Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 124 of 170
Found at i:37927823 original size:11 final size:12
Alignment explanation
Indices: 37927802--37927836 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
37927792 ATTTTCATAA
37927802 TAAAATATTAAT
1 TAAAATATTAAT
37927814 TAAAAT-TTAAT
1 TAAAATATTAAT
37927825 TAAAATATTAAT
1 TAAAATATTAAT
37927837 ATTATAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAATATTAAT
Found at i:37932194 original size:24 final size:22
Alignment explanation
Indices: 37932146--37932195 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
37932136 ATTCATTAAT
*
37932146 TCATTTACATAGTATCACATTC
1 TCATTTACATAGTATCACATAC
37932168 TCATTTAAGCATA-TATCACAATAC
1 TCATTT-A-CATAGTATCAC-ATAC
37932192 TCAT
1 TCAT
37932196 AAACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 11 0.46
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (22 bp):
TCATTTACATAGTATCACATAC
Found at i:37938612 original size:43 final size:42
Alignment explanation
Indices: 37938509--37938648 Score: 183
Period size: 42 Copynumber: 3.3 Consensus size: 42
37938499 CGTTGTAGAA
* *
37938509 AAACGCCACTACAAAACATGACCTTTAGCGGCGCTTTCCCAC
1 AAACGCCGCTACAAAACATGACCTTTAGCGGCGTTTTCCCAC
*
37938551 AAATGCCGCTA-AACAACATGACCTTTAGCGGCGTTTTCCCCAC
1 AAACGCCGCTACAA-AACATGACCTTTAGCGGCGTTTT-CCCAC
* * *
37938594 AAACGCCGCTACAGAACATGGACCTTTAGCGGCACTTTTCCCAA
1 AAACGCCGCTACAAAACAT-GACCTTTAGCGGC-GTTTTCCCAC
37938638 AAACGCCGCTA
1 AAACGCCGCTA
37938649 AAGTTCATGT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 31 0.36
43 20 0.23
44 29 0.34
45 4 0.05
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTACAAAACATGACCTTTAGCGGCGTTTTCCCAC
Found at i:37939046 original size:21 final size:21
Alignment explanation
Indices: 37939022--37939066 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
37939012 TTCTGCTTTG
* * *
37939022 CTCTACTTCCTTCGTTGCTGC
1 CTCTACTTCCCTCGCTGCTAC
*
37939043 CTCTGCTTCCCTCGCTGCTAC
1 CTCTACTTCCCTCGCTGCTAC
37939064 CTC
1 CTC
37939067 CGCTTTAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.04, C:0.44, G:0.13, T:0.38
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCTAC
Found at i:37939071 original size:21 final size:21
Alignment explanation
Indices: 37939027--37939071 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
37939017 CTTTGCTCTA
* * * *
37939027 CTTCCTTCGTTGCTGCCTCTG
1 CTTCCCTCGCTGCTACCTCCG
37939048 CTTCCCTCGCTGCTACCTCCG
1 CTTCCCTCGCTGCTACCTCCG
37939069 CTT
1 CTT
37939072 TAAGTCGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.44, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTCCCTCGCTGCTACCTCCG
Found at i:37941515 original size:26 final size:26
Alignment explanation
Indices: 37941479--37941531 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
37941469 TTGAATAAAA
37941479 AGGGGTCGCTAAGTGCAGATTCCCCG
1 AGGGGTCGCTAAGTGCAGATTCCCCG
* *
37941505 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTCGCTAAGTGCAGATTCCCCG
37941531 A
1 A
37941532 ATTATTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.34, T:0.23
Consensus pattern (26 bp):
AGGGGTCGCTAAGTGCAGATTCCCCG
Found at i:37941560 original size:42 final size:42
Alignment explanation
Indices: 37941508--37941742 Score: 196
Period size: 42 Copynumber: 5.6 Consensus size: 42
37941498 TTCCCCGAGG
* *
37941508 GGTTGCTAAGTGCTGATTCC-CCGAATTATTGATTCTAAATGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTATTGATTGTAAA-GT
* *
37941550 GGTTTCTAAGTGCTGATTCCACCGTA-TATTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTA-TTGATTGT-AAAGT
* * * * * * *
37941593 GGATGCTATGTGCTGATTCC-TCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTATTGATTGTAAA-GT
37941635 GGTTGCTAAGTGCTGATTCCACCGTATCT-TTGATTGTGAAAG-
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TATTGATTGT-AAAGT
* * * *
37941677 GGTTTGCTATGTGCTGATTCC-CTGTATCACTGAATT-TAAAGT
1 GG-TTGCTAAGTGCTGATTCCACCGTATTATTG-ATTGTAAAGT
* *
37941719 GGTTCCTAAGTGCTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCACCG
37941743 AGTAACGGAT
Statistics
Matches: 152, Mismatches: 28, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
41 22 0.14
42 63 0.41
43 61 0.40
44 6 0.04
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTATTGATTGTAAAGT
Found at i:37941606 original size:43 final size:43
Alignment explanation
Indices: 37941505--37941697 Score: 182
Period size: 43 Copynumber: 4.5 Consensus size: 43
37941495 AGATTCCCCG
* * *
37941505 AGGGGTTGCTAAGTGCTGATTCC-CCGAAT-TATTGATTCT-AA
1 AGGGGTTGCTATGTGCTGATTCCACCGTATAT-TTGATTGTGAA
* * *
37941546 ATGTGGTTTCTAAGTGCTGATTCCACCGTATATTTGATTGTGAA
1 A-GGGGTTGCTATGTGCTGATTCCACCGTATATTTGATTGTGAA
* * * * *
37941590 AGGGGATGCTATGTGCTGATTCC-TCGTATCA-CTGAATAT-AA
1 AGGGGTTGCTATGTGCTGATTCCACCGTAT-ATTTGATTGTGAA
* *
37941631 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAA
1 AGG-GGTTGCTATGTGCTGATTCCACCGTATATTTGATTGTGAA
*
37941675 AGGGTTTGCTATGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATTCC
37941698 CTGTATCACT
Statistics
Matches: 122, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
41 6 0.05
42 48 0.39
43 59 0.48
44 9 0.07
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (43 bp):
AGGGGTTGCTATGTGCTGATTCCACCGTATATTTGATTGTGAA
Found at i:37941648 original size:85 final size:83
Alignment explanation
Indices: 37941505--37941742 Score: 314
Period size: 85 Copynumber: 2.8 Consensus size: 83
37941495 AGATTCCCCG
* * * * * * *
37941505 AGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAATGTGGTTTCTAAGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATT-CCCGTATCACTGAATATAAA-GTGGTTCCTAAGTGCTGATTCC
37941570 ACCGTATATTTGATTGTGAA
64 ACCGTATATTTGATTGTGAA
* *
37941590 AGGGGATGCTATGTGCTGATTCCTCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATTCC-CGTATCACTGAATATAAA-GTGGTTCCTAAGTGCTGATTCC
*
37941655 ACCGTATCTTTGATTGTGAA
64 ACCGTATATTTGATTGTGAA
* * *
37941675 AGGGTTTGCTATGTGCTGATTCCCTGTATCACTGAATTTAAAGTGGTTCCTAAGTGCTGAATCCA
1 AGGGGTTGCTATGTGCTGATTCCC-GTATCACTGAATATAAAGTGGTTCCTAAGTGCTGATTCCA
37941740 CCG
65 CCG
37941743 AGTAACGGAT
Statistics
Matches: 136, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
84 27 0.20
85 109 0.80
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (83 bp):
AGGGGTTGCTATGTGCTGATTCCCGTATCACTGAATATAAAGTGGTTCCTAAGTGCTGATTCCAC
CGTATATTTGATTGTGAA
Found at i:37950450 original size:12 final size:12
Alignment explanation
Indices: 37950433--37950458 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37950423 AAATCTACCC
37950433 AAATCCATTTCG
1 AAATCCATTTCG
37950445 AAATCCATTTCG
1 AAATCCATTTCG
37950457 AA
1 AA
37950459 GTCGATGGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
AAATCCATTTCG
Found at i:37950724 original size:41 final size:40
Alignment explanation
Indices: 37950652--37950740 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 40
37950642 TTCTCCTAGC
* ** *
37950652 GCCGCTAATACTCGACCTTTTGTGGCTTTTTTTTCATAAAT
1 GCCGCTAATACTCGACCTATTGCAGC-GTTTTTTCATAAAT
* * *
37950693 GCCGCTAATGCTTGACCTATTGCAGCGTTTTTTCGTAAAT
1 GCCGCTAATACTCGACCTATTGCAGCGTTTTTTCATAAAT
*
37950733 GCCACTAA
1 GCCGCTAA
37950741 AAAGCCAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 19 0.47
41 21 0.52
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (40 bp):
GCCGCTAATACTCGACCTATTGCAGCGTTTTTTCATAAAT
Found at i:37950813 original size:18 final size:18
Alignment explanation
Indices: 37950790--37950826 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
37950780 TGATTTTTTG
37950790 CAGCGTTTTTATCATAAA
1 CAGCGTTTTTATCATAAA
*
37950808 CAGCGTTTTTCTCATAAA
1 CAGCGTTTTTATCATAAA
37950826 C
1 C
37950827 GCCACTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (18 bp):
CAGCGTTTTTATCATAAA
Found at i:37957100 original size:19 final size:19
Alignment explanation
Indices: 37957076--37957127 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
37957066 AAAAATAAAA
37957076 AAAATTCAAAATAATTTTC
1 AAAATTCAAAATAATTTTC
* *
37957095 AAAATTTTAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTC
37957115 AAAATTCAAAATA
1 AAAATTCAAAATA
37957128 TTTATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:37957137 original size:19 final size:19
Alignment explanation
Indices: 37957075--37957137 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
37957065 AAAAAATAAA
37957075 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
* *
37957094 CAAAATTTTAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
37957114 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
37957133 AAAAA
1 AAAAA
37957138 CTCCAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 4 0.11
19 15 0.42
20 17 0.47
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:37962073 original size:16 final size:17
Alignment explanation
Indices: 37962034--37962074 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
37962024 CACGTAAAAC
* *
37962034 TAATCTAATTTTTTATA
1 TAATTTAATATTTTATA
37962051 TAA-TTAATATTTTA-A
1 TAATTTAATATTTTATA
37962066 TAATTTAAT
1 TAATTTAAT
37962075 TATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTTAATATTTTATA
Found at i:37966938 original size:32 final size:32
Alignment explanation
Indices: 37966902--37966965 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
37966892 TAAAGAAGAA
37966902 AAACATATTAACAGCGGATCTAAAGCAAAATC
1 AAACATATTAACAGCGGATCTAAAGCAAAATC
37966934 AAACATATTAACAGCGGATCTAAAGCAAAATC
1 AAACATATTAACAGCGGATCTAAAGCAAAATC
37966966 CATGAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (32 bp):
AAACATATTAACAGCGGATCTAAAGCAAAATC
Found at i:37967882 original size:33 final size:36
Alignment explanation
Indices: 37967838--37967908 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 36
37967828 TCACCTATTC
37967838 TCTCATCTCTTTTATTAT-TAAATTTT-TATCCTAA
1 TCTCATCTCTTTTATTATCTAAATTTTCTATCCTAA
* * *
37967872 TCTC-TCTCTTTTTTTCTCTCAATTTTCTATCCTAA
1 TCTCATCTCTTTTATTATCTAAATTTTCTATCCTAA
37967907 TC
1 TC
37967909 GTTTGTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 11 0.34
34 11 0.34
35 10 0.31
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (36 bp):
TCTCATCTCTTTTATTATCTAAATTTTCTATCCTAA
Found at i:37968795 original size:13 final size:13
Alignment explanation
Indices: 37968777--37968801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37968767 GAATTTACTT
37968777 GTGTGAAAATTTC
1 GTGTGAAAATTTC
37968790 GTGTGAAAATTT
1 GTGTGAAAATTT
37968802 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:37970693 original size:41 final size:41
Alignment explanation
Indices: 37970636--37970780 Score: 263
Period size: 41 Copynumber: 3.5 Consensus size: 41
37970626 GACTTTAAGT
37970636 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
37970677 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
37970718 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
37970759 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
37970781 ATATGTTAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:37972744 original size:19 final size:19
Alignment explanation
Indices: 37972720--37972756 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
37972710 ACAAACACCA
37972720 ATCGACCGACCACCACAAC
1 ATCGACCGACCACCACAAC
37972739 ATCGACCGACCACCACAA
1 ATCGACCGACCACCACAA
37972757 ACACCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.46, G:0.11, T:0.05
Consensus pattern (19 bp):
ATCGACCGACCACCACAAC
Found at i:37975515 original size:19 final size:19
Alignment explanation
Indices: 37975478--37975515 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
37975468 CTAATTAATT
*
37975478 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
37975497 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
37975516 GAAAAAGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:37977016 original size:23 final size:23
Alignment explanation
Indices: 37976989--37977098 Score: 97
Period size: 23 Copynumber: 5.0 Consensus size: 23
37976979 GGCTTTGCCG
*
37976989 ATCAGGCACTTTATGTGTTGTAT
1 ATCAGGCACTTTATGTGTCGTAT
37977012 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* * **
37977035 TTCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTAT
* **
37977056 ATCAGGCACCTCGTG-GTCGT-T
1 ATCAGGCACTTTATGTGTCGTAT
*
37977077 -TTAGGCAC-TTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
37977098 A
1 A
37977099 CTGATCAGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.04
20 16 0.22
21 17 0.23
23 38 0.51
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:37977082 original size:20 final size:21
Alignment explanation
Indices: 37977025--37977084 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
37977015 AGGCACTTTA
37977025 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGT-TTT-AGGCACCTCG
* *
37977048 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTTTTAGGCACCTCG
37977069 TG-GTCGTTTTAGGCAC
1 TGTGTCGTTTTAGGCAC
37977085 TTATGTGTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.36
21 12 0.36
22 1 0.03
23 8 0.24
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.33
Consensus pattern (21 bp):
TGTGTCGTTTTAGGCACCTCG
Found at i:37977365 original size:19 final size:19
Alignment explanation
Indices: 37977341--37977378 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
37977331 AGTAAAGGTA
*
37977341 ATTAAAGTT-ATGACATAAT
1 ATTAAAATTGATG-CATAAT
37977360 ATTAAAATTGATGCATAAT
1 ATTAAAATTGATGCATAAT
37977379 TAAAAGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (19 bp):
ATTAAAATTGATGCATAAT
Found at i:37980856 original size:14 final size:13
Alignment explanation
Indices: 37980837--37980875 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
37980827 TTATGCAAGC
37980837 AACAATATAATGAT
1 AACAATA-AATGAT
*
37980851 AACAATAATATAAT
1 AACAATAA-ATGAT
37980865 AACAATAAATG
1 AACAATAAATG
37980876 TAATACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (13 bp):
AACAATAAATGAT
Found at i:37981939 original size:13 final size:15
Alignment explanation
Indices: 37981912--37981943 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
37981902 CTGATTTGTA
37981912 AAAAAATGAATAAAT
1 AAAAAATGAATAAAT
37981927 AAAAAAT-AA-AAAT
1 AAAAAATGAATAAAT
37981940 AAAA
1 AAAA
37981944 GGAAAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAAATGAATAAAT
Found at i:37982306 original size:21 final size:21
Alignment explanation
Indices: 37982280--37982320 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
37982270 TAATCTGGGC
37982280 TTGTT-TTT-GTTTTGGG-TT
1 TTGTTGTTTAGTTTTGGGCTT
37982298 TTGTTGTTTAGTTTTGGGCTT
1 TTGTTGTTTAGTTTTGGGCTT
37982319 TT
1 TT
37982321 AGCCCGGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 8 0.40
21 4 0.20
ACGTcount: A:0.02, C:0.02, G:0.27, T:0.68
Consensus pattern (21 bp):
TTGTTGTTTAGTTTTGGGCTT
Found at i:37984507 original size:10 final size:9
Alignment explanation
Indices: 37984481--37984506 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
37984471 TTTAAATCAT
37984481 AAAAAAAAC
1 AAAAAAAAC
37984490 AAAAAAAAC
1 AAAAAAAAC
37984499 AAAAAAAA
1 AAAAAAAA
37984507 AAGAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:37985862 original size:18 final size:18
Alignment explanation
Indices: 37985839--37985875 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
37985829 TAGTTTACCT
37985839 ATGTATTTTACTTTTAAA
1 ATGTATTTTACTTTTAAA
37985857 ATGTATTTTACTTTTAAA
1 ATGTATTTTACTTTTAAA
37985875 A
1 A
37985876 AAGAGCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
ATGTATTTTACTTTTAAA
Found at i:37992036 original size:6 final size:6
Alignment explanation
Indices: 37992027--37992061 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
37992017 TATATATATA
37992027 TGTTGG TGTTGG TGTTGG TGTTGG TGTTGG TGTTG
1 TGTTGG TGTTGG TGTTGG TGTTGG TGTTGG TGTTG
37992062 AAGTGAGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (6 bp):
TGTTGG
Found at i:37992501 original size:16 final size:16
Alignment explanation
Indices: 37992476--37992511 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37992466 CGGTTTGCTC
*
37992476 TAATGGAATAGAGGCG
1 TAATGAAATAGAGGCG
*
37992492 TAATGAAATAGATGCG
1 TAATGAAATAGAGGCG
37992508 TAAT
1 TAAT
37992512 AGCAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (16 bp):
TAATGAAATAGAGGCG
Found at i:37992556 original size:45 final size:44
Alignment explanation
Indices: 37992491--37992587 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
37992481 GAATAGAGGC
* *
37992491 GTAATGAAATAGATGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATA-CAATTC-ATGTGTTTGGTTGAAT
* ** *
37992536 GTAATGGAATAGAGGTGTAATATTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATACAATTCATGTGTTTGGTTGAAT
*
37992580 GGAATGGA
1 GTAATGGA
37992588 GGTGTAATAG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.55
45 19 0.43
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATACAATTCATGTGTTTGGTTGAAT
Found at i:37992771 original size:18 final size:17
Alignment explanation
Indices: 37992744--37992778 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
37992734 TTATTATTAA
*
37992744 ATATATTTTAATCAAAAT
1 ATATAATTTAAT-AAAAT
37992762 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
37992779 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:37992818 original size:61 final size:61
Alignment explanation
Indices: 37992753--37993069 Score: 258
Period size: 61 Copynumber: 5.3 Consensus size: 61
37992743 AATATATTTT
* *
37992753 AATCAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAA
1 AATCAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTA
* * * * * * * * * *
37992814 AATCATAATATATGATACT-ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTT
1 AATCAAAATATATGAT-TTAATAAAATTCTTAATAAT-CAAT-ATTCTTATATGAATTTACTTA
* *
37992873 AATTAAAATATATGGTTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTA
1 AATCAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTA
* * * * * * * * * *
37992934 AATCATAATATATGATAGT-ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTT
1 AATCAAAATATATGAT-TTAATAAAATTCTTAATAAT-CAAT-ATTCTTATATGAATTTACTTA
* * *
37992993 AATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAA
1 AATCAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTA
*
37993054 AATCATAATATATGAT
1 AATCAAAATATATGAT
37993070 ACTATAAAAT
Statistics
Matches: 188, Mismatches: 52, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
58 4 0.02
59 67 0.36
60 32 0.17
61 81 0.43
62 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (61 bp):
AATCAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTA
Found at i:37993005 original size:18 final size:17
Alignment explanation
Indices: 37992984--37993018 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
37992974 TTATTATTAA
*
37992984 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
37993002 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
37993019 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:37993125 original size:18 final size:17
Alignment explanation
Indices: 37993102--37993138 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
37993092 AATTATTATT
37993102 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
37993118 AAATATATGATTTAATA
1 AAATATATGATTTAATA
37993135 AAAT
1 AAAT
37993139 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:37993148 original size:120 final size:120
Alignment explanation
Indices: 37992730--37993139 Score: 766
Period size: 120 Copynumber: 3.4 Consensus size: 120
37992720 ATATTTTAAC
*
37992730 ATAATTATTATTAAATATATTTTAATCAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
37992795 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
**
37992850 ATAATTATTATTAAATATATTTTAATTAAAATATATGGTTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
* *
37992915 TCTTATATGAATTTACTTAAATCATAATATATGATAGTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
37992970 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
37993035 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
37993090 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
37993140 TAAAATAATT
Statistics
Matches: 280, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 280 1.00
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:37993174 original size:47 final size:46
Alignment explanation
Indices: 37993121--37993361 Score: 175
Period size: 47 Copynumber: 5.3 Consensus size: 46
37993111 TTAATTAAAA
*
37993121 TATATG-ATTTAATAAAATTTAAAATAATTATTACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT
* *
37993168 TATATGAATTTGTATAATTTAAAATAATTATTAT--TAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * *
37993213 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
* *
37993259 TATATGAATTTATATAATTTAAAATAATTA--ATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * * *
37993304 TA-AT-AATGATATATAATTTCATAA-AATTCTTAATAATAAATATTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
37993350 TATATGAATTTA
1 TATATGAATTTA
37993362 CTAAAATCAT
Statistics
Matches: 152, Mismatches: 20, Indels: 44
0.70 0.09 0.20
Matches are distributed among these distances:
43 6 0.04
44 46 0.30
45 18 0.12
46 13 0.09
47 59 0.39
48 10 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT
Found at i:37993195 original size:101 final size:98
Alignment explanation
Indices: 37993078--37993361 Score: 312
Period size: 91 Copynumber: 3.0 Consensus size: 98
37993068 ATACTATAAA
* *
37993078 ATATAATTTGAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTT-A
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAA-TAAAATATAT-ATTT-ATAAAATTTCA
37993142 AAATAATTATT-ACTAATAAATTTTCTTATATGAATTT
63 AAA-AATTATTGA-TAATAAATTTTCTTATATGAATTT
* *
37993179 GTATAATTTAAAATAATTATTATTAAATATAATTTAAT--AATA-ATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
*
37993237 AATTCTTGATAATAAATTTTCTTATATGAATTT
66 AATTATTGATAATAAATTTTCTTATATGAATTT
* * *
37993270 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT--AAT-GATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
* * *
37993328 AATTCTTAATAATAAATATTCTTATATGAATTT
66 AATTATTGATAATAAATTTTCTTATATGAATTT
37993361 A
1 A
37993362 CTAAAATCAT
Statistics
Matches: 171, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
91 122 0.71
92 4 0.02
93 2 0.01
94 1 0.01
96 1 0.01
97 2 0.01
98 4 0.02
100 1 0.01
101 34 0.20
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (98 bp):
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
AATTATTGATAATAAATTTTCTTATATGAATTT
Found at i:37993230 original size:44 final size:43
Alignment explanation
Indices: 37993180--37993322 Score: 139
Period size: 44 Copynumber: 3.2 Consensus size: 43
37993170 TATGAATTTG
37993180 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
* * * *
37993224 TATAATTTCATAA-AATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-AT--TAAATATAAT-TTA-AT-AATATA
*
37993271 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
37993315 TATAATTT
1 TATAATTT
37993323 CATAAAATTC
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.39
45 10 0.13
46 10 0.13
47 22 0.28
48 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATATA
Found at i:37993251 original size:91 final size:91
Alignment explanation
Indices: 37993146--37993361 Score: 369
Period size: 91 Copynumber: 2.4 Consensus size: 91
37993136 AATTTAAAAT
* * * *
37993146 AATTATTACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
37993211 TTTAATAATAATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
37993237 AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
*
37993302 TTTAATAATGATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
37993328 AATTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTA
37993362 CTAAAATCAT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 117 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:38002652 original size:53 final size:53
Alignment explanation
Indices: 38002572--38002798 Score: 211
Period size: 53 Copynumber: 4.3 Consensus size: 53
38002562 AGGGGTATAA
*
38002572 CAGTCATTTAACCCTAT-GTGGGTATTTCAGTCATTTGACCCTTCGAGGGTATTTT
1 CAGTCATTT-ACCCT-TCG-GGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
* * *
38002627 GA-TCATTGTACCCTTCGGGGTATTTCGGTTATTTTACCCTTCGAGGGTA-TTT
1 CAGTCATT-TACCCTTCGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
* * * *
38002679 CAGTTATTTCACCCTTCAAGGGCATTTCAGTCATTTTACCTTTCG-GGG--TTTT
1 CAGTCATTT-ACCCTTC-GGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
* * *
38002731 CAGTCATTTTACCCTTTGGGGTATTTC-GATCATTTTACCTTTCGA-GATA-TTT
1 CAGTCA-TTTACCCTTCGGGGTATTTCAG-TCATTTTACCCTTCGAGGGTATTTT
38002783 CAGTCATTTTACCCTT
1 CAGTCA-TTTACCCTT
38002799 TCGATCATTT
Statistics
Matches: 145, Mismatches: 16, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
50 1 0.01
51 24 0.17
52 38 0.26
53 47 0.32
54 33 0.23
55 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (53 bp):
CAGTCATTTACCCTTCGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
Found at i:38002664 original size:26 final size:26
Alignment explanation
Indices: 38002563--38002798 Score: 228
Period size: 27 Copynumber: 9.0 Consensus size: 26
38002553 TTCATCTCTA
** *
38002563 GGGGTATAACAGTCATTTAACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCT-TC
*
38002589 GTGGGTATTTCAGTCATTTGACCCTTC
1 G-GGGTATTTCAGTCATTTTACCCTTC
* *
38002616 GAGGGTATTT-TGATCATTGTACCCTTC
1 G-GGGTATTTCAG-TCATTTTACCCTTC
* *
38002643 GGGGTATTTCGGTTATTTTACCCTTC
1 GGGGTATTTCAGTCATTTTACCCTTC
* *
38002669 GAGGGTATTTCAGTTATTTCACCCTTC
1 G-GGGTATTTCAGTCATTTTACCCTTC
* * *
38002696 AAGGGCATTTCAGTCATTTTACCTTTC
1 -GGGGTATTTCAGTCATTTTACCCTTC
*
38002723 GGGGT-TTTCAGTCATTTTACCCTTT
1 GGGGTATTTCAGTCATTTTACCCTTC
*
38002748 GGGGTATTTC-GATCATTTTACCTTTC
1 GGGGTATTTCAG-TCATTTTACCCTTC
* *
38002774 GAGATATTTCAGTCATTTTACCCTT
1 GGGGTATTTCAGTCATTTTACCCTT
38002799 TCGATCATTT
Statistics
Matches: 175, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
25 24 0.14
26 63 0.36
27 88 0.50
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (26 bp):
GGGGTATTTCAGTCATTTTACCCTTC
Found at i:38002808 original size:26 final size:24
Alignment explanation
Indices: 38002702--38002808 Score: 92
Period size: 26 Copynumber: 4.2 Consensus size: 24
38002692 CTTCAAGGGC
*
38002702 ATTTCAGTCATTTTACCTTTCGGGGT
1 ATTTCAGTCATTTTACCTTTC--GAT
* *
38002728 -TTTCAGTCATTTTACCCTTTGGGGT
1 ATTTCAGTCATTTTA-CCTTT-CGAT
38002753 ATTTC-GATCATTTTACCTTTCGAGAT
1 ATTTCAG-TCATTTTACCTTTC--GAT
38002779 ATTTCAGTCATTTTACCCTTTCGAT
1 ATTTCAGTCATTTTA-CCTTTCGAT
38002804 CATTT
1 -ATTT
38002809 TATCCTTCGA
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
25 26 0.38
26 36 0.52
27 7 0.10
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.48
Consensus pattern (24 bp):
ATTTCAGTCATTTTACCTTTCGAT
Found at i:38002818 original size:43 final size:44
Alignment explanation
Indices: 38002754--38002839 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
38002744 CTTTGGGGTA
38002754 TTTCGATCATTTTACCTTTCGA-GATATTTCAGTCATTTTACCC
1 TTTCGATCATTTTACCTTTCGAGGATATTTCAGTCATTTTACCC
* *
38002797 TTTCGATCATTTTATCC-TTCGAGGTTATTTCGGTCATTTTACC
1 TTTCGATCATTTTA-CCTTTCGAGGATATTTCAGTCATTTTACC
38002840 ACGAATCGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 19 0.49
44 20 0.51
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.48
Consensus pattern (44 bp):
TTTCGATCATTTTACCTTTCGAGGATATTTCAGTCATTTTACCC
Found at i:38008694 original size:35 final size:35
Alignment explanation
Indices: 38008648--38008717 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
38008638 GAATATCACC
38008648 ATAGGAGGGGAGAAGAGATTTGATTCAAGCTTTCT
1 ATAGGAGGGGAGAAGAGATTTGATTCAAGCTTTCT
* *
38008683 ATAGGAGGGGAGAAGAGATTTTATTTAAGCTTTCT
1 ATAGGAGGGGAGAAGAGATTTGATTCAAGCTTTCT
38008718 CTTTGCATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.07, G:0.30, T:0.31
Consensus pattern (35 bp):
ATAGGAGGGGAGAAGAGATTTGATTCAAGCTTTCT
Found at i:38020610 original size:13 final size:13
Alignment explanation
Indices: 38020589--38020621 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38020579 ACTTAAATCA
*
38020589 ATTACAATAACTT
1 ATTATAATAACTT
38020602 ATTATAATAACTT
1 ATTATAATAACTT
38020615 ATTATAA
1 ATTATAA
38020622 GCTTTAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTATAATAACTT
Found at i:38026770 original size:4 final size:4
Alignment explanation
Indices: 38026761--38026814 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
38026751 GGATTACTTG
* * *
38026761 TACA TACA TACA TACA TACA TACA TACA TTCA TACA TACA CACA CACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
38026809 CACA TA
1 TACA TA
38026815 TATATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (4 bp):
TACA
Found at i:38041704 original size:22 final size:22
Alignment explanation
Indices: 38041676--38041719 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
38041666 TAACTTATAA
38041676 AATAATAACAATCTTCCTCCAT
1 AATAATAACAATCTTCCTCCAT
38041698 AATAATAACAATCTTCCTCCAT
1 AATAATAACAATCTTCCTCCAT
38041720 TCCTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAATAACAATCTTCCTCCAT
Found at i:38043352 original size:57 final size:57
Alignment explanation
Indices: 38043247--38043354 Score: 128
Period size: 57 Copynumber: 1.9 Consensus size: 57
38043237 GAATGAATTT
* * * *
38043247 ATTTCCTTTTTCTATTTTTTTTTCCATTTTGAAGAAAACCACATTCATTTCTAAATG
1 ATTTCATTTCTCTATTTTATTTTCCATTTTGAAGAAAACCACAATCATTTCTAAATG
* * **
38043304 ATTTCATTTCTCTATTTTCATTTT-CTTTTTGGAGAAAACCTTAATCATTTC
1 ATTTCATTTCTCTATTTT-ATTTTCCATTTTGAAGAAAACCACAATCATTTC
38043355 ACCATTTCTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
57 38 0.90
58 4 0.10
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.52
Consensus pattern (57 bp):
ATTTCATTTCTCTATTTTATTTTCCATTTTGAAGAAAACCACAATCATTTCTAAATG
Found at i:38044901 original size:18 final size:19
Alignment explanation
Indices: 38044863--38044905 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
38044853 AGAATAAGAA
* *
38044863 AAATATAATGTGGACATTG
1 AAATGTAATGTGGAAATTG
38044882 AAATGTAATGT-GAAATTG
1 AAATGTAATGTGGAAATTG
38044900 AAATGT
1 AAATGT
38044906 GTAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (19 bp):
AAATGTAATGTGGAAATTG
Found at i:38052287 original size:17 final size:17
Alignment explanation
Indices: 38052260--38052293 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
38052250 TTAAGAAATA
38052260 AAAAAACGAAAAAGAAAG
1 AAAAAACG-AAAAGAAAG
38052278 AAAAAA-GAAAAGAAAG
1 AAAAAACGAAAAGAAAG
38052294 GGAGAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 1 0.06
18 6 0.38
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAACGAAAAGAAAG
Found at i:38055726 original size:188 final size:192
Alignment explanation
Indices: 38055395--38055774 Score: 588
Period size: 188 Copynumber: 2.0 Consensus size: 192
38055385 TTTGCTGATA
* *
38055395 GTGCATCCTGCTTGGAGCATTATCTCTATACAAATTTCAACCCTCATTTGGGACAAAAAAACCCA
1 GTGCATCCTACTTGGAGCATTATCTCTATACAAATTTCAACCCTCACTTGGGACAAAAAAACCCA
* * * *
38055460 TCATATATATCCTGAGATATATTTTCAAAACTCATCTCGTCAATATTAATGCATTGTGATAAATA
66 TCACATATATCCTGAGATATATTTTCAAAACCCATCTCATCAATATTAATGCACTGTGATAAATA
* * *
38055525 ATTTACTAAAATATCGGATCAAACTAGTATTAAAAATGTGTACAATTTTAAAAACTAATATT
131 ATTTACTAAAATATCGGATCAAACTAGTATTAAAAATGTGAAAAAATTTAAAAACTAATATT
* * * *
38055587 GTGCGTCCTACTTGGAGCGTTATCTCTCTACAAA-TTCAACTCTCACTTGGGAC-AAAAAACCCA
1 GTGCATCCTACTTGGAGCATTATCTCTATACAAATTTCAACCCTCACTTGGGACAAAAAAACCCA
*
38055650 -C-CATATATCCTGAGATATATTTTCAGAACCCATCTCATCAATATTAATGCACTGTGATAAATA
66 TCACATATATCCTGAGATATATTTTCAAAACCCATCTCATCAATATTAATGCACTGTGATAAATA
* *
38055713 ATTTACTAAAATATTGGATCAAACTAGTATTAAGAATGTGAAAAAATTTAAAAACTAATATT
131 ATTTACTAAAATATCGGATCAAACTAGTATTAAAAATGTGAAAAAATTTAAAAACTAATATT
38055775 TCATCCCAAA
Statistics
Matches: 172, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
188 114 0.66
189 1 0.01
190 10 0.06
191 17 0.10
192 30 0.17
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (192 bp):
GTGCATCCTACTTGGAGCATTATCTCTATACAAATTTCAACCCTCACTTGGGACAAAAAAACCCA
TCACATATATCCTGAGATATATTTTCAAAACCCATCTCATCAATATTAATGCACTGTGATAAATA
ATTTACTAAAATATCGGATCAAACTAGTATTAAAAATGTGAAAAAATTTAAAAACTAATATT
Found at i:38056362 original size:15 final size:15
Alignment explanation
Indices: 38056331--38056388 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
38056321 TTTAAGAAAA
38056331 AATTATAATA-AACAT
1 AATTATAATATAA-AT
38056346 AATTATAATATAAAT
1 AATTATAATATAAAT
* *
38056361 AA-TA-CATCTAAAT
1 AATTATAATATAAAT
*
38056374 AATTATAATTTAAAT
1 AATTATAATATAAAT
38056389 TTAAATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 9 0.25
14 4 0.11
15 21 0.58
16 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATAATATAAAT
Found at i:38056406 original size:5 final size:5
Alignment explanation
Indices: 38056396--38056420 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38056386 AATTTAAATT
38056396 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
38056421 TGGTTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:38061325 original size:29 final size:30
Alignment explanation
Indices: 38061290--38061357 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
38061280 TAGTATATTG
*
38061290 TAAAATTATACTTTAATC-TTTAAAAATAA
1 TAAAATTATAATTTAATCTTTTAAAAATAA
* * *
38061319 TAAAATTTTAATTTAATCTTTTCAAAATTA
1 TAAAATTATAATTTAATCTTTTAAAAATAA
38061349 TAAATATTA
1 TAAA-ATTA
38061358 AAAATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 16 0.50
30 13 0.41
31 3 0.09
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAATTATAATTTAATCTTTTAAAAATAA
Found at i:38066533 original size:15 final size:15
Alignment explanation
Indices: 38066513--38066542 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38066503 GAAGTGTCCA
*
38066513 AAATATGTTTAATTT
1 AAATATATTTAATTT
38066528 AAATATATTTAATTT
1 AAATATATTTAATTT
38066543 GGGTTGGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
AAATATATTTAATTT
Found at i:38069229 original size:19 final size:19
Alignment explanation
Indices: 38069205--38069244 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38069195 GTTAAAACTC
* *
38069205 TATTTTAGAGTAATTAAAA
1 TATTTTAAAATAATTAAAA
*
38069224 TATTTTAAAATAATTTAAA
1 TATTTTAAAATAATTAAAA
38069243 TA
1 TA
38069245 ATATTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TATTTTAAAATAATTAAAA
Found at i:38075876 original size:2 final size:2
Alignment explanation
Indices: 38075869--38075966 Score: 187
Period size: 2 Copynumber: 49.0 Consensus size: 2
38075859 TGAATGGTTA
38075869 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
38075911 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
38075953 TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG
38075967 ATTGAAACTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.50
Consensus pattern (2 bp):
TG
Found at i:38077512 original size:24 final size:24
Alignment explanation
Indices: 38077472--38077518 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38077462 AAAGGGAAAT
*
38077472 AAGAGAAAGTGATGGAAAATGTTG
1 AAGAGAAAGTGAAGGAAAATGTTG
*
38077496 AAGAGAAAG-GAAAGGAAAGTGTT
1 AAGAGAAAGTG-AAGGAAAATGTT
38077519 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
AAGAGAAAGTGAAGGAAAATGTTG
Found at i:38079271 original size:291 final size:291
Alignment explanation
Indices: 38078747--38079332 Score: 1154
Period size: 291 Copynumber: 2.0 Consensus size: 291
38078737 TATAAATGTT
*
38078747 AGATAAAAATGGAGTGTCTGAAAATTAATTAGTAAACTCCGGTAATGCCTCATACCCTATTTCGG
1 AGATAAAAATGGAGTGTCTAAAAATTAATTAGTAAACTCCGGTAATGCCTCATACCCTATTTCGG
38078812 TGTCGAATACGGGTAAGGGGTGTTACATATACATTTAGTGACTTGTTGTGATATACAATTTAACA
66 TGTCGAATACGGGTAAGGGGTGTTACATATACATTTAGTGACTTGTTGTGATATACAATTTAACA
38078877 CACGACTGTGTGTCACACATAATTACACAATTCGCCAAATGATGAGTACCATTCACAGACAGCCG
131 CACGACTGTGTGTCACACATAATTACACAATTCGCCAAATGATGAGTACCATTCACAGACAGCCG
38078942 ATATGTCAGTTTACTATTCTTTGGCGTATACAATACACCCATATGACCATTCAGACAAAACTTCT
196 ATATGTCAGTTTACTATTCTTTGGCGTATACAATACACCCATATGACCATTCAGACAAAACTTCT
38079007 TCATGTTAGCCACATACCCAGATCCATAGTC
261 TCATGTTAGCCACATACCCAGATCCATAGTC
38079038 AGATAAAAATGGAGTGTCTAAAAATTAATTAGTAAACTCCGGTAATGCCTCATACCCTATTTCGG
1 AGATAAAAATGGAGTGTCTAAAAATTAATTAGTAAACTCCGGTAATGCCTCATACCCTATTTCGG
38079103 TGTCGAATACGGGTAAGGGGTGTTACATATACATTTAGTGACTTGTTGTGATATACAATTTAACA
66 TGTCGAATACGGGTAAGGGGTGTTACATATACATTTAGTGACTTGTTGTGATATACAATTTAACA
38079168 CACGACTGTGTGTCACACATAATTACACAATTCGCCAAATGATGAGTACCATTCACAGACAGCCG
131 CACGACTGTGTGTCACACATAATTACACAATTCGCCAAATGATGAGTACCATTCACAGACAGCCG
*
38079233 ATATGTCAGTTTACTATTCTTTGGCGTATGCAATACACCCATATGACCATTCAGACAAAACTTCT
196 ATATGTCAGTTTACTATTCTTTGGCGTATACAATACACCCATATGACCATTCAGACAAAACTTCT
38079298 TCATGTTAGCCACATACCCAGATCCATAGTC
261 TCATGTTAGCCACATACCCAGATCCATAGTC
38079329 AGAT
1 AGAT
38079333 TCATATCATT
Statistics
Matches: 293, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
291 293 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (291 bp):
AGATAAAAATGGAGTGTCTAAAAATTAATTAGTAAACTCCGGTAATGCCTCATACCCTATTTCGG
TGTCGAATACGGGTAAGGGGTGTTACATATACATTTAGTGACTTGTTGTGATATACAATTTAACA
CACGACTGTGTGTCACACATAATTACACAATTCGCCAAATGATGAGTACCATTCACAGACAGCCG
ATATGTCAGTTTACTATTCTTTGGCGTATACAATACACCCATATGACCATTCAGACAAAACTTCT
TCATGTTAGCCACATACCCAGATCCATAGTC
Found at i:38082633 original size:78 final size:78
Alignment explanation
Indices: 38082540--38082973 Score: 717
Period size: 78 Copynumber: 5.6 Consensus size: 78
38082530 AACTAATAGT
* **
38082540 GGATAATATATGTATATACATGTATATGTTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTA
1 GGAT-ATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTA
38082605 TATATATAAAGTTC
65 TATATATAAAGTTC
**
38082619 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGCCTGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
38082684 ATATATAAAGTTC
66 ATATATAAAGTTC
* ** *
38082697 GGATATATATGTATATACACGAATAAATTCTTGAATTTAGTTAAAAGTATGCCTATTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
38082762 ATATATAAAGTTC
66 ATATATAAAGTTC
*
38082775 GGATATATATGTATGTACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
38082840 ATATATAAAGTTC
66 ATATATAAAGTTC
* *
38082853 GGATGTATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTAAGTATGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
38082918 ATATATAAAGTTC
66 ATATATAAAGTTC
** *
38082931 GGATATACGTGTATATACATGAATAAGTT-TTGAATTTAGTTAA
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAA
38082974 TGTTGAATGT
Statistics
Matches: 336, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
77 14 0.04
78 318 0.95
79 4 0.01
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (78 bp):
GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTAT
ATATATAAAGTTC
Found at i:38083714 original size:41 final size:41
Alignment explanation
Indices: 38083669--38083825 Score: 228
Period size: 41 Copynumber: 3.8 Consensus size: 41
38083659 CATTTCGGAC
* **
38083669 TATAAGTCTAGCAGGCTAAAAGCCGGTG-TACTGAATCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGAT-CTGAATCAGGT
38083710 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
*
38083751 TATAAGCCTAGAAGGCTAAGTGCCGGTGATCTGAATCAGGCT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG-T
*
38083793 T-TAAGCCTAACAGGCTAAGTGCCGGTGAATCTG
1 TATAAGCCTAGCAGGCTAAGTGCCGGTG-ATCTG
38083826 TTTAAATTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
41 99 0.93
42 8 0.07
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
Found at i:38083734 original size:82 final size:82
Alignment explanation
Indices: 38083635--38083821 Score: 197
Period size: 82 Copynumber: 2.3 Consensus size: 82
38083625 GACTTTATGT
* * * *
38083635 CTAGCAGGCT-TGATGCCGGTGAAAC-ATTTC-GGACTATAAGTCTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTAAG-TGCCGGTGAAACTA-ATCAGG-CTATAAGCCTAGAAGGCTAAAAGCCGGTG
38083697 -TACTGAATCAGG-TTATAAGC
63 AT-CTGAATCAGGCTT-TAAGC
* * **
38083717 CTAGCAGGCTAAGTGCCGGTG-ATCTGAATCAGGTTATAAGCCTAGAAGGCTAAGTGCCGGTGAT
1 CTAGCAGGCTAAGTGCCGGTGAAACT-AATCAGGCTATAAGCCTAGAAGGCTAAAAGCCGGTGAT
38083781 CTGAATCAGGCTTTAAGC
65 CTGAATCAGGCTTTAAGC
*
38083799 CTAACAGGCTAAGTGCCGGTGAA
1 CTAGCAGGCTAAGTGCCGGTGAA
38083822 TCTGTTTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
81 2 0.02
82 79 0.89
83 8 0.09
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (82 bp):
CTAGCAGGCTAAGTGCCGGTGAAACTAATCAGGCTATAAGCCTAGAAGGCTAAAAGCCGGTGATC
TGAATCAGGCTTTAAGC
Found at i:38087894 original size:19 final size:19
Alignment explanation
Indices: 38087870--38087916 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
38087860 CGACGTCTTT
*
38087870 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
38087889 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
38087908 TATGCATTA
1 TTTGCATTA
38087917 AAGTCCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:38095161 original size:51 final size:51
Alignment explanation
Indices: 38095054--38095185 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 51
38095044 ACTTCACCAG
* * **
38095054 AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAACAATG
1 AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAAAA
* * *
38095105 GAGAGACCAAGGTGAAAACCCGTAAAGGGCGCTTTGAATTCTAAAAAAAAA
1 AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAAAA
38095156 AAGAGAAAGGCCAAGGTGAAAACCCGCAAA
1 AAGAG--A--CCAAGGTGAAAACCCGCAAA
38095186 TGGCCCCTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 48 0.71
53 1 0.01
55 19 0.28
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (51 bp):
AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAAAA
Found at i:38096491 original size:45 final size:44
Alignment explanation
Indices: 38096347--38096509 Score: 152
Period size: 44 Copynumber: 3.7 Consensus size: 44
38096337 AATCTTATTT
* * * * *
38096347 CCCTGAAGTTGCAGTGGAGCAGATTAAAG-TCACTAATCTTATCC
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACGAGTCCTATCC
* * * * *
38096391 CCTTGAAGTTGCAGTGGGGCAGA-TCGAAGTTACCAG-CCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGACT-GAAGATACGAGTCC-TATCC
*
38096435 CCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAGTCCTATCC
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CGAGTCCTATCC
**
38096480 CCCTGAAGTTGCAGCAGAGCAGACTGAAGA
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGA
38096510 CAGCGAATAT
Statistics
Matches: 97, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
43 2 0.02
44 57 0.59
45 36 0.37
46 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACGAGTCCTATCC
Found at i:38096515 original size:45 final size:45
Alignment explanation
Indices: 38096430--38096515 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
38096420 TTACCAGCCT
* ** *
38096430 TATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAGTCC
1 TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGAGTCC
*
38096475 TATCCCCCTGAAGTTGCAGCAGAGCAGACTGAAGACAGCGA
1 TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGA
38096516 ATATTATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (45 bp):
TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGAGTCC
Found at i:38098189 original size:3 final size:3
Alignment explanation
Indices: 38098183--38098214 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
38098173 TTTGTGTTGT
38098183 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38098215 TACTCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38098337 original size:15 final size:15
Alignment explanation
Indices: 38098319--38098353 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
38098309 GTTATTATAA
38098319 TTATTATTACTATTT
1 TTATTATTACTATTT
*
38098334 TTATTATTAGTATTT
1 TTATTATTACTATTT
38098349 TTATT
1 TTATT
38098354 TTGTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTATTACTATTT
Found at i:38100015 original size:17 final size:17
Alignment explanation
Indices: 38099990--38100043 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
38099980 AAGAATTCGT
*
38099990 CAAATCATAGATCTCGC
1 CAAAACATAGATCTCGC
* *
38100007 CAAAACATAAATCTCAC
1 CAAAACATAGATCTCGC
*
38100024 CAAAACATAGATTTCGC
1 CAAAACATAGATCTCGC
38100041 CAA
1 CAA
38100044 TCAGCACATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.20
Consensus pattern (17 bp):
CAAAACATAGATCTCGC
Found at i:38101902 original size:44 final size:44
Alignment explanation
Indices: 38101839--38101923 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
38101829 GGTTTTTTTC
* *
38101839 TCCCACTTAAACTTTGATTAATGTAGATTATTTTAATATTAGTT
1 TCCCACTTAAACTCTGATTAATGTAGATTAGTTTAATATTAGTT
* *
38101883 TCCCACTTAAACTCTGATTAGTGTAGGTTAGTTTAATATTA
1 TCCCACTTAAACTCTGATTAATGTAGATTAGTTTAATATTA
38101924 TTTGACCTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.45
Consensus pattern (44 bp):
TCCCACTTAAACTCTGATTAATGTAGATTAGTTTAATATTAGTT
Found at i:38104671 original size:23 final size:22
Alignment explanation
Indices: 38104616--38104671 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
38104606 CTATTACGTA
*
38104616 GATATAACTGC-TTGGAGACAC
1 GATATAACTGCAGTGGAGACAC
***
38104637 GATATGTTTGCAAGTGGAGACAC
1 GATATAACTGC-AGTGGAGACAC
38104660 GATATAACTGCA
1 GATATAACTGCA
38104672 TAATTTGGCT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
21 8 0.31
22 1 0.04
23 17 0.65
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (22 bp):
GATATAACTGCAGTGGAGACAC
Found at i:38108054 original size:13 final size:14
Alignment explanation
Indices: 38108024--38108056 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
38108014 GAGCTCTATT
*
38108024 TTTTTATTTTTTAT
1 TTTTTATTTTTTAC
38108038 TTTTTA-TTTTTAC
1 TTTTTATTTTTTAC
38108051 TTTTTA
1 TTTTTA
38108057 GCTCTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTTTTAC
Found at i:38108056 original size:7 final size:7
Alignment explanation
Indices: 38108023--38108048 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38108013 AGAGCTCTAT
38108023 TTTTTTA
1 TTTTTTA
38108030 TTTTTTA
1 TTTTTTA
38108037 TTTTTTA
1 TTTTTTA
38108044 TTTTT
1 TTTTT
38108049 ACTTTTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:38110074 original size:17 final size:17
Alignment explanation
Indices: 38110052--38110085 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38110042 GACATCTTTA
38110052 ATTTTTCATGCTAAAAT
1 ATTTTTCATGCTAAAAT
*
38110069 ATTTTTCATGTTAAAAT
1 ATTTTTCATGCTAAAAT
38110086 TAGCGACCTA
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:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTTCATGCTAAAAT
Found at i:38110497 original size:17 final size:17
Alignment explanation
Indices: 38110471--38110760 Score: 170
Period size: 17 Copynumber: 16.4 Consensus size: 17
38110461 TTTTTAATGG
38110471 AATTTTTGAAACACGAA
1 AATTTTTGAAACACGAA
* *
38110488 AATCTTTGAAACACGGA
1 AATTTTTGAAACACGAA
** * *
38110505 TTTTTTTTAAACACGAC
1 AATTTTTGAAACACGAA
*
38110522 AATTTTTTAAACACGAGA
1 AATTTTTGAAACACGA-A
* * *
38110540 ATTTTTTCAAAACACAAA
1 AATTTTT-GAAACACGAA
*
38110558 AAGTTTTTAAAACACGAA
1 AA-TTTTTGAAACACGAA
* * *
38110576 AATTTGTGAAACACTAG
1 AATTTTTGAAACACGAA
* ** *
38110593 AGTCGTTGAAAACACGGA
1 AATTTTTG-AAACACGAA
* *
38110611 AATTTGTGAAAACACAAA
1 AATTTTTG-AAACACGAA
* *
38110629 AATTTTTGAAACATGGA
1 AATTTTTGAAACACGAA
*
38110646 AATTTTTAGAAAACACAAA
1 AATTTTT-G-AAACACGAA
* * *
38110665 AATTTTTGGATCACCG-G
1 AATTTTTGAAACA-CGAA
*
38110682 AATTTTTGAAAACACGAG
1 AATTTTTG-AAACACGAA
*
38110700 GATTTTTGAAACACGAA
1 AATTTTTGAAACACGAA
** *
38110717 TTTTTTTTTGAAAATACGAA
1 --AATTTTTG-AAACACGAA
38110737 AATTTTTGAAAACAC-AA
1 AATTTTTG-AAACACGAA
38110754 AATTTTT
1 AATTTTT
38110761 TTTGAAAACA
Statistics
Matches: 207, Mismatches: 54, Indels: 24
0.73 0.19 0.08
Matches are distributed among these distances:
17 98 0.47
18 70 0.34
19 31 0.15
20 8 0.04
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (17 bp):
AATTTTTGAAACACGAA
Found at i:38110641 original size:35 final size:35
Alignment explanation
Indices: 38110471--38110760 Score: 196
Period size: 35 Copynumber: 8.2 Consensus size: 35
38110461 TTTTTAATGG
* *
38110471 AATTTTTG-AAACACGAAAATCTTTGAAACACGG-
1 AATTTTTGAAAACACAAAAATTTTTGAAACACGGA
* ** * * *
38110504 ATTTTTTTTAAACACGACAATTTTTTAAACACGAGA
1 AATTTTTGAAAACACAAAAATTTTTGAAACACG-GA
* * * *
38110540 ATTTTTTCAAAACACAAAAAGTTTTTAAAACACGAA
1 AATTTTTGAAAACACAAAAA-TTTTTGAAACACGGA
* * * * **
38110576 AATTTGTG-AAACACTAGAGTCGTTGAAAACACGGA
1 AATTTTTGAAAACACAAAAATTTTTG-AAACACGGA
* *
38110611 AATTTGTGAAAACACAAAAATTTTTGAAACATGGA
1 AATTTTTGAAAACACAAAAATTTTTGAAACACGGA
* *
38110646 AATTTTTAGAAAACACAAAAATTTTTGGATCACCGG-
1 AATTTTT-GAAAACACAAAAATTTTTGAAACA-CGGA
* **
38110682 AATTTTTGAAAACACGAGGATTTTTGAAACAC-GA
1 AATTTTTGAAAACACAAAAATTTTTGAAACACGGA
* * * *
38110716 ATTTTTTTTTGAAAATACGAAAATTTTTGAAAACAC-AA
1 A---ATTTTTGAAAACACAAAAATTTTTG-AAACACGGA
38110754 AATTTTT
1 AATTTTT
38110761 TTTGAAAACA
Statistics
Matches: 202, Mismatches: 42, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
33 7 0.03
34 26 0.13
35 63 0.31
36 63 0.31
37 35 0.17
38 8 0.04
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (35 bp):
AATTTTTGAAAACACAAAAATTTTTGAAACACGGA
Found at i:38110735 original size:20 final size:19
Alignment explanation
Indices: 38110684--38110770 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 19
38110674 ATCACCGGAA
***
38110684 TTTTTGAAAACACG-AGGA
1 TTTTTGAAAACACGAATTT
38110702 TTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACGAA-TTT
* **
38110721 TTTTTGAAAATACGAA-AA
1 TTTTTGAAAACACGAATTT
*
38110739 TTTTTGAAAACACAAAATTT
1 TTTTTGAAAACAC-GAATTT
38110759 TTTTTGAAAACA
1 TTTTTGAAAACA
38110771 TGAGAATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
17 7 0.13
18 19 0.35
19 8 0.15
20 20 0.37
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTTTGAAAACACGAATTT
Found at i:38110742 original size:37 final size:37
Alignment explanation
Indices: 38110473--38110799 Score: 168
Period size: 36 Copynumber: 9.1 Consensus size: 37
38110463 TTTAATGGAA
* * *
38110473 TTTTTG-AAACACGAAAATCTTTGAAACACG-GATTT
1 TTTTTGAAAACACGAGAATTTTTGAAACACGAAATTT
* *
38110508 TTTTT--AAACACGACAATTTTTTAAACACGAGAA--T
1 TTTTTGAAAACACGAGAATTTTTGAAACACGA-AATTT
* * * * *
38110542 TTTTTCAAAACACAAAAAGTTTTTAAAACACGAAA--A
1 TTTTTGAAAACACGAGAA-TTTTTGAAACACGAAATTT
* * * **
38110578 TTTGTG-AAACACTAGAGTCGTTGAAAACACGGAAA---
1 TTTTTGAAAACACGAGAATTTTTG-AAACAC-GAAATTT
* * * *
38110613 TTTGTGAAAACACAAAAATTTTTGAAACATGGAAA--T
1 TTTTTGAAAACACGAGAATTTTTGAAACA-CGAAATTT
* * * * * *
38110649 TTTTAGAAAACACAAAAATTTTTGGATCACCGGAA---
1 TTTTTGAAAACACGAGAATTTTTGAAACA-CGAAATTT
* *
38110684 TTTTTGAAAACACGAGGATTTTTGAAACACGAATTTT
1 TTTTTGAAAACACGAGAATTTTTGAAACACGAAATTT
* * *
38110721 TTTTTGAAAATACGAAAATTTTTGAAAACACAAAATTT
1 TTTTTGAAAACACGAGAATTTTTG-AAACACGAAATTT
* * *
38110759 TTTTTGAAAACATGAGAA-TTTTGAAAGACGAAATCT
1 TTTTTGAAAACACGAGAATTTTTGAAACACGAAATTT
38110795 TTTTT
1 TTTTT
38110800 ATTTTTATTT
Statistics
Matches: 230, Mismatches: 48, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
34 33 0.14
35 57 0.25
36 75 0.33
37 39 0.17
38 26 0.11
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (37 bp):
TTTTTGAAAACACGAGAATTTTTGAAACACGAAATTT
Found at i:38110779 original size:38 final size:38
Alignment explanation
Indices: 38110684--38110784 Score: 134
Period size: 37 Copynumber: 2.7 Consensus size: 38
38110674 ATCACCGGAA
* * *
38110684 TTTTTGAAAACACGAGGATTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACGAGAATTTTTGAAAACACAAAATTT
* *
38110721 TTTTTGAAAATACGAAAATTTTTGAAAACACAAAATTT
1 TTTTTGAAAACACGAGAATTTTTGAAAACACAAAATTT
*
38110759 TTTTTGAAAACATGAGAA-TTTTGAAA
1 TTTTTGAAAACACGAGAATTTTTGAAA
38110785 GACGAAATCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 29 0.53
38 26 0.47
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (38 bp):
TTTTTGAAAACACGAGAATTTTTGAAAACACAAAATTT
Found at i:38110780 original size:20 final size:20
Alignment explanation
Indices: 38110702--38110770 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
38110692 AACACGAGGA
* *
38110702 TTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACAAAATTT
*
38110721 TTTTTGAAAATACGAAAA---
1 TTTTTGAAAACAC-AAAATTT
38110739 TTTTTGAAAACACAAAATTT
1 TTTTTGAAAACACAAAATTT
38110759 TTTTTGAAAACA
1 TTTTTGAAAACA
38110771 TGAGAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.10
18 12 0.29
19 6 0.15
20 17 0.41
21 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTTGAAAACACAAAATTT
Found at i:38110798 original size:38 final size:36
Alignment explanation
Indices: 38110684--38110799 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 36
38110674 ATCACCGGAA
*
38110684 TTTTTGAAAACACGAGGATTTTTGAAACACG-AATTTT
1 TTTTTGAAAACACGA-GAATTTTGAAA-ACGAAATTTT
* * * *
38110721 TTTTTGAAAATACGAAAATTTTTGAAAACACAAAATTT
1 TTTTTGAAAACACGAGAA-TTTTGAAAAC-GAAATTTT
* *
38110759 TTTTTGAAAACATGAGAATTTTGAAAGACGAAATCTT
1 TTTTTGAAAACACGAGAATTTTGAAA-ACGAAATTTT
38110796 TTTT
1 TTTT
38110800 ATTTTTATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
36 3 0.05
37 39 0.61
38 22 0.34
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTTTGAAAACACGAGAATTTTGAAAACGAAATTTT
Found at i:38111409 original size:7 final size:7
Alignment explanation
Indices: 38111394--38111457 Score: 76
Period size: 7 Copynumber: 8.9 Consensus size: 7
38111384 AAATTAAACA
38111394 TTTTCTT
1 TTTTCTT
*
38111401 TTCTCTT
1 TTTTCTT
*
38111408 TTCTCTT
1 TTTTCTT
38111415 TTTTCTT
1 TTTTCTT
38111422 TTTTCCTT
1 TTTT-CTT
38111430 TTTTCTT
1 TTTTCTT
38111437 TCTTT-TT
1 T-TTTCTT
38111444 TTTCTCTT
1 TTT-TCTT
38111452 TTTTCT
1 TTTTCT
38111458 CCTCTCTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
6 2 0.04
7 34 0.67
8 15 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:38111416 original size:14 final size:14
Alignment explanation
Indices: 38111394--38111469 Score: 80
Period size: 14 Copynumber: 5.3 Consensus size: 14
38111384 AAATTAAACA
38111394 TTTTCTTTTCTCTT
1 TTTTCTTTTCTCTT
* *
38111408 TTCTCTTTTTTCTT
1 TTTTCTTTTCTCTT
*
38111422 TTTTCCTTTTTTCTT
1 TTTT-CTTTTCTCTT
*
38111437 TCTTTTTTTTCTCTT
1 T-TTTCTTTTCTCTT
**
38111452 TTTTCTCCTCTCTT
1 TTTTCTTTTCTCTT
38111466 TTTT
1 TTTT
38111470 TCGGCCTGCC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
14 29 0.56
15 20 0.38
16 3 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTCTCTT
Found at i:38111420 original size:9 final size:9
Alignment explanation
Indices: 38111406--38111458 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
38111396 TTCTTTTCTC
38111406 TTTTCTCTT
1 TTTTCTCTT
38111415 TTTTCT-TT
1 TTTTCTCTT
* *
38111423 TTTCCTTTTT
1 TTTTC-TCTT
*
38111433 TCTTTCTTTT
1 T-TTTCTCTT
38111443 TTTTCTCTT
1 TTTTCTCTT
38111452 TTTTCTC
1 TTTTCTC
38111459 CTCTCTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 6 0.16
9 21 0.55
10 8 0.21
11 3 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:38111430 original size:22 final size:21
Alignment explanation
Indices: 38111395--38111457 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
38111385 AATTAAACAT
*
38111395 TTTCTTTTCTCTTTTCTCTTT
1 TTTCTTTTCTCTTTTTTCTTT
*
38111416 TTTCTTTTTTCCTTTTTTCTTT
1 TTTCTTTTCT-CTTTTTTCTTT
*
38111438 CTTTTTTTTCTCTTTTTTCT
1 -TTTCTTTTCTCTTTTTTCT
38111458 CCTCTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 9 0.25
22 19 0.53
23 8 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTCTTTTCTCTTTTTTCTTT
Found at i:38111467 original size:22 final size:21
Alignment explanation
Indices: 38111421--38111468 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
38111411 TCTTTTTTCT
* *
38111421 TTTTTCCTTTTTTCTTTCTTT
1 TTTTTCCTTTTTTCTCTCTTC
38111442 TTTTTCTCTTTTTTCTC-CTCTC
1 TTTTTC-CTTTTTTCTCTCT-TC
38111464 TTTTT
1 TTTTT
38111469 TTCGGCCTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCCTTTTTTCTCTCTTC
Found at i:38111673 original size:17 final size:17
Alignment explanation
Indices: 38111651--38111691 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
38111641 ACTGAATTAA
38111651 TTTTTTTATTTTTTATT
1 TTTTTTTATTTTTTATT
*
38111668 TTTTTTTATTTTTTCTT
1 TTTTTTTATTTTTTATT
*
38111685 TCTTTTT
1 TTTTTTT
38111692 CTTCTTCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTATTTTTTATT
Found at i:38111686 original size:4 final size:4
Alignment explanation
Indices: 38111679--38111759 Score: 78
Period size: 4 Copynumber: 20.0 Consensus size: 4
38111669 TTTTTTATTT
* *
38111679 TTTC TTTC TTTT TCTTC -TTC CTTC -TTC TTTC -TTC TTTC TTTC TTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
38111725 TTTC TTCTC TTTTC TTTC TCTTT TTTC TTTC TTTC
1 TTTC TT-TC -TTTC TTTC T-TTC TTTC TTTC TTTC
38111760 CCGATCAACC
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
3 9 0.14
4 46 0.70
5 9 0.14
6 2 0.03
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:38111713 original size:26 final size:27
Alignment explanation
Indices: 38111679--38111757 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
38111669 TTTTTTATTT
*
38111679 TTTCTTTCTTTTTCTTC-TTCCTTCTTC
1 TTTC-TTCTTTCTCTTCTTTCCTTCTTC
*
38111706 TTTCTTCTTTCT-TTCTTTCTTTCTTC
1 TTTCTTCTTTCTCTTCTTTCCTTCTTC
* *
38111732 TCTT-TTCTTTCTCTTTTTTCTTTCTT
1 T-TTCTTCTTTCTCTTCTTTCCTTCTT
38111758 TCCCGATCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 3 0.07
26 25 0.54
27 18 0.39
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTCTTCTTTCTCTTCTTTCCTTCTTC
Found at i:38111753 original size:7 final size:7
Alignment explanation
Indices: 38111652--38111759 Score: 62
Period size: 7 Copynumber: 15.0 Consensus size: 7
38111642 CTGAATTAAT
*
38111652 TTTTTTA
1 TTTTTTC
*
38111659 TTTTTTA
1 TTTTTTC
38111666 TTTTTT-
1 TTTTTTC
38111672 TTTATTT-
1 TTT-TTTC
38111679 TTTCTTTC
1 TTT-TTTC
38111687 -TTTTTC
1 TTTTTTC
38111693 TTCTTCCTTC
1 TT-TT--TTC
*
38111703 TTCTTTC
1 TTTTTTC
*
38111710 TTCTTTC
1 TTTTTTC
38111717 TTTCTTTC
1 TTT-TTTC
*
38111725 TTTCTTC
1 TTTTTTC
*
38111732 TCTTTTC
1 TTTTTTC
*
38111739 -TTTCTC
1 TTTTTTC
38111745 TTTTTTC
1 TTTTTTC
38111752 TTTCTTTC
1 TTT-TTTC
38111760 CCGATCAACC
Statistics
Matches: 83, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
6 11 0.13
7 53 0.64
8 13 0.16
9 1 0.01
10 5 0.06
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:38111927 original size:22 final size:21
Alignment explanation
Indices: 38111873--38111928 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
38111863 TCTTCTTTGC
38111873 TCTTTTCTTCTT-CTTTTTCTT
1 TCTTTT-TTCTTGCTTTTTCTT
* *
38111894 TCTTTTTGCTTGCTTGTTTTTT
1 TCTTTTTTCTTGCTT-TTTCTT
38111916 TCTTTTTTCTTGC
1 TCTTTTTTCTTGC
38111929 CTCTTGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 17 0.57
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (21 bp):
TCTTTTTTCTTGCTTTTTCTT
Found at i:38112298 original size:29 final size:29
Alignment explanation
Indices: 38112256--38112360 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
38112246 CAAAACCTCT
* *
38112256 AGGGTCAAAGTGTAATTTTGGAAAATTTA
1 AGGGTCAAAATGTAATTTTAGAAAATTTA
* *
38112285 AGGGTCAAAATGTAATTTCAAGAAAGTTT-
1 AGGGTCAAAATGTAATTT-TAGAAAATTTA
* *
38112314 AGGGTCAAAATATAATTTTAAAAAAATTTA
1 AGGGTCAAAATGTAATTTT-AGAAAATTTA
* *
38112344 GGGGTCAAAATGCAATT
1 AGGGTCAAAATGTAATT
38112361 GTGTAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
29 41 0.66
30 21 0.34
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (29 bp):
AGGGTCAAAATGTAATTTTAGAAAATTTA
Found at i:38112698 original size:24 final size:24
Alignment explanation
Indices: 38112666--38112719 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
38112656 TAAAAAATAC
* *
38112666 CTCAGCGTGTGATCCGAGGCTCAA
1 CTCACCGTGTGACCCGAGGCTCAA
38112690 CTCACCGTGTGACCCGAGGCTCAA
1 CTCACCGTGTGACCCGAGGCTCAA
38112714 CTCACC
1 CTCACC
38112720 TCTCGCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.19
Consensus pattern (24 bp):
CTCACCGTGTGACCCGAGGCTCAA
Found at i:38112872 original size:77 final size:77
Alignment explanation
Indices: 38112690--38112995 Score: 386
Period size: 77 Copynumber: 4.0 Consensus size: 77
38112680 CGAGGCTCAA
* *
38112690 CTCACCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAA-AAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAACAAA
38112754 AATTTAAAAGAAATAC
64 AA-TTAAAA-AAATAC
* * * * * *
38112770 CTTAGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAA
38112834 TTAAAAAAATAC
66 TTAAAAAAATAC
* * * ** * * *
38112846 ATCGGCGTGCGACCCGAGACTCAACTCACCTCAGGCAATATGAGCTGATTTTTGAAAAATAGAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAA
*
38112911 TT--TAAAATAC
66 TTAAAAAAATAC
38112921 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGCAAAAACAAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAAAA
38112986 ATTAAAAAAA
65 ATTAAAAAAA
38112996 ATAATTTTTG
Statistics
Matches: 193, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
75 55 0.28
76 23 0.12
77 62 0.32
78 11 0.06
79 34 0.18
80 8 0.04
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (77 bp):
CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAA
TTAAAAAAATAC
Found at i:38112951 original size:75 final size:74
Alignment explanation
Indices: 38112690--38112980 Score: 341
Period size: 75 Copynumber: 3.8 Consensus size: 74
38112680 CGAGGCTCAA
* * *
38112690 CTCACCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAAAAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAAAGAA
38112755 ATTTAAAAGAAATAC
64 ATTT---A-AAATAC
* * * * *
38112770 CTTAGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-AGAAA
*
38112834 TTAAAAAAATAC
65 TT--TAAAATAC
* * * ** *
38112846 ATCGGCGTGCGACCCGAGACTCAACTCACCTCAGGCAATATGAGCTGATTTTTGAAAAATAGAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-AGAAA
38112911 TTTAAAATAC
65 TTTAAAATAC
*
38112921 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGCAAAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
38112981 CAAAAATTAA
Statistics
Matches: 180, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
74 1 0.01
75 59 0.33
76 12 0.07
77 57 0.32
78 9 0.05
79 34 0.19
80 8 0.04
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (74 bp):
CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAAAT
TTAAAATAC
Found at i:38113798 original size:1 final size:1
Alignment explanation
Indices: 38113794--38113851 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
38113784 TTTTTCCTTC
* * * * * * *
38113794 TTTTTTCTTTTTCTTTTTTCTTTTTTTTTTGTTTTTGTTTTTTTTGTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38113852 AGGCATAATA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:38113807 original size:13 final size:13
Alignment explanation
Indices: 38113791--38113850 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
38113781 TAATTTTTCC
38113791 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
38113804 TTCTTTTTTC-TT
1 TTCTTTTTTCTTT
*
38113816 TT-TTTTTTGTTT
1 TTCTTTTTTCTTT
* *
38113828 TTGTTTTTTTTGTT
1 TTCTTTTTTCT-TT
*
38113842 TTGTTTTTT
1 TTCTTTTTT
38113851 TAGGCATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
11 6 0.14
12 8 0.19
13 17 0.40
14 11 0.26
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:38113811 original size:24 final size:24
Alignment explanation
Indices: 38113784--38113836 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
38113774 TTCATATTAA
38113784 TTTTTCCTTCTTTTTTCTTTTTCT
1 TTTTTCCTTCTTTTTTCTTTTTCT
* * * *
38113808 TTTTTCTTTTTTTTTTGTTTTTGT
1 TTTTTCCTTCTTTTTTCTTTTTCT
38113832 TTTTT
1 TTTTT
38113837 TTGTTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (24 bp):
TTTTTCCTTCTTTTTTCTTTTTCT
Found at i:38113834 original size:14 final size:14
Alignment explanation
Indices: 38113816--38113851 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
38113806 CTTTTTTCTT
38113816 TTTTTTTTGTTTTTG
1 TTTTTTTTG-TTTTG
38113831 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
38113845 TTTTTTT
1 TTTTTTT
38113852 AGGCATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:38121226 original size:17 final size:17
Alignment explanation
Indices: 38121206--38121327 Score: 86
Period size: 17 Copynumber: 6.9 Consensus size: 17
38121196 TTTTTTAAAT
38121206 GAAATTTTTGAAACACG
1 GAAATTTTTGAAACACG
*
38121223 GAAATTTTAGAAACAC-
1 GAAATTTTTGAAACACG
* *
38121239 GAATTGTTTTTTAAACAC-
1 GAA--ATTTTTGAAACACG
38121257 GACAATTTTTGAAACACG
1 GA-AATTTTTGAAACACG
* * *
38121275 AGAATTTTTTCAAAACACA
1 -GAAATTTTT-GAAACACG
* *
38121294 AAAATTTTTTAAAACACG
1 GAAA-TTTTTGAAACACG
* *
38121312 AAAATTTCTGAAACAC
1 GAAATTTTTGAAACAC
38121328 TAGAGCTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.04
17 36 0.43
18 31 0.37
19 14 0.17
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (17 bp):
GAAATTTTTGAAACACG
Found at i:38121284 original size:35 final size:33
Alignment explanation
Indices: 38121206--38121314 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 33
38121196 TTTTTTAAAT
* *
38121206 GAAA-TTTTTGAAACACGGAAATTTTAGAAACAC
1 GAAATTTTTTAAAACAC-GAAATTTTTGAAACAC
* *
38121239 GAATTGTTTTTTAAACACGACAATTTTTGAAACAC
1 GAAAT-TTTTTAAAACACGA-AATTTTTGAAACAC
* *
38121274 GAGAATTTTTTCAAAACACAAAAATTTTTTAAAACAC
1 GA-AATTTTTT-AAAACAC-GAAA-TTTTTGAAACAC
38121311 GAAA
1 GAAA
38121315 ATTTCTGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
33 3 0.05
34 2 0.03
35 31 0.50
36 12 0.19
37 14 0.23
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (33 bp):
GAAATTTTTTAAAACACGAAATTTTTGAAACAC
Found at i:38121290 original size:19 final size:18
Alignment explanation
Indices: 38121210--38121318 Score: 91
Period size: 18 Copynumber: 6.1 Consensus size: 18
38121200 TTAAATGAAA
* *
38121210 TTTTTGAAACACGGAAA-
1 TTTTTAAAACACGAAAAT
*
38121227 -TTTTAGAAACACG-AATT
1 TTTTTA-AAACACGAAAAT
* *
38121244 GTTTTTTAAACACGACAA-
1 -TTTTTAAAACACGAAAAT
* *
38121262 TTTTTGAAACACGAGAAT
1 TTTTTAAAACACGAAAAT
*
38121280 TTTTTCAAAACACAAAAAT
1 TTTTT-AAAACACGAAAAT
38121299 TTTTTAAAACACGAAAAT
1 TTTTTAAAACACGAAAAT
38121317 TT
1 TT
38121319 CTGAAACACT
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
16 6 0.08
17 22 0.30
18 26 0.35
19 20 0.27
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (18 bp):
TTTTTAAAACACGAAAAT
Found at i:38121400 original size:18 final size:18
Alignment explanation
Indices: 38121379--38121494 Score: 71
Period size: 18 Copynumber: 6.4 Consensus size: 18
38121369 GGATCACCGG
38121379 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
38121397 AATTTTCT--AAACACCAG
1 AATTTT-TGAAAACACGAA
* *
38121414 AATTTTTGAAAACATGAG
1 AATTTTTGAAAACACGAA
*
38121432 GATTTTTG-AAACAC-AA
1 AATTTTTGAAAACACGAA
* *
38121448 AATTTTTTTTTTGAAAATATGAA
1 AA-----TTTTTGAAAACACGAA
*
38121471 AATTTTTGAAAACAC-AG
1 AATTTTTGAAAACACGAA
38121488 AATTTTT
1 AATTTTT
38121495 TTTTTGAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
16 3 0.04
17 26 0.35
18 31 0.41
19 1 0.01
21 6 0.08
22 4 0.05
23 4 0.05
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:38121437 original size:35 final size:35
Alignment explanation
Indices: 38121346--38121494 Score: 115
Period size: 35 Copynumber: 4.1 Consensus size: 35
38121336 TTTTTTAAAT
* * * * *
38121346 TTTTTCAAAACACAAAAATTTTTGGATCACCGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCAGAA
38121381 TTTTTGAAAACACGAAAATTTTCT-AAACACCAGAA
1 TTTTTGAAAACACGAAAATTTT-TGAAACACCAGAA
* ** *
38121416 TTTTTGAAAACATGAGGATTTTTGAAACA-CAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCAGAA
* *
38121450 TTTTTTTTTTGAAAATATGAAAATTTTTGAAA-ACACAGAA
1 -----TTTTTGAAAACACGAAAATTTTTGAAACAC-CAGAA
38121490 TTTTT
1 TTTTT
38121495 TTTTTGAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
34 5 0.05
35 57 0.62
36 1 0.01
38 1 0.01
39 24 0.26
40 4 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCAGAA
Found at i:38121476 original size:39 final size:39
Alignment explanation
Indices: 38121416--38121535 Score: 161
Period size: 40 Copynumber: 3.1 Consensus size: 39
38121406 AACACCAGAA
*
38121416 TTTTTGAAAACATGAGGATTTTTGAAACACAAAATTTTT
1 TTTTTGAAAACATGAGAATTTTTGAAACACAAAATTTTT
* * *
38121455 TTTTTGAAAATATGAAAATTTTTGAAAACACAGAATTTTT
1 TTTTTGAAAACATGAGAATTTTTG-AAACACAAAATTTTT
* * *
38121495 TTTTTGAAAACATGAGAA-TTTTGAAAGACGAAATCTTT
1 TTTTTGAAAACATGAGAATTTTTGAAACACAAAATTTTT
38121533 TTT
1 TTT
38121536 ATTTTTATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 14 0.20
39 26 0.37
40 30 0.43
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (39 bp):
TTTTTGAAAACATGAGAATTTTTGAAACACAAAATTTTT
Found at i:38121499 original size:23 final size:23
Alignment explanation
Indices: 38121473--38121516 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
38121463 AATATGAAAA
38121473 TTTTTGAAAACA-CAGAATTTTT
1 TTTTTGAAAACATCAGAATTTTT
*
38121495 TTTTTGAAAACATGAGAATTTT
1 TTTTTGAAAACATCAGAATTTT
38121517 GAAAGACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (23 bp):
TTTTTGAAAACATCAGAATTTTT
Found at i:38121534 original size:40 final size:37
Alignment explanation
Indices: 38121416--38121535 Score: 141
Period size: 39 Copynumber: 3.1 Consensus size: 37
38121406 AACACCAGAA
*
38121416 TTTTTGAAAACATGAGGATTTTTGAAACACAAAATTTTT
1 TTTTTGAAAACATGA-GAATTTTGAAA-ACAAAATTTTT
* *
38121455 TTTTTGAAAATATGAAAATTTTTGAAAACACAGAATTTTT
1 TTTTTGAAAACATGAGAA-TTTTGAAAACA-A-AATTTTT
* *
38121495 TTTTTGAAAACATGAGAATTTTGAAAGACGAAATCTTT
1 TTTTTGAAAACATGAGAATTTTGAAA-ACAAAATTTTT
38121533 TTT
1 TTT
38121536 ATTTTTATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
38 13 0.19
39 32 0.46
40 25 0.36
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTTTGAAAACATGAGAATTTTGAAAACAAAATTTTT
Found at i:38121964 original size:17 final size:17
Alignment explanation
Indices: 38121935--38121978 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
38121925 AAAATTATTT
*
38121935 AAAA-TAAAATAAAATA
1 AAAATTAAATTAAAATA
*
38121951 AAAATTAAATTAAATTA
1 AAAATTAAATTAAAATA
38121968 AAAATATAAAT
1 AAAAT-TAAAT
38121979 ACAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATTAAATTAAAATA
Found at i:38122145 original size:7 final size:7
Alignment explanation
Indices: 38122129--38122179 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
38122119 TTAAACCTTT
38122129 TTTTTCTC
1 TTTTT-TC
38122137 TTTTTTC
1 TTTTTTC
38122144 TTTTTTCC
1 TTTTTT-C
38122152 TTTTTTC
1 TTTTTTC
38122159 TTTTTT-
1 TTTTTTC
* *
38122165 TTCTCTC
1 TTTTTTC
38122172 TTTTTTC
1 TTTTTTC
38122179 T
1 T
38122180 CCTCTCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 4 0.11
7 21 0.57
8 12 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:38122154 original size:15 final size:16
Alignment explanation
Indices: 38122128--38122164 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
38122118 ATTAAACCTT
38122128 TTTTTTCTCTTTTTTC
1 TTTTTTCTCTTTTTTC
38122144 TTTTTTC-CTTTTTTC
1 TTTTTTCTCTTTTTTC
38122159 TTTTTT
1 TTTTTT
38122165 TTCTCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:38122162 original size:20 final size:20
Alignment explanation
Indices: 38122126--38122179 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
38122116 AAATTAAACC
38122126 TTTTTTT-TCTCTTTTTTC-
1 TTTTTTTCTCTCTTTTTTCT
38122144 --TTTTT-TC-CTTTTTTCT
1 TTTTTTTCTCTCTTTTTTCT
38122160 TTTTTTTCTCTCTTTTTTCT
1 TTTTTTTCTCTCTTTTTTCT
38122180 CCTCTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.26
16 7 0.23
18 5 0.16
19 2 0.06
20 9 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTCTCTCTTTTTTCT
Found at i:38122176 original size:14 final size:14
Alignment explanation
Indices: 38122157--38122193 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
38122147 TTTCCTTTTT
38122157 TCTTTTTTTT-CTC
1 TCTTTTTTTTCCTC
*
38122170 TCTTTTTTCTCCTC
1 TCTTTTTTTTCCTC
38122184 TCTTTTTTTT
1 TCTTTTTTTT
38122194 AGCCTGCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TCTTTTTTTTCCTC
Found at i:38122180 original size:9 final size:9
Alignment explanation
Indices: 38122128--38122176 Score: 59
Period size: 8 Copynumber: 5.7 Consensus size: 9
38122118 ATTAAACCTT
38122128 TTTTTTCTC
1 TTTTTTCTC
38122137 -TTTTT-TC
1 TTTTTTCTC
38122144 TTTTTTC-C
1 TTTTTTCTC
*
38122152 TTTTTTCTT
1 TTTTTTCTC
38122161 TTTTTTCTC
1 TTTTTTCTC
38122170 TCTTTTT
1 T-TTTTT
38122177 TCTCCTCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.06
8 18 0.53
9 9 0.26
10 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:38122191 original size:35 final size:34
Alignment explanation
Indices: 38122126--38122192 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
38122116 AAATTAAACC
** *
38122126 TTTTTTTTCTCTTTTTTCTTTTTTCCTTTTTTCT
1 TTTTTTTTCTCTTTTTTCTCCTCTCCTTTTTTCT
*
38122160 TTTTTTTCTCTCTTTTTTCTCCTCTCTTTTTTT
1 TTTTTTT-TCTCTTTTTTCTCCTCTCCTTTTTT
38122193 TAGCCTGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 7 0.25
35 21 0.75
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTTTTTCTCTTTTTTCTCCTCTCCTTTTTTCT
Found at i:38122476 original size:29 final size:29
Alignment explanation
Indices: 38122433--38122537 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
38122423 AAAACTTCTA
* * **
38122433 GGGTCAAAGTGTAATTTTGGAAAATTTAG
1 GGGTCAAAATATAATTTAAGAAAATTTAG
*
38122462 GGGTCAAAATATAATTTCAAGAAAGTTTA-
1 GGGTCAAAATATAATTT-AAGAAAATTTAG
*
38122491 GAGTCAAAATATAAATTTAAGAAAATTTAG
1 GGGTCAAAATAT-AATTTAAGAAAATTTAG
*
38122521 GGGTCAAAATACAATTT
1 GGGTCAAAATATAATTT
38122538 TGTAAAAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 41 0.64
30 23 0.36
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (29 bp):
GGGTCAAAATATAATTTAAGAAAATTTAG
Found at i:38132285 original size:411 final size:411
Alignment explanation
Indices: 38131523--38132319 Score: 1540
Period size: 411 Copynumber: 1.9 Consensus size: 411
38131513 TTGGAATCGG
38131523 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
1 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
38131588 GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
66 GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
*
38131653 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAGC
131 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
38131718 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
196 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
*
38131783 ATGGTGTGTAGGGATGGGTGGGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
261 ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
*
38131848 GTGTAGAGGATGGGGGTAGGACTCGCTATCTCTGTTCTGTTTTTCTGATTCTGATAATTGTTCTC
326 GTGTAGAGGATGGGGGTAGGACTCGCTATCTCTGTTCTATTTTTCTGATTCTGATAATTGTTCTC
38131913 GGAGATGGGTGCATATTACCT
391 GGAGATGGGTGCATATTACCT
38131934 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
1 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
*
38131999 GTGTATTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
66 GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
38132064 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
131 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
38132129 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
196 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
*
38132194 ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTTGGAGATGGT
261 ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
*
38132259 GTGTAGAGGATGGGGGTAGGACTCGCTATCTCTGTTCTATTTTTTTGATTCTGATAATTGT
326 GTGTAGAGGATGGGGGTAGGACTCGCTATCTCTGTTCTATTTTTCTGATTCTGATAATTGT
38132320 ATCTATTATG
Statistics
Matches: 380, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
411 380 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (411 bp):
GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
GTGTAGAGGATGGGGGTAGGACTCGCTATCTCTGTTCTATTTTTCTGATTCTGATAATTGTTCTC
GGAGATGGGTGCATATTACCT
Found at i:38133894 original size:12 final size:12
Alignment explanation
Indices: 38133877--38133901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38133867 CTTTTTTAAA
38133877 GACAGTTTGAGG
1 GACAGTTTGAGG
38133889 GACAGTTTGAGG
1 GACAGTTTGAGG
38133901 G
1 G
38133902 TTTTGATTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.44, T:0.24
Consensus pattern (12 bp):
GACAGTTTGAGG
Found at i:38140042 original size:20 final size:21
Alignment explanation
Indices: 38140017--38140076 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
38140007 TTGTACGGGA
38140017 TTGCAC-TTTAGTGCCTCTGT
1 TTGCACATTTAGTGCCTCTGT
* **
38140037 TTGCACTTTTA-TGCCTCTAA
1 TTGCACATTTAGTGCCTCTGT
*
38140057 TTACACATTT-GTGCCTCTGT
1 TTGCACATTTAGTGCCTCTGT
38140077 CTGTACTTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (21 bp):
TTGCACATTTAGTGCCTCTGT
Done.