanation
Indices: 58303617--58303802 Score: 282
Period size: 94 Copynumber: 2.0 Consensus size: 94
58303607 ACTAATCAAT
* * * * *
58303617 GAGCTGTTTGGAGTTGCGATTGTAAATCAACTAACTTAGAAAAAATTGTTCATGATCGTAAATCA
1 GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAAAAATTGTTCATGATCATAAATCA
*
58303682 ATGAACTTAGGTTATGATCGTAAATCAGC
66 ATGAACTCAGGTTATGATCGTAAATCAGC
* * *
58303711 GAGCTATTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAATAAATTGTTCATGATTATAAATCA
1 GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAAAAATTGTTCATGATCATAAATCA
*
58303776 ATGAACTCAGGTTGTGATCGTAAATCA
66 ATGAACTCAGGTTATGATCGTAAATCA
58303803 ATGAGCCTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (94 bp):
GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAAAAATTGTTCATGATCATAAATCA
ATGAACTCAGGTTATGATCGTAAATCAGC
Found at i:58303856 original size:130 final size:130
Alignment explanation
Indices: 58303696--58304033 Score: 444
Period size: 130 Copynumber: 2.6 Consensus size: 130
58303686 ACTTAGGTTA
* * * * *
58303696 TGATCGTAAATCAGCGAGCTATTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAATAAATTGTT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAAGAAATTGTT
* * *
58303761 CATGATTATAAATCAATGAACTCAGGTTGTGATCGTAAATCAATGAGCCTTAATAATATCAACCG
66 CATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACCG
** * * * *
58303826 TGATTGTAAATCAATGAGTTGTTTGGAGTTGCA-ATTGTAAATCAGCTAACTAAAAAGAAATTGT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTG-AGATCGTAAATCAGCTAACTCAGAAGAAATTGT
* * * * *
58303890 TCATGATTGTCAATCAATGAACTTAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAGCT
65 TCATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACC
58303955 G
130 G
* * *
58303956 TGATCATAAATCAGCGAGTTGTTTGGAGTTGCGATCGTAAATCAACTAACTCAGAAGAAATTGTT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAAGAAATTGTT
* *
58304021 TATGATCATAAAT
66 CATGATTATAAAT
58304034 TAGTGAGCCT
Statistics
Matches: 176, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
130 175 0.99
131 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (130 bp):
TGATCATAAATCAACGAGTTGTTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAAGAAATTGTT
CATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACCG
Found at i:58304507 original size:63 final size:63
Alignment explanation
Indices: 58304408--58304534 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
58304398 TCTTGTAGGG
*
58304408 CCCTTCCTAATTGGAATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
1 CCCTTCCCAATTGGAATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
*
58304471 CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
1 CCCTTCCCAATTGGAATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
58304534 C
1 C
58304535 AAGACTAGAC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.39
Consensus pattern (63 bp):
CCCTTCCCAATTGGAATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
Found at i:58313453 original size:33 final size:33
Alignment explanation
Indices: 58313406--58313470 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
58313396 TTTGCATGGT
* *
58313406 GATGCGAACCCACCACGTTCAAG-CTCATGTAAG
1 GATGCAAACCCACCACGTGCAAGCCT-ATGTAAG
*
58313439 GATGCAAACTCACCACGTGCAAGCCTATGTAA
1 GATGCAAACCCACCACGTGCAAGCCTATGTAA
58313471 AGGTGCGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.18
Consensus pattern (33 bp):
GATGCAAACCCACCACGTGCAAGCCTATGTAAG
Found at i:58321336 original size:2 final size:2
Alignment explanation
Indices: 58321329--58321693 Score: 309
Period size: 2 Copynumber: 180.5 Consensus size: 2
58321319 TAAAATTCAA
* *
58321329 AT AT AT AT AG AT AT CAT AT AT AT AT AT GAT AT AT AT CAT AT AG
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT AT AT AT -AT AT AT
*
58321372 AT AT AT AG AT AT A- AT AT AT AT AT AT AT AT GAT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT
* * * * *
58321415 AT AT AT AT CT GT AT CAT -T AT AG AT AT AT AC AT AT CT 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
* * *
58321457 AT AT AT CAT -T AT AT AT AT AT TT AT CT AT A- AT GAT CT 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
* * * *
58321499 AT AT AT AT GAT AT CT AT AT AT CT AT AT AT AT -T AT AT CT AT CT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
58321541 AT AT AT AT AT A- AT AG AT AT AT AT AT CAT AT CT AT AT CAT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT -AT AT AT
* *
58321584 AT AT AT AT AG AT AT AT AG AT AT A- AT AT AT AT AT GAT 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
* * *
58321626 AT AT A- AC AT AT AT AT CAT -T AT AT AT AT AT AG AT AT GT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
58321667 AT CT AT A- AT GAT CT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT A
58321694 CGATGATTAT
Statistics
Matches: 291, Mismatches: 48, Indels: 48
0.75 0.12 0.12
Matches are distributed among these distances:
1 10 0.03
2 253 0.87
3 28 0.10
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:58328747 original size:31 final size:30
Alignment explanation
Indices: 58328707--58328765 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
58328697 AGATGATCAT
58328707 TAAATTATTTGAAAGTTTGTATTTAAGTTA
1 TAAATTATTTGAAAGTTTGTATTTAAGTTA
* *
58328737 TAAACTTATTTGTAAGTTTTTATTTAAGT
1 TAAA-TTATTTGAAAGTTTGTATTTAAGT
58328766 CTATGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.53
Consensus pattern (30 bp):
TAAATTATTTGAAAGTTTGTATTTAAGTTA
Found at i:58329822 original size:23 final size:22
Alignment explanation
Indices: 58329783--58329827 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
58329773 TATTAAAATA
* * *
58329783 ATAAAATTATATTTTTACTTTC
1 ATAAAAATATATATTTAATTTC
58329805 ATAAAAATATATAATTTAATTTC
1 ATAAAAATATAT-ATTTAATTTC
58329828 GACCTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAAATATATATTTAATTTC
Found at i:58330453 original size:13 final size:13
Alignment explanation
Indices: 58330435--58330460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58330425 AATTAATGTT
58330435 TTGATAGGGATAA
1 TTGATAGGGATAA
58330448 TTGATAGGGATAA
1 TTGATAGGGATAA
58330461 GTTTTCAGGC
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:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TTGATAGGGATAA
Found at i:58333102 original size:48 final size:49
Alignment explanation
Indices: 58333050--58333142 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
58333040 TTGTTTGAAC
*
58333050 ATTTGTGTTTGATATGCAAA-AAATGGAGAAAGTTAAATTTATATAAAA
1 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATATAAAA
58333098 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
1 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
58333143 CTACTTCCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 19 0.44
49 24 0.56
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (49 bp):
ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATATAAAA
Found at i:58345490 original size:27 final size:27
Alignment explanation
Indices: 58345448--58345580 Score: 175
Period size: 27 Copynumber: 5.0 Consensus size: 27
58345438 GTCACTAGAT
58345448 ACAGATAT-TGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
58345474 ACAGATATATGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
* * *
58345501 TCAGATA-ATTGTGGCATAGCCACCAGG
1 ACAGATATA-TGTGGCAGAGCCACCAGA
58345528 ACAGATATATGTGGCAGAGCCACCA-A
1 ACAGATATATGTGGCAGAGCCACCAGA
*
58345554 ATCAGATA-ATTGTGGCATAGCCACCAG
1 A-CAGATATA-TGTGGCAGAGCCACCAG
58345581 GACGCTTCCT
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
26 11 0.12
27 82 0.87
28 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
ACAGATATATGTGGCAGAGCCACCAGA
Found at i:58345581 original size:54 final size:54
Alignment explanation
Indices: 58345449--58345583 Score: 236
Period size: 54 Copynumber: 2.5 Consensus size: 54
58345439 TCACTAGATA
* * *
58345449 CAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
58345502 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
1 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
58345556 CAGATAATTGTGGCATAGCCACCAGGAC
1 CAGATAATTGTGGCATAGCCACCAGGAC
58345584 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 5 0.06
54 73 0.94
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (54 bp):
CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
Found at i:58347207 original size:26 final size:26
Alignment explanation
Indices: 58347177--58347232 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
58347167 TGAAATTCCC
58347177 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58347203 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58347229 ATCA
1 ATCA
58347233 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:58350678 original size:20 final size:20
Alignment explanation
Indices: 58350624--58350678 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
58350614 GTTATGGAGC
58350624 ATTACTAAAAATTTCAGAACA
1 ATTACT-AAAATTTCAGAACA
*
58350645 ATTAC-AGATAATTT-AGATCA
1 ATTACTA-A-AATTTCAGAACA
58350665 ATTACTAAACATTT
1 ATTACTAAA-ATTT
58350679 TTCAAAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTACTAAAATTTCAGAACA
Found at i:58359345 original size:17 final size:17
Alignment explanation
Indices: 58359325--58359372 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
58359315 TTTTACCCAT
*
58359325 TAAATTCTTTTAATTCA
1 TAAATTCTTCTAATTCA
*
58359342 TAAAATTC-ACTAATTCA
1 T-AAATTCTTCTAATTCA
*
58359359 AAAATTCTTCTAAT
1 TAAATTCTTCTAAT
58359373 GTCTTAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.24
17 13 0.52
18 6 0.24
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTCTTCTAATTCA
Found at i:58359871 original size:32 final size:32
Alignment explanation
Indices: 58359830--58359893 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
58359820 AAGCTTTAGG
58359830 GCCATTTATAACCTTGGAAACAAGAAATTGAC
1 GCCATTTATAACCTTGGAAACAAGAAATTGAC
*
58359862 GCCATTTATAACGTTGGAAACAAGAAATTGAC
1 GCCATTTATAACCTTGGAAACAAGAAATTGAC
58359894 TCTTACACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (32 bp):
GCCATTTATAACCTTGGAAACAAGAAATTGAC
Found at i:58361922 original size:51 final size:51
Alignment explanation
Indices: 58361833--58361938 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
58361823 AAACATCTGC
* *
58361833 TCATATGAAATAATAGTTCTTACCAAATGAAAACTCATGCAAAATAATAGT
1 TCATATGAAATAATAGTTCATACCAAATGAAAACTCATGCAAAATAAAAGT
* * *
58361884 TCATATGAAAT-ATCAGTTCATATCGAAT-AACAATTCATGCAAAATAAAAGT
1 TCATATGAAATAAT-AGTTCATACCAAATGAA-AACTCATGCAAAATAAAAGT
58361935 TCAT
1 TCAT
58361939 GCTCCATCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.08
51 44 0.92
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (51 bp):
TCATATGAAATAATAGTTCATACCAAATGAAAACTCATGCAAAATAAAAGT
Found at i:58371342 original size:14 final size:14
Alignment explanation
Indices: 58371323--58371352 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58371313 TATTTTCAAG
58371323 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
58371337 ATAGATTCACGCAT
1 ATAGATTAACGCAT
58371351 AT
1 AT
58371353 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:58377240 original size:28 final size:28
Alignment explanation
Indices: 58377191--58377259 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
58377181 CTTAAAACCC
* *
58377191 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGATAATTTTGCTCTT
58377218 TAGGGGTAATTTCGATAATTTTGCTCTT
1 TAGGGGTAATTTCGATAATTTTGCTCTT
58377246 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
58377260 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGATAATTTTGCTCTT
Found at i:58379091 original size:19 final size:18
Alignment explanation
Indices: 58379054--58379097 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
58379044 ATACATACAG
58379054 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
58379071 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
58379090 TACTAATT
1 TAATAATT
58379098 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:58382999 original size:21 final size:20
Alignment explanation
Indices: 58382970--58383024 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
58382960 AAAAACTCTT
58382970 TAAC-TGATTGAAGAAAAGTC
1 TAACTTGATTGAA-AAAAGTC
** *
58382990 TAACTTGATTGAAACCATTC
1 TAACTTGATTGAAAAAAGTC
*
58383010 TAACTTGATTTAAAA
1 TAACTTGATTGAAAA
58383025 GTTGACTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
TAACTTGATTGAAAAAAGTC
Found at i:58385993 original size:10 final size:10
Alignment explanation
Indices: 58385978--58386008 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
58385968 TAAATAAAAC
58385978 ATAACATAAA
1 ATAACATAAA
58385988 ATAACATAAA
1 ATAACATAAA
*
58385998 ATAAAATAAA
1 ATAACATAAA
58386008 A
1 A
58386009 CAAAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAACATAAA
Found at i:58385995 original size:15 final size:15
Alignment explanation
Indices: 58385975--58386006 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58385965 AATTAAATAA
*
58385975 AACATAACATAAAAT
1 AACATAAAATAAAAT
58385990 AACATAAAATAAAAT
1 AACATAAAATAAAAT
58386005 AA
1 AA
58386007 AACAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (15 bp):
AACATAAAATAAAAT
Found at i:58386854 original size:12 final size:14
Alignment explanation
Indices: 58386837--58386869 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
58386827 TAAAGAAATA
58386837 ATAAATTG-AT-TG
1 ATAAATTGAATATG
58386849 ATAAATTGAATATG
1 ATAAATTGAATATG
58386863 ATAAATT
1 ATAAATT
58386870 ACAATTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 2 0.11
14 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (14 bp):
ATAAATTGAATATG
Found at i:58387509 original size:34 final size:34
Alignment explanation
Indices: 58387455--58387535 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
58387445 TTATATTTTT
* * *
58387455 AATATTGGTGTGAAAGTCAATGATATATTTTAAG
1 AATATTGGTATGGAACTCAATGATATATTTTAAG
* * * *
58387489 CATATTGTTATGGAACTCAATGGTATATTTTGAG
1 AATATTGGTATGGAACTCAATGATATATTTTAAG
58387523 AATATTGGTATGG
1 AATATTGGTATGG
58387536 TGATAGAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (34 bp):
AATATTGGTATGGAACTCAATGATATATTTTAAG
Found at i:58393448 original size:13 final size:13
Alignment explanation
Indices: 58393430--58393463 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
58393420 GCACACGCCC
58393430 GTGTCCCTGGCCT
1 GTGTCCCTGGCCT
58393443 GTGTCCCTGGCCT
1 GTGTCCCTGGCCT
58393456 GTGTCCCT
1 GTGTCCCT
58393464 CACATGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.29, T:0.32
Consensus pattern (13 bp):
GTGTCCCTGGCCT
Found at i:58397053 original size:38 final size:38
Alignment explanation
Indices: 58397001--58397080 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
58396991 TTTAATAAGT
* ** *
58397001 ATATGGATACATGAAATGGACCATGATTTGGATTAATG
1 ATATAGATACATGAAATAAACCATGATTTAGATTAATG
*
58397039 ATATAGATATATGAAATAAACCATGATTTAGATTAATG
1 ATATAGATACATGAAATAAACCATGATTTAGATTAATG
58397077 ATAT
1 ATAT
58397081 GGATTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (38 bp):
ATATAGATACATGAAATAAACCATGATTTAGATTAATG
Found at i:58400389 original size:21 final size:19
Alignment explanation
Indices: 58400351--58400398 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
58400341 AGATAATTTT
*
58400351 CTTTATTTTATGTTTTAAC
1 CTTTATTTTATATTTTAAC
58400370 CTTTATTATTACTATTTTAAC
1 CTTTATT-TTA-TATTTTAAC
*
58400391 TTTTATTT
1 CTTTATTT
58400399 AACACATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 14 0.56
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (19 bp):
CTTTATTTTATATTTTAAC
Found at i:58400983 original size:13 final size:13
Alignment explanation
Indices: 58400965--58400996 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
58400955 AGGGTGACAA
58400965 ACCTAGTATATTT
1 ACCTAGTATATTT
58400978 ACCTAGTATATTT
1 ACCTAGTATATTT
*
58400991 AACTAG
1 ACCTAG
58400997 CGTGTGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (13 bp):
ACCTAGTATATTT
Found at i:58401427 original size:22 final size:22
Alignment explanation
Indices: 58401384--58401427 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
58401374 TTTTGTTGCT
* *
58401384 TCCATTTTCAGCACCTTTGCTG
1 TCCATTTTCAGCACCATAGCTG
58401406 TCCATTTT-AGTCACCATAGCTG
1 TCCATTTTCAG-CACCATAGCTG
58401428 CACCTCATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (22 bp):
TCCATTTTCAGCACCATAGCTG
Found at i:58402974 original size:15 final size:15
Alignment explanation
Indices: 58402954--58402983 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58402944 GAGATTGCCA
58402954 AACATGCCAAGAAGG
1 AACATGCCAAGAAGG
58402969 AACATGCCAAGAAGG
1 AACATGCCAAGAAGG
58402984 TCCATCCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.27, T:0.07
Consensus pattern (15 bp):
AACATGCCAAGAAGG
Found at i:58422188 original size:13 final size:13
Alignment explanation
Indices: 58422170--58422194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58422160 GCCAACCATT
58422170 TATAGATTTTTTC
1 TATAGATTTTTTC
58422183 TATAGATTTTTT
1 TATAGATTTTTT
58422195 TGTTCTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TATAGATTTTTTC
Found at i:58428746 original size:23 final size:23
Alignment explanation
Indices: 58428718--58428763 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
58428708 TGGGGAGAGG
58428718 TTATCAGAAAATAATTTGATTAT
1 TTATCAGAAAATAATTTGATTAT
58428741 TTATCAGAAAATAATTTGATTAT
1 TTATCAGAAAATAATTTGATTAT
58428764 CTTTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (23 bp):
TTATCAGAAAATAATTTGATTAT
Found at i:58435031 original size:46 final size:44
Alignment explanation
Indices: 58434964--58435140 Score: 194
Period size: 46 Copynumber: 3.9 Consensus size: 44
58434954 TGTAACCCGC
58434964 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGTATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GG-ATTCGCAT
* *
58435010 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATTCGC-A--T
* *** * *
58435056 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG--ATTCGCAT
*
58435103 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAT
58435141 GCCCAAAACA
Statistics
Matches: 110, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 6 0.05
45 2 0.02
46 66 0.60
47 31 0.28
49 3 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATTCGCAT
Found at i:58435084 original size:93 final size:93
Alignment explanation
Indices: 58434972--58435143 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
58434962 GCCCATAAGT
*
58434972 GAACTCGGACTCAACTCAACGAGCTCAGG-TATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
58435036 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* * *
58435065 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
58435130 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
58435144 CAAAACATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:58444487 original size:124 final size:124
Alignment explanation
Indices: 58444265--58444489 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 124
58444255 GAATTATGTG
* * * * * * *
58444265 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
* **
58444330 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
*
58444389 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
*
58444454 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
58444490 CCGGGTTAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 3 0.03
124 85 0.97
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (124 bp):
AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
Found at i:58444611 original size:40 final size:40
Alignment explanation
Indices: 58444484--58444613 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
58444474 TTGCTGGAAA
* * *
58444484 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
58444524 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
* *
58444564 TTCTATCCGGGCTAAGACCTGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
58444604 TTATATCCGG
1 TTATATCCGG
58444614 TTGTATTCCA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:58463582 original size:56 final size:56
Alignment explanation
Indices: 58463515--58463627 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
58463505 TTATTTACTC
* *
58463515 TAACTTCCAGAAGAATGATGACATAAACATTTATCAAATCTCTTCAAGTGATCATT
1 TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTTCAAGTGATCATT
*
58463571 TAACTTCCAGAAGAATAATGATATAAACATTTACCAAATCTCTTCAAGTGATCATT
1 TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTTCAAGTGATCATT
58463627 T
1 T
58463628 GAAAAACTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (56 bp):
TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTTCAAGTGATCATT
Found at i:58468541 original size:60 final size:54
Alignment explanation
Indices: 58468423--58468530 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
58468413 AAATTAACCA
*
58468423 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAATAAAATT
1 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
*
58468477 TGATAATGTATGGTTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
1 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
58468531 GAACTGTGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (54 bp):
TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
Found at i:58471185 original size:13 final size:14
Alignment explanation
Indices: 58471155--58471185 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
58471145 TTCTTCTTTC
58471155 TTTTCTTTCGTTCT
1 TTTTCTTTCGTTCT
58471169 TTTTCTTTC-TTCT
1 TTTTCTTTCGTTCT
58471182 TTTT
1 TTTT
58471186 ACCATACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTCTTTCGTTCT
Found at i:58471201 original size:3 final size:3
Alignment explanation
Indices: 58471195--58471271 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
58471185 TACCATACTA
58471195 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58471243 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
58471272 ATAATGCATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:58472358 original size:22 final size:22
Alignment explanation
Indices: 58472301--58472348 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
58472291 TCACTTGCCG
58472301 AGAAACACCTTCATATTGTAAT
1 AGAAACACCTTCATATTGTAAT
58472323 AGAAACACCTTCATATTGTAAT
1 AGAAACACCTTCATATTGTAAT
58472345 AGAA
1 AGAA
58472349 TTTATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (22 bp):
AGAAACACCTTCATATTGTAAT
Found at i:58475860 original size:15 final size:15
Alignment explanation
Indices: 58475840--58475869 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58475830 TAAAGCCTCC
58475840 TTTTAAACAATCATT
1 TTTTAAACAATCATT
58475855 TTTTAAACAATCATT
1 TTTTAAACAATCATT
58475870 GTTTCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTTAAACAATCATT
Found at i:58498418 original size:27 final size:26
Alignment explanation
Indices: 58498378--58498468 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
58498368 CATAAATTTT
* * *
58498378 TTTTTTTAAATTTTGTTAATTTTAGA
1 TTTTTATATATTTTTTTAATTTTAGA
**
58498404 TTTTTATATATTTTTTTGAATTTTCTA
1 TTTTTATATATTTTTTT-AATTTTAGA
* * *
58498431 TATTTATAAATTGTTTTTTATTTTTATGA
1 TTTTTATATA-T-TTTTTTAATTTTA-GA
58498460 TTTTTATAT
1 TTTTTATAT
58498469 TTATAAAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
26 14 0.29
27 15 0.31
28 6 0.12
29 14 0.29
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.68
Consensus pattern (26 bp):
TTTTTATATATTTTTTTAATTTTAGA
Found at i:58498419 original size:19 final size:19
Alignment explanation
Indices: 58498397--58498435 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
58498387 ATTTTGTTAA
*
58498397 TTTTAGATTTTTATATATT
1 TTTTAGAATTTTATATATT
* *
58498416 TTTTTGAATTTTCTATATT
1 TTTTAGAATTTTATATATT
58498435 T
1 T
58498436 ATAAATTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTAGAATTTTATATATT
Found at i:58498420 original size:29 final size:29
Alignment explanation
Indices: 58498388--58498468 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 29
58498378 TTTTTTTAAA
58498388 TTTTGTTAATTTTAGATTTTTATATATT-
1 TTTTGTTAATTTTAGATTTTTATATATTG
* ** * *
58498416 TTTT-TGAATTTTCTATATTTATAAATTG
1 TTTTGTTAATTTTAGATTTTTATATATTG
*
58498444 TTTT-TTATTTTTATGATTTTTATAT
1 TTTTGTTAATTTTA-GATTTTTATAT
58498469 TTATAAAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
27 18 0.45
28 14 0.35
29 8 0.20
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (29 bp):
TTTTGTTAATTTTAGATTTTTATATATTG
Found at i:58499442 original size:16 final size:17
Alignment explanation
Indices: 58499409--58499445 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
58499399 TGACTCCACC
58499409 AAATAAAATATTTAAAA
1 AAATAAAATATTTAAAA
58499426 AAATAATAAT-TTTAAAA
1 AAATAA-AATATTTAAAA
58499443 AAA
1 AAA
58499446 GAATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAAATATTTAAAA
Found at i:58504083 original size:3 final size:3
Alignment explanation
Indices: 58504075--58504138 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
58504065 CTGTTACCAA
58504075 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
58504123 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
58504139 TCCAATTTAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:58514912 original size:21 final size:21
Alignment explanation
Indices: 58514888--58514934 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
58514878 TTAAATTATT
58514888 TTAAATATA-ATAAAAATAAAA
1 TTAAATATATAT-AAAATAAAA
*
58514909 TTAATTATATATAAAATAAAA
1 TTAAATATATATAAAATAAAA
*
58514930 ATAAA
1 TTAAA
58514935 AATTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAATATATATAAAATAAAA
Found at i:58515254 original size:13 final size:14
Alignment explanation
Indices: 58515238--58515266 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
58515228 ATTTTAGTCA
58515238 TTAATTTA-ATTTT
1 TTAATTTATATTTT
58515251 TTAATTTATATTTT
1 TTAATTTATATTTT
58515265 TT
1 TT
58515267 GTCAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTAATTTATATTTT
Found at i:58515906 original size:35 final size:35
Alignment explanation
Indices: 58515849--58515916 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
58515839 AAAGCCTACT
* * *
58515849 GAATCTTAATTTGATTAATATTAGTATAATTGTCA
1 GAATCTTAACTTAATTAATATTAGCATAATTGTCA
**
58515884 GAATCTTAACTTAATTTGTATTAGCATAATTGT
1 GAATCTTAACTTAATTAATATTAGCATAATTGT
58515917 TAATATAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (35 bp):
GAATCTTAACTTAATTAATATTAGCATAATTGTCA
Found at i:58516835 original size:14 final size:15
Alignment explanation
Indices: 58516816--58516844 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58516806 TGATTTTTCT
58516816 AAAAAAGAAA-TAAA
1 AAAAAAGAAACTAAA
58516830 AAAAAAGAAACTAAA
1 AAAAAAGAAACTAAA
58516845 CAATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAGAAACTAAA
Found at i:58517110 original size:9 final size:9
Alignment explanation
Indices: 58517085--58517128 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
58517075 CCGATGAGGA
*
58517085 AACAGCAAC
1 AACAGCAGC
*
58517094 AACTGCAGC
1 AACAGCAGC
58517103 AACAGCAGC
1 AACAGCAGC
*
58517112 AGCAGCAGC
1 AACAGCAGC
*
58517121 AGCAGCAG
1 AACAGCAG
58517129 ATGACTACGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.41, C:0.32, G:0.25, T:0.02
Consensus pattern (9 bp):
AACAGCAGC
Found at i:58517111 original size:3 final size:3
Alignment explanation
Indices: 58517098--58517128 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
58517088 AGCAACAACT
*
58517098 GCA GCA ACA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G
58517129 ATGACTACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:58517113 original size:12 final size:12
Alignment explanation
Indices: 58517087--58517127 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
58517077 GATGAGGAAA
* *
58517087 CAGCAACAACTG
1 CAGCAACAGCAG
58517099 CAGCAACAGCAG
1 CAGCAACAGCAG
*
58517111 CAGCAGCAGCAG
1 CAGCAACAGCAG
58517123 CAGCA
1 CAGCA
58517128 GATGACTACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.39, C:0.34, G:0.24, T:0.02
Consensus pattern (12 bp):
CAGCAACAGCAG
Found at i:58529785 original size:14 final size:15
Alignment explanation
Indices: 58529768--58529801 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
58529758 TTAAATGCTG
58529768 AAAAAA-TAAATATT
1 AAAAAAGTAAATATT
*
58529782 AAAAAAGTAAGTATT
1 AAAAAAGTAAATATT
58529797 AAAAA
1 AAAAA
58529802 TTTAAAGTTA
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:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAAAGTAAATATT
Found at i:58532466 original size:37 final size:37
Alignment explanation
Indices: 58532413--58532497 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
58532403 GTTTATTTCC
*
58532413 TAAAATAAAATCTTTAAAAGATAATATAATATTAAAA
1 TAAAATAAAATATTTAAAAGATAATATAATATTAAAA
* * *
58532450 TAAAATAAAATATTTAAAGGATAATATTATTTTAAAA
1 TAAAATAAAATATTTAAAAGATAATATAATATTAAAA
58532487 TAAAATAAAAT
1 TAAAATAAAAT
58532498 TTGAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (37 bp):
TAAAATAAAATATTTAAAAGATAATATAATATTAAAA
Found at i:58532475 original size:19 final size:19
Alignment explanation
Indices: 58532416--58532497 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 19
58532406 TATTTCCTAA
*
58532416 AATAAAATCTTTAAAAGAT
1 AATAAAATATTTAAAAGAT
* * *
58532435 AATATAATA-TTAAAATAA
1 AATAAAATATTTAAAAGAT
*
58532453 AATAAAATATTTAAAGGAT
1 AATAAAATATTTAAAAGAT
** * *
58532472 AATATTAT-TTTAAAATAA
1 AATAAAATATTTAAAAGAT
58532490 AATAAAAT
1 AATAAAAT
58532498 TTGAAAAAAA
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
18 28 0.60
19 19 0.40
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (19 bp):
AATAAAATATTTAAAAGAT
Found at i:58532493 original size:18 final size:18
Alignment explanation
Indices: 58532414--58532509 Score: 68
Period size: 18 Copynumber: 5.3 Consensus size: 18
58532404 TTTATTTCCT
*
58532414 AAAATAAAATCTTTAAAAG
1 AAAATATAAT-TTTAAAAG
* * *
58532433 ATAATATAATATTAAAAT
1 AAAATATAATTTTAAAAG
* *
58532451 AAAATAAAATATTTAAAGG
1 AAAATATAAT-TTTAAAAG
* * *
58532470 ATAATATTATTTTAAAAT
1 AAAATATAATTTTAAAAG
* *
58532488 AAAATAAAATTTGAAAA-
1 AAAATATAATTTTAAAAG
58532505 AAAAT
1 AAAAT
58532510 CTGCATGTAA
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
17 5 0.09
18 33 0.57
19 20 0.34
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAATATAATTTTAAAAG
Found at i:58536766 original size:5 final size:5
Alignment explanation
Indices: 58536731--58536797 Score: 62
Period size: 5 Copynumber: 12.6 Consensus size: 5
58536721 AAATAGAAAG
* * *
58536731 ATTTT ATTTT GTTTT GTTTT GTTTT ATTTTT ATTTT ATTATTT ATATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT A-T-TTT AT-TTT
*
58536780 ATATT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATT
58536798 AATTTAGGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
5 38 0.69
6 13 0.24
7 4 0.07
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:58536780 original size:18 final size:18
Alignment explanation
Indices: 58536753--58536787 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58536743 TTTGTTTTGT
* *
58536753 TTTATTTTTATTTTATTA
1 TTTATATTTATATTATTA
58536771 TTTATATTTATATTATT
1 TTTATATTTATATTATT
58536788 TTATTTTATT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATATTTATATTATTA
Found at i:58541570 original size:42 final size:42
Alignment explanation
Indices: 58541504--58541617 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
58541494 GGTTTTGGGG
* *
58541504 ATTCTAAGGCTGAAATAGGACTGTTTGGCT-GCAGAGATATAGC
1 ATTCT-AGGCTGGAATAGAACTGTTTGG-TAGCAGAGATATAGC
* * *
58541547 ATTCTGGGCTGGAATAGAACTGTTTGGTAGCAGGGATATGGC
1 ATTCTAGGCTGGAATAGAACTGTTTGGTAGCAGAGATATAGC
* *
58541589 ATTTTAGGTTGGAATAGAACTGTTTGGTA
1 ATTCTAGGCTGGAATAGAACTGTTTGGTA
58541618 CCATGGATAG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 56 0.90
43 5 0.08
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.32
Consensus pattern (42 bp):
ATTCTAGGCTGGAATAGAACTGTTTGGTAGCAGAGATATAGC
Found at i:58541731 original size:10 final size:10
Alignment explanation
Indices: 58541718--58541797 Score: 67
Period size: 10 Copynumber: 7.8 Consensus size: 10
58541708 ATTAATATTT
58541718 AAATAAAATA
1 AAATAAAATA
58541728 AAAT-AAATA
1 AAATAAAATA
58541737 AAATAAAATAA
1 AAATAAAAT-A
58541748 TAAATAATAA-A
1 -AAATAA-AATA
* *
58541759 TAATAAAAAA
1 AAATAAAATA
*
58541769 AAATAATA-A
1 AAATAAAATA
58541778 AAATAAAAATAA
1 AAAT-AAAAT-A
58541790 AAATAAAA
1 AAATAAAA
58541798 AGAAAGATTG
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
9 16 0.28
10 23 0.40
11 6 0.10
12 11 0.19
13 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAAAATA
Found at i:58541736 original size:14 final size:14
Alignment explanation
Indices: 58541717--58541790 Score: 75
Period size: 14 Copynumber: 5.3 Consensus size: 14
58541707 TATTAATATT
58541717 TAAATAAAATAAAA
1 TAAATAAAATAAAA
58541731 TAAATAAAATAAAA
1 TAAATAAAATAAAA
58541745 T-AAT-AAATAATAA
1 TAAATAAAATAA-AA
*
58541758 -ATAATAAAAAAAAA
1 TA-AATAAAATAAAA
58541772 T-AATAAAAATAAAAA
1 TAAAT-AAAAT-AAAA
58541787 TAAA
1 TAAA
58541791 AATAAAAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
12 6 0.12
13 8 0.16
14 24 0.48
15 10 0.20
16 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAATAAAATAAAA
Found at i:58541754 original size:7 final size:6
Alignment explanation
Indices: 58541718--58541798 Score: 74
Period size: 6 Copynumber: 12.5 Consensus size: 6
58541708 ATTAATATTT
*
58541718 AAAT-A AAATAA AATAAATA AAATAAA ATAATAA ATAATAA ATAATAA
1 AAATAA AAATAA AA-ATA-A AAAT-AA A-AATAA A-AATAA A-AATAA
*
58541765 AAAAAA ATAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA A-AATAA AAATAA AAATAA AAATAA AAA
58541799 GAAAGATTGG
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.06
6 28 0.42
7 27 0.41
8 7 0.11
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:58541797 original size:27 final size:26
Alignment explanation
Indices: 58541722--58541798 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 26
58541712 ATATTTAAAT
58541722 AAAAT-AAAATAAATAAAATAAAATAATA
1 AAAATAAAAAT-AA-AAAA-AAAATAATA
58541750 AATAATAAATAAT-AAAAAAAAATAATA
1 AA-AATAAA-AATAAAAAAAAAATAATA
58541777 AAAATAAAAATAAAAATAAAAA
1 AAAATAAAAATAAAAA-AAAAA
58541799 GAAAGATTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
25 3 0.07
26 10 0.23
27 16 0.36
28 6 0.14
29 4 0.09
30 2 0.05
31 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (26 bp):
AAAATAAAAATAAAAAAAAAATAATA
Found at i:58545573 original size:27 final size:26
Alignment explanation
Indices: 58545543--58545604 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
58545533 AGATAATTAA
58545543 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
58545570 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
58545597 AATAAAAT
1 AATAAAAT
58545605 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:58549039 original size:46 final size:44
Alignment explanation
Indices: 58548935--58549042 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
58548925 TGTCTTTGAC
** * * *
58548935 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
58548979 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
58549025 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
58549043 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:58551830 original size:6 final size:5
Alignment explanation
Indices: 58551799--58551848 Score: 55
Period size: 5 Copynumber: 9.2 Consensus size: 5
58551789 ATAGAAAGAC
*
58551799 TTTAT TTTGT TTTAT TTTATT ATTTAT ATTTAT ATTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTA-T -TTTAT -TTTAT -TTTAT TTTAT TTTAT
58551848 T
1 T
58551849 AATTTAGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 23 0.56
6 14 0.34
7 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:58556554 original size:169 final size:169
Alignment explanation
Indices: 58556261--58556598 Score: 505
Period size: 169 Copynumber: 2.0 Consensus size: 169
58556251 CCTTCAATAG
* * * *
58556261 TAACCCACAAGACCCAAAAAACTACGGATCTTAGAAACGTTCCTAGGTTGTTTCCAATCAAGCAC
1 TAACCCACAAGACCCAAAAAAATACGGATCTCAAAAACGTTCCTAGGCTGTTTCCAATCAAGCAC
* * *
58556326 AGCCTCAATCTTTCTAGGATCAACTCAAATCCATTCAGCAAAAACTACGTACCCTAGAAATGTTA
66 AGCCTCAACCTTTCTAGGATCAACTCAAACCCATTCAGCAAAAACTACGTACACTAGAAATGTTA
* * * *
58556391 TTTCCTGTAATCATAATTCACATTTGCTCAACTTAGCGT
131 TTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
* * * *
58556430 TAACCCGCAAGACCCAAAAAAATGCGGATCTCAAAAAGGTTCCTAGGCTGTTTCCTATCAAGCAC
1 TAACCCACAAGACCCAAAAAAATACGGATCTCAAAAACGTTCCTAGGCTGTTTCCAATCAAGCAC
* * * *
58556495 GGCCTCAACCTTTCTAGGATCAACTCAGACCCATTCAGTAGAAACTACGTACACTAGAAATGTTA
66 AGCCTCAACCTTTCTAGGATCAACTCAAACCCATTCAGCAAAAACTACGTACACTAGAAATGTTA
58556560 TTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
131 TTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
58556599 AGAGCTACTT
Statistics
Matches: 150, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
169 150 1.00
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (169 bp):
TAACCCACAAGACCCAAAAAAATACGGATCTCAAAAACGTTCCTAGGCTGTTTCCAATCAAGCAC
AGCCTCAACCTTTCTAGGATCAACTCAAACCCATTCAGCAAAAACTACGTACACTAGAAATGTTA
TTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
Found at i:58557627 original size:27 final size:27
Alignment explanation
Indices: 58557597--58557659 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
58557587 ATGGATTAGT
*
58557597 ACAATAATCTCATCAGAAGTACACTCA
1 ACAATAATCTCACCAGAAGTACACTCA
* *
58557624 ACAATAATCTGACCGGAAGTACACTCA
1 ACAATAATCTCACCAGAAGTACACTCA
58557651 ACAATAATC
1 ACAATAATC
58557660 CTCAAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (27 bp):
ACAATAATCTCACCAGAAGTACACTCA
Found at i:58564132 original size:15 final size:15
Alignment explanation
Indices: 58564112--58564164 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
58564102 AATGTAGAAT
*
58564112 CAAATAATTACGATA
1 CAAATAATTACAATA
*
58564127 CAAATACATTA-AAAA
1 CAAATA-ATTACAATA
*
58564142 TCAAATTATTACAATA
1 -CAAATAATTACAATA
58564158 CAAATAA
1 CAAATAA
58564165 ATTATAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.26
Consensus pattern (15 bp):
CAAATAATTACAATA
Found at i:58564144 original size:31 final size:31
Alignment explanation
Indices: 58564109--58564173 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
58564099 TTAAATGTAG
* *
58564109 AATCAAATAATTACGATACAAATACATTAAA
1 AATCAAATAATTACAATACAAATAAATTAAA
* *
58564140 AATCAAATTATTACAATACAAATAAATTATA
1 AATCAAATAATTACAATACAAATAAATTAAA
58564171 AAT
1 AAT
58564174 AATTGGAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (31 bp):
AATCAAATAATTACAATACAAATAAATTAAA
Found at i:58568365 original size:16 final size:18
Alignment explanation
Indices: 58568329--58568366 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58568319 ATTCGATACG
*
58568329 TGTTTGTATATGTTAGCA
1 TGTTTGTATATGATAGCA
58568347 TGTTTGTATAT-AT-GCA
1 TGTTTGTATATGATAGCA
58568363 TGTT
1 TGTT
58568367 ATGAGTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (18 bp):
TGTTTGTATATGATAGCA
Found at i:58568515 original size:2 final size:2
Alignment explanation
Indices: 58568508--58568545 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
58568498 TGTTCTAATC
*
58568508 AT AT AT AT AT AT AT AT AT AT AT AT GT 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
58568546 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58568550 original size:2 final size:2
Alignment explanation
Indices: 58568545--58568569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58568535 TATATATATA
58568545 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
58568570 ATATATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:58574298 original size:40 final size:39
Alignment explanation
Indices: 58574174--58574297 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
58574164 GCATGATACT
*
58574174 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
58574213 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
* * * * *
58574252 TGGAAATATATCCGGGCTTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAACATATCCGGACTTGAGGT-CCGCAGGCTATGTGC
*
58574292 TAGAAA
1 TGGAAA
58574298 TTGGACTCGG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 58 0.75
40 19 0.25
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
Found at i:58581887 original size:12 final size:12
Alignment explanation
Indices: 58581866--58581898 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
58581856 TGGTTTGTAC
*
58581866 GTGAATTAAGAT
1 GTGAAATAAGAT
58581878 GTGAAATAAGAT
1 GTGAAATAAGAT
58581890 GTGAAATAA
1 GTGAAATAA
58581899 ATAATTCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.27
Consensus pattern (12 bp):
GTGAAATAAGAT
Found at i:58582160 original size:39 final size:39
Alignment explanation
Indices: 58582106--58582216 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
58582096 GCATGATACT
58582106 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
*
58582145 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
* * * *
58582184 TGGAAATATATCCGGGCTTAAAGTCCGCAGGCT
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCT
58582217 TTTGCTAGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
Found at i:58584789 original size:117 final size:119
Alignment explanation
Indices: 58584524--58584797 Score: 392
Period size: 121 Copynumber: 2.3 Consensus size: 119
58584514 TAGAAAGGGA
* *
58584524 AAGTATCCAAAGTCCTAACAAAACATAATTATACAATTACAAGTCATGCACATCATCTAATATAG
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
* * *
58584589 GTAATGTATCCAAGAAAGGTTCAAAATATAATATTATCAAAGAAAGTTCAAAGAGG
66 GTAATGTA--CAAGAAAAGTTCAAAATATAATACTACCAAAGAAAGTTCAAAGAGG
* * *
58584645 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCATATCATCTCAGATTG
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
* *
58584710 GTAATGTA-AAGAAAAGTTC-AAATATAATACTACC-ATGAAAAGTTCAAAGATG
66 GTAATGTACAAGAAAAGTTCAAAATATAATACTACCAAAG-AAAGTTCAAAGAGG
* *
58584762 AAGTATTCAAAGTTCTAACAAAACCTAATTATACAA
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAA
58584798 AGCCTAAGAA
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
116 2 0.01
117 60 0.43
118 10 0.07
121 68 0.49
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (119 bp):
AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
GTAATGTACAAGAAAAGTTCAAAATATAATACTACCAAAGAAAGTTCAAAGAGG
Done.