Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 179 of 214
Found at i:52600182 original size:21 final size:21
Alignment explanation
Indices: 52600136--52600189 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
52600126 CCCTAATTAA
* *
52600136 TCTAACTTCTAGCCCCTAACC
1 TCTAACTCCTAACCCCTAACC
* *
52600157 CCTAACTCCTAACCCCTAACT
1 TCTAACTCCTAACCCCTAACC
*
52600178 TCTAACCCCTAA
1 TCTAACTCCTAA
52600190 ACCATAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.44, G:0.02, T:0.26
Consensus pattern (21 bp):
TCTAACTCCTAACCCCTAACC
Found at i:52600913 original size:82 final size:81
Alignment explanation
Indices: 52600766--52600917 Score: 259
Period size: 81 Copynumber: 1.9 Consensus size: 81
52600756 ACACTGACAA
* * *
52600766 CTAATCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTA
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
52600831 ACCTGACCCCGAATCT
66 ACCTGACCCCGAATCT
*
52600847 CTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAAATCCT
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAACCCTAAACCCT
52600912 AACCTG
65 AACCTG
52600918 TCACTGAATC
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 34 0.52
82 32 0.48
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.30
Consensus pattern (81 bp):
CTAACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
ACCTGACCCCGAATCT
Found at i:52600927 original size:82 final size:81
Alignment explanation
Indices: 52600766--52600927 Score: 252
Period size: 82 Copynumber: 2.0 Consensus size: 81
52600756 ACACTGACAA
* * *
52600766 CTAATCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTA
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
*
52600831 ACCTGACCCCGAATCT
66 ACCTGACACCGAATCT
*
52600847 CTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAAATCCT
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAACCCTAAACCCT
* *
52600912 AACCTGTCACTGAATC
65 AACCTGACACCGAATC
52600928 CATAAACCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 34 0.47
82 39 0.53
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (81 bp):
CTAACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
ACCTGACACCGAATCT
Found at i:52600976 original size:21 final size:21
Alignment explanation
Indices: 52600932--52600977 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
52600922 TGAATCCATA
* *
52600932 AACCTTAAATCCCTAACTCTT
1 AACCTTAAATCCCTAACCCCT
*
52600953 AACCTTTAATCCCTAACCCCT
1 AACCTTAAATCCCTAACCCCT
52600974 AACC
1 AACC
52600978 CATAAACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.28
Consensus pattern (21 bp):
AACCTTAAATCCCTAACCCCT
Found at i:52601003 original size:14 final size:14
Alignment explanation
Indices: 52600984--52601013 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52600974 AACCCATAAA
52600984 CCTTAAATCACAAC
1 CCTTAAATCACAAC
*
52600998 CCTTAAATCAGAAC
1 CCTTAAATCACAAC
52601012 CC
1 CC
52601014 CTAATCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.37, G:0.03, T:0.20
Consensus pattern (14 bp):
CCTTAAATCACAAC
Found at i:52601046 original size:22 final size:21
Alignment explanation
Indices: 52601012--52601053 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
52601002 AAATCAGAAC
52601012 CCCTAATCCATAATCCATAAG
1 CCCTAATCCATAATCCATAAG
*
52601033 CCCTAATTCCATAATCTATAA
1 CCCTAA-TCCATAATCCATAA
52601054 ACCTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (21 bp):
CCCTAATCCATAATCCATAAG
Found at i:52601139 original size:21 final size:22
Alignment explanation
Indices: 52601099--52601142 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
52601089 CCTAAATTAG
*
52601099 CCATATATATATATACCCTAAA
1 CCATATATATATAAACCCTAAA
52601121 CCATATATAT-TAAACCCTAAA
1 CCATATATATATAAACCCTAAA
52601142 C
1 C
52601143 TATAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (22 bp):
CCATATATATATAAACCCTAAA
Found at i:52601447 original size:89 final size:89
Alignment explanation
Indices: 52601344--52601523 Score: 333
Period size: 89 Copynumber: 2.0 Consensus size: 89
52601334 TTATTTCTAC
*
52601344 GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTCAATTAAAAATAAATTGAATTTTAAT
1 GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
52601409 TAATATAAATAAACAAATTAAATA
66 TAATATAAATAAACAAATTAAATA
*
52601433 GTGTCATTATTTCAAATTTATCTATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
1 GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
*
52601498 TAATATAAATAAATAAATTAAATA
66 TAATATAAATAAACAAATTAAATA
52601522 GT
1 GT
52601524 AAATAGACAG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (89 bp):
GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
TAATATAAATAAACAAATTAAATA
Found at i:52601604 original size:41 final size:41
Alignment explanation
Indices: 52601547--52601781 Score: 346
Period size: 41 Copynumber: 5.7 Consensus size: 41
52601537 AAATGTTCTT
*
52601547 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
52601588 GCGGCGCTGTTACAAAAACGCCGCTAAAGAACTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
52601629 GCGGCGCTTATCCAAAAACGCCACTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
52601670 GCGGCGCTTCTCCATAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
52601711 GCGGCGCTTTTCCAAAAACGCCGCTAAA-AATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAA-CTGAGCATTA
**
52601752 GCGGCGCTTTTTTTAAAAACGCCGCTAAAG
1 GCGGCGC-TTTTCCAAAAACGCCGCTAAAG
52601782 CTCGAAAGGC
Statistics
Matches: 175, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 155 0.89
42 19 0.11
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
Found at i:52601873 original size:40 final size:39
Alignment explanation
Indices: 52601818--52601954 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
52601808 GGGCTTAGGG
* * *
52601818 TTTTTTGCGGCGTTTTTCCAAAAATCGCCGCTAATACTCA
1 TTTTTAGCGGCGTTTTT-CAAAAACCGCCGCTAATGCTCA
* *
52601858 TTTTTAGTGGCGTTTTTGAAAAACCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAACCGCCGCTAATGCTC-A
* * * ** * *
52601898 TCTTTAGCGGCATTTTACGTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAACCGCCGCTAATGC-TCA
52601938 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
52601955 TGTCCAAACG
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
39 18 0.23
40 59 0.76
41 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAACCGCCGCTAATGCTCA
Found at i:52602470 original size:39 final size:39
Alignment explanation
Indices: 52602427--52602510 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
52602417 TCTCATGATT
52602427 TACAACTTTATTGCTTACACCGTTTCTTCTTTGAGAAAC
1 TACAACTTTATTGCTTACACCGTTTCTTCTTTGAGAAAC
*
52602466 TACAATTTTATTGCTTACACCGTTTCTTCTTTGAGAAAC
1 TACAACTTTATTGCTTACACCGTTTCTTCTTTGAGAAAC
52602505 TA-AACT
1 TACAACT
52602511 CAATAAGCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 3 0.07
39 40 0.93
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (39 bp):
TACAACTTTATTGCTTACACCGTTTCTTCTTTGAGAAAC
Found at i:52612741 original size:45 final size:45
Alignment explanation
Indices: 52612677--52612836 Score: 302
Period size: 45 Copynumber: 3.6 Consensus size: 45
52612667 TGTCCTGAAG
52612677 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
1 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
52612722 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
1 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
*
52612767 ACAAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
1 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
*
52612812 ACTAGGAAGGAACCTGAGGATGGTG
1 ACTAGGAAGGAGCCTGAGGATGGTG
52612837 AGAACAGAAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.26, C:0.09, G:0.47, T:0.17
Consensus pattern (45 bp):
ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
Found at i:52615726 original size:10 final size:10
Alignment explanation
Indices: 52615688--52615726 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
52615678 TTATTTAAGC
52615688 AAAAAAAAA-
1 AAAAAAAAAG
52615697 AAAAAAAAA-
1 AAAAAAAAAG
52615706 AAAAAAAAAG
1 AAAAAAAAAG
*
52615716 AAAAAAGAAG
1 AAAAAAAAAG
52615726 A
1 A
52615727 GGGTGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 18 0.64
10 10 0.36
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:52615737 original size:1 final size:1
Alignment explanation
Indices: 52615688--52615721 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
52615678 TTATTTAAGC
*
52615688 AAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
52615722 GAAGAGGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:52618849 original size:23 final size:24
Alignment explanation
Indices: 52618823--52618882 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
52618813 TTTCATAAAA
52618823 ATATAATATAATAAAATTAA-ATT
1 ATATAATATAATAAAATTAATATT
* *
52618846 ATAT-ATAATATTAATATTAATATT
1 ATATAAT-ATAATAAAATTAATATT
*
52618870 AAATAAATATAAT
1 ATAT-AATATAAT
52618883 TATATACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 2 0.07
23 15 0.52
24 6 0.21
25 4 0.14
26 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAATATAATAAAATTAATATT
Found at i:52618858 original size:17 final size:18
Alignment explanation
Indices: 52618822--52618879 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
52618812 TTTTCATAAA
*
52618822 AATATAATATAATAAAATT
1 AATATTATAT-ATAAAATT
*
52618841 AA-ATTATATATAATATT
1 AATATTATATATAAAATT
* *
52618858 AATATTA-ATATTAAATA
1 AATATTATATATAAAATT
52618875 AATAT
1 AATAT
52618880 AATTATATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 21 0.64
18 10 0.30
19 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTATATATAAAATT
Found at i:52619830 original size:3 final size:3
Alignment explanation
Indices: 52619822--52619865 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
52619812 ATCATGAAAT
52619822 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52619866 GAAAAATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:52620137 original size:26 final size:26
Alignment explanation
Indices: 52620102--52620155 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
52620092 CATTTTTACT
52620102 ATAATAAAAATATATAATTTAATTTA
1 ATAATAAAAATATATAATTTAATTTA
52620128 ATAATAAAAATATATAATTTAATTTA
1 ATAATAAAAATATATAATTTAATTTA
52620154 AT
1 AT
52620156 TCCCCCCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAATAAAAATATATAATTTAATTTA
Found at i:52622597 original size:4 final size:4
Alignment explanation
Indices: 52622588--52622612 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52622578 TTTAGTCCTC
52622588 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
52622613 GATTTTTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:52626794 original size:17 final size:17
Alignment explanation
Indices: 52626772--52626805 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52626762 ATCCACTAAT
*
52626772 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
52626789 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
52626806 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:52631433 original size:17 final size:17
Alignment explanation
Indices: 52631411--52631444 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52631401 ATCCACTAAT
*
52631411 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
52631428 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
52631445 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:52641132 original size:73 final size:73
Alignment explanation
Indices: 52641040--52641176 Score: 238
Period size: 73 Copynumber: 1.9 Consensus size: 73
52641030 TGGCCAGGCC
52641040 GTGTGTCTCACATGGTCAAGAGACACGCCTATGTCTCAAGCCATGTGGACATTCGAAATAGGGGC
1 GTGTGTCTCACATGGTCAAGAGACACGCCTATGTCTCAAGCCATGTGGACATTCGAAATAGGGGC
52641105 ACACGGCT
66 ACACGGCT
* * * *
52641113 GTGTGTCTCACATGGTCAAGAGACACGTCTGTGTCTCAGGCCGTGTGGACATTCGAAATAGGGG
1 GTGTGTCTCACATGGTCAAGAGACACGCCTATGTCTCAAGCCATGTGGACATTCGAAATAGGGG
52641177 TACATGGCCG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (73 bp):
GTGTGTCTCACATGGTCAAGAGACACGCCTATGTCTCAAGCCATGTGGACATTCGAAATAGGGGC
ACACGGCT
Found at i:52641547 original size:54 final size:54
Alignment explanation
Indices: 52641461--52641576 Score: 205
Period size: 54 Copynumber: 2.1 Consensus size: 54
52641451 TAGTATGCTC
*
52641461 ACACGGGCATGTGGCTTGGCCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
1 ACACGGGCATGTGGCTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
* *
52641515 ACATGGGCATGTGGCTTGACCGTGTGACCCAAGTCATTAAGCACCCTAATTTGG
1 ACACGGGCATGTGGCTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
52641569 ACACGGGC
1 ACACGGGC
52641577 TGGGACACAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.22
Consensus pattern (54 bp):
ACACGGGCATGTGGCTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
Found at i:52642684 original size:25 final size:24
Alignment explanation
Indices: 52642620--52642734 Score: 95
Period size: 24 Copynumber: 4.7 Consensus size: 24
52642610 AGCTCTTTCA
* *
52642620 AGCCATATAACGGGAAGCTCAAGTG
1 AGCCAT-TAACGGGAAGCTCCAGAG
* * * *
52642645 AGTCGTGTAACGGAAAGCTCCGGAG
1 AGCCAT-TAACGGGAAGCTCCAGAG
* * *
52642670 AGCCATTAACGGGAAGTTCAAGCG
1 AGCCATTAACGGGAAGCTCCAGAG
* * *
52642694 AGCCAATATCGAGAAGCTCCAGAG
1 AGCCATTAACGGGAAGCTCCAGAG
52642718 AGCCATTAATCGGGAAG
1 AGCCATTAA-CGGGAAG
52642735 TTCATAAGAG
Statistics
Matches: 66, Mismatches: 23, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
24 38 0.58
25 28 0.42
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.16
Consensus pattern (24 bp):
AGCCATTAACGGGAAGCTCCAGAG
Found at i:52642744 original size:25 final size:24
Alignment explanation
Indices: 52642668--52642807 Score: 81
Period size: 25 Copynumber: 5.7 Consensus size: 24
52642658 AAAGCTCCGG
*
52642668 AGAGCCATTAACGGGAAGTTCA-A
1 AGAGCCATTATCGGGAAGTTCATA
* * * * *
52642691 GCGAGCCAATATCGAGAAGCTCCA-G
1 -AGAGCCATTATCGGGAAG-TTCATA
52642716 AGAGCCATTAATCGGGAAGTTCATA
1 AGAGCCATT-ATCGGGAAGTTCATA
*
52642741 AGAGCCAGTTATCGGGATGCTT--TGA
1 AGAGCCA-TTATCGGGAAG-TTCAT-A
* * *
52642766 AGAGCTAATTATCGAGAAGCTCATA
1 AGAGC-CATTATCGGGAAGTTCATA
* *
52642791 AGAGCCATAAACGGGAA
1 AGAGCCATTATCGGGAA
52642808 TCTCGTAAGA
Statistics
Matches: 87, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
24 34 0.39
25 47 0.54
26 6 0.07
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
AGAGCCATTATCGGGAAGTTCATA
Found at i:52644656 original size:42 final size:42
Alignment explanation
Indices: 52644603--52644702 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
52644593 CTATATGAAT
*
52644603 GGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAATG
1 GGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAACG
* *
52644645 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAACG
*
52644687 GGGACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
52644703 TACCGAGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAACG
Found at i:52648127 original size:27 final size:27
Alignment explanation
Indices: 52648089--52648141 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
52648079 TAGGAAAAGA
52648089 AAAAGAAAAAAAAGGGAAGAA-GAAAAC
1 AAAAGAAAAAAAAGGGAA-AATGAAAAC
*
52648116 AAAAGAAGAAAAAGGGAAAATGAAAA
1 AAAAGAAAAAAAAGGGAAAATGAAAA
52648142 AGAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAAAAAGGGAAAATGAAAAC
Found at i:52648708 original size:18 final size:18
Alignment explanation
Indices: 52648682--52648717 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52648672 TCATTGATGG
52648682 ATCTCATATTGAGATTGT
1 ATCTCATATTGAGATTGT
*
52648700 ATCTTATATTGAGATTGT
1 ATCTCATATTGAGATTGT
52648718 GAATGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (18 bp):
ATCTCATATTGAGATTGT
Found at i:52656140 original size:20 final size:20
Alignment explanation
Indices: 52656117--52656164 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
52656107 ATTTATTTAT
*
52656117 TAAAATAAAAATTTTATAAA
1 TAAAATAAAAATCTTATAAA
* *
52656137 TAAAATCATAATCTTATAAA
1 TAAAATAAAAATCTTATAAA
52656157 TAAAATAA
1 TAAAATAA
52656165 TTTAAGGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAAAAATCTTATAAA
Found at i:52666985 original size:43 final size:43
Alignment explanation
Indices: 52666924--52667127 Score: 275
Period size: 43 Copynumber: 4.7 Consensus size: 43
52666914 GCTCTTCCCT
52666924 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* * * *
52666967 CCGCTAAAGACCAGGACCTTTAGCGACGCTTTTCCCAAAAATG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
*
52667010 CCGCTAAAGA-CAATGACCTTTAGCGGCGTTTTTCCCACAAACG
1 CCGCTAAAGACCAA-GACCTTTAGCGGCGCTTTTCCCACAAACG
* ** *
52667053 CCGCTAATGACCAAGACCTTTAGCGGCGCTTTTCCCTGAAGCG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* ** *
52667096 CCGCTAAAAAATAAGACCTTTAGCGACGCTTT
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTT
52667128 CTCCAAAAAC
Statistics
Matches: 140, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 2 0.01
43 135 0.96
44 3 0.02
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (43 bp):
CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
Found at i:52668077 original size:23 final size:23
Alignment explanation
Indices: 52668051--52668482 Score: 286
Period size: 23 Copynumber: 19.0 Consensus size: 23
52668041 AATGGAAAGT
*
52668051 AGCACTTTAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTGC
*
52668074 AGCAAC-TGAACACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTGC
52668097 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTGC
* * *
52668120 AGCACTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTGC
* *
52668142 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTGC
*
52668165 AGCAGC-TAAATACTTCAATTTGC
1 AGCA-CTTAAACACTTCAATTTGC
*
52668188 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTGC
* * **
52668211 ATCATTTAAACACTAAAATTTGC
1 AGCACTTAAACACTTCAATTTGC
* **
52668234 AGTACTT-AACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTGC
* * * *
52668256 AACATTTATACA-TCTCAA-TTAC
1 AGCACTTAAACACT-TCAATTTGC
* *
52668278 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTGC
52668301 AGCAAC-TAAACACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTGC
*
52668324 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTGC
* * *
52668347 AACATTTAAACACTTAAATTTGC
1 AGCACTTAAACACTTCAATTTGC
**
52668370 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTGC
* * * * *
52668393 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTGC
* * *
52668415 AACGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTGC
*
52668438 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTGC
*
52668461 TGCACTTAAACACTTCAATTTG
1 AGCACTTAAACACTTCAATTTG
52668483 AAGAACTATC
Statistics
Matches: 320, Mismatches: 65, Indels: 48
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.00
22 68 0.21
23 246 0.77
24 5 0.02
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (23 bp):
AGCACTTAAACACTTCAATTTGC
Found at i:52668180 original size:68 final size:67
Alignment explanation
Indices: 52668088--52668480 Score: 341
Period size: 68 Copynumber: 5.8 Consensus size: 67
52668078 ACTGAACACT
* * * *
52668088 TCAATTTGCAGCACTTAAACACTTCAATTTGCAGCACTTATACACCTCAATTACAGCGATAAAAC
1 TCAATTTCCAGCAC-TAAATACTTCAATTTGCAGCACTTAAACACCTCAATTACAACGATAAAAC
52668153 ATC
65 ATC
* * *
52668156 TCAATTTCCAGCAGCTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTTACATC-ATTTAA
1 TCAATTTCCAGCA-CTAAATACTTCAATTTGCAGCACTTAAACACCTCAA-TTACAACGA-TAAA
52668220 ACA-C
63 ACATC
* * * ** * * * * *
52668224 TAAAATTTGCAGTACTTAACATA--TCAATTAACAACATTTATACATCTCAATTACAGCGATAAA
1 T-CAATTTCCAGCAC-TAA-ATACTTCAATTTGCAGCACTTAAACACCTCAATTACAACGATAAA
52668287 ACATC
63 ACATC
* * *
52668292 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAAC-ATTTAA
1 TCAATTTCCAGC-ACTAAATACTTCAATTTGCAGCACTTAAACACCTCAA-TTACAACGA-TAAA
52668356 ACA-C
63 ACATC
* * * ** * * *
52668360 TTAAATTTGCAGCACTTAA-ACATATCAATTAACAACATTTATACACCTCAATTACAACGATAAA
1 -TCAATTTCCAGCACTAAATAC-T-TCAATTTGCAGCACTTAAACACCTCAATTACAACGATAAA
52668424 ACATC
63 ACATC
* *
52668429 TCAATTTCCAGCAACTAAATACTTCAATTTGCTGCACTTAAACACTTCAATT
1 TCAATTTCCAGC-ACTAAATACTTCAATTTGCAGCACTTAAACACCTCAATT
52668481 TGAAGAACTA
Statistics
Matches: 254, Mismatches: 51, Indels: 40
0.74 0.15 0.12
Matches are distributed among these distances:
66 2 0.01
67 25 0.10
68 146 0.57
69 76 0.30
70 5 0.02
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.31
Consensus pattern (67 bp):
TCAATTTCCAGCACTAAATACTTCAATTTGCAGCACTTAAACACCTCAATTACAACGATAAAACA
TC
Found at i:52668245 original size:91 final size:89
Alignment explanation
Indices: 52668057--52668481 Score: 289
Period size: 91 Copynumber: 4.7 Consensus size: 89
52668047 AAGTAGCACT
* * * *
52668057 TTAACA-CTTCAATTTGCAGCAACTGAACACTTCAATTTGCAGCACTTAAACACTTCAATTTGCA
1 TTAACATC-TCAATTTACAGCAACTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTTACA
* *
52668121 GCACTTATACACCTCAATTACAG-C
65 GCATTTAAACACCTCAATTACAGAC
* * *
52668145 GATAAAACATCTCAATTTCCAGCAGCTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTTA
1 --T-TAACATCTCAATTTACAGCAACTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTTA
* * *
52668210 CATCATTTAAACA-CTAAAATTTGCAGTAC
63 CAGCATTTAAACACCT-CAA-TTACAG-AC
* ** * *
52668239 TTAACATATCAA-TTA-A-CAACATTTATACATCTCAA-TTACAGCGA-TAAAACA-TCTCAATT
1 TTAACATCTCAATTTACAGCAAC-TAAATAC-T-TCAATTTGCAGC-ACTTAAACACT-TCAATT
* ** * *
52668298 TCCAGCAACTAAACACTTCAATTTGCAGCAC
61 TACAGCATTTAAACACCTCAA-TTACAG-AC
* ** * * *
52668329 TTAAACA-CTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACA-TATCAATTAA
1 TT-AACATC-TCAATTTACAGCAACTAAATACTTCAATTTGCAGCACTTAAACACT-TCAATTTA
* *
52668392 CAACATTTATACACCTCAATTACA-AC
63 CAGCATTTAAACACCTCAATTACAGAC
* * *
52668418 GATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGCTGCACTTAAACACTTCAATTT
1 --T-TAACATCTCAATTTACAGCAACTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTT
52668482 GAAGAACTAT
Statistics
Matches: 258, Mismatches: 53, Indels: 47
0.72 0.15 0.13
Matches are distributed among these distances:
88 3 0.01
89 9 0.03
90 48 0.19
91 144 0.56
92 46 0.18
93 5 0.02
94 3 0.01
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (89 bp):
TTAACATCTCAATTTACAGCAACTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTTACAG
CATTTAAACACCTCAATTACAGAC
Found at i:52668446 original size:137 final size:137
Alignment explanation
Indices: 52668051--52668481 Score: 668
Period size: 137 Copynumber: 3.2 Consensus size: 137
52668041 AATGGAAAGT
* * * ** * *
52668051 AGCACTTTAACACTTCAATTTGCAGCAACTGAACACTTCAATTTGCAGCACTTAAACACT-TCAA
1 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACA-TATCAA
** * * *
52668115 TTTGCAGCACTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAGCTAAATACTT
65 TTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAATACTT
52668180 CAATTTGC
130 CAATTTGC
* * *
52668188 AGCACTTAAACACTTCAATTTACATCATTTAAACACTAAAATTTGCAGTACTT-AACATATCAAT
1 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
* *
52668252 TAACAACATTTATACATCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTC
66 TAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAATACTTC
52668317 AATTTGC
131 AATTTGC
52668324 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
1 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
*
52668389 TAACAACATTTATACACCTCAATTACAACGATAAAACATCTCAATTTCCAGCAACTAAATACTTC
66 TAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAATACTTC
52668454 AATTTGC
131 AATTTGC
*
52668461 TGCACTTAAACACTTCAATTT
1 AGCACTTAAACACTTCAATTT
52668482 GAAGAACTAT
Statistics
Matches: 269, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
135 1 0.00
136 124 0.46
137 144 0.54
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (137 bp):
AGCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
TAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAATACTTC
AATTTGC
Found at i:52668908 original size:41 final size:39
Alignment explanation
Indices: 52668825--52668908 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
52668815 GCACAATACA
* **
52668825 ATATAAAAAGCATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
*
52668864 ATATAAAAAGCATATATAAATATATGTATGTCACAGAAACT
1 ATATAAAAAGCATATATAAATATATGAATGT-ACAGAAA-T
52668905 ATAT
1 ATAT
52668909 TCATTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 30 0.77
40 4 0.10
41 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (39 bp):
ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
Found at i:52671389 original size:30 final size:26
Alignment explanation
Indices: 52671329--52671378 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
52671319 GAATTATTGT
52671329 TTTTTTATAAATTGATTTATTTTTTG
1 TTTTTTATAAATTGATTTATTTTTTG
52671355 TTTTTTATAAATTGATTTATTTTT
1 TTTTTTATAAATTGATTTATTTTT
52671379 GTGGCGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (26 bp):
TTTTTTATAAATTGATTTATTTTTTG
Found at i:52671395 original size:27 final size:25
Alignment explanation
Indices: 52671330--52671392 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 25
52671320 AATTATTGTT
*
52671330 TTTTTATAAATTGATTTATTTTTTGT
1 TTTTTAT-AATTGATTTATTTTTTGG
52671356 TTTTTATAAATTGATTTATTTTTGTGGCG
1 TTTTTAT-AATTGATTTATTTTT-T-G-G
52671385 TTTTTATA
1 TTTTTATA
52671393 TTGCTTACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 23 0.70
27 1 0.03
28 2 0.06
29 7 0.21
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65
Consensus pattern (25 bp):
TTTTTATAATTGATTTATTTTTTGG
Found at i:52671543 original size:89 final size:89
Alignment explanation
Indices: 52671440--52671602 Score: 249
Period size: 89 Copynumber: 1.8 Consensus size: 89
52671430 GGAAATTTTT
* * *
52671440 TTTCATTTTGAACAAAAAT-ACGCCGTTTTGCTATTCTAAAAA-AATTTTATTTTGTTTTTTATA
1 TTTCATTTTGAAC-AAAATGACACCGTTTTGCTATGC-AAAAATAATTTTATTTTATTTTTTATA
52671503 AATTGATTTATAAAAAAACGCCGCTA
64 AATTGATTTATAAAAAAACGCCGCTA
**
52671529 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCAAAAATTTTTTTATTTTATTTTTTATAAA
1 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCAAAAATAATTTTATTTTATTTTTTATAAA
52671594 TTGATTTAT
66 TTGATTTAT
52671603 TTTTTGCTGC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 10 0.15
89 57 0.85
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.47
Consensus pattern (89 bp):
TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCAAAAATAATTTTATTTTATTTTTTATAAA
TTGATTTATAAAAAAACGCCGCTA
Found at i:52672327 original size:14 final size:14
Alignment explanation
Indices: 52672308--52672341 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
52672298 AACCTTAAAT
52672308 CCCTAAC-TCTTAAC
1 CCCTAACATC-TAAC
52672322 CCCTAACATCTAAC
1 CCCTAACATCTAAC
52672336 CCCTAA
1 CCCTAA
52672342 ACCCTAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACATCTAAC
Found at i:52672378 original size:20 final size:20
Alignment explanation
Indices: 52672341--52672380 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52672331 CTAACCCCTA
*
52672341 AACCCTAAACCTTAAATCCC
1 AACCCTAAACCATAAATCCC
52672361 AACCCTTAAACCAT-AATCCC
1 AACCC-TAAACCATAAATCCC
52672381 TAAATCCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCTAAACCATAAATCCC
Found at i:52672389 original size:15 final size:14
Alignment explanation
Indices: 52672367--52672401 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
52672357 TCCCAACCCT
52672367 TAAACCATAATCCC
1 TAAACCATAATCCC
*
52672381 TAAATCCATACTCCC
1 TAAA-CCATAATCCC
52672396 TAAACC
1 TAAACC
52672402 TTAAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:52672594 original size:22 final size:23
Alignment explanation
Indices: 52672564--52672619 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
52672554 CCCTAACTCG
* *
52672564 ACCCCTAAATCCCTAA-CTTTTA
1 ACCCCTAAACCCCTAACCTTCTA
*
52672586 ATCCCTAAACCCCTAACCTTCTA
1 ACCCCTAAACCCCTAACCTTCTA
52672609 ACCCCTAAACC
1 ACCCCTAAACC
52672620 TTAAATCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (23 bp):
ACCCCTAAACCCCTAACCTTCTA
Found at i:52673098 original size:73 final size:73
Alignment explanation
Indices: 52672913--52673099 Score: 286
Period size: 73 Copynumber: 2.6 Consensus size: 73
52672903 AGATAAAATA
* * * *
52672913 TTTTTAGCAGCGCTTT-TCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTG
1 TTTTTTGCGGCGCTTTCT-CAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGCCGTTG
52672977 GGCTTAGGT
65 GGCTTAGGT
* *
52672986 TTTTTTGCGACGCTTTCCCAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGCCGTTGG
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGCCGTTGG
52673051 GCTTAGGT
66 GCTTAGGT
* *
52673059 TTTTTTGCGGCGCTTTCTCAAAAACGCAGCTAAAGCCCTGA
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCTGA
52673100 GCATTAGCGC
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
73 103 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (73 bp):
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGCCGTTGG
GCTTAGGT
Found at i:52673194 original size:113 final size:114
Alignment explanation
Indices: 52672996--52673318 Score: 459
Period size: 113 Copynumber: 2.8 Consensus size: 114
52672986 TTTTTTGCGA
** * *
52672996 CGCTTTCCCAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTT
*
52673061 TTTTGCGGCGCTTTCTCAAAAACGCAGCTAAAGCCCTGAGCATTAG-CG
66 TTTTGCGGCGCTTTCCCAAAAACGCAGCTAAAGCCCTGAGCATTAGTCG
* * * * * *
52673109 CGCTTTCTTAAAAATGCCGCCAAATCCCCAAAAGCTCAAAAAACGGCGTCATGGGGCTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTT
* * * ** *
52673174 TTTTGTGGCGCTTTCCCAAAAACGCCGCTAAAGTCCTGAGTTTTAGTGG
66 TTTTGCGGCGCTTTCCCAAAAACGCAGCTAAAGCCCTGAGCATTAGTCG
*
52673223 CGCTTTCTTATAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTT
* *
52673288 TTTTGCGGCGCTTTTCCAAAAACGCAACTAA
66 TTTTGCGGCGCTTTCCCAAAAACGCAGCTAA
52673319 TGCTTATTTT
Statistics
Matches: 181, Mismatches: 28, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
113 95 0.52
114 86 0.48
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (114 bp):
CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTT
TTTTGCGGCGCTTTCCCAAAAACGCAGCTAAAGCCCTGAGCATTAGTCG
Found at i:52679397 original size:12 final size:13
Alignment explanation
Indices: 52679374--52679428 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
52679364 AGTTTGGCAA
52679374 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
52679387 TACTTTTAAAAAA
1 TACTTTTGAAAAG
52679400 TATGCTTTTGAAAAG
1 TA--CTTTTGAAAAG
**
52679415 TGTTTTTGAAAAG
1 TACTTTTGAAAAG
52679428 T
1 T
52679429 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 24 0.71
15 10 0.29
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:52680384 original size:58 final size:58
Alignment explanation
Indices: 52680315--52680427 Score: 208
Period size: 58 Copynumber: 1.9 Consensus size: 58
52680305 AAGTGATAGA
*
52680315 TGAAAAATCTTATATGCTAGGTCTATTGCAGAAATAGCTTAAGAATATAAAGCAACTC
1 TGAAAAATCTTATATGCTAGGTCTATTACAGAAATAGCTTAAGAATATAAAGCAACTC
*
52680373 TGAAAAATCTTATATGCTAGGTCTATTACAGAAATAGCTTGAGAATATAAAGCAA
1 TGAAAAATCTTATATGCTAGGTCTATTACAGAAATAGCTTAAGAATATAAAGCAA
52680428 TTCAAGTGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (58 bp):
TGAAAAATCTTATATGCTAGGTCTATTACAGAAATAGCTTAAGAATATAAAGCAACTC
Found at i:52688623 original size:63 final size:63
Alignment explanation
Indices: 52688541--52688713 Score: 215
Period size: 63 Copynumber: 2.8 Consensus size: 63
52688531 TGTGCCAGGC
* * * * * *
52688541 CGTGTGT-CAGGTCGTGTAACTTATCATTTTAGAATTAGAGTCACACGGACTAGAGACATGGG
1 CGTGTGTCCAGGCCGTGTAACTTATCGTTTTGGAATTAGAGTCACACGGACCAGAGACACGAG
* *
52688603 CGTGTGTCCAGGCCGTGTAACTTA-CTGTTTTGGAATTAGAGTCACACGGGCCAGAGGCACGAG
1 CGTGTGTCCAGGCCGTGTAACTTATC-GTTTTGGAATTAGAGTCACACGGACCAGAGACACGAG
* ** *
52688666 CTTGTGTCCAGGCTATGTAACTTATTGTTTTGGAATTAGAGTCACACG
1 CGTGTGTCCAGGCCGTGTAACTTATCGTTTTGGAATTAGAGTCACACG
52688714 AGTCAGGGAT
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
62 8 0.08
63 88 0.92
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (63 bp):
CGTGTGTCCAGGCCGTGTAACTTATCGTTTTGGAATTAGAGTCACACGGACCAGAGACACGAG
Found at i:52688735 original size:63 final size:62
Alignment explanation
Indices: 52688555--52688737 Score: 197
Period size: 63 Copynumber: 2.9 Consensus size: 62
52688545 TGTCAGGTCG
** * * * * *
52688555 TGTAACTTATCATTTTAGAATTAGAGTCACACGGACTAGAGACATGGGCGTGTGTCCAGGCCG
1 TGTAACTTATTGTTTTGGAATTAGAGTCACACGGAC-AGGGACACGGGCATGTGTCCAGGCCA
* * * * *
52688618 TGTAACTTACTGTTTTGGAATTAGAGTCACACGGGCCAGAGG-CACGAGCTTGTGTCCAGGCTA
1 TGTAACTTATTGTTTTGGAATTAGAGTCACAC-GGACAG-GGACACGGGCATGTGTCCAGGCCA
* *
52688681 TGTAACTTATTGTTTTGGAATTAGAGTCACACGAGTCAGGGATACGGGCATGTGTCC
1 TGTAACTTATTGTTTTGGAATTAGAGTCACACG-GACAGGGACACGGGCATGTGTCC
52688738 TCGCTGTGTG
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
62 3 0.03
63 93 0.93
64 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (62 bp):
TGTAACTTATTGTTTTGGAATTAGAGTCACACGGACAGGGACACGGGCATGTGTCCAGGCCA
Found at i:52689901 original size:18 final size:17
Alignment explanation
Indices: 52689868--52689906 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52689858 TTTTATCAAT
52689868 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52689886 TGTGAATTAT-TATTGAA
1 TGTGAATTATAT-TTGAA
52689903 TGTG
1 TGTG
52689907 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52690162 original size:23 final size:23
Alignment explanation
Indices: 52690132--52690207 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
52690122 AATGTTATTG
*
52690132 ATCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
52690155 ATCAGTGGTAGGTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
52690178 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
52690201 ATCAGTG
1 ATCAGTG
52690208 TGGTACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:52691428 original size:49 final size:49
Alignment explanation
Indices: 52691365--52691503 Score: 197
Period size: 49 Copynumber: 2.8 Consensus size: 49
52691355 CAATAAGTGA
* *
52691365 TATGTAATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
* *
52691414 TATGTGATTACGTGTAAGACCATTGCTGGGCTATGGCATCAGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
** * * *
52691463 TATGTGATTACACGCAAGACCATAGTTGGACTATGGCATCG
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
52691504 AGAAAATAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 79 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (49 bp):
TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
Found at i:52696329 original size:15 final size:15
Alignment explanation
Indices: 52696296--52696329 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52696286 GTGCGGTGTT
* *
52696296 TGTGTTGTGTTGTGT
1 TGTGTTGTGTTGGGC
52696311 TGTGTTGTGTTGGGC
1 TGTGTTGTGTTGGGC
52696326 TGTG
1 TGTG
52696330 CTGCATAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.44, T:0.53
Consensus pattern (15 bp):
TGTGTTGTGTTGGGC
Found at i:52696332 original size:5 final size:5
Alignment explanation
Indices: 52696295--52696322 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52696285 TGTGCGGTGT
52696295 TTGTG TTGTG TTGTG TTGTG TTGTG TTG
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTG
52696323 GGCTGTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (5 bp):
TTGTG
Found at i:52700318 original size:2 final size:2
Alignment explanation
Indices: 52700311--52700339 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52700301 AACTTGAAGA
52700311 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52700340 AGCTTTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52706879 original size:6 final size:6
Alignment explanation
Indices: 52706868--52706899 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
52706858 GGCATGTCAT
52706868 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
52706900 AAACCCTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:52721218 original size:23 final size:23
Alignment explanation
Indices: 52721192--52721240 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
52721182 TTTCTTACTA
52721192 TAGTAATTTTCGAGATATTACAG
1 TAGTAATTTTCGAGATATTACAG
* *
52721215 TAGTAATTTTCGGGATGTTACAG
1 TAGTAATTTTCGAGATATTACAG
52721238 TAG
1 TAG
52721241 ATAGGACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (23 bp):
TAGTAATTTTCGAGATATTACAG
Found at i:52724588 original size:27 final size:27
Alignment explanation
Indices: 52724558--52724612 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
52724548 TCTCGGAGGA
52724558 GCCAATGGTGGAGCCTATCTGACAGGC
1 GCCAATGGTGGAGCCTATCTGACAGGC
*
52724585 GCCAATGGTGGAGCCTTTCTGACAGGC
1 GCCAATGGTGGAGCCTATCTGACAGGC
52724612 G
1 G
52724613 TCACTGCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (27 bp):
GCCAATGGTGGAGCCTATCTGACAGGC
Found at i:52730166 original size:45 final size:44
Alignment explanation
Indices: 52730100--52730190 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
52730090 TTTGGTTCGT
* * *
52730100 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGATTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGATTGAA
* ***
52730145 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGATTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGATTGAA
52730189 TG
1 TG
52730191 AAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGATTGAA
Found at i:52730376 original size:18 final size:17
Alignment explanation
Indices: 52730355--52730389 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52730345 TTATTATTAA
*
52730355 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52730373 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52730390 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52730503 original size:14 final size:15
Alignment explanation
Indices: 52730454--52730505 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52730444 GTAAAATATA
52730454 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
52730469 TATTAAATATATTAT
1 AATTAAATATATTAT
52730484 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
52730497 AATTTAATA
1 AATTAAATA
52730506 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:52730623 original size:14 final size:15
Alignment explanation
Indices: 52730574--52730625 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52730564 GTAAAATATA
52730574 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
52730589 TATTAAATATATTAT
1 AATTAAATATATTAT
52730604 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
52730617 AATTTAATA
1 AATTAAATA
52730626 AAATTGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:52730761 original size:120 final size:120
Alignment explanation
Indices: 52730338--52730750 Score: 724
Period size: 120 Copynumber: 3.4 Consensus size: 120
52730328 ATCATATTTA
*
52730338 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
52730403 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
52730458 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
52730523 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
52730578 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTGTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
52730643 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* * *
52730698 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
52730751 TAAAATAATT
Statistics
Matches: 284, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 7 0.02
120 275 0.97
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:52730837 original size:24 final size:25
Alignment explanation
Indices: 52730791--52730838 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
52730781 TATGAATTTG
52730791 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
52730817 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
52730839 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:52730842 original size:92 final size:92
Alignment explanation
Indices: 52730746--52730955 Score: 232
Period size: 92 Copynumber: 2.3 Consensus size: 92
52730736 TGATTTAATA
* * *
52730746 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
52730808 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
52730838 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
52730903 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* *
52730928 ATAATTTCATAAAATTCTTAATAATAAA
1 A-AATTTCAAAAAATTCATAATAATAAA
52730956 ATGTTCTTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
90 2 0.02
91 30 0.29
92 62 0.61
93 8 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:52730963 original size:92 final size:92
Alignment explanation
Indices: 52730781--52730974 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 92
52730771 AATTATATTT
* * * *
52730781 TATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAATTAATATTAAATTTCA
1 TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
* *
52730846 TAAAATTCTTGATAATAAATTTTCTTA
66 TAAAATTCTTAATAATAAATGTTCTTA
*
52730873 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAGTG-ATA-TATAATTT
1 TATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAATGAATATTA-AATTT
52730935 CATAAAATTCTTAATAATAAAATGTTCTTA
64 CATAAAATTCTTAATAAT-AAATGTTCTTA
*
52730965 TATCAATTTA
1 TATGAATTTA
52730975 GTAAAATCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
90 2 0.02
91 25 0.27
92 61 0.67
93 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
TAAAATTCTTAATAATAAATGTTCTTA
Found at i:52734012 original size:33 final size:33
Alignment explanation
Indices: 52733973--52734048 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
52733963 ATTATAAAGC
*
52733973 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
52734006 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
52734039 ATGTATAATT
1 ATGTATAATT
52734049 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:52734146 original size:37 final size:37
Alignment explanation
Indices: 52734091--52734172 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
52734081 GTATAAATAT
* * *
52734091 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAGC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTCAAC
*
52734128 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTCAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTCAAC
52734165 ATTGATTA
1 ATTGATTA
52734173 ATAAATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTCAAC
Found at i:52741909 original size:40 final size:40
Alignment explanation
Indices: 52741854--52741934 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
52741844 TAAAATATCG
52741854 ATAGATACACATGTAGTACACTCGAAGTGTACAAAACTGT
1 ATAGATACACATGTAGTACACTCGAAGTGTACAAAACTGT
52741894 ATAGATACACATGTAGTACACTCGAAGTGTACAAAACTGT
1 ATAGATACACATGTAGTACACTCGAAGTGTACAAAACTGT
52741934 A
1 A
52741935 ATCTGTCAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (40 bp):
ATAGATACACATGTAGTACACTCGAAGTGTACAAAACTGT
Found at i:52746450 original size:13 final size:13
Alignment explanation
Indices: 52746432--52746456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52746422 TCAAACGATC
52746432 AAATTTTTACACG
1 AAATTTTTACACG
52746445 AAATTTTTACAC
1 AAATTTTTACAC
52746457 ATATTAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATTTTTACACG
Found at i:52751413 original size:24 final size:24
Alignment explanation
Indices: 52751381--52751431 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
52751371 TATATATCGT
*
52751381 TTTTAAGAATAACTAGTTATAATG
1 TTTTAAGAATAACTAGCTATAATG
* *
52751405 TTTTCAGAATAATTAGCTATAATG
1 TTTTAAGAATAACTAGCTATAATG
52751429 TTT
1 TTT
52751432 CTAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (24 bp):
TTTTAAGAATAACTAGCTATAATG
Found at i:52757857 original size:21 final size:21
Alignment explanation
Indices: 52757831--52757873 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
52757821 CGCGAAACTG
52757831 AGTAGACCACCGCAACAACCA
1 AGTAGACCACCGCAACAACCA
52757852 AGTAGACCACCGCAACAACCA
1 AGTAGACCACCGCAACAACCA
52757873 A
1 A
52757874 AGGTGGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.14, T:0.05
Consensus pattern (21 bp):
AGTAGACCACCGCAACAACCA
Found at i:52760188 original size:19 final size:19
Alignment explanation
Indices: 52760166--52760205 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52760156 TTGAGAAAAT
*
52760166 TATT-TTTAATTATTTATTA
1 TATTATTTAATCA-TTATTA
52760185 TATTATTTAATCATTATTA
1 TATTATTTAATCATTATTA
52760204 TA
1 TA
52760206 ACAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTTAATCATTATTA
Found at i:52772432 original size:3 final size:3
Alignment explanation
Indices: 52772417--52772448 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52772407 GGAACCATGC
*
52772417 TGT TGT GGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
52772449 ATGGTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (3 bp):
TGT
Found at i:52773615 original size:25 final size:25
Alignment explanation
Indices: 52773587--52773637 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
52773577 AGAAAGTAAA
52773587 TTAA-AATTTATATTTATTTTA-ATAT
1 TTAATAATTT-TATTT-TTTTATATAT
52773612 TTAATAATTTTATTTTTTTATATAT
1 TTAATAATTTTATTTTTTTATATAT
52773637 T
1 T
52773638 ATAGTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.21
25 14 0.58
26 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTAATAATTTTATTTTTTTATATAT
Found at i:52773634 original size:23 final size:26
Alignment explanation
Indices: 52773586--52773647 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 26
52773576 TAGAAAGTAA
52773586 ATTAA-AATTTATATTTATTTTAATAT
1 ATTAATAATTT-TATTTATTTTAATAT
52773612 -TTAATAATTTTATTT-TTTT-ATAT
1 ATTAATAATTTTATTTATTTTAATAT
*
52773635 ATT-ATAGTTTTAT
1 ATTAATAATTTTAT
52773648 ATAAAGGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 13 0.39
24 6 0.18
25 9 0.27
26 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTAATAATTTTATTTATTTTAATAT
Found at i:52783619 original size:2 final size:2
Alignment explanation
Indices: 52783612--52783640 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52783602 CAGTTGGCAA
52783612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52783641 TGGAGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52785720 original size:23 final size:24
Alignment explanation
Indices: 52785675--52785724 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
52785665 AACACGTCAA
*
52785675 TTTTTTCTTCAATATAGTTTACTTT
1 TTTTTTCTTCAATATAG-CTACTTT
*
52785700 TTTTTTCTTCAATTTA-CTACTTT
1 TTTTTTCTTCAATATAGCTACTTT
52785723 TT
1 TT
52785725 CTATCTTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
25 15 0.65
ACGTcount: A:0.18, C:0.14, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTTCTTCAATATAGCTACTTT
Found at i:52788957 original size:4 final size:4
Alignment explanation
Indices: 52788948--52788972 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52788938 AAGTGTATGA
52788948 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
52788973 GTAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:52790128 original size:20 final size:19
Alignment explanation
Indices: 52790095--52790172 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 19
52790085 ATCAACATTT
52790095 AATTAATTTCTTAATATTTTAA
1 AATT-ATTT-TTAA-ATTTTAA
*
52790117 AATTATTTTTAAATAATTAA
1 AATTATTTTTAAAT-TTTAA
* *
52790137 AATGATTTTTAACTTTTAA
1 AATTATTTTTAAATTTTAA
* *
52790156 AAATAGTTTTATAATTT
1 AATTATTTTTA-AATTT
52790173 ATTGAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.30
20 24 0.52
21 4 0.09
22 4 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTATTTTTAAATTTTAA
Found at i:52792313 original size:18 final size:19
Alignment explanation
Indices: 52792282--52792323 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
52792272 GTTGCCCTTA
*
52792282 TGTATTTTGCATTGTTTATT
1 TGTATTTT-CATTGATTATT
*
52792302 TGTATTTT-ATTGATTCTT
1 TGTATTTTCATTGATTATT
52792320 TGTA
1 TGTA
52792324 ACTCATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64
Consensus pattern (19 bp):
TGTATTTTCATTGATTATT
Found at i:52796815 original size:19 final size:18
Alignment explanation
Indices: 52796779--52796831 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
52796769 GTTCAGATTC
52796779 AAAAA-CAAAAAAAAAAG
1 AAAAATCAAAAAAAAAAG
*
52796796 AAAAATCAAAAAAGAGAAG
1 AAAAATCAAAAAA-AAAAG
52796815 AAAAAT-AAAAATAAAAA
1 AAAAATCAAAAA-AAAAA
52796832 ACAAAGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 15 0.48
19 11 0.35
ACGTcount: A:0.83, C:0.04, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAATCAAAAAAAAAAG
Found at i:52796818 original size:25 final size:24
Alignment explanation
Indices: 52796790--52796885 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 24
52796780 AAAACAAAAA
52796790 AAAAAGAAAAATCAAAAAAGAGAAG
1 AAAAAGAAAAAT-AAAAAAGAGAAG
* *
52796815 AAAAATAAAAATAAAAAACA-AAGG
1 AAAAAGAAAAATAAAAAAGAGAA-G
*
52796839 TCAAAATG-AAAATGAAAAAGAGAGAAG
1 --AAAAAGAAAAAT-AAAAA-AGAGAAG
*
52796866 AAAAGAGAAAAA-AGAAAAGA
1 AAAA-AGAAAAATAAAAAAGA
52796886 AAATGAGAGG
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
23 2 0.04
24 11 0.20
25 24 0.43
26 10 0.18
27 7 0.12
28 2 0.04
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAAAGAAAAATAAAAAAGAGAAG
Found at i:52796868 original size:19 final size:20
Alignment explanation
Indices: 52796841--52796893 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
52796831 AACAAAGGTC
*
52796841 AAAATGAAAATGA-AAAAGAG
1 AAAA-GAAAATGAGAAAAAAG
*
52796861 AGAAGAAAA-GAGAAAAAAG
1 AAAAGAAAATGAGAAAAAAG
52796880 AAAAGAAAATGAGA
1 AAAAGAAAATGAGA
52796894 GGCCAATGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.07
19 19 0.68
20 7 0.25
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.06
Consensus pattern (20 bp):
AAAAGAAAATGAGAAAAAAG
Found at i:52798636 original size:86 final size:86
Alignment explanation
Indices: 52798479--52799097 Score: 986
Period size: 86 Copynumber: 7.2 Consensus size: 86
52798469 CAGATCAGTG
* * *
52798479 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAACCTTGCATCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
52798544 TTGGTTGTAGTAGAGCTGGTTA
65 TCGGTTGTAGTGGAGCTGGTTA
* * *
52798566 AAGAAGTAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAACATTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
*
52798631 CGGTTGCAGTGGAGCTGGTTA
66 CGGTTGTAGTGGAGCTGGTTA
*
52798652 AAGAAGCAGATCTTGCCTTCTTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
*
52798717 CGGTTGTAGTAGAGCTGGTTA
66 CGGTTGTAGTGGAGCTGGTTA
* * *
52798738 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGAAGATTGAAAACAAAGCTTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
52798803 CGGTTGTAGTGGAGCTGGTTA
66 CGGTTGTAGTGGAGCTGGTTA
* * * *
52798824 AAAAAGTAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGTCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
52798889 CGGTTGTAGTGGAGCTGGTTA
66 CGGTTGTAGTGGAGCTGGTTA
*
52798910 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
52798975 CGGTTGTAGTGGAGCTGGTTA
66 CGGTTGTAGTGGAGCTGGTTA
* * *
52798996 AAGATAGCAGATCTTGCCTTCCTGTATTAACAGTGAAGTAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* * *
52799061 TCGGTTGCAGTAGAGCTGGTTG
65 TCGGTTGTAGTGGAGCTGGTTA
52799083 AAGATAGCAGATCTT
1 AAGA-AGCAGATCTT
52799098 CCCCTTCTGC
Statistics
Matches: 494, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
86 400 0.81
87 94 0.19
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (86 bp):
AAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
CGGTTGTAGTGGAGCTGGTTA
Found at i:52799315 original size:44 final size:44
Alignment explanation
Indices: 52799222--52799324 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 44
52799212 ATCACATCGG
*
52799222 GTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAGAAAATAA
1 GTCTTATCTCCCTGAAGTCACAGTGGAGCAGACTGAGAAAATAA
* * *
52799266 GTCTTATCACCCTGAAGTCACAGTAGG-GTAGACTGAAGAAGCA-AA
1 GTCTTATCTCCCTGAAGTCACAGT-GGAGCAGACTG-AGAA-AATAA
52799311 -TCTTATCTCCCTGA
1 GTCTTATCTCCCTGA
52799325 GGTTGTAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
44 42 0.82
45 8 0.16
46 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTCACAGTGGAGCAGACTGAGAAAATAA
Found at i:52799414 original size:45 final size:44
Alignment explanation
Indices: 52799309--52799431 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
52799299 TGAAGAAGCA
* * *
52799309 AATCTTATCTCCCTGAGGTTGTAGTAGAGCAGATTAAATTCGAT
1 AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGTCAAT
* * * *
52799353 AATCCTATCTCCCTGAAGTTGTAGTTGAGCGGATTGAAGT-AAT
1 AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGTCAAT
* * *
52799396 AAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 -A-ATCTTATCTCCCTGAAGTTGTAGTAGAGCAGAT
52799432 CGCATCAAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 2 0.03
44 35 0.55
45 27 0.42
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGTCAAT
Found at i:52800337 original size:18 final size:19
Alignment explanation
Indices: 52800316--52800356 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52800306 GGTTTCTGGG
52800316 TTTTCTT-CTGTTTTCTTT
1 TTTTCTTCCTGTTTTCTTT
* *
52800334 TTTTTTTCCTTTTTTCTTT
1 TTTTCTTCCTGTTTTCTTT
52800353 TTTT
1 TTTT
52800357 GGTTTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTCTTCCTGTTTTCTTT
Found at i:52801693 original size:18 final size:19
Alignment explanation
Indices: 52801662--52801703 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
52801652 GTTGCCCTTA
*
52801662 TGTATTTTGCATTGTTTATT
1 TGTATTTT-CATTGATTATT
*
52801682 TGTATTTT-ATTGATTCTT
1 TGTATTTTCATTGATTATT
52801700 TGTA
1 TGTA
52801704 ACTCATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64
Consensus pattern (19 bp):
TGTATTTTCATTGATTATT
Found at i:52804985 original size:20 final size:19
Alignment explanation
Indices: 52804956--52805003 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
52804946 TCTAATTTTT
*
52804956 TAAGATTTTATAATTGAGAA
1 TAAGAGTTTAT-ATTGAGAA
52804976 TAAGAG-TT-TATTGAGAA
1 TAAGAGTTTATATTGAGAA
52804993 TAAGAGTTTAT
1 TAAGAGTTTAT
52805004 GTTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.56
18 3 0.12
19 3 0.12
20 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (19 bp):
TAAGAGTTTATATTGAGAA
Found at i:52804990 original size:17 final size:17
Alignment explanation
Indices: 52804968--52805003 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52804958 AGATTTTATA
52804968 ATTGAGAATAAGAGTTT
1 ATTGAGAATAAGAGTTT
52804985 ATTGAGAATAAGAGTTT
1 ATTGAGAATAAGAGTTT
52805002 AT
1 AT
52805004 GTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (17 bp):
ATTGAGAATAAGAGTTT
Found at i:52806374 original size:8 final size:8
Alignment explanation
Indices: 52806361--52806394 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
52806351 TAGAACACAT
52806361 AAAAAAA-
1 AAAAAAAG
52806368 AAAAAAAG
1 AAAAAAAG
52806376 AAAAAAAG
1 AAAAAAAG
52806384 AAAAAAAG
1 AAAAAAAG
52806392 AAA
1 AAA
52806395 GTCATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:52806503 original size:29 final size:29
Alignment explanation
Indices: 52806461--52806520 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
52806451 AAAACGAGGA
52806461 AAGAAAATTTATTCATGTAGTATCATCTG
1 AAGAAAATTTATTCATGTAGTATCATCTG
52806490 AAGAAAATTTATTCATGTAGTATCATCTG
1 AAGAAAATTTATTCATGTAGTATCATCTG
52806519 AA
1 AA
52806521 CTTTCAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (29 bp):
AAGAAAATTTATTCATGTAGTATCATCTG
Found at i:52818791 original size:23 final size:22
Alignment explanation
Indices: 52818740--52818823 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 22
52818730 CACAGCTCGT
* *
52818740 ATGAGCTTACAGTTTCAACTCTA
1 ATGAGCTTACCGTTTCAGCTC-A
**
52818763 CGGAGCTTACCGTTTCAGCTCA
1 ATGAGCTTACCGTTTCAGCTCA
52818785 ATAGAGCTTACCGTTTATCAGCTCGGA
1 AT-GAGCTTACCG-TT-TCAGCTC--A
52818812 ATGAGCTTACCG
1 ATGAGCTTACCG
52818824 ATCATGGCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
22 1 0.02
23 27 0.54
24 2 0.04
25 7 0.14
26 10 0.20
27 3 0.06
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (22 bp):
ATGAGCTTACCGTTTCAGCTCA
Found at i:52825318 original size:15 final size:16
Alignment explanation
Indices: 52825300--52825333 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
52825290 TTTTCTCCTT
52825300 GTTC-TTTTTATTTTG
1 GTTCTTTTTTATTTTG
52825315 GTTCTTTTTTATTTTG
1 GTTCTTTTTTATTTTG
52825331 GTT
1 GTT
52825334 AATCTACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.74
Consensus pattern (16 bp):
GTTCTTTTTTATTTTG
Found at i:52827517 original size:33 final size:30
Alignment explanation
Indices: 52827453--52827528 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
52827443 GCGGTGGATT
52827453 TGGTGGTGGCGTTGAAAGGGGAGGTTGTGA
1 TGGTGGTGGCGTTGAAAGGGGAGGTTGTGA
52827483 TGGTGGTGGCGTTGAAAGGGGAGGTTGTGA
1 TGGTGGTGGCGTTGAAAGGGGAGGTTGTGA
* *
52827513 TGATGGTGGCGGTGAA
1 TGGTGGTGGCGTTGAA
52827529 CTAACAGGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.17, C:0.04, G:0.53, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGCGTTGAAAGGGGAGGTTGTGA
Found at i:52827629 original size:21 final size:21
Alignment explanation
Indices: 52827595--52827655 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
52827585 CGGTTGAGTA
* *
52827595 GATGGTGTTGGTGGAGGTGGT
1 GATGGAGTTTGTGGAGGTGGT
52827616 GATGGAGTTTGTGGAGGTGGT
1 GATGGAGTTTGTGGAGGTGGT
52827637 GATGGAGTTTGTGGAGGTG
1 GATGGAGTTTGTGGAGGTG
52827656 ATGGCCTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.13, C:0.00, G:0.54, T:0.33
Consensus pattern (21 bp):
GATGGAGTTTGTGGAGGTGGT
Found at i:52832068 original size:12 final size:12
Alignment explanation
Indices: 52832029--52832060 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
52832019 TATACATATA
52832029 TATTATTTTACT
1 TATTATTTTACT
*
52832041 TAATATTTTACT
1 TATTATTTTACT
52832053 TATTATTT
1 TATTATTT
52832061 GTATTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTATTTTACT
Found at i:52835571 original size:18 final size:17
Alignment explanation
Indices: 52835538--52835576 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52835528 TTGTATAAAT
52835538 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52835556 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
52835573 TGTG
1 TGTG
52835577 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52835708 original size:8 final size:8
Alignment explanation
Indices: 52835695--52835723 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52835685 CACTAGAGAC
52835695 CAGTGTTA
1 CAGTGTTA
52835703 CAGTGTTA
1 CAGTGTTA
52835711 CAGTGTTA
1 CAGTGTTA
52835719 CAGTG
1 CAGTG
52835724 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:52835837 original size:23 final size:23
Alignment explanation
Indices: 52835810--52835882 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
52835800 AGTGTTATTG
52835810 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
52835833 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52835856 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52835879 ATCA
1 ATCA
52835883 ATGTGGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:52846620 original size:48 final size:48
Alignment explanation
Indices: 52846549--52846645 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
52846539 TTAATAAATA
*
52846549 AGTATAATTCAACATTTCCTGCCAACCACAGTCTCAAGCAATGAATTT
1 AGTATAATTCAACATTTCCTGCCAACCACAATCTCAAGCAATGAATTT
52846597 AGTATAATTCAACATTTCCTGCCAACCACAATCTCAAGCAATGAATTT
1 AGTATAATTCAACATTTCCTGCCAACCACAATCTCAAGCAATGAATTT
52846645 A
1 A
52846646 CTCAATCGAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (48 bp):
AGTATAATTCAACATTTCCTGCCAACCACAATCTCAAGCAATGAATTT
Found at i:52846867 original size:46 final size:46
Alignment explanation
Indices: 52846797--52847065 Score: 398
Period size: 46 Copynumber: 5.8 Consensus size: 46
52846787 ACAATGCTAT
*
52846797 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
52846843 AACTCAGTATGGTTTTCGTTACTGAAATACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
52846889 AACTCAGTATAGTTTTCTTTACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * * *
52846935 AACTCAGTATGATTTT-TGTTATTAAAATACCTTACCTACTTCTT-AC
1 AACTCAGTATGGTTTTCT-TTACTGAAATACCATACCTACTT-TTCAC
*
52846981 AACTCAGTATGGTTTTCTTTACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
52847027 AACTCAGTATGGTTTTCTTTACAGAAATGCCATACCTAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
52847066 GTTCCACACT
Statistics
Matches: 198, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
45 3 0.02
46 192 0.97
47 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
Found at i:52847316 original size:17 final size:17
Alignment explanation
Indices: 52847296--52847332 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
52847286 TTTAAAATAC
52847296 TTTTAAAATAT-TTTTAT
1 TTTTAAAATATATTTT-T
52847313 TTTTAAAATATATTTTT
1 TTTTAAAATATATTTTT
52847330 TTT
1 TTT
52847333 GTTTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAAATATATTTTT
Found at i:52848810 original size:25 final size:24
Alignment explanation
Indices: 52848728--52849119 Score: 215
Period size: 23 Copynumber: 16.6 Consensus size: 24
52848718 ATCTACCCTG
* *
52848728 TTTGGACAGCTTTTATACATC-AA
1 TTTGGACAGCATTTATACACCAAA
*
52848751 TTTGGACAGCATTTATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* *
52848775 -CTAGACAGCATTT-TCACACCAAAA
1 TTTGGACAGCATTTAT-ACACC-AAA
* *
52848799 TTTGGACAGCATATATACAAC-AA
1 TTTGGACAGCATTTATACACCAAA
* *
52848822 TTTGTG-CAGCATATATACAACAAA
1 TTTG-GACAGCATTTATACACCAAA
* *
52848846 -TT-GAGTAGCATTTTTACACCAAAA
1 TTTGGA-CAGCATTTATACACC-AAA
* * *
52848870 ATTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
52848894 -TTGGGCAGCATATATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* *
52848917 -TT-GAGCAGCATTTTTACATCAAA
1 TTTGGA-CAGCATTTATACACCAAA
* * *
52848940 ATTGGACAGCATATATACAAC-AA
1 TTTGGACAGCATTTATACACCAAA
* ** *
52848963 TTTGGGCAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* *
52848987 -TT-GAGCAGCATTTTTACATCAAAA
1 TTTGGA-CAGCATTTATACA-CCAAA
* * *
52849011 ATTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
52849035 -TTGGGCAGCATATATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
*
52849058 -TT-GAGCAGCATTTTTACACCAAAA
1 TTTGGA-CAGCATTTATACACC-AAA
* * * *
52849082 TTTGGAAAGCATATATATAAC-AA
1 TTTGGACAGCATTTATACACCAAA
*
52849105 TTTGGGCAGCATTTA
1 TTTGGACAGCATTTA
52849120 AGCATCAAAA
Statistics
Matches: 288, Mismatches: 57, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
21 1 0.00
22 4 0.01
23 183 0.64
24 39 0.14
25 54 0.19
26 7 0.02
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (24 bp):
TTTGGACAGCATTTATACACCAAA
Found at i:52848831 original size:23 final size:22
Alignment explanation
Indices: 52848800--52849116 Score: 238
Period size: 23 Copynumber: 13.5 Consensus size: 22
52848790 ACACCAAAAT
*
52848800 TTGGACAGCATATATACAACAAT
1 TTGG-CAGCATATATACAACAAA
52848823 TTGTGCAGCATATATACAACAAA
1 TTG-GCAGCATATATACAACAAA
* * * *
52848846 TTGAGTAGCATTTTTACACCAAAAA
1 TTG-GCAGCATATATACA--ACAAA
52848871 TTGGACAGCATATATACAACAAA
1 TTGG-CAGCATATATACAACAAA
* *
52848894 TTGGGCAGCATATATATACCAAA
1 TT-GGCAGCATATATACAACAAA
* * *
52848917 TTGAGCAGCATTTTTACATCAAAA
1 TTG-GCAGCATATATACAAC-AAA
*
52848941 TTGGACAGCATATATACAACAAT
1 TTGG-CAGCATATATACAACAAA
*
52848964 TTGGGCAGCATAAATACAACAAA
1 TT-GGCAGCATATATACAACAAA
* * *
52848987 TTGAGCAGCATTTTTACATCAAAAA
1 TTG-GCAGCATATATACA--ACAAA
52849012 TTGGACAGCATATATACAACAAA
1 TTGG-CAGCATATATACAACAAA
* *
52849035 TTGGGCAGCATATATATACCAAA
1 TT-GGCAGCATATATACAACAAA
* * *
52849058 TTGAGCAGCATTTTTACACCAAAA
1 TTG-GCAGCATATATACAAC-AAA
* * *
52849082 TTTGGAAAGCATATATATAACAAT
1 -TTGG-CAGCATATATACAACAAA
52849106 TTGGGCAGCAT
1 TT-GGCAGCAT
52849117 TTAAGCATCA
Statistics
Matches: 234, Mismatches: 41, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
22 3 0.01
23 148 0.63
24 35 0.15
25 48 0.21
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (22 bp):
TTGGCAGCATATATACAACAAA
Found at i:52848856 original size:71 final size:71
Alignment explanation
Indices: 52848728--52849116 Score: 557
Period size: 71 Copynumber: 5.5 Consensus size: 71
52848718 ATCTACCCTG
* * * * * * *
52848728 TTTGGACAGCTTTTATACATCAATTTGGACAGCATTTATATACCAAACT-AGACAGCATTTTCAC
1 TTTGGACAGCATATATACAACAATTTGGGCAGCATATATATACCAAATTGAG-CAGCATTTTTAC
52848792 ACCAAAA
65 ACCAAAA
* * * *
52848799 TTTGGACAGCATATATACAACAATTTGTGCAGCATATATACAACAAATTGAGTAGCATTTTTACA
1 TTTGGACAGCATATATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
52848864 CCAAAA
66 CCAAAA
* *
52848870 ATTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
1 TTTGGACAGCATATATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
*
52848935 TCAAAA
66 CCAAAA
* * *
52848941 -TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACA
1 TTTGGACAGCATATATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
*
52849005 TCAAAA
66 CCAAAA
* *
52849011 ATTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
1 TTTGGACAGCATATATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
52849076 CCAAAA
66 CCAAAA
* *
52849082 TTTGGAAAGCATATATATAACAATTTGGGCAGCAT
1 TTTGGACAGCATATATACAACAATTTGGGCAGCAT
52849117 TTAAGCATCA
Statistics
Matches: 285, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
70 66 0.23
71 217 0.76
72 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (71 bp):
TTTGGACAGCATATATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACA
CCAAAA
Found at i:52848990 original size:141 final size:142
Alignment explanation
Indices: 52848729--52849116 Score: 618
Period size: 141 Copynumber: 2.7 Consensus size: 142
52848719 TCTACCCTGT
* * * * * * * *
52848729 TTGGACAGCTTTTATACATCAATTTGGACAGCATTTATATACCAAACT-AGACAGCATTTTCACA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAG-CAGCATTTTTACA
* * *
52848793 CCAAAATTTGGACAGCATATATACAACAATTTGTGCAGCATATATACAACAAATTGAGTAGCATT
65 CCAAAATTTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATT
52848858 TTTACACCAAAAA
130 TTTACACCAAAAA
*
52848871 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
52848936 CAAAA-TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTT
66 CAAAATTTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTT
*
52849000 TTACATCAAAAA
131 TTACACCAAAAA
52849012 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
* *
52849077 CAAAATTTGGAAAGCATATATATAACAATTTGGGCAGCAT
66 CAAAATTTGGACAGCATATATACAACAATTTGGGCAGCAT
52849117 TTAAGCATCA
Statistics
Matches: 228, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
141 136 0.60
142 90 0.39
143 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (142 bp):
TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
CAAAATTTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTT
TTACACCAAAAA
Found at i:52849858 original size:24 final size:25
Alignment explanation
Indices: 52849830--52849911 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 25
52849820 TTCGAAAATA
*
52849830 TTTAATAAGTTCGCACACTTAGTGC
1 TTTAATAAATTCGCACACTTAGTGC
*
52849855 TTAATAATCAATTTCGCACACTTAGTGC
1 TT--TAAT-AAATTCGCACACTTAGTGC
*
52849883 TTTACAATTAAACTCGCACACTTAGTGC
1 TTT--AA-TAAATTCGCACACTTAGTGC
52849911 T
1 T
52849912 AATCTCATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.04
26 1 0.02
27 4 0.08
28 40 0.83
29 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (25 bp):
TTTAATAAATTCGCACACTTAGTGC
Found at i:52849871 original size:28 final size:28
Alignment explanation
Indices: 52849839--52849911 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
52849829 ATTTAATAAG
* *
52849839 TTCGCACACTTAGTGCTTAATAATCAAT
1 TTCGCACACTTAGTGCTTAACAATCAAA
* *
52849867 TTCGCACACTTAGTGCTTTACAATTAAA
1 TTCGCACACTTAGTGCTTAACAATCAAA
*
52849895 CTCGCACACTTAGTGCT
1 TTCGCACACTTAGTGCT
52849912 AATCTCATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (28 bp):
TTCGCACACTTAGTGCTTAACAATCAAA
Found at i:52851638 original size:32 final size:32
Alignment explanation
Indices: 52851596--52851656 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
52851586 TTTTTTGAAA
52851596 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
52851628 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
52851657 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:52851649 original size:20 final size:20
Alignment explanation
Indices: 52851615--52851656 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52851605 AACTATTTAA
** *
52851615 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
52851635 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
52851655 AT
1 AT
52851657 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:52854342 original size:13 final size:11
Alignment explanation
Indices: 52854315--52854348 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
52854305 TTTTTATAAT
52854315 TAAAATATTAA
1 TAAAATATTAA
52854326 TAAAATATCTAAA
1 TAAAATAT-T-AA
52854339 TAAAATATTA
1 TAAAATATTA
52854349 TCACAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:52857698 original size:25 final size:24
Alignment explanation
Indices: 52857658--52857704 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
52857648 AAAAATTCTA
52857658 TTTTTTATATTTGAAATTTAATTT
1 TTTTTTATATTTGAAATTTAATTT
52857682 TTTTTTA-ATTTAAGAAATTTAAT
1 TTTTTTATATTT--GAAATTTAAT
52857705 CTATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 7 0.33
25 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTTTATATTTGAAATTTAATTT
Found at i:52876892 original size:32 final size:31
Alignment explanation
Indices: 52876823--52876900 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
52876813 ACTACACTAG
* *
52876823 TAGTCACCTAACTATTATTAAATTACTTTTT
1 TAGTCACCCAACTATTAATAAATTACTTTTT
* * *
52876854 TGGTCACCCAATTATTAATAAATTGCTTTTTT
1 TAGTCACCCAACTATTAATAAATTAC-TTTTT
*
52876886 TAGTCACTCAACTAT
1 TAGTCACCCAACTAT
52876901 GAAAAGTTAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 21 0.55
32 17 0.45
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (31 bp):
TAGTCACCCAACTATTAATAAATTACTTTTT
Found at i:52903376 original size:5 final size:5
Alignment explanation
Indices: 52903363--52903407 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
52903353 CCGACCCTAT
* * *
52903363 TCTCA TCTCG TCTCA TCTCG TCTCC TCTCG TCATCG TCTCG TCTC
1 TCTCG TCTCG TCTCG TCTCG TCTCG TCTCG TC-TCG TCTCG TCTC
52903408 CCCTTGTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.07, C:0.42, G:0.11, T:0.40
Consensus pattern (5 bp):
TCTCG
Found at i:52903378 original size:10 final size:10
Alignment explanation
Indices: 52903363--52903407 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
52903353 CCGACCCTAT
52903363 TCTCATCTCG
1 TCTCATCTCG
52903373 TCTCATCTCG
1 TCTCATCTCG
*
52903383 TCTCCTCTCG
1 TCTCATCTCG
*
52903393 TCATCGTCTCG
1 TC-TCATCTCG
52903404 TCTC
1 TCTC
52903408 CCCTTGTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.07, C:0.42, G:0.11, T:0.40
Consensus pattern (10 bp):
TCTCATCTCG
Found at i:52903455 original size:15 final size:15
Alignment explanation
Indices: 52903423--52903454 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52903413 GTCACGCTGC
52903423 TTTCTTTTCTTTCTT
1 TTTCTTTTCTTTCTT
52903438 TTTCTTTTCTTT-TT
1 TTTCTTTTCTTTCTT
52903452 TTT
1 TTT
52903455 TGTCTCGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:52903703 original size:14 final size:14
Alignment explanation
Indices: 52903684--52903710 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52903674 GCCTATTCAA
52903684 TAATAATCCATAAC
1 TAATAATCCATAAC
52903698 TAATAATCCATAA
1 TAATAATCCATAA
52903711 GCCTAATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATAATCCATAAC
Found at i:52907334 original size:21 final size:21
Alignment explanation
Indices: 52907296--52907335 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52907286 ATCTTTTACC
* * *
52907296 AAAATTATTTTTTTAATATTT
1 AAAAATATTTTGTGAATATTT
52907317 AAAAATATTTTGTGAATAT
1 AAAAATATTTTGTGAATAT
52907336 AAATATAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
AAAAATATTTTGTGAATATTT
Found at i:52914365 original size:16 final size:17
Alignment explanation
Indices: 52914328--52914368 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
52914318 TTTCCATTTA
*
52914328 TCTATTTTTTCATCCCT
1 TCTAATTTTTCATCCCT
*
52914345 T-TAATTTTTCAT-CTT
1 TCTAATTTTTCATCCCT
52914360 TCTAATTTT
1 TCTAATTTT
52914369 CTTTTCACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 17 0.81
17 1 0.05
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (17 bp):
TCTAATTTTTCATCCCT
Done.