Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 2 of 93
Found at i:457758 original size:69 final size:69
Alignment explanation
Indices: 457566--457784 Score: 235
Period size: 69 Copynumber: 3.2 Consensus size: 69
457556 ATTTTTTTAA
* * ** * * *
457566 ACATGACGTGTAACAATCTAACCATGACGTGTCACATGTTTTTGTACATGACGTGTCACATGTTT
1 ACATGATGTGTAACAACCTAATAATGGCATGTCACATGTTTTTGTACATGACGTGTCACATATTT
*
457631 CTGT
66 TTGT
* * * * * *
457635 -CATGGTGTGTAACAACCTAATCATGGCGTGTTACATGTTTCTGTACATGACGTGTCACATTTTT
1 ACATGATGTGTAACAACCTAATAATGGCATGTCACATGTTTTTGTACATGACGTGTCACATATTT
457699 TTGT
66 TTGT
* * ** *
457703 ACATAATGTGTAACAACCTAATAATGGCATGTCACATATTTTTACACAT-AGCGTGTAACATATT
1 ACATGATGTGTAACAACCTAATAATGGCATGTCACATGTTTTTGTACATGA-CGTGTCACATATT
457767 TTTGT
65 TTTGT
*
457772 ACATGACGTGTAA
1 ACATGATGTGTAA
457785 TATCATAGTG
Statistics
Matches: 126, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
68 60 0.48
69 66 0.52
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (69 bp):
ACATGATGTGTAACAACCTAATAATGGCATGTCACATGTTTTTGTACATGACGTGTCACATATTT
TTGT
Found at i:457775 original size:24 final size:24
Alignment explanation
Indices: 457736--457784 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
457726 ATGGCATGTC
457736 ACATATTTTTACACAT-AGCGTGTA
1 ACATATTTTTACACATGA-CGTGTA
**
457760 ACATATTTTTGTACATGACGTGTA
1 ACATATTTTTACACATGACGTGTA
457784 A
1 A
457785 TATCATAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (24 bp):
ACATATTTTTACACATGACGTGTA
Found at i:475399 original size:44 final size:45
Alignment explanation
Indices: 475284--475407 Score: 130
Period size: 46 Copynumber: 2.8 Consensus size: 45
475274 ATATTTTATT
** *
475284 TTTTAATATTAAATATTATTTAGTTATAAT-AAAATGTTTAATTAGC
1 TTTTAATACAAAATATTATTTAATTATAATAAAAATGTTT-ATTA-C
*
475330 TTTTAATACAAAATATTATTAAATTATAATAAAAATGTGTT-TGTA-
1 TTTTAATACAAAATATTATTTAATTATAATAAAAATGT-TTAT-TAC
* *
475375 TTTTGATA-AAAATATTATTTAATTATAGTAAAA
1 TTTTAATACAAAATATTATTTAATTATAATAAAA
475408 GTTATTTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
44 23 0.34
45 7 0.10
46 27 0.40
47 9 0.13
48 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (45 bp):
TTTTAATACAAAATATTATTTAATTATAATAAAAATGTTTATTAC
Found at i:475406 original size:22 final size:22
Alignment explanation
Indices: 475339--475407 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
475329 CTTTTAATAC
* *
475339 AAAATATTATTAAATTATAATA
1 AAAATATTATTTAATTATAGTA
* *
475361 AAAATGTGT-TTGT-ATT-TTGATA
1 AAAATAT-TATT-TAATTATAG-TA
475383 AAAATATTATTTAATTATAGTA
1 AAAATATTATTTAATTATAGTA
475405 AAA
1 AAA
475408 GTTATTTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
21 3 0.09
22 29 0.83
23 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
AAAATATTATTTAATTATAGTA
Found at i:489107 original size:2 final size:2
Alignment explanation
Indices: 489100--489138 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
489090 AAATAAACGA
* *
489100 AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG GG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
489139 AAAGAAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:503945 original size:12 final size:12
Alignment explanation
Indices: 503908--503958 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
503898 ACCAGGAGCG
*
503908 GGATCTTGACCT
1 GGATCTAGACCT
*
503920 AGATCTAGACCT
1 GGATCTAGACCT
*
503932 GGATCTAGATCT
1 GGATCTAGACCT
503944 GGATCGT-GACCT
1 GGATC-TAGACCT
503956 GGA
1 GGA
503959 CTGCTCTCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 32 0.97
13 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (12 bp):
GGATCTAGACCT
Found at i:515770 original size:42 final size:41
Alignment explanation
Indices: 515724--515816 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
515714 CGCAAGAGAT
* *
515724 GGACTGTACTTGGCTGAC-TGTGGATTGTAACTTGGAGAGGTA
1 GGACTGTACTTGG-TGACGTG-GGACTATAACTTGGAGAGGTA
* * *
515766 GGACTATAGCTTGGTGACGTGGGACTATAACTTGGTGAGGTT
1 GGACTGTA-CTTGGTGACGTGGGACTATAACTTGGAGAGGTA
515808 GGACTGTAC
1 GGACTGTAC
515817 CCTGGAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 35 0.81
43 7 0.16
ACGTcount: A:0.22, C:0.13, G:0.35, T:0.30
Consensus pattern (41 bp):
GGACTGTACTTGGTGACGTGGGACTATAACTTGGAGAGGTA
Found at i:515790 original size:21 final size:21
Alignment explanation
Indices: 515751--515812 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
515741 CTGTGGATTG
* * *
515751 TAACTTGGAGAGGTAGGACTA
1 TAACTTGGTGACGTGGGACTA
*
515772 TAGCTTGGTGACGTGGGACTA
1 TAACTTGGTGACGTGGGACTA
* *
515793 TAACTTGGTGAGGTTGGACT
1 TAACTTGGTGACGTGGGACT
515813 GTACCCTGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.29
Consensus pattern (21 bp):
TAACTTGGTGACGTGGGACTA
Found at i:515830 original size:42 final size:42
Alignment explanation
Indices: 515751--515851 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
515741 CTGTGGATTG
* * * * *
515751 TAACTTGGAGAGGTAGGACTATAGCTTGGTGACGTGGGACTA
1 TAACTTGGTGAGGTAGGACTATACCCTGGAGAAGTGGGACTA
* * *
515793 TAACTTGGTGAGGTTGGACTGTACCCTGGAGAAGTGGGGCTA
1 TAACTTGGTGAGGTAGGACTATACCCTGGAGAAGTGGGACTA
*
515835 TAAGC-TGGTGAAGTAGG
1 TAA-CTTGGTGAGGTAGG
515852 GCTGTATGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.26
Consensus pattern (42 bp):
TAACTTGGTGAGGTAGGACTATACCCTGGAGAAGTGGGACTA
Found at i:515847 original size:21 final size:21
Alignment explanation
Indices: 515818--516082 Score: 108
Period size: 21 Copynumber: 12.6 Consensus size: 21
515808 GGACTGTACC
*
515818 CTGGAGAAGTGGGGCTATAAG
1 CTGGTGAAGTGGGGCTATAAG
* * *
515839 CTGGTGAAGTAGGGCTGTATG
1 CTGGTGAAGTGGGGCTATAAG
* * * *
515860 ATGGAGATGTGGGGCTATAGG
1 CTGGTGAAGTGGGGCTATAAG
** * * *
515881 AGGGTGAGGTTGGGCTGTAAG
1 CTGGTGAAGTGGGGCTATAAG
** * * * * *
515902 AAGGAGATGTAGGGCTGTATG
1 CTGGTGAAGTGGGGCTATAAG
* * * * * *
515923 ATGGGGATGTTGGGCTGTATG
1 CTGGTGAAGTGGGGCTATAAG
* * *
515944 ATGGAGAAGTGGGGCTATATG
1 CTGGTGAAGTGGGGCTATAAG
* * *
515965 CGGGTGAAGTGGGGCTGTATG
1 CTGGTGAAGTGGGGCTATAAG
*
515986 CTGGTGAAGTTGGGCTATATA-
1 CTGGTGAAGTGGGGCTATA-AG
* *
516007 CGGGTGAAGTGGGGCTGT-AG
1 CTGGTGAAGTGGGGCTATAAG
* *
516027 CTAGGTGAAGTTGGACTAT-AG
1 CT-GGTGAAGTGGGGCTATAAG
*
516048 CTGG-GAGATGTGGGACTATAA-
1 CTGGTGA-A-GTGGGGCTATAAG
516069 CTTGGTGAAGTGGG
1 C-TGGTGAAGTGGG
516083 ACTGTAACTT
Statistics
Matches: 192, Mismatches: 44, Indels: 16
0.76 0.17 0.06
Matches are distributed among these distances:
19 3 0.02
20 4 0.02
21 178 0.93
22 5 0.03
23 2 0.01
ACGTcount: A:0.22, C:0.08, G:0.45, T:0.26
Consensus pattern (21 bp):
CTGGTGAAGTGGGGCTATAAG
Found at i:515857 original size:42 final size:42
Alignment explanation
Indices: 515819--516025 Score: 202
Period size: 42 Copynumber: 4.9 Consensus size: 42
515809 GACTGTACCC
* *
515819 TGGAGAAGTGGGGCTATAAGCTGGTGAAGTAGGGCTGTATGA
1 TGGAGAAGTGGGGCTATAAGCGGGTGAAGTTGGGCTGTATGA
* * * * *
515861 TGGAGATGTGGGGCTATAGGAGGGTGAGGTTGGGCTGTAAGA
1 TGGAGAAGTGGGGCTATAAGCGGGTGAAGTTGGGCTGTATGA
* * * * * * *
515903 AGGAGATGTAGGGCTGTATGATGGG-GATGTTGGGCTGTATGA
1 TGGAGAAGTGGGGCTATAAG-CGGGTGAAGTTGGGCTGTATGA
* * *
515945 TGGAGAAGTGGGGCTATATGCGGGTGAAGTGGGGCTGTATGC
1 TGGAGAAGTGGGGCTATAAGCGGGTGAAGTTGGGCTGTATGA
* * *
515987 TGGTGAAGTTGGGCTATATA-CGGGTGAAGTGGGGCTGTA
1 TGGAGAAGTGGGGCTATA-AGCGGGTGAAGTTGGGCTGTA
516026 GCTAGGTGAA
Statistics
Matches: 137, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
41 3 0.02
42 131 0.96
43 3 0.02
ACGTcount: A:0.22, C:0.07, G:0.46, T:0.26
Consensus pattern (42 bp):
TGGAGAAGTGGGGCTATAAGCGGGTGAAGTTGGGCTGTATGA
Found at i:515888 original size:84 final size:84
Alignment explanation
Indices: 515799--516025 Score: 231
Period size: 84 Copynumber: 2.7 Consensus size: 84
515789 ACTATAACTT
* ** *
515799 GGTGAGGTTGGACTGTACCCTGGAGAAGTGGGGCTATAAGCTGGTGAAGTAGGGCTGTATGATGG
1 GGTGAGGTTGGGCTGTAAGCTGGAGAAGTAGGGCTATAAGCTGGTGAAGTAGGGCTGTATGATGG
*
515864 AGATGTGGGGCTATAGGAG
66 AGAAGTGGGGCTATAGGAG
** * * * * * * *
515883 GGTGAGGTTGGGCTGTAAGAAGGAGATGTAGGGCTGTATGATGGGGATGTTGGGCTGTATGATGG
1 GGTGAGGTTGGGCTGTAAGCTGGAGAAGTAGGGCTATAAGCTGGTGAAGTAGGGCTGTATGATGG
* *
515948 AGAAGTGGGGCTATATGCG
66 AGAAGTGGGGCTATAGGAG
* * * * * * *
515967 GGTGAAGTGGGGCTGTATGCTGGTGAAGTTGGGCTATATA-CGGGTGAAGTGGGGCTGTA
1 GGTGAGGTTGGGCTGTAAGCTGGAGAAGTAGGGCTATA-AGCTGGTGAAGTAGGGCTGTA
516026 GCTAGGTGAA
Statistics
Matches: 111, Mismatches: 31, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
84 111 1.00
ACGTcount: A:0.21, C:0.08, G:0.45, T:0.26
Consensus pattern (84 bp):
GGTGAGGTTGGGCTGTAAGCTGGAGAAGTAGGGCTATAAGCTGGTGAAGTAGGGCTGTATGATGG
AGAAGTGGGGCTATAGGAG
Found at i:516016 original size:63 final size:62
Alignment explanation
Indices: 515823--516037 Score: 207
Period size: 63 Copynumber: 3.4 Consensus size: 62
515813 GTACCCTGGA
* * *
515823 GAAGTGGGGCTATAAGCTGGTGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATAGGAGGGT
1 GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTTGGGCTATA-TAGGGT
* * * * * * * * * *
515886 GAGGTTGGGCTGTAAGAAGGAGATGTAGGGCTGTATGATGGGGATGTTGGGCTGTATGATGGA
1 GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTTGGGCTATAT-AGGGT
* * * * * *
515949 GAAGTGGGGCTATATGCGGGTGAAGTGGGGCTGTATGCTGGTGAAGTTGGGCTATATACGGGT
1 GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTTGGGCTATATA-GGGT
*
516012 GAAGTGGGGCTGT-AGCTAGGTGAAGT
1 GAAGTGGGGCTATAAGC-AGGTGAAGT
516038 TGGACTATAG
Statistics
Matches: 118, Mismatches: 31, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
62 3 0.03
63 115 0.97
ACGTcount: A:0.22, C:0.07, G:0.46, T:0.26
Consensus pattern (62 bp):
GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTTGGGCTATATAGGGT
Found at i:516034 original size:42 final size:42
Alignment explanation
Indices: 515934--516046 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 42
515924 TGGGGATGTT
* * * *
515934 GGGCTGTATGATGGAGAAGTGGGGCTATATGCGGGTGAAGTG
1 GGGCTGTATGCTGGTGAAGTTGGGCTATATACGGGTGAAGTG
515976 GGGCTGTATGCTGGTGAAGTTGGGCTATATACGGGTGAAGTG
1 GGGCTGTATGCTGGTGAAGTTGGGCTATATACGGGTGAAGTG
*
516018 GGGCTGTA-GCTAGGTGAAGTTGGACTATA
1 GGGCTGTATGCT-GGTGAAGTTGGGCTATA
516047 GCTGGGAGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 3 0.05
42 62 0.95
ACGTcount: A:0.21, C:0.09, G:0.43, T:0.27
Consensus pattern (42 bp):
GGGCTGTATGCTGGTGAAGTTGGGCTATATACGGGTGAAGTG
Found at i:516061 original size:42 final size:41
Alignment explanation
Indices: 515973--516109 Score: 132
Period size: 42 Copynumber: 3.3 Consensus size: 41
515963 TGCGGGTGAA
* * *
515973 GTGGGGCTGTATGCTGGTGAAGTTGGGCTATATAC-GGGTGAA
1 GTGGGGCTGTA-GCTGGTGAAGTTGGACTATA-ACTGGGAGAT
*
516015 GTGGGGCTGTAGCTAGGTGAAGTTGGACTATAGCTGGGAGAT
1 GTGGGGCTGTAGCT-GGTGAAGTTGGACTATAACTGGGAGAT
* * * * * *
516057 GTGGGACTATAACTTGGTGAAGTGGGACTGTAACTTGGAGAT
1 GTGGGGCTGTAGC-TGGTGAAGTTGGACTATAACTGGGAGAT
*
516099 GTAGGGCTGTA
1 GTGGGGCTGTA
516110 ACTTGGAGAG
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
41 4 0.05
42 73 0.94
43 1 0.01
ACGTcount: A:0.22, C:0.09, G:0.41, T:0.28
Consensus pattern (41 bp):
GTGGGGCTGTAGCTGGTGAAGTTGGACTATAACTGGGAGAT
Found at i:516083 original size:21 final size:21
Alignment explanation
Indices: 515987--516094 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
515977 GGCTGTATGC
515987 TGGTGAAGTTGGG-CTATATAC-
1 TGGTGAAG-TGGGACTATA-ACT
* * * *
516008 GGGTGAAGTGGGGCTGTAGCT
1 TGGTGAAGTGGGACTATAACT
* * *
516029 AGGTGAAGTTGGACTATAGCT
1 TGGTGAAGTGGGACTATAACT
* * *
516050 GGGAGATGTGGGACTATAACT
1 TGGTGAAGTGGGACTATAACT
*
516071 TGGTGAAGTGGGACTGTAACT
1 TGGTGAAGTGGGACTATAACT
516092 TGG
1 TGG
516095 AGATGTAGGG
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 5 0.07
21 64 0.93
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.28
Consensus pattern (21 bp):
TGGTGAAGTGGGACTATAACT
Found at i:516108 original size:21 final size:21
Alignment explanation
Indices: 516051--516118 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
516041 ACTATAGCTG
*
516051 GGAGATGTGGGACTATAACTT
1 GGAGATGTGGGACTGTAACTT
* *
516072 GGTGAAGTGGGACTGTAACTT
1 GGAGATGTGGGACTGTAACTT
516093 GGAGATGTAGGG-CTGTAACTT
1 GGAGATGT-GGGACTGTAACTT
516114 GGAGA
1 GGAGA
516119 GGTAGGGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 38 0.93
22 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.38, T:0.26
Consensus pattern (21 bp):
GGAGATGTGGGACTGTAACTT
Found at i:516123 original size:21 final size:21
Alignment explanation
Indices: 516066--516130 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
516056 TGTGGGACTA
*
516066 TAACTTGGTGAAGT-GGGACTG
1 TAACTTGGAGAAGTAGGG-CTG
*
516087 TAACTTGGAGATGTAGGGCTG
1 TAACTTGGAGAAGTAGGGCTG
*
516108 TAACTTGGAGAGGTAGGGCTG
1 TAACTTGGAGAAGTAGGGCTG
516129 TA
1 TA
516131 GCTCGGTGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 37 0.93
22 3 0.08
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.28
Consensus pattern (21 bp):
TAACTTGGAGAAGTAGGGCTG
Found at i:516130 original size:42 final size:42
Alignment explanation
Indices: 516033--516118 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
516023 GTAGCTAGGT
* * * * *
516033 GAAGTTGGACTATAGCTGGGAGATGTGGGACTATAACTTGGT
1 GAAGTGGGACTGTAACTTGGAGATGTGGGACTATAACTTGGA
*
516075 GAAGTGGGACTGTAACTTGGAGATGTAGGG-CTGTAACTTGGA
1 GAAGTGGGACTGTAACTTGGAGATGT-GGGACTATAACTTGGA
516117 GA
1 GA
516119 GGTAGGGCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 34 0.92
43 3 0.08
ACGTcount: A:0.27, C:0.09, G:0.37, T:0.27
Consensus pattern (42 bp):
GAAGTGGGACTGTAACTTGGAGATGTGGGACTATAACTTGGA
Found at i:516141 original size:21 final size:21
Alignment explanation
Indices: 516084--516142 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
516074 TGAAGTGGGA
* *
516084 CTGTAACTTGGAGATGTAGGG
1 CTGTAACTCGGAGAGGTAGGG
*
516105 CTGTAACTTGGAGAGGTAGGG
1 CTGTAACTCGGAGAGGTAGGG
* *
516126 CTGTAGCTCGGTGAGGT
1 CTGTAACTCGGAGAGGT
516143 CGGAGAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.41, T:0.27
Consensus pattern (21 bp):
CTGTAACTCGGAGAGGTAGGG
Found at i:516249 original size:21 final size:21
Alignment explanation
Indices: 516234--516309 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
516224 TGTGGGGCTG
*
516234 TACCCAGGAGAGGTGGGACTA
1 TACCCAGGAGAGGTAGGACTA
*
516255 TACCCAGGAGATGTAGGACTA
1 TACCCAGGAGAGGTAGGACTA
* *
516276 TAACCAGGAGAGGTAGGACTG
1 TACCCAGGAGAGGTAGGACTA
* *
516297 TAGCCAGGGGAGG
1 TACCCAGGAGAGG
516310 ATGGACTGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.38, T:0.14
Consensus pattern (21 bp):
TACCCAGGAGAGGTAGGACTA
Found at i:516315 original size:21 final size:21
Alignment explanation
Indices: 516270--516349 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
516260 AGGAGATGTA
* *
516270 GGACTATAACCAGGAGAGG-T
1 GGACTGTAACCAGGGGAGGAT
*
516290 AGGACTGTAGCCAGGGGAGGAT
1 -GGACTGTAACCAGGGGAGGAT
* * * *
516312 GGACTGTATCCTGGAGATGAT
1 GGACTGTAACCAGGGGAGGAT
*
516333 GGGCTGTAACCAGGGGA
1 GGACTGTAACCAGGGGA
516350 CGACGTAGGA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
21 46 0.98
22 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.40, T:0.17
Consensus pattern (21 bp):
GGACTGTAACCAGGGGAGGAT
Found at i:522184 original size:223 final size:223
Alignment explanation
Indices: 521796--522235 Score: 745
Period size: 223 Copynumber: 2.0 Consensus size: 223
521786 AAAAATAGCT
* * *
521796 ATGAAGCCAAATATCACTCACTACCCCAATTGTAAATATTGCCCGCTCATAACATAAACGATTAA
1 ATGAAGCCAAATATCAATCACTACCCCAATTGTAAATATTGCCCACTCAGAACATAAACGATTAA
*
521861 AACATGCCTTTCCTTTTGTATGCTTCATGTTCACTTTCAATTACTTCAAAATATCATATCAAACA
66 AACATGCCTTTCCTTTTGTATGCTTCAAGTTCACTTTCAATTACTTCAAAATATCATATCAAACA
*
521926 ACACGCAAGTTACTGCACTCCTTCACACATAGTTATGCTCTTTGCATTATATGGAAACTAATAAT
131 ACACACAAGTTACTGCACTCCTTCACACATAGTTATGCTCTTTGCATTATATGGAAACTAATAAT
*
521991 CCAGAACCGGAAAAATGCTATCTATCCA
196 CCACAACCGGAAAAATGCTATCTATCCA
522019 ATGAAGCCAAATATCAATCACTACCCCAATTGTAAATATTGCCCACTCAGAACATAAACGATTAA
1 ATGAAGCCAAATATCAATCACTACCCCAATTGTAAATATTGCCCACTCAGAACATAAACGATTAA
*
522084 AACATGCCTTTCCTTTTGTATGCTTCAAGTTCACTTTCAATTACTTCAAAATATCATATCATACA
66 AACATGCCTTTCCTTTTGTATGCTTCAAGTTCACTTTCAATTACTTCAAAATATCATATCAAACA
* * * * *
522149 ACCCATAAGTTACTGCACTCCTTCACACGTAGTTATGCTCTTTGCGTTATATGGAAACTAATAGT
131 ACACACAAGTTACTGCACTCCTTCACACATAGTTATGCTCTTTGCATTATATGGAAACTAATAAT
* **
522214 CCACATCCGGAATCATGCTATC
196 CCACAACCGGAAAAATGCTATC
522236 CAATGATAAC
Statistics
Matches: 202, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
223 202 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (223 bp):
ATGAAGCCAAATATCAATCACTACCCCAATTGTAAATATTGCCCACTCAGAACATAAACGATTAA
AACATGCCTTTCCTTTTGTATGCTTCAAGTTCACTTTCAATTACTTCAAAATATCATATCAAACA
ACACACAAGTTACTGCACTCCTTCACACATAGTTATGCTCTTTGCATTATATGGAAACTAATAAT
CCACAACCGGAAAAATGCTATCTATCCA
Found at i:539895 original size:15 final size:15
Alignment explanation
Indices: 539871--539912 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
539861 TTTTTATATT
*
539871 TAATAAAAATATAAAA
1 TAATATAAATA-AAAA
539887 TAAT-TAAATAAAAA
1 TAATATAAATAAAAA
*
539901 TTATATAAATAA
1 TAATATAAATAA
539913 CTTCACTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAATATAAATAAAAA
Found at i:542554 original size:3 final size:3
Alignment explanation
Indices: 542546--542577 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
542536 CTTTTGAAAC
542546 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
542578 TCATTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:545724 original size:6 final size:6
Alignment explanation
Indices: 545708--545741 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
545698 ATCAGACAAG
*
545708 GAAAAA TAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
545742 CCCTTTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:546076 original size:29 final size:29
Alignment explanation
Indices: 546017--546073 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
546007 ATTATTTTAT
*
546017 ATTTTATATTTAAAATATATTAAAATAAA
1 ATTTTATATTTAAAATATATAAAAATAAA
*
546046 ATTTTAT-TTT-AATTATATAAAAATAAA
1 ATTTTATATTTAAAATATATAAAAATAAA
546073 A
1 A
546074 AATAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.62
28 3 0.12
29 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTTATATTTAAAATATATAAAAATAAA
Found at i:550078 original size:15 final size:15
Alignment explanation
Indices: 550058--550087 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
550048 TCATCAAACT
550058 AGAGGAAGAAGAAGA
1 AGAGGAAGAAGAAGA
*
550073 AGAGGAAGGAGAAGA
1 AGAGGAAGAAGAAGA
550088 CTAAAGATCA
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:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
AGAGGAAGAAGAAGA
Found at i:551328 original size:2 final size:2
Alignment explanation
Indices: 551321--551347 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
551311 ACTCCTTAAC
551321 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
551348 GATTTCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:565364 original size:16 final size:16
Alignment explanation
Indices: 565310--565364 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
565300 GTTTTTATTT
565310 TTAACATAAAAATATA
1 TTAACATAAAAATATA
*
565326 TTATA-A-AAAAATAAATT
1 TTA-ACATAAAAAT--ATA
565343 TTAACATAAAAATATA
1 TTAACATAAAAATATA
565359 TTAACA
1 TTAACA
565365 ATCAAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 6 0.19
16 13 0.41
17 7 0.22
18 6 0.19
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAACATAAAAATATA
Found at i:574351 original size:2 final size:2
Alignment explanation
Indices: 574344--574389 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
574334 TCAGTAATCC
574344 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
574386 CT CT
1 CT CT
574390 GTGTCTTGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:600687 original size:2 final size:2
Alignment explanation
Indices: 600682--600716 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
600672 AGGAAAAATA
* *
600682 AG AG AG AG AA AG AG TG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
600717 AGCAGAGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:603748 original size:8 final size:8
Alignment explanation
Indices: 603737--603773 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
603727 ATTTGTGTTC
603737 TAAGTACA
1 TAAGTACA
603745 TAAGTACA
1 TAAGTACA
603753 TAAGTAC-
1 TAAGTACA
*
603760 -CAGTACA
1 TAAGTACA
603767 TAAGTAC
1 TAAGTAC
603774 TGGATCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
6 5 0.20
8 20 0.80
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (8 bp):
TAAGTACA
Found at i:603766 original size:14 final size:14
Alignment explanation
Indices: 603747--603773 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
603737 TAAGTACATA
603747 AGTACATAAGTACC
1 AGTACATAAGTACC
603761 AGTACATAAGTAC
1 AGTACATAAGTAC
603774 TGGATCACTT
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:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (14 bp):
AGTACATAAGTACC
Found at i:603845 original size:1 final size:1
Alignment explanation
Indices: 603839--603869 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
603829 TCTCCCGGCG
*
603839 CCCCCCCCCCCCCCCCCCCCGCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
603870 GNNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:603870 original size:11 final size:11
Alignment explanation
Indices: 603837--603870 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
603827 TCTCTCCCGG
603837 CGCCCCCCCCC
1 CGCCCCCCCCC
603848 C-CCCCCCCCC
1 CGCCCCCCCCC
603858 CGCCCCCCCCC
1 CGCCCCCCCCC
603869 CG
1 CG
603871 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.91, G:0.09, T:0.00
Consensus pattern (11 bp):
CGCCCCCCCCC
Found at i:604713 original size:20 final size:20
Alignment explanation
Indices: 604677--604714 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
604667 GGAGCATCGC
*
604677 TTTCTAGAGATGTTCTTTGA
1 TTTCTAAAGATGTTCTTTGA
604697 TTTCTAAAG-TGTGTCTTT
1 TTTCTAAAGATGT-TCTTT
604715 CTCCTTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCTAAAGATGTTCTTTGA
Found at i:606120 original size:2 final size:2
Alignment explanation
Indices: 606113--606137 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
606103 TAAATTCATA
606113 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
606138 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:606299 original size:2 final size:2
Alignment explanation
Indices: 606292--606316 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
606282 TTAACTACTA
606292 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
606317 CATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:609760 original size:29 final size:30
Alignment explanation
Indices: 609734--609788 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
609724 GTTTTTCTCT
* *
609734 TTTA-TTAT-TATTTATTATTTTTATTCTA
1 TTTATTTATATATTCATAATTTTTATTCTA
609762 TTTATTTATATATTCATAATTTTTATT
1 TTTATTTATATATTCATAATTTTTATT
609789 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 15 0.65
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (30 bp):
TTTATTTATATATTCATAATTTTTATTCTA
Found at i:615192 original size:6 final size:6
Alignment explanation
Indices: 615181--615207 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
615171 ACCATGTTGT
615181 TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TAT
615208 ATTTTATGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:615850 original size:34 final size:35
Alignment explanation
Indices: 615798--615878 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
615788 AACTTGTAAT
* * * *
615798 ATTATTTAAGTTGTTATTTG-GATATTTATTTTT-
1 ATTATTTAAATTGATATTTGAGAGAGTTATTTTTG
*
615831 AGTTATTTAAATTGATATTTGAGAGAGTTGTTTTTG
1 A-TTATTTAAATTGATATTTGAGAGAGTTATTTTTG
615867 ATTATTTAAATT
1 ATTATTTAAATT
615879 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 1 0.03
34 17 0.43
35 21 0.52
36 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (35 bp):
ATTATTTAAATTGATATTTGAGAGAGTTATTTTTG
Found at i:619574 original size:4 final size:4
Alignment explanation
Indices: 619565--619589 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
619555 CAACTCTCCT
619565 CCTC CCTC CCTC CCTC CCTC CCTC C
1 CCTC CCTC CCTC CCTC CCTC CCTC C
619590 AATTTTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CCTC
Found at i:625700 original size:48 final size:48
Alignment explanation
Indices: 625629--625727 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
625619 TAAAGGCTTG
*
625629 ATATCTATTATCTTTGACAATATCAATAAACATGAAATCAGAGGCATT
1 ATATCGATTATCTTTGACAATATCAATAAACATGAAATCAGAGGCATT
625677 ATATCGATTATCTTTGACAATATCAATAAACATGAAATCAGAGGCATT
1 ATATCGATTATCTTTGACAATATCAATAAACATGAAATCAGAGGCATT
625725 ATA
1 ATA
625728 CAAAATATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (48 bp):
ATATCGATTATCTTTGACAATATCAATAAACATGAAATCAGAGGCATT
Found at i:657556 original size:68 final size:68
Alignment explanation
Indices: 657443--657579 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
657433 CATTGGTCAG
* * * *
657443 ACATCTCAAACAAATAGCACTTTTCTTGGGCCTTATCCTGTCACGTGCCAGGACTTGGACTCAAT
1 ACATCTCAAACAAATAGCACTTTTCTTCGGCCTTATCCTGCCACGTGCCAGGACTTGAACCCAAT
657508 TCC
66 TCC
*
657511 ACATCTCAAACAAATAGCACTTTTCTTCGGCTTTATCCTGCCACGTGCCAGGACTTGAACCCAAT
1 ACATCTCAAACAAATAGCACTTTTCTTCGGCCTTATCCTGCCACGTGCCAGGACTTGAACCCAAT
657576 TCC
66 TCC
657579 A
1 A
657580 TTCGGTCTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (68 bp):
ACATCTCAAACAAATAGCACTTTTCTTCGGCCTTATCCTGCCACGTGCCAGGACTTGAACCCAAT
TCC
Found at i:660895 original size:23 final size:23
Alignment explanation
Indices: 660851--660895 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
660841 CAGTGCAATA
*
660851 ATTTATAAAATTTAAATCTTTAC
1 ATTTATAAAATTAAAATCTTTAC
*
660874 ATTTCTAAAATTAATAAT-TTTA
1 ATTTATAAAATTAA-AATCTTTA
660896 ATTAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTATAAAATTAAAATCTTTAC
Found at i:660976 original size:21 final size:19
Alignment explanation
Indices: 660925--660976 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
660915 AAAATTTTTT
*
660925 TATTATTTATATTGATATAA
1 TATT-TTTATATTGACATAA
660945 TATTTGATTATATTGACATGATA
1 TATTT--TTATATTGACAT-A-A
660968 TATTTTTAT
1 TATTTTTAT
660977 TGGGGGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 4 0.15
21 15 0.56
22 1 0.04
23 6 0.22
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (19 bp):
TATTTTTATATTGACATAA
Found at i:661621 original size:2 final size:2
Alignment explanation
Indices: 661614--661639 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
661604 ATTCACAAAC
661614 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
661640 TAAATCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:693277 original size:34 final size:34
Alignment explanation
Indices: 693237--693302 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
693227 TTTCCCTCCA
* **
693237 TCTTTGTCTTTTTGGGCCGATTTGTTCCCTCATC
1 TCTTTGTCTTTTTGGGCCAATTCCTTCCCTCATC
693271 TCTTTGTCTTTTTGGGCCAATTCCTTCCCTCA
1 TCTTTGTCTTTTTGGGCCAATTCCTTCCCTCA
693303 CCGTCCCTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.08, C:0.29, G:0.15, T:0.48
Consensus pattern (34 bp):
TCTTTGTCTTTTTGGGCCAATTCCTTCCCTCATC
Found at i:705748 original size:118 final size:118
Alignment explanation
Indices: 705540--705775 Score: 436
Period size: 118 Copynumber: 2.0 Consensus size: 118
705530 ATAAAAACAA
* *
705540 ACACATCATCAGATTCAACAATCCAATACCTTCCACGTTGGTTCCCCCATGATATGATAGTCATG
1 ACACATCATCAGATTCAACAATCCAATACCTTCCACGTTGGCTACCCCATGATATGATAGTCATG
705605 CTGCATGCTAAATGGCATAGAGCCCCGGACGTGCATCCCAGATGGCAGAGGTT
66 CTGCATGCTAAATGGCATAGAGCCCCGGACGTGCATCCCAGATGGCAGAGGTT
* *
705658 ACACATCATCAGATTCAACAATCGAATACCTTCCACGTTGGCTACCCCATGATTTGATAGTCATG
1 ACACATCATCAGATTCAACAATCCAATACCTTCCACGTTGGCTACCCCATGATATGATAGTCATG
705723 CTGCATGCTAAATGGCATAGAGCCCCGGACGTGCATCCCAGATGGCAGAGGTT
66 CTGCATGCTAAATGGCATAGAGCCCCGGACGTGCATCCCAGATGGCAGAGGTT
705776 TGCGTGCGCA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (118 bp):
ACACATCATCAGATTCAACAATCCAATACCTTCCACGTTGGCTACCCCATGATATGATAGTCATG
CTGCATGCTAAATGGCATAGAGCCCCGGACGTGCATCCCAGATGGCAGAGGTT
Found at i:706994 original size:33 final size:33
Alignment explanation
Indices: 706952--707017 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
706942 TCGTGTCTCT
*
706952 TTCTTAATTTGGAAGGTGGGTCAGAATAAGAGG
1 TTCTTAATTTGGAAGGTGAGTCAGAATAAGAGG
706985 TTCTTAATTTGGAAGGTGAGTCAGAATAAGAGG
1 TTCTTAATTTGGAAGGTGAGTCAGAATAAGAGG
707018 AGAGGCTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (33 bp):
TTCTTAATTTGGAAGGTGAGTCAGAATAAGAGG
Found at i:707269 original size:21 final size:23
Alignment explanation
Indices: 707220--707270 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
707210 TCAGTGGCTT
**
707220 GTTCCTTAAGATATTAGTTGCTC
1 GTTCCTTAAGATATTAGTTGCAA
707243 GTTCCTTAAGATATTAG-TG-AA
1 GTTCCTTAAGATATTAGTTGCAA
707264 GTTCCTT
1 GTTCCTT
707271 GCCCTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 2 0.08
23 17 0.65
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (23 bp):
GTTCCTTAAGATATTAGTTGCAA
Found at i:724519 original size:13 final size:12
Alignment explanation
Indices: 724498--724528 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
724488 AAATTATGCG
724498 AATTTATTATAT
1 AATTTATTATAT
724510 AATTTGATTATAT
1 AATTT-ATTATAT
724523 AATTTA
1 AATTTA
724529 ATTCATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
AATTTATTATAT
Found at i:732357 original size:18 final size:19
Alignment explanation
Indices: 732330--732367 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
732320 CAATAGGGAC
732330 ATTTTGTCCC-C-ACTGCT
1 ATTTTGTCCCTCAACTGCT
732347 ATTTATGTCCCTCAACTGCT
1 ATTT-TGTCCCTCAACTGCT
732367 A
1 A
732368 GACTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 1 0.06
20 7 0.39
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (19 bp):
ATTTTGTCCCTCAACTGCT
Found at i:736284 original size:57 final size:57
Alignment explanation
Indices: 736215--736508 Score: 560
Period size: 57 Copynumber: 5.2 Consensus size: 57
736205 GTTTTAAAGG
736215 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736272 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736329 ATAGGATGTTGTAGGATTGGA-T-GA-TCT-AAGTGATTTTGTAGATTCAGCTCAGC
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736382 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736439 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736496 ATAGGATGTTGTA
1 ATAGGATGTTGTA
736509 TTCATCTAGA
Statistics
Matches: 233, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
53 47 0.20
54 4 0.02
55 4 0.02
56 4 0.02
57 174 0.75
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (57 bp):
ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
Found at i:736412 original size:110 final size:114
Alignment explanation
Indices: 736215--736508 Score: 560
Period size: 110 Copynumber: 2.6 Consensus size: 114
736205 GTTTTAAAGG
736215 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
736280 TTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
66 TTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736329 ATAGGATGTTGTAGGATTGGA-T-GA-TCT-AAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
736390 TTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
66 TTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
736439 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
1 ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
736504 TTGTA
66 TTGTA
736509 TTCATCTAGA
Statistics
Matches: 176, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
110 104 0.59
111 4 0.02
112 4 0.02
113 4 0.02
114 60 0.34
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (114 bp):
ATAGGATGTTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGCATAGGATG
TTGTAGGATTGGATTGGATTCTCAAGTGATTTTGTAGATTCAGCTCAGC
Found at i:759056 original size:2 final size:2
Alignment explanation
Indices: 759049--759131 Score: 118
Period size: 2 Copynumber: 41.5 Consensus size: 2
759039 TAAAACTCAT
759049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TNA -A CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA
759091 -A CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
759132 CTGCAACATG
Statistics
Matches: 75, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.04
2 70 0.93
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:763911 original size:132 final size:132
Alignment explanation
Indices: 763673--763937 Score: 467
Period size: 132 Copynumber: 2.0 Consensus size: 132
763663 CCAGGTGTTG
763673 AAATCAATAGCCATTACCAAACTAAAGGAAGGATACACCTGTATAACATAATTCATGAAACTAAA
1 AAATCAATAGCCATTACCAAACTAAAGGAAGGATACACCTGTATAACATAATTCATGAAACTAAA
* * * * *
763738 ATCCTGGCGATACTCAATCAAATTGACAACTATCATGACTAGACCCCTAAAGAAAGGCTGCACTT
66 ATCCTGGCCAGACTCAATCAAATTGACAACCATCATAACTAGACCACTAAAGAAAGGCTGCACTT
763803 CA
131 CA
*
763805 AAATCAATAGCCATTACCAAACTAAAGGAAGGATACACCTGTATACCATAATTCATGAAACTAAA
1 AAATCAATAGCCATTACCAAACTAAAGGAAGGATACACCTGTATAACATAATTCATGAAACTAAA
*
763870 ATCCTGGCCAGACTTAATCAAATTGACAACCATCATAACTAGACCACTAAAGAAAGGCTGCACTT
66 ATCCTGGCCAGACTCAATCAAATTGACAACCATCATAACTAGACCACTAAAGAAAGGCTGCACTT
763935 CA
131 CA
763937 A
1 A
763938 TTTCCAATCA
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 126 1.00
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (132 bp):
AAATCAATAGCCATTACCAAACTAAAGGAAGGATACACCTGTATAACATAATTCATGAAACTAAA
ATCCTGGCCAGACTCAATCAAATTGACAACCATCATAACTAGACCACTAAAGAAAGGCTGCACTT
CA
Found at i:775802 original size:18 final size:18
Alignment explanation
Indices: 775781--775820 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
775771 GTATATACGT
775781 TTAAACACGATAACACGA
1 TTAAACACGATAACACGA
*
775799 TTAAACATGATAACACGA
1 TTAAACACGATAACACGA
775817 TTAA
1 TTAA
775821 GTAAACGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (18 bp):
TTAAACACGATAACACGA
Found at i:778168 original size:2 final size:2
Alignment explanation
Indices: 778161--778188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
778151 TTTATAATTA
778161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
778189 TATTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:778613 original size:2 final size:2
Alignment explanation
Indices: 778606--778670 Score: 67
Period size: 2 Copynumber: 31.5 Consensus size: 2
778596 GTTCACCCTT
* * *
778606 TA TA TA TA TA TA TA AA CA TA TA TA TA CTT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
**
778649 TA TA TA GCG TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA T
778671 CTAATTTAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:778661 original size:23 final size:23
Alignment explanation
Indices: 778612--778670 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
778602 CCTTTATATA
* * *
778612 TATATATAAACATATATATACTT
1 TATATATATATATATATATACTG
778635 TATATATATATATATATATAGC-G
1 TATATATATATATATATATA-CTG
778658 TATATATATATAT
1 TATATATATATAT
778671 CTAATTTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (23 bp):
TATATATATATATATATATACTG
Found at i:782611 original size:2 final size:2
Alignment explanation
Indices: 782601--782631 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
782591 CAGGGAAAAA
*
782601 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
782632 AATAACTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:827975 original size:13 final size:13
Alignment explanation
Indices: 827959--828023 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 13
827949 ATAAGATATT
827959 ATAATTTAATTAA
1 ATAATTTAATTAA
* *
827972 ATAATAATATTTTATA
1 ATAAT-TTA-ATTA-A
827988 ATAATTTTAATTAA
1 ATAA-TTTAATTAA
828002 ATAATTT-ATATAA
1 ATAATTTAAT-TAA
*
828015 ATATTTTAA
1 ATAATTTAA
828024 CCCTCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
12 2 0.05
13 17 0.41
14 8 0.20
15 6 0.15
16 7 0.17
17 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATAATTTAATTAA
Found at i:827981 original size:24 final size:24
Alignment explanation
Indices: 827930--828004 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
827920 TTATAGTACC
* *
827930 ATATTATAATATAATTTTAATAAG
1 ATATTATAATATAATTTAAATAAA
*
827954 ATATTATAATTTAA-TTAAATAATA
1 ATATTATAATATAATTTAAATAA-A
* * *
827978 ATATT-TTATAATAATTTTAATTAA
1 ATATTATAAT-ATAATTTAAATAAA
828002 ATA
1 ATA
828005 ATTTATATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 10 0.24
24 25 0.61
25 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
ATATTATAATATAATTTAAATAAA
Found at i:827997 original size:26 final size:26
Alignment explanation
Indices: 827968--828023 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
827958 TATAATTTAA
*
827968 TTAAAT-AATAATATTTTAT-AATAATT
1 TTAAATAAATAAT-TTATATAAAT-ATT
*
827994 TTAATTAAATAATTTATATAAATATT
1 TTAAATAAATAATTTATATAAATATT
828020 TTAA
1 TTAA
828024 CCCTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAAATAAATAATTTATATAAATATT
Found at i:829581 original size:2 final size:2
Alignment explanation
Indices: 829574--829616 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
829564 TAAGTAGGAA
829574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
829616 A
1 A
829617 CGTGAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:830279 original size:10 final size:10
Alignment explanation
Indices: 830264--830298 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
830254 CTTTAAGTCC
830264 ATGTATATAT
1 ATGTATATAT
830274 ATG--TATAT
1 ATGTATATAT
830282 ATGTATATAT
1 ATGTATATAT
830292 ATGTATA
1 ATGTATA
830299 GAATCTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (10 bp):
ATGTATATAT
Found at i:830287 original size:18 final size:18
Alignment explanation
Indices: 830264--830298 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
830254 CTTTAAGTCC
830264 ATGTATATATATGTATAT
1 ATGTATATATATGTATAT
830282 ATGTATATATATGTATA
1 ATGTATATATATGTATA
830299 GAATCTCTTG
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:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
ATGTATATATATGTATAT
Found at i:832641 original size:174 final size:174
Alignment explanation
Indices: 832343--832733 Score: 611
Period size: 174 Copynumber: 2.2 Consensus size: 174
832333 AGAACACTTA
* *
832343 TTGGTACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCTGATTCTGATGGCACCTTG
1 TTGGTACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTC
*
832408 CATGACTGAGCTATTCCGGATCTTGTTGCTCATACCCTCTTTCCGATTAAGCTCCTCTTCTGCCT
66 CATGACTGAGCTATTCCGGATCTTGTTGCTCATACCCTCTTTCCGATTAAGCTCCTCTTCCGCCT
* * *
832473 GATCTCGTCTAGCTCTTCGTTCTTCAGTCACTGGAAAAAACTTC
131 GATCTCGTCTAGCTCTTCGATCTTCACTCACTGGAAAAAACCTC
** * * *
832517 TTGGTATGATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTGGGATTTTGATGGCAGCTTC
1 TTGGTACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTC
* *
832582 CATGACTGATCTATTCCGGATCTTGTTGCTCTTACCCTCTTTCCGATTAAGCTCCTCTTCCGCCT
66 CATGACTGAGCTATTCCGGATCTTGTTGCTCATACCCTCTTTCCGATTAAGCTCCTCTTCCGCCT
* *
832647 GTTTTCGTCTAGCTCTTCGATCTTCACTCACTGGAAAAAACCTC
131 GATCTCGTCTAGCTCTTCGATCTTCACTCACTGGAAAAAACCTC
*
832691 TTGGTACCATCAGCAGCTGATGAAGCGATTACCATGGCTGAGC
1 TTGGTACCATCAGCAG-T--TGAAGCGATTGCCATGGCTGAGC
832734 CAGGCATGGT
Statistics
Matches: 196, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
174 173 0.88
175 1 0.01
177 22 0.11
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (174 bp):
TTGGTACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTC
CATGACTGAGCTATTCCGGATCTTGTTGCTCATACCCTCTTTCCGATTAAGCTCCTCTTCCGCCT
GATCTCGTCTAGCTCTTCGATCTTCACTCACTGGAAAAAACCTC
Found at i:833661 original size:20 final size:20
Alignment explanation
Indices: 833638--833675 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
833628 AGAGTGTGTC
833638 GAAAACAAG-AACAAGAAAAG
1 GAAAAC-AGCAACAAGAAAAG
*
833658 GAAAGCAGCAACAAGAAA
1 GAAAACAGCAACAAGAAA
833676 GGTCTGCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.66, C:0.13, G:0.21, T:0.00
Consensus pattern (20 bp):
GAAAACAGCAACAAGAAAAG
Found at i:834520 original size:21 final size:21
Alignment explanation
Indices: 834483--834523 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
834473 AAGAAGAAGG
*
834483 AGAAGAAGTAGATGATGGAGA
1 AGAAGAAGTAGAAGATGGAGA
834504 AGAAGAAG-AGGAAGATGGAG
1 AGAAGAAGTA-GAAGATGGAG
834524 GATTGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.10
Consensus pattern (21 bp):
AGAAGAAGTAGAAGATGGAGA
Found at i:844720 original size:15 final size:15
Alignment explanation
Indices: 844700--844729 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
844690 CAATGCATTA
844700 TAAACAGAACCAAAC
1 TAAACAGAACCAAAC
844715 TAAACAGAACCAAAC
1 TAAACAGAACCAAAC
844730 AGCCAACCCA
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:0.60, C:0.27, G:0.07, T:0.07
Consensus pattern (15 bp):
TAAACAGAACCAAAC
Found at i:915822 original size:56 final size:56
Alignment explanation
Indices: 915755--915868 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 56
915745 AAGTGTGTAT
** *
915755 AAAGCATTGCTCACCTAAACCCTAATGCTTCACCCATTTTTGTTGATATAGCATAC
1 AAAGCATTGCTCACCTAAACCCTAACCCTTCACCCATTTTTGTTGATATAACATAC
* * *
915811 AAAGCATTGCTCACTTAAACCCTAACCCTTCACTCATTTTTGTTGATCTAACATAC
1 AAAGCATTGCTCACCTAAACCCTAACCCTTCACCCATTTTTGTTGATATAACATAC
915867 AA
1 AA
915869 TCGAGCCATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (56 bp):
AAAGCATTGCTCACCTAAACCCTAACCCTTCACCCATTTTTGTTGATATAACATAC
Found at i:916061 original size:33 final size:33
Alignment explanation
Indices: 916019--916084 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
916009 TAAGAATTAA
916019 AAAAATTTTAGATTATGATATTATGTTGTTGAG
1 AAAAATTTTAGATTATGATATTATGTTGTTGAG
* * *
916052 AAAAATTTTAGATTTTGATGTTCTGTTGTTGAG
1 AAAAATTTTAGATTATGATATTATGTTGTTGAG
916085 TTTTTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.47
Consensus pattern (33 bp):
AAAAATTTTAGATTATGATATTATGTTGTTGAG
Found at i:918404 original size:51 final size:51
Alignment explanation
Indices: 918320--918422 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
918310 ACTTTCTGAA
* * * *
918320 CTTTTTGGGTTGGAGTGAGCGTTTCATTTATCCGGAGACTGGCCTTTGGAC
1 CTTTTTGGGTTGGAGTGAGAGTTTCATTCATCCGGAAACTGGCCTTTAGAC
*
918371 CTTTTTGGGTTGGAGTGAGAGTTTGATTCATCCGGAAACTGGCCTTTAGAC
1 CTTTTTGGGTTGGAGTGAGAGTTTCATTCATCCGGAAACTGGCCTTTAGAC
918422 C
1 C
918423 CTATATCTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.36
Consensus pattern (51 bp):
CTTTTTGGGTTGGAGTGAGAGTTTCATTCATCCGGAAACTGGCCTTTAGAC
Found at i:928461 original size:18 final size:18
Alignment explanation
Indices: 928420--928455 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
928410 AATCAAAACA
928420 AAAAACTTTAATCAGATT
1 AAAAACTTTAATCAGATT
*
928438 AAAAAC-TTAATCCGATT
1 AAAAACTTTAATCAGATT
928455 A
1 A
928456 GCAAACCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAAACTTTAATCAGATT
Found at i:929988 original size:9 final size:9
Alignment explanation
Indices: 929971--930000 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
929961 ATATTTTTAT
929971 TTAATCGTG
1 TTAATCGTG
*
929980 TTAAACGTG
1 TTAATCGTG
929989 TTAATCGTG
1 TTAATCGTG
929998 TTA
1 TTA
930001 TTAATCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TTAATCGTG
Found at i:943651 original size:24 final size:24
Alignment explanation
Indices: 943623--943684 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
943613 GAAGCCTGTC
943623 AAGGAGAAGAAACCGAAAGCGCCG
1 AAGGAGAAGAAACCGAAAGCGCCG
**
943647 AAGGAGAAGAAACCGAAAGTTCCG
1 AAGGAGAAGAAACCGAAAGCGCCG
943671 AAGGAGAAGAAACC
1 AAGGAGAAGAAACC
943685 AAGACAGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.48, C:0.18, G:0.31, T:0.03
Consensus pattern (24 bp):
AAGGAGAAGAAACCGAAAGCGCCG
Found at i:943698 original size:24 final size:24
Alignment explanation
Indices: 943623--943698 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
943613 GAAGCCTGTC
943623 AAGGAGAAGAAACCGAA-AGC-GCCG
1 AAGGAGAAGAAACC-AAGA-CAGCCG
*
943647 AAGGAGAAGAAACC--GAAAGTTCCG
1 AAGGAGAAGAAACCAAGACAG--CCG
*
943671 AAGGAGAAGAAACCAAGACAGCCA
1 AAGGAGAAGAAACCAAGACAGCCG
943695 AAGG
1 AAGG
943699 CTGCTGCACA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
22 2 0.05
24 37 0.86
26 4 0.09
ACGTcount: A:0.49, C:0.18, G:0.30, T:0.03
Consensus pattern (24 bp):
AAGGAGAAGAAACCAAGACAGCCG
Found at i:945372 original size:53 final size:53
Alignment explanation
Indices: 945278--945378 Score: 121
Period size: 53 Copynumber: 1.9 Consensus size: 53
945268 AAATTTCATC
* * **
945278 TTTAATTGAATATTATACCTTTTCGAGTAAATTTTTTAATTCTAAATTTTGAT
1 TTTAATTGAATATTATACATTTTCGAGTAAACTTTCCAATTCTAAATTTTGAT
* ** * *
945331 TTTAATTGGATATTATACATTTTTTAGTAGACTTTCCAATTCTGAATT
1 TTTAATTGAATATTATACATTTTCGAGTAAACTTTCCAATTCTAAATT
945379 GACACCGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (53 bp):
TTTAATTGAATATTATACATTTTCGAGTAAACTTTCCAATTCTAAATTTTGAT
Found at i:945770 original size:13 final size:14
Alignment explanation
Indices: 945752--945790 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
945742 TTCATTAACT
945752 ATTTTAAA-TATAA
1 ATTTTAAATTATAA
*
945765 ATTTTAAATTTTAA
1 ATTTTAAATTATAA
*
945779 ATTTTAATTTAT
1 ATTTTAAATTAT
945791 TTTTATGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTTAAATTATAA
Found at i:945774 original size:7 final size:7
Alignment explanation
Indices: 945752--945785 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
945742 TTCATTAACT
945752 ATTTTAA
1 ATTTTAA
*
945759 A-TATAA
1 ATTTTAA
945765 ATTTTAA
1 ATTTTAA
945772 ATTTTAA
1 ATTTTAA
945779 ATTTTAA
1 ATTTTAA
945786 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATTTTAA
Found at i:946175 original size:24 final size:24
Alignment explanation
Indices: 946129--946183 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
946119 TTTTTAATAG
*
946129 TTTATTAAAAATATTATGAAATTA
1 TTTATTTAAAATATTATGAAATTA
* *
946153 -TTATTTAAAATTTTAATGTAATTA
1 TTTATTTAAAATATT-ATGAAATTA
946177 TTTATTT
1 TTTATTT
946184 TTATTTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.46
24 8 0.31
25 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTATTTAAAATATTATGAAATTA
Found at i:956533 original size:3 final size:3
Alignment explanation
Indices: 956525--956580 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
956515 CAGAAGCAAT
* *
956525 GAA GAA GAA GAA GACA -AA CGAA G-A GAA GGA GAA GGA GAA GAA GAA
1 GAA GAA GAA GAA GA-A GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA
956570 GAA GAA GAA GA
1 GAA GAA GAA GA
956581 TGAGCAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 39 0.87
4 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:959241 original size:29 final size:29
Alignment explanation
Indices: 959209--959267 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
959199 AATGTTGAGG
*
959209 CTCAACATGTAGGCTTAAACGTTCTACCA
1 CTCAACATGTAGGCTTAAACATTCTACCA
959238 CTCAACATGTAGGCTTAAACATTCTACCA
1 CTCAACATGTAGGCTTAAACATTCTACCA
959267 C
1 C
959268 ACCATGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (29 bp):
CTCAACATGTAGGCTTAAACATTCTACCA
Found at i:961002 original size:2 final size:2
Alignment explanation
Indices: 960997--961024 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
960987 TGGGGGGAAA
960997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
961025 TTTTCCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:998270 original size:24 final size:24
Alignment explanation
Indices: 998223--998267 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
998213 TTTTTTATTT
*
998223 TTAATTATTATTTTTAAAATTTAA
1 TTAATTATTATTATTAAAATTTAA
998247 TTAATT-TTATTATTAAAATTT
1 TTAATTATTATTATTAAAATTT
998268 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTAATTATTATTATTAAAATTTAA
Found at i:1006673 original size:18 final size:19
Alignment explanation
Indices: 1006640--1006677 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1006630 GAATCTTTGT
*
1006640 AACAAAAATGGGAGAAAAG
1 AACAAAAATGGAAGAAAAG
1006659 AACAAAAA-GGAAGAAAAG
1 AACAAAAATGGAAGAAAAG
1006677 A
1 A
1006678 CATGTAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.03
Consensus pattern (19 bp):
AACAAAAATGGAAGAAAAG
Found at i:1038439 original size:18 final size:19
Alignment explanation
Indices: 1038405--1038440 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1038395 AATTTTAAAT
1038405 TTTTTAATTTATATTATTA
1 TTTTTAATTTATATTATTA
*
1038424 TTTTTATTTTAT-TTATT
1 TTTTTAATTTATATTATT
1038441 CATATGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTAATTTATATTATTA
Found at i:1038586 original size:15 final size:16
Alignment explanation
Indices: 1038552--1038600 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1038542 GTCATATTTT
* *
1038552 TTTTATGTTATATAAA
1 TTTTATTTTTTATAAA
1038568 TTTTATTTTTTAT-AA
1 TTTTATTTTTTATAAA
* *
1038583 TTTTAATTTTTAAAAA
1 TTTTATTTTTTATAAA
1038599 TT
1 TT
1038601 AATAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTATTTTTTATAAA
Found at i:1038786 original size:18 final size:17
Alignment explanation
Indices: 1038765--1038847 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 17
1038755 AAAATAAAAA
1038765 ATTTTTAATTATATATAT
1 ATTTTTAATTAT-TATAT
*
1038783 ATTTTTAACTATT-TAT
1 ATTTTTAATTATTATAT
*
1038799 ATTTTATAAATTATAAAATTAT
1 ATTTT-T-AATTAT--TA-TAT
1038821 ATTTTT-ATTATTA-AT
1 ATTTTTAATTATTATAT
1038836 ATTTTT-ATTATT
1 ATTTTTAATTATT
1038848 GATTGAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
15 14 0.25
16 8 0.15
17 3 0.05
18 16 0.29
19 5 0.09
21 1 0.02
22 8 0.15
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAATTATTATAT
Found at i:1038837 original size:15 final size:15
Alignment explanation
Indices: 1038819--1038847 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1038809 TTATAAAATT
1038819 ATATTTTTATTATTA
1 ATATTTTTATTATTA
1038834 ATATTTTTATTATT
1 ATATTTTTATTATT
1038848 GATTGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTTTTATTATTA
Found at i:1046410 original size:4 final size:4
Alignment explanation
Indices: 1046397--1046449 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
1046387 ACACACACAC
* * * * *
1046397 ACAT ATAT ACAT ACAT ACAT ACAA ACAT ACAT ACAT AAAT ATAT ATAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1046445 ACAT A
1 ACAT A
1046450 TATAAAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:1046442 original size:2 final size:2
Alignment explanation
Indices: 1046435--1046498 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
1046425 ACATACATAA
* *
1046435 AT AT AT AT AT AC AT AT AT A- AA AT AT -T AT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1046473 AT -T AT AT AT TT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1046499 TTTTATATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
1 6 0.12
2 45 0.88
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1046452 original size:10 final size:10
Alignment explanation
Indices: 1046435--1046498 Score: 59
Period size: 9 Copynumber: 7.0 Consensus size: 10
1046425 ACATACATAA
1046435 ATATATATAT
1 ATATATATAT
*
1046445 ACATATATA-
1 ATATATATAT
*
1046454 AAATAT-TAT
1 ATATATATAT
1046463 AT-TATAT-T
1 ATATATATAT
1046471 ATAT-TATAT
1 ATATATATAT
*
1046480 ATTTATATA-
1 ATATATATAT
1046489 ATATATATAT
1 ATATATATAT
1046499 TTTTATATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
8 11 0.26
9 20 0.47
10 12 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:1046464 original size:20 final size:20
Alignment explanation
Indices: 1046423--1046495 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
1046413 ACATACAAAC
*
1046423 ATACATACAT-AAATATATAT
1 ATACATATATAAAATAT-TAT
1046443 ATACATATATAAAATATTAT
1 ATACATATATAAAATATTAT
* * *
1046463 ATTATATTATATTATATATTTAT
1 A-TACA-TATATAAAATA-TTAT
1046486 ATA-ATATATA
1 ATACATATATA
1046496 TATTTTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 18 0.41
21 10 0.23
22 11 0.25
23 5 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
ATACATATATAAAATATTAT
Found at i:1046466 original size:5 final size:5
Alignment explanation
Indices: 1046456--1046499 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
1046446 CATATATAAA
*
1046456 ATATT ATATT ATATT ATATT ATA-T AT-TT ATATA ATATAT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T ATATT
1046500 TTTATATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 6 0.18
5 24 0.71
6 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:1046500 original size:17 final size:17
Alignment explanation
Indices: 1046437--1046505 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
1046427 ATACATAAAT
**
1046437 ATATATATACATATATA
1 ATATATATATTTATATA
* *
1046454 AAATAT-TATATTATATT
1 ATATATATAT-TTATATA
1046471 ATATTATATATTTATATA
1 ATA-TATATATTTATATA
*
1046489 ATATATATATTTTTATA
1 ATATATATATTTATATA
1046506 TCACCTACCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
16 2 0.05
17 25 0.60
18 12 0.29
19 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATTTATATA
Found at i:1048400 original size:2 final size:2
Alignment explanation
Indices: 1048393--1048442 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1048383 NNNNNNNNNN
1048393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1048435 AT AT AT AT
1 AT AT AT AT
1048443 TTAGTGTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1059355 original size:69 final size:69
Alignment explanation
Indices: 1059268--1059405 Score: 172
Period size: 69 Copynumber: 2.0 Consensus size: 69
1059258 GATTTTATCT
* * *
1059268 ATAAAAAATAAAATAACTATAAAAAATCATTAAATATATGTTACCGTTAATTGA-TTGAAAATAA
1 ATAAAAAATAAAAAAACTATAAAAAATCATTAAATACATATTACCGTTAATTGATTTG-AAATAA
1059332 AAAAA
65 AAAAA
* * * *
1059337 ATAAACAAA-AAAAAAACTATTAGAGATCATTAAATACATATTACTGTTAATTGATTTGAAATAA
1 ATAAA-AAATAAAAAAACTATAAAAAATCATTAAATACATATTACCGTTAATTGATTTGAAATAA
*
1059401 GAAAA
65 AAAAA
1059406 TAATTGAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 53 0.90
70 6 0.10
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (69 bp):
ATAAAAAATAAAAAAACTATAAAAAATCATTAAATACATATTACCGTTAATTGATTTGAAATAAA
AAAA
Found at i:1059676 original size:3 final size:3
Alignment explanation
Indices: 1059670--1059696 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1059660 ATAATAATAA
1059670 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1059697 AAAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1060080 original size:106 final size:106
Alignment explanation
Indices: 1059861--1060177 Score: 553
Period size: 106 Copynumber: 3.0 Consensus size: 106
1059851 TGTCACAACG
* * *
1059861 ACAAGGTATAGGCTCCTAATGAACCAAGTCTCCTAATTCCAAACTAGCAAGCCAGCTAGCTAGCC
1 ACAAGGTACAGGCTCCTAATAAACCAAGTCTTCTAATTCCAAACTAGCAAGCCAGCTAG---G-C
1059926 CTCCATGGAGCTCAAAAGTCACCAAATTCTCTGGCACCCACAGCA
62 CTCCATGGAGCTCAAAAGTCACCAAATTCTCTGGCACCCACAGCA
1059971 ACAAGGTACAGGCTCCTAATAAACCAAGTCTTCTAATTCCAAACTAGCAAGCCAGCTAGGCCTCC
1 ACAAGGTACAGGCTCCTAATAAACCAAGTCTTCTAATTCCAAACTAGCAAGCCAGCTAGGCCTCC
1060036 ATGGAGCTCAAAAGTCACCAAATTCTCTGGCACCCACAGCA
66 ATGGAGCTCAAAAGTCACCAAATTCTCTGGCACCCACAGCA
*
1060077 ACAAGGTACAGGCTCCTAATAAACCAAGTCTTCTAATTCCAAACTAGCAAGCCAGCTAGCCCTCC
1 ACAAGGTACAGGCTCCTAATAAACCAAGTCTTCTAATTCCAAACTAGCAAGCCAGCTAGGCCTCC
*
1060142 ATGGAGCTCAAAAGTCAGCAAATTCTCTGGCACCCA
66 ATGGAGCTCAAAAGTCACCAAATTCTCTGGCACCCA
1060178 GTCTAGTGTC
Statistics
Matches: 202, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
106 145 0.72
107 1 0.00
110 56 0.28
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.19
Consensus pattern (106 bp):
ACAAGGTACAGGCTCCTAATAAACCAAGTCTTCTAATTCCAAACTAGCAAGCCAGCTAGGCCTCC
ATGGAGCTCAAAAGTCACCAAATTCTCTGGCACCCACAGCA
Found at i:1062368 original size:2 final size:2
Alignment explanation
Indices: 1062363--1062391 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1062353 ATATATATAT
1062363 GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1062392 CCATAAGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1063313 original size:27 final size:27
Alignment explanation
Indices: 1063280--1063439 Score: 84
Period size: 27 Copynumber: 6.0 Consensus size: 27
1063270 TATTAATATT
1063280 TAAATTATCAATTATTAATATTTAAAA
1 TAAATTATCAATTATTAATATTTAAAA
* * *
1063307 TAAATTATAAATTATTACTATATAAAAA
1 TAAATTATCAATTATTAATAT-TTAAAA
* * ** *
1063335 TAAA--ATAAATGA-GCATA-ATAAAA
1 TAAATTATCAATTATTAATATTTAAAA
* * *
1063358 TTTAAATT-T-TA-TA-TAAAATACTAATAA
1 --TAAATTATCAATTATTAATAT-TTAA-AA
* *
1063385 TGAAATTATCCATTATTAATATTTTAAA
1 T-AAATTATCAATTATTAATATTTAAAA
*
1063413 TAAATTAACAATTATTAATATTTAAAA
1 TAAATTATCAATTATTAATATTTAAAA
1063440 AATAAATAAA
Statistics
Matches: 98, Mismatches: 22, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
23 4 0.04
24 3 0.03
25 8 0.08
26 16 0.16
27 45 0.46
28 13 0.13
29 4 0.04
30 5 0.05
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTATCAATTATTAATATTTAAAA
Found at i:1063383 original size:106 final size:106
Alignment explanation
Indices: 1063253--1063449 Score: 281
Period size: 106 Copynumber: 1.9 Consensus size: 106
1063243 AATATTAATA
* * *
1063253 TTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTAAAATAAATTATA-A
1 TTAAATTATAAATAAAATACTAATAATGAAATTATCAATTATTAATATTTAAAATAAATTA-ACA
*
1063317 ATTATTACTATAT-AAAAATAAAATAAATGAGCATAATAAAAT
65 ATTATTAATATATAAAAAAT-AAATAAATGAGCATAATAAAAT
* * * *
1063359 TTAAATTTTATATAAAATACTAATAATGAAATTATCCATTATTAATATTTTAAATAAATTAACAA
1 TTAAATTATAAATAAAATACTAATAATGAAATTATCAATTATTAATATTTAAAATAAATTAACAA
*
1063424 TTATTAATATTTAAAAAATAAATAAA
66 TTATTAATATATAAAAAATAAATAAA
1063450 ATAAAAAATT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 1 0.01
106 73 0.91
107 6 0.08
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (106 bp):
TTAAATTATAAATAAAATACTAATAATGAAATTATCAATTATTAATATTTAAAATAAATTAACAA
TTATTAATATATAAAAAATAAATAAATGAGCATAATAAAAT
Found at i:1063449 original size:33 final size:31
Alignment explanation
Indices: 1063409--1063537 Score: 100
Period size: 33 Copynumber: 4.0 Consensus size: 31
1063399 ATTAATATTT
1063409 TAAATAAATTAACAATTATTAATATTTAAAAAA
1 TAAATAAATTAA-AA-TATTAATATTTAAAAAA
* * * * **
1063442 TAAATAAAATAAAAAATTAATCATAATAATATT
1 TAAATAAATTAAAATATTAAT-AT-TTAAAAAA
*
1063475 TAAATTAAA-TAAAATATTAATATTTTAAAATA
1 TAAA-TAAATTAAAATATTAATA-TTTAAAAAA
* * *
1063507 TTAA-AGATTAAATTATTAATATTTAAAAAA
1 TAAATAAATTAAAATATTAATATTTAAAAAA
1063537 T
1 T
1063538 CAAACAAAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
30 11 0.14
31 18 0.23
32 13 0.17
33 31 0.40
34 4 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (31 bp):
TAAATAAATTAAAATATTAATATTTAAAAAA
Found at i:1063532 original size:15 final size:16
Alignment explanation
Indices: 1063484--1063534 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
1063474 TTAAATTAAA
*
1063484 TAAAATATTAATATTT
1 TAAAATATTAATAGTT
*
1063500 TAAAATATTAA-AGAT
1 TAAAATATTAATAGTT
*
1063515 TAAATTATTAATA-TT
1 TAAAATATTAATAGTT
1063530 TAAAA
1 TAAAA
1063535 AATCAAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAAATATTAATAGTT
Found at i:1066023 original size:6 final size:6
Alignment explanation
Indices: 1066014--1066060 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
1066004 AGGAGGAAAT
* * *
1066014 GGTGGC GGTGGA GGTGGC GGTGGC GGTGGT GGTGGT GGTGGC GGTGG
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGG
1066061 AGGAGGAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.02, C:0.09, G:0.68, T:0.21
Consensus pattern (6 bp):
GGTGGC
Found at i:1066035 original size:18 final size:18
Alignment explanation
Indices: 1066014--1066063 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1066004 AGGAGGAAAT
1066014 GGTGGCGGTGGAGGTGGC
1 GGTGGCGGTGGAGGTGGC
* *
1066032 GGTGGCGGTGGTGGTGGT
1 GGTGGCGGTGGAGGTGGC
1066050 GGTGGCGGTGGAGG
1 GGTGGCGGTGGAGG
1066064 AGGAGGAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.04, C:0.08, G:0.68, T:0.20
Consensus pattern (18 bp):
GGTGGCGGTGGAGGTGGC
Found at i:1066473 original size:3 final size:3
Alignment explanation
Indices: 1066465--1066494 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1066455 NNNNNNNNGC
1066465 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1066495 GGGTGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1072907 original size:19 final size:18
Alignment explanation
Indices: 1072872--1072945 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 18
1072862 AAACAACCAC
*
1072872 CTTTCTGTTCTTATTCTTT
1 CTTTCT-TTCTTCTTCTTT
1072891 CTTTCTTTCTTTCTTC-TT
1 CTTTCTTTC-TTCTTCTTT
* *
1072909 CGTCTACTTTCTTTTTC-TT
1 C-T-TTCTTTCTTCTTCTTT
*
1072928 -TTTCTTTGTTCTTCTTT
1 CTTTCTTTCTTCTTCTTT
1072945 C
1 C
1072946 GTAAGAATTC
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
16 10 0.23
17 3 0.07
18 6 0.14
19 19 0.43
20 6 0.14
ACGTcount: A:0.03, C:0.24, G:0.04, T:0.69
Consensus pattern (18 bp):
CTTTCTTTCTTCTTCTTT
Found at i:1072934 original size:16 final size:17
Alignment explanation
Indices: 1072872--1072934 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
1072862 AAACAACCAC
*
1072872 CTTTCTGTTCTTATTCTTT
1 CTTTCT-TTCTTTTTC-TT
1072891 CTTTCTTTCTTTCTTCTT
1 CTTTCTTTCTTT-TTCTT
*
1072909 CGTCTACTTTCTTTTTCTT
1 C-T-TTCTTTCTTTTTCTT
1072928 -TTTCTTT
1 CTTTCTTT
1072935 GTTCTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 5 0.13
17 1 0.03
18 8 0.21
19 15 0.39
20 9 0.24
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.70
Consensus pattern (17 bp):
CTTTCTTTCTTTTTCTT
Found at i:1098286 original size:45 final size:45
Alignment explanation
Indices: 1098235--1098346 Score: 170
Period size: 45 Copynumber: 2.5 Consensus size: 45
1098225 GAATATGACG
*
1098235 TGTAACAACCTAACCATGGCGTGTTACATGTTTTTGTACATAGCA
1 TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATAGCA
* * **
1098280 TGTAACAACCTAACCATGACGTGTCATATGTTTTTGTACATAGTG
1 TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATAGCA
*
1098325 TGTAACAATCTAACCATGGCGT
1 TGTAACAACCTAACCATGGCGT
1098347 ATAACAACCT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATAGCA
Found at i:1098397 original size:45 final size:45
Alignment explanation
Indices: 1098339--1098584 Score: 183
Period size: 45 Copynumber: 5.4 Consensus size: 45
1098329 ACAATCTAAC
* *
1098339 CATGGCGTATAACAACCTAACCATAGCATGTCATATGTTTTTGTA
1 CATGGCGTGTAACAACCTAACCATAGCATGTCACATGTTTTTGTA
* * * * ** * *
1098384 CACGGCGTGTAACAACCTAACTATAACGTACCAGATGTTTTTATA
1 CATGGCGTGTAACAACCTAACCATAGCATGTCACATGTTTTTGTA
* ** * ** ** *
1098429 TATGATGTGTAACAAATCTAATTAGGGCGTGTCACATGTTTTTGTA
1 CATGGCGTGTAAC-AACCTAACCATAGCATGTCACATGTTTTTGTA
* * * * *
1098475 CATGACATGTAACAACCTAACCAT-GACATATCATATGTTTTTATA
1 CATGGCGTGTAACAACCTAACCATAG-CATGTCACATGTTTTTGTA
* *
1098520 TC-TGGCGTGTAACAACCAAACTC-TGGCATGTCACATGTTTTTGTA
1 -CATGGCGTGTAACAACCTAAC-CATAGCATGTCACATGTTTTTGTA
**
1098565 CATACCGTGTAACAACCTAA
1 CATGGCGTGTAACAACCTAA
1098585 TCATGGCGTA
Statistics
Matches: 153, Mismatches: 42, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
44 2 0.01
45 115 0.75
46 36 0.24
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (45 bp):
CATGGCGTGTAACAACCTAACCATAGCATGTCACATGTTTTTGTA
Found at i:1098438 original size:111 final size:112
Alignment explanation
Indices: 1098237--1098449 Score: 277
Period size: 111 Copynumber: 1.9 Consensus size: 112
1098227 ATATGACGTG
* * * * *
1098237 TAACAACCTAACCATGGCGTGTTACATGTTTTTGTACATAGCATGTAACAACCTAACCATGACGT
1 TAACAACCTAACCATAGCATGTCACATGTTTTTGTACACAGCATGTAACAACCTAACCATAACGT
** * *
1098302 GTCATATGTTTTTGTACATAGTGTGTAAC-AATCTAACCATGGCGTA
66 ACCAGATGTTTTTATACATAGTGTGTAACAAATCTAACCATGGCGTA
* * * *
1098348 TAACAACCTAACCATAGCATGTCATATGTTTTTGTACACGGCGTGTAACAACCTAACTATAACGT
1 TAACAACCTAACCATAGCATGTCACATGTTTTTGTACACAGCATGTAACAACCTAACCATAACGT
*
1098413 ACCAGATGTTTTTATATAT-GATGTGTAACAAATCTAA
66 ACCAGATGTTTTTATACATAG-TGTGTAACAAATCTAA
1098450 TTAGGGCGTG
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
110 1 0.01
111 78 0.91
112 7 0.08
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (112 bp):
TAACAACCTAACCATAGCATGTCACATGTTTTTGTACACAGCATGTAACAACCTAACCATAACGT
ACCAGATGTTTTTATACATAGTGTGTAACAAATCTAACCATGGCGTA
Found at i:1098530 original size:91 final size:90
Alignment explanation
Indices: 1098364--1098589 Score: 256
Period size: 91 Copynumber: 2.5 Consensus size: 90
1098354 CCTAACCATA
* * * * * *
1098364 GCATGTCATATGTTTTTGTACACGGCGTGTAACAACCTAACTATAACGTACCAGATGTTTTTATA
1 GCATGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGACATACCAGATGTTTTTATA
* * * *
1098429 TATGATGTGTAACAAATCTAATTAGG
66 TATGACGTGTAAC-AACCAAACTAGG
* * * *
1098455 GCGTGTCACATGTTTTTGTACATGACATGTAACAACCTAACCATGACATATCATATGTTTTTATA
1 GCATGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGACATACCAGATGTTTTTATA
* * **
1098520 TCTGGCGTGTAACAACCAAACTCTG
66 TATGACGTGTAACAACCAAACTAGG
*
1098545 GCATGTCACATGTTTTTGTACAT-ACCGTGTAACAACCTAATCATG
1 GCATGTCACATGTTTTTGTACATGA-CGTGTAACAACCTAACCATG
1098590 GCGTATAACA
Statistics
Matches: 113, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 47 0.42
91 65 0.58
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (90 bp):
GCATGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGACATACCAGATGTTTTTATA
TATGACGTGTAACAACCAAACTAGG
Found at i:1098600 original size:21 final size:21
Alignment explanation
Indices: 1098574--1098627 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1098564 ACATACCGTG
*
1098574 TAACAACCTAATCATGGCGTA
1 TAACAACCTAACCATGGCGTA
1098595 TAACAACCTAACCATGGCGTA
1 TAACAACCTAACCATGGCGTA
*
1098616 TAACAACTTAAC
1 TAACAACCTAAC
1098628 AATGACGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (21 bp):
TAACAACCTAACCATGGCGTA
Found at i:1098666 original size:24 final size:24
Alignment explanation
Indices: 1098629--1098687 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1098619 CAACTTAACA
* *
1098629 ATGACGTGTCATATGTTTTTGTAC
1 ATGACGTATAATATGTTTTTGTAC
*
1098653 ATGACGTATAATATGTTTTTGTAT
1 ATGACGTATAATATGTTTTTGTAC
*
1098677 ATAACGTATAA
1 ATGACGTATAA
1098688 CAACTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (24 bp):
ATGACGTATAATATGTTTTTGTAC
Found at i:1100507 original size:23 final size:22
Alignment explanation
Indices: 1100479--1100521 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1100469 TGATTTTAAG
*
1100479 TTTTAATATTAACATTTTATTTC
1 TTTTAA-AATAACATTTTATTTC
*
1100502 TTTTAAAATAATATTTTATT
1 TTTTAAAATAACATTTTATT
1100522 AATAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAATAACATTTTATTTC
Done.