Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 100 of 228
Found at i:28929986 original size:48 final size:48
Alignment explanation
Indices: 28929925--28930021 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 48
28929915 TCAGTCATAC
*
28929925 AAATCATAAACAAATCA-ATCATACTA-ATCACATACAAATCAATCATTT
1 AAATCATAAACAAATCAGA-CAT-CTACATCACAGACAAATCAATCATTT
* * * *
28929973 AAATCATAGACAAATTAGACATTTACATCACGGACAAATCAATCATTT
1 AAATCATAAACAAATCAGACATCTACATCACAGACAAATCAATCATTT
28930021 A
1 A
28930022 CACTTGAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 2 0.05
48 39 0.93
49 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (48 bp):
AAATCATAAACAAATCAGACATCTACATCACAGACAAATCAATCATTT
Found at i:28930019 original size:24 final size:24
Alignment explanation
Indices: 28929934--28930023 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
28929924 CAAATCATAA
* *
28929934 ACAAATCAATCATACTA-ATCACAT
1 ACAAATCAATCAT-TTACATCACAG
* *
28929958 ACAAATCAATCATTTAAATCATAG
1 ACAAATCAATCATTTACATCACAG
* *
28929982 ACAAATTAGA-CATTTACATCACGG
1 ACAAATCA-ATCATTTACATCACAG
28930006 ACAAATCAATCATTTACA
1 ACAAATCAATCATTTACA
28930024 CTTGAGGGGC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
23 3 0.05
24 51 0.93
25 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (24 bp):
ACAAATCAATCATTTACATCACAG
Found at i:28930080 original size:27 final size:27
Alignment explanation
Indices: 28930041--28930449 Score: 379
Period size: 27 Copynumber: 15.2 Consensus size: 27
28930031 GGCAAAATAG
* * *
28930041 TTTACCCTCTAGGGGCATTACGGTTAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* *
28930068 TTTACCTTATAGGGGTATTACGGTAAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * * * * * *
28930095 TTTATCTTACAAGGGCATTACGATTAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * *
28930122 TTTACCCTACAGGAGTATTACAGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * ** * *
28930149 TTAACCTTATAGCAGTATTACAGTTAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * *
28930176 TTTACCCTTTAGGGGCATTACTGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
*
28930203 TTTACCCTACAGGGGTATTACGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * * *
28930230 TTAACCCTATAAGGGTATTATGATCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* *
28930257 TTTACCCTACAGGGGCATTACGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * *
28930284 TTTATCCTACAGGGGTATTACGATCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* ** * *
28930311 TTAACCCTATAAAGGTCTAACGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * *
28930338 TTTACCCTACAGGGGCATTACGGTTAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* *
28930365 TTTACCCTATAGGGGTATTTCAGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* *
28930392 TTAACCCTATAGGGGTATTATGGTCA-
1 TTTACCCTATAGGGGTATTACGGTCAT
* *
28930418 TTTACCCTATAGGGGCATTAGGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
28930445 TTTAC
1 TTTAC
28930450 AAATATTGGG
Statistics
Matches: 304, Mismatches: 77, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
26 23 0.08
27 281 0.92
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
TTTACCCTATAGGGGTATTACGGTCAT
Found at i:28930461 original size:81 final size:81
Alignment explanation
Indices: 28930041--28930449 Score: 457
Period size: 81 Copynumber: 5.1 Consensus size: 81
28930031 GGCAAAATAG
* * * * * * * * *
28930041 TTTACCCT-CTAGGGGCATTACGGTTATTTTACCTTATAGGGGTATTACGGTAATTTTATCTTAC
1 TTTACCCTAC-AGGGGTATTACAGTCATTTAACCCTATAAGGGTATTACGGTCATTTTACCCTAC
* * *
28930105 AAGGGCATTACGATTAT
65 AGGGGCATTACGGTCAT
* * * * * **
28930122 TTTACCCTACAGGAGTATTACAGTCATTTAACCTTAT-AGCAGTATTACAGTTATTTTACCCTTT
1 TTTACCCTACAGGGGTATTACAGTCATTTAACCCTATAAG-GGTATTACGGTCATTTTACCCTAC
*
28930186 AGGGGCATTACTGTCAT
65 AGGGGCATTACGGTCAT
* * *
28930203 TTTACCCTACAGGGGTATTACGGTCATTTAACCCTATAAGGGTATTATGATCATTTTACCCTACA
1 TTTACCCTACAGGGGTATTACAGTCATTTAACCCTATAAGGGTATTACGGTCATTTTACCCTACA
28930268 GGGGCATTACGGTCAT
66 GGGGCATTACGGTCAT
* * * *
28930284 TTTATCCTACAGGGGTATTAC-GATCATTTAACCCTATAAAGGTCTAACGGTCATTTTACCCTAC
1 TTTACCCTACAGGGGTATTACAG-TCATTTAACCCTATAAGGGTATTACGGTCATTTTACCCTAC
*
28930348 AGGGGCATTACGGTTAT
65 AGGGGCATTACGGTCAT
* * * * *
28930365 TTTACCCTATAGGGGTATTTCAGTCATTTAACCCTATAGGGGTATTATGGTCA-TTTACCCTATA
1 TTTACCCTACAGGGGTATTACAGTCATTTAACCCTATAAGGGTATTACGGTCATTTTACCCTACA
*
28930429 GGGGCATTAGGGTCAT
66 GGGGCATTACGGTCAT
28930445 TTTAC
1 TTTAC
28930450 AAATATTGGG
Statistics
Matches: 277, Mismatches: 46, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
80 31 0.11
81 242 0.87
82 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (81 bp):
TTTACCCTACAGGGGTATTACAGTCATTTAACCCTATAAGGGTATTACGGTCATTTTACCCTACA
GGGGCATTACGGTCAT
Found at i:28932656 original size:27 final size:27
Alignment explanation
Indices: 28932616--28932902 Score: 292
Period size: 27 Copynumber: 10.7 Consensus size: 27
28932606 TTGGGCTGTA
*
28932616 AAAATTACCGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * * *
28932643 AGAATTATTGAAATACCTTCGAAAGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * ** *
28932670 AAAATTACCGAAATACCTTTAAAAGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * * *
28932697 CAAATTA-CTAAAATACCCCCGCAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
28932724 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
28932751 AAAATTATCGAAATACACTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* ** * *
28932778 AAAATTATTGAAATACATTCAAAGGAT
1 AAAATTATCGAAATACCCTCGAAGGGT
** *
28932805 AAAATTATTAAAATACCCTCCAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
28932832 AAAATTACCGAAATATCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
28932859 AAAATTACCGAAATACCC-CTAAAGGGT
1 AAAATTATCGAAATACCCTC-GAAGGGT
28932886 AAAATT-TCGAAATACCC
1 AAAATTATCGAAATACCC
28932903 CTAGGAGATG
Statistics
Matches: 217, Mismatches: 40, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
26 12 0.06
27 204 0.94
28 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGAAGGGT
Found at i:28933125 original size:26 final size:26
Alignment explanation
Indices: 28933084--28933187 Score: 138
Period size: 26 Copynumber: 4.0 Consensus size: 26
28933074 TTTGCCATAA
* *
28933084 ATTACTGTTACTGGCAACTTTGCTGC
1 ATTACTGATACTGGCAGCTTTGCTGC
* *
28933110 GA-TATTGATACTGGCAGCTCTGCTGC
1 -ATTACTGATACTGGCAGCTTTGCTGC
* *
28933136 ATTACTGTTACTTGCAGCTTTGCTGC
1 ATTACTGATACTGGCAGCTTTGCTGC
28933162 ATTACTGATACTGGCAGCTTTGCTGC
1 ATTACTGATACTGGCAGCTTTGCTGC
28933188 GATATTGGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
25 1 0.02
26 64 0.97
27 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (26 bp):
ATTACTGATACTGGCAGCTTTGCTGC
Found at i:28933171 original size:52 final size:52
Alignment explanation
Indices: 28933084--28933187 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
28933074 TTTGCCATAA
*
28933084 ATTACTGTTACTGGCAACTTTGCTGCGATATTGATACTGGCAGCTCTGCTGC
1 ATTACTGTTACTGGCAACTTTGCTGCGATACTGATACTGGCAGCTCTGCTGC
* * *
28933136 ATTACTGTTACTTGCAGCTTTGCTGC-ATTACTGATACTGGCAGCTTTGCTGC
1 ATTACTGTTACTGGCAACTTTGCTGCGA-TACTGATACTGGCAGCTCTGCTGC
28933188 GATATTGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (52 bp):
ATTACTGTTACTGGCAACTTTGCTGCGATACTGATACTGGCAGCTCTGCTGC
Found at i:28933365 original size:30 final size:30
Alignment explanation
Indices: 28933296--28933382 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 30
28933286 TGCATTTGTA
*
28933296 CTGATTACTGTTTTGGGCTAAGGCCCACACT
1 CTGA-TACTGTATTGGGCTAAGGCCCACACT
*
28933327 AT--TACTGTATTGGGCTAAGGCCCACACT
1 CTGATACTGTATTGGGCTAAGGCCCACACT
*
28933355 CTGATACTGTATTGGGCTATGGCCCACA
1 CTGATACTGTATTGGGCTAAGGCCCACA
28933383 TACTGCTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 26 0.52
30 23 0.46
31 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (30 bp):
CTGATACTGTATTGGGCTAAGGCCCACACT
Found at i:28933393 original size:30 final size:30
Alignment explanation
Indices: 28933301--28933394 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
28933291 TTGTACTGAT
*
28933301 TACTGTTTTGGGCTAAGGCCCACACTA-T-
1 TACTGTATTGGGCTAAGGCCCACACTACTG
28933329 TACTGTATTGGGCTAAGGCCCACACT-CTG
1 TACTGTATTGGGCTAAGGCCCACACTACTG
*
28933358 ATACTGTATTGGGCTATGGCCCACA-TACTG
1 -TACTGTATTGGGCTAAGGCCCACACTACTG
28933388 CTACTGT
1 -TACTGT
28933395 TTAAGGCTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
28 26 0.44
29 1 0.02
30 32 0.54
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (30 bp):
TACTGTATTGGGCTAAGGCCCACACTACTG
Found at i:28934574 original size:21 final size:21
Alignment explanation
Indices: 28934550--28934593 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28934540 GCTATGCATG
28934550 CATGAAAAATTTATGAGATTT
1 CATGAAAAATTTATGAGATTT
28934571 CATGAAAAATTTATGAGATTT
1 CATGAAAAATTTATGAGATTT
28934592 CA
1 CA
28934594 ACTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (21 bp):
CATGAAAAATTTATGAGATTT
Found at i:28942363 original size:159 final size:160
Alignment explanation
Indices: 28942162--28942452 Score: 426
Period size: 161 Copynumber: 1.8 Consensus size: 160
28942152 AAGAGTTTAT
28942162 ATTTTTAAAATAAAAATATTTTTTAAAATCATATTAAAGGAAAAGTTTAA-ATTCTTAAAACAAA
1 ATTTTTAAAATAAAAATATTTTTTAAAATCATATTAAAGGAAAAGTTTAATATTCTTAAAACAAA
28942226 GTTTTGATCTTCT-TCAACTATTTCAAAATAAAATTTTGATTTTTAAGAAAAATAGTGATTTTTT
66 GTTTTGATCTT-TGTCAACTATTTCAAAATAAAATTTTGATTTTTAAGAAAAATAGTGATTTTTT
28942290 AATAAAAAAAAAAAAGGAAGAGAAAGTTCAG
130 AATAAAAAAAAAAAAGGAAGAGAAAGTTCAG
* * * * * *
28942321 ATTTTTAAAATAAATATATGTTTTT-TAGTCATTTTAAAGGAAAAGTTTAATTTTTTTTAAAACA
1 ATTTTTAAAATAAAAATAT-TTTTTAAAATCATATTAAAGGAAAAGTTTAA-TATTCTTAAAACA
* ** * * *
28942385 AAGTTTTGATCTTTGTCAATTATTTTGAAATAAATTTTTTATTTTTAAGAAAAGTAGTGATTTTT
64 AAGTTTTGATCTTTGTCAACTATTTCAAAATAAAATTTTGATTTTTAAGAAAAATAGTGATTTTT
28942450 TAA
129 TAA
28942453 AAGAAAACTT
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
159 40 0.34
160 6 0.05
161 70 0.60
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (160 bp):
ATTTTTAAAATAAAAATATTTTTTAAAATCATATTAAAGGAAAAGTTTAATATTCTTAAAACAAA
GTTTTGATCTTTGTCAACTATTTCAAAATAAAATTTTGATTTTTAAGAAAAATAGTGATTTTTTA
ATAAAAAAAAAAAAGGAAGAGAAAGTTCAG
Found at i:28952403 original size:15 final size:14
Alignment explanation
Indices: 28952380--28952410 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28952370 AAAAACAATA
28952380 AAACCAAAAAAAAG
1 AAACCAAAAAAAAG
28952394 AAACCAAAAAAAAG
1 AAACCAAAAAAAAG
28952408 AAA
1 AAA
28952411 GAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.13, G:0.06, T:0.00
Consensus pattern (14 bp):
AAACCAAAAAAAAG
Found at i:28952416 original size:14 final size:14
Alignment explanation
Indices: 28952360--28952418 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
28952350 TTGCCTAAAT
*
28952360 AAAAAGAAAGAAAA
1 AAAAAGAAACAAAA
* *
28952374 ACAATA-AAACCAAA
1 A-AAAAGAAACAAAA
*
28952388 AAAAAGAAACCAAA
1 AAAAAGAAACAAAA
*
28952402 AAAAAGAAAGAAAA
1 AAAAAGAAACAAAA
28952416 AAA
1 AAA
28952419 TAGTGAGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 3 0.08
14 31 0.84
15 3 0.08
ACGTcount: A:0.81, C:0.08, G:0.08, T:0.02
Consensus pattern (14 bp):
AAAAAGAAACAAAA
Found at i:28952882 original size:42 final size:42
Alignment explanation
Indices: 28952823--28953251 Score: 525
Period size: 42 Copynumber: 10.2 Consensus size: 42
28952813 AAGGAAAACA
** *
28952823 TTCATTGCATTTAGAGGCATAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
28952865 TTCATTACATTTAGAGGCCCAGGCGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
28952907 TTTATTGCATTTAAAGGCCCAAGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
28952949 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
28952991 TTTATTGTATTTAGAGGCCCAAGTGTGGAGTTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
28953033 TTCATTGCATTTAGAGGCCTATGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
28953075 TTTATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTCACTC
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
28953117 TTCATTGCATTTAGAGACTCAGGTGTGGAGGTTCATTCATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * **
28953159 TTCATTGCATTTAGAGACCCAGGTGTGGAAGTCTGTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
28953201 TCCATTGCATTTAAAAGCCCAAGTATGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
28953243 TTCATTGCA
1 TTCATTGCA
28953252 ATGTATATGA
Statistics
Matches: 330, Mismatches: 57, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 330 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:28954378 original size:156 final size:155
Alignment explanation
Indices: 28954083--28954380 Score: 447
Period size: 156 Copynumber: 1.9 Consensus size: 155
28954073 TTTTTAAAAA
* *
28954083 AAGAGAAAGTTTATATTTGTAAAATAAAAATATGTTTTTTAGTCATATTAAAAGAAATGTTTAAA
1 AAGAGAAAGTTTAGATTTGTAAAATAAAAATATGTTTTATAGTCATATTAAAAGAAATGTTTAAA
* *
28954148 TTCTTAAAACAAAATTTTGACCTTTTTCAACTATTTCAAAATAAAATTTTTATTTTTAAGAAAAA
66 TTCTTAAAACAAAATTTTGACCTTATTCAACTATTTCAAAATAAAATTTTGATTTTTAAGAAAAA
*
28954213 TAGTGATTTTTTTTAAAAAAAAGAG
131 TAATGATTTTTTTTAAAAAAAAGAG
* *
28954238 AAGAGAAAGTTTAGATTT-TGAAAATAAAAATATGTTTTATAGTCATTTTAAAGGAAAAT-TTTA
1 AAGAGAAAGTTTAGATTTGT-AAAATAAAAATATGTTTTATAGTCATATTAAAAG-AAATGTTTA
* * * * *
28954301 AATTTTTTAAAACAAATTTTTGATCTTATTCAACTATTTCAAAATAAAGTTTTGATTTTTAGGAA
64 AA-TTCTTAAAACAAAATTTTGACCTTATTCAACTATTTCAAAATAAAATTTTGATTTTTAAGAA
28954366 AAATAATGATTTTTT
128 AAATAATGATTTTTT
28954381 AAAGAAAACT
Statistics
Matches: 128, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
154 1 0.01
155 54 0.42
156 73 0.57
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (155 bp):
AAGAGAAAGTTTAGATTTGTAAAATAAAAATATGTTTTATAGTCATATTAAAAGAAATGTTTAAA
TTCTTAAAACAAAATTTTGACCTTATTCAACTATTTCAAAATAAAATTTTGATTTTTAAGAAAAA
TAATGATTTTTTTTAAAAAAAAGAG
Found at i:28955552 original size:32 final size:32
Alignment explanation
Indices: 28955510--28955585 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
28955500 GACCAAAATT
*
28955510 TCAAAGTTATTTTTCCAGATTTTAATGAGATC
1 TCAAACTTATTTTTCCAGATTTTAATGAGATC
*
28955542 TCAAACTTATTTTTCCATATTTTAATGAGATC
1 TCAAACTTATTTTTCCAGATTTTAATGAGATC
28955574 TCAAAC-TATTTT
1 TCAAACTTATTTT
28955586 AAAATTCAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 6 0.14
32 36 0.86
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (32 bp):
TCAAACTTATTTTTCCAGATTTTAATGAGATC
Found at i:28957437 original size:47 final size:47
Alignment explanation
Indices: 28957379--28957637 Score: 396
Period size: 47 Copynumber: 5.6 Consensus size: 47
28957369 GATAATTGTG
* *
28957379 ATGTG-AA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28957424 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28957471 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28957518 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
28957565 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28957612 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
28957638 TCCCGAAGGG
Statistics
Matches: 196, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 5 0.03
46 2 0.01
47 189 0.96
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:28963552 original size:42 final size:42
Alignment explanation
Indices: 28963505--28963602 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
28963495 GTGTCTTCAC
* *** *
28963505 TCGTGTAACTCACTAAGTAGGGTCACACAGCCATGTTGTAGG
1 TCGTGTAACTCACTAACTAGCCACACACAGCCATGTCGTAGG
* * *
28963547 TCGTGTAACTCTCTGACTTGCCACACACAGCCATGTCGTAGG
1 TCGTGTAACTCACTAACTAGCCACACACAGCCATGTCGTAGG
*
28963589 CCGTGTAACTCACT
1 TCGTGTAACTCACT
28963603 GACTTAAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (42 bp):
TCGTGTAACTCACTAACTAGCCACACACAGCCATGTCGTAGG
Found at i:28963605 original size:42 final size:42
Alignment explanation
Indices: 28963528--28963607 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
28963518 TAAGTAGGGT
* * *
28963528 CACACAGCCATGTTGTAGGTCGTGTAACTCTCTGACTTGCCA
1 CACACAGCCATGTCGTAGGCCGTGTAACTCACTGACTTGCCA
28963570 CACACAGCCATGTCGTAGGCCGTGTAACTCACTGACTT
1 CACACAGCCATGTCGTAGGCCGTGTAACTCACTGACTT
28963608 AAAACACTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (42 bp):
CACACAGCCATGTCGTAGGCCGTGTAACTCACTGACTTGCCA
Found at i:28975599 original size:53 final size:53
Alignment explanation
Indices: 28975530--28975636 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
28975520 TTTATGTTGG
*
28975530 GCTGCTATACCTATTGCATTTGATTTTAGTTTGAATGCTTTGATTTAAGTAAA
1 GCTGCTATACCTATTGCATTTGATTTTAGGTTGAATGCTTTGATTTAAGTAAA
28975583 GCTGCTATACCTATTGCATTTGATTTTAGGTTGAATGCTTTGATTTAAGTAAA
1 GCTGCTATACCTATTGCATTTGATTTTAGGTTGAATGCTTTGATTTAAGTAAA
28975636 G
1 G
28975637 ATGGAATAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (53 bp):
GCTGCTATACCTATTGCATTTGATTTTAGGTTGAATGCTTTGATTTAAGTAAA
Found at i:28992491 original size:38 final size:38
Alignment explanation
Indices: 28992427--28992504 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
28992417 AGGTAATGAC
*
28992427 TTTACACCTCTTCGATCATTACCCTGTAAGTAAATTCA
1 TTTACACCTCTTCAATCATTACCCTGTAAGTAAATTCA
* *
28992465 TTTACACCTCTTCAATTATTATCCTGTAAGTAAATTCA
1 TTTACACCTCTTCAATCATTACCCTGTAAGTAAATTCA
28992503 TT
1 TT
28992505 CGGCTTCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.41
Consensus pattern (38 bp):
TTTACACCTCTTCAATCATTACCCTGTAAGTAAATTCA
Found at i:28993149 original size:210 final size:207
Alignment explanation
Indices: 28992630--28993217 Score: 685
Period size: 207 Copynumber: 2.8 Consensus size: 207
28992620 CTTCAGCAAC
* * * * *
28992630 CATCTTACTAAGCAAGCTTGTTGCTTCTCCACATTGT-CCTGAATTGCATAATCCATGTATTAAA
1 CATCCTACTAAACAAGCTTGTCGCTTCTCCACATT-TACCTGAATTGCACAATCCAAGTATTAAA
* * * * * * * *** *
28992694 CTACTGTAGGTGACGATGTCTGGTTTCAGATCTCTCTGAATCATTAATTTGTACAAGGTAATGGC
65 CAACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAGTTCCAACATGGTAATGGC
* * *
28992759 TTCTTCAATCTTTTTTTCTTTGCACAAAGCATTGATTAAAGAGCTTAAGGTTTCCACATCAGGCT
130 TTCTTCAATCTTCTTTTCCTTGCACAAAGCATTGATTAAAGAGCTTAAAGTTTCCACATCAGGCT
28992824 GGACTCCATTCAA
195 GGACTCCATTCAA
* * * * * ** * * *
28992837 CATCCTACTAAACAAGCTAGCCACTCCTGCACAACTACCTAAACTCCACAATCCAAGTATTAAA-
1 CATCCTACTAAACAAGCTTGTCGCTTCTCCACATTTACCTGAATTGCACAATCCAAGTATTAAAC
* * * * *
28992901 AAGCAGTGGGTGACAATGTCAGGTATTACATTTCTCTGACTCATTAGTTCCAACATGCTAATGGC
66 AA-CTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAGTTCCAACATGGTAATGGC
* * * * *
28992966 TTCTTCATTCTTGTTTTCCTTGTACAAAGCATTGATTAAAGATCTTAAAGTTTCCATATCAGGCT
130 TTCTTCAATCTTCTTTTCCTTGCACAAAGCATTGATTAAAGAGCTTAAAGTTTCCACATCAGGCT
28993031 GGACTCCTCCATTCAA
195 GGA---CTCCATTCAA
* * * *
28993047 CATCCTACTAAACAAGCTTGTGGCTTCTTCACATTTATCTGAATTGCACAATCCACGTATTAAAC
1 CATCCTACTAAACAAGCTTGTCGCTTCTCCACATTTACCTGAATTGCACAATCCAAGTATTAAAC
* *
28993112 AATTGTAGGTGACAATGTCAGGTTTTACACCTCTCTGACTCATTAGTTCCAACATGGTAATGGCT
66 AACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAGTTCCAACATGGTAATGGCT
* * *
28993177 TCTTCAGTCCTCTTTTCCTTGCACAAGGCATTGATTAAAGA
131 TCTTCAATCTTCTTTTCCTTGCACAAAGCATTGATTAAAGA
28993218 ATTGAAAGTT
Statistics
Matches: 312, Mismatches: 63, Indels: 9
0.81 0.16 0.02
Matches are distributed among these distances:
206 2 0.01
207 155 0.50
210 153 0.49
211 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (207 bp):
CATCCTACTAAACAAGCTTGTCGCTTCTCCACATTTACCTGAATTGCACAATCCAAGTATTAAAC
AACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAGTTCCAACATGGTAATGGCT
TCTTCAATCTTCTTTTCCTTGCACAAAGCATTGATTAAAGAGCTTAAAGTTTCCACATCAGGCTG
GACTCCATTCAA
Found at i:28993246 original size:210 final size:210
Alignment explanation
Indices: 28992630--28993501 Score: 747
Period size: 210 Copynumber: 4.2 Consensus size: 210
28992620 CTTCAGCAAC
* * * * *
28992630 CATCTTACTAAGCAAGCTTGTTGCTTCTCCACATTGT-CCTGAATTGCATAATCCATGTATTAAA
1 CATCCTACTAAACAAGCTTGTTGCTTCTTCACATT-TACCTGAACTGCACAATCCATGTATTAAA
* * * * * * *** *
28992694 CTACTGTAGGTGACGATGTCTGGTTTCAGATCTCTCTGAATCATTAATTTGTACAAGGTAATGGC
65 CAACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAATTCCAACATGGTAATGGC
* * * * * * * *
28992759 TTCTTCAATCTTTTTTTCTTTGCACAAAGCATTGATTAAAGAGCTT-AAGGTTTCCACATCAGGC
130 TTCTTCAGTCCTCTTTTCCTTGCACAAAGCATTGATTAAAGA-ATTGAAAGTTACCACATCAGGA
28992823 TGGA---CTCCATTCAA
194 TGGACTCCTCCATTCAA
* *** * * ** * * *
28992837 CATCCTACTAAACAAGCTAGCCACTCCTGCACAACTACCTAAACTCCACAATCCAAGTATTAAA-
1 CATCCTACTAAACAAGCTTGTTGCTTCTTCACATTTACCTGAACTGCACAATCCATGTATTAAAC
* * * * * *
28992901 AAGCAGTGGGTGACAATGTCAGGTATTACATTTCTCTGACTCATTAGTTCCAACATGCTAATGGC
66 AA-CTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAATTCCAACATGGTAATGGC
* * * * * * * *
28992966 TTCTTCATTCTTGTTTTCCTTGTACAAAGCATTGATTAAAG-ATCTTAAAGTTTCCATATCAGGC
130 TTCTTCAGTCCTCTTTTCCTTGCACAAAGCATTGATTAAAGAAT-TGAAAGTTACCACATCAGGA
28993030 TGGACTCCTCCATTCAA
194 TGGACTCCTCCATTCAA
* * * *
28993047 CATCCTACTAAACAAGCTTGTGGCTTCTTCACATTTATCTGAATTGCACAATCCACGTATTAAAC
1 CATCCTACTAAACAAGCTTGTTGCTTCTTCACATTTACCTGAACTGCACAATCCATGTATTAAAC
* * *
28993112 AATTGTAGGTGACAATGTCAGGTTTTACACCTCTCTGACTCATTAGTTCCAACATGGTAATGGCT
66 AACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAATTCCAACATGGTAATGGCT
* * *
28993177 TCTTCAGTCCTCTTTTCCTTGCACAAGGCATTGATTAAAGAATTGAAAGTTACTACATCAAGATG
131 TCTTCAGTCCTCTTTTCCTTGCACAAAGCATTGATTAAAGAATTGAAAGTTACCACATCAGGATG
* *
28993242 GACTCCTGCATTCAT
196 GACTCCTCCATTCAA
* * * * * * * * * * * *
28993257 CATTCTATTGAGCACGGTTGTTGCTTCCGTC-CATTTGCCCGAACTGCA-AAACTCATATATTGA
1 CATCCTACTAAACAAGCTTGTTGCTT-CTTCACATTTACCTGAACTGCACAATC-CATGTATTAA
* ** * * * * ** *
28993320 ACAATTGTTTGTGACAACGTTAGGTTTTACATTTCTCTGTA-TCATTAATTCCAGCACAGTAAAG
64 ACAACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTG-ACTCATTAATTCCAACATGGTAATG
** * * *
28993384 GCTTCTGAAGTCCTCTTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAAGTCACAACATCAGG
128 GCTTCTTCAGTCCTCTTTTCCTTGCACAAAGCATTGATTAAAGAATTGAAAGTTACCACATCAGG
* *
28993449 ATGGACTCCTTCATTCAT
193 ATGGACTCCTCCATTCAA
* * * * * * *
28993467 CGTTCTATTGAGCAAGCTTGTTGTTTCTTCCCATT
1 CATCCTACTAAACAAGCTTGTTGCTTCTTCACATT
28993502 GCCCAGAATG
Statistics
Matches: 541, Mismatches: 111, Indels: 23
0.80 0.16 0.03
Matches are distributed among these distances:
205 1 0.00
206 3 0.01
207 151 0.28
209 6 0.01
210 372 0.69
211 8 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (210 bp):
CATCCTACTAAACAAGCTTGTTGCTTCTTCACATTTACCTGAACTGCACAATCCATGTATTAAAC
AACTGTAGGTGACAATGTCAGGTTTTACATCTCTCTGACTCATTAATTCCAACATGGTAATGGCT
TCTTCAGTCCTCTTTTCCTTGCACAAAGCATTGATTAAAGAATTGAAAGTTACCACATCAGGATG
GACTCCTCCATTCAA
Found at i:29005885 original size:19 final size:18
Alignment explanation
Indices: 29005861--29005931 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 18
29005851 ATTCCAAAAA
*
29005861 TAATATTATTTTAATATCT
1 TAATATTAATTTAATA-CT
29005880 TAATATTTAATTTAATACT
1 TAATA-TTAATTTAATACT
29005899 T-ATATTAA--TAATA-T
1 TAATATTAATTTAATACT
*
29005913 T-TTATTAATTTAATA-T
1 TAATATTAATTTAATACT
29005929 TAA
1 TAA
29005932 AGTGATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.18
15 5 0.11
16 7 0.16
17 4 0.09
18 3 0.07
19 8 0.18
20 10 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTAATTTAATACT
Found at i:29007419 original size:15 final size:15
Alignment explanation
Indices: 29007401--29007430 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29007391 TCATAACTTT
*
29007401 TTTACATTATTTATA
1 TTTAAATTATTTATA
29007416 TTTAAATTATTTATA
1 TTTAAATTATTTATA
29007431 GTTTTACTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAAATTATTTATA
Found at i:29011204 original size:464 final size:464
Alignment explanation
Indices: 29010336--29011274 Score: 1853
Period size: 464 Copynumber: 2.0 Consensus size: 464
29010326 TGGTGGGTTT
29010336 GAGAATAAAGATGGAAATAAATCCGATGTCGATCCAGTCTGAGAGCCCGATGCTGACGATTTATA
1 GAGAATAAAGATGGAAATAAATCCGATGTCGATCCAGTCTGAGAGCCCGATGCTGACGATTTATA
29010401 AATTGCATTAATTTCTAAACTGGAGCATGTTCCAATTGAACCAAAATATGGTAAAGAGGGTGAAG
66 AATTGCATTAATTTCTAAACTGGAGCATGTTCCAATTGAACCAAAATATGGTAAAGAGGGTGAAG
29010466 ATGTATAAGAGGATCCATGGTTCATGGTTTACTCGCCTCCAACCCACATGCATAATGTCGACCTA
131 ATGTATAAGAGGATCCATGGTTCATGGTTTACTCGCCTCCAACCCACATGCATAATGTCGACCTA
29010531 TCAACAGAGGATGGGTTGGAGTTTGTAGAAATACCACACAGGAGGCCAGACAGCACAAGTTCTTC
196 TCAACAGAGGATGGGTTGGAGTTTGTAGAAATACCACACAGGAGGCCAGACAGCACAAGTTCTTC
29010596 GTTGGAATTGGGTGACTTGGAAGTGGACAAGGAGTTTTTCAGTAAAGATGGTTTTGTCATTGTAG
261 GTTGGAATTGGGTGACTTGGAAGTGGACAAGGAGTTTTTCAGTAAAGATGGTTTTGTCATTGTAG
29010661 TGAAGCGATATAGCATCAAGAACGGGGTTAACTTCCACGTGGCTAAATCCTGATCTGAGAAGTTT
326 TGAAGCGATATAGCATCAAGAACGGGGTTAACTTCCACGTGGCTAAATCCTGATCTGAGAAGTTT
29010726 GAGGCCAAGTGTGCAATGCAAGATAGTAGATGCGCATGGAAAATAATGGCTTCTATTAAGAAGAC
391 GAGGCCAAGTGTGCAATGCAAGATAGTAGATGCGCATGGAAAATAATGGCTTCTATTAAGAAGAC
29010791 AGGGTTGTA
456 AGGGTTGTA
29010800 GAGAATAAAGATGGAAATAAATCCGATGTCGATCCAGTCTGAGAGCCCGATGCTGACGATTTATA
1 GAGAATAAAGATGGAAATAAATCCGATGTCGATCCAGTCTGAGAGCCCGATGCTGACGATTTATA
29010865 AATTGCATTAATTTCTAAACTGGAGCATGTTCCAATTGAACCAAAATATGGTAAAGAGGGTGAAG
66 AATTGCATTAATTTCTAAACTGGAGCATGTTCCAATTGAACCAAAATATGGTAAAGAGGGTGAAG
29010930 ATGTATAAGAGGATCCATGGTTCATGGTTTACTCGCCTCCAACCCACATGCATAATGTCGACCTA
131 ATGTATAAGAGGATCCATGGTTCATGGTTTACTCGCCTCCAACCCACATGCATAATGTCGACCTA
*
29010995 TCAACAGAGGATGGGTTGGAGTTTGTAGAAATACCACACAGGAGGCCAGACAGCATAAGTTCTTC
196 TCAACAGAGGATGGGTTGGAGTTTGTAGAAATACCACACAGGAGGCCAGACAGCACAAGTTCTTC
29011060 GTTGGAATTGGGTGACTTGGAAGTGGACAAGGAGTTTTTCAGTAAAGATGGTTTTGTCATTGTAG
261 GTTGGAATTGGGTGACTTGGAAGTGGACAAGGAGTTTTTCAGTAAAGATGGTTTTGTCATTGTAG
29011125 TGAAGCGATATAGCATCAAGAACGGGGTTAACTTCCACGTGGCTAAATCCTGATCTGAGAAGTTT
326 TGAAGCGATATAGCATCAAGAACGGGGTTAACTTCCACGTGGCTAAATCCTGATCTGAGAAGTTT
29011190 GAGGCCAAGTGTGCAATGCAAGATAGTAGATGCGCATGGAAAATAATGGCTTCTATTAAGAAGAC
391 GAGGCCAAGTGTGCAATGCAAGATAGTAGATGCGCATGGAAAATAATGGCTTCTATTAAGAAGAC
29011255 AGGGTTGTA
456 AGGGTTGTA
29011264 GATG-ATAAAGA
1 GA-GAATAAAGA
29011275 AGTTTACCAC
Statistics
Matches: 473, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
464 472 1.00
465 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (464 bp):
GAGAATAAAGATGGAAATAAATCCGATGTCGATCCAGTCTGAGAGCCCGATGCTGACGATTTATA
AATTGCATTAATTTCTAAACTGGAGCATGTTCCAATTGAACCAAAATATGGTAAAGAGGGTGAAG
ATGTATAAGAGGATCCATGGTTCATGGTTTACTCGCCTCCAACCCACATGCATAATGTCGACCTA
TCAACAGAGGATGGGTTGGAGTTTGTAGAAATACCACACAGGAGGCCAGACAGCACAAGTTCTTC
GTTGGAATTGGGTGACTTGGAAGTGGACAAGGAGTTTTTCAGTAAAGATGGTTTTGTCATTGTAG
TGAAGCGATATAGCATCAAGAACGGGGTTAACTTCCACGTGGCTAAATCCTGATCTGAGAAGTTT
GAGGCCAAGTGTGCAATGCAAGATAGTAGATGCGCATGGAAAATAATGGCTTCTATTAAGAAGAC
AGGGTTGTA
Found at i:29022767 original size:28 final size:28
Alignment explanation
Indices: 29022704--29022854 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
29022694 ATATTAAGTC
* *
29022704 CGCATACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29022731 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29022759 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29022787 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
29022815 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
29022844 CGCACACTTAG
1 CGCACACTTAG
29022855 CGCCAATCTC
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 20 0.18
28 76 0.68
29 16 0.14
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:29038657 original size:22 final size:22
Alignment explanation
Indices: 29038632--29038673 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29038622 ATTCTGCTCT
* *
29038632 CTATGTTGCGACATTGCATCTC
1 CTATGTTACGACATAGCATCTC
29038654 CTATGTTACGACATAGCATC
1 CTATGTTACGACATAGCATC
29038674 CAATATTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (22 bp):
CTATGTTACGACATAGCATCTC
Found at i:29039733 original size:20 final size:20
Alignment explanation
Indices: 29039696--29039733 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29039686 TAGATACATA
*
29039696 TATAAATTATCAATTAATCT
1 TATAAATTATAAATTAATCT
29039716 TATAAATT-TAAATATAAT
1 TATAAATTATAAAT-TAAT
29039734 ATTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAATTATAAATTAATCT
Found at i:29044229 original size:28 final size:28
Alignment explanation
Indices: 29044197--29044252 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
29044187 CCACCAACTC
29044197 TTCTCTTCAATTTTTCTTTACTTTCCCT
1 TTCTCTTCAATTTTTCTTTACTTTCCCT
*
29044225 TTCTCTTCAATTTTTTTTTACTTTCCCT
1 TTCTCTTCAATTTTTCTTTACTTTCCCT
29044253 CCTCTTTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (28 bp):
TTCTCTTCAATTTTTCTTTACTTTCCCT
Found at i:29046556 original size:14 final size:14
Alignment explanation
Indices: 29046537--29046566 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29046527 AGAAAGAAAG
*
29046537 AAAATTGAAAAGAA
1 AAAATTAAAAAGAA
29046551 AAAATTAAAAAGAA
1 AAAATTAAAAAGAA
29046565 AA
1 AA
29046567 TAGGAGAGGA
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:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAATTAAAAAGAA
Found at i:29047368 original size:18 final size:18
Alignment explanation
Indices: 29047345--29047380 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29047335 CTTAAGTGTA
29047345 TAACCATCAACTCAACAC
1 TAACCATCAACTCAACAC
29047363 TAACCATCAACTCAACAC
1 TAACCATCAACTCAACAC
29047381 CTATCGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (18 bp):
TAACCATCAACTCAACAC
Found at i:29052095 original size:79 final size:77
Alignment explanation
Indices: 29051993--29052215 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 77
29051983 GCTCCTCGTT
* *
29051993 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCAC-AATGCCTTCGGGACTTAGCCCGG
*
29052058 ATTTAGTAACTCGCA
63 AATTAGTAACTCGCA
*
29052073 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCAC-AATGCCTTCGGGACTTAGCCCGG
*
29052136 AATTAGTATCTCGCA
63 AATTAGTAACTCGCA
* * * * *
29052151 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCACAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAATGCCTTCGGGACTTAGCCCGG
29052215 A
63 A
29052216 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 47 0.38
79 56 0.45
80 20 0.16
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (77 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAATGCCTTCGGGACTTAGCCCGGAAT
TAGTAACTCGCA
Found at i:29052110 original size:39 final size:40
Alignment explanation
Indices: 29051993--29052215 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
29051983 GCTCCTCGTT
* *
29051993 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
29052033 CGAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29052073 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29052112 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29052151 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29052192 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29052216 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 62 0.38
41 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29057825 original size:8 final size:9
Alignment explanation
Indices: 29057801--29057825 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29057791 AAATTATAAT
29057801 TTTAAAAAC
1 TTTAAAAAC
29057810 TTTAAAAAC
1 TTTAAAAAC
29057819 TTTAAAA
1 TTTAAAA
29057826 TTAACTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (9 bp):
TTTAAAAAC
Found at i:29064042 original size:25 final size:26
Alignment explanation
Indices: 29064000--29064048 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
29063990 TTTAAAAATT
*
29064000 TTGAGTGACTAAATTAAAA-AAATAG
1 TTGAGTGACTAAAATAAAACAAATAG
29064025 TTGAGTGA-TCAAAATAAAACAAAT
1 TTGAGTGACT-AAAATAAAACAAAT
29064049 TAAATAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.76
26 4 0.19
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (26 bp):
TTGAGTGACTAAAATAAAACAAATAG
Found at i:29064288 original size:76 final size:77
Alignment explanation
Indices: 29064169--29064317 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 77
29064159 GACGAAATTG
* * * *
29064169 TTTTTCTATAATATTACTAAATGTGACATTTAAATATATTTATAATTTAATTTAAAATAATTATT
1 TTTTTCTATAATATTACTAAATGTGAAATTTAAATATAATTATAAATTAATTTAAAATAATTAGT
29064234 TAACATTTGCCC
66 TAACATTTGCCC
* *
29064246 TTTTTCTATCATATTATTAAA-GTGAAATTTAAATATAATTATAAATTAATTTAAAATAATTAGT
1 TTTTTCTATAATATTACTAAATGTGAAATTTAAATATAATTATAAATTAATTTAAAATAATTAGT
*
29064310 TAATATTT
66 TAACATTT
29064318 AAATAATAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 46 0.71
77 19 0.29
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (77 bp):
TTTTTCTATAATATTACTAAATGTGAAATTTAAATATAATTATAAATTAATTTAAAATAATTAGT
TAACATTTGCCC
Found at i:29066076 original size:13 final size:14
Alignment explanation
Indices: 29066060--29066088 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29066050 AATTTGAATA
29066060 TATTTTTAA-TATT
1 TATTTTTAATTATT
29066073 TATTTTTAATTATT
1 TATTTTTAATTATT
29066087 TA
1 TA
29066089 GGAAGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTTTAATTATT
Found at i:29074889 original size:14 final size:14
Alignment explanation
Indices: 29074866--29074907 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
29074856 ATAGGATAGG
*
29074866 ATTTTGTTTATTTT
1 ATTTTATTTATTTT
*
29074880 ATTTTATTTAGTTT
1 ATTTTATTTATTTT
*
29074894 ATTTTATTAATTTT
1 ATTTTATTTATTTT
29074908 TGAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
ATTTTATTTATTTT
Found at i:29075704 original size:21 final size:21
Alignment explanation
Indices: 29075662--29075707 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29075652 GTCTGCCCAT
* *
29075662 ACGGTCGTGTACCTTAGCCAC
1 ACGGCCGTGTACCTTAGACAC
29075683 ACGGCCGTGTACCTCT-GACAC
1 ACGGCCGTGTACCT-TAGACAC
29075704 ACGG
1 ACGG
29075708 TCTAAACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.20, C:0.35, G:0.26, T:0.20
Consensus pattern (21 bp):
ACGGCCGTGTACCTTAGACAC
Found at i:29083918 original size:18 final size:18
Alignment explanation
Indices: 29083895--29083948 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
29083885 CTTCTAGGGC
29083895 TCGCATACATATAAAGGT
1 TCGCATACATATAAAGGT
* *
29083913 TCGCATACATATGAGGGT
1 TCGCATACATATAAAGGT
*
29083931 TCGTATACATATAAAGGT
1 TCGCATACATATAAAGGT
29083949 AATAAGTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (18 bp):
TCGCATACATATAAAGGT
Found at i:29088704 original size:29 final size:29
Alignment explanation
Indices: 29088672--29088931 Score: 259
Period size: 29 Copynumber: 9.1 Consensus size: 29
29088662 TAAGTGAGCA
*
29088672 TTTGTGGCTATCTCTGTTATAAGGAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
*
29088701 TTTGTGGCTA--TCT-TTGAAAGGACA-CC
1 TTTGTGGCTATCTCTGTTAAAAGGA-AGCC
* * *
29088727 TTTGTGGTTATCTCTGTTATAAGAAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
*
29088756 TTTGTGGCTATCTCTGTTAAAAGAAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
* * *
29088785 TTTGTGGCGATCTTTATTATAAA-GAAGCC
1 TTTGTGGCTATCTCTGTTA-AAAGGAAGCC
*
29088814 TTTGTGGCTATCTCTGTTAAAAGGATGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
* **
29088843 TTTATGGCTATCTCTGTTAAAAACATAG-C
1 TTTGTGGCTATCTCTGTTAAAAGGA-AGCC
*
29088872 TTTGTGGCTATCT-TAGTT-AAATGAATGCC
1 TTTGTGGCTATCTCT-GTTAAAAGGAA-GCC
* *
29088901 -TTGTGGCAAACTCTGTTAAAAGGAACGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAA-GCC
29088930 TT
1 TT
29088932 CTTGGTGAGA
Statistics
Matches: 190, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
26 18 0.09
27 5 0.03
28 26 0.14
29 136 0.72
30 5 0.03
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (29 bp):
TTTGTGGCTATCTCTGTTAAAAGGAAGCC
Found at i:29088858 original size:87 final size:85
Alignment explanation
Indices: 29088676--29088931 Score: 288
Period size: 87 Copynumber: 3.0 Consensus size: 85
29088666 TGAGCATTTG
* * * * *
29088676 TGGCTATCTCTGTTATAAGGAAGCCTTTGTGGCTATCTT-TGAAAGGACA-CCTTTGTGGTTATC
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTGTGGCTATCTTATTAAAAGA-AGCCTTTGTGGCTATC
* * *
29088739 TCTGTTATAAGAAAGCCTTTG
65 TCTGTTAAAAGGAAGCCTTTA
*
29088760 TGGCTATCTCTGTTAAAAGAAAGCCTTTGTGGCGATCTTTATTATAAAGAAGCCTTTGTGGCTAT
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTGTGGCTATC-TTATTA-AAAGAAGCCTTTGTGGCTAT
*
29088825 CTCTGTTAAAAGGATGCCTTTA
64 CTCTGTTAAAAGGAAGCCTTTA
* *
29088847 TGGCTATCTCTGTTAAAA-ACATAG-CTTTGTGGCTATCTTAGTTAAATGAATGCC-TTGTGGCA
1 TGGCTATCTCTGTTAAAAGA-A-AGCCTTTGTGGCTATCTTA-TTAAAAGAA-GCCTTTGTGGCT
*
29088909 AACTCTGTTAAAAGGAACGCCTT
62 ATCTCTGTTAAAAGGAA-GCCTT
29088932 CTTGGTGAGA
Statistics
Matches: 148, Mismatches: 15, Indels: 15
0.83 0.08 0.08
Matches are distributed among these distances:
84 34 0.23
85 2 0.01
86 34 0.23
87 76 0.51
88 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (85 bp):
TGGCTATCTCTGTTAAAAGAAAGCCTTTGTGGCTATCTTATTAAAAGAAGCCTTTGTGGCTATCT
CTGTTAAAAGGAAGCCTTTA
Found at i:29089744 original size:15 final size:15
Alignment explanation
Indices: 29089724--29089755 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29089714 TTAAGAATGC
*
29089724 TTCTCAAAAGTGCTT
1 TTCTCAAAAGTACTT
29089739 TTCTCAAAAGTACTT
1 TTCTCAAAAGTACTT
29089754 TT
1 TT
29089756 AAGGAGAAGC
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:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCTCAAAAGTACTT
Found at i:29104884 original size:13 final size:12
Alignment explanation
Indices: 29104861--29104934 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 12
29104851 AGTCATTGGC
29104861 AAAAA-GAAAGA
1 AAAAAGGAAAGA
29104872 AAAAGAGGAAAG-
1 AAAA-AGGAAAGA
29104884 -AAAAGGAAAG-
1 AAAAAGGAAAGA
* *
29104894 GAGAAGGAGAAGA
1 AAAAAGGA-AAGA
29104907 AAAAA-GAAAGAA
1 AAAAAGGAAAG-A
29104919 AAAGAAGGAAAGA
1 AAA-AAGGAAAGA
29104932 AAA
1 AAA
29104935 GGAAAGGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
10 7 0.13
11 16 0.31
12 10 0.19
13 14 0.27
14 5 0.10
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAAGA
Found at i:29104893 original size:5 final size:5
Alignment explanation
Indices: 29104877--29104947 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
29104867 AAAGAAAAAG
* * * * *
29104877 AGGAA AGAAA AGGAA AGGAGA AGGAGA AGAAAA AAGAA AGAAA AAG-A
1 AGGAA AGGAA AGGAA AGGA-A AGGA-A AG-GAA AGGAA AGGAA AGGAA
*
29104924 AGGAA AGAAA AGGAA AGGAA AGGA
1 AGGAA AGGAA AGGAA AGGAA AGGA
29104948 GAAGAGAGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
4 3 0.06
5 36 0.71
6 11 0.22
7 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:29104906 original size:29 final size:26
Alignment explanation
Indices: 29104880--29104990 Score: 85
Period size: 25 Copynumber: 4.3 Consensus size: 26
29104870 GAAAAAGAGG
29104880 AAAGAAAAGGAAAGGAGAAGGAGAAGAAA
1 AAAG-AAAGGAAAGGAGAAGGAGAAG--A
*
29104909 AAAGAAA-GAAA-AAGAAGGA-AAGA
1 AAAGAAAGGAAAGGAGAAGGAGAAGA
29104932 AAAGGAAAGGAAAGGAGAAGAGAGAA-A
1 AAA-GAAAGGAAAGGAGAAG-GAGAAGA
* *
29104959 AAA-AAAAGAAGAGG-GAAGGA-AGGA
1 AAAGAAAGGAA-AGGAGAAGGAGAAGA
29104983 AAA-AAAGG
1 AAAGAAAGG
29104991 TAATTTTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
23 5 0.07
24 14 0.20
25 17 0.24
26 15 0.21
27 10 0.14
28 5 0.07
29 4 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (26 bp):
AAAGAAAGGAAAGGAGAAGGAGAAGA
Found at i:29104947 original size:46 final size:47
Alignment explanation
Indices: 29104861--29104969 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 47
29104851 AGTCATTGGC
29104861 AAAAAGAAAGAAAAAG-AGGAAAGAAAAGGAAAGGAGAAGGAGAAGA
1 AAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGGAGAAGA
29104907 AAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA-AAGGAGAAGA
1 AAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGGAGAAGA
* *
29104953 GAGAA-AAA-AAAAAGAAG
1 AAAAAGAAAGAAAAAGAAG
29104970 AGGGAAGGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
44 9 0.15
45 3 0.05
46 29 0.48
47 19 0.32
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (47 bp):
AAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGGAGAAGA
Found at i:29105728 original size:27 final size:27
Alignment explanation
Indices: 29105698--29105752 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
29105688 AAAGAGGCTG
29105698 ATGGAGGAGAATAAAAAGGCGGCACCA
1 ATGGAGGAGAATAAAAAGGCGGCACCA
*
29105725 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGGAGAATAAAAAGGCGGCACCA
29105752 A
1 A
29105753 AATGTGACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.35, T:0.07
Consensus pattern (27 bp):
ATGGAGGAGAATAAAAAGGCGGCACCA
Found at i:29108279 original size:14 final size:14
Alignment explanation
Indices: 29108238--29108290 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
29108228 TTTTTGTATA
*
29108238 AATTTAATTATTCC
1 AATTTAATTATTCT
29108252 AATTTAATTATTCT
1 AATTTAATTATTCT
29108266 AATTTAATTATTCT
1 AATTTAATTATTCT
*
29108280 AGTTTTAATTA
1 A-ATTTAATTA
29108291 GTATGCTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 28 0.78
15 8 0.22
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:29111630 original size:22 final size:23
Alignment explanation
Indices: 29111604--29111658 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
29111594 TATTAATCTT
29111604 AATAACTA-AAATTAAAACAAAA-
1 AATAACTACAAATT-AAACAAAAC
*
29111626 AATAA-TACAAATTATACAAAAC
1 AATAACTACAAATTAAACAAAAC
*
29111648 AATAACAACAA
1 AATAACTACAA
29111659 TGTAATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 15 0.54
23 4 0.14
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (23 bp):
AATAACTACAAATTAAACAAAAC
Found at i:29111853 original size:27 final size:27
Alignment explanation
Indices: 29111823--29111900 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
29111813 CCACTTAGTA
* *
29111823 TGGCACCATCGGTGCCGTCAATCTCCT
1 TGGCACCATCGGTGCCGTCAATCACAT
*
29111850 TGGCACCATCGGTGCCGCCAATCACAT
1 TGGCACCATCGGTGCCGTCAATCACAT
* *
29111877 TGGCACCTTTGGTGCCGTCAATCA
1 TGGCACCATCGGTGCCGTCAATCA
29111901 AGAACCCTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.18, C:0.35, G:0.23, T:0.24
Consensus pattern (27 bp):
TGGCACCATCGGTGCCGTCAATCACAT
Found at i:29112836 original size:20 final size:20
Alignment explanation
Indices: 29112811--29112852 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29112801 TTCTTACGAA
29112811 TTTATAAAATTTTACAATTT
1 TTTATAAAATTTTACAATTT
***
29112831 TTTATATTTTTTTACAATTT
1 TTTATAAAATTTTACAATTT
29112851 TT
1 TT
29112853 ATATTCTTCT
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:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATAAAATTTTACAATTT
Found at i:29113149 original size:90 final size:92
Alignment explanation
Indices: 29112979--29113149 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 92
29112969 AAGCAGTGGT
* ** * * *
29112979 TTAATTGCTTTTTTTGAAAAAAGTTTAAGAGTTTTTTTTTGATACATTTTGAAAGTTCAAGTACC
1 TTAATTGCTTATTTTGAAAAAAGTTT-AGAGGATCTTTTTAATACATTTTAAAAGTTCAAGTACC
* *
29113044 TAATTGAGTGCAAAAAAAAGGTAGGGGC
65 TAAATGACTGCAAAAAAAAGGTAGGGGC
*
29113072 TTAATTGCTTATTTTGAAAAAA-TTT-GAGGATCTTTTTAATATATTTTAAAAGTTCAAGTACCT
1 TTAATTGCTTATTTTGAAAAAAGTTTAGAGGATCTTTTTAATACATTTTAAAAGTTCAAGTACCT
*
29113135 AAATGACTGTAAAAA
66 AAATGACTGCAAAAA
29113150 GGAAAGCAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
90 44 0.65
92 3 0.04
93 21 0.31
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (92 bp):
TTAATTGCTTATTTTGAAAAAAGTTTAGAGGATCTTTTTAATACATTTTAAAAGTTCAAGTACCT
AAATGACTGCAAAAAAAAGGTAGGGGC
Found at i:29114521 original size:15 final size:15
Alignment explanation
Indices: 29114501--29114530 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29114491 TGGACATCAC
29114501 CCCCCAAGGTTAACA
1 CCCCCAAGGTTAACA
29114516 CCCCCAAGGTTAACA
1 CCCCCAAGGTTAACA
29114531 AAGCACTTCC
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:0.33, C:0.40, G:0.13, T:0.13
Consensus pattern (15 bp):
CCCCCAAGGTTAACA
Found at i:29123590 original size:11 final size:11
Alignment explanation
Indices: 29123574--29123599 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29123564 ATTTTTTTAT
29123574 TTTTAAAATAC
1 TTTTAAAATAC
29123585 TTTTAAAATAC
1 TTTTAAAATAC
29123596 TTTT
1 TTTT
29123600 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:29123611 original size:10 final size:10
Alignment explanation
Indices: 29123596--29123659 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 10
29123586 TTTAAAATAC
29123596 TTTTTTTAAA
1 TTTTTTTAAA
29123606 -TTTTTTAAA
1 TTTTTTTAAA
*
29123615 -GTTTTTAAA
1 TTTTTTTAAA
*
29123624 TTTTTTAAAAA
1 TTTTTT-TAAA
29123635 TACTTTTTT-AA
1 T--TTTTTTAAA
*
29123646 TTTTTTTTAA
1 TTTTTTTAAA
29123656 TTTT
1 TTTT
29123660 AAAATATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 23 0.51
10 10 0.22
11 7 0.16
13 5 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:29123621 original size:18 final size:18
Alignment explanation
Indices: 29123598--29123632 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29123588 TAAAATACTT
29123598 TTTTTAAATTTTTTAAAG
1 TTTTTAAATTTTTTAAAG
29123616 TTTTTAAATTTTTTAAA
1 TTTTTAAATTTTTTAAA
29123633 AATACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTTTTTAAAG
Found at i:29123630 original size:41 final size:41
Alignment explanation
Indices: 29123564--29123691 Score: 163
Period size: 41 Copynumber: 3.1 Consensus size: 41
29123554 AAATATTTTT
* * *
29123564 ATTTTTTTATTTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
*
29123605 ATTTTTTAAAGTTTTTAAAT-TTTTTAAAAATAC-TTTTTTAA
1 ATTTTTTAAA-TTTTAAAATATTTTT-AAAATACTTTTTTTAA
* *
29123646 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-A
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
29123686 ATTTTT
1 ATTTTT
29123692 GTTTTAATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
40 21 0.28
41 39 0.52
42 15 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (41 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
Found at i:29123652 original size:9 final size:9
Alignment explanation
Indices: 29123597--29123632 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
29123587 TTAAAATACT
29123597 TTTTTTAAA
1 TTTTTTAAA
29123606 TTTTTTAAA
1 TTTTTTAAA
*
29123615 GTTTTTAAA
1 TTTTTTAAA
29123624 TTTTTTAAA
1 TTTTTTAAA
29123633 AATACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:29123768 original size:30 final size:30
Alignment explanation
Indices: 29123734--29123809 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
29123724 ATTTAAAAAA
*
29123734 CGGGCCGGGCCCGGGTTTATGAATTTTTCC
1 CGGGCCGGGCCCGGGCTTATGAATTTTTCC
29123764 CGGGCCGGGCCCGGGCTTATGAATTTTTCC
1 CGGGCCGGGCCCGGGCTTATGAATTTTTCC
*
29123794 CGGGCCGGGCCTGGGC
1 CGGGCCGGGCCCGGGC
29123810 AAAATTCTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.08, C:0.30, G:0.38, T:0.24
Consensus pattern (30 bp):
CGGGCCGGGCCCGGGCTTATGAATTTTTCC
Found at i:29130916 original size:36 final size:38
Alignment explanation
Indices: 29130835--29130920 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
29130825 AAACTTTTAC
* *
29130835 TCCTAGCCCTAGATTTAAACTCTAAAGATATCTTATAA
1 TCCTAGCCCTAGATTTAAACGCTAAAGATATCTAATAA
29130873 TCCTAGCCCTAGATTTAAACGCTAAAGA-A-CTAATAA
1 TCCTAGCCCTAGATTTAAACGCTAAAGATATCTAATAA
*
29130909 TCGTAGCCCTAG
1 TCCTAGCCCTAG
29130921 TGATTAGCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 17 0.38
37 1 0.02
38 27 0.60
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (38 bp):
TCCTAGCCCTAGATTTAAACGCTAAAGATATCTAATAA
Found at i:29141334 original size:42 final size:42
Alignment explanation
Indices: 29141278--29141358 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
29141268 CCTAATTGGG
* * *
29141278 AAAATAATTCCCTTATTCTAATAAGCTACTTAAAGATAAGGA
1 AAAATAATACCCTTATTCTAATAAACTACTAAAAGATAAGGA
29141320 AAAATAATACCCTTATTCTAATAAACTACTAAAAGATAA
1 AAAATAATACCCTTATTCTAATAAACTACTAAAAGATAA
29141359 AATAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (42 bp):
AAAATAATACCCTTATTCTAATAAACTACTAAAAGATAAGGA
Found at i:29142807 original size:295 final size:295
Alignment explanation
Indices: 29142277--29142871 Score: 1190
Period size: 295 Copynumber: 2.0 Consensus size: 295
29142267 CTTGCCCTTG
29142277 TGAGTAACCTTATTTTTTAACAACTTGAGTGAACCGTTCAAACCAAGCTCAAGGAGACTGCTTTA
1 TGAGTAACCTTATTTTTTAACAACTTGAGTGAACCGTTCAAACCAAGCTCAAGGAGACTGCTTTA
29142342 GACCATACAAAGATTTTCTAAGCTTACATATTCGAGTTCCAAATTTTTCTTCAAAACCTAGAGGA
66 GACCATACAAAGATTTTCTAAGCTTACATATTCGAGTTCCAAATTTTTCTTCAAAACCTAGAGGA
29142407 GGATCCATGTAAACTTCTTCTTCAAGTTTCCCATTTAGGAAAACATTCTTCACTTCTAGCTGCTG
131 GGATCCATGTAAACTTCTTCTTCAAGTTTCCCATTTAGGAAAACATTCTTCACTTCTAGCTGCTG
29142472 TAAGGACCAATCAAGATTAACAGCAATTGATAAAAGACCTCTAACAGAATTTAATTTGGCTATTG
196 TAAGGACCAATCAAGATTAACAGCAATTGATAAAAGACCTCTAACAGAATTTAATTTGGCTATTG
29142537 GAGCAAATGTTTCAAGATAATCTATCACGTTTGTT
261 GAGCAAATGTTTCAAGATAATCTATCACGTTTGTT
29142572 TGAGTAACCTTATTTTTTAACAACTTGAGTGAACCGTTCAAACCAAGCTCAAGGAGACTGCTTTA
1 TGAGTAACCTTATTTTTTAACAACTTGAGTGAACCGTTCAAACCAAGCTCAAGGAGACTGCTTTA
29142637 GACCATACAAAGATTTTCTAAGCTTACATATTCGAGTTCCAAATTTTTCTTCAAAACCTAGAGGA
66 GACCATACAAAGATTTTCTAAGCTTACATATTCGAGTTCCAAATTTTTCTTCAAAACCTAGAGGA
29142702 GGATCCATGTAAACTTCTTCTTCAAGTTTCCCATTTAGGAAAACATTCTTCACTTCTAGCTGCTG
131 GGATCCATGTAAACTTCTTCTTCAAGTTTCCCATTTAGGAAAACATTCTTCACTTCTAGCTGCTG
29142767 TAAGGACCAATCAAGATTAACAGCAATTGATAAAAGACCTCTAACAGAATTTAATTTGGCTATTG
196 TAAGGACCAATCAAGATTAACAGCAATTGATAAAAGACCTCTAACAGAATTTAATTTGGCTATTG
29142832 GAGCAAATGTTTCAAGATAATCTATCACGTTTGTT
261 GAGCAAATGTTTCAAGATAATCTATCACGTTTGTT
29142867 TGAGT
1 TGAGT
29142872 GTACTGTTTA
Statistics
Matches: 300, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 300 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (295 bp):
TGAGTAACCTTATTTTTTAACAACTTGAGTGAACCGTTCAAACCAAGCTCAAGGAGACTGCTTTA
GACCATACAAAGATTTTCTAAGCTTACATATTCGAGTTCCAAATTTTTCTTCAAAACCTAGAGGA
GGATCCATGTAAACTTCTTCTTCAAGTTTCCCATTTAGGAAAACATTCTTCACTTCTAGCTGCTG
TAAGGACCAATCAAGATTAACAGCAATTGATAAAAGACCTCTAACAGAATTTAATTTGGCTATTG
GAGCAAATGTTTCAAGATAATCTATCACGTTTGTT
Found at i:29145498 original size:41 final size:41
Alignment explanation
Indices: 29145453--29145533 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
29145443 AATCTAATTG
** *
29145453 GGAAAATAATTTTCTTATTCTAATAAACTACTAAAAGATAA
1 GGAAAATAATTCCCTTATTCTAAAAAACTACTAAAAGATAA
*
29145494 GGAAAATGATTCCCTTATTCTAAAAAACTACTAAAAGATA
1 GGAAAATAATTCCCTTATTCTAAAAAACTACTAAAAGATA
29145534 TAATAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (41 bp):
GGAAAATAATTCCCTTATTCTAAAAAACTACTAAAAGATAA
Found at i:29145547 original size:41 final size:41
Alignment explanation
Indices: 29145466--29145547 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
29145456 AAATAATTTT
* *
29145466 CTTATTCTAATAAACTACTAAAAGATAAGGAAAATGATTCC
1 CTTATTCTAAAAAACTACTAAAAGATAAAGAAAATGATTCC
*
29145507 CTTATTCTAAAAAACTACTAAAAGATATAATAAAAT-ATTCC
1 CTTATTCTAAAAAACTACTAAAAGATA-AAGAAAATGATTCC
29145548 TAGAATATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 31 0.84
42 6 0.16
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (41 bp):
CTTATTCTAAAAAACTACTAAAAGATAAAGAAAATGATTCC
Found at i:29156472 original size:165 final size:165
Alignment explanation
Indices: 29156200--29156695 Score: 920
Period size: 165 Copynumber: 3.0 Consensus size: 165
29156190 GAAAGTTGAT
*
29156200 ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCTGAAGTGCCACAATACGAAAGGTA
1 ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCTGAAGTGCCACAATATGAAAGGTA
29156265 ACTCAAAAAAAGTAGCTGTTGATGCTAATCAGATCACAGGACAATAGCAAATAGGTGAAATGGGG
66 ACTCAAAAAAAGTAGCTGTTGATGCTAATCAGATCACAGGACAATAGCAAATAGGTGAAATGGGG
29156330 TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
131 TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
* *
29156365 ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCCGAAGTGCTACAATATGAAAGGTA
1 ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCTGAAGTGCCACAATATGAAAGGTA
* * * *
29156430 ACTCGAAAAAAGCAGCTGTTGATGCCAATCAAATCACAGGACAATAGCAAATAGGTGAAATGGGG
66 ACTCAAAAAAAGTAGCTGTTGATGCTAATCAGATCACAGGACAATAGCAAATAGGTGAAATGGGG
29156495 TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
131 TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
29156530 ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCTGAAGTGCCACAATATGAAAGGTA
1 ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCTGAAGTGCCACAATATGAAAGGTA
*
29156595 ACTCAAAAAAAGTAGCTGTTGATGCTAATCAGATCACAGAACAATAGCAAATAGGTGAAATGGGG
66 ACTCAAAAAAAGTAGCTGTTGATGCTAATCAGATCACAGGACAATAGCAAATAGGTGAAATGGGG
29156660 TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
131 TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
29156695 A
1 A
29156696 CAAGCTGATT
Statistics
Matches: 317, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 317 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (165 bp):
ATTCCTCTCAATTGACAAATACTAGAAAACTAAAGTGGGGCTGAAGTGCCACAATATGAAAGGTA
ACTCAAAAAAAGTAGCTGTTGATGCTAATCAGATCACAGGACAATAGCAAATAGGTGAAATGGGG
TGAAAAATTTTGGTCTAAGCTGAAAATCAGATTTA
Found at i:29163752 original size:17 final size:18
Alignment explanation
Indices: 29163719--29163753 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29163709 TTTGTCAATA
*
29163719 TTTTTAAATTATAAAAAG
1 TTTTCAAATTATAAAAAG
29163737 TTTTCAAATTATAAAAA
1 TTTTCAAATTATAAAAA
29163754 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTTCAAATTATAAAAAG
Found at i:29163974 original size:24 final size:26
Alignment explanation
Indices: 29163929--29163982 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
29163919 ACTCGACTTT
*
29163929 TTTTTTAATTTTTGATAAGGTTAGGG
1 TTTTTTAATTTTTGATAAGGTTAGGA
**
29163955 TTTTTTAA-TTTTG-TTGGGTTAGGA
1 TTTTTTAATTTTTGATAAGGTTAGGA
29163979 TTTT
1 TTTT
29163983 ATGAGCGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
25 5 0.20
26 8 0.32
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (26 bp):
TTTTTTAATTTTTGATAAGGTTAGGA
Found at i:29176670 original size:40 final size:40
Alignment explanation
Indices: 29176626--29176834 Score: 267
Period size: 40 Copynumber: 5.2 Consensus size: 40
29176616 GTACAAACAG
29176626 GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACTTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACTTAT
* * * *
29176666 GTGCATTCAAGGGTACTGAAGTACAAACAAGAGCATTTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACTTAT
* * * *
29176706 GTGCATGCAAGGGTATCGAAGTACAAACAAGGGGACTTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACTTAT
* *
29176746 ATGCATTCAGGGGTACCGAAGTACAAA-TAGAGGCACTTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAAG-GGCACTTAT
* * * * *
29176786 GTGTATTCAGGAGTACCGAAGTACAAATACGGGCACCTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACTTAT
29176826 GTGCATTCA
1 GTGCATTCA
29176835 TATATATATA
Statistics
Matches: 144, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
39 2 0.01
40 141 0.98
41 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (40 bp):
GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACTTAT
Found at i:29176696 original size:20 final size:20
Alignment explanation
Indices: 29176636--29176696 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
29176626 GTGCATTCAG
*
29176636 GGGTACCGAAGTACAAACAA
1 GGGTACTGAAGTACAAACAA
* * * * **
29176656 GGGCACTTATGTGCATTCAA
1 GGGTACTGAAGTACAAACAA
29176676 GGGTACTGAAGTACAAACAA
1 GGGTACTGAAGTACAAACAA
29176696 G
1 G
29176697 AGCATTTATG
Statistics
Matches: 28, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
GGGTACTGAAGTACAAACAA
Found at i:29178207 original size:25 final size:25
Alignment explanation
Indices: 29178179--29178228 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29178169 TAGATAATAT
*
29178179 GCCAC-AAGGTCTTTACAGAATATGC
1 GCCACAAAGG-CTTTACAAAATATGC
29178204 GCCACAAAGGCTTTACAAAATATGC
1 GCCACAAAGGCTTTACAAAATATGC
29178229 CATGACAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (25 bp):
GCCACAAAGGCTTTACAAAATATGC
Found at i:29182369 original size:27 final size:27
Alignment explanation
Indices: 29182339--29182816 Score: 356
Period size: 27 Copynumber: 17.8 Consensus size: 27
29182329 TCATTTCCTA
**
29182339 AGGGTATAACAGTCATTTTACCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATG
29182366 AGGGTATTTC-GTTCATTTTACCCTATG
1 AGGGTATTTCAG-TCATTTTACCCTATG
** *
29182393 AGGGTATTTTGGTCATTTCACCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATG
* ** *
29182420 GGGGTATTTTGGTCATTTTACCTTAT-
1 AGGGTATTTCAGTCATTTTACCCTATG
29182446 AGGGATATTTCAGAT-ATTTTACCCTAT-
1 AGGG-TATTTCAG-TCATTTTACCCTATG
29182473 AGGGGTATTTC-GATCATTTTACCCTATG
1 A-GGGTATTTCAG-TCATTTTACCCTATG
* * *
29182501 GGGGTAATTC-GATTATTTTACCCTATG
1 AGGGTATTTCAG-TCATTTTACCCTATG
* *
29182528 -GGGTATTTCAATCATTTTATCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATG
* **
29182554 AGAGTATTTCAGTCATTCTT-TTCTAT-
1 AGGGTATTTCAGTCATT-TTACCCTATG
* * *
29182580 AGGGGTATTTAAGTTATTCTACCCTATG
1 A-GGGTATTTCAGTCATTTTACCCTATG
* * * *
29182608 GGGGTATTTCGGTCATTCTACCATATG
1 AGGGTATTTCAGTCATTTTACCCTATG
* *
29182635 AGGCTATTTC-GATCATTCTACCCTATG
1 AGGGTATTTCAG-TCATTTTACCCTATG
* * *
29182662 -GGGTTATTTCGGTCATTCTATCCTATG
1 AGGG-TATTTCAGTCATTTTACCCTATG
* * *
29182689 -GGGTATTTCGGTCATTCTACCTTAT-
1 AGGGTATTTCAGTCATTTTACCCTATG
* *
29182714 AGGGGTATTTCAGTTATTTTACCTTATG
1 A-GGGTATTTCAGTCATTTTACCCTATG
* * *
29182742 GGGGTATTTC-GATCATTTAATCCTATG
1 AGGGTATTTCAG-TCATTTTACCCTATG
* * *
29182769 GGGGTATTTAAGCCATTTTACCCT-TG
1 AGGGTATTTCAGTCATTTTACCCTATG
* **
29182795 GGGGTATTTTGGTCATTTTACC
1 AGGGTATTTCAGTCATTTTACC
29182817 TATTTTGGGA
Statistics
Matches: 376, Mismatches: 54, Indels: 43
0.79 0.11 0.09
Matches are distributed among these distances:
26 75 0.20
27 292 0.78
28 9 0.02
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
AGGGTATTTCAGTCATTTTACCCTATG
Found at i:29182397 original size:54 final size:54
Alignment explanation
Indices: 29182339--29182816 Score: 395
Period size: 54 Copynumber: 8.9 Consensus size: 54
29182329 TCATTTCCTA
** *
29182339 AGGGTATAACAGTCATTTTACCCTATGAGGGTATTTCGTTCATTTTACCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
** * * * * *
29182393 AGGGTATTTTGGTCATTTCACCCTATGGGGGTATTTTGGTCATTTTACCTTAT-
1 AGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
29182446 AGGGATATTTCAGAT-ATTTTACCCTAT-AGGGGTATTTCGATCATTTTACCCTATG
1 AGGG-TATTTCAG-TCATTTTACCCTATGA-GGGTATTTCGATCATTTTACCCTATG
* * * * *
29182501 GGGGTAATTC-GATTATTTTACCCTATG-GGGTATTTCAATCATTTTATCCTATG
1 AGGGTATTTCAG-TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
* ** * * *
29182554 AGAGTATTTCAGTCATTCTT-TTCTAT-AGGGGTATTT-AAGTTATTCTACCCTATG
1 AGGGTATTTCAGTCATT-TTACCCTATGA-GGGTATTTCGA-TCATTTTACCCTATG
* * * * * *
29182608 GGGGTATTTCGGTCATTCTACCATATGAGGCTATTTCGATCATTCTACCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
* * * * * *
29182662 -GGGTTATTTCGGTCATTCTATCCTATG-GGGTATTTCGGTCATTCTACCTTAT-
1 AGGG-TATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
* * * * *
29182714 AGGGGTATTTCAGTTATTTTACCTTATGGGGGTATTTCGATCATTTAATCCTATG
1 A-GGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
* * * * * *
29182769 GGGGTATTTAAGCCATTTTACCCT-TGGGGGTATTTTGGTCATTTTACC
1 AGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACC
29182817 TATTTTGGGA
Statistics
Matches: 342, Mismatches: 63, Indels: 39
0.77 0.14 0.09
Matches are distributed among these distances:
53 112 0.33
54 224 0.65
55 6 0.02
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (54 bp):
AGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG
Found at i:29182603 original size:107 final size:105
Alignment explanation
Indices: 29182348--29182803 Score: 366
Period size: 107 Copynumber: 4.3 Consensus size: 105
29182338 AAGGGTATAA
* * * * * * * * *
29182348 CAGTCATTTTACCCTAT-GAGGGTATTTCGTTCATTTTACCCTATGAGGGTATTTTGGTCATTTC
1 CAGTCATTCTATCCTATAG-GGGTATTTAG-TCATTCTACCCTATGGGGGTATTTCGATTATTTT
* * * *
29182412 ACCCTATGGGGGTATTTTGGTCATTTTA-CCTTATAGGGATATTT
64 ACCATAT-GGGGTATTTCGATCATTTTATCC-TAT-GGGGTATTT
* * * * *
29182456 CAGAT-ATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTAATTCGATTATTTT
1 CAG-TCATTCTATCCTATAGGGGTATTTAG-TCATTCTACCCTATGGGGGTATTTCGATTATTTT
* * *
29182520 ACCCTATGGGGTATTTCAATCATTTTATCCTATGAGAGTATTT
64 ACCATATGGGGTATTTCGATCATTTTATCCTATG-GGGTATTT
* * * * * *
29182563 CAGTCATTCTTTTCTATAGGGGTATTTAAGTTATTCTACCCTATGGGGGTATTTCGGTCATTCTA
1 CAGTCATTCTATCCTATAGGGGTATTT-AGTCATTCTACCCTATGGGGGTATTTCGATTATTTTA
* * *
29182628 CCATATGAGGCTATTTCGATCATTCTACCCTATGGGGTTATTT
65 CCATATG-GGGTATTTCGATCATTTTATCCTATGGGG-TATTT
* * * *
29182671 CGGTCATTCTATCCTAT-GGGGTATTTCGGTCATTCTACCTTATAGGGGTATTTC-AGTTATTTT
1 CAGTCATTCTATCCTATAGGGGTATTT-AGTCATTCTACCCTATGGGGGTATTTCGA-TTATTTT
* *
29182734 ACCTTATGGGGGTATTTCGATCATTTAATCCTATGGGGGTATTT
64 ACCATAT-GGGGTATTTCGATCATTTTATCCTAT-GGGGTATTT
* * * * *
29182778 AAGCCATTTTACCCT-TGGGGGTATTT
1 CAGTCATTCTATCCTATAGGGGTATTT
29182804 TGGTCATTTT
Statistics
Matches: 286, Mismatches: 50, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
106 3 0.01
107 172 0.60
108 109 0.38
109 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (105 bp):
CAGTCATTCTATCCTATAGGGGTATTTAGTCATTCTACCCTATGGGGGTATTTCGATTATTTTAC
CATATGGGGTATTTCGATCATTTTATCCTATGGGGTATTT
Found at i:29182777 original size:134 final size:133
Alignment explanation
Indices: 29182351--29182819 Score: 550
Period size: 134 Copynumber: 3.5 Consensus size: 133
29182341 GGTATAACAG
* * * *
29182351 TCATTTTACCCTATGAGGGTATTTCGTTCATTTTACCCTATGAGGGTATTTTGGTCATTTCACCC
1 TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATG-GGGTATTTCGGTCATTTTATCC
* * * * *
29182416 TATGGGGGTATTTTGGTCATTTTACCTTATAGGGATATTTCAGATATTTTACCCTATAGGGGTAT
65 TAT-GGGGTATTTCGGTCATTCTACCTTATAGGGGTATTTCAGTTATTTTACCCTATGGGGGTAT
29182481 TTCGA
129 TTCGA
* * * **
29182486 TCATTTTACCCTATGGGGGTAATTCGATTATTTTACCCTATGGGGTATTTCAATCATTTTATCCT
1 TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGGGGTATTTCGGTCATTTTATCCT
* * ** * *
29182551 ATGAGAGTATTTCAGTCATTCT-TTTCTATAGGGGTATTTAAGTTATTCTACCCTATGGGGGTAT
66 ATG-GGGTATTTCGGTCATTCTACCT-TATAGGGGTATTTCAGTTATTTTACCCTATGGGGGTAT
*
29182615 TTCGG
129 TTCGA
* * * * *
29182620 TCATTCTACCATATGAGGCTATTTCGATCATTCTACCCTATGGGGTTATTTCGGTCATTCTATCC
1 TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGGGG-TATTTCGGTCATTTTATCC
*
29182685 TATGGGGTATTTCGGTCATTCTACCTTATAGGGGTATTTCAGTTATTTTACCTTATGGGGGTATT
65 TATGGGGTATTTCGGTCATTCTACCTTATAGGGGTATTTCAGTTATTTTACCCTATGGGGGTATT
29182750 TCGA
130 TCGA
* * * * * *
29182754 TCATTTAATCCTATGGGGGTATTT-AAGCCATTTTACCCT-TGGGGGTATTTTGGTCATTTTA-C
1 TCATTTTACCCTATGAGGGTATTTCGA-TCATTTTACCCTAT-GGGGTATTTCGGTCATTTTATC
29182816 CTAT
64 CTAT
29182820 TTTGGGATCT
Statistics
Matches: 278, Mismatches: 50, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
132 5 0.02
133 18 0.06
134 196 0.71
135 59 0.21
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (133 bp):
TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGGGGTATTTCGGTCATTTTATCCT
ATGGGGTATTTCGGTCATTCTACCTTATAGGGGTATTTCAGTTATTTTACCCTATGGGGGTATTT
CGA
Found at i:29191181 original size:15 final size:15
Alignment explanation
Indices: 29191157--29191188 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29191147 TATGCATGCA
*
29191157 AAATATAAAAGACAT
1 AAATACAAAAGACAT
29191172 AAATACAAAAGACAT
1 AAATACAAAAGACAT
29191187 AA
1 AA
29191189 TAGTGAAATG
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:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:29197196 original size:23 final size:23
Alignment explanation
Indices: 29197160--29197210 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
29197150 AAAAATGGTT
29197160 AAAT-TACCATATAAATCCATTC
1 AAATATACCATATAAATCCATTC
*
29197182 AAATATACTATATAAATCCATTC
1 AAATATACCATATAAATCCATTC
29197205 AAATAT
1 AAATAT
29197211 GCATTCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATACCATATAAATCCATTC
Found at i:29207839 original size:14 final size:14
Alignment explanation
Indices: 29207822--29207870 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
29207812 TTCATTTTCC
29207822 ACCTGCCATTACAT
1 ACCTGCCATTACAT
* *
29207836 ACCTCCACACTCTGCAT
1 ACCTGC-CA-T-TACAT
29207853 ACCTGCCATTACAT
1 ACCTGCCATTACAT
29207867 ACCT
1 ACCT
29207871 TCACACTCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 13 0.46
15 3 0.11
16 3 0.11
17 9 0.32
ACGTcount: A:0.27, C:0.41, G:0.06, T:0.27
Consensus pattern (14 bp):
ACCTGCCATTACAT
Found at i:29207855 original size:17 final size:17
Alignment explanation
Indices: 29207833--29207884 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
29207823 CCTGCCATTA
29207833 CATACCTCCACACTCTG
1 CATACCTCCACACTCTG
* *
29207850 CATACCTGC-CA-T-TA
1 CATACCTCCACACTCTG
*
29207864 CATACCTTCACACTCTG
1 CATACCTCCACACTCTG
29207881 CATA
1 CATA
29207885 TCATTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 9 0.32
15 3 0.11
16 3 0.11
17 13 0.46
ACGTcount: A:0.27, C:0.40, G:0.06, T:0.27
Consensus pattern (17 bp):
CATACCTCCACACTCTG
Found at i:29207860 original size:31 final size:31
Alignment explanation
Indices: 29207822--29207884 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
29207812 TTCATTTTCC
29207822 ACCTGCCATTACATACCTCCACACTCTGCAT
1 ACCTGCCATTACATACCTCCACACTCTGCAT
*
29207853 ACCTGCCATTACATACCTTCACACTCTGCAT
1 ACCTGCCATTACATACCTCCACACTCTGCAT
29207884 A
1 A
29207885 TCATTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.40, G:0.06, T:0.27
Consensus pattern (31 bp):
ACCTGCCATTACATACCTCCACACTCTGCAT
Found at i:29208376 original size:36 final size:36
Alignment explanation
Indices: 29208336--29208408 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
29208326 CTTATAAAGA
* *
29208336 GAAAGTTCTATAATTTAGTTACTTAGAATTACTGTT
1 GAAAGTTCTATAATTTAGTTACCTAGAATTACAGTT
* *
29208372 GAAAGTTTTATATTTTAGTTACCTAGAATTACAGTT
1 GAAAGTTCTATAATTTAGTTACCTAGAATTACAGTT
29208408 G
1 G
29208409 TACTTATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (36 bp):
GAAAGTTCTATAATTTAGTTACCTAGAATTACAGTT
Found at i:29215083 original size:21 final size:21
Alignment explanation
Indices: 29215059--29215100 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29215049 TAACTTTTTC
*
29215059 TTCTTCAGCAACAACTTCCTT
1 TTCTGCAGCAACAACTTCCTT
*
29215080 TTCTGCAGCATCAACTTCCTT
1 TTCTGCAGCAACAACTTCCTT
29215101 CTCAACAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.38
Consensus pattern (21 bp):
TTCTGCAGCAACAACTTCCTT
Found at i:29221178 original size:21 final size:21
Alignment explanation
Indices: 29221154--29221196 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29221144 TGTGGCTGCA
29221154 TTTGAATG-TGCTGATTGTAGT
1 TTTG-ATGTTGCTGATTGTAGT
* *
29221175 TTTGCTGTTGTTGATTGTAGT
1 TTTGATGTTGCTGATTGTAGT
29221196 T
1 T
29221197 CCCTTGTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.14, C:0.05, G:0.28, T:0.53
Consensus pattern (21 bp):
TTTGATGTTGCTGATTGTAGT
Found at i:29229794 original size:101 final size:101
Alignment explanation
Indices: 29229580--29229826 Score: 318
Period size: 101 Copynumber: 2.5 Consensus size: 101
29229570 TTAACTATTA
* * * * *
29229580 TCATT-CGATACACGTAGTAGCCTTCACATAGTTCTACACACGTG-TTCAAACTTTTCGGTTCAC
1 TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATTCAAACTATCCGGTACAC
* *
29229643 GTAGTAGCCTACACATAGTACTACACACGTGACCAT
66 ATAGTAGCCTACACATAGTACTACACACGCGACCAT
* * * * * *
29229679 TAATATCTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATTGAAGCTATCCGGTACG
1 TCAT-TCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATTCAAACTATCCGGTACA
* * *
29229744 CATAGTAGCCTGCACATAGTACTACACATGCGACCTT
65 CATAGTAGCCTACACATAGTACTACACACGCGACCAT
*
29229781 TCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGA
1 TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGA
29229827 CCATCACTTT
Statistics
Matches: 126, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
99 3 0.02
100 1 0.01
101 75 0.60
102 47 0.37
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (101 bp):
TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATTCAAACTATCCGGTACAC
ATAGTAGCCTACACATAGTACTACACACGCGACCAT
Found at i:29235454 original size:26 final size:27
Alignment explanation
Indices: 29235425--29235489 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29235415 TTTAAATTAT
*
29235425 TAATTATTTTAAATTAA-TTAAAAATC
1 TAATTATCTTAAATTAATTTAAAAATC
* * * *
29235451 TAATCATCCTAACTTAATTTAAAATTC
1 TAATTATCTTAAATTAATTTAAAAATC
29235478 TAATTATCTTAA
1 TAATTATCTTAA
29235490 CTAAAATCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATTATCTTAAATTAATTTAAAAATC
Found at i:29235521 original size:53 final size:53
Alignment explanation
Indices: 29235373--29235802 Score: 160
Period size: 53 Copynumber: 8.3 Consensus size: 53
29235363 CTAAACTCCG
* * *
29235373 AATTATCTTAACTAAAATCTAAATTATTACCTAATCTATTGATTTAAATTATT
1 AATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAATTTAAATTACT
* * * * ** *
29235426 AATTATTTTAAATTAATTAAAAATCTAATCATCCTAA-C--TTAATTTAAAATT-CT
1 AATTATCTTAACTAAAATCTAAAT-T-ATTAT-CTAATCTATTAATTT-AAATTACT
*
29235479 AATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAA-TTAAATTCCT
1 AATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAATTTAAATTACT
* * * * *
29235531 AATTTTATTATCT-AAAT-TAAAACTCTAATTATCCTAA--T-TCAATTTAAACT-CAT
1 AATTATCTTAACTAAAATCT-AAA-T-T-ATTAT-CTAATCTATTAATTTAAATTAC-T
* * * *
29235584 AATTATC-T-A-T---ATCTAAATTATTACCTAATATTTTAATTTAAATTATT
1 AATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAATTTAAATTACT
* * * ** * ***
29235631 AATCATC-TAAATAAATTAGAAATCTAATTATTCTAA--T-TTAGTTTAAACCCCT
1 AATTATCTTAACTAAAATCTAAAT-T-ATTA-TCTAATCTATTAATTTAAATTACT
* * * * *
29235683 AATTACCTTAACTAAAATCAAAATTATTATCTAACCTGTTAA-TTAAATTCCT
1 AATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAATTTAAATTACT
* * * *
29235735 AACTATCTT-ATTTAAAT-TAAAATTTCAATTATCCTAA--T-TTAATTTAAACT-CT
1 AATTATCTTAACTAAAATCT-AAA-TT--ATTAT-CTAATCTATTAATTTAAATTACT
29235787 AATTATCTTAACTAAA
1 AATTATCTTAACTAAA
29235803 TTAAATCTCT
Statistics
Matches: 281, Mismatches: 57, Indels: 78
0.68 0.14 0.19
Matches are distributed among these distances:
44 4 0.01
45 4 0.01
46 2 0.01
47 19 0.07
48 6 0.02
49 2 0.01
50 11 0.04
51 30 0.11
52 74 0.26
53 89 0.32
54 20 0.07
55 16 0.06
56 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.43
Consensus pattern (53 bp):
AATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAATTTAAATTACT
Found at i:29235576 original size:105 final size:103
Alignment explanation
Indices: 29235364--29235802 Score: 428
Period size: 105 Copynumber: 4.2 Consensus size: 103
29235354 CGAGGAACCC
* * *
29235364 TAAACTCCGAATTATCTTAACTAAAATCTAAATTATTACCTAATCTATTGATTTAAATTATTAAT
1 TAAACT-CTAATTATCTTAACTAAAATCTAAATTATTACCTAATCTATT-AATTAAATTACTAAT
* * *
29235429 TATT-TTAAATTAATTAAAAATCTAATCATCCTAACTTAATT
64 T-TTATTAAATAAATT-AAAATCTAATTATCCTAATTTAATT
* * *
29235470 TAAAATTCTAATTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAATTAAATTCCTAATT
1 T-AAACTCTAATTATCTTAACTAAAATCTAAATTATTACCTAATCTATTAATTAAATTACTAATT
** *
29235535 TTATTATCTAAATTAAAACTCTAATTATCCTAATTCAATT
65 TTATTAAATAAATTAAAA-TCTAATTATCCTAATTTAATT
* * *
29235575 TAAACTCATAATTATC-T-A-T---ATCTAAATTATTACCTAATATTTTAATTTAAATTATTAA-
1 TAAACTC-TAATTATCTTAACTAAAATCTAAATTATTACCTAATCTATTAA-TTAAATTACTAAT
* * *
29235633 -TCATCTAAATAAATTAGAAATCTAATTATTCTAATTTAGTT
64 TTTAT-TAAATAAATTA-AAATCTAATTATCCTAATTTAATT
* * * * * * * *
29235674 TAAACCCCTAATTACCTTAACTAAAATCAAAATTATTATCTAACCTGTTAATTAAATTCCTAACT
1 TAAA-CTCTAATTATCTTAACTAAAATCTAAATTATTACCTAATCTATTAATTAAATTACTAATT
* * ** *
29235739 ATCTTATTTAAATTAAAATTTCAATTATCCTAATTTAATT
65 TTATTAAATAAATTAAAATCT-AATTATCCTAATTTAATT
29235779 TAAACTCTAATTATCTTAACTAAA
1 TAAACTCTAATTATCTTAACTAAA
29235803 TTAAATCTCT
Statistics
Matches: 273, Mismatches: 43, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
98 3 0.01
99 61 0.22
100 16 0.06
101 1 0.00
102 2 0.01
103 1 0.00
104 45 0.16
105 98 0.36
106 42 0.15
107 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.43
Consensus pattern (103 bp):
TAAACTCTAATTATCTTAACTAAAATCTAAATTATTACCTAATCTATTAATTAAATTACTAATTT
TATTAAATAAATTAAAATCTAATTATCCTAATTTAATT
Found at i:29235753 original size:26 final size:25
Alignment explanation
Indices: 29235723--29235824 Score: 80
Period size: 26 Copynumber: 3.9 Consensus size: 25
29235713 CTAACCTGTT
*
29235723 AATTAAATTCCTAACTATCTTATTTA
1 AATTAAATT-CTAATTATCTTATTTA
*
29235749 AATTAAAATT-TCAATTATCCTAATTTA
1 AATT-AAATTCT-AATTAT-CTTATTTA
* * **
29235776 ATTTAAACTCTAATTATCTTAACTA
1 AATTAAATTCTAATTATCTTATTTA
*
29235801 AATTAAATCTCTAATCATCGTTAT
1 AATTAAAT-TCTAATTATC-TTAT
29235825 ATATTTTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
25 12 0.20
26 28 0.47
27 19 0.32
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (25 bp):
AATTAAATTCTAATTATCTTATTTA
Found at i:29235753 original size:204 final size:203
Alignment explanation
Indices: 29235389--29235805 Score: 568
Period size: 204 Copynumber: 2.0 Consensus size: 203
29235379 CTTAACTAAA
* * * * *
29235389 ATCTAAATTATTACCTAATCTATTGATTTAAATTATTAATTATTTTAAATTAATTAAAAATCTAA
1 ATCTAAATTATTACCTAATATATTAATTTAAATTATTAATCATTCTAAATAAATTAAAAATCTAA
** * * *
29235454 TCATCCTAACTTAATTTAAAATTCTAATTATCTTAACTAAAATCTAAATTATTATCTAATCTATT
66 TCATCCTAACTTAATTTAAAACCCTAATTACCTTAACTAAAATCAAAATTATTATCTAACCTATT
* *
29235519 AATTAAATTCCTAATTTTATTATCTAAATTAAAA-CTCTAATTATCCTAATTCAATTTAAACTCA
131 AATTAAATTCCTAACTATATTATCTAAATTAAAATCTC-AATTATCCTAATTCAATTTAAACTC-
29235583 TAATTATCTAT
194 TAATTATCT-T
* *
29235594 ATCTAAATTATTACCTAATATTTTAATTTAAATTATTAATCA-TCTAAATAAATTAGAAATCTAA
1 ATCTAAATTATTACCTAATATATTAATTTAAATTATTAATCATTCTAAATAAATTAAAAATCTAA
* * * * * *
29235658 TTATTCTAATTTAGTTTAAACCCCTAATTACCTTAACTAAAATCAAAATTATTATCTAACCTGTT
66 TCATCCTAACTTAATTTAAAACCCTAATTACCTTAACTAAAATCAAAATTATTATCTAACCTATT
* * * *
29235723 AATTAAATTCCTAACTATCTTATTTAAATTAAAATTTCAATTATCCTAATTTAATTTAAACTCTA
131 AATTAAATTCCTAACTATATTATCTAAATTAAAATCTCAATTATCCTAATTCAATTTAAACTCTA
29235788 ATTATCTT
196 ATTATCTT
*
29235796 AACTAAATTA
1 ATCTAAATTA
29235806 AATCTCTAAT
Statistics
Matches: 186, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
202 10 0.05
203 9 0.05
204 127 0.68
205 40 0.22
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (203 bp):
ATCTAAATTATTACCTAATATATTAATTTAAATTATTAATCATTCTAAATAAATTAAAAATCTAA
TCATCCTAACTTAATTTAAAACCCTAATTACCTTAACTAAAATCAAAATTATTATCTAACCTATT
AATTAAATTCCTAACTATATTATCTAAATTAAAATCTCAATTATCCTAATTCAATTTAAACTCTA
ATTATCTT
Found at i:29237518 original size:29 final size:29
Alignment explanation
Indices: 29237476--29237563 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
29237466 AAGTGAACAT
* * * * *
29237476 CGATACAAAATACCTGATAATATGGTCAC
1 CGATACATAGTACCTAATAAAATAGTCAC
29237505 CGATACATAGTACCTAATAAAATAGTCAC
1 CGATACATAGTACCTAATAAAATAGTCAC
* * * *
29237534 TGGTACATAGCACCTAATAAATATAATCAC
1 CGATACATAGTACCTAATAAA-ATAGTCAC
29237564 TGGCACATAG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 42 0.86
30 7 0.14
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (29 bp):
CGATACATAGTACCTAATAAAATAGTCAC
Found at i:29237566 original size:30 final size:29
Alignment explanation
Indices: 29237508--29237573 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
29237498 TGGTCACCGA
* *
29237508 TACATAGTACCTAATAAAATAGTCACTGG
1 TACATAGCACCTAATAAAATAATCACTGG
29237537 TACATAGCACCTAATAAATATAATCACTGG
1 TACATAGCACCTAATAAA-ATAATCACTGG
*
29237567 CACATAG
1 TACATAG
29237574 TGCTTGATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (29 bp):
TACATAGCACCTAATAAAATAATCACTGG
Found at i:29240542 original size:16 final size:16
Alignment explanation
Indices: 29240517--29240559 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
29240507 GCTCGCATAT
* * *
29240517 CATAGTTCACATTCAG
1 CATAGCTCACATGCAA
29240533 CATAGCTCACATGCAA
1 CATAGCTCACATGCAA
*
29240549 CATTGCTCACA
1 CATAGCTCACA
29240560 ATTATTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.26
Consensus pattern (16 bp):
CATAGCTCACATGCAA
Found at i:29242222 original size:25 final size:24
Alignment explanation
Indices: 29242194--29242252 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 24
29242184 ATGCTCATAT
29242194 GAGCTATGAATCGGTATGCTCTCAC
1 GAGCTAT-AATCGGTATGCTCTCAC
29242219 GAGCTATAGATCGGTATGCTCTCAC
1 GAGCTATA-ATCGGTATGCTCTCAC
29242244 GAGCTATAA
1 GAGCTATAA
29242253 ATCACTAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (24 bp):
GAGCTATAATCGGTATGCTCTCAC
Found at i:29249876 original size:25 final size:25
Alignment explanation
Indices: 29249848--29249896 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29249838 TATGAATTGG
*
29249848 TATGCTCTCATGAGCTATAAATCGA
1 TATGCTCTCAGGAGCTATAAATCGA
* *
29249873 TATGCTTTTAGGAGCTATAAATCG
1 TATGCTCTCAGGAGCTATAAATCG
29249897 GTAACCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (25 bp):
TATGCTCTCAGGAGCTATAAATCGA
Found at i:29251210 original size:27 final size:27
Alignment explanation
Indices: 29251180--29251234 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
29251170 GTTTGCACAT
29251180 AGAATAGTTTGCATAAGAACATAGCTC
1 AGAATAGTTTGCATAAGAACATAGCTC
29251207 AGAATAGTTTGCATAAGAACATAGCTC
1 AGAATAGTTTGCATAAGAACATAGCTC
29251234 A
1 A
29251235 CTTAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (27 bp):
AGAATAGTTTGCATAAGAACATAGCTC
Found at i:29267033 original size:38 final size:38
Alignment explanation
Indices: 29266972--29267164 Score: 235
Period size: 38 Copynumber: 5.1 Consensus size: 38
29266962 GTAAATTTTC
* * *
29266972 AATA-CACCGGCACAAAGCCTGCTAGGCACATAGCGCA
1 AATATCACCGGCACAAAGCCTGCTAGGCACACAGCTCG
* * * *
29267009 AATATCACCGGCACACAGCTTGCTAGACACACAGCTTG
1 AATATCACCGGCACAAAGCCTGCTAGGCACACAGCTCG
*
29267047 AATATCACCGGCACAAAGCCTACTAGGCACACAGCTCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACACAGCTCG
* * *
29267085 AATATCACTGGCACAAAGCTTGCTAGGCACACAGTTCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACACAGCTCG
** * * *
29267123 AATATCACTAGCACAAAGCCTACTAGGCACATAGCCCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACACAGCTCG
29267161 AATA
1 AATA
29267165 ACATTACATT
Statistics
Matches: 133, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
37 4 0.03
38 129 0.97
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.16
Consensus pattern (38 bp):
AATATCACCGGCACAAAGCCTGCTAGGCACACAGCTCG
Found at i:29267105 original size:76 final size:76
Alignment explanation
Indices: 29266972--29267164 Score: 273
Period size: 76 Copynumber: 2.6 Consensus size: 76
29266962 GTAAATTTTC
* * * *
29266972 AATA-CACCGGCACAAAGCCTGCTAGGCACATAGCGCAAATATCACCGGCACACAGCTTGCTAGA
1 AATATCACCGGCACAAAGCCTACTAGGCACATAGCCCGAATATCACCGGCACAAAGCTTGCTAGA
29267036 CACACAGCTT-G
66 CACACAG-TTCG
* * * *
29267047 AATATCACCGGCACAAAGCCTACTAGGCACACAGCTCGAATATCACTGGCACAAAGCTTGCTAGG
1 AATATCACCGGCACAAAGCCTACTAGGCACATAGCCCGAATATCACCGGCACAAAGCTTGCTAGA
29267112 CACACAGTTCG
66 CACACAGTTCG
**
29267123 AATATCACTAGCACAAAGCCTACTAGGCACATAGCCCGAATA
1 AATATCACCGGCACAAAGCCTACTAGGCACATAGCCCGAATA
29267165 ACATTACATT
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 6 0.06
76 99 0.94
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.16
Consensus pattern (76 bp):
AATATCACCGGCACAAAGCCTACTAGGCACATAGCCCGAATATCACCGGCACAAAGCTTGCTAGA
CACACAGTTCG
Found at i:29269607 original size:28 final size:28
Alignment explanation
Indices: 29269567--29269625 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
29269557 GCGTATAATA
29269567 GAATTTCTAATAATGTGTAATGAAATTT
1 GAATTTCTAATAATGTGTAATGAAATTT
29269595 GAATTTCTAATAATGTGTAATGAAATTT
1 GAATTTCTAATAATGTGTAATGAAATTT
29269623 GAA
1 GAA
29269626 GCAAATGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (28 bp):
GAATTTCTAATAATGTGTAATGAAATTT
Found at i:29270017 original size:18 final size:17
Alignment explanation
Indices: 29269993--29270032 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 17
29269983 AAATTATTTT
29269993 TAAAATTTAGAAAATTATA
1 TAAAA-TTA-AAAATTATA
29270012 -AAAATTAAAAATTATA
1 TAAAATTAAAAATTATA
29270028 TAAAA
1 TAAAA
29270033 GTAGATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.45
17 7 0.35
18 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATTAAAAATTATA
Found at i:29270024 original size:16 final size:17
Alignment explanation
Indices: 29269993--29270037 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
29269983 AAATTATTTT
*
29269993 TAAAATTTAGAAAATTA
1 TAAAAATTAGAAAATTA
29270010 TAAAAATTA-AAAATTA
1 TAAAAATTAGAAAATTA
*
29270026 TATAAAAGTAGA
1 TA-AAAATTAGA
29270038 TAAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 14 0.58
18 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (17 bp):
TAAAAATTAGAAAATTA
Found at i:29270059 original size:19 final size:21
Alignment explanation
Indices: 29270017--29270060 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
29270007 TTATAAAAAT
* *
29270017 TAAAAATTATATAAAAGTAGA
1 TAAAAATTATATAAAAATAAA
29270038 TAAAAATT-T-TAAAAATAAA
1 TAAAAATTATATAAAAATAAA
29270057 TAAA
1 TAAA
29270061 GGGAGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 8 0.38
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAAATTATATAAAAATAAA
Found at i:29281457 original size:49 final size:49
Alignment explanation
Indices: 29281358--29281457 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
29281348 TTATTTTATT
* * * * * *
29281358 TTAGAATAAGGTTTTTCAACTTTATTACACTTCATCTATTTGATATTGA
1 TTAGAATAAGGTGTTTCAACCTCACTACACTCCATCTATTAGATATTGA
*
29281407 TTAGAATAAGGTGTTTCAACCTCACTACACTCCTTCTATTAGA-ATATGA
1 TTAGAATAAGGTGTTTCAACCTCACTACACTCCATCTATTAGATAT-TGA
29281456 TT
1 TT
29281458 TTACAAGCCC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.05
49 41 0.95
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (49 bp):
TTAGAATAAGGTGTTTCAACCTCACTACACTCCATCTATTAGATATTGA
Found at i:29282546 original size:31 final size:32
Alignment explanation
Indices: 29282499--29282571 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 32
29282489 ACAAAATTTC
*
29282499 ACATGAA-TTTTGGTTTAATTTGTAATATTAT
1 ACATGAACTTTTGGTTTAATTTGCAATATTAT
*
29282530 ACATGAGCTTTT-GTTTAATTTGCAATATTAT
1 ACATGAACTTTTGGTTTAATTTGCAATATTAT
*
29282561 GCATGAACTTT
1 ACATGAACTTT
29282572 GACTTTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (32 bp):
ACATGAACTTTTGGTTTAATTTGCAATATTAT
Found at i:29283428 original size:21 final size:20
Alignment explanation
Indices: 29283394--29283434 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
29283384 TTAGTTTGAT
29283394 TTTTTTATATAATTT-ATAA
1 TTTTTTATATAATTTGATAA
29283413 TTTTTTATATTAAATTTGATAA
1 TTTTTTATA-T-AATTTGATAA
29283435 ATTAATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 1 0.05
21 5 0.26
22 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTTATATAATTTGATAA
Found at i:29285433 original size:3 final size:3
Alignment explanation
Indices: 29285425--29285454 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29285415 TTTGAGCCGT
29285425 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
29285455 GTTAGATGAT
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:29293017 original size:22 final size:22
Alignment explanation
Indices: 29292958--29293020 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 22
29292948 AAAGATTTCT
29292958 TTATAATTTATATCTTAAACTAAA
1 TTATAATTTAT-T-TTAAACTAAA
*
29292982 -TATAAAGTTGATTTTAAA-TAAA
1 TTAT-AA-TTTATTTTAAACTAAA
29293004 TTATATATTTATTTTAA
1 TTATA-ATTTATTTTAA
29293021 TATTTTACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
22 14 0.42
23 12 0.36
24 3 0.09
25 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (22 bp):
TTATAATTTATTTTAAACTAAA
Found at i:29294244 original size:20 final size:20
Alignment explanation
Indices: 29294215--29294264 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29294205 CATATATCCT
* *
29294215 AATTTTATTTTATTCCAATC
1 AATTTGATTTGATTCCAATC
**
29294235 AATTTGATTTGATTTTAATC
1 AATTTGATTTGATTCCAATC
*
29294255 AAATTGATTT
1 AATTTGATTT
29294265 AATTGCTCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (20 bp):
AATTTGATTTGATTCCAATC
Found at i:29295054 original size:21 final size:21
Alignment explanation
Indices: 29295028--29295069 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29295018 TAAATTATAA
29295028 ATATTTTA-ACATTAAAAATAT
1 ATATTTTATA-ATTAAAAATAT
*
29295049 ATATTTTATAATTAAATATAT
1 ATATTTTATAATTAAAAATAT
29295070 TTTCTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTTTATAATTAAAAATAT
Found at i:29295112 original size:23 final size:24
Alignment explanation
Indices: 29295058--29295113 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29295048 TATATTTTAT
* *
29295058 AATTAAATATATTTTCTTTTAACA
1 AATTAAATATATTTTATATTAACA
29295082 AATTAAATATATTTTATAATT-AC-
1 AATTAAATATATTTTAT-ATTAACA
29295105 AATTAAATA
1 AATTAAATA
29295114 ATATAGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.31
24 18 0.62
25 2 0.07
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTAAATATATTTTATATTAACA
Found at i:29303166 original size:22 final size:22
Alignment explanation
Indices: 29303138--29303182 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
29303128 AGTCATTGTG
29303138 AAAAAAAATCAATAAAAAA-TTT
1 AAAAAAAATCAA-AAAAAAGTTT
*
29303160 AAAAAAATTCAAAAAAAAGTTT
1 AAAAAAAATCAAAAAAAAGTTT
29303182 A
1 A
29303183 TTTTATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAAAAATCAAAAAAAAGTTT
Found at i:29304340 original size:13 final size:12
Alignment explanation
Indices: 29304322--29304363 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
29304312 TGTGAGCGAG
29304322 AAAAGAACATTGA
1 AAAAGAA-ATTGA
29304335 AAAAGAAATTG-
1 AAAAGAAATTGA
29304346 -AAAGAAA-TGA
1 AAAAGAAATTGA
29304356 AAAAGAAA
1 AAAAGAAA
29304364 AAGATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:29304423 original size:12 final size:12
Alignment explanation
Indices: 29304406--29304481 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
29304396 AGTGAAAAGC
29304406 AAAAAGAGATTG
1 AAAAAGAGATTG
*
29304418 AAAAAGAAATTG
1 AAAAAGAGATTG
*
29304430 --AAAGAGA-AG
1 AAAAAGAGATTG
*
29304439 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
29304454 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
29304466 AAAGAGAGCTTG
1 AAAAAGAGATTG
29304478 AAAA
1 AAAA
29304482 GAAATCGAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:29304447 original size:15 final size:15
Alignment explanation
Indices: 29304429--29304462 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29304419 AAAAGAAATT
29304429 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
29304444 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
29304459 GAAA
1 GAAA
29304463 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:29306872 original size:34 final size:34
Alignment explanation
Indices: 29306806--29306873 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
29306796 ATGTGTCCTA
*
29306806 ATGTGGCTGCCAAATTTATTAAGCCTTGTTGACC
1 ATGTGGCTGCCAAATTTATTAAGCCTTATTGACC
* * * *
29306840 ATGTGGCTGTCGAATTTATTATGTCTTATTGACC
1 ATGTGGCTGCCAAATTTATTAAGCCTTATTGACC
29306874 CCTTTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (34 bp):
ATGTGGCTGCCAAATTTATTAAGCCTTATTGACC
Found at i:29307050 original size:72 final size:72
Alignment explanation
Indices: 29306932--29307121 Score: 290
Period size: 72 Copynumber: 2.6 Consensus size: 72
29306922 GCAGGTACAT
* *
29306932 GGACGGCAATTAAAGAGAAAGGTTGCTGCTGCATTTTTCCAAGCTGCCGAATTTAATGTGTGCAT
1 GGACGGCATTTAAAGAG-AAGGTTGCTGCTGCATTTTTCCAAGCTGCCAAATTTAATGTGTGCAT
29306997 GGGACTTG
65 GGGACTTG
*
29307005 GGACGGCATTTAAAGAGAAGGTTGCTGCTGCCTTTTTCCAAGCTGCCAAATTTAATGTGTGCATG
1 GGACGGCATTTAAAGAGAAGGTTGCTGCTGCATTTTTCCAAGCTGCCAAATTTAATGTGTGCATG
29307070 GGACTTG
66 GGACTTG
* * * * * *
29307077 GGACGACATTAAAAGAGGAGGCTGCTGTTGCATTTTTCTAAGCTG
1 GGACGGCATTTAAAGAGAAGGTTGCTGCTGCATTTTTCCAAGCTG
29307122 ATTATTCAGC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 91 0.85
73 16 0.15
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (72 bp):
GGACGGCATTTAAAGAGAAGGTTGCTGCTGCATTTTTCCAAGCTGCCAAATTTAATGTGTGCATG
GGACTTG
Found at i:29307973 original size:43 final size:42
Alignment explanation
Indices: 29307869--29308079 Score: 133
Period size: 43 Copynumber: 4.8 Consensus size: 42
29307859 CAAATCCATT
*
29307869 TAGAACATAACCTTTAGC-GACGTTT-CTCACAAAAAAATGCCACTA
1 TAGAACATAACCTTTAGCGGAC-TTTCCTCAC----AAACGCCACTA
* * * *
29307914 TATAACATCACATTTAGCGGAACTTTCCTCACAAACGCCGCTA
1 TAGAACATAACCTTTAGCGG-ACTTTCCTCACAAACGCCACTA
*
29307957 TAGAACATAACCTTTAGC-GACGTTT-CTCACAAAAAAATGCCACTA
1 TAGAACATAACCTTTAGCGGAC-TTTCCTCAC----AAACGCCACTA
* * * ** *
29308002 TATAACATGACATTTAATGGCACTTTCCTCACAAACGCCGCTA
1 TAGAACATAACCTTTAGCGG-ACTTTCCTCACAAACGCCACTA
* ** *
29308045 AAGAACATGGCCTTTAGCGGCACTTTCCCCACAAA
1 TAGAACATAACCTTTAGCGG-ACTTTCCTCACAAA
29308080 AACATCGCTA
Statistics
Matches: 131, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
41 7 0.05
42 4 0.03
43 61 0.47
45 37 0.28
46 8 0.06
47 14 0.11
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (42 bp):
TAGAACATAACCTTTAGCGGACTTTCCTCACAAACGCCACTA
Found at i:29308009 original size:45 final size:45
Alignment explanation
Indices: 29307872--29308009 Score: 169
Period size: 45 Copynumber: 3.1 Consensus size: 45
29307862 ATCCATTTAG
29307872 AACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATAT
1 AACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATAT
* * * * *
29307917 AACATCACATTTAGCGGAAC-TTTCCTCAC----AAACGCCGCTATAG
1 AACATAACCTTTAGC-G-ACGTTT-CTCACAAAAAAATGCCACTATAT
29307960 AACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATAT
1 AACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATAT
29308005 AACAT
1 AACAT
29308010 GACATTTAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
41 7 0.09
42 4 0.05
43 24 0.32
45 29 0.39
46 4 0.05
47 7 0.09
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.25
Consensus pattern (45 bp):
AACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATAT
Found at i:29308027 original size:88 final size:88
Alignment explanation
Indices: 29307869--29308063 Score: 327
Period size: 88 Copynumber: 2.2 Consensus size: 88
29307859 CAAATCCATT
*
29307869 TAGAACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATATAACATCACATTTAGCGG
1 TAGAACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATATAACATCACATTTAACGG
29307934 AACTTTCCTCACAAACGCCGCTA
66 AACTTTCCTCACAAACGCCGCTA
* *
29307957 TAGAACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATATAACATGACATTTAATGG
1 TAGAACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATATAACATCACATTTAACGG
*
29308022 CACTTTCCTCACAAACGCCGCTA
66 AACTTTCCTCACAAACGCCGCTA
* **
29308045 AAGAACATGGCCTTTAGCG
1 TAGAACATAACCTTTAGCG
29308064 GCACTTTCCC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 100 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (88 bp):
TAGAACATAACCTTTAGCGACGTTTCTCACAAAAAAATGCCACTATATAACATCACATTTAACGG
AACTTTCCTCACAAACGCCGCTA
Found at i:29308081 original size:88 final size:88
Alignment explanation
Indices: 29307870--29308171 Score: 279
Period size: 88 Copynumber: 3.4 Consensus size: 88
29307860 AAATCCATTT
* * * * *
29307870 AGAACATAACCTTTAGC-G-ACGTTTCTCACAAAAAAATGCCACTATATAACATCACATTTAGCG
1 AGAACATGACCTTTAGCGGCAC-TTTC-CCCACAAAAATGCCACTATATAACATGACATTTAGTG
* *
29307933 GAACTTTCCTCACAAACGCCGCTAT
64 GCACTTTCCTCACAAACGCCGCTAA
* * * *
29307958 AGAACATAACCTTTAGC-G-ACGTTTCTCACAAAAAAATGCCACTATATAACATGACATTTAATG
1 AGAACATGACCTTTAGCGGCAC-TTTC-CCCACAAAAATGCCACTATATAACATGACATTTAGTG
29308021 GCACTTTCCTCACAAACGCCGCTAA
64 GCACTTTCCTCACAAACGCCGCTAA
* *** * * * * * *
29308046 AGAACATGGCCTTTAGCGGCACTTTCCCCACAAAAACATCGCTATAAAATATGCCCTTTAGTGAC
1 AGAACATGACCTTTAGCGGCACTTTCCCCACAAAAATGCCACTATATAACATGACATTTAGTGGC
* *
29308111 GCTTTCCCCACAAACGTCGCTAGCTAA
66 ACTTTCCTCACAAACG-C-C--GCTAA
* *
29308138 AGAGCATGACCTTTAGCGACACTTTCCCCACAAA
1 AGAACATGACCTTTAGCGGCACTTTCCCCACAAA
29308172 CGCCACTACT
Statistics
Matches: 184, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
88 139 0.76
89 6 0.03
90 3 0.02
92 36 0.20
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (88 bp):
AGAACATGACCTTTAGCGGCACTTTCCCCACAAAAATGCCACTATATAACATGACATTTAGTGGC
ACTTTCCTCACAAACGCCGCTAA
Done.