Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 123 of 352
Found at i:39429630 original size:37 final size:37
Alignment explanation
Indices: 39429574--39429652 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
39429564 CCGAGCTCTA
* *
39429574 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
39429611 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
39429648 AAGAC
1 AAGAC
39429653 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:39430403 original size:19 final size:19
Alignment explanation
Indices: 39430379--39430421 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
39430369 GCTGGGATTG
39430379 GGATTGGGATTAAATAATA
1 GGATTGGGATTAAATAATA
39430398 GGATTGGGATTAAATAATA
1 GGATTGGGATTAAATAATA
39430417 GGATT
1 GGATT
39430422 AAATAATAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
GGATTGGGATTAAATAATA
Found at i:39430420 original size:13 final size:13
Alignment explanation
Indices: 39430404--39430431 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39430394 AATAGGATTG
39430404 GGATTAAATAATA
1 GGATTAAATAATA
39430417 GGATTAAATAATA
1 GGATTAAATAATA
39430430 GG
1 GG
39430432 TAAACTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (13 bp):
GGATTAAATAATA
Found at i:39434333 original size:32 final size:32
Alignment explanation
Indices: 39434283--39434345 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
39434273 CACACGGGCT
39434283 AGGCCAAGCTGAGCGTGTAGGCCACATGGGTA
1 AGGCCAAGCTGAGCGTGTAGGCCACATGGGTA
*
39434315 AGGCCAATCT-AGCTGTGTAGGCCACATGGGT
1 AGGCCAAGCTGAGC-GTGTAGGCCACATGGGT
39434346 GTGTGGGCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (32 bp):
AGGCCAAGCTGAGCGTGTAGGCCACATGGGTA
Found at i:39435858 original size:14 final size:14
Alignment explanation
Indices: 39435839--39435878 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39435829 TTGATTGGCT
39435839 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
39435853 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
39435867 GGAAAATGTTTT
1 GTAAAATGTTTT
39435879 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:39435891 original size:34 final size:35
Alignment explanation
Indices: 39435847--39435913 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
39435837 CTGTAAAATG
* *
39435847 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
39435881 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
39435914 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:39435900 original size:20 final size:20
Alignment explanation
Indices: 39435862--39435901 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39435852 CGTAAAATGA
**
39435862 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
39435882 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
39435902 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:39440472 original size:49 final size:49
Alignment explanation
Indices: 39440391--39440513 Score: 133
Period size: 49 Copynumber: 2.5 Consensus size: 49
39440381 CTTGTTGTGT
*** * *
39440391 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGA
1 GTCAGTGTAAGACCTGTCTGGGACACAACATCGAC-CTCAATAGATGAAA
* * *
39440440 G-CTAGTGTAAGACCTGTCTGGGATACAACATCGGCCTCAATATATGAAA
1 GTC-AGTGTAAGACCTGTCTGGGACACAACATCGACCTCAATAGATGAAA
*
39440489 GTCAGTGTAAGACCTCTCTGGGACA
1 GTCAGTGTAAGACCTGTCTGGGACA
39440514 TGATATCGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
48 2 0.03
49 58 0.95
50 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (49 bp):
GTCAGTGTAAGACCTGTCTGGGACACAACATCGACCTCAATAGATGAAA
Found at i:39450055 original size:31 final size:31
Alignment explanation
Indices: 39450017--39450079 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
39450007 CCTATATTGT
*
39450017 AGTAAACATGTATCTGTTTTCTGTTTATTTG
1 AGTAAACATGTATCTGTTTTCTATTTATTTG
* *
39450048 AGTAAACATGTATTTTTTTTCTATTTATTTG
1 AGTAAACATGTATCTGTTTTCTATTTATTTG
39450079 A
1 A
39450080 ATAATGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (31 bp):
AGTAAACATGTATCTGTTTTCTATTTATTTG
Found at i:39450072 original size:27 final size:32
Alignment explanation
Indices: 39450008--39450078 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
39449998 GGAATTATGC
39450008 CTATATTGTAGTAAACATGTATCTGTTTTCTGT
1 CTAT-TTGTAGTAAACATGTATCTGTTTTCTGT
* * * *
39450041 TTATTTG-AGTAAACATGTATTTTTTTTCTAT
1 CTATTTGTAGTAAACATGTATCTGTTTTCTGT
*
39450072 TTATTTG
1 CTATTTG
39450079 AATAATGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 28 0.82
32 3 0.09
33 3 0.09
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (32 bp):
CTATTTGTAGTAAACATGTATCTGTTTTCTGT
Found at i:39451575 original size:7 final size:7
Alignment explanation
Indices: 39451563--39451591 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
39451553 GTGAGTATTT
39451563 ATATGAG
1 ATATGAG
39451570 ATATGAG
1 ATATGAG
39451577 ATATGAG
1 ATATGAG
39451584 AT-TGAG
1 ATATGAG
39451590 AT
1 AT
39451592 GGTTTCGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (7 bp):
ATATGAG
Found at i:39452291 original size:42 final size:42
Alignment explanation
Indices: 39452244--39452327 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
39452234 TTATATTTAG
39452244 GCAAGATAGTGCATTTATATAATTGACCATTTAGGTAGTTTT
1 GCAAGATAGTGCATTTATATAATTGACCATTTAGGTAGTTTT
39452286 GCAAGATAGTGCATTTATATAATTGACCATTTAGGTAGTTTT
1 GCAAGATAGTGCATTTATATAATTGACCATTTAGGTAGTTTT
39452328 TAGAGGTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (42 bp):
GCAAGATAGTGCATTTATATAATTGACCATTTAGGTAGTTTT
Found at i:39456631 original size:56 final size:55
Alignment explanation
Indices: 39456517--39456701 Score: 264
Period size: 56 Copynumber: 3.3 Consensus size: 55
39456507 TCGTAAACAC
* *
39456517 ATATCAGAATCACATATCGATGCCAACGTA-TGAATGTGGACTTACTCCCACACAT
1 ATATCA-AATCACATATCGATGCCAACGTATTAAACGTGGACTTACTCCCACACAT
39456572 ATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGACTTACTCCCACACAT
1 ATATC-AAATCACATATCGATGCCAACGTATTAAACGTGGACTTACTCCCACACAT
* * * *
39456628 ATATCAGAATCACATATCGATGCCAGCGTATTAAACGTGGTCTTACTCACACATAT
1 ATATCA-AATCACATATCGATGCCAACGTATTAAACGTGGACTTACTCCCACACAT
*
39456684 ATATTAAAGTCACATATC
1 ATATCAAA-TCACATATC
39456702 TATTCCACAT
Statistics
Matches: 119, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
55 31 0.26
56 88 0.74
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (55 bp):
ATATCAAATCACATATCGATGCCAACGTATTAAACGTGGACTTACTCCCACACAT
Found at i:39457305 original size:19 final size:19
Alignment explanation
Indices: 39457269--39457307 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39457259 CATGGCTTAT
* * *
39457269 TATTATTTTATGAGATATA
1 TATTATATTATAACATATA
39457288 TATTATATTATAACATATA
1 TATTATATTATAACATATA
39457307 T
1 T
39457308 TAATTTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTATATTATAACATATA
Found at i:39468708 original size:27 final size:27
Alignment explanation
Indices: 39468678--39468729 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
39468668 GTTTATAAGT
*
39468678 TTTTAAAATTTATGTTTTAATGTGTGA
1 TTTTAAAATTTATATTTTAATGTGTGA
39468705 TTTTAAAATTTATATTTTAATGTGT
1 TTTTAAAATTTATATTTTAATGTGT
39468730 AAGGATTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTGTGA
Found at i:39472012 original size:23 final size:24
Alignment explanation
Indices: 39471984--39472046 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
39471974 TTTATGTATT
*
39471984 ATATTATATATA-AT-TGTTTTTTC
1 ATATTATATATATATGTG-TTTTTA
39472007 ATATTATATATATATGTGTTTTTA
1 ATATTATATATATATGTGTTTTTA
*
39472031 ATATTATGTTATATAT
1 ATATTAT-ATATATAT
39472047 ATTATGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 12 0.34
24 14 0.40
25 9 0.26
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (24 bp):
ATATTATATATATATGTGTTTTTA
Found at i:39482602 original size:40 final size:40
Alignment explanation
Indices: 39482558--39482782 Score: 305
Period size: 40 Copynumber: 5.7 Consensus size: 40
39482548 GCTCCTCGTT
*
39482558 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
39482598 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
39482638 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
39482678 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
39482717 CAAATACCTTC-GGATCTTAGTCCGGATTTGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
39482758 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39482783 CATCATTCAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 119 0.72
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39482742 original size:119 final size:120
Alignment explanation
Indices: 39482558--39482782 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 120
39482548 GCTCCTCGTT
* *
39482558 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGG
*
39482623 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATTTAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
39482678 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCC
* * *
39482740 GGATTTGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATTTAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
39482783 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
118 4 0.04
119 66 0.72
120 22 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGG
ATTTAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:39490542 original size:38 final size:40
Alignment explanation
Indices: 39490426--39490608 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
39490416 GCTCCTCGTT
* *
39490426 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
39490466 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
39490506 CAAATGCCTTC-GG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
39490544 CAAATGCCTTC-GGATCTTAGTCCGG-ATTGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAATTAGTAAC-TCGCA
39490584 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39490609 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
38 35 0.28
39 23 0.18
40 66 0.52
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:39490543 original size:78 final size:81
Alignment explanation
Indices: 39490426--39490608 Score: 227
Period size: 78 Copynumber: 2.3 Consensus size: 81
39490416 GCTCCTCGTT
* *
39490426 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
39490489 GGATTTAGTAAC-TCGCA
65 GGA-TTAGTAACTTAGCA
* **
39490506 CAAATGCCTTC-GG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
39490568 GATTGGTCACTTAGCA
66 GATTAGTAACTTAGCA
39490584 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39490609 CATCATTCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
77 15 0.17
78 50 0.56
79 14 0.16
80 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATTAGTAACTTAGCA
Found at i:39495315 original size:86 final size:86
Alignment explanation
Indices: 39495095--39495481 Score: 413
Period size: 86 Copynumber: 4.4 Consensus size: 86
39495085 CTGCTTTCAG
* * * * * * ***
39495095 AAATCAACTCATATTGCAAGAGGTAAGTTGATCCTC-GGATCACATGCCGAGGTATTTTCAAAAC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA-CAC--GCTGAGGTAATGTCAATTT
* *
39495159 CTGT-TTTCAAGTTTCT-GTTTGTCAA
63 CTGTCTTT-AA-TTTCTACTTT-TCCA
* * *
39495184 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGTTAATGTCAATTTTTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATGTCAATTTCTG
39495249 TCTTTAATTTCTACTTTTCCA
66 TCTTTAATTTCTACTTTTCCA
*
39495270 AAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATGTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATGTCAATTTCTG
39495335 TCTTTAATTTCTACTTTTCCA
66 TCTTTAATTTCTACTTTTCCA
* * * * * *
39495356 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACACTGAGGTATTTTCAATTTCCG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATGTCAATTTCTG
* * * *
39495421 T-TTTCCAACTTATGCTTTTCAAAAA
66 TCTTT--AATTTCTACTTTTC---CA
*
39495446 AAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
39495482 GGGTCGCACA
Statistics
Matches: 261, Mismatches: 29, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
85 3 0.01
86 149 0.57
87 31 0.12
88 3 0.01
89 37 0.14
90 38 0.15
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (86 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATGTCAATTTCTG
TCTTTAATTTCTACTTTTCCA
Found at i:39495606 original size:14 final size:14
Alignment explanation
Indices: 39495575--39495609 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39495565 CACTGAGGTA
*
39495575 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
*
39495589 TTTTCAATTTCTAT
1 TTTTCAATTTCTAC
39495603 TTTTCAA
1 TTTTCAA
39495610 AATAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:39498174 original size:93 final size:93
Alignment explanation
Indices: 39498006--39498177 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
39497996 CGCCCATAAG
* * * *
39498006 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCA
* *
39498071 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* *
39498099 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCA
39498164 ACGAGCTCGGATGC
66 ACGAGCTCGGATGC
39498178 TCAACCATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:39498193 original size:46 final size:46
Alignment explanation
Indices: 39497999--39498180 Score: 181
Period size: 46 Copynumber: 3.9 Consensus size: 46
39497989 TGTAACTCGC
* * * * *
39497999 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCACAT
* * * * *
39498045 CCATGAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-C---TCACAT
* * *
39498095 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCACAT
*
39498138 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCA
39498181 ACCATCCTAG
Statistics
Matches: 110, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
44 1 0.01
45 2 0.02
46 66 0.60
47 29 0.26
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCACAT
Found at i:39500342 original size:12 final size:12
Alignment explanation
Indices: 39500325--39500357 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39500315 TATTATTTTG
39500325 TTCTTTTTCTTC
1 TTCTTTTTCTTC
*
39500337 TTCTTTTTGTTC
1 TTCTTTTTCTTC
39500349 TT-TTTTTCT
1 TTCTTTTTCT
39500358 ACTCATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:39501145 original size:22 final size:22
Alignment explanation
Indices: 39501120--39501168 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
39501110 CCCGTATTTA
*
39501120 ATATACTTATGTATT-ATATTAT
1 ATATAATT-TGTATTCATATTAT
* *
39501142 ATATAATTTTTTTTCATATTAT
1 ATATAATTTGTATTCATATTAT
39501164 ATATA
1 ATATA
39501169 TGTGTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATAATTTGTATTCATATTAT
Found at i:39501176 original size:22 final size:22
Alignment explanation
Indices: 39501135--39501185 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
39501125 CTTATGTATT
* *
39501135 ATATTATATATAATTTTTTTTC
1 ATATTATATATAATTGTTTTTA
39501157 ATATTATATAT-ATGTGTTTTTA
1 ATATTATATATAAT-TGTTTTTA
39501179 ATATTAT
1 ATATTAT
39501186 GTTATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
ATATTATATATAATTGTTTTTA
Found at i:39501201 original size:40 final size:42
Alignment explanation
Indices: 39501157--39501234 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 42
39501147 ATTTTTTTTC
* * *
39501157 ATATTATATATATGTGTTTTTAATATTA-T-GTTATATATAT
1 ATATTATATATATATATTTTCAATATTATTAGTTATATATAT
*
39501197 ATATTATGTATATATATTTTCAATATTATTAGTTATAT
1 ATATTATATATATATATTTTCAATATTATTAGTTATAT
39501235 TTTCTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 24 0.75
41 1 0.03
42 7 0.22
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56
Consensus pattern (42 bp):
ATATTATATATATATATTTTCAATATTATTAGTTATATATAT
Found at i:39514868 original size:40 final size:40
Alignment explanation
Indices: 39514813--39514893 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
39514803 TTATGATCGA
*
39514813 ATTGTAACTTTTTGTAGTTAAGTGTTCAAAATAAAAATTT
1 ATTGTAACTTTTTGTAGTTAAGTGATCAAAATAAAAATTT
39514853 ATTGTAACTTTTTGTAGTTAAGTGATCAAAATAAAAATTT
1 ATTGTAACTTTTTGTAGTTAAGTGATCAAAATAAAAATTT
39514893 A
1 A
39514894 CTCATAGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (40 bp):
ATTGTAACTTTTTGTAGTTAAGTGATCAAAATAAAAATTT
Found at i:39519736 original size:47 final size:47
Alignment explanation
Indices: 39519670--39519988 Score: 252
Period size: 47 Copynumber: 6.7 Consensus size: 47
39519660 TTGTTTGTGT
*
39519670 GCTAGTGT-AGAACATGTCTGGGACAT-GCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACATTATGAGA
* * *
39519716 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG--CATTGAGATCAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATT---ATGAGA
*
39519764 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGA-GATGAG-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-AC-ATTATGAGA
* * *
39519809 TC-AGTGTAAGACCATGTTTGGGACATGGCATCGGCACGGATATGTGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC--AT-TATGAGA
* * * * * *
39519858 GTTAGTGCAAGACCATGTCTGGGACATGGCGTCGGC-CTTAGTTTTAATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC--A-TTATGAGA
* *
39519907 GTTAGTGTAAAACCATGT-TCGGGACATGGCATC-G-AC-TTGATGGATGA
1 GCTAGTGTAAGACCATGTCT-GGGACATGGCATCGGCACATT-AT-GA-GA
39519954 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG
39519989 TATTATACCC
Statistics
Matches: 219, Mismatches: 30, Indels: 46
0.74 0.10 0.16
Matches are distributed among these distances:
44 11 0.05
45 21 0.10
46 28 0.13
47 61 0.28
48 31 0.14
49 35 0.16
50 32 0.15
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTATGAGA
Found at i:39519922 original size:99 final size:96
Alignment explanation
Indices: 39519719--39519988 Score: 244
Period size: 96 Copynumber: 2.8 Consensus size: 96
39519709 TATGAGAGCC
* *
39519719 AGTGTAAGACCATG-TCTGGGACATGGCATC-AGCAT--TGAGATCAGAGCTAGTGTAAGA-CAT
1 AGTGTAAAACCATGTTC-GGGACATGGCATCGA-CATGATG-GAT--GAGCTAGTGCAAGACCAT
*
39519779 GTCTGGGACAT-GCATCGG-C-TACG----AGATGAGTC
61 GTCTGGGACATGGCATCGGCCTTA-GTTTTA-AT-AGTT
* * *
39519811 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACGGAT-ATGTGA-GAGTTAGTGCAAGACCAT
1 AGTGTAAAACCATGTTCGGGACATGGCATC-G-AC--ATGATG-GATGAGCTAGTGCAAGACCAT
*
39519874 GTCTGGGACATGGCGTCGGCCTTAGTTTTAATAGTT
61 GTCTGGGACATGGCATCGGCCTTAGTTTTAATAGTT
* *
39519910 AGTGTAAAACCATGTTCGGGACATGGCATCGACTTGATGGATGAGCTAGTGTAAGACCATGTCTG
1 AGTGTAAAACCATGTTCGGGACATGGCATCGACATGATGGATGAGCTAGTGCAAGACCATGTCTG
39519975 GGACATGGCATCGG
66 GGACATGGCATCGG
39519989 TATTATACCC
Statistics
Matches: 149, Mismatches: 12, Indels: 30
0.78 0.06 0.16
Matches are distributed among these distances:
92 27 0.18
93 1 0.01
94 13 0.09
95 18 0.12
96 45 0.30
97 8 0.05
98 3 0.02
99 31 0.21
100 2 0.01
101 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.25
Consensus pattern (96 bp):
AGTGTAAAACCATGTTCGGGACATGGCATCGACATGATGGATGAGCTAGTGCAAGACCATGTCTG
GGACATGGCATCGGCCTTAGTTTTAATAGTT
Found at i:39525294 original size:28 final size:28
Alignment explanation
Indices: 39525262--39525328 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
39525252 CCGTGTCTAT
* *
39525262 TGCCCATGTCCCTCACACGGCCATGACA
1 TGCCCGTGTCCCTCACACGGCAATGACA
*
39525290 TGCCCGTGTCCCTTACACGGCAATGACA
1 TGCCCGTGTCCCTCACACGGCAATGACA
*
39525318 CGCCCGTGTCC
1 TGCCCGTGTCC
39525329 TAGCCCGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.19
Consensus pattern (28 bp):
TGCCCGTGTCCCTCACACGGCAATGACA
Found at i:39527947 original size:48 final size:48
Alignment explanation
Indices: 39527875--39528243 Score: 421
Period size: 48 Copynumber: 7.8 Consensus size: 48
39527865 CTCACACCCT
* *
39527875 AAGTGCCAATATCATGGCCCGAAGCCAAATCAATG-AAGTTCGCACCTG
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAA-CTCGCACCTG
** * *
39527923 AAGTGCCGATATCATGGCTTGAAGCCAAATCAATGTAACTCGCACTTA
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTG
* * * * *
39527971 AAATGTCGATATCATGGCTCAAAGCCAAATCAATG-AAGTTCGCA-CTCG
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAA-CTCGCACCT-G
* * *
39528019 AAGTGCCGATATCATGACCCGAAGCC--A--AATGTAACTCACACTTG
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTG
* * *
39528063 AAGTGCTGATATCATGGCCCGAAGCCAAATCAATGTAACACGCACCCG
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTG
* * *
39528111 AAGTGTCAATATCATGGCCCGAAGCCAAATCAATGTAACTCTCA-CTCG
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCT-G
* ** *
39528159 AAGTGTCGATATCATGGCCCGAAGCCAAATCAATGTAACTTACACCCG
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTG
*
39528207 AAGTGCCGATATCATGGCCCAAAGCCAAATCAATGTA
1 AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTA
39528244 TTCCCTAATG
Statistics
Matches: 271, Mismatches: 39, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
44 33 0.12
45 3 0.01
46 2 0.01
47 4 0.01
48 226 0.83
49 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (48 bp):
AAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTG
Found at i:39528047 original size:96 final size:97
Alignment explanation
Indices: 39527883--39528243 Score: 479
Period size: 96 Copynumber: 3.8 Consensus size: 97
39527873 CTAAGTGCCA
* **
39527883 ATATCATGGCCCGAAGCCAAATCAATG-AAGTTCGCACCTGAAGTGCCGATATCATGGCTTGAAG
1 ATATCATGGCCCGAAGCCAAATCAATGTAAGTTCGCACCCGAAGTGCCGATATCATGGCCCGAAG
* * *
39527947 CCAAATCAATGTAACTCGCACTTAAAATGTCG
66 CCAAATCAATGTAACTCACACTTGAAGTGTCG
* * * *
39527979 ATATCATGGCTCAAAGCCAAATCAATG-AAGTTCGCACTCGAAGTGCCGATATCATGACCCGAAG
1 ATATCATGGCCCGAAGCCAAATCAATGTAAGTTCGCACCCGAAGTGCCGATATCATGGCCCGAAG
39528043 CC--A--AATGTAACTCACACTTGAAGTG-CTG
66 CCAAATCAATGTAACTCACACTTGAAGTGTC-G
** * *
39528071 ATATCATGGCCCGAAGCCAAATCAATGTAA-CACGCACCCGAAGTGTCAATATCATGGCCCGAAG
1 ATATCATGGCCCGAAGCCAAATCAATGTAAGTTCGCACCCGAAGTGCCGATATCATGGCCCGAAG
* *
39528135 CCAAATCAATGTAACTCTCACTCGAAGTGTCG
66 CCAAATCAATGTAACTCACACTTGAAGTGTCG
* * *
39528167 ATATCATGGCCCGAAGCCAAATCAATGTAACTT-ACACCCGAAGTGCCGATATCATGGCCCAAAG
1 ATATCATGGCCCGAAGCCAAATCAATGTAAGTTCGCACCCGAAGTGCCGATATCATGGCCCGAAG
39528231 CCAAATCAATGTA
66 CCAAATCAATGTA
39528244 TTCCCTAATG
Statistics
Matches: 231, Mismatches: 26, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
91 1 0.00
92 75 0.32
93 2 0.01
94 2 0.01
96 150 0.65
97 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (97 bp):
ATATCATGGCCCGAAGCCAAATCAATGTAAGTTCGCACCCGAAGTGCCGATATCATGGCCCGAAG
CCAAATCAATGTAACTCACACTTGAAGTGTCG
Found at i:39528186 original size:188 final size:188
Alignment explanation
Indices: 39527883--39528236 Score: 514
Period size: 188 Copynumber: 1.9 Consensus size: 188
39527873 CTAAGTGCCA
** * * **
39527883 ATATCATGGCCCGAAGCCAAATCAATGAAGTTCGCACCTGAAGTGCCGATATCATGGCTTGAAGC
1 ATATCATGGCCCGAAGCCAAATCAATGAAGCACGCACCCGAAGTGCCAATATCATGGCCCGAAGC
* * *
39527948 CAAATCAATGTAACTCGCACTTAAAATGTCGATATCATGGCTCAAAGCCAAATCAATG-AAGTTC
66 CAAATCAATGTAACTCGCACTCAAAATGTCGATATCATGGCCCAAAGCCAAATCAATGTAACTT-
* * *
39528012 GCACTCGAAGTGCCGATATCATGACCCGAAGCCAAATGTAACTCACACTTGAAGTGCTG
130 ACACCCGAAGTGCCGATATCATGACCCAAAGCCAAATGTAACTCACACTTGAAGTGCTG
*
39528071 ATATCATGGCCCGAAGCCAAATCAATGTAA-CACGCACCCGAAGTGTCAATATCATGGCCCGAAG
1 ATATCATGGCCCGAAGCCAAATCAATG-AAGCACGCACCCGAAGTGCCAATATCATGGCCCGAAG
* * * *
39528135 CCAAATCAATGTAACTCTCACTCGAAGTGTCGATATCATGGCCCGAAGCCAAATCAATGTAACTT
65 CCAAATCAATGTAACTCGCACTCAAAATGTCGATATCATGGCCCAAAGCCAAATCAATGTAACTT
*
39528200 ACACCCGAAGTGCCGATATCATGGCCCAAAGCCAAAT
130 ACACCCGAAGTGCCGATATCATGACCCAAAGCCAAAT
39528237 CAATGTATTC
Statistics
Matches: 146, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
188 140 0.96
189 6 0.04
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (188 bp):
ATATCATGGCCCGAAGCCAAATCAATGAAGCACGCACCCGAAGTGCCAATATCATGGCCCGAAGC
CAAATCAATGTAACTCGCACTCAAAATGTCGATATCATGGCCCAAAGCCAAATCAATGTAACTTA
CACCCGAAGTGCCGATATCATGACCCAAAGCCAAATGTAACTCACACTTGAAGTGCTG
Found at i:39530633 original size:23 final size:23
Alignment explanation
Indices: 39530607--39530659 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
39530597 TTTTTTTTTA
39530607 ATTTCA-ATTAATTTTCTAA-TTTC
1 ATTTCATATTAA-TTTC-AACTTTC
*
39530630 ATTTCATATTCATTTCAACTTTC
1 ATTTCATATTAATTTCAACTTTC
39530653 ATTTCAT
1 ATTTCAT
39530660 TTTATATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 21 0.78
24 4 0.15
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTCATATTAATTTCAACTTTC
Found at i:39530635 original size:5 final size:5
Alignment explanation
Indices: 39530625--39530755 Score: 84
Period size: 5 Copynumber: 24.2 Consensus size: 5
39530615 TAATTTTCTA
*
39530625 ATTTC ATTTC ATATTC ATTTC AACTTTC ATTTC ATTTT ATATTC ATTTCAC
1 ATTTC ATTTC AT-TTC ATTTC -A-TTTC ATTTC ATTTC AT-TTC ATTT--C
* * * * *
39530676 ATTTC ATTTC ATTTT TTTTC ATTTC ATTTC AATTT- TTTCTC ATTTT ATTTGA
1 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC -ATTTC ATT-TC ATTTC ATTT-C
* *
39530728 ATTTC ATTTGA ATTTT ATTTC AATTTC A
1 ATTTC ATTT-C ATTTC ATTTC -ATTTC A
39530756 CTTATTTTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
4 2 0.02
5 59 0.59
6 30 0.30
7 9 0.09
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.60
Consensus pattern (5 bp):
ATTTC
Found at i:39530690 original size:28 final size:28
Alignment explanation
Indices: 39530625--39530701 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
39530615 TAATTTTCTA
*
39530625 ATTTCATTTCATATTCATTTCAACTTTC
1 ATTTCATTTTATATTCATTTCAACTTTC
39530653 ATTTCATTTTATATTCATTTC-ACATTTC
1 ATTTCATTTTATATTCATTTCAAC-TTTC
*
39530681 ATTTCATTTT-TTTTCATTTCA
1 ATTTCATTTTATATTCATTTCA
39530702 TTTCAATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 11 0.24
28 34 0.76
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTCATTTTATATTCATTTCAACTTTC
Found at i:39530712 original size:21 final size:21
Alignment explanation
Indices: 39530651--39530731 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
39530641 ATTTCAACTT
* *
39530651 TCATTTCATTTTATATTCATTTC
1 TCATTTCATTTCA-ATT-TTTTC
* *
39530674 ACATTTCATTTC-ATTTTTTT
1 TCATTTCATTTCAATTTTTTC
39530694 TCATTTCATTTCAATTTTTTC
1 TCATTTCATTTCAATTTTTTC
* *
39530715 TCATTTTATTTGAATTT
1 TCATTTCATTTCAATTT
39530732 CATTTGAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.29
21 25 0.51
23 10 0.20
ACGTcount: A:0.21, C:0.15, G:0.01, T:0.63
Consensus pattern (21 bp):
TCATTTCATTTCAATTTTTTC
Found at i:39530736 original size:11 final size:11
Alignment explanation
Indices: 39530717--39530755 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39530707 ATTTTTTCTC
*
39530717 ATTTTATTTGA
1 ATTTCATTTGA
39530728 ATTTCATTTGA
1 ATTTCATTTGA
* *
39530739 ATTTTATTTCA
1 ATTTCATTTGA
39530750 ATTTCA
1 ATTTCA
39530756 CTTATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (11 bp):
ATTTCATTTGA
Found at i:39530765 original size:22 final size:22
Alignment explanation
Indices: 39530717--39530758 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39530707 ATTTTTTCTC
* *
39530717 ATTTTATTTGAATTTCATTTGA
1 ATTTTATTTCAATTTCACTTGA
39530739 ATTTTATTTCAATTTCACTT
1 ATTTTATTTCAATTTCACTT
39530759 ATTTTTTTAG
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:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTATTTCAATTTCACTTGA
Found at i:39530814 original size:17 final size:16
Alignment explanation
Indices: 39530776--39530808 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39530766 TAGTTAAAAC
39530776 TTTATTTTTTTCTCAT
1 TTTATTTTTTTCTCAT
39530792 TTTATTTTTTT-TCAT
1 TTTATTTTTTTCTCAT
39530807 TT
1 TT
39530809 CATATTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTTTTCTCAT
Found at i:39530928 original size:34 final size:37
Alignment explanation
Indices: 39530850--39530937 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 37
39530840 TTTTTTTCTC
*
39530850 ATTTTATTTTAATTTCAAATTTTTTTCTTCTTCAGTTAA
1 ATTTCATTTTAATTTCAAATTTTTTTCTTCTT-A-TTAA
39530889 ATTTCATTTT-ATTT-AAATTTTTTTC-TCATT-TTAA
1 ATTTCATTTTAATTTCAAATTTTTTTCTTC-TTATTAA
*
39530923 ATTTCATTTAAATTT
1 ATTTCATTTTAATTT
39530938 TTTTAAATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
34 13 0.29
35 4 0.09
36 2 0.04
37 13 0.29
38 4 0.09
39 9 0.20
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.62
Consensus pattern (37 bp):
ATTTCATTTTAATTTCAAATTTTTTTCTTCTTATTAA
Found at i:39531196 original size:27 final size:28
Alignment explanation
Indices: 39531166--39531224 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
39531156 TTCATTTCAA
*
39531166 ATTTCTTTTAAATTTCA-TT-ATTTTCTT
1 ATTTCATTTAAATTTCATTTCATTTT-TT
*
39531193 ATTTCATTTGAATTTCATTTCATTTTTT
1 ATTTCATTTAAATTTCATTTCATTTTTT
39531221 ATTT
1 ATTT
39531225 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.54
28 8 0.29
29 5 0.18
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTTCATTTAAATTTCATTTCATTTTTT
Found at i:39531638 original size:22 final size:22
Alignment explanation
Indices: 39531598--39531660 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 22
39531588 TTATATTTTT
39531598 ATTTCAATTTCTATT-CAATTTGA
1 ATTTC-ATTTC-ATTCCAATTTGA
*
39531621 ATTTCATTTCATTCCAATTTTA
1 ATTTCATTTCATTCCAATTTGA
39531643 ATTTCATTTCATTCCAAT
1 ATTTCATTTCATTCCAAT
39531661 AAAAAAGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 3 0.08
22 30 0.79
23 5 0.13
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTCATTTCATTCCAATTTGA
Found at i:39531730 original size:6 final size:6
Alignment explanation
Indices: 39531691--39531738 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
39531681 TTAAATATAA
* * *
39531691 TTTCAT TTT-AA TTTCA- TTTCAT TTCCAA TTTCAT TTTCAT TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
39531737 TT
1 TT
39531739 CCCTTTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTCAT
Found at i:39531745 original size:12 final size:12
Alignment explanation
Indices: 39531690--39531745 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
39531680 TTTAAATATA
*
39531690 ATTT-CATTTTA
1 ATTTCCATTTTC
39531701 ATTT-CA-TTTC
1 ATTTCCATTTTC
*
39531711 ATTTCCAATTTC
1 ATTTCCATTTTC
*
39531723 ATTTTCATTTTC
1 ATTTCCATTTTC
*
39531735 ATTTCCCTTTT
1 ATTTCCATTTT
39531746 TACTTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
10 7 0.18
11 8 0.21
12 23 0.61
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTCCATTTTC
Found at i:39531883 original size:27 final size:28
Alignment explanation
Indices: 39531853--39531916 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
39531843 TGTATTAATT
39531853 AATATATTTA-ATCAATTGTATAATTTG
1 AATATATTTATATCAATTGTATAATTTG
** * *
39531880 AATA-AAGTATGTCATTTGTATAATTTG
1 AATATATTTATATCAATTGTATAATTTG
*
39531907 TATATATTTA
1 AATATATTTA
39531917 CAACGTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 3 0.11
27 22 0.79
28 3 0.11
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (28 bp):
AATATATTTATATCAATTGTATAATTTG
Found at i:39534793 original size:12 final size:11
Alignment explanation
Indices: 39534763--39534787 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39534753 TTTAACTAAT
39534763 AAAGCAAACAA
1 AAAGCAAACAA
39534774 AAAGCAAACAA
1 AAAGCAAACAA
39534785 AAA
1 AAA
39534788 CTCAAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAGCAAACAA
Found at i:39540192 original size:15 final size:15
Alignment explanation
Indices: 39540174--39540203 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39540164 GTTGTTTAAA
39540174 TTTTAAAATATATTT
1 TTTTAAAATATATTT
*
39540189 TTTTAAATTATATTT
1 TTTTAAAATATATTT
39540204 AGAATAAATT
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:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAAAATATATTT
Found at i:39542329 original size:18 final size:20
Alignment explanation
Indices: 39542295--39542331 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
39542285 AAACGACAAT
39542295 AAAACAATGGCAAAACAACA
1 AAAACAATGGCAAAACAACA
39542315 AAAACAAT-G-AAAACAAC
1 AAAACAATGGCAAAACAAC
39542332 GGCAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.68, C:0.19, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAACAATGGCAAAACAACA
Found at i:39545104 original size:28 final size:31
Alignment explanation
Indices: 39545073--39545130 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
39545063 GAAATATCCA
39545073 TACATAAT-AAA-AATACATAT-ATATATAG
1 TACATAATAAAAGAATACATATAATATATAG
*
39545101 TACATATTAAAAGAATACATATAATATATA
1 TACATAATAAAAGAATACATATAATATATA
39545131 TTTCAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 3 0.12
30 9 0.35
31 7 0.27
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (31 bp):
TACATAATAAAAGAATACATATAATATATAG
Found at i:39545160 original size:22 final size:24
Alignment explanation
Indices: 39545104--39545160 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
39545094 TATATAGTAC
* *
39545104 ATATTAAAAGAATACATATAATAT
1 ATATTAAAAGAATAAAGATAATAT
**
39545128 ATATTTCAAGAA-AAAGATAATA-
1 ATATTAAAAGAATAAAGATAATAT
39545150 ATATTAAAAGA
1 ATATTAAAAGA
39545161 GTAACTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 9 0.33
23 8 0.30
24 10 0.37
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (24 bp):
ATATTAAAAGAATAAAGATAATAT
Found at i:39546683 original size:7 final size:7
Alignment explanation
Indices: 39546671--39546719 Score: 80
Period size: 7 Copynumber: 6.9 Consensus size: 7
39546661 TCAGGAGTGT
39546671 GGGTTTA
1 GGGTTTA
39546678 GGGTTTTA
1 GGG-TTTA
39546686 GGGTTTA
1 GGGTTTA
39546693 GGGTTTA
1 GGGTTTA
*
39546700 GGTTTTA
1 GGGTTTA
39546707 GGGTTTA
1 GGGTTTA
39546714 GGGTTT
1 GGGTTT
39546720 TGTGTATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
7 32 0.82
8 7 0.18
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (7 bp):
GGGTTTA
Found at i:39546705 original size:21 final size:22
Alignment explanation
Indices: 39546671--39546719 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
39546661 TCAGGAGTGT
39546671 GGGTTTAGGGTTTTAGGGTTTA
1 GGGTTTAGGGTTTTAGGGTTTA
39546693 GGGTTTA-GGTTTTAGGGTTTA
1 GGGTTTAGGGTTTTAGGGTTTA
39546714 GGGTTT
1 GGGTTT
39546720 TGTGTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (22 bp):
GGGTTTAGGGTTTTAGGGTTTA
Found at i:39547747 original size:227 final size:229
Alignment explanation
Indices: 39547324--39547770 Score: 541
Period size: 231 Copynumber: 1.9 Consensus size: 229
39547314 TGTGATCTTG
** *
39547324 AGCTCAACTCATTTCTCGCAATATGAATTGATTCTTTAAAAACAGACATTAAAACAGAAATTGAA
1 AGCTCAACTCACCTCTCGCAATATGAATTGATTCTTTAAAAACAGACACTAAAACAGAAATTGAA
* *
39547389 AATAGCTCAGCACGTGAGCCAAAGCGCAACTCACCTCTCGCAATATGAGTTGGTCTTTTTGAAAC
66 AATACCTCAGCACGTGAGCCAAAGCGCAACTCACCTCTCGCAATATGAGTTGGTATTTTTGAAAC
*
39547454 TTAATTTAAAAAATAAATTTTTGAAAATACCTCGCCATGTGACCCGAGGCTCAACTCACCTCTCG
131 TTAAATT--AAAATAAA-TTTTGAAAATACCTCGCCATGTGACCCGAGGCTCAACTCACCTCTCG
* *
39547519 CACTATGAGTTGATTTTTTTGAAAAACAGAAATTAAA
193 CAATATGAGTTGATTTTCTTGAAAAACAGAAATTAAA
* * *
39547556 AGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAACATGA-ACTAAAACGGAAATTGA
1 AGCTCAACTCACCTCTCGCAATATGAATTGATTCTTTAAAAACA-GACACTAAAACAGAAATTGA
* * * * * * * *
39547619 GAATTCCTCAGCATGTGAGCC-GAGACTCAACTTACTTCTCGTAATATGAGTT-G-ATTTTTGAA
65 AAATACCTCAGCACGTGAGCCAAAG-CGCAACTCACCTCTCGCAATATGAGTTGGTATTTTTG-A
* * * * *
39547681 AAGTATAAATT-AAATAGAA-TTTGGAAATACCTCAG-CGTGTGACCTGAGGTTCAACTCACCTC
128 AACT-TAAATTAAAATA-AATTTTGAAAATACCTC-GCCATGTGACCCGAGGCTCAACTCACCTC
39547743 TCGCAATATGAGTTGATTTTCTTGAAAA
190 TCGCAATATGAGTTGATTTTCTTGAAAA
39547771 GTAGAAACTG
Statistics
Matches: 185, Mismatches: 24, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
227 63 0.34
228 6 0.03
229 8 0.04
230 7 0.04
231 69 0.37
232 32 0.17
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (229 bp):
AGCTCAACTCACCTCTCGCAATATGAATTGATTCTTTAAAAACAGACACTAAAACAGAAATTGAA
AATACCTCAGCACGTGAGCCAAAGCGCAACTCACCTCTCGCAATATGAGTTGGTATTTTTGAAAC
TTAAATTAAAATAAATTTTGAAAATACCTCGCCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTCTTGAAAAACAGAAATTAAA
Found at i:39547831 original size:89 final size:86
Alignment explanation
Indices: 39547557--39547853 Score: 320
Period size: 86 Copynumber: 3.4 Consensus size: 86
39547547 GAAATTAAAA
* * * *
39547557 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA-CATGAACTAAAACGGAAATT-GA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGTA-GAAATTAAACAGAAATTGGA
* *
39547619 GAATTCCTCAGCATGTGAGCC-GAG
65 -AATACCTCAGCGTGT-A-CCTGAG
* * * * * * *
39547643 ACTCAACTTACTTCTCGTAATATGAGTTGA-TTTTTGAAAAGTATAAATTAAATAGAATTTGGAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGTAGAAATTAAACAGAAATTGGAA
39547707 ATACCTCAGCGTGTGACCTGAG
66 ATACCTCAGCGTGT-ACCTGAG
*
39547729 GTTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGTAGAAACTGATAAACAGAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAGTAGAAA-T--TAAACAGAAATT
*
39547794 -GAAATTACCTCGGCGTGT-CCTGAG
62 GGAAA-TACCTCAGCGTGTACCTGAG
39547818 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
39547854 TTATATACCT
Statistics
Matches: 179, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
85 2 0.01
86 90 0.50
87 6 0.03
88 15 0.08
89 40 0.22
90 4 0.02
91 22 0.12
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (86 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGTAGAAATTAAACAGAAATTGGAA
ATACCTCAGCGTGTACCTGAG
Found at i:39547892 original size:60 final size:60
Alignment explanation
Indices: 39547799--39547911 Score: 208
Period size: 60 Copynumber: 1.9 Consensus size: 60
39547789 AAATTGAAAT
*
39547799 TACCTCGGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTATA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTATA
*
39547859 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGGAATATGAGTTGATTTT
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
39547912 CAAAAAGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (60 bp):
TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTATA
Found at i:39547977 original size:73 final size:72
Alignment explanation
Indices: 39547858--39547997 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 72
39547848 TTTTTTTTAT
* * *
39547858 ATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGGAATATGAGTTG-ATTTTCAAAAAGCAG
1 ATACCTCAACGTCTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-AAAAA-CAG
39547922 AAATTGGAA
64 AAATTGGAA
* ** *
39547931 ATACCTCAACGTCTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
1 ATACCTCAACGTCTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAA
39547996 AT
66 AT
39547998 AAAAATATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 7 0.12
73 47 0.80
74 5 0.08
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (72 bp):
ATACCTCAACGTCTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAA
ATTGGAA
Found at i:39548898 original size:46 final size:45
Alignment explanation
Indices: 39548812--39548899 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
39548802 TGTGTTAATC
* *
39548812 AAGACGCCCTTTTCGGGTTTTCACCTTGAATCTCTCTTTTTTTTT
1 AAGACGCCCTTTTCGGGTTTTCACCTTGAATCCCCCTTTTTTTTT
* *
39548857 AAGATGCCCTTTATCGGGTTTTCACCTTG-ATCCCCCATTTTTT
1 AAGACGCCCTTT-TCGGGTTTTCACCTTGAATCCCCCTTTTTTT
39548900 CTTTTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 22 0.58
46 16 0.42
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.45
Consensus pattern (45 bp):
AAGACGCCCTTTTCGGGTTTTCACCTTGAATCCCCCTTTTTTTTT
Found at i:39559958 original size:26 final size:30
Alignment explanation
Indices: 39559929--39559995 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 30
39559919 TTAGTAATAT
*
39559929 AAAATA-ATATGTA-CA-TAAGATAACA-A
1 AAAATACATATATACCACTAAGATAACATA
* *
39559955 AAAA-ATATATATACCACTAATATAACATA
1 AAAATACATATATACCACTAAGATAACATA
39559984 AAAATACATATA
1 AAAATACATATA
39559996 CAATTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.03
26 10 0.30
27 2 0.06
28 9 0.27
29 5 0.15
30 6 0.18
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAATACATATATACCACTAAGATAACATA
Found at i:39560003 original size:28 final size:28
Alignment explanation
Indices: 39559948--39560004 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
39559938 TGTACATAAG
* *
39559948 ATAACAAAAAAATATATATACCACTAAT
1 ATAACAAAAAAATACATATACAACTAAT
* *
39559976 ATAACATAAAAATACATATACAATTAAT
1 ATAACAAAAAAATACATATACAACTAAT
39560004 A
1 A
39560005 ATATGAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.26
Consensus pattern (28 bp):
ATAACAAAAAAATACATATACAACTAAT
Found at i:39560411 original size:25 final size:25
Alignment explanation
Indices: 39560352--39560411 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
39560342 TATGTAGTAC
*
39560352 ATATTAAAAG-AATACATATAATAT
1 ATATTAAAAGAAAAACATATAATAT
** *
39560376 ATATTTCAAGAAAAAGATAATAATA-
1 ATATTAAAAGAAAAACAT-ATAATAT
39560401 ATATTAAAAGA
1 ATATTAAAAGA
39560412 GTAACTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 8 0.29
25 14 0.50
26 6 0.21
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (25 bp):
ATATTAAAAGAAAAACATATAATAT
Found at i:39562171 original size:46 final size:46
Alignment explanation
Indices: 39562118--39562293 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
39562108 TATTTGGGCA
39562118 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * * * *
39562164 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-GCG
* * *
39562211 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
39562257 -CCTGAGCTCGTTGAGTTGAGTTCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39562294 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
45 3 0.03
46 65 0.62
47 36 0.35
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:39562273 original size:93 final size:93
Alignment explanation
Indices: 39562114--39562286 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
39562104 GGGATATTTG
* *
39562114 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCGAACTCGTTGAG
39562179 TTGAGTCCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* *
39562207 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCC-GAACTCGTTGA
*
39562271 GTTGAGTTCGAGTTCG
65 GTTGAGTCCGAGTTCG
39562287 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:39565477 original size:40 final size:40
Alignment explanation
Indices: 39565394--39565579 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
39565384 TTGAATGATG
* * * *
39565394 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
39565434 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39565474 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39565514 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39565555 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39565580 AACGAGTAGC
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 122 0.92
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39565586 original size:80 final size:79
Alignment explanation
Indices: 39565447--39565612 Score: 228
Period size: 80 Copynumber: 2.1 Consensus size: 79
39565437 GGACTAAGAT
* **
39565447 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
*
39565511 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAATC
*
39565527 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
39565591 ATATCCGGTTAAATT
65 AAATCCGGTTAAATC
39565606 CCGAAGG
1 CCGAAGG
39565613 TACGTGATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
79 16 0.21
80 59 0.77
81 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAATC
Found at i:39568507 original size:15 final size:15
Alignment explanation
Indices: 39568468--39568547 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
39568458 GTATCTTGGG
*
39568468 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
39568483 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
39568498 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
39568513 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
39568528 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
39568542 TTTCTT
1 TTTCTT
39568548 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:39568537 original size:30 final size:30
Alignment explanation
Indices: 39568459--39568546 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
39568449 CATAGTATCG
* * *
39568459 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
39568489 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
39568519 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
39568547 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:39570986 original size:46 final size:46
Alignment explanation
Indices: 39570930--39571108 Score: 173
Period size: 46 Copynumber: 3.9 Consensus size: 46
39570920 GGATATTTGG
*
39570930 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* ** * * * *
39570976 GCGTCCGAACTCGTTGAGTTGAGTCCGAGTT-TGTGAAATGTA-ACTA
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA
* * *
39571022 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACCTATGGATGTGA
1 -GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* * * * *
39571069 ACACCCGAGCTCGTTGATTTGAGTCCGAGTTCGCTTATGG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39571109 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
45 1 0.01
46 68 0.66
47 34 0.33
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:39571091 original size:93 final size:93
Alignment explanation
Indices: 39570929--39571099 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
39570919 GGGATATTTG
* * **
39570929 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAG
39570994 TTGAGTCCGAGTTTGTGAAATGTAACTA
66 TTGAGTCCGAGTTTGTGAAATGTAACTA
** * * *
39571022 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACCTATGGATGTGAACACCCGAGCTCGTTGAT
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAG
39571087 TTGAGTCCGAGTT
66 TTGAGTCCGAGTT
39571100 CGCTTATGGG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAG
TTGAGTCCGAGTTTGTGAAATGTAACTA
Found at i:39572603 original size:40 final size:41
Alignment explanation
Indices: 39572555--39572690 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
39572545 CACACTAGTG
* *
39572555 CACCCAGTGCCTTATCGGAT-AATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATAAATTCGAAGTAGTAAATTGA
* * *
39572595 CACTCAGTGTCTCATTGAATAAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATAAATTCGAAGTAGTAAATTGA
* * ** *
39572636 CACCCAGTGTCTCATTGGTTAAATT-G-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATAAATTCGAAGTAGTAAATTGA
39572673 CACCCAGTGCCTCATCGA
1 CACCCAGTGCCTCATCGA
39572691 CTCGAAGTCA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
37 24 0.29
39 1 0.01
40 16 0.19
41 42 0.51
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAATAAATTCGAAGTAGTAAATTGA
Found at i:39572620 original size:41 final size:41
Alignment explanation
Indices: 39572575--39572687 Score: 153
Period size: 41 Copynumber: 2.9 Consensus size: 41
39572565 CTTATCGGAT
*
39572575 AATTCGAAGTAGTAAATTGACACTCAGTGTCTCATTGAATA
1 AATTCGAAGTAGTAAATTGACACCCAGTGTCTCATTGAATA
**
39572616 AATTCGAAGTAGTAAATTGACACCCAGTGTCTCATTGGTTA
1 AATTCGAAGTAGTAAATTGACACCCAGTGTCTCATTGAATA
* *
39572657 AATT-G-A--AGTAAATTGGCACCCAGTGCCTCAT
1 AATTCGAAGTAGTAAATTGACACCCAGTGTCTCAT
39572688 CGACTCGAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
37 23 0.34
39 1 0.01
40 1 0.01
41 42 0.63
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
AATTCGAAGTAGTAAATTGACACCCAGTGTCTCATTGAATA
Found at i:39574993 original size:29 final size:29
Alignment explanation
Indices: 39574930--39575007 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
39574920 CAAAGAAGAA
* **
39574930 AAAAGAAAATAAAGAAATAAATATTTGAT
1 AAAAGAAAATAAAGAAATAAAAATTCAAT
39574959 AAAAGAAAATAAAGAAA-AAAAATTCAAT
1 AAAAGAAAATAAAGAAATAAAAATTCAAT
* * *
39574987 ATTAAGAAAATGAAGGAATAA
1 A-AAAGAAAATAAAGAAATAA
39575008 CAGATAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.22
29 30 0.73
30 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.12, T:0.19
Consensus pattern (29 bp):
AAAAGAAAATAAAGAAATAAAAATTCAAT
Found at i:39575027 original size:4 final size:4
Alignment explanation
Indices: 39575011--39575133 Score: 106
Period size: 4 Copynumber: 30.2 Consensus size: 4
39575001 GGAATAACAG
* * * * *
39575011 ATAA ATGA ATAA ATAA ATTAAA ACAA ATAA GTAA ATAA ATGA AT-A ATAT
1 ATAA ATAA ATAA ATAA A-T-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* ** * *
39575060 ATAA ATAA GTAA ATAA ATAA GCAA ATGA ATAAA ATAAA ATGA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA
39575109 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
39575134 AGGAAACAGT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
3 6 0.06
4 78 0.81
5 9 0.09
6 3 0.03
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:39575127 original size:49 final size:46
Alignment explanation
Indices: 39575011--39575128 Score: 150
Period size: 49 Copynumber: 2.5 Consensus size: 46
39575001 GGAATAACAG
* *
39575011 ATAAATGAATAAATAAATTAA-AACAAATAAGTAAATAAATGAATA
1 ATAAATAAATAAATAAATAAATAACAAATAAGTAAATAAATGAATA
* *
39575056 ATATATAAATAAGTAAATAAATAAGCAAATGAA-TAAAATAAAATGAATA
1 ATAAATAAATAAATAAATAAATAA-CAAAT-AAGT-AAAT-AAATGAATA
39575105 ATAAATAAATAAATAAATAAATAA
1 ATAAATAAATAAATAAATAAATAA
39575129 ATAAAAGGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
45 17 0.27
46 2 0.03
47 6 0.10
48 6 0.10
49 31 0.50
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (46 bp):
ATAAATAAATAAATAAATAAATAACAAATAAGTAAATAAATGAATA
Found at i:39576896 original size:44 final size:44
Alignment explanation
Indices: 39576786--39576904 Score: 130
Period size: 45 Copynumber: 2.7 Consensus size: 44
39576776 GATTTGTAAC
* * *
39576786 TTGTAACTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAAAT
1 TTGTAACTTTAATCTGCTCCACTACAACTTTAAGGAAATAAAAT
* * * * * *
39576830 TAGCTATCTTCAATCTGCTCCACTACTACTTTAAGGAGATAAGAT
1 TTG-TAACTTTAATCTGCTCCACTACAACTTTAAGGAAATAAAAT
* *
39576875 TTGTAGCTTTAATCTGCTCCACTGCAACTT
1 TTGTAACTTTAATCTGCTCCACTACAACTT
39576905 CAGGGAGGTA
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 25 0.42
45 35 0.58
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (44 bp):
TTGTAACTTTAATCTGCTCCACTACAACTTTAAGGAAATAAAAT
Found at i:39576917 original size:44 final size:44
Alignment explanation
Indices: 39576786--39576919 Score: 151
Period size: 44 Copynumber: 3.0 Consensus size: 44
39576776 GATTTGTAAC
* * *
39576786 TTGTAACTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAAAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* * * * * *
39576830 TAGCTATCTTCAATCTGCTCCACTACTACTTTAAGGAGATAAGAT
1 TTG-TAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* * *
39576875 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGGTAAGAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
39576919 T
1 T
39576920 CACCACGGTG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
44 37 0.51
45 35 0.49
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (44 bp):
TTGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
Found at i:39586134 original size:42 final size:42
Alignment explanation
Indices: 39586075--39586183 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
39586065 TACCATACCA
** *
39586075 ATGCCATATCCCAGATATGGTCTTACGTGAAA-TCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTAC-ACAAAGTCTCATATCG
* *
39586117 ATGCCATATCCAAGATATGGTCTTGCACAAAGTCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATATCG
*
39586159 ATGTCATATCCCAGATATGGTCTTA
1 ATGCCATATCCCAGATATGGTCTTA
39586184 AACATTGTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 3 0.05
42 55 0.95
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATATCG
Found at i:39590014 original size:28 final size:28
Alignment explanation
Indices: 39589974--39590038 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
39589964 ATGTACTAGA
*
39589974 ATACCCCTATGTATGCAAAATTACCAT-T
1 ATACCCCTATGTATGCAAAATGACC-TCT
39590002 ATACCCCTATGTATGCAAAATGACCTCT
1 ATACCCCTATGTATGCAAAATGACCTCT
39590030 ATACCCCTA
1 ATACCCCTA
39590039 GGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTCT
Found at i:39590245 original size:29 final size:28
Alignment explanation
Indices: 39590154--39590234 Score: 135
Period size: 28 Copynumber: 2.9 Consensus size: 28
39590144 CTAGTGGCTA
*
39590154 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAATTATCTGTTCTGGTGGCAC
39590182 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAATTATCTGTTCTGGTGGCAC
*
39590210 TGCCACAAAATATCTGTATCTGGTG
1 TGCCACAAATTATCTGT-TCTGGTG
39590235 ACTCTGTCAC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 43 0.86
29 7 0.14
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAATTATCTGTTCTGGTGGCAC
Found at i:39590259 original size:56 final size:55
Alignment explanation
Indices: 39590154--39590259 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 55
39590144 CTAGTGGCTA
* *
39590154 TGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTTCTGGTGGCAC
* * *
39590210 TGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-TCTGG
39590260 CAGCCATGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
55 8 0.19
56 21 0.49
57 14 0.33
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (55 bp):
TGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTTCTGGTGGCAC
Found at i:39596562 original size:49 final size:49
Alignment explanation
Indices: 39596505--39596729 Score: 279
Period size: 49 Copynumber: 4.5 Consensus size: 49
39596495 TATCTGGTAG
39596505 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA
* * ** * *
39596554 CATAGTAGCCTGCACTTAGTACTACACAAGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACA
* * * * * * *
39596604 CATAGTAGCTTGCACTTAGTTCTACACACGTGATCGAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACA
* *
39596655 CATAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATTCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA
*
39596704 CGTAGTAGCCTGCACTTAGTACTACA
1 CATAGTAGCCTGCACTTAGTACTACA
39596730 AACGTGACCT
Statistics
Matches: 149, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
49 66 0.44
50 45 0.30
51 38 0.26
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA
Found at i:39596678 original size:101 final size:98
Alignment explanation
Indices: 39596505--39596738 Score: 290
Period size: 101 Copynumber: 2.4 Consensus size: 98
39596495 TATCTGGTAG
* *
39596505 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACATAGTAGCCTGCACT
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTGCACT
*
39596570 TAGTACTACACAAGTGACCTAACCA-TCTGATACA
66 TAGTACTACACAAGCGACC-AACCATTC-GATACA
* * * * * *
39596604 CATAGTAGCTTGCACTTAGTTCTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCTTGCA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACATAGTAGCCTGCA
* ** *
39596669 CTTAGTACTACACATGCGACCAATTATTCGGTACA
64 CTTAGTACTACACAAGCGACCAACCATTCGATACA
* *
39596704 CGTAGTAGCCTGCACTTAGTACTACAAACGTGACC
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACC
39596739 TCACAATAGA
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
99 30 0.26
100 40 0.35
101 44 0.39
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (98 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTGCACT
TAGTACTACACAAGCGACCAACCATTCGATACA
Found at i:39601318 original size:46 final size:45
Alignment explanation
Indices: 39601268--39601541 Score: 191
Period size: 46 Copynumber: 5.9 Consensus size: 45
39601258 CACTGACACA
39601268 TCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACG
1 TCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTT-CG
*** * *
39601314 TCTCG-AGGTTAAAGCATGTCCCAGACATGTCTTACACTAGCACTCG
1 TCTCGTA-GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TTCG
* * * * * *
39601360 TCTC-AATGTCGATGCCATGTCCCAGACATGGTCTCATACT-GAC-ACA
1 TCTCGTA-GCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTTCG
* * *
39601406 TCTCGTAGCCGATGCATGTCCCTGACATGTCTTACACTAGAATTTG
1 TCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTAG-CTTCG
* * *
39601452 TCTCAATA-CCGATGCCATGTCCCAGACATGATCTTACACTGGCTCTCA
1 TCTC-GTAGCCGATG-CATGTCCCAGACATG-TCTTACACTAGCT-TCG
* * * * *
39601500 TAAT-GTGGCCGATGCATGTACCAGAAATGTCATACACTAGCT
1 T-CTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCT
39601542 CACACAAGTG
Statistics
Matches: 178, Mismatches: 35, Indels: 30
0.73 0.14 0.12
Matches are distributed among these distances:
44 8 0.04
45 16 0.09
46 78 0.44
47 48 0.27
48 27 0.15
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (45 bp):
TCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCG
Found at i:39609174 original size:10 final size:10
Alignment explanation
Indices: 39609159--39609184 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39609149 TTATACTTAA
39609159 TTTTGATTAT
1 TTTTGATTAT
39609169 TTTTGATTAT
1 TTTTGATTAT
39609179 TTTTGA
1 TTTTGA
39609185 CAGATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (10 bp):
TTTTGATTAT
Found at i:39611198 original size:14 final size:14
Alignment explanation
Indices: 39611179--39611205 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39611169 AGAATATTGT
39611179 GATATGGGCTTTAA
1 GATATGGGCTTTAA
39611193 GATATGGGCTTTA
1 GATATGGGCTTTA
39611206 GAAAAACTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (14 bp):
GATATGGGCTTTAA
Found at i:39612046 original size:20 final size:19
Alignment explanation
Indices: 39612007--39612046 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39611997 ACTTTACTAG
* *
39612007 AAAACAAATCTCTTTACAT
1 AAAACAAATATATTTACAT
39612026 AAAACAAATATATTATACAT
1 AAAACAAATATATT-TACAT
39612046 A
1 A
39612047 TACAGCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAACAAATATATTTACAT
Found at i:39613256 original size:27 final size:27
Alignment explanation
Indices: 39613154--39613249 Score: 156
Period size: 27 Copynumber: 3.6 Consensus size: 27
39613144 CTAAATTGAA
39613154 AAAATGACTATTTTGCCCTTATGTGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
*
39613181 AAAATGACTGTTTTGCCCTTATGTGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
* *
39613208 AAAATAACTATTTTTCCCTTATGTGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
*
39613235 AAAATGACTGTTTTG
1 AAAATGACTATTTTG
39613250 TATTTATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (27 bp):
AAAATGACTATTTTGCCCTTATGTGGT
Found at i:39615128 original size:50 final size:50
Alignment explanation
Indices: 39615074--39615235 Score: 229
Period size: 50 Copynumber: 3.3 Consensus size: 50
39615064 CTAAGATAGG
* ** *
39615074 AGTTACATAATGCATGACACAATTTATGATGCAATCTTAACTAACATGAG
1 AGTTACATAATGCATGTCATTATTTATGATGCAATCTTAACTAACATGAA
* *
39615124 AGTTACATAATGCATGTCATTATGTATGATGCAA-CTTAACTAACATAAA
1 AGTTACATAATGCATGTCATTATTTATGATGCAATCTTAACTAACATGAA
* *
39615173 AGTTACATAATGCATGTCATTATTTATGATGC-ATACTTAAATAGCATGAA
1 AGTTACATAATGCATGTCATTATTTATGATGCAAT-CTTAACTAACATGAA
39615223 AGTTACATAATGC
1 AGTTACATAATGC
39615236 CCGACTTTAT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
48 1 0.01
49 44 0.44
50 55 0.55
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (50 bp):
AGTTACATAATGCATGTCATTATTTATGATGCAATCTTAACTAACATGAA
Found at i:39615163 original size:99 final size:101
Alignment explanation
Indices: 39615050--39615235 Score: 261
Period size: 99 Copynumber: 1.9 Consensus size: 101
39615040 TTCATTAAAA
* **
39615050 GATGCAAACTTTAACTAAGATAGGAGTTACATAATGCATGACACAATTTATGATGCA-ATCTTAA
1 GATGCAAACTTTAACTAACATAAAAGTTACATAATGCATGACACAATTTATGATGCATA-CTTAA
* *
39615114 CTAACATGAGAGTTACATAATGCATGTCATTATGTAT
65 ATAACATGAAAGTTACATAATGCATGTCATTATGTAT
* **
39615151 GATGC-AAC-TTAACTAACATAAAAGTTACATAATGCATGTCATTATTTATGATGCATACTTAAA
1 GATGCAAACTTTAACTAACATAAAAGTTACATAATGCATGACACAATTTATGATGCATACTTAAA
*
39615214 TAGCATGAAAGTTACATAATGC
66 TAACATGAAAGTTACATAATGC
39615236 CCGACTTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 66 0.88
100 4 0.05
101 5 0.07
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (101 bp):
GATGCAAACTTTAACTAACATAAAAGTTACATAATGCATGACACAATTTATGATGCATACTTAAA
TAACATGAAAGTTACATAATGCATGTCATTATGTAT
Found at i:39615181 original size:49 final size:49
Alignment explanation
Indices: 39615050--39615235 Score: 228
Period size: 50 Copynumber: 3.7 Consensus size: 49
39615040 TTCATTAAAA
* ** * **
39615050 GATGCAAACTTTAACTAAGATAGGAGTTACATAATGCATGACACAATTTAT
1 GATGC-AAC-TTAACTAACATAAAAGTTACATAATGCATGTCATTATTTAT
* * *
39615101 GATGCAATCTTAACTAACATGAGAGTTACATAATGCATGTCATTATGTAT
1 GATGCAA-CTTAACTAACATAAAAGTTACATAATGCATGTCATTATTTAT
39615151 GATGCAACTTAACTAACATAAAAGTTACATAATGCATGTCATTATTTAT
1 GATGCAACTTAACTAACATAAAAGTTACATAATGCATGTCATTATTTAT
* * *
39615200 GATGCATACTTAAATAGCATGAAAGTTACATAATGC
1 GATGCA-ACTTAACTAACATAAAAGTTACATAATGC
39615236 CCGACTTTAT
Statistics
Matches: 120, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 45 0.38
50 69 0.57
51 6 0.05
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (49 bp):
GATGCAACTTAACTAACATAAAAGTTACATAATGCATGTCATTATTTAT
Found at i:39619943 original size:31 final size:31
Alignment explanation
Indices: 39619905--39619965 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39619895 ATTGTATAAT
39619905 TTTCTCTTTA-GTTTTAGACTTTAGTTTTTCC
1 TTTCTC-TTAGGTTTTAGACTTTAGTTTTTCC
* * *
39619936 TTTCTCTTAGGTTTTGGATTTTATTTTTTC
1 TTTCTCTTAGGTTTTAGACTTTAGTTTTTC
39619966 ATTCTTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.64
Consensus pattern (31 bp):
TTTCTCTTAGGTTTTAGACTTTAGTTTTTCC
Found at i:39636850 original size:10 final size:10
Alignment explanation
Indices: 39636835--39636883 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
39636825 ATTAGAATAT
39636835 TTAATTTTAA
1 TTAATTTTAA
39636845 TTAATTTGATAA
1 TTAATTT--TAA
* *
39636857 TAAATTTTGA
1 TTAATTTTAA
*
39636867 TTTATTTTAA
1 TTAATTTTAA
39636877 TTAATTT
1 TTAATTT
39636884 GATAATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 22 0.71
12 9 0.29
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:39636875 original size:32 final size:33
Alignment explanation
Indices: 39636833--39636894 Score: 117
Period size: 32 Copynumber: 1.9 Consensus size: 33
39636823 TTATTAGAAT
39636833 ATTTAATTTTAATTAATTTGATAATAAATTTTG
1 ATTTAATTTTAATTAATTTGATAATAAATTTTG
39636866 ATTT-ATTTTAATTAATTTGATAATAAATT
1 ATTTAATTTTAATTAATTTGATAATAAATT
39636895 ATTAGCTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (33 bp):
ATTTAATTTTAATTAATTTGATAATAAATTTTG
Found at i:39639210 original size:18 final size:18
Alignment explanation
Indices: 39639187--39639223 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39639177 GAAAACGAAA
39639187 AAGAAGGAAAG-GATGAAG
1 AAGAA-GAAAGAGATGAAG
39639205 AAGAAGAAAGAGATGAAG
1 AAGAAGAAAGAGATGAAG
39639223 A
1 A
39639224 GACATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAGAGATGAAG
Found at i:39653897 original size:45 final size:44
Alignment explanation
Indices: 39653821--39653910 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
39653811 ATCTTTCTTT
39653821 TTCGAAGTTAGGGACAGTCCCGATACAAAATCCATAGTGACTCTA
1 TTCGAAGTTAGGGACAGTCCCGATACAAAAT-CATAGTGACTCTA
* * ** * *
39653866 TTCGGAGTTAGGGGCAGTCTTGATGCGAAATCATAGTGACTCTA
1 TTCGAAGTTAGGGACAGTCCCGATACAAAATCATAGTGACTCTA
39653910 T
1 T
39653911 CCCTTTTCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TTCGAAGTTAGGGACAGTCCCGATACAAAATCATAGTGACTCTA
Found at i:39657167 original size:31 final size:31
Alignment explanation
Indices: 39657132--39657195 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
39657122 CCTTTTCATA
39657132 TTTCATATTTCATAACACTGGGCAAAAGCCT
1 TTTCATATTTCATAACACTGGGCAAAAGCCT
** **
39657163 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCAAAAGCCT
39657194 TT
1 TT
39657196 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCAAAAGCCT
Found at i:39657485 original size:50 final size:48
Alignment explanation
Indices: 39657404--39657511 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 48
39657394 CTGGAGGCCT
*
39657404 AGCCTCTTTTAATAACTGGGGCAAAGCCCTTTT-GATAAACTAGGGCAAA
1 AGCC-CTTTTAATAACTAGGGCAAAGCCCTTTTCGATAAACTAGGGC-AA
* *
39657453 AGCCCTTTTAATAAACTAGGGCAAAAGCCCTTTTCGGTAAACTAGGGCAT
1 AGCCCTTTTAAT-AACTAGGGC-AAAGCCCTTTTCGATAAACTAGGGCAA
39657503 AGCCCTTTT
1 AGCCCTTTT
39657512 TGCACTTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
48 8 0.15
49 12 0.23
50 21 0.40
51 12 0.23
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (48 bp):
AGCCCTTTTAATAACTAGGGCAAAGCCCTTTTCGATAAACTAGGGCAA
Found at i:39657512 original size:26 final size:25
Alignment explanation
Indices: 39657404--39657511 Score: 132
Period size: 25 Copynumber: 4.4 Consensus size: 25
39657394 CTGGAGGCCT
* *
39657404 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTAGGGCAAA
39657428 AGCCCTTTTGATAAACTAGGGCAAA
1 AGCCCTTTTGATAAACTAGGGCAAA
*
39657453 AGCCCTTTTAATAAACTAGGGCAAA
1 AGCCCTTTTGATAAACTAGGGCAAA
* *
39657478 AGCCCTTTTCGGTAAACTAGGGC-AT
1 AGCCCTTTT-GATAAACTAGGGCAAA
39657503 AGCCCTTTT
1 AGCCCTTTT
39657512 TGCACTTCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
23 7 0.09
24 12 0.16
25 45 0.60
26 11 0.15
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTAGGGCAAA
Found at i:39657582 original size:20 final size:20
Alignment explanation
Indices: 39657559--39657605 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
39657549 TTATGAATAC
39657559 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
39657578 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
39657599 ATCATGT
1 ATCATGT
39657606 ATATCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:39661866 original size:23 final size:22
Alignment explanation
Indices: 39661812--39661897 Score: 120
Period size: 22 Copynumber: 3.9 Consensus size: 22
39661802 GAGTCATGGT
*
39661812 CGGTAAGCTCTTTTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
* *
39661834 CAGTAAGCTCTATTGAGTTGAAA
1 CGGTAAGCTCTATTGAGCTG-AA
39661857 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
39661879 CGGTAAGCTCTCA-TGAGCT
1 CGGTAAGCTCT-ATTGAGCT
39661898 AAAAAAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 36 0.63
23 21 0.37
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (22 bp):
CGGTAAGCTCTATTGAGCTGAA
Found at i:39661909 original size:45 final size:45
Alignment explanation
Indices: 39661815--39661934 Score: 118
Period size: 45 Copynumber: 2.6 Consensus size: 45
39661805 TCATGGTCGG
* * * ***
39661815 TAAGCTCTTTTGAGCTGAACAGTAAGCTCTATTGAGTTGAAACGG
1 TAAGCTCTATTGAGCTGAACAGTAAGCTCTATTGAGCTAAAAAAA
*
39661860 TAAGCTCTATTGAGCTGAACGGTAAGCTCTCA-TGAGCTAAAAAAA
1 TAAGCTCTATTGAGCTGAACAGTAAGCTCT-ATTGAGCTAAAAAAA
* *
39661905 TAAGCTCT-TACGAGTTGAATCAGTAAGCTC
1 TAAGCTCTAT-TGAGCTGAA-CAGTAAGCTC
39661935 ATACGAGCTG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.02
45 51 0.82
46 10 0.16
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
TAAGCTCTATTGAGCTGAACAGTAAGCTCTATTGAGCTAAAAAAA
Found at i:39666586 original size:17 final size:17
Alignment explanation
Indices: 39666551--39666606 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
39666541 ATATTGCCTA
* *
39666551 GCAGATAGTATCGCATG
1 GCAGATTGTATCGCTTG
*
39666568 GCAGATTGTATCGGTTG
1 GCAGATTGTATCGCTTG
* * *
39666585 GCAAACTGTATTGCTTG
1 GCAGATTGTATCGCTTG
39666602 GCAGA
1 GCAGA
39666607 CAATATCGAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (17 bp):
GCAGATTGTATCGCTTG
Found at i:39669207 original size:20 final size:20
Alignment explanation
Indices: 39669184--39669230 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39669174 GGTTAGATCA
*
39669184 CAATACTGGCAGTTTACTTG
1 CAATACTGGCAGCTTACTTG
* **
39669204 CAATACTGTCAGCTTGTTTG
1 CAATACTGGCAGCTTACTTG
39669224 CAATACT
1 CAATACT
39669231 AGTGGCTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
CAATACTGGCAGCTTACTTG
Found at i:39669247 original size:60 final size:60
Alignment explanation
Indices: 39669145--39669286 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 60
39669135 TTACATTCAT
* * * * *
39669145 AATACTGGCAGCTTGTCTATAATACTGGTGGTTAGATCACAATACTGGCAGTTTA-CTTGC
1 AATACTGTCAGCTTGTCTACAATACTAGTGGCTAGATCACAATACTGACAGTTTATC-TGC
* * * *
39669205 AATACTGTCAGCTTGTTTGCAATACTAGTGGCTAGA-CTACAATATTGATAGTTTATCTGC
1 AATACTGTCAGCTTGTCTACAATACTAGTGGCTAGATC-ACAATACTGACAGTTTATCTGC
*
39669265 AATACTGGT-AGCTTGTCCACAA
1 AATACT-GTCAGCTTGTCTACAA
39669287 ATTGGTGTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 63 0.94
61 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (60 bp):
AATACTGTCAGCTTGTCTACAATACTAGTGGCTAGATCACAATACTGACAGTTTATCTGC
Found at i:39673892 original size:28 final size:29
Alignment explanation
Indices: 39673839--39673899 Score: 99
Period size: 28 Copynumber: 2.1 Consensus size: 29
39673829 TGAGCATGAC
39673839 TATAAATGTGAATTGGGCCTGATGGGCCA
1 TATAAATGTGAATTGGGCCTGATGGGCCA
39673868 TATAAATGTG-ATTGGGCCT-AGTGGGCCA
1 TATAAATGTGAATTGGGCCTGA-TGGGCCA
39673896 TATA
1 TATA
39673900 CAGGTATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 1 0.03
28 20 0.65
29 10 0.32
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (29 bp):
TATAAATGTGAATTGGGCCTGATGGGCCA
Found at i:39678755 original size:14 final size:15
Alignment explanation
Indices: 39678736--39678770 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
39678726 CAAAACTAAT
*
39678736 ATTTTTACAA-TTTC
1 ATTTTTACAACATTC
39678750 ATTTTTACAACATTC
1 ATTTTTACAACATTC
39678765 ATTTTT
1 ATTTTT
39678771 CTTTAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTACAACATTC
Found at i:39679103 original size:24 final size:24
Alignment explanation
Indices: 39679060--39679105 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39679050 AACTCACTAG
*
39679060 ATTTTACAATTTAAGTTTTCATAA
1 ATTTTACAATTTAAGATTTCATAA
39679084 ATTTTACAATTTCAA-ATTTCAT
1 ATTTTACAATTT-AAGATTTCAT
39679106 CCGAGGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTACAATTTAAGATTTCATAA
Found at i:39679502 original size:41 final size:41
Alignment explanation
Indices: 39679440--39679524 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
39679430 TGCACCCCAC
*
39679440 TACATCGGTGCAGTTACAGTTAGGGACAATTGCCCGCTTAG
1 TACACCGGTGCAGTTACAGTTAGGGACAATTGCCCGCTTAG
*
39679481 TACACCGGTGCAGTTACAGTTAGTGACAATTGCCCGCTTAG
1 TACACCGGTGCAGTTACAGTTAGGGACAATTGCCCGCTTAG
39679522 TAC
1 TAC
39679525 TTCATTGGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.27
Consensus pattern (41 bp):
TACACCGGTGCAGTTACAGTTAGGGACAATTGCCCGCTTAG
Found at i:39684229 original size:16 final size:14
Alignment explanation
Indices: 39684205--39684238 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
39684195 TAATTTAGCC
39684205 ATTTTTTATTTTAA
1 ATTTTTTATTTTAA
39684219 TATTTTGTTATTTTAA
1 -ATTTT-TTATTTTAA
39684235 ATTT
1 ATTT
39684239 AATTTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
ATTTTTTATTTTAA
Found at i:39686700 original size:43 final size:44
Alignment explanation
Indices: 39686634--39686790 Score: 175
Period size: 43 Copynumber: 3.7 Consensus size: 44
39686624 AACTCGTACA
*
39686634 ATGCCAA-TGTCCCAAACATGGTCTTACATGTAATCAAATATTG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATATTG
*
39686677 ATGCC-ACTGTCCCAGACAAGGTCTTACATG-AAGTCAAATA-TG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGTAA-TCAAATATTG
* * * *
39686719 ATGCCGA-TGTCCTAGACATGGTCTTACACGTAAATCTCAA-ATTG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGT-AATC-AAATATTG
*
39686763 ATGCCAAC-GTCCCAGACGTGGTCTTACA
1 ATGCCAACTGTCCCAGACATGGTCTTACA
39686791 CAAAATCACA
Statistics
Matches: 97, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
42 30 0.31
43 37 0.38
44 30 0.31
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATATTG
Found at i:39686786 original size:86 final size:85
Alignment explanation
Indices: 39686634--39686790 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 85
39686624 AACTCGTACA
*
39686634 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCAAATATTGATGCCACTGTCCCAGACAAGGT
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAATCAAATATTGATGCCACTGTCCCAGACAAGGT
39686699 CTTACATGAAGTCAAATATG
66 CTTACATGAAGTCAAATATG
* * * * **
39686719 ATGCCGATGTCCTAGACATGGTCTTACACGTAAATCTCAA-ATTGATGCCAAC-GTCCCAGACGT
1 ATGCCAATGTCCCAAACATGGTCTTACACGT-AATC-AAATATTGATGCC-ACTGTCCCAGACAA
39686782 GGTCTTACA
63 GGTCTTACA
39686791 CAAAATCACA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
85 27 0.44
86 31 0.50
87 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (85 bp):
ATGCCAATGTCCCAAACATGGTCTTACACGTAATCAAATATTGATGCCACTGTCCCAGACAAGGT
CTTACATGAAGTCAAATATG
Found at i:39693910 original size:20 final size:20
Alignment explanation
Indices: 39693882--39693920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39693872 CTAAGAACTA
39693882 TGTGATCTGAGCTCATGATT
1 TGTGATCTGAGCTCATGATT
* *
39693902 TGTGGTCTGAGTTCATGAT
1 TGTGATCTGAGCTCATGAT
39693921 ATATATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGATT
Found at i:39716010 original size:15 final size:15
Alignment explanation
Indices: 39715987--39716048 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
39715977 CATGAAAACT
*
39715987 AAGATAAAGAAGTCC
1 AAGATAAAGAAATCC
*
39716002 AAGACAAAGAAATCC
1 AAGATAAAGAAATCC
*
39716017 TAGATAAAGAAATCC
1 AAGATAAAGAAATCC
*
39716032 AAGAGACAA-AAATCC
1 AAGATA-AAGAAATCC
39716047 AA
1 AA
39716049 TATACAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
15 38 0.95
16 2 0.05
ACGTcount: A:0.58, C:0.16, G:0.15, T:0.11
Consensus pattern (15 bp):
AAGATAAAGAAATCC
Found at i:39730695 original size:25 final size:26
Alignment explanation
Indices: 39730667--39730741 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
39730657 CTGGAGGCCT
39730667 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCCTCTTTTAATAAACTGGGGCAAA
*
39730692 AGCCAT-TTTTGATAAACTGGGGCAAA
1 AGCC-TCTTTTAATAAACTGGGGCAAA
**
39730718 AGCC-CTTTTCGGTAAACTGGGGCA
1 AGCCTCTTTT-AATAAACTGGGGCA
39730742 TAGCCCTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 14 0.32
26 30 0.68
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (26 bp):
AGCCTCTTTTAATAAACTGGGGCAAA
Found at i:39730746 original size:25 final size:26
Alignment explanation
Indices: 39730680--39730751 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
39730670 CTCTTTTAAT
* *
39730680 AACTGGGGCAAAAGCCATTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGATA
*
39730706 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGATA
*
39730732 AACTGGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
39730752 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 10 0.24
26 32 0.76
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGATA
Found at i:39743276 original size:29 final size:29
Alignment explanation
Indices: 39743214--39743303 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 29
39743204 TATATACATG
* *
39743214 CATATGGCCCACTAGGCCC-AATC-TCATT
1 CATATGACCCATTAGGCCCAAATCAT-ATT
39743242 CATATGACCCATTAGGCCCAAATCATATT
1 CATATGACCCATTAGGCCCAAATCATATT
* * *
39743271 CGTATGACCTATTAGGCCCAAATCACATT
1 CATATGACCCATTAGGCCCAAATCATATT
39743300 CATA
1 CATA
39743304 CGGTCTATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
28 17 0.31
29 36 0.67
30 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (29 bp):
CATATGACCCATTAGGCCCAAATCATATT
Found at i:39743311 original size:29 final size:29
Alignment explanation
Indices: 39743226--39743333 Score: 128
Period size: 29 Copynumber: 3.8 Consensus size: 29
39743216 TATGGCCCAC
* *
39743226 TAGGCCC-AATCTCATTCATATGACCCAT
1 TAGGCCCAAATCACATTCATATGACCTAT
* *
39743254 TAGGCCCAAATCATATTCGTATGACCTAT
1 TAGGCCCAAATCACATTCATATGACCTAT
* **
39743283 TAGGCCCAAATCACATTCATACGGTCTAT
1 TAGGCCCAAATCACATTCATATGACCTAT
* *
39743312 TAGCCCCAAATCACAGTCATAT
1 TAGGCCCAAATCACATTCATAT
39743334 TCATGCTTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 7 0.10
29 60 0.90
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (29 bp):
TAGGCCCAAATCACATTCATATGACCTAT
Found at i:39747236 original size:40 final size:40
Alignment explanation
Indices: 39747137--39747341 Score: 263
Period size: 40 Copynumber: 5.1 Consensus size: 40
39747127 TGGATGATAA
*
39747137 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
39747178 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39747218 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39747258 CCGAGCTAAGTCCTGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39747298 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
39747338 CCGG
1 CCGG
39747342 TTAAATTTCG
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.01
40 117 0.80
41 23 0.16
42 4 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.