Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 121 of 172
Found at i:40230663 original size:26 final size:26
Alignment explanation
Indices: 40230623--40230672 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
40230613 AGTGGCCGGG
40230623 TTGACCAACTAGTTCTATTAACTAAT
1 TTGACCAACTAGTTCTATTAACTAAT
*
40230649 TTGACCAACTGGTTCTATTAACTA
1 TTGACCAACTAGTTCTATTAACTA
40230673 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (26 bp):
TTGACCAACTAGTTCTATTAACTAAT
Found at i:40231591 original size:15 final size:16
Alignment explanation
Indices: 40231571--40231604 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40231561 AATTTTTTAA
40231571 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
40231586 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
40231602 AAA
1 AAA
40231605 ATTGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:40235661 original size:20 final size:19
Alignment explanation
Indices: 40235638--40235702 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
40235628 AAAATTACAA
40235638 AAAAAATTTAAAATAATTT
1 AAAAAATTTAAAATAATTT
*
40235657 GAAAAAATTAAAAATAATTT
1 -AAAAAATTTAAAATAATTT
**
40235677 TTAAAATTTAAAAT-ATTT
1 AAAAAATTTAAAATAATTT
40235695 ATAAAAAT
1 A-AAAAAT
40235703 CAAAATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 4 0.11
19 16 0.42
20 18 0.47
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAAATTTAAAATAATTT
Found at i:40235701 original size:19 final size:20
Alignment explanation
Indices: 40235639--40235702 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 20
40235629 AAATTACAAA
40235639 AAAAATTTAAAATAATTTGA-
1 AAAAATTTAAAATAATTT-AT
*
40235659 AAAAATTAAAAATAATTT-T
1 AAAAATTTAAAATAATTTAT
*
40235678 TAAAATTTAAAAT-ATTTAT
1 AAAAATTTAAAATAATTTAT
40235697 AAAAAT
1 AAAAAT
40235703 CAAAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 17 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTAT
Found at i:40235714 original size:17 final size:17
Alignment explanation
Indices: 40235672--40235714 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
40235662 AATTAAAAAT
* *
40235672 AATTTT-TAAAATTTAA
1 AATTTTATAAAAATCAA
40235688 AATATTTATAAAAATCAA
1 AAT-TTTATAAAAATCAA
40235706 AATTTTATA
1 AATTTTATA
40235715 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 9 0.39
18 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTTATAAAAATCAA
Found at i:40235739 original size:20 final size:20
Alignment explanation
Indices: 40235714--40235753 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40235704 AAAATTTTAT
40235714 ATTTTTAAAAAAATTATAAA
1 ATTTTTAAAAAAATTATAAA
* *
40235734 ATTTTTCAAAAAATTCTAAA
1 ATTTTTAAAAAAATTATAAA
40235754 GAATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTAAAAAAATTATAAA
Found at i:40238395 original size:21 final size:21
Alignment explanation
Indices: 40238369--40238422 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
40238359 GTTTAAGCCT
40238369 CACACGTCCGTGGAGGCAATG
1 CACACGTCCGTGGAGGCAATG
*
40238390 CACACGCCCGTGGAGGCAATG
1 CACACGTCCGTGGAGGCAATG
40238411 CACACGTCCGTG
1 CACACGTCCGTG
40238423 TGCTTTGGGA
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:0.22, C:0.33, G:0.31, T:0.13
Consensus pattern (21 bp):
CACACGTCCGTGGAGGCAATG
Found at i:40247888 original size:20 final size:21
Alignment explanation
Indices: 40247848--40247896 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
40247838 AGTCCATAAA
40247848 ATCACATTTCATAATCTCAAT
1 ATCACATTTCATAATCTCAAT
40247869 ATCACATTTCATAA-CTCAAT
1 ATCACATTTCATAATCTCAAT
40247889 ATCACATT
1 ATCACATT
40247897 CACTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (21 bp):
ATCACATTTCATAATCTCAAT
Found at i:40248926 original size:31 final size:31
Alignment explanation
Indices: 40248891--40248954 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
40248881 ATTTAACCCC
40248891 ATATTTTCAAAATTTTCCATAATAATCCTCA
1 ATATTTTCAAAATTTTCCATAATAATCCTCA
*
40248922 ATATTTTCAAAATTTTCCTTAATAATCCTCA
1 ATATTTTCAAAATTTTCCATAATAATCCTCA
40248953 AT
1 AT
40248955 GTACAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATTTTCAAAATTTTCCATAATAATCCTCA
Found at i:40250508 original size:28 final size:28
Alignment explanation
Indices: 40250476--40250529 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40250466 TAGACTTAAC
40250476 CGTATTGAATCAACTAAGAAACTATCAT
1 CGTATTGAATCAACTAAGAAACTATCAT
* *
40250504 CGTATTGAATCAACTAATAGACTATC
1 CGTATTGAATCAACTAAGAAACTATC
40250530 TATGTGTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (28 bp):
CGTATTGAATCAACTAAGAAACTATCAT
Found at i:40255088 original size:47 final size:47
Alignment explanation
Indices: 40255019--40255115 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
40255009 GATGACTAAG
40255019 TCACTTCCTATAACCAAATTTGAGCATTGCTTAGACTTGGTTGGTGT
1 TCACTTCCTATAACCAAATTTGAGCATTGCTTAGACTTGGTTGGTGT
*
40255066 TCACTTCCTATAACCAAGTTTGAGCATTGCTTAGACTTGGTTGGTGT
1 TCACTTCCTATAACCAAATTTGAGCATTGCTTAGACTTGGTTGGTGT
40255113 TCA
1 TCA
40255116 TTGTTGAACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (47 bp):
TCACTTCCTATAACCAAATTTGAGCATTGCTTAGACTTGGTTGGTGT
Found at i:40261525 original size:12 final size:12
Alignment explanation
Indices: 40261508--40261552 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
40261498 CGAGATCCGA
40261508 AGCTAGAGCACT
1 AGCTAGAGCACT
40261520 AGCTAGAGCACT
1 AGCTAGAGCACT
*
40261532 AGCTAGAGCACC
1 AGCTAGAGCACT
40261544 AGCTAGAGC
1 AGCTAGAGC
40261553 TTGCGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.13
Consensus pattern (12 bp):
AGCTAGAGCACT
Found at i:40282030 original size:29 final size:29
Alignment explanation
Indices: 40281988--40282046 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
40281978 CCATTTTTAC
40281988 TTAAATTCATGCAAATCCGGTTAAATTCT
1 TTAAATTCATGCAAATCCGGTTAAATTCT
40282017 TTAAATTCATGCAAATCCGGTTAAATTCT
1 TTAAATTCATGCAAATCCGGTTAAATTCT
40282046 T
1 T
40282047 GTCAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (29 bp):
TTAAATTCATGCAAATCCGGTTAAATTCT
Found at i:40290612 original size:28 final size:29
Alignment explanation
Indices: 40290568--40290626 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
40290558 ACCCATTTAA
40290568 AACTCTATTTTGATAAGATTGATAGCAGG
1 AACTCTATTTTGATAAGATTGATAGCAGG
* *
40290597 AACT-TATTTTGGTAAGATTGATATCAGG
1 AACTCTATTTTGATAAGATTGATAGCAGG
40290625 AA
1 AA
40290627 TGAGGAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (29 bp):
AACTCTATTTTGATAAGATTGATAGCAGG
Found at i:40295055 original size:13 final size:13
Alignment explanation
Indices: 40295037--40295062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40295027 AAGTAATCGA
40295037 ACACGGGCGTGTC
1 ACACGGGCGTGTC
40295050 ACACGGGCGTGTC
1 ACACGGGCGTGTC
40295063 CCTACCGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:40299418 original size:24 final size:22
Alignment explanation
Indices: 40299389--40299435 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
40299379 ATAATCTTTA
40299389 TTATATAATTATATCTATTAT-AAT
1 TTATAT-ATTA-ATCT-TTATCAAT
40299413 TTATATATTAATCTTTATCAAT
1 TTATATATTAATCTTTATCAAT
40299435 T
1 T
40299436 AGCATAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 4 0.18
24 6 0.27
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATATTAATCTTTATCAAT
Found at i:40307425 original size:6 final size:6
Alignment explanation
Indices: 40307410--40307439 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40307400 TTTGAGTCCC
40307410 TTTA-T TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT T
40307440 AAAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:40309725 original size:16 final size:17
Alignment explanation
Indices: 40309699--40309732 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
40309689 GATAACCTCT
40309699 TTGATTTATATGATAAA
1 TTGATTTATATGATAAA
40309716 TTGA-TTATATGATAAA
1 TTGATTTATATGATAAA
40309732 T
1 T
40309733 ATTTGTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
TTGATTTATATGATAAA
Found at i:40325315 original size:34 final size:33
Alignment explanation
Indices: 40325277--40325348 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
40325267 GCCCTTTTTC
*
40325277 CAGTAACAATGGCAGTCTAGGCCTAAGCCCATTT
1 CAGTAACAATGCCAGT-TAGGCCTAAGCCCATTT
* * *
40325311 CAGTAATAGTGCCAGTTGGGCCTAAGCCCATTT
1 CAGTAACAATGCCAGTTAGGCCTAAGCCCATTT
40325344 CAGTA
1 CAGTA
40325349 CAGTATGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (33 bp):
CAGTAACAATGCCAGTTAGGCCTAAGCCCATTT
Found at i:40345804 original size:76 final size:76
Alignment explanation
Indices: 40345696--40345957 Score: 287
Period size: 76 Copynumber: 3.4 Consensus size: 76
40345686 CAAACAATAG
* * * *
40345696 GTGTACCCTGCACTAGTCGGATAAACTGACAATTTTTTGTACCTAGCGCTAGTTAG-ATAACTTG
1 GTGTGCCCAGCACTAGTCGGATAAACTGACAATATTTTGTGCCTAGCGCTAGTTAGAATAAC-TG
40345760 ACGATATCAAAT
65 ACGATATCAAAT
* * * * * * *
40345772 GTGTGTCCAGCACTAG-CTGGATAAACCGACAATGTTTTGCGCCCAGCGCTAGTCAGAAAAACTG
1 GTGTGCCCAGCACTAGTC-GGATAAACTGACAATATTTTGTGCCTAGCGCTAGTTAGAATAACTG
40345836 ACGATATCAAAT
65 ACGATATCAAAT
* * * ** * * *
40345848 GTATGCCCAACACTAGTCAGATAAACTGACAATAAATTGTGCCTAGCACTAG-TCGAATAAACCG
1 GTGTGCCCAGCACTAGTCGGATAAACTGACAATATTTTGTGCCTAGCGCTAGTTAGAAT-AACTG
40345912 ACGATATCAAAT
65 ACGATATCAAAT
* *
40345924 GTGTGCCCAGCACTAGTCGAATAAACTGAAAATA
1 GTGTGCCCAGCACTAGTCGGATAAACTGACAATA
40345958 CATACATAAT
Statistics
Matches: 152, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
75 4 0.03
76 143 0.94
77 5 0.03
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (76 bp):
GTGTGCCCAGCACTAGTCGGATAAACTGACAATATTTTGTGCCTAGCGCTAGTTAGAATAACTGA
CGATATCAAAT
Found at i:40345864 original size:40 final size:40
Alignment explanation
Indices: 40345812--40345952 Score: 177
Period size: 40 Copynumber: 3.6 Consensus size: 40
40345802 AATGTTTTGC
* *
40345812 GCCCAGCGCTAGTCAGAA-AAACTGACGATATCAAATGTAT
1 GCCCAGCACTAGTC-GAATAAACTGACGATATCAAATGTGT
*
40345852 GCCCAACACTAGTC-AGATAAACTGAC-A-AT-AAAT-TGT
1 GCCCAGCACTAGTCGA-ATAAACTGACGATATCAAATGTGT
* *
40345888 GCCTAGCACTAGTCGAATAAACCGACGATATCAAATGTGT
1 GCCCAGCACTAGTCGAATAAACTGACGATATCAAATGTGT
40345928 GCCCAGCACTAGTCGAATAAACTGA
1 GCCCAGCACTAGTCGAATAAACTGA
40345953 AAATACATAC
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
36 23 0.27
37 6 0.07
38 5 0.06
39 6 0.07
40 46 0.53
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (40 bp):
GCCCAGCACTAGTCGAATAAACTGACGATATCAAATGTGT
Found at i:40345908 original size:36 final size:37
Alignment explanation
Indices: 40345768--40345957 Score: 147
Period size: 40 Copynumber: 5.0 Consensus size: 37
40345758 TGACGATATC
* * *
40345768 AAATGTGTGTCCAGCACTAG-CTGGATAAACCGACAAT
1 AAATGTGTGCCCAGCACTAGTC-GAATAAACTGACAAT
** * * *
40345805 -GTTTTGCGCCCAGCGCTAGTCAGAA-AAACTGACGATAT
1 AAATGTGTGCCCAGCACTAGTC-GAATAAACTGAC-A-AT
* *
40345843 CAAATGTATGCCCAACACTAGTC-AGATAAACTGACAAT
1 -AAATGTGTGCCCAGCACTAGTCGA-ATAAACTGACAAT
* *
40345881 AAAT-TGTGCCTAGCACTAGTCGAATAAACCGACGATAT
1 AAATGTGTGCCCAGCACTAGTCGAATAAACTGAC-A-AT
*
40345919 CAAATGTGTGCCCAGCACTAGTCGAATAAACTGAAAAT
1 -AAATGTGTGCCCAGCACTAGTCGAATAAACTGACAAT
40345957 A
1 A
40345958 CATACATAAT
Statistics
Matches: 118, Mismatches: 23, Indels: 24
0.72 0.14 0.15
Matches are distributed among these distances:
36 43 0.36
37 11 0.09
38 9 0.08
39 7 0.06
40 48 0.41
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATGTGTGCCCAGCACTAGTCGAATAAACTGACAAT
Found at i:40349731 original size:497 final size:497
Alignment explanation
Indices: 40348797--40352993 Score: 8369
Period size: 497 Copynumber: 8.4 Consensus size: 497
40348787 GCAGTTCCGG
40348797 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40348862 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40348927 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40348992 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40349057 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40349122 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40349187 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40349252 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40349294 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40349359 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40349424 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40349489 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40349554 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40349619 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40349684 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40349749 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40349791 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40349856 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40349921 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40349986 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40350051 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40350116 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40350181 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40350246 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40350288 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40350353 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40350418 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40350483 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40350548 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40350613 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40350678 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40350743 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40350785 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40350850 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40350915 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40350980 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40351045 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40351110 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40351175 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40351240 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40351282 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40351347 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40351412 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40351477 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40351542 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40351607 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40351672 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40351737 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40351779 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40351844 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40351909 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40351974 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40352039 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
40352104 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40352169 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
40352234 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40352276 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40352341 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40352406 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40352471 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
196 CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
40352536 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
261 AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
*
40352601 AAAACTTTC-AAAATAATTAACATGTTTCTATAACTTTTCACAATATATCCTCAAAATATTATAA
326 AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
40352665 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
391 TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
*
40352730 CATTCAATTCGCAATTTCTCATGTTCATAATTTAAATCATAT
456 CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
40352772 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
1 CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
40352837 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
66 TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
40352902 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
131 GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
40352967 CCATTTACTTTAATTCTTTTGGGCCCA
196 CCATTTACTTTAATTCTTTTGGGCCCA
40352994 TTTGTCACTT
Statistics
Matches: 3698, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
496 382 0.10
497 3316 0.90
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.34
Consensus pattern (497 bp):
CACTAGCAATTTCCATTTAATTCACGTACAATTCAATGACATCAAATTCAAAACTAATACGTATT
TACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTATGAAATTCTCAATTTA
GCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAATACACTACCACTTAT
CCATTTACTTTAATTCTTTTGGGCCCAACCCCCCTTCCCCGTATCCAACACCGGAATAGGGTACG
AGGCATTACCAAAACACATACACTTGTAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATT
AAAACTTTCAAAAATAATTAACATGTTTCTATAACTTTTCACAATATATTCTCAAAATATTATAA
TCATAATAATTAGGGCCTGCGAGACCCGATACATACTCATGCAATTTAATGCTTCATTTCCATTT
CATTCAATTCGCAATTTCTCATGCTCATAATTTAAATCATAT
Found at i:40353155 original size:37 final size:37
Alignment explanation
Indices: 40353094--40353359 Score: 392
Period size: 37 Copynumber: 7.0 Consensus size: 37
40353084 TACGTATGAT
* *
40353094 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40353129 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40353166 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40353203 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40353240 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40353277 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T--AGC
*
40353320 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 ---CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40353360 TAAAGCTATC
Statistics
Matches: 215, Mismatches: 5, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
35 9 0.04
36 3 0.01
37 159 0.74
39 2 0.01
40 4 0.02
41 1 0.00
42 1 0.00
43 4 0.02
44 2 0.01
46 30 0.14
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:40353330 original size:46 final size:46
Alignment explanation
Indices: 40353277--40353689 Score: 520
Period size: 46 Copynumber: 8.6 Consensus size: 46
40353267 TAAGTGTAGC
* *
40353277 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
40353323 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * * *
40353369 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGTAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
40353415 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
40353467 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
*
40353513 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
40353565 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * *
40353611 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
40353663 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40353690 AGTACTCAAA
Statistics
Matches: 327, Mismatches: 22, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
46 198 0.61
48 2 0.01
49 2 0.01
50 2 0.01
52 123 0.38
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
Found at i:40353477 original size:98 final size:98
Alignment explanation
Indices: 40353277--40353689 Score: 667
Period size: 98 Copynumber: 4.3 Consensus size: 98
40353267 TAAGTGTAGC
* * **
40353277 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC--T----TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
40353336 GTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* * *
40353369 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGTAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
40353434 GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
40353467 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
40353532 GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
40353565 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
40353630 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
40353663 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40353690 AGTACTCAAA
Statistics
Matches: 303, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
92 52 0.17
94 1 0.00
98 250 0.83
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
Found at i:40365388 original size:42 final size:42
Alignment explanation
Indices: 40365329--40365413 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
40365319 AAATAAGTAT
40365329 ATCTAACAATCAAGCTTCCAACAAAACCAATTAGCATCAAAG
1 ATCTAACAATCAAGCTTCCAACAAAACCAATTAGCATCAAAG
*
40365371 ATCTAACAATCAAGCTTCTAACAAAACCAATTAGCATCAAAG
1 ATCTAACAATCAAGCTTCCAACAAAACCAATTAGCATCAAAG
40365413 A
1 A
40365414 CATTCAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.25, G:0.07, T:0.20
Consensus pattern (42 bp):
ATCTAACAATCAAGCTTCCAACAAAACCAATTAGCATCAAAG
Found at i:40369631 original size:24 final size:24
Alignment explanation
Indices: 40369604--40369650 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40369594 ATGAGATATC
* *
40369604 GACCTTTTCGTTGATATCTTTTTT
1 GACCTTTTCATTGATATCCTTTTT
*
40369628 GACCTTTTCATTTATATCCTTTT
1 GACCTTTTCATTGATATCCTTTT
40369651 CAATCTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.09, T:0.57
Consensus pattern (24 bp):
GACCTTTTCATTGATATCCTTTTT
Found at i:40369928 original size:76 final size:75
Alignment explanation
Indices: 40369724--40369928 Score: 196
Period size: 76 Copynumber: 2.7 Consensus size: 75
40369714 TGCCGGACGG
* * *
40369724 ATAAACCATAACAAAGTTTTGTGCCTAGCGCTAGTCGGATAAACCAATAATATCAAATGTGTGCC
1 ATAAACC--AACAATGTTTTGTGCCCAGCGCTAGTAGGATAAACCAA-AATATCAAATGTGTGCC
* ***
40369789 CAACATTAGTTGG
63 CAACACTAGTCAA
* * * * *
40369802 ATAAACCGACAATGTTTTGCGCCCAGCGCTAATAGGATAAATCGACAATATCAAATGTGTG-CCA
1 ATAAACCAACAATGTTTTGTGCCCAGCGCTAGTAGGATAAA-CCAAAATATCAAATGTGTGCCCA
40369866 AGCACTAGTCAA
65 A-CACTAGTCAA
* * * * *
40369878 ATTAACCAATAATGATTTTGTGCCCAGTGCTAGTTGAATAAACCAAAATAT
1 ATAAACCAACAATG-TTTTGTGCCCAGCGCTAGTAGGATAAACCAAAATAT
40369929 ACATACATAA
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
75 4 0.04
76 67 0.66
77 24 0.24
78 7 0.07
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (75 bp):
ATAAACCAACAATGTTTTGTGCCCAGCGCTAGTAGGATAAACCAAAATATCAAATGTGTGCCCAA
CACTAGTCAA
Found at i:40374479 original size:39 final size:41
Alignment explanation
Indices: 40374390--40374529 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 41
40374380 CCGTAATAAT
* * * * *
40374390 CTCGCACACTTAGTGTCATTTCAATAAACCAGAGCTATCTCGGTA
1 CTCGCACACTTAGTGCCA--TCAAT-AGCCAAAGCTATTTC-GAA
*
40374435 -TCGCACACTTAGTGCC-TCAATAGCCGAAGCTATTTC-AA
1 CTCGCACACTTAGTGCCATCAATAGCCAAAGCTATTTCGAA
*** *
40374473 CTCGCACACTTAGTGCCATTTGTAGCCAAATCTATTTCGAA
1 CTCGCACACTTAGTGCCATCAATAGCCAAAGCTATTTCGAA
40374514 C-CGCACACTTAGTGCC
1 CTCGCACACTTAGTGCC
40374530 GAACATAGTC
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
38 1 0.01
39 16 0.20
40 41 0.51
41 8 0.10
44 15 0.19
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (41 bp):
CTCGCACACTTAGTGCCATCAATAGCCAAAGCTATTTCGAA
Found at i:40376401 original size:3 final size:3
Alignment explanation
Indices: 40376389--40376418 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40376379 AACACACTCC
40376389 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40376419 TGGTTAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:40377667 original size:76 final size:74
Alignment explanation
Indices: 40377535--40377827 Score: 304
Period size: 76 Copynumber: 3.9 Consensus size: 74
40377525 TCTTAGTGAG
* * *
40377535 CAAATATTTGTCG-GAATCCGACTAGTGTTGGGCATACATTTAACATCGTCGATTCATCCGACTA
1 CAAATATTTGTCGTTAATCTGACTAGTGTTGGGCACACATTTAACATCGTCGATTCATCCGACTA
40377599 GCGTAGGGCA
66 GCGT-GGGCA
* * * * * *
40377609 CACATATTTGTCAGTTAATCTGACTAGTGCTGGGAACACATTTAACATTGTCGGTTCATCTGACT
1 CAAATATTTGTC-GTTAATCTGACTAGTGTTGGGCACACATTTAACATCGTCGATTCATCCGACT
*
40377674 AGCACTGGGCA
65 AGC-GTGGGCA
* * *
40377685 CAAATATTTGTCGGTTAAT-TCAACTAGTGTTAGGCACACATTTAACATCGTCGGTTCATCCGAC
1 CAAATATTTGTC-GTTAATCT-GACTAGTGTTGGGCACACATTTAACATCGTCGATTCATCCGAC
* **
40377749 TAGTGCTGGATA
64 TAGCG-TGGGCA
* * * * *
40377761 CAAATCTTTGTCGATTAATCTGACTAGTGTTGGGCACAC-TTTTACTATTGTCGATTTATCCAAC
1 CAAATATTTGTCG-TTAATCTGACTAGTGTTGGGCACACATTTAAC-ATCGTCGATTCATCCGAC
40377825 TAG
64 TAG
40377828 GCTGGGTGCA
Statistics
Matches: 181, Mismatches: 30, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
74 11 0.06
75 8 0.04
76 160 0.88
77 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (74 bp):
CAAATATTTGTCGTTAATCTGACTAGTGTTGGGCACACATTTAACATCGTCGATTCATCCGACTA
GCGTGGGCA
Found at i:40377671 original size:40 final size:39
Alignment explanation
Indices: 40377616--40377813 Score: 119
Period size: 40 Copynumber: 5.2 Consensus size: 39
40377606 GCACACATAT
*
40377616 TTGTCAGTTAATCTGACTAGTGCTGGGAACACATTTAACA
1 TTGTCGGTTAATCTGACTAGTGCTGGG-ACACATTTAACA
* ** *
40377656 TTGTCGGTTCATCTGACTAGCACTGGG-CACA---AATA
1 TTGTCGGTTAATCTGACTAGTGCTGGGACACATTTAACA
* * *
40377691 TTTGTCGGTTAAT-TCAACTAGTGTTAGGCACACATTTAACA
1 -TTGTCGGTTAATCT-GACTAGTGCT-GGGACACATTTAACA
* * * * *
40377732 TCGTCGGTTCATCCGACTAGTGCT-GGATACA---AATCT
1 TTGTCGGTTAATCTGACTAGTGCTGGGACACATTTAA-CA
* * *
40377768 TTGTCGATTAATCTGACTAGTGTTGGG-CACACTTTTACTA
1 TTGTCGGTTAATCTGACTAGTGCTGGGACACA-TTTAAC-A
40377808 TTGTCG
1 TTGTCG
40377814 ATTTATCCAA
Statistics
Matches: 115, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
35 6 0.05
36 40 0.35
37 4 0.03
38 13 0.11
39 1 0.01
40 48 0.42
41 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (39 bp):
TTGTCGGTTAATCTGACTAGTGCTGGGACACATTTAACA
Found at i:40377852 original size:152 final size:152
Alignment explanation
Indices: 40377535--40377827 Score: 371
Period size: 152 Copynumber: 1.9 Consensus size: 152
40377525 TCTTAGTGAG
* * * *
40377535 CAAATATTTGTCGG--AATCCGACTAGTGTTGGGCATACATTTAACATCGTCGATTCATCCGACT
1 CAAATATTTGTCGGTTAATTCAACTAGTGTTAGGCACACATTTAACATCGTCGATTCATCCGACT
* * *
40377598 AGCGTAGGGCACACATATTTGTCAGTTAATCTGACTAGTGCTGGGAACACATTTAACATTGTCGG
66 AGCGTAGGACACAAATATTTGTCAGTTAATCTGACTAGTGCTGGGAACACATTTAACATTGTCGA
**
40377663 TTCATCTGACTAGCACTGGGCA
131 TTCATCCAACTAGCACTGGGCA
*
40377685 CAAATATTTGTCGGTTAATTCAACTAGTGTTAGGCACACATTTAACATCGTCGGTTCATCCGACT
1 CAAATATTTGTCGGTTAATTCAACTAGTGTTAGGCACACATTTAACATCGTCGATTCATCCGACT
* * * * * *
40377750 AGTGCT-GGATACAAATCTTTGTC-GATTAATCTGACTAGTGTTGGGCACAC-TTTTACTATTGT
66 AGCG-TAGGACACAAATATTTGTCAG-TTAATCTGACTAGTGCTGGGAACACATTTAAC-ATTGT
*
40377812 CGATTTATCCAACTAG
128 CGATTCATCCAACTAG
40377828 GCTGGGTGCA
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
150 14 0.12
151 6 0.05
152 100 0.83
153 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (152 bp):
CAAATATTTGTCGGTTAATTCAACTAGTGTTAGGCACACATTTAACATCGTCGATTCATCCGACT
AGCGTAGGACACAAATATTTGTCAGTTAATCTGACTAGTGCTGGGAACACATTTAACATTGTCGA
TTCATCCAACTAGCACTGGGCA
Found at i:40379681 original size:26 final size:26
Alignment explanation
Indices: 40379651--40379703 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40379641 TTCCTGAGAG
*
40379651 AGTGTTAATTGTGTTGTTTTGTTATT
1 AGTGTTAATTGTGTTGTTTCGTTATT
40379677 AGTGTTAATTGTGTTGTTTCGTTATT
1 AGTGTTAATTGTGTTGTTTCGTTATT
40379703 A
1 A
40379704 CAAGGAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.02, G:0.23, T:0.58
Consensus pattern (26 bp):
AGTGTTAATTGTGTTGTTTCGTTATT
Found at i:40381083 original size:12 final size:13
Alignment explanation
Indices: 40381047--40381084 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
40381037 AAATATTTGA
40381047 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
40381060 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
40381074 CTTG-TCTTAAT
1 CTTGTTCTTAAT
40381085 ATTTCAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:40386083 original size:20 final size:20
Alignment explanation
Indices: 40386058--40386124 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
40386048 GATATAATAT
40386058 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
40386078 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40386098 ACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGC
40386118 ACATGAT
1 ACATGAT
40386125 GAATTCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40386085 original size:11 final size:11
Alignment explanation
Indices: 40386069--40386124 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40386059 CATGATTGAT
40386069 ATGATATGCAC
1 ATGATATGCAC
*
40386080 ATGATATG--T
1 ATGATATGCAC
40386089 ATGATATGCAC
1 ATGATATGCAC
*
40386100 ATGATATG--T
1 ATGATATGCAC
*
40386109 ATGAAATGCAC
1 ATGATATGCAC
40386120 ATGAT
1 ATGAT
40386125 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40386203 original size:26 final size:26
Alignment explanation
Indices: 40386174--40386268 Score: 156
Period size: 26 Copynumber: 3.7 Consensus size: 26
40386164 GAGGAAGTGC
40386174 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40386200 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
40386226 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
40386252 AAAAGGG-TTTTGCCCCA
1 AAAAGGGCTTATGCCCCA
40386269 ATTATTAAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
25 9 0.14
26 57 0.86
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40389909 original size:46 final size:46
Alignment explanation
Indices: 40389842--40390011 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 46
40389832 AACCCGCCCC
* *
40389842 TAAGTGAACTTGGACTCAACTCAACGAGCTCGGACGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * * * * *
40389888 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCATCCA
* * *
40389934 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
40389981 TAAGTGAACTCGAACTCAACTCAACGTGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
40390012 AGATGCTCAA
Statistics
Matches: 98, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
45 2 0.02
46 61 0.62
47 33 0.34
48 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:40390017 original size:93 final size:93
Alignment explanation
Indices: 40389847--40390017 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
40389837 GCCCCTAAGT
* * *
40389847 GAACTTGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
40389912 CAAGTTCGGATGCCTAGTTACATTTCAC
66 CAAGTTCAGATGCCTAGTTACATTTCAC
*
40389940 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
**
40390005 CGTGTTCAGATGC
66 CAAGTTCAGATGC
40390018 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CAAGTTCAGATGCCTAGTTACATTTCAC
Found at i:40392440 original size:15 final size:15
Alignment explanation
Indices: 40392414--40392469 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
40392404 CAAGGAAACC
40392414 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
40392429 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
40392444 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
40392459 GAATAAAGAAA
1 GAATAAAGAAA
40392470 CCCAAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:40395974 original size:40 final size:40
Alignment explanation
Indices: 40395916--40396133 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
40395906 CGGATGATAA
* *
40395916 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
40395956 CTGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40395996 CCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40396036 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40396076 CCGGGCTAAGTCCCAAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
40396116 CC-GGCTAAATCCTGAAGG
1 CCGGGCTAAGTCCCGAAGG
40396134 TACTTGGTTT
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 143 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40404238 original size:40 final size:40
Alignment explanation
Indices: 40404183--40404356 Score: 228
Period size: 40 Copynumber: 4.4 Consensus size: 40
40404173 TGATAACCGA
* *
40404183 GCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGG
40404223 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* *
40404263 GCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* * *
40404303 GATAAGTTCCGAAGGCATTTGAGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
* *
40404342 GCTAAATTCCGAAGG
1 GCTAAGTCCCGAAGG
40404357 TACTTGGTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
39 16 0.13
40 104 0.86
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:40407182 original size:93 final size:93
Alignment explanation
Indices: 40407074--40407337 Score: 483
Period size: 93 Copynumber: 2.8 Consensus size: 93
40407064 GCCTCTAAGT
* ** * *
40407074 GAACTAGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40407139 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
40407167 GAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40407232 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
40407260 GAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40407325 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40407338 TCAACCATCC
Statistics
Matches: 166, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 166 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40407183 original size:47 final size:47
Alignment explanation
Indices: 40407120--40407288 Score: 213
Period size: 47 Copynumber: 3.6 Consensus size: 47
40407110 ATCCATAAGT
40407120 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* * * * *
40407167 GAACTCGGACTCAACTCAACGATTTCGGA---C-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--TTCA-C
40407213 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
*
40407260 GAACTCGGACTCAACTCAACGATTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
40407289 CATTCGCATC
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 28 0.27
47 56 0.55
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40407334 original size:46 final size:46
Alignment explanation
Indices: 40407069--40407334 Score: 260
Period size: 46 Copynumber: 5.7 Consensus size: 46
40407059 AACCCGCCTC
* * * *
40407069 TAAGTGAACTAGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
40407115 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
40407163 TCA-CGAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
40407208 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
40407256 TCA-CGAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40407301 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40407335 TGCTCAACCA
Statistics
Matches: 178, Mismatches: 24, Indels: 36
0.75 0.10 0.15
Matches are distributed among these distances:
42 4 0.02
43 8 0.04
44 2 0.01
45 4 0.02
46 87 0.49
47 56 0.31
48 4 0.02
49 2 0.01
50 7 0.04
51 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40413343 original size:8 final size:8
Alignment explanation
Indices: 40413332--40413359 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40413322 TTAAAACGAT
40413332 AAATGCCG
1 AAATGCCG
40413340 AAATGCCG
1 AAATGCCG
40413348 AAATGCCG
1 AAATGCCG
40413356 AAAT
1 AAAT
40413360 TCTGGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (8 bp):
AAATGCCG
Found at i:40413499 original size:21 final size:20
Alignment explanation
Indices: 40413473--40413512 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40413463 GCATTACGAT
40413473 AAGTTGGGCCTCAAGGGGCTG
1 AAGTTGGGCC-CAAGGGGCTG
*
40413494 AAGTTGGGCCCAATGGGCT
1 AAGTTGGGCCCAAGGGGCT
40413513 TTCGGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (20 bp):
AAGTTGGGCCCAAGGGGCTG
Found at i:40413870 original size:9 final size:10
Alignment explanation
Indices: 40413858--40413914 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
40413848 TACGTGGGAT
40413858 ATGATAT-AC
1 ATGATATGAC
*
40413867 ATGAT-TGAT
1 ATGATATGAC
40413876 ATGATATGCAC
1 ATGATATG-AC
*
40413887 ATGATATG-T
1 ATGATATGAC
40413896 ATGATATGCAC
1 ATGATATG-AC
40413907 ATGATATG
1 ATGATATG
40413915 TATGAAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (10 bp):
ATGATATGAC
Found at i:40413890 original size:20 final size:20
Alignment explanation
Indices: 40413857--40413931 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
40413847 ATACGTGGGA
40413857 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
40413874 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
40413895 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
40413915 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
40413932 GAATTCATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:40413892 original size:11 final size:11
Alignment explanation
Indices: 40413876--40413931 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40413866 CATGATTGAT
40413876 ATGATATGCAC
1 ATGATATGCAC
*
40413887 ATGATATG--T
1 ATGATATGCAC
40413896 ATGATATGCAC
1 ATGATATGCAC
*
40413907 ATGATATG--T
1 ATGATATGCAC
*
40413916 ATGAAATGCAC
1 ATGATATGCAC
40413927 ATGAT
1 ATGAT
40413932 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40414048 original size:25 final size:26
Alignment explanation
Indices: 40413981--40414052 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
40413971 GAGGAAGTGC
* **
40413981 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
40414007 AAAAAGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
40414033 AAAAGGGCTT-TACCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40414053 ATTAAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 9 0.22
26 31 0.77
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:40420273 original size:55 final size:55
Alignment explanation
Indices: 40420212--40420388 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
40420202 ATATTAAGTC
* * *
40420212 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
40420267 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
40420322 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
40420378 CGCACACTTAG
1 CGCACACTTAG
40420389 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:40420276 original size:28 final size:27
Alignment explanation
Indices: 40420212--40420363 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
40420202 ATATTAAGTC
* *
40420212 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
40420239 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
40420267 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
40420294 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
40420322 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
40420349 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40420364 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40426234 original size:40 final size:40
Alignment explanation
Indices: 40426182--40426299 Score: 200
Period size: 40 Copynumber: 3.0 Consensus size: 40
40426172 AGCCTGGATG
* *
40426182 TAACAACGAGCACAAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
* *
40426222 TAGCAACCAGCACGAATGCCTTCGGGACTTAACCCAGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
40426262 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGA
40426300 TAAAATCCTC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (40 bp):
TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
Found at i:40452221 original size:21 final size:23
Alignment explanation
Indices: 40452195--40452254 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 23
40452185 GTTTTAAAAA
*
40452195 TTGTTTTAGTA-TTATTTTTAT-
1 TTGTTTTAATATTTATTTTTATG
*
40452216 TTGTTTTAATATTTGTTTTTATG
1 TTGTTTTAATATTTATTTTTATG
*
40452239 TT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
40452255 GATTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 16 0.48
22 15 0.45
23 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (23 bp):
TTGTTTTAATATTTATTTTTATG
Found at i:40452275 original size:27 final size:25
Alignment explanation
Indices: 40452224--40452275 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
40452214 ATTTGTTTTA
* *
40452224 ATATTTGTTTTTATGTTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAAT
40452249 ATATTTGATTTATTATATTTTTAAAAT
1 ATATTTG-TTT-TTATATTTTTAAAAT
40452276 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 3 0.13
27 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (25 bp):
ATATTTGTTTTTATATTTTTAAAAT
Found at i:40452576 original size:29 final size:29
Alignment explanation
Indices: 40452534--40452603 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
40452524 ATACATCAGA
40452534 CATGCTAACATTGATATTGCCCCTACCAC
1 CATGCTAACATTGATATTGCCCCTACCAC
40452563 CATGCTAACATTGATATTGCCCCTACCAC
1 CATGCTAACATTGATATTGCCCCTACCAC
*
40452592 CATG-TAGCATTG
1 CATGCTAACATTG
40452604 CAAGTGGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (29 bp):
CATGCTAACATTGATATTGCCCCTACCAC
Found at i:40471097 original size:24 final size:25
Alignment explanation
Indices: 40471043--40471098 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
40471033 TATTTAAAGG
* * *
40471043 TTTAGAATAGATACTATAAAAGCAA
1 TTTAAAATAAATAATATAAAAGCAA
40471068 TTTAAAATAAATAATATAAAA-CAA
1 TTTAAAATAAATAATATAAAAGCAA
40471092 TTTAAAA
1 TTTAAAA
40471099 ATCATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (25 bp):
TTTAAAATAAATAATATAAAAGCAA
Found at i:40471410 original size:26 final size:26
Alignment explanation
Indices: 40471381--40471449 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
40471371 CACATATAAA
*
40471381 AAAAAAGTTTAAAGTAAATAACATAT
1 AAAAAAGTTTAAAATAAATAACATAT
* *
40471407 AAAAATA-TTTAAAATAAATAATATGT
1 AAAAA-AGTTTAAAATAAATAACATAT
**
40471433 AAAGGAGTTTAAAATAA
1 AAAAAAGTTTAAAATAA
40471450 CTGATGCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.03
26 34 0.94
27 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.29
Consensus pattern (26 bp):
AAAAAAGTTTAAAATAAATAACATAT
Found at i:40471745 original size:17 final size:17
Alignment explanation
Indices: 40471725--40471758 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40471715 TAAAATAATC
*
40471725 TAAAGTAAAGAATATAT
1 TAAAATAAAGAATATAT
*
40471742 TAAAATAAATAATATAT
1 TAAAATAAAGAATATAT
40471759 GGGAAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TAAAATAAAGAATATAT
Found at i:40478252 original size:28 final size:28
Alignment explanation
Indices: 40478221--40478320 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
40478211 CTGACTGATT
*
40478221 TCGCACACATAGCGCTCGATTAAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* * *
40478249 TCGCACACATAGTGCCTCAATTACCA-ATC
1 TCGCACACATAGTG-CTCGATTA-AAGAAC
*
40478278 TCGCACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
*
40478306 TCACACACATAGTGC
1 TCGCACACATAGTGC
40478321 CTCAACTACT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.02
28 35 0.58
29 23 0.38
30 1 0.02
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (28 bp):
TCGCACACATAGTGCTCGATTAAAGAAC
Found at i:40478288 original size:57 final size:57
Alignment explanation
Indices: 40478221--40478381 Score: 214
Period size: 57 Copynumber: 2.8 Consensus size: 57
40478211 CTGACTGATT
* * *
40478221 TCGCACACATAGCGCTCGATTAAAGAACTCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* **
40478278 TCGCACACATAGTGCTCGATTGAAGAACTCACACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* ** * * *
40478335 TGGCGTACATAGTGCTCGGTTGAAGAACTTGCACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCA
40478382 TAACTCCAAC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
Found at i:40478453 original size:40 final size:40
Alignment explanation
Indices: 40478409--40478695 Score: 477
Period size: 40 Copynumber: 7.2 Consensus size: 40
40478399 CCTTCGAGGT
* *
40478409 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
*
40478449 TTAGCCCGGATACATTACTAGCACGAATGCGCTTCGGAAC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
* * *
40478489 TTAACCTGGATACATTACTAGCATGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
40478529 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
*
40478569 TTAGCCCGGATATATTACTAGCACGAATGCTCTTCGG-AC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
*
40478608 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
* *
40478648 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
40478688 TTAGCCCG
1 TTAGCCCG
40478696 AATATATATA
Statistics
Matches: 232, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
39 37 0.16
40 195 0.84
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
Found at i:40478672 original size:119 final size:120
Alignment explanation
Indices: 40478409--40478702 Score: 491
Period size: 119 Copynumber: 2.5 Consensus size: 120
40478399 CCTTCGAGGT
* *
40478409 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATTACTAGCACG
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATTACTAGCACG
* * *
40478474 AATGCGCTTCGGAACTTAACCTGGATACATTACTAGCATGAATGCTCTTCGGAAC
66 AATGCGCTTCGGAACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
40478529 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATTACTAGCACG
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATTACTAGCACG
* *
40478594 AATGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
66 AATGCGCTTCGGAACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
40478648 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGAATATAT
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATAT
40478703 ATAACTCTCA
Statistics
Matches: 163, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 90 0.55
120 73 0.45
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (120 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATTACTAGCACG
AATGCGCTTCGGAACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:40480042 original size:37 final size:37
Alignment explanation
Indices: 40479985--40480087 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
40479975 CGAATAGTCC
*
40479985 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
* *
40480022 CCACACGTAGTCATCAGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
40480059 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
40480088 ATATATTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:40480286 original size:48 final size:48
Alignment explanation
Indices: 40480228--40481141 Score: 1774
Period size: 48 Copynumber: 19.0 Consensus size: 48
40480218 ATATACACAC
*
40480228 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480276 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480324 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480372 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480420 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480468 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480516 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480564 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480612 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480660 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480708 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480756 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480804 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480852 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480900 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480948 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40480996 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
40481044 CTCTCATACATAATTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
40481092 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40481140 AT
1 AT
40481142 ATTTATCTTG
Statistics
Matches: 857, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 857 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.33
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:40487922 original size:71 final size:71
Alignment explanation
Indices: 40487805--40488264 Score: 472
Period size: 71 Copynumber: 6.5 Consensus size: 71
40487795 CCCCTAGTCA
* * ** * * *
40487805 CCCAACTATCATATTAAAGCTCACAGGTGAAAAACTACAGCTTCCAACACAGTTAGCTAGAGTTA
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
*
40487870 GAAACT
66 CAAACT
* ** * * * *
40487876 CCCAACTATCATATTAAATCTTGCAGGTGAAAGACCGCAGCCTCCAACACAGTTAGCAAGAGTTC
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
40487941 CAAACT
66 CAAACT
* * * ** * * * * * *
40487947 CTCAGCTATCATATTAAGGCTTATAAGTGAAAAATCGCAGCCTCCAACATAGTTACCGATAGTTA
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
40488012 CAAACT
66 CAAACT
* * * * *
40488018 CCCAACTGTCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCTAATATAGTT-GACGAGAGTT
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAG-CGAGAGTT
40488082 ACAAACT
65 ACAAACT
* * * ** * ** * * * *
40488089 TCCAGCTGTCATATTAAGGGTCACAGGTGAAAAATCGTAGCTTCCAACACAATTAGTGAAAGTTA
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
40488154 CAAACT
66 CAAACT
* * * *
40488160 CCTAACTGTCATATTAAGGCTTGTAGGTAAAAAACCACAGCCTCTAACACAGTTAGCGAGAGTTA
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
40488225 CAAACT
66 CAAACT
*
40488231 CTCAACTGTCATATTAAGGCTTGCAGGTGAAAAA
1 CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAA
40488265 TTGCAGCCCC
Statistics
Matches: 316, Mismatches: 71, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
71 315 1.00
72 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (71 bp):
CCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
CAAACT
Found at i:40488080 original size:142 final size:142
Alignment explanation
Indices: 40487810--40488272 Score: 536
Period size: 142 Copynumber: 3.3 Consensus size: 142
40487800 AGTCACCCAA
* * * * * *
40487810 CTATCATATTAAAGCTCACAGGTGAAAAA-CTACAGCTTCCAACACAGTTAGCTAGAGTTAGAAA
1 CTATCATATTAAGGCTCACAGGTGAAAAATC-GCAGCCTCCAACACAGTTAGCGAAAGTTACAAA
* ** * * * *
40487874 CTCCCAACTATCATATTAAATCTTGCAGGTGAAAGACCGCAGCCTCCAACACAGTTAGCAAGAGT
65 CTCCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCTAACACAGTTAGCGAGAGT
*
40487939 TCCAAACTCTCAG
130 TACAAACTCTCAG
* * * * * *
40487952 CTATCATATTAAGGCTTATAAGTGAAAAATCGCAGCCTCCAACATAGTTACCGATAGTTACAAAC
1 CTATCATATTAAGGCTCACAGGTGAAAAATCGCAGCCTCCAACACAGTTAGCGAAAGTTACAAAC
* * * *
40488017 TCCCAACTGTCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCTAATATAGTT-GACGAGAGT
66 TCCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCTAACACAGTTAG-CGAGAGT
40488081 TACAAACT-TCCAG
130 TACAAACTCT-CAG
* * * * * *
40488094 CTGTCATATTAAGGGTCACAGGTGAAAAATCGTAGCTTCCAACACAATTAGTGAAAGTTACAAAC
1 CTATCATATTAAGGCTCACAGGTGAAAAATCGCAGCCTCCAACACAGTTAGCGAAAGTTACAAAC
* * *
40488159 TCCTAACTGTCATATTAAGGCTTGTAGGTAAAAAACCACAGCCTCTAACACAGTTAGCGAGAGTT
66 TCCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCTAACACAGTTAGCGAGAGTT
*
40488224 ACAAACTCTCAA
131 ACAAACTCTCAG
* ** *
40488236 CTGTCATATTAAGGCTTGCAGGTGAAAAATTGCAGCC
1 CTATCATATTAAGGCTCACAGGTGAAAAATCGCAGCC
40488273 CCTAAAATAA
Statistics
Matches: 267, Mismatches: 49, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
141 2 0.01
142 262 0.98
143 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (142 bp):
CTATCATATTAAGGCTCACAGGTGAAAAATCGCAGCCTCCAACACAGTTAGCGAAAGTTACAAAC
TCCCAACTGTCATATTAAGGCTTGCAGGTGAAAAACCACAGCCTCTAACACAGTTAGCGAGAGTT
ACAAACTCTCAG
Found at i:40488174 original size:213 final size:213
Alignment explanation
Indices: 40487805--40488264 Score: 521
Period size: 213 Copynumber: 2.2 Consensus size: 213
40487795 CCCCTAGTCA
* * * * * *
40487805 CCCAACTATCATATTAAAGCTCACAGGTGAAAAACTACAGCTTCCAACACAGTTAGCTAGAGTTA
1 CCCAACTGTCATATTAAGGCTCGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
* * ** * *
40487870 GAAACTCCCAACTATCATATTAAATCTTGCAGGTGAAAGACCGCAGCCTCCAACACAGTTAGCAA
66 CAAACTCCCAACTATCATATTAAAGCTCACAGGTGAAAAACCGCAGCCTCCAACACAATTAGCAA
* * * * * *
40487935 GAGTTCCAAACTCTCAGCTATCATATTAAGGCTTATAAGTGAAAAATCGCAGCCTCCAACATAGT
131 GAGTTACAAACTCTCAACTATCATATTAAGGCTTATAAGTAAAAAACCACAGCCTCCAACACAGT
*
40488000 TACCGATAGTTACAAACT
196 TACCGAGAGTTACAAACT
* * * *
40488018 CCCAACTGTCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCTAATATAGTT-GACGAGAGTT
1 CCCAACTGTCATATTAAGGCTCGCAGGTGAAAAACCACAGCCTCCAACACAGTTAG-CGAGAGTT
* * * * * * * * *
40488082 ACAAACTTCCAGCTGTCATATTAAGGGTCACAGGTGAAAAATCGTAGCTTCCAACACAATTAGTG
65 ACAAACTCCCAACTATCATATTAAAGCTCACAGGTGAAAAACCGCAGCCTCCAACACAATTAG-C
* * * *
40488147 AA-AGTTACAAACTC-CTAACTGTCATATTAAGGCTTGTAGGTAAAAAACCACAGCCTCTAACAC
129 AAGAGTTACAAACTCTC-AACTATCATATTAAGGCTTATAAGTAAAAAACCACAGCCTCCAACAC
*
40488210 AGTTAGCGAGAGTTACAAACT
193 AGTTACCGAGAGTTACAAACT
* *
40488231 CTCAACTGTCATATTAAGGCTTGCAGGTGAAAAA
1 CCCAACTGTCATATTAAGGCTCGCAGGTGAAAAA
40488265 TTGCAGCCCC
Statistics
Matches: 204, Mismatches: 40, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
212 2 0.01
213 200 0.98
214 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (213 bp):
CCCAACTGTCATATTAAGGCTCGCAGGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA
CAAACTCCCAACTATCATATTAAAGCTCACAGGTGAAAAACCGCAGCCTCCAACACAATTAGCAA
GAGTTACAAACTCTCAACTATCATATTAAGGCTTATAAGTAAAAAACCACAGCCTCCAACACAGT
TACCGAGAGTTACAAACT
Found at i:40515551 original size:54 final size:54
Alignment explanation
Indices: 40515469--40515574 Score: 212
Period size: 54 Copynumber: 2.0 Consensus size: 54
40515459 GCTAAATGTG
40515469 TTATTTTAGATCAAGAAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAAA
1 TTATTTTAGATCAAGAAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAAA
40515523 TTATTTTAGATCAAGAAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAA
1 TTATTTTAGATCAAGAAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAA
40515575 GATTGTGGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (54 bp):
TTATTTTAGATCAAGAAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAAA
Found at i:40518472 original size:53 final size:53
Alignment explanation
Indices: 40518392--40518497 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
40518382 TCTGCAGCCA
40518392 GTGTAGGGAACTCGAGATTTGTTAAACCCGAGTGCCAGCGATGTGGTAGAAAT
1 GTGTAGGGAACTCGAGATTTGTTAAACCCGAGTGCCAGCGATGTGGTAGAAAT
*
40518445 GTGTAGGGAACTCGAGATTTGTTAAACCCGAGTGCCAGCGGTGTGGTAGAAAT
1 GTGTAGGGAACTCGAGATTTGTTAAACCCGAGTGCCAGCGATGTGGTAGAAAT
40518498 CATTTTGGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (53 bp):
GTGTAGGGAACTCGAGATTTGTTAAACCCGAGTGCCAGCGATGTGGTAGAAAT
Found at i:40521705 original size:200 final size:200
Alignment explanation
Indices: 40521362--40521764 Score: 788
Period size: 200 Copynumber: 2.0 Consensus size: 200
40521352 ATGGACAATC
40521362 AGAGAGAGTAATTTAGATTCTTGAAGACATGTTCAGATGTTGCGTATTGGAATTTCAAGATAGTT
1 AGAGAGAGTAATTTAGATTCTTGAAGACATGTTCAGATGTTGCGTATTGGAATTTCAAGATAGTT
40521427 CGGAAAGGTACTTACCATTGGTAGAATTTGCTTATAATAATAGTTATCAGACAAGTTTGAAGATG
66 CGGAAAGGTACTTACCATTGGTAGAATTTGCTTATAATAATAGTTATCAGACAAGTTTGAAGATG
*
40521492 GCACCTTATGAAGCATTATATGGTCGTAAATGTCGGACGCCGTTGTATTGGACTGAACTCAAGGA
131 GCACCTTATGAAGCATTATATGGTCGTAAATGTCGGACGCCATTGTATTGGACTGAACTCAAGGA
40521557 AAATT
196 AAATT
40521562 AGAGAGAGTAATTTAGATTCTTGAAGACATGTTCAGATGTTGCGTATTGGAATTTCAAGATAGTT
1 AGAGAGAGTAATTTAGATTCTTGAAGACATGTTCAGATGTTGCGTATTGGAATTTCAAGATAGTT
*
40521627 CGGAAAGGTACTTACCATTGGTAGAATTTGCTTATAATAATAGTTATTAGACAAGTTTGAAGATG
66 CGGAAAGGTACTTACCATTGGTAGAATTTGCTTATAATAATAGTTATCAGACAAGTTTGAAGATG
40521692 GCACCTTATGAAGCATTATATGGTCGTAAATGTCGGACGCCATTGTATTGGACTGAACTCAAGGA
131 GCACCTTATGAAGCATTATATGGTCGTAAATGTCGGACGCCATTGTATTGGACTGAACTCAAGGA
40521757 AAATT
196 AAATT
40521762 AGA
1 AGA
40521765 TTTATGGAGT
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (200 bp):
AGAGAGAGTAATTTAGATTCTTGAAGACATGTTCAGATGTTGCGTATTGGAATTTCAAGATAGTT
CGGAAAGGTACTTACCATTGGTAGAATTTGCTTATAATAATAGTTATCAGACAAGTTTGAAGATG
GCACCTTATGAAGCATTATATGGTCGTAAATGTCGGACGCCATTGTATTGGACTGAACTCAAGGA
AAATT
Found at i:40522826 original size:22 final size:22
Alignment explanation
Indices: 40522797--40522868 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
40522787 TGTTTCAAGC
40522797 TTCCAAGCTCCATAGTAAGTGA
1 TTCCAAGCTCCATAGTAAGTGA
* * * *
40522819 TTCGAAGCTCCGT-TTCAA--GC
1 TTCCAAGCTCCATAGT-AAGTGA
40522839 TTCCAAGCTCCATAGTAAGTGA
1 TTCCAAGCTCCATAGTAAGTGA
40522861 TTCCAAGC
1 TTCCAAGC
40522869 CCGTTTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 14 0.37
21 2 0.05
22 22 0.58
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (22 bp):
TTCCAAGCTCCATAGTAAGTGA
Found at i:40522847 original size:42 final size:41
Alignment explanation
Indices: 40522788--40522874 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 41
40522778 GCTAGGGTTT
*
40522788 GTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCGAAGCTCC
1 GTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGC-CC
40522830 GTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCC
1 GTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCC
40522871 GTTT
1 GTTT
40522875 TTAATGATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 6 0.14
42 38 0.86
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (41 bp):
GTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCC
Found at i:40523738 original size:46 final size:46
Alignment explanation
Indices: 40523684--40523856 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
40523674 TGGTTGAGCA
*
40523684 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
40523730 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGCAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
40523777 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
40523823 -CCTGAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40523857 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 7 0.07
45 5 0.05
46 58 0.54
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:40523840 original size:93 final size:93
Alignment explanation
Indices: 40523681--40523851 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
40523671 GGATGGTTGA
*
40523681 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCAAACTCGTTGAGT
40523746 TGAGTCCGAGTTCGTGAGATGCAACTAG
66 TGAGTCCGAGTTCGTGAGATGCAACTAG
* * *
40523774 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-AAACTCGTTGAG
*
40523838 TTGAGTTCGAGTTC
65 TTGAGTCCGAGTTC
40523852 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGCAACTAG
Found at i:40533734 original size:58 final size:58
Alignment explanation
Indices: 40533644--40533756 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
40533634 TTTTTATTCA
40533644 TGCTGGATGTCCGCAACAAGTTAGGAATCTGAAGGTATTAATCAATACATCAATCTCC
1 TGCTGGATGTCCGCAACAAGTTAGGAATCTGAAGGTATTAATCAATACATCAATCTCC
*
40533702 TGCTGGATGTCCGCACCAAGTTAGGAATCTGAAGGTATTAATCAATACATCAATC
1 TGCTGGATGTCCGCAACAAGTTAGGAATCTGAAGGTATTAATCAATACATCAATC
40533757 CTCATTCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (58 bp):
TGCTGGATGTCCGCAACAAGTTAGGAATCTGAAGGTATTAATCAATACATCAATCTCC
Found at i:40535781 original size:72 final size:72
Alignment explanation
Indices: 40535688--40535827 Score: 271
Period size: 72 Copynumber: 1.9 Consensus size: 72
40535678 CCGTTATTAG
*
40535688 AAATCAAGATTGAAGCTCAAGAATATTTTTTTTTTCATTTCAAAAATCAAGTTTGAGTTTATAAG
1 AAATCAAGATTGAAGCGCAAGAATATTTTTTTTTTCATTTCAAAAATCAAGTTTGAGTTTATAAG
40535753 GTTTTAA
66 GTTTTAA
40535760 AAATCAAGATTGAAGCGCAAGAATATTTTTTTTTTCATTTCAAAAATCAAGTTTGAGTTTATAAG
1 AAATCAAGATTGAAGCGCAAGAATATTTTTTTTTTCATTTCAAAAATCAAGTTTGAGTTTATAAG
40535825 GTT
66 GTT
40535828 AGTTGATAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (72 bp):
AAATCAAGATTGAAGCGCAAGAATATTTTTTTTTTCATTTCAAAAATCAAGTTTGAGTTTATAAG
GTTTTAA
Found at i:40542750 original size:20 final size:19
Alignment explanation
Indices: 40542727--40542768 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
40542717 AGATTATATA
40542727 TATTAT-ATTATATAATTGAT
1 TATTATAATTAT-TAATTG-T
40542747 TATTATAATTATTAATTGT
1 TATTATAATTATTAATTGT
40542766 TAT
1 TAT
40542769 GGTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTATAATTATTAATTGT
Found at i:40543137 original size:13 final size:13
Alignment explanation
Indices: 40543091--40543142 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
40543081 TTATTAAGTT
40543091 AATAAAATAAA-A
1 AATAAAATAAAGA
*
40543103 TAATAAAAGAAATGA
1 -AATAAAATAAA-GA
40543118 AATAAAATAAAGA
1 AATAAAATAAAGA
* *
40543131 AACAAAACAAAG
1 AATAAAATAAAG
40543143 TAAAGAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 10 0.30
15 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:40543975 original size:40 final size:40
Alignment explanation
Indices: 40543905--40543991 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
40543895 AATTTATGGG
* * *
40543905 TTACTAAATATTGTTTTGAATACGGAATTGAACTGTGAAA
1 TTACTGAATATTGTTATGAATACGGAATTGAACTGTAAAA
* * *
40543945 TTACTGAATATTGTTATGTATACTGTATTGAACTGTAAAA
1 TTACTGAATATTGTTATGAATACGGAATTGAACTGTAAAA
*
40543985 TTTCTGA
1 TTACTGA
40543992 TGAAAAGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41
Consensus pattern (40 bp):
TTACTGAATATTGTTATGAATACGGAATTGAACTGTAAAA
Found at i:40544272 original size:18 final size:19
Alignment explanation
Indices: 40544245--40544285 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
40544235 GTGTGTCGAA
* *
40544245 TACTGTTACCGTTACT-AT
1 TACTGCTACCGTCACTGAT
40544263 TACTGCTACCGTCACTGAT
1 TACTGCTACCGTCACTGAT
40544282 TACT
1 TACT
40544286 ATTTAGGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (19 bp):
TACTGCTACCGTCACTGAT
Found at i:40550026 original size:34 final size:34
Alignment explanation
Indices: 40549983--40550050 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
40549973 AAATGTAACN
*
40549983 AAAGGGCCAAAATGACAAATATGTCATTAAGTAA
1 AAAGGGCCAAAATGACAAATATGCCATTAAGTAA
**
40550017 AAAGGGCCAAAATGGTAAATATGCCATTAAGTAA
1 AAAGGGCCAAAATGACAAATATGCCATTAAGTAA
40550051 TGGTTGAGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (34 bp):
AAAGGGCCAAAATGACAAATATGCCATTAAGTAA
Found at i:40550164 original size:3 final size:3
Alignment explanation
Indices: 40550156--40550217 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
40550146 TGGTTTTATG
* * *
40550156 TTA TTA TTA GTA TTA ATA TTA -AA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
40550203 CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
40550218 AAGATAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:40550519 original size:13 final size:14
Alignment explanation
Indices: 40550501--40550547 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
40550491 TTATTAAGTT
40550501 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
40550514 AATAAAAGAAATGA
1 AATAAAATAAAAGA
40550528 AATAAAAT-AAAGA
1 AATAAAATAAAAGA
*
40550541 AACAAAA
1 AATAAAA
40550548 CAAAGTAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:40551382 original size:40 final size:40
Alignment explanation
Indices: 40551312--40551398 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
40551302 AATTTATGAG
* *
40551312 TTACTGAATATTGTTTTGAATACCGAATTGAACTGTGAAA
1 TTACTGAATATTGTTATGAATACCGAATTGAACTGTAAAA
* * *
40551352 TTACTGAATATTGTTATGTATACTGTATTGAACTGTAAAA
1 TTACTGAATATTGTTATGAATACCGAATTGAACTGTAAAA
*
40551392 TTTCTGA
1 TTACTGA
40551399 TGAAACGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (40 bp):
TTACTGAATATTGTTATGAATACCGAATTGAACTGTAAAA
Found at i:40553138 original size:21 final size:20
Alignment explanation
Indices: 40553114--40553154 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
40553104 ACAAATACGA
40553114 ATGCAAATAAAAATGAAAAAT
1 ATGCAAATAAAAA-GAAAAAT
* *
40553135 ATGCAATTGAAAAGAAAAAT
1 ATGCAAATAAAAAGAAAAAT
40553155 CAAAAGCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (20 bp):
ATGCAAATAAAAAGAAAAAT
Found at i:40555408 original size:5 final size:5
Alignment explanation
Indices: 40555392--40555434 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
40555382 TAGGAAGATA
*
40555392 TTATT TTGTT TTATT TTATTAT TTATT ATTATT TTATT TTATT
1 TTATT TTATT TTATT TTA-T-T TTATT -TTATT TTATT TTATT
40555435 AATTTAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 22 0.67
6 7 0.21
7 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:40559269 original size:47 final size:47
Alignment explanation
Indices: 40559206--40559359 Score: 245
Period size: 47 Copynumber: 3.3 Consensus size: 47
40559196 CCCTTCGGGA
*
40559206 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* * * *
40559253 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
40559300 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
40559347 CTTATCACATATA
1 CTTATCACATATA
40559360 CATATCTTGT
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:40566919 original size:20 final size:20
Alignment explanation
Indices: 40566878--40566919 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40566868 ATTTTGTACG
*
40566878 TTGGCCCATTTTCTCTTTTT
1 TTGGCCCATTTTCTCTTCTT
40566898 TTGGCCCA-TTTCTCGTTCTT
1 TTGGCCCATTTTCTC-TTCTT
40566918 TT
1 TT
40566920 CACTCTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.05, C:0.26, G:0.12, T:0.57
Consensus pattern (20 bp):
TTGGCCCATTTTCTCTTCTT
Found at i:40567179 original size:47 final size:47
Alignment explanation
Indices: 40567107--40567201 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
40567097 TAACGACGTT
* *
40567107 AAAAAGCGCTTTTTGGGAGGTAACCCAAATTTATTTTCATTTATTTA
1 AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
40567154 AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
1 AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
40567201 A
1 A
40567202 TTTTTAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (47 bp):
AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
Found at i:40568811 original size:21 final size:21
Alignment explanation
Indices: 40568787--40568831 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40568777 CCACTCTTGA
40568787 TATG-TTAAATATTCATGATGC
1 TATGATTAAATATT-ATGATGC
* *
40568808 TATGATTAATTATTTTGATGC
1 TATGATTAAATATTATGATGC
40568829 TAT
1 TAT
40568832 TGGTTGGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (21 bp):
TATGATTAAATATTATGATGC
Found at i:40570081 original size:4 final size:4
Alignment explanation
Indices: 40570072--40570112 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
40570062 TTTCTTGTGC
* *
40570072 ATAA ATAA ATAC ATAA ATAA ATAC ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
40570113 GGTTCAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:40570088 original size:12 final size:12
Alignment explanation
Indices: 40570071--40570112 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
40570061 TTTTCTTGTG
40570071 CATAAATAAATA
1 CATAAATAAATA
40570083 CATAAATAAATA
1 CATAAATAAATA
40570095 CATAAATAAATA
1 CATAAATAAATA
*
40570107 AATAAA
1 CATAAA
40570113 GGTTCAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
CATAAATAAATA
Found at i:40570896 original size:12 final size:13
Alignment explanation
Indices: 40570879--40570907 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40570869 ATTATTTTGT
40570879 TTTATTTTATT-A
1 TTTATTTTATTAA
40570891 TTTATTTTATTAA
1 TTTATTTTATTAA
40570904 TTTA
1 TTTA
40570908 GGTTAGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTATTAA
Found at i:40576361 original size:20 final size:20
Alignment explanation
Indices: 40576328--40576402 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
40576318 ATACGTGGGT
40576328 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
40576345 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
40576366 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
40576386 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
40576403 GTAATCATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:40576363 original size:11 final size:11
Alignment explanation
Indices: 40576347--40576402 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40576337 CATGATTGAT
40576347 ATGATATGCAC
1 ATGATATGCAC
*
40576358 ATGATATG--T
1 ATGATATGCAC
40576367 ATGATATGCAC
1 ATGATATGCAC
*
40576378 ATGATATG--T
1 ATGATATGCAC
*
40576387 ATGAAATGCAC
1 ATGATATGCAC
40576398 ATGAT
1 ATGAT
40576403 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40576481 original size:26 final size:26
Alignment explanation
Indices: 40576452--40576523 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
40576442 GAGGAAGTGC
**
40576452 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
40576478 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
40576504 AAAAGGGCTT-CGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40576524 ATTAAAGAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 9 0.21
26 34 0.79
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:40579816 original size:220 final size:221
Alignment explanation
Indices: 40579434--40579884 Score: 841
Period size: 220 Copynumber: 2.0 Consensus size: 221
40579424 TAGATAAACT
40579434 CTTTAGGGCGGTGCCTTTAGAGACACAAGGTAAGATTTTTGAAGGAGATTTGATGGAGCTGCCAT
1 CTTTAGGGCGGTGCCTTTAGAGACACAAGGTAAGATTTTTGAAGGAGATTTGATGGAGCTGCCAT
*
40579499 TTGGGGATTTTGATCTTATATTGGGAATGGACTGGCTAACTAAGCATAAGGCGACGTTGGATTGT
66 TTGGGGATTTTGATCTTATATTGGGAATGGACTGGCTAACTAAGCATAAGGCAACGTTGGATTGT
40579564 GCTGCAAAGAGAATGGTACTAAGAACTGCTGAAGATGAGGAGATAATGGTCATAGGGGAACGAAA
131 GCTGCAAAGAGAATGGTACTAAGAACTGCTGAAGATGAGGAGATAATGGTCATAGGGGAACGAAA
40579629 GAATTATTTGTCCAATGTTGTTTT-G
196 GAATTATTTGTCCAATGTTGTTTTGG
*
40579654 CTTTAGGGCGGTGCTTTTAGAGACACAAGGTAAGATTTTTGAAGGAGATTTGATGGAGCTGCCAT
1 CTTTAGGGCGGTGCCTTTAGAGACACAAGGTAAGATTTTTGAAGGAGATTTGATGGAGCTGCCAT
* * *
40579719 TTGGGTATTTTGATCTTATCTTGGGAATGGACTGGCTAACTAAGCATAAGGCAATGTTGGATTGT
66 TTGGGGATTTTGATCTTATATTGGGAATGGACTGGCTAACTAAGCATAAGGCAACGTTGGATTGT
40579784 GCTGCAAAGAGAATGGTACTAAGAACTGCTGAAGATGAGGAGATAATGGTCATAGGGGAACGAAA
131 GCTGCAAAGAGAATGGTACTAAGAACTGCTGAAGATGAGGAGATAATGGTCATAGGGGAACGAAA
40579849 GAATTATTTGTCCAATGTTGTTTTGG
196 GAATTATTTGTCCAATGTTGTTTTGG
40579875 CTTTAAGGGC
1 CTTT-AGGGC
40579885 CGAGAAGTTG
Statistics
Matches: 224, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
220 214 0.96
221 5 0.02
222 5 0.02
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (221 bp):
CTTTAGGGCGGTGCCTTTAGAGACACAAGGTAAGATTTTTGAAGGAGATTTGATGGAGCTGCCAT
TTGGGGATTTTGATCTTATATTGGGAATGGACTGGCTAACTAAGCATAAGGCAACGTTGGATTGT
GCTGCAAAGAGAATGGTACTAAGAACTGCTGAAGATGAGGAGATAATGGTCATAGGGGAACGAAA
GAATTATTTGTCCAATGTTGTTTTGG
Found at i:40584217 original size:9 final size:10
Alignment explanation
Indices: 40584205--40584261 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
40584195 TACGTGGGAT
40584205 ATGATAT-AC
1 ATGATATGAC
*
40584214 ATGAT-TGAT
1 ATGATATGAC
40584223 ATGATATGCAC
1 ATGATATG-AC
*
40584234 ATGATATG-T
1 ATGATATGAC
40584243 ATGATATGCAC
1 ATGATATG-AC
40584254 ATGATATG
1 ATGATATG
40584262 TATGAAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (10 bp):
ATGATATGAC
Found at i:40584237 original size:20 final size:20
Alignment explanation
Indices: 40584204--40584278 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
40584194 ATACGTGGGA
40584204 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
40584221 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
40584242 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
40584262 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
40584279 GAATTCATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:40584239 original size:11 final size:11
Alignment explanation
Indices: 40584223--40584278 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40584213 CATGATTGAT
40584223 ATGATATGCAC
1 ATGATATGCAC
*
40584234 ATGATATG--T
1 ATGATATGCAC
40584243 ATGATATGCAC
1 ATGATATGCAC
*
40584254 ATGATATG--T
1 ATGATATGCAC
*
40584263 ATGAAATGCAC
1 ATGATATGCAC
40584274 ATGAT
1 ATGAT
40584279 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40584357 original size:26 final size:26
Alignment explanation
Indices: 40584328--40584399 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
40584318 GAGGAAGTGC
*
40584328 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40584354 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
40584380 AAAAGGGCTT-TACCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40584400 ATTAAAGAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 9 0.20
26 35 0.80
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40585507 original size:13 final size:13
Alignment explanation
Indices: 40585489--40585521 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40585479 CTGTGTCTCT
40585489 CACACGGTCGAGA
1 CACACGGTCGAGA
40585502 CACACGGTCGAGA
1 CACACGGTCGAGA
40585515 CACACGG
1 CACACGG
40585522 CCGTGTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.33, G:0.30, T:0.06
Consensus pattern (13 bp):
CACACGGTCGAGA
Found at i:40586620 original size:42 final size:43
Alignment explanation
Indices: 40586498--40586706 Score: 126
Period size: 42 Copynumber: 4.9 Consensus size: 43
40586488 AGTAAGATGC
* * * ** * *
40586498 CAATGCCATATCCTAGATATGCTCTTACATGGGA-TCACATAT
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCATAT
* * *
40586540 CAAAGCCAATAGCCCA-ACTATGGTC--ATACACGATGTCTCATAT
1 CAATGCC-ATATCCCAGA-TATGGTCTTATACA-GAAGTCTCATAT
* * *
40586583 CGATGTCATATCCCAGATATGGTCTTATA-AGAAGTCTCATTTT
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCA-TAT
* * * * * * * **
40586626 TAAAGCCATGTCCCAAACATGGTCTTATACA-AAATCACATGC
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCATAT
*
40586668 CTATGCCATATCCCAGATATGGTCTTATACAGAA-TCTCA
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCA
40586707 ATAACCCTAA
Statistics
Matches: 123, Mismatches: 34, Indels: 20
0.69 0.19 0.11
Matches are distributed among these distances:
41 2 0.02
42 60 0.49
43 57 0.46
44 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (43 bp):
CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCATAT
Found at i:40616425 original size:13 final size:13
Alignment explanation
Indices: 40616404--40616449 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
40616394 AATATAATTT
*
40616404 TAAACATTAAATA
1 TAAATATTAAATA
40616417 TAAATATTAAA-A
1 TAAATATTAAATA
40616429 TAAA-ATATAAATA
1 TAAATAT-TAAATA
40616442 TATAATAT
1 TA-AATAT
40616450 ACAAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.07
12 9 0.32
13 13 0.46
14 2 0.07
15 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:40616439 original size:19 final size:20
Alignment explanation
Indices: 40616389--40616442 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
40616379 TACATAATAT
*
40616389 ATAATAATAT-AATTTTAAAC
1 ATAA-AATATAAATATTAAAC
*
40616409 ATTAAATATAAATATTAAA-
1 ATAAAATATAAATATTAAAC
40616428 ATAAAATATAAATAT
1 ATAAAATATAAATAT
40616443 ATAATATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAATATAAATATTAAAC
Found at i:40619200 original size:27 final size:27
Alignment explanation
Indices: 40619170--40619347 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40619160 ATATTGAGTC
* * * *
40619170 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40619197 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40619224 CGCACACTTAGTGCCACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40619252 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40619279 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40619306 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40619333 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40619348 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 25 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40619309 original size:82 final size:81
Alignment explanation
Indices: 40619191--40619346 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40619181 TGCTATATAA
* *
40619191 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40619256 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40619273 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40619337 CACTTAGTGC
65 CACTTAGTGC
40619347 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40628109 original size:28 final size:27
Alignment explanation
Indices: 40628048--40628172 Score: 187
Period size: 28 Copynumber: 4.6 Consensus size: 27
40628038 ATATTAAGTC
* *
40628048 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
40628075 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
40628103 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* *
40628131 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
40628158 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40628173 GCACAATTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
27 39 0.43
28 50 0.56
29 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:40628161 original size:55 final size:55
Alignment explanation
Indices: 40628048--40628172 Score: 198
Period size: 55 Copynumber: 2.3 Consensus size: 55
40628038 ATATTAAGTC
* *
40628048 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
* *
40628103 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCA-ATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCATACT
40628158 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40628173 GCACAATTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
55 38 0.58
56 27 0.42
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
Found at i:40646726 original size:55 final size:55
Alignment explanation
Indices: 40646605--40646747 Score: 144
Period size: 55 Copynumber: 2.6 Consensus size: 55
40646595 TTATCAATGG
* *
40646605 CCGTGGGCGAACCTACCAAAACAACACGGGCGTAAGACACGCCCGTGCCTAGAAA
1 CCGTGGGCGAACCTACCAAAACAACACGGGCGTAAGACACACCCGTGCCTAAAAA
** * * ** * **
40646660 CATTGGTCGAACCTATCAAATTAACACGGGTGTGCGACACACCCGTGCC-AAACAA
1 CCGTGGGCGAACCTACCAAAACAACACGGGCGTAAGACACACCCGTGCCTAAA-AA
* * *
40646715 CCGTGGGCGAACTTGCCAAAACAACACAGGCGT
1 CCGTGGGCGAACCTACCAAAACAACACGGGCGT
40646748 GGGAGAAGCG
Statistics
Matches: 66, Mismatches: 21, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
54 2 0.03
55 64 0.97
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.13
Consensus pattern (55 bp):
CCGTGGGCGAACCTACCAAAACAACACGGGCGTAAGACACACCCGTGCCTAAAAA
Found at i:40651092 original size:16 final size:16
Alignment explanation
Indices: 40651071--40651102 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40651061 GTTATTATTT
40651071 TCTGAATCGTATGATA
1 TCTGAATCGTATGATA
*
40651087 TCTGAATTGTATGATA
1 TCTGAATCGTATGATA
40651103 AATATTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (16 bp):
TCTGAATCGTATGATA
Found at i:40677104 original size:92 final size:92
Alignment explanation
Indices: 40676937--40677162 Score: 251
Period size: 92 Copynumber: 2.5 Consensus size: 92
40676927 AGGCCAAATA
* * *
40676937 AGATAATAGTACGCAGCATAGCTGACGTACGTACAGTACAGTGCAATGCGGTAATCCACTGTACA
1 AGATAATAGTACGCAGCATAGCTAACGTACGTACAGTACAGTGCAATGCGGTAAACCACTATACA
40677002 GTCATGTTGCAGTTACACTGCCAGATC
66 GTCATGTTGCAGTTACACTGCCAGATC
* * * ** *
40677029 AGATAATAGTATGTAGCATAGCTAACGTACGTACGGTACAGTGTGATGCGGTAAACCGCTATACC
1 AGATAATAGTACGCAGCATAGCTAACGTACGTACAGTACAGTGCAATGCGGTAAACCACTATA-C
* * * * * *
40677094 AGTTAT-TTGCAGTCAAACTACCATATT
65 AGTCATGTTGCAGTTACACTGCCAGATC
* *
40677121 AGATAA-AGGTACGCAGCAGAGCTGAA-GTATGTACAGTACAGT
1 AGATAATA-GTACGCAGCATAGCT-AACGTACGTACAGTACAGT
40677163 CTTCCTTCTC
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
91 1 0.01
92 102 0.92
93 8 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (92 bp):
AGATAATAGTACGCAGCATAGCTAACGTACGTACAGTACAGTGCAATGCGGTAAACCACTATACA
GTCATGTTGCAGTTACACTGCCAGATC
Found at i:40682097 original size:16 final size:16
Alignment explanation
Indices: 40682078--40682108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40682068 CTTCTTCACT
40682078 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
40682094 TACTTACTTACTTAA
1 TACTCACTTACTTAA
40682109 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:40682114 original size:20 final size:20
Alignment explanation
Indices: 40682075--40682114 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40682065 AAACTTCTTC
* *
40682075 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
40682095 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
40682115 TTATTAATAC
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:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:40682486 original size:55 final size:52
Alignment explanation
Indices: 40682300--40682554 Score: 234
Period size: 55 Copynumber: 4.8 Consensus size: 52
40682290 ACACGGGTAC
* * * *
40682300 CTTACCATTGCCATGACTTGTCATGGTCTTACATGGTATCCTT---T-TAAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTATAGAA
* * *
40682349 CTTACCATTGCCATGTCTTGATATGGTCTTACATGGTATCCTTGCCGTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCC-TATAGAA
* * *
40682402 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCC-TATAG-AA
* * * *
40682457 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCT-TAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTATAG-AA
*
40682510 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
40682555 CAACCTAATG
Statistics
Matches: 170, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
49 40 0.24
52 2 0.01
53 48 0.28
54 11 0.06
55 67 0.39
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (52 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTATAGAA
Found at i:40682491 original size:108 final size:110
Alignment explanation
Indices: 40682347--40682547 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
40682337 ATCCTTTTAA
* * *
40682347 AACTTACCATTGCCATGTCTTGATATGGTCTTACATGGTATCCTTGCCGTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCGTA-GAAACCTCACCAA
40682410 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * *
40682455 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCGTAGAAACCTCACCAAT
40682520 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
40682548 TATCCTTCAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.57
109 7 0.08
110 28 0.34
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCGTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Done.