Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 15 of 199
Found at i:6315212 original size:23 final size:21
Alignment explanation
Indices: 6315154--6315233 Score: 115
Period size: 22 Copynumber: 3.7 Consensus size: 21
6315144 GCTTTAAGAG
* *
6315154 GAATTTGAGAGGAATTTGAGA
1 GAATTTGAGAGAAATATGAGA
6315175 GGAATTTGAGAGAAATATGAGA
1 -GAATTTGAGAGAAATATGAGA
6315197 GAATATTGGAGAGAAATATGAGA
1 GAAT-TT-GAGAGAAATATGAGA
6315220 GAATTTGAGAGAAA
1 GAATTTGAGAGAAA
6315234 GGATTTAAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
21 12 0.22
22 23 0.43
23 19 0.35
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (21 bp):
GAATTTGAGAGAAATATGAGA
Found at i:6333221 original size:14 final size:14
Alignment explanation
Indices: 6333202--6333238 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6333192 TTTCTTTTTC
6333202 AGAAAGAAAAAAAA
1 AGAAAGAAAAAAAA
*
6333216 AGAAAGAAAAGAAA
1 AGAAAGAAAAAAAA
6333230 AGAAGAGAA
1 AGAA-AGAA
6333239 GATGTGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAAAA
Found at i:6341604 original size:25 final size:25
Alignment explanation
Indices: 6341576--6341623 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6341566 TTGCATAATT
*
6341576 ATGTCATGATT-CTATCACTACAATC
1 ATGTCA-GATTACTATCACAACAATC
6341601 ATGTCAGATTACTATCACAACAA
1 ATGTCAGATTACTATCACAACAA
6341624 CCTTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (25 bp):
ATGTCAGATTACTATCACAACAATC
Found at i:6349297 original size:31 final size:31
Alignment explanation
Indices: 6349204--6349299 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
6349194 GGCAAATTAC
*
6349204 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
*
6349235 AAGAGTAATTGAATTCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
6349267 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
6349298 AA
1 AA
6349300 ATTATCTAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:6349396 original size:3 final size:3
Alignment explanation
Indices: 6349388--6349412 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6349378 GAATTAAGTA
6349388 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
6349413 TACATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6349885 original size:12 final size:12
Alignment explanation
Indices: 6349868--6349893 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6349858 GTCGTAGTCG
6349868 GAGGATGTATTA
1 GAGGATGTATTA
6349880 GAGGATGTATTA
1 GAGGATGTATTA
6349892 GA
1 GA
6349894 AAAAGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (12 bp):
GAGGATGTATTA
Found at i:6351664 original size:3 final size:3
Alignment explanation
Indices: 6351656--6351684 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6351646 TATAATTTAA
6351656 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
6351685 CTAAAATTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6363928 original size:16 final size:16
Alignment explanation
Indices: 6363907--6363939 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6363897 TTGAACTCTG
6363907 TTGCAACTTGAGGTTA
1 TTGCAACTTGAGGTTA
6363923 TTGCAACTTGAGGTTA
1 TTGCAACTTGAGGTTA
6363939 T
1 T
6363940 CTATGAAGCG
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:0.12, G:0.24, T:0.39
Consensus pattern (16 bp):
TTGCAACTTGAGGTTA
Found at i:6376099 original size:26 final size:26
Alignment explanation
Indices: 6376063--6376112 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
6376053 ACAACGAGAA
*
6376063 TGTCAACTAAACTAGTAGGGGTGATT
1 TGTCAACTAAACTAGTAGAGGTGATT
*
6376089 TGTCAACTAAATTAGTAGAGGTGA
1 TGTCAACTAAACTAGTAGAGGTGA
6376113 GTTTAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (26 bp):
TGTCAACTAAACTAGTAGAGGTGATT
Found at i:6377535 original size:11 final size:11
Alignment explanation
Indices: 6377518--6377555 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
6377508 TTTTTAATCA
6377518 AATATATATTT
1 AATATATATTT
* *
6377529 TATATATATTA
1 AATATATATTT
6377540 AATATATATTT
1 AATATATATTT
6377551 AATAT
1 AATAT
6377556 GAGTCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:6378450 original size:21 final size:20
Alignment explanation
Indices: 6378413--6378451 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6378403 TGACAAACTG
*
6378413 TTGTTATTATAAGTAAAAAA
1 TTGTTATAATAAGTAAAAAA
*
6378433 TTGTTATAAATAATTAAAA
1 TTGTTAT-AATAAGTAAAA
6378452 TAAAACCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
TTGTTATAATAAGTAAAAAA
Found at i:6390768 original size:19 final size:21
Alignment explanation
Indices: 6390740--6390778 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6390730 AAATTTTAGT
*
6390740 TTTTTTAAA-TATTT-TTATA
1 TTTTTAAAATTATTTGTTATA
6390759 TTTTTAAAATTATTTGTTAT
1 TTTTTAAAATTATTTGTTAT
6390779 CATGACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTAAAATTATTTGTTATA
Found at i:6393606 original size:9 final size:8
Alignment explanation
Indices: 6393585--6393615 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6393575 AAAATAAAAA
6393585 TAAAAATT
1 TAAAAATT
6393593 TAAAAATT
1 TAAAAATT
*
6393601 TAAAAAGT
1 TAAAAATT
6393609 TAAAAAT
1 TAAAAAT
6393616 ATCATAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (8 bp):
TAAAAATT
Found at i:6397658 original size:19 final size:19
Alignment explanation
Indices: 6397617--6397658 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6397607 TCAGAATTTT
* *
6397617 TATTTTTATTTTTAAATTG
1 TATTTTTATTTATAAATTA
6397636 TATTTTTATTTAATAAA-TA
1 TATTTTTATTT-ATAAATTA
6397655 TATT
1 TATT
6397659 ATTTTCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTTATTTATAAATTA
Found at i:6404548 original size:51 final size:51
Alignment explanation
Indices: 6404467--6404574 Score: 182
Period size: 51 Copynumber: 2.1 Consensus size: 51
6404457 AGTACTTCTC
*
6404467 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAATGACA
*
6404518 AGTGGCAAGTGATAAGT-GATAGCTTCAGCTACACTTATCTGATCAATGACA
1 AGTGACAAGTGATAAGTAG-TAGCTTCAGCTACACTTATCTGATCAATGACA
6404569 AGTGAC
1 AGTGAC
6404575 TTATCTAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAATGACA
Found at i:6404576 original size:23 final size:23
Alignment explanation
Indices: 6404550--6404597 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
6404540 CTTCAGCTAC
*
6404550 ACTTATCTGATCAATGACAAGTG
1 ACTTATCTAATCAATGACAAGTG
*
6404573 ACTTATCTAATCAGTGACAAGTG
1 ACTTATCTAATCAATGACAAGTG
6404596 AC
1 AC
6404598 AAGTGATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (23 bp):
ACTTATCTAATCAATGACAAGTG
Found at i:6404588 original size:74 final size:74
Alignment explanation
Indices: 6404499--6404647 Score: 262
Period size: 74 Copynumber: 2.0 Consensus size: 74
6404489 CTTCAGCTAC
* *
6404499 ACTTATCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAA
1 ACTTATCTAATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAA
6404564 TGACAAGTG
66 TGACAAGTG
* *
6404573 ACTTATCTAATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
1 ACTTATCTAATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAA
6404638 TGACAAGTG
66 TGACAAGTG
6404647 A
1 A
6404648 TGAGTGGTAG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (74 bp):
ACTTATCTAATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAA
TGACAAGTG
Found at i:6404659 original size:44 final size:44
Alignment explanation
Indices: 6404592--6404735 Score: 227
Period size: 44 Copynumber: 3.3 Consensus size: 44
6404582 ATCAGTGACA
* *
6404592 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATC
6404636 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATC
* * *
6404680 AGTGACAAGTAATGAGTGGTAGCTTTAGCTACACTTATATGATT
1 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATC
6404724 AG-GTACAAGTGA
1 AGTG-ACAAGTGA
6404736 CAAGTGATAA
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 1 0.01
44 92 0.99
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (44 bp):
AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:6422512 original size:22 final size:22
Alignment explanation
Indices: 6422487--6422530 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6422477 CATATAAAAT
*
6422487 TATAATAAATCTTTAATAGTAA
1 TATAATAAATCTTTAACAGTAA
*
6422509 TATAATAAGTCTTTAACAGTAA
1 TATAATAAATCTTTAACAGTAA
6422531 ACACAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
TATAATAAATCTTTAACAGTAA
Found at i:6423406 original size:6 final size:6
Alignment explanation
Indices: 6423395--6423428 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6423385 TCAAGAACCG
* *
6423395 TGGGAT TGGGAT TGGGAT TGAGAT TGAGAT TGGG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGG
6423429 CTTATTAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (6 bp):
TGGGAT
Found at i:6425279 original size:3 final size:3
Alignment explanation
Indices: 6425271--6425301 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6425261 TCTCGAGGTC
*
6425271 CAT CAT CAT CAT CAT CAT CAT CAT CAC CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
6425302 CTGTAGGGAG
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:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:6430409 original size:318 final size:318
Alignment explanation
Indices: 6429832--6430467 Score: 1236
Period size: 318 Copynumber: 2.0 Consensus size: 318
6429822 CAAGAAAAAT
6429832 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
1 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
* *
6429897 CATTTAACCAGTGCCAATGGTCAAATCAAATCCTTTTTCTGAATCACTCTGGATGTAAAACATGA
66 CATTTAACCAGTGCCAATGGTCAAATCAAATCCTCTTTCTGAATCACTCGGGATGTAAAACATGA
*
6429962 AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTTACG
131 AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACG
*
6430027 ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCCAGAACCAAATATGCAGATA
196 ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCAAGAACCAAATATGCAGATA
6430092 CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
261 CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
6430150 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
1 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
6430215 CATTTAACCAGTGCCAATGGTCAAATCAAATCCTCTTTCTGAATCACTCGGGATGTAAAACATGA
66 CATTTAACCAGTGCCAATGGTCAAATCAAATCCTCTTTCTGAATCACTCGGGATGTAAAACATGA
6430280 AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACG
131 AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACG
6430345 ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCAAGAACCAAATATGCAGATA
196 ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCAAGAACCAAATATGCAGATA
6430410 CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
261 CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
6430468 TTCTAGCAGG
Statistics
Matches: 314, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
318 314 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (318 bp):
CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
CATTTAACCAGTGCCAATGGTCAAATCAAATCCTCTTTCTGAATCACTCGGGATGTAAAACATGA
AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACG
ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCAAGAACCAAATATGCAGATA
CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
Found at i:6453079 original size:16 final size:16
Alignment explanation
Indices: 6453080--6453132 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
6453070 AAAATTAAAA
*
6453080 AAAATTAAAAGTATTTT
1 AAAATTAAAA-TAATTT
*
6453097 AAAATTAAAATACTTT
1 AAAATTAAAATAATTT
*
6453113 AAAATTAAAAAAATTT
1 AAAATTAAAATAATTT
6453129 AAAA
1 AAAA
6453133 AAAGCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 23 0.70
17 10 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATTAAAATAATTT
Found at i:6453114 original size:27 final size:27
Alignment explanation
Indices: 6453056--6453116 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
6453046 AAAAATTTAT
6453056 TTTAAAAATATTTTAAAATTAAAAAAA
1 TTTAAAAATATTTTAAAATTAAAAAAA
* * * *
6453083 ATTAAAAGTATTTTAAAATTAAAATAC
1 TTTAAAAATATTTTAAAATTAAAAAAA
6453110 TTTAAAA
1 TTTAAAA
6453117 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
TTTAAAAATATTTTAAAATTAAAAAAA
Found at i:6453133 original size:17 final size:17
Alignment explanation
Indices: 6453079--6453133 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
6453069 TAAAATTAAA
**
6453079 AAAAATTAAAAGTATTT
1 AAAAATTAAAAAAATTT
* * *
6453096 TAAAATTAAAATACTTT
1 AAAAATTAAAAAAATTT
6453113 -AAAATTAAAAAAATTT
1 AAAAATTAAAAAAATTT
6453129 AAAAA
1 AAAAA
6453134 AAGCATTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATTAAAAAAATTT
Found at i:6453156 original size:42 final size:42
Alignment explanation
Indices: 6453016--6453180 Score: 144
Period size: 43 Copynumber: 4.0 Consensus size: 42
6453006 TAAATACCAA
* * **
6453016 AAAATTATTTTAAAAATTAAAACAAAAATAAAAAATTTATTTT
1 AAAATTATTTTTAAAATTAAAA-AAAATTAAAAAAAGTATTTT
*
6453059 AAAAATA-TTTTAAAATTAAAAAAAATT---AAAAGTATTTT
1 AAAATTATTTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
* * *
6453097 AAAATTAAAATACTTTAAAATTAAAAAAATTTAAAAAAAGCATTTT
1 AAAATT---AT-TTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
* * *
6453143 AAAAGTATTTTT-AAATTTAAAAAAA-TAAAAAAATTATT
1 AAAATTATTTTTAAAATTAAAAAAAATTAAAAAAAGTATT
6453181 GTATTCGGGC
Statistics
Matches: 99, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
38 14 0.14
40 11 0.11
41 17 0.17
42 16 0.16
43 26 0.26
46 15 0.15
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (42 bp):
AAAATTATTTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
Found at i:6454756 original size:87 final size:87
Alignment explanation
Indices: 6454610--6454777 Score: 327
Period size: 87 Copynumber: 1.9 Consensus size: 87
6454600 GGGGAAACAA
6454610 CAACTAAATCTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGA
1 CAACTAAATCTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGA
6454675 GTATTAAGGGTCTCATGAATAG
66 GTATTAAGGGTCTCATGAATAG
*
6454697 CAACTAAATCTGGGATAGGTTTGTTTGTGATAGTAGTAGTAGGATCAGGAGGTATAATGAGGAGA
1 CAACTAAATCTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGA
6454762 GTATTAAGGGTCTCAT
66 GTATTAAGGGTCTCAT
6454778 CTTCATTAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.30
Consensus pattern (87 bp):
CAACTAAATCTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGA
GTATTAAGGGTCTCATGAATAG
Found at i:6465448 original size:6 final size:6
Alignment explanation
Indices: 6465432--6465466 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
6465422 AAGTAGCCAT
*
6465432 TTTTCC CTTTCC TTTTCC TTTTCC TTTTCAC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTC-C TTTT
6465467 GTTTTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTCC
Found at i:6484868 original size:6 final size:6
Alignment explanation
Indices: 6484818--6484851 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
6484808 TTAAATATAC
6484818 AATTGA AATTGA AATTGA AATTGA AATTGA AATT
1 AATTGA AATTGA AATTGA AATTGA AATTGA AATT
6484852 ATAAGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
AATTGA
Found at i:6485566 original size:14 final size:14
Alignment explanation
Indices: 6485544--6485573 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6485534 TTTAATTATT
6485544 ATATATTTAATGAA
1 ATATATTTAATGAA
*
6485558 ATATTTTTAATGAA
1 ATATATTTAATGAA
6485572 AT
1 AT
6485574 TAAAATTCTT
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:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATATTTAATGAA
Found at i:6489827 original size:21 final size:21
Alignment explanation
Indices: 6489801--6489841 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6489791 ATCTGCTCAA
* *
6489801 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6489822 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6489842 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:6493838 original size:6 final size:6
Alignment explanation
Indices: 6493827--6493851 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6493817 TAAGCATTAA
6493827 AGACAC AGACAC AGACAC AGACAC A
1 AGACAC AGACAC AGACAC AGACAC A
6493852 TACATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AGACAC
Found at i:6498429 original size:21 final size:21
Alignment explanation
Indices: 6498403--6498443 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6498393 ATCTGCTCAA
* *
6498403 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6498424 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6498444 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:6501700 original size:33 final size:33
Alignment explanation
Indices: 6501661--6501728 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
6501651 TTTAGTTATA
6501661 GTTAATTGTATAAATTTAACGGTTGATATAGTT
1 GTTAATTGTATAAATTTAACGGTTGATATAGTT
6501694 GTTAATTGTATAAATTTAACGGTTGATATAGTT
1 GTTAATTGTATAAATTTAACGGTTGATATAGTT
6501727 GT
1 GT
6501729 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (33 bp):
GTTAATTGTATAAATTTAACGGTTGATATAGTT
Found at i:6502013 original size:16 final size:16
Alignment explanation
Indices: 6501992--6502028 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6501982 GAGTGAAAGG
*
6501992 AAATTGGAAGGATAAA
1 AAATTGAAAGGATAAA
*
6502008 AAATTGAAAGTATAAA
1 AAATTGAAAGGATAAA
6502024 AAATT
1 AAATT
6502029 AAAAACGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (16 bp):
AAATTGAAAGGATAAA
Found at i:6521918 original size:20 final size:20
Alignment explanation
Indices: 6521884--6521925 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6521874 AACTGTTTAA
** *
6521884 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
6521904 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
6521924 AT
1 AT
6521926 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:6523958 original size:11 final size:11
Alignment explanation
Indices: 6523941--6523970 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6523931 AGGTTTGACT
6523941 TTGTTGATTGA
1 TTGTTGATTGA
*
6523952 TTTTTGATTGA
1 TTGTTGATTGA
6523963 TTGTTGAT
1 TTGTTGAT
6523971 AGATCATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (11 bp):
TTGTTGATTGA
Found at i:6535011 original size:16 final size:16
Alignment explanation
Indices: 6534963--6535014 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
6534953 TTTGGTTCGC
6534963 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
6534979 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6534995 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6535011 TGTA
1 TGTA
6535015 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.02, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6535079 original size:44 final size:45
Alignment explanation
Indices: 6534995--6535085 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
6534985 GGATTAGAGG
* * *
6534995 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
6535040 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
6535084 TG
1 TG
6535086 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:6535271 original size:18 final size:17
Alignment explanation
Indices: 6535250--6535284 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6535240 TTATTATTAA
*
6535250 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6535268 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6535285 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6535532 original size:17 final size:18
Alignment explanation
Indices: 6535491--6535526 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6535481 TTATTATTAA
* *
6535491 ATATATTTTAATTAAAAT
1 ATATAATTTAATAAAAAT
6535509 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
6535527 CTTAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:6535723 original size:119 final size:120
Alignment explanation
Indices: 6535233--6535854 Score: 1142
Period size: 119 Copynumber: 5.2 Consensus size: 120
6535223 ATCATATTTA
6535233 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
6535298 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
6535353 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAA-T-AATT
*
6535417 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
6535474 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAATCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
6535539 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
6535594 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAA-AAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
6535658 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
6535713 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAA-AAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
6535777 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
6535832 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
6535855 AACTTGAAAA
Statistics
Matches: 491, Mismatches: 8, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
119 215 0.44
120 160 0.33
121 115 0.23
122 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:6535847 original size:241 final size:241
Alignment explanation
Indices: 6535233--6535854 Score: 1144
Period size: 241 Copynumber: 2.6 Consensus size: 241
6535223 ATCATATTTA
6535233 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
6535298 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
* *
6535363 TTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGATAATATTCTTAT
131 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATTGAATAATATTCTTAT
*
6535428 ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 ATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
6535474 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAATCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
6535539 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
*
6535604 TTATTAAATATATTTTAATTAAACTATATAATTTAA-AAAATTCTTAA-T-AATTAATATTCTTA
131 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATTGAA-TAATATTCTTA
6535666 TATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
195 TATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
6535713 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAA-AAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
6535777 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
6535842 TTATTAAATATAT
131 TTATTAAATATAT
6535855 AACTTGAAAA
Statistics
Matches: 372, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
238 96 0.26
239 103 0.28
240 10 0.03
241 163 0.44
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (241 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATTGAATAATATTCTTAT
ATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:6538906 original size:33 final size:33
Alignment explanation
Indices: 6538867--6538976 Score: 136
Period size: 33 Copynumber: 3.3 Consensus size: 33
6538857 ATTATAAAGC
6538867 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
6538900 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
6538933 AATGT-T-ATTGTCCCTAAAA-AACATTGTTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
6538966 ATGTATAATTG
1 ATGTATAATTG
6538977 TTGGTTTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
32 9 0.14
33 49 0.74
34 8 0.12
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:6538983 original size:51 final size:51
Alignment explanation
Indices: 6538923--6539037 Score: 214
Period size: 51 Copynumber: 2.3 Consensus size: 51
6538913 CTAAAATTAC
6538923 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATGTATAA
6538974 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
6539025 TTGTTGGTTTAAT
1 TTGTTGGTTTAAT
6539038 TGTTGGTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 1 0.02
51 62 0.98
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.47
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
Found at i:6539010 original size:33 final size:33
Alignment explanation
Indices: 6538973--6539077 Score: 92
Period size: 33 Copynumber: 3.3 Consensus size: 33
6538963 TGTATGTATA
6538973 ATTGTTGGTTTAATGTTATTTACCCTAAAAAAC
1 ATTGTTGGTTTAATGTTATTTACCCTAAAAAAC
* * ** *****
6539006 ATTGTTGGTGT-ATGTATAATT--GTTGGTTTA-
1 ATTGTTGGTTTAATGT-TATTTACCCTAAAAAAC
6539036 ATTGTTGGTTTAATGTTATTTACCCTAAAAAAC
1 ATTGTTGGTTTAATGTTATTTACCCTAAAAAAC
6539069 ATTGTTGGT
1 ATTGTTGGT
6539078 GTATGATAAT
Statistics
Matches: 49, Mismatches: 18, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
30 14 0.29
31 6 0.12
32 6 0.12
33 23 0.47
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTGTTGGTTTAATGTTATTTACCCTAAAAAAC
Found at i:6539039 original size:12 final size:12
Alignment explanation
Indices: 6539022--6539049 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6539012 GGTGTATGTA
6539022 TAATTGTTGGTT
1 TAATTGTTGGTT
6539034 TAATTGTTGGTT
1 TAATTGTTGGTT
6539046 TAAT
1 TAAT
6539050 GTTATTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (12 bp):
TAATTGTTGGTT
Found at i:6539049 original size:63 final size:62
Alignment explanation
Indices: 6538971--6539088 Score: 227
Period size: 63 Copynumber: 1.9 Consensus size: 62
6538961 GGTGTATGTA
6538971 TAATTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAATTGTTGGTT
1 TAATTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATG-ATAATTGTTGGTT
6539034 TAATTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAATT
1 TAATTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAATT
6539089 TTTACGTATA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 6 0.11
63 49 0.89
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (62 bp):
TAATTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAATTGTTGGTT
Found at i:6539262 original size:86 final size:86
Alignment explanation
Indices: 6539155--6539335 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
6539145 TTCTCTCCAC
6539155 ATAA-AATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
6539219 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
6539240 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
6539305 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
6539326 ATAATAATTA
1 ATAATAATTA
6539336 CAATTATATT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (86 bp):
ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
TTAATATTAAAGATAAAAATT
Found at i:6542393 original size:31 final size:31
Alignment explanation
Indices: 6542358--6542420 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
6542348 TATAATTTTA
*
6542358 TTATTAAATTATTTAAAAGTTTTTATTTAAG
1 TTATTAAATTATTCAAAAGTTTTTATTTAAG
*
6542389 TTATTGAATTATTCAAAAGTTTTTATTTAAG
1 TTATTAAATTATTCAAAAGTTTTTATTTAAG
6542420 T
1 T
6542421 GATTGGGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (31 bp):
TTATTAAATTATTCAAAAGTTTTTATTTAAG
Found at i:6545948 original size:3 final size:3
Alignment explanation
Indices: 6545936--6545976 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
6545926 CTACTACTAC
*
6545936 TAT TAC 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 TAT TA
6545977 ACAACTAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6547575 original size:71 final size:71
Alignment explanation
Indices: 6547438--6547588 Score: 250
Period size: 71 Copynumber: 2.1 Consensus size: 71
6547428 GGGGAATCAT
*
6547438 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAATATACAATGG
6547503 ATATCG
66 ATATCG
***
6547509 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAA-ATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAATATACAATG
6547573 GATATCG
65 GATATCG
6547580 CACTTAGCA
1 CACTTAGCA
6547589 CCACCAATGA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
71 66 0.88
72 9 0.12
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAATATACAATGG
ATATCG
Found at i:6547617 original size:103 final size:104
Alignment explanation
Indices: 6547508--6547730 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
6547498 AATGGATATC
6547508 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAA-ATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
6547572 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
6547611 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
6547676 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
6547715 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
6547731 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 57 0.51
104 54 0.48
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:6554528 original size:26 final size:26
Alignment explanation
Indices: 6554492--6554543 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
6554482 CACCACTGAA
* *
6554492 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
6554518 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
6554544 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:6554620 original size:70 final size:71
Alignment explanation
Indices: 6554504--6554654 Score: 250
Period size: 72 Copynumber: 2.1 Consensus size: 71
6554494 GGGGAATCAT
6554504 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTT-CATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAATATACAATGG
6554568 ATATCG
66 ATATCG
* ***
6554574 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAATATATGGTG
1 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAATATACAATG
6554639 GATATCG
65 GATATCG
6554646 CACTTAGCA
1 CACTTAGCA
6554655 CCACCAATGA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
70 16 0.21
71 28 0.37
72 31 0.41
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAATATACAATGG
ATATCG
Found at i:6554750 original size:102 final size:104
Alignment explanation
Indices: 6554573--6554794 Score: 351
Period size: 102 Copynumber: 2.2 Consensus size: 104
6554563 AATGGATATC
*
6554573 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAATATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
6554638 GGATATCGCACTTAGCACCACCAATGAA-CCGGGAATCA
66 GGATATCGCACATAGCACCACCAATAAATCCGGGAATCA
6554676 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
6554740 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGAT-ATCGCACATAGCACCACCAATAAATCCGGGAATCA
**
6554779 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
6554795 TTTATATACA
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
102 69 0.63
103 41 0.37
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACATAGCACCACCAATAAATCCGGGAATCA
Found at i:6571027 original size:124 final size:124
Alignment explanation
Indices: 6570807--6571051 Score: 472
Period size: 124 Copynumber: 2.0 Consensus size: 124
6570797 TAATCAGAAC
*
6570807 AAGGAATAGACAACAACAACAGCAACAATAGTAAAATTTAATTAATCTGATAATGTTCTATTTAA
1 AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
*
6570872 AGTTAACCTAATAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCTAAT
66 AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCTAAT
6570931 AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
1 AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
6570996 AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCT
66 AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCT
6571052 CCAAAAGCCT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (124 bp):
AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCTAAT
Found at i:6573562 original size:36 final size:39
Alignment explanation
Indices: 6573522--6573614 Score: 138
Period size: 41 Copynumber: 2.4 Consensus size: 39
6573512 GAACAACACT
6573522 TGGTAGAA-TT-AAA-AATTCACACATAACAATCATCTA
1 TGGTAGAACTTGAAACAATTCACACATAACAATCATCTA
*
6573558 TGGTAGAACTTGAAACTCAGTTCACACATAACAATCATCTA
1 TGGTAGAACTTGAAA--CAATTCACACATAACAATCATCTA
6573599 TGGTAGAACTTGAAAC
1 TGGTAGAACTTGAAAC
6573615 TCAGTACTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
36 8 0.16
37 2 0.04
38 3 0.06
39 1 0.02
41 37 0.73
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (39 bp):
TGGTAGAACTTGAAACAATTCACACATAACAATCATCTA
Found at i:6573594 original size:41 final size:41
Alignment explanation
Indices: 6573537--6573619 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
6573527 GAATTAAAAA
6573537 TTCACACATAACAATCATCTATGGTAGAACTTGAAACTCAG
1 TTCACACATAACAATCATCTATGGTAGAACTTGAAACTCAG
6573578 TTCACACATAACAATCATCTATGGTAGAACTTGAAACTCAG
1 TTCACACATAACAATCATCTATGGTAGAACTTGAAACTCAG
6573619 T
1 T
6573620 ACTCAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.28
Consensus pattern (41 bp):
TTCACACATAACAATCATCTATGGTAGAACTTGAAACTCAG
Found at i:6579265 original size:17 final size:18
Alignment explanation
Indices: 6579233--6579266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6579223 AAAATTTTTA
*
6579233 TTTAAACTTATTAAATTT
1 TTTAAAATTATTAAATTT
6579251 TTTAAAATT-TTAAATT
1 TTTAAAATTATTAAATT
6579267 AGTAAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAAATTATTAAATTT
Found at i:6592770 original size:3 final size:3
Alignment explanation
Indices: 6592762--6592800 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
6592752 TTCGTTTTAG
*
6592762 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
6592801 ACCTCGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6596391 original size:25 final size:27
Alignment explanation
Indices: 6596357--6596419 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
6596347 CATATTTTTC
*
6596357 AAATAGATGAACT-AATTTTTTTTAAT
1 AAATAAATGAACTGAATTTTTTTTAAT
* **
6596383 -ATTAAATGAACTGTTTTTTTTTTAAT
1 AAATAAATGAACTGAATTTTTTTTAAT
6596409 AAATAAATGAA
1 AAATAAATGAA
6596420 AAACAAGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 10 0.33
26 11 0.37
27 9 0.30
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (27 bp):
AAATAAATGAACTGAATTTTTTTTAAT
Found at i:6602547 original size:17 final size:18
Alignment explanation
Indices: 6602525--6602560 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6602515 TGATAGAGTG
*
6602525 TGTATAATAA-ACTAAAA
1 TGTATAAAAATACTAAAA
6602542 TGTATAAAAATACTAAAA
1 TGTATAAAAATACTAAAA
6602560 T
1 T
6602561 AAAGCTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
TGTATAAAAATACTAAAA
Found at i:6604844 original size:12 final size:12
Alignment explanation
Indices: 6604827--6604861 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
6604817 TGCAGTGAGA
*
6604827 TGCTTTTGCTTT
1 TGCTTTTGCATT
6604839 TGCTTTTGCATT
1 TGCTTTTGCATT
*
6604851 TGCATTTGCAT
1 TGCTTTTGCAT
6604862 GTTGGACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.17, G:0.17, T:0.57
Consensus pattern (12 bp):
TGCTTTTGCATT
Found at i:6608135 original size:24 final size:25
Alignment explanation
Indices: 6608104--6608168 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
6608094 TCTCAAGCAC
*
6608104 TATAACGGGAAGCTCAT-TGAGCCA
1 TATAACGGGAAGCTCATCCGAGCCA
* * **
6608128 TGTAACGGGAAGCTTATCCGAGCTT
1 TATAACGGGAAGCTCATCCGAGCCA
6608153 TATAACGGGAAGCTCA
1 TATAACGGGAAGCTCA
6608169 CAAAGAGCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (25 bp):
TATAACGGGAAGCTCATCCGAGCCA
Found at i:6608181 original size:25 final size:24
Alignment explanation
Indices: 6608153--6608200 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
6608143 ATCCGAGCTT
6608153 TATAACGGGAAGCTCACAAAGAGCC
1 TATAACGGGAAGCTC-CAAAGAGCC
* * *
6608178 TATATCGGGTAGCTCCGAAGAGC
1 TATAACGGGAAGCTCCAAAGAGC
6608201 ACTTTAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (24 bp):
TATAACGGGAAGCTCCAAAGAGCC
Found at i:6609448 original size:64 final size:64
Alignment explanation
Indices: 6609372--6609495 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
6609362 ATGAAGAGTC
* * ** * * * *
6609372 ATATATCAGGACGCTCATAAAGAGTTGCGGTATGTCCGCAATATATGCAGGATAAATACCAATT
1 ATATAACAGGACGCTCACAAAGAACTGCGGTATATCCACAACATATGCACGATAAATACCAATT
* *
6609436 ATATAACAGGACGCTCACAAAGAACTGCGGTATATTCACAACATATGCACGATCAATACC
1 ATATAACAGGACGCTCACAAAGAACTGCGGTATATCCACAACATATGCACGATAAATACC
6609496 GATCGGGATG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (64 bp):
ATATAACAGGACGCTCACAAAGAACTGCGGTATATCCACAACATATGCACGATAAATACCAATT
Found at i:6613582 original size:15 final size:16
Alignment explanation
Indices: 6613557--6613590 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
6613547 TCCTTTCTCA
6613557 AAACGCTATAATGGAT
1 AAACGCTATAATGGAT
6613573 AAAC-CTATAATGGAT
1 AAACGCTATAATGGAT
6613588 AAA
1 AAA
6613591 TTTTCCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
AAACGCTATAATGGAT
Found at i:6617132 original size:3 final size:3
Alignment explanation
Indices: 6617124--6617153 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6617114 TTAGAAAATG
6617124 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6617154 TTGATGACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6617830 original size:118 final size:116
Alignment explanation
Indices: 6617661--6617894 Score: 344
Period size: 118 Copynumber: 2.0 Consensus size: 116
6617651 AACATAGGCA
* * * *
6617661 TTAACATGAGATTTAAAAGAGTAAAATAATTTTTGGAAAGAGTGATTAAGTGTGATATATATAAT
1 TTAACATGAAATTTAAAAGAGCAAAATAATTTTTGGAAAGAGTGATTAAGTGTCATATATATAAA
* *
6617726 TTGTAATATCAAAACT-GGAAGAATAATATATACTTAAACATGCTTGAATCT
66 TTGTAATATCAAAA-TGGGAAGAATAATACATACTTAAACATACTTGAATCT
* *
6617777 TTAACATGAAATTTAAAAAGAGCAAAATAATGTTTTTGAAAGAGTGATTAAGTGTCATGTATATA
1 TTAACATGAAATTT-AAAAGAGCAAAATAAT-TTTTGGAAAGAGTGATTAAGTGTCATATATATA
* *
6617842 AATTGTATTATCAAAATGGGAAGAATAATACATACTTAACCATACTTGAATCT
64 AATTGTAATATCAAAATGGGAAGAATAATACATACTTAAACATACTTGAATCT
6617895 GTATGTTTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
116 13 0.12
117 16 0.15
118 76 0.72
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (116 bp):
TTAACATGAAATTTAAAAGAGCAAAATAATTTTTGGAAAGAGTGATTAAGTGTCATATATATAAA
TTGTAATATCAAAATGGGAAGAATAATACATACTTAAACATACTTGAATCT
Found at i:6620549 original size:22 final size:22
Alignment explanation
Indices: 6620510--6620566 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
6620500 CGGCCTATTT
** *
6620510 TTTTAATAAATACCAAAAAATTA
1 TTTTAA-AAATAAAAAAAAAGTA
6620533 TTTTAAAAATAAAAAAAAAAGTA
1 TTTTAAAAAT-AAAAAAAAAGTA
6620556 TTTTAAAAATA
1 TTTTAAAAATA
6620567 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTTAAAAATAAAAAAAAAGTA
Found at i:6620563 original size:11 final size:11
Alignment explanation
Indices: 6620525--6620614 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
6620515 ATAAATACCA
6620525 AAAAATTATTTT
1 AAAAA-TATTTT
****
6620537 AAAAATAAAAA
1 AAAAATATTTT
6620548 AAAAAGTATTTT
1 AAAAA-TATTTT
6620560 AAAAATATTTT
1 AAAAATATTTT
6620571 --AAA-A--TT
1 AAAAATATTTT
* **
6620577 AAAAAAATTAA
1 AAAAATATTTT
6620588 AAAAAGTATTTT
1 AAAAA-TATTTT
6620600 AAAAATATTTT
1 AAAAATATTTT
6620611 AAAA
1 AAAA
6620615 TTAAAAAATA
Statistics
Matches: 58, Mismatches: 13, Indels: 15
0.67 0.15 0.17
Matches are distributed among these distances:
6 2 0.03
8 4 0.07
9 4 0.07
11 28 0.48
12 20 0.34
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:6620579 original size:40 final size:40
Alignment explanation
Indices: 6620535--6620626 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
6620525 AAAAATTATT
6620535 TTAAAAATAAAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAATAAAAAAAAAAGTATTTTAAAAATATTTTAAAA
*
6620575 TTAAAAA-AATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAATAA-AAAAAAAAGTATTTTAAAAATATTTTAAAA
6620615 TTAAAAAATAAA
1 TT-AAAAATAAA
6620627 TATATTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 2 0.04
40 38 0.81
41 5 0.11
42 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (40 bp):
TTAAAAATAAAAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:6629921 original size:22 final size:23
Alignment explanation
Indices: 6629874--6629923 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6629864 GGACCCTATT
* *
6629874 TATTTTTATTATAATATAATTAA
1 TATTTTTATTATAAAAAAATTAA
6629897 TATTTTT-TTATAAAAAAAATT-A
1 TATTTTTATTAT-AAAAAAATTAA
6629919 TATTT
1 TATTT
6629924 ATCTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTTATTATAAAAAAATTAA
Found at i:6637925 original size:33 final size:32
Alignment explanation
Indices: 6637834--6637925 Score: 76
Period size: 33 Copynumber: 2.8 Consensus size: 32
6637824 GGTAACACCT
* * * *
6637834 CAATAAGGAGGCCGAGTAGCGGTGATGATCCCC
1 CAATAAGCAGGTCAAGTAGCGG-GATGATACCC
* ** * *
6637867 CTATAAGCATATTAAGCAGCTGGGATGATACCC
1 CAATAAGCAGGTCAAGTAGC-GGGATGATACCC
6637900 CAATAAGCAGGTCAAGTAGCAGGGAT
1 CAATAAGCAGGTCAAGTAGC-GGGAT
6637926 ACCCCTGTAA
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (32 bp):
CAATAAGCAGGTCAAGTAGCGGGATGATACCC
Found at i:6639217 original size:9 final size:9
Alignment explanation
Indices: 6639205--6639234 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6639195 AATCGAATCA
6639205 AGTTATTCG
1 AGTTATTCG
6639214 AGTTATTCG
1 AGTTATTCG
*
6639223 AATTATTCG
1 AGTTATTCG
6639232 AGT
1 AGT
6639235 CAACTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
AGTTATTCG
Found at i:6639427 original size:19 final size:19
Alignment explanation
Indices: 6639376--6639436 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
6639366 TCTCTTAACG
* *
6639376 AAAAATCAAAATAATTTTC
1 AAAATTCAAAATAATTTTT
*
6639395 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
6639415 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
6639433 AAAA
1 AAAA
6639437 ATTTTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.25
19 11 0.31
20 16 0.44
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:6639437 original size:19 final size:19
Alignment explanation
Indices: 6639376--6639439 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
6639366 TCTCTTAACG
6639376 AAAAA-TCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
* *
6639394 CAAAATTTGAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
6639414 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
6639433 AAAAATT
1 AAAAATT
6639440 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 4 0.11
19 21 0.57
20 12 0.32
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:6639498 original size:24 final size:22
Alignment explanation
Indices: 6639447--6639499 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
6639437 ATTTTAAAAA
*
6639447 TATAAATTTTAAAAAAATATAT
1 TATAAAATTTAAAAAAATATAT
* *
6639469 CA-AAAATTTAATAAAATAATAAT
1 TATAAAATTTAAAAAAAT-AT-AT
6639492 TATAAAAT
1 TATAAAAT
6639500 CAAAATAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 13 0.54
22 3 0.12
23 3 0.12
24 5 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TATAAAATTTAAAAAAATATAT
Found at i:6653601 original size:15 final size:14
Alignment explanation
Indices: 6653581--6653615 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
6653571 GAGAGTGGGA
6653581 AAAAAAAGAAAACTG
1 AAAAAAAG-AAACTG
*
6653596 AAAAAAAGGAACTG
1 AAAAAAAGAAACTG
6653610 AAAAAA
1 AAAAAA
6653616 TTGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (14 bp):
AAAAAAAGAAACTG
Found at i:6654383 original size:84 final size:84
Alignment explanation
Indices: 6654242--6654410 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 84
6654232 ATGCTATATC
* *
6654242 TGTAATATCCCGAAAATTACTATAGTAAGAAAATAGGTATATTTGATATAGTAAAATAAGGAAAT
1 TGTAATATCCCGAAAATTACTACAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
**
6654307 AAAATGTTAAAAAGCAAAA
66 AAAATGACAAAAAGCAAAA
*
6654326 TGTAATATCCCGAAAATTACTACAGTAAGAAAGTAGGTATACTTGATATAGTAAAATAAGGAAAT
1 TGTAATATCCCGAAAATTACTACAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
*
6654391 AAAGTGACAAAAAGCAAAA
66 AAAATGACAAAAAGCAAAA
6654410 T
1 T
6654411 TTTGATTTAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (84 bp):
TGTAATATCCCGAAAATTACTACAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
AAAATGACAAAAAGCAAAA
Found at i:6658388 original size:28 final size:29
Alignment explanation
Indices: 6658357--6658412 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
6658347 TATTATTATT
*
6658357 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
6658385 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
6658413 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:6658740 original size:3 final size:3
Alignment explanation
Indices: 6658732--6658770 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6658722 GTGAGGTAAG
6658732 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
6658771 GAGTGGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6659184 original size:37 final size:39
Alignment explanation
Indices: 6659125--6659220 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
6659115 CGGATAGATT
* * * *
6659125 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
6659162 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
6659201 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
6659221 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:6664853 original size:36 final size:36
Alignment explanation
Indices: 6664781--6664929 Score: 226
Period size: 36 Copynumber: 4.1 Consensus size: 36
6664771 ACTCAGGATG
* * * *
6664781 CTTATGAGAGGAAAATGGGATGTAAAACAGTATATCA
1 CTTATAAGAGGAAAATGAGAT-TTAAACAGTTTATCA
6664818 CTTATAAGAGGAAAATGAGATTTAAACAGTTTATCA
1 CTTATAAGAGGAAAATGAGATTTAAACAGTTTATCA
*
6664854 CTTATAAGAGGAAAATGAGATTTAAACAGCTTATCA
1 CTTATAAGAGGAAAATGAGATTTAAACAGTTTATCA
*
6664890 CTTACAAGAGGAAAATGAGATTTAGAACAGTTTATCA
1 CTTATAAGAGGAAAATGAGATTTA-AACAGTTTATCA
6664927 CTT
1 CTT
6664930 CAGCAATAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 71 0.68
37 33 0.32
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (36 bp):
CTTATAAGAGGAAAATGAGATTTAAACAGTTTATCA
Found at i:6666577 original size:13 final size:14
Alignment explanation
Indices: 6666553--6666581 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6666543 CATTTATTGT
6666553 TTAAATAAATATCA
1 TTAAATAAATATCA
6666567 TTAAA-AAATATCA
1 TTAAATAAATATCA
6666580 TT
1 TT
6666582 TAATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAATAAATATCA
Found at i:6666584 original size:14 final size:15
Alignment explanation
Indices: 6666552--6666584 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6666542 TCATTTATTG
6666552 TTTAAATAAATATCA
1 TTTAAATAAATATCA
6666567 -TTAAA-AAATATCA
1 TTTAAATAAATATCA
6666580 TTTAA
1 TTTAA
6666585 TGTTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTAAATAAATATCA
Found at i:6667655 original size:57 final size:54
Alignment explanation
Indices: 6667558--6667688 Score: 149
Period size: 57 Copynumber: 2.4 Consensus size: 54
6667548 CAAATTATCA
* * *
6667558 AAAGATTCATTGATTCGATCTAGAAAAAAACCATCCGTTTCGTCATACACATCGTTG
1 AAAGATTTATTGATTCCATCTAGAAAAAAACCATCCGTTTCG---TACACATCATTG
* * *
6667615 GAAGATTTATTGATTCCA-CTGAGAAAAAAGCCA-CTTGTTTCGTACACATCATTG
1 AAAGATTTATTGATTCCATCT-AGAAAAAAACCATC-CGTTTCGTACACATCATTG
6667669 AAAGATTTATTGATTCCATC
1 AAAGATTTATTGATTCCATC
6667689 GAGTAATATG
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
54 28 0.44
55 1 0.02
56 3 0.05
57 32 0.50
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (54 bp):
AAAGATTTATTGATTCCATCTAGAAAAAAACCATCCGTTTCGTACACATCATTG
Found at i:6678466 original size:27 final size:27
Alignment explanation
Indices: 6678436--6678489 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6678426 CCTTGGCTGC
6678436 TCACGTCTCCTCTGACCCGCGTCTGAA
1 TCACGTCTCCTCTGACCCGCGTCTGAA
6678463 TCACGTCTCCTCTGACCCGCGTCTGAA
1 TCACGTCTCCTCTGACCCGCGTCTGAA
6678490 CTGCTCGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.41, G:0.19, T:0.26
Consensus pattern (27 bp):
TCACGTCTCCTCTGACCCGCGTCTGAA
Found at i:6685899 original size:18 final size:18
Alignment explanation
Indices: 6685872--6685964 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
6685862 TACGACCGTT
6685872 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
6685890 TACGGCACTATTCACATA
1 TACGGTACTATTCACGTA
* *
6685908 TACAGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
6685926 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
6685944 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
6685962 TAC
1 TAC
6685965 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:6693762 original size:9 final size:9
Alignment explanation
Indices: 6693704--6693762 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
6693694 TCAAAAAATT
6693704 AAATTTAAA
1 AAATTTAAA
*
6693713 AAA-ATAAA
1 AAATTTAAA
*
6693721 AAATTTTAA
1 AAATTTAAA
6693730 AAATCTTATATA
1 AAAT-TTA-A-A
*
6693742 AAATTTACA
1 AAATTTAAA
6693751 AAATTTAAA
1 AAATTTAAA
6693760 AAA
1 AAA
6693763 AAGCTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.17
9 22 0.55
10 2 0.05
11 4 0.10
12 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATTTAAA
Found at i:6694107 original size:23 final size:25
Alignment explanation
Indices: 6694081--6694126 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
6694071 AAATGTTTAA
*
6694081 ATTTAGGATA-AATTTAA-ATTTTG
1 ATTTAAGATATAATTTAATATTTTG
*
6694104 ATTTAATATATAATTTAATATTT
1 ATTTAAGATATAATTTAATATTT
6694127 AAACTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 7 0.37
25 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (25 bp):
ATTTAAGATATAATTTAATATTTTG
Found at i:6696283 original size:17 final size:18
Alignment explanation
Indices: 6696243--6696283 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
6696233 AATCAAAATT
*
6696243 TATAAATCAAATTGCATA
1 TATAAATAAAATTGCATA
*
6696261 TA-AAATAAAATTG-ATG
1 TATAAATAAAATTGCATA
6696277 TATAAAT
1 TATAAAT
6696284 TTGATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 14 0.70
18 2 0.10
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (18 bp):
TATAAATAAAATTGCATA
Found at i:6696434 original size:2 final size:2
Alignment explanation
Indices: 6696427--6696459 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6696417 TAATAAAATT
6696427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6696460 AAGAACACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6706002 original size:59 final size:59
Alignment explanation
Indices: 6705910--6706047 Score: 258
Period size: 59 Copynumber: 2.3 Consensus size: 59
6705900 TTACAGCGGG
* *
6705910 ATTACCAGTCCAGGCAAAATCCCCTACAATGACAATTACTCTAATGAGCTTGGGTCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTACAATGACAATTACTCTAATGAGCTTGGATCTGA
6705969 ATTACCAGTCCAGGCTAAATCCCCTACAATGACAATTACTCTAATGAGCTTGGATCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTACAATGACAATTACTCTAATGAGCTTGGATCTGA
6706028 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
6706048 TCAGACCCTA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 77 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (59 bp):
ATTACCAGTCCAGGCTAAATCCCCTACAATGACAATTACTCTAATGAGCTTGGATCTGA
Found at i:6708737 original size:4 final size:4
Alignment explanation
Indices: 6708728--6708752 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6708718 AATGAATTAC
6708728 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
6708753 TGTATCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:6710389 original size:13 final size:13
Alignment explanation
Indices: 6710371--6710410 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
6710361 AGTAGAAGTG
*
6710371 ACAATTTTATTAA
1 ACAATTTTATCAA
*
6710384 ACAATTTTTATCAG
1 ACAA-TTTTATCAA
6710398 ACAATTTTATCAA
1 ACAATTTTATCAA
6710411 CCATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (13 bp):
ACAATTTTATCAA
Found at i:6718286 original size:7 final size:7
Alignment explanation
Indices: 6718274--6718298 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6718264 GAGGCTTGGA
6718274 TCCACTG
1 TCCACTG
6718281 TCCACTG
1 TCCACTG
6718288 TCCACTG
1 TCCACTG
6718295 TCCA
1 TCCA
6718299 TTGGACCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.12, T:0.28
Consensus pattern (7 bp):
TCCACTG
Found at i:6722670 original size:21 final size:20
Alignment explanation
Indices: 6722631--6722667 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6722621 AATTTTCAAT
6722631 TTTTATAAAACTGAATATTG
1 TTTTATAAAACTGAATATTG
6722651 TTTTATAAAA-TGAATAT
1 TTTTATAAAACTGAATAT
6722668 ATTTGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTTATAAAACTGAATATTG
Found at i:6729612 original size:5 final size:5
Alignment explanation
Indices: 6729602--6729631 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
6729592 TCCACCCAGG
6729602 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
6729632 TGTTGGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:6741082 original size:11 final size:11
Alignment explanation
Indices: 6741068--6741097 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6741058 AAAATAAAAA
6741068 TAAAATTATTT
1 TAAAATTATTT
*
6741079 TAAAAGTATTT
1 TAAAATTATTT
6741090 TAAAATTA
1 TAAAATTA
6741098 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:6743199 original size:20 final size:20
Alignment explanation
Indices: 6743174--6743223 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6743164 TGGCTTAAAA
6743174 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
6743194 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
6743211 GTGGTAGTGGATT
1 TTGGTAGTGGATT
6743224 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:6747826 original size:20 final size:20
Alignment explanation
Indices: 6747801--6747850 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6747791 TGGCTTAAAA
6747801 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
6747821 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
6747838 GTGGTAGTGGATT
1 TTGGTAGTGGATT
6747851 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:6750105 original size:12 final size:13
Alignment explanation
Indices: 6750075--6750117 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
6750065 TTTTATTTTT
6750075 AATTAAAACTATA
1 AATTAAAACTATA
6750088 AATTAAAA-TATA
1 AATTAAAACTATA
*
6750100 ATTTAAAAACTATCA
1 AATT-AAAACTAT-A
6750115 AAT
1 AAT
6750118 AAATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 3 0.12
15 3 0.12
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTAAAACTATA
Found at i:6750159 original size:13 final size:14
Alignment explanation
Indices: 6750120--6750178 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
6750110 TATCAAATAA
*
6750120 ATTTTATTATTAAAT
1 ATTTTATTA-AAAAT
* *
6750135 A-TTTAATCAAAAT
1 ATTTTATTAAAAAT
6750148 ATTTT-TTAAAAAT
1 ATTTTATTAAAAAT
6750161 AAATTTTATTAAAAAT
1 --ATTTTATTAAAAAT
6750177 AT
1 AT
6750179 ATAAGCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
13 11 0.31
14 10 0.29
15 6 0.17
16 8 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTATTAAAAAT
Found at i:6750172 original size:16 final size:15
Alignment explanation
Indices: 6750148--6750177 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6750138 TAATCAAAAT
6750148 ATTTTTTAAAAATAA
1 ATTTTTTAAAAATAA
6750163 ATTTTATTAAAAATA
1 ATTTT-TTAAAAATA
6750178 TATAAGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTTTTAAAAATAA
Found at i:6751315 original size:3 final size:3
Alignment explanation
Indices: 6751307--6751335 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6751297 GGTAGAGTAG
6751307 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
6751336 GAAACTGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:6755108 original size:18 final size:17
Alignment explanation
Indices: 6755085--6755119 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
6755075 GAATAGATTT
6755085 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
6755103 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
6755120 ACCCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:6765168 original size:29 final size:29
Alignment explanation
Indices: 6765135--6765194 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
6765125 AAATCCAATT
6765135 TTAACTTAGTGGATAATTTGCCAAAAGGC
1 TTAACTTAGTGGATAATTTGCCAAAAGGC
6765164 TTAACTTAGTGGATAATTTGCCAAAAGGC
1 TTAACTTAGTGGATAATTTGCCAAAAGGC
6765193 TT
1 TT
6765195 TTATTACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (29 bp):
TTAACTTAGTGGATAATTTGCCAAAAGGC
Found at i:6766386 original size:20 final size:19
Alignment explanation
Indices: 6766350--6766394 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6766340 TTTAAAAAAA
*
6766350 TTAAAAATGTATAAAAATT
1 TTAAAAATATATAAAAATT
*
6766369 TTAAAAATATATGTAAAATT
1 TTAAAAATATAT-AAAAATT
*
6766389 CTAAAA
1 TTAAAA
6766395 GCATATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
TTAAAAATATATAAAAATT
Found at i:6768023 original size:31 final size:30
Alignment explanation
Indices: 6767962--6768023 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
6767952 TAATATACAA
* *
6767962 TTTTATACATGAATTTTGATTTTGTGTAAT
1 TTTTATACATAAATTTTGATTTTGTCTAAT
6767992 TTTTATACATAAAATTTTGA-TTTGATCTAAT
1 TTTTATACAT-AAATTTTGATTTTG-TCTAAT
6768023 T
1 T
6768024 ATTGTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (30 bp):
TTTTATACATAAATTTTGATTTTGTCTAAT
Found at i:6768240 original size:29 final size:30
Alignment explanation
Indices: 6768206--6768267 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
6768196 GTTTCACGTG
*
6768206 TATAATTACAC-CAAATTAAAATTCATATA
1 TATAATTACACACAAATTAAAATTCACATA
*
6768235 TATAATTACACATTAAATTAAAATTCACATA
1 TATAATTACACA-CAAATTAAAATTCACATA
6768266 TA
1 TA
6768268 ACTTTTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.38
31 18 0.62
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (30 bp):
TATAATTACACACAAATTAAAATTCACATA
Found at i:6768268 original size:29 final size:28
Alignment explanation
Indices: 6768206--6768268 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
6768196 GTTTCACGTG
*
6768206 TATAATTACACCAAATTAAAATTCATATA
1 TATAATTACACCAAATTAAAATTCA-ACA
*
6768235 TATAATTACACATTAAATTAAAATTC-ACA
1 TATAATTACAC--CAAATTAAAATTCAACA
6768264 TATAA
1 TATAA
6768269 CTTTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 18 0.60
31 12 0.40
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (28 bp):
TATAATTACACCAAATTAAAATTCAACA
Found at i:6773849 original size:14 final size:14
Alignment explanation
Indices: 6773832--6773859 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6773822 CTCACATTTC
6773832 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
6773846 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
6773860 CATTTCTGCT
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:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:6773850 original size:19 final size:18
Alignment explanation
Indices: 6773812--6773856 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
6773802 TACGGTATGC
6773812 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
6773829 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
6773848 TTCTTTTCT
1 TTCTTTTCT
6773857 CCACATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:6773875 original size:19 final size:18
Alignment explanation
Indices: 6773812--6773875 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
6773802 TACGGTATGC
*
6773812 TTCTTTTCTTCT-CACAT
1 TTCTCTTCTTCTCCACAT
* *
6773829 TTCTTTTCTTTTCTC-CAT
1 TTCTCTTCTTCTC-CACAT
6773847 TT-TCTT-TTCTCCACAT
1 TTCTCTTCTTCTCCACAT
6773863 TTCTGCTTCTTCT
1 TTCT-CTTCTTCT
6773876 TCCAAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
15 1 0.03
16 9 0.24
17 15 0.39
18 8 0.21
19 5 0.13
ACGTcount: A:0.08, C:0.30, G:0.02, T:0.61
Consensus pattern (18 bp):
TTCTCTTCTTCTCCACAT
Found at i:6776886 original size:17 final size:18
Alignment explanation
Indices: 6776861--6776906 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
6776851 TATAAGAATA
*
6776861 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
6776878 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
6776896 ATTAAATTATA
1 ATTAAATTATA
6776907 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:6777484 original size:19 final size:20
Alignment explanation
Indices: 6777433--6777489 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
6777423 TTAAAATTTT
*
6777433 AAAAATTAAAAAACATTTAA
1 AAAAATTAAAAATCATTTAA
*
6777453 AAAAATAAAAAATCA-TTAA
1 AAAAATTAAAAATCATTTAA
** *
6777472 AATTATTAAAAATTATTT
1 AAAAATTAAAAATCATTT
6777490 TTTAATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTAAAAATCATTTAA
Found at i:6779677 original size:14 final size:14
Alignment explanation
Indices: 6779635--6779664 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6779625 AGGTTGATTA
6779635 TTTTCTTCATACTC
1 TTTTCTTCATACTC
*
6779649 TTTTCTTCATATTC
1 TTTTCTTCATACTC
6779663 TT
1 TT
6779665 CATATTCTTT
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:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTCTTCATACTC
Found at i:6785197 original size:51 final size:51
Alignment explanation
Indices: 6785099--6785259 Score: 270
Period size: 51 Copynumber: 3.2 Consensus size: 51
6785089 TGAGTACTTC
* *
6785099 TGATCAGTGACAAGTGATAAGTGGT-AGTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAG
6785149 TGATAAGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAG
* * *
6785200 TGATAACTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAG
6785251 TGATAAGTG
1 TGATAAGTG
6785260 GTAGCTTAGC
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 24 0.23
51 80 0.77
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAG
Done.