Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 128 of 161
Found at i:40263987 original size:14 final size:14
Alignment explanation
Indices: 40263968--40264011 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
40263958 TGGGAAGTCC
40263968 CTGTATTGTAAGGA
1 CTGTATTGTAAGGA
*
40263982 CTGTA-T-CAA--A
1 CTGTATTGTAAGGA
40263992 CTGTATTGTAAGGA
1 CTGTATTGTAAGGA
40264006 CTGTAT
1 CTGTAT
40264012 CAAATTAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
11 1 0.04
12 4 0.17
13 1 0.04
14 12 0.50
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (14 bp):
CTGTATTGTAAGGA
Found at i:40263995 original size:24 final size:24
Alignment explanation
Indices: 40263968--40264015 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
40263958 TGGGAAGTCC
40263968 CTGTATTGTAAGGACTGTATCAAA
1 CTGTATTGTAAGGACTGTATCAAA
40263992 CTGTATTGTAAGGACTGTATCAAA
1 CTGTATTGTAAGGACTGTATCAAA
40264016 TTAGTCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (24 bp):
CTGTATTGTAAGGACTGTATCAAA
Found at i:40267842 original size:20 final size:19
Alignment explanation
Indices: 40267815--40267856 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
40267805 CATTTTTTTA
*
40267815 TATATATTTTTACTATTAT
1 TATATATTATTACTATTAT
40267834 TATACTATTATTACTATTAT
1 TATA-TATTATTACTATTAT
40267854 TAT
1 TAT
40267857 GTTACATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATATTATTACTATTAT
Found at i:40271621 original size:44 final size:44
Alignment explanation
Indices: 40271573--40271656 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
40271563 GATCAAAGAC
*
40271573 AACAGATCTTGTCTTCCCATTCTGGTGGCGAAGTAGATTGGAAA
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGGAAA
* *
40271617 AACAGATTTTGTCTTTCCATACTGGTGGCGAAGTAGATTG
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTG
40271657 AAGATTACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGGAAA
Found at i:40275235 original size:26 final size:28
Alignment explanation
Indices: 40275201--40275252 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
40275191 TACTTTTATA
*
40275201 AAAAATATATGAAA-ATTTT-TAATTCC
1 AAAAATATATAAAATATTTTCTAATTCC
*
40275227 AAAATTATATAAAATATTTTCTAATT
1 AAAAATATATAAAATATTTTCTAATT
40275253 TTAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 5 0.23
28 5 0.23
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
AAAAATATATAAAATATTTTCTAATTCC
Found at i:40275549 original size:19 final size:17
Alignment explanation
Indices: 40275516--40275581 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 17
40275506 TTAAAATTAT
40275516 ATTTATATATGTTTTTTAA
1 ATTTATATA--TTTTTTAA
40275535 ATATTA-ATATATTTTTATA
1 AT-TTATATAT-TTTTTA-A
*
40275554 ATTTTTATATTTTTTAA
1 ATTTATATATTTTTTAA
40275571 ATTT-TATATTT
1 ATTTATATATTT
40275582 CTTATATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
16 7 0.17
17 6 0.14
18 14 0.33
19 12 0.29
20 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTATATATTTTTTAA
Found at i:40275562 original size:17 final size:17
Alignment explanation
Indices: 40275542--40275587 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
40275532 TAAATATTAA
*
40275542 TATATTTTTATAATTTT
1 TATATTTTTATAAATTT
40275559 TATATTTTT-TAAATTT
1 TATATTTTTATAAATTT
40275575 TATATTTCTTATA
1 TATATTT-TTATA
40275588 TATTCACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 13 0.50
17 11 0.42
18 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTTTATAAATTT
Found at i:40275575 original size:16 final size:16
Alignment explanation
Indices: 40275527--40275581 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
40275517 TTTATATATG
40275527 TTTTTTAAATATTAATATA
1 TTTTTTAAAT-TT--TATA
*
40275546 TTTTTATAATTTTTATA
1 TTTTT-TAAATTTTATA
40275563 TTTTTTAAATTTTATA
1 TTTTTTAAATTTTATA
40275579 TTT
1 TTT
40275582 CTTATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 13 0.39
17 9 0.27
19 7 0.21
20 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAAATTTTATA
Found at i:40275588 original size:9 final size:8
Alignment explanation
Indices: 40275542--40275588 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
40275532 TAAATATTAA
40275542 TATATTTT
1 TATATTTT
40275550 TATAATTTT
1 TAT-ATTTT
40275559 TATATTTT
1 TATATTTT
*
40275567 T-TAAATTT
1 TAT-ATTTT
40275575 TATATTTCT
1 TATATTT-T
40275584 TATAT
1 TATAT
40275589 ATTCACTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 1 0.03
8 17 0.52
9 15 0.45
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (8 bp):
TATATTTT
Found at i:40277289 original size:18 final size:17
Alignment explanation
Indices: 40277266--40277300 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
40277256 TTTCTAGACT
40277266 TTTAACTAACCCATATAA
1 TTTAACTAACCCA-ATAA
40277284 TTTAACTAACCCAATAA
1 TTTAACTAACCCAATAA
40277301 ACAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (17 bp):
TTTAACTAACCCAATAA
Found at i:40278691 original size:80 final size:80
Alignment explanation
Indices: 40278566--40278774 Score: 214
Period size: 80 Copynumber: 2.6 Consensus size: 80
40278556 TATAACAGTT
*
40278566 ATTTTACCC-TATGGAGGTATTT-TAGTAATTTTA-CCATTC-AGGGGTATTTC-GATAATTTTA
1 ATTTTACCCAT-TGG-GGTATTTCGA-TAATTTTACCCA-TCGA-GGGTATTTCAG-TAATTTTA
**
40278626 -CCATTCGGGGGTATTTCGGTA
60 CCCA-TCAAGGGTATTTCGGTA
*
40278647 ATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATC
1 ATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATC
*
40278712 AAGGGTATTTCGGTC
66 AAGGGTATTTCGGTA
* * * * *
40278727 ATTTTACACATTGAGGGTACTTCGATCATTTTACGCATAGAGGGTATT
1 ATTTTACCCATTG-GGGTATTTCGATAATTTTACCCATCGAGGGTATT
40278775 ACTGTCATTT
Statistics
Matches: 111, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
80 59 0.53
81 51 0.46
82 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (80 bp):
ATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATC
AAGGGTATTTCGGTA
Found at i:40278709 original size:27 final size:26
Alignment explanation
Indices: 40278566--40278774 Score: 167
Period size: 27 Copynumber: 7.8 Consensus size: 26
40278556 TATAACAGTT
* *
40278566 ATTTTACCCTATGGA-GGTATTTTAGTA
1 ATTTTACCC-ATCGAGGGTA-TTTCGTA
40278593 ATTTTA-CCATTC-AGGGGTATTTCGATA
1 ATTTTACCCA-TCGA-GGGTATTTCG-TA
*
40278620 ATTTTA-CCATTCGGGGGTATTTCGGTA
1 ATTTTACCCA-TCGAGGGTATTTC-GTA
*
40278647 ATTTTACCCATTG-GGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCG-TA
*
40278673 ATTTTACCCATCGAGGGTATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTC-GTA
* *
40278700 ATTTTACCCATCAAGGGTATTTCGGTC
1 ATTTTACCCATCGAGGGTATTTC-GTA
* * * *
40278727 ATTTTACACATTGAGGGTACTTCGATC
1 ATTTTACCCATCGAGGGTATTTCG-TA
* *
40278754 ATTTTACGCATAGAGGGTATT
1 ATTTTACCCATCGAGGGTATT
40278775 ACTGTCATTT
Statistics
Matches: 156, Mismatches: 15, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.02
26 31 0.20
27 117 0.75
28 5 0.03
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (26 bp):
ATTTTACCCATCGAGGGTATTTCGTA
Found at i:40278743 original size:54 final size:53
Alignment explanation
Indices: 40278581--40278774 Score: 187
Period size: 54 Copynumber: 3.6 Consensus size: 53
40278571 ACCCTATGGA
* * *
40278581 GGTATTTTAGTAATTTTA-CCATTCAGGGGTATTTCGATAATTTTAC-CATTCGGG
1 GGTATTTCAGTAATTTTACCCA-T-AAGGGTATTTCGATAATTTTACACATT-GAG
* ** * *
40278635 GGTATTTCGGTAATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAG
1 GGTATTTCAGTAATTTTACCCATAAGGGTATTTCGATAATTTTACACATTGAG
* * *
40278688 GGTATTTCAGTCATTTTACCCATCAAGGGTATTTCGGTCATTTTACACATTGAG
1 GGTATTTCAGTAATTTTACCCAT-AAGGGTATTTCGATAATTTTACACATTGAG
* * *
40278742 GGTACTTC-GATCATTTTACGCATAGAGGGTATT
1 GGTATTTCAG-TAATTTTACCCATA-AGGGTATT
40278775 ACTGTCATTT
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
53 46 0.38
54 71 0.59
55 3 0.03
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (53 bp):
GGTATTTCAGTAATTTTACCCATAAGGGTATTTCGATAATTTTACACATTGAG
Found at i:40278782 original size:81 final size:80
Alignment explanation
Indices: 40278634--40278784 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 80
40278624 TACCATTCGG
* * * *
40278634 GGGTATTTCGGTAATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGT
1 GGGTATTTCGGTAATTTTACACATTGGGGTACTTCGATAATTTTACCCATAGAGGGTATTACAGT
40278699 CATTTTACCCATCAA
66 CATTTTACCCATCAA
* * * *
40278714 GGGTATTTCGGTCATTTTACACATTGAGGGTACTTCGATCATTTTACGCATAGAGGGTATTACTG
1 GGGTATTTCGGTAATTTTACACATTG-GGGTACTTCGATAATTTTACCCATAGAGGGTATTACAG
40278779 TCATTT
65 TCATTT
40278785 AACAACATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
80 24 0.39
81 38 0.61
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (80 bp):
GGGTATTTCGGTAATTTTACACATTGGGGTACTTCGATAATTTTACCCATAGAGGGTATTACAGT
CATTTTACCCATCAA
Found at i:40283048 original size:37 final size:37
Alignment explanation
Indices: 40282996--40283079 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
40282986 CATGACCATA
* * * *
40282996 GCATAATCTAGGGAGGTCCACCAGATTTGCCTATATG
1 GCATAATCCAGGGAGGTCCACCAAATTCGCCTACATG
* **
40283033 GGATAATCCAGGGAGGTCTGCCAAATTCGCCTACATG
1 GCATAATCCAGGGAGGTCCACCAAATTCGCCTACATG
40283070 GCATAATCCA
1 GCATAATCCA
40283080 ACGGAGGCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (37 bp):
GCATAATCCAGGGAGGTCCACCAAATTCGCCTACATG
Found at i:40289574 original size:4 final size:4
Alignment explanation
Indices: 40289565--40289637 Score: 64
Period size: 4 Copynumber: 17.8 Consensus size: 4
40289555 CAACCCAATT
40289565 TTTA TTTA TTTA TTTA TTTA -TTA TTTTA TTTA -TTA CTTTA TTTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA TTTA
40289613 TATTA TTTA -TTA CTTTA TTTTA TTT
1 T-TTA TTTA TTTA -TTTA -TTTA TTT
40289638 TAATAAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
3 10 0.17
4 31 0.53
5 18 0.31
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40289582 original size:12 final size:12
Alignment explanation
Indices: 40289565--40289632 Score: 77
Period size: 12 Copynumber: 5.6 Consensus size: 12
40289555 CAACCCAATT
40289565 TTTATTTATTTA-
1 TTTATTTA-TTAC
*
40289577 TTTATTTATTAT
1 TTTATTTATTAC
40289589 TTTATTTATTAC
1 TTTATTTATTAC
*
40289601 TTTATTTTATT-T
1 TTTA-TTTATTAC
40289613 TATTATTTATTAC
1 T-TTATTTATTAC
40289626 TTTATTT
1 TTTATTT
40289633 TATTTTAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.06
12 36 0.73
13 10 0.20
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTATTAC
Found at i:40289637 original size:25 final size:25
Alignment explanation
Indices: 40289566--40289639 Score: 109
Period size: 25 Copynumber: 3.0 Consensus size: 25
40289556 AACCCAATTT
40289566 TTATTTATTTA-TTTA-TTTATTATT-
1 TTATTTA-TTACTTTATTTTATT-TTA
40289590 TTATTTATTACTTTATTTTATTTTA
1 TTATTTATTACTTTATTTTATTTTA
40289615 TTATTTATTACTTTATTTTATTTTA
1 TTATTTATTACTTTATTTTATTTTA
40289640 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
23 3 0.06
24 13 0.28
25 31 0.66
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (25 bp):
TTATTTATTACTTTATTTTATTTTA
Found at i:40291334 original size:13 final size:13
Alignment explanation
Indices: 40291318--40291342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40291308 TATTAAAGAT
40291318 GATTTAATTTTAG
1 GATTTAATTTTAG
40291331 GATTTAATTTTA
1 GATTTAATTTTA
40291343 TTTATCTTTA
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:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
GATTTAATTTTAG
Found at i:40300184 original size:46 final size:46
Alignment explanation
Indices: 40300132--40300226 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
40300122 AAAAAGATAG
*
40300132 AAACCAAAATATTATCTCCTAAACTTTAGTATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
40300178 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
40300224 AAA
1 AAA
40300227 AGAAAATAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:40303637 original size:33 final size:34
Alignment explanation
Indices: 40303554--40303643 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
40303544 GGTTAACCAG
*
40303554 CCAGCACACCAAATGCTCATATGAGCCAGCCCAT
1 CCAGCACACCAAATGCTCATATGAGCCAACCCAT
* *
40303588 CCAGCACACCAGATGCTCATATGAGCCAATCCAT
1 CCAGCACACCAAATGCTCATATGAGCCAACCCAT
* *
40303622 -CAGTACACCAAATGCTCGTATG
1 CCAGCACACCAAATGCTCATATG
40303644 GCAAAATCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 19 0.38
34 31 0.62
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (34 bp):
CCAGCACACCAAATGCTCATATGAGCCAACCCAT
Found at i:40303652 original size:33 final size:33
Alignment explanation
Indices: 40303555--40303655 Score: 114
Period size: 34 Copynumber: 3.0 Consensus size: 33
40303545 GTTAACCAGC
* **
40303555 CAGCACACCAAATGCTCATATGAGCCAGCCCAT
1 CAGCACACCAAATGCTCATATGAGCAAATCCAT
* *
40303588 CCAGCACACCAGATGCTCATATGAGCCAATCCAT
1 -CAGCACACCAAATGCTCATATGAGCAAATCCAT
* *
40303622 CAGTACACCAAATGCTCGTATG-GCAAAATCCAT
1 CAGCACACCAAATGCTCATATGAGC-AAATCCAT
40303655 C
1 C
40303656 CTTCACACCA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
32 2 0.03
33 27 0.46
34 30 0.51
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.18
Consensus pattern (33 bp):
CAGCACACCAAATGCTCATATGAGCAAATCCAT
Found at i:40313520 original size:32 final size:31
Alignment explanation
Indices: 40313479--40313542 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
40313469 ACGTGAAACC
* *
40313479 GCTCGTGTGGTAAGTCGTGTGATCAAACATA
1 GCTCGTGTGGTAAGCCGTGCGATCAAACATA
* * *
40313510 NGCTCTTGTGGTAGGCCGTGCGATCGAACATA
1 -GCTCGTGTGGTAAGCCGTGCGATCAAACATA
40313542 G
1 G
40313543 GTGTGTGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.27
Consensus pattern (31 bp):
GCTCGTGTGGTAAGCCGTGCGATCAAACATA
Found at i:40322752 original size:14 final size:16
Alignment explanation
Indices: 40322721--40322752 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
40322711 AAAGGAAATC
40322721 AATGTAGAAAATTGTG
1 AATGTAGAAAATTGTG
40322737 AATGT-GAAAA-TGTG
1 AATGTAGAAAATTGTG
40322751 AA
1 AA
40322753 AAAAATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (16 bp):
AATGTAGAAAATTGTG
Found at i:40324551 original size:12 final size:12
Alignment explanation
Indices: 40324534--40324559 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40324524 CCGTGTGGCT
40324534 CACATGGCCTAC
1 CACATGGCCTAC
40324546 CACATGGCCTAC
1 CACATGGCCTAC
40324558 CA
1 CA
40324560 TACGGTCATG
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:0.27, C:0.42, G:0.15, T:0.15
Consensus pattern (12 bp):
CACATGGCCTAC
Found at i:40330325 original size:30 final size:29
Alignment explanation
Indices: 40330262--40330540 Score: 134
Period size: 30 Copynumber: 9.4 Consensus size: 29
40330252 TGGTTGACCC
* * * * *
40330262 ATCCCTTTTCGTAATTCGATAATTGAAATT
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
*
40330292 ATCCCTTTTCATAGTTCGACAGTCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
* * * * *
40330322 ATCCTTTTTCATAATTTGATAGTGGTCACT
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
* ** * * * *
40330352 ATCCCTTTTCATTGTTTAATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
* * * *
40330382 ATCCCTTTTCATAATTGGATAGCCGAAGCC
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
* *
40330412 ATCCCTTTTCATAGTTCGATGGTC-ATCACC
1 ATCCCTTTTCATAGTTCGATAGTCGA--ACT
* * * * *
40330442 GTCCCTTTTCATTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
* *
40330471 ATCCCTTTTCATAATT-GACAGTCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
* * *
40330500 ATCCCCTTTCTTA-TTCGATAGTCAAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
40330529 ATCCCTTTTCAT
1 ATCCCTTTTCAT
40330541 TTGTTGATGA
Statistics
Matches: 193, Mismatches: 47, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
28 3 0.02
29 66 0.34
30 122 0.63
31 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAGTTCGATAGTCGAACT
Found at i:40330391 original size:60 final size:60
Alignment explanation
Indices: 40330322--40330483 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 60
40330312 AGTCGAAGCT
* * * * * **
40330322 ATCCTTTTTCATAATTTGATAGTGGTCACTATCCCTTTTCATTGTTTAATGGTTGTCACC
1 ATCCCTTTTCATAATTTGATAGTCGTCACCATCCCTTTTCATAGTTCAATGGTCATCACC
* * * *
40330382 ATCCCTTTTCATAATTGGATAGCCG-AAGCCATCCCTTTTCATAGTTCGATGGTCATCACC
1 ATCCCTTTTCATAATTTGATAGTCGTCA-CCATCCCTTTTCATAGTTCAATGGTCATCACC
* *
40330442 GTCCCTTTTCAT--TGTTGATGGTCGTCACCATCCCTTTTCATA
1 ATCCCTTTTCATAAT-TTGATAGTCGTCACCATCCCTTTTCATA
40330484 ATTGACAGTC
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
58 1 0.01
59 23 0.28
60 59 0.71
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGTCGTCACCATCCCTTTTCATAGTTCAATGGTCATCACC
Found at i:40330421 original size:90 final size:88
Alignment explanation
Indices: 40330292--40330541 Score: 288
Period size: 90 Copynumber: 2.8 Consensus size: 88
40330282 AATTGAAATT
* * * ** *
40330292 ATCCCTTTTCATAGTTCGACAGTCGAAGCTATCCTTTTTCATAATTTGATAGTGGTCACTATCCC
1 ATCCCTTTTCATAATT-GACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCACCATCCC
*
40330357 TTTTCATTGTTTAATGGTTGTCACC
65 TTTTCATTG-TTAATGGTCGTCACC
* * * * * *
40330382 ATCCCTTTTCATAATTGGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGGTCATCACCGTCCC
1 ATCCCTTTTCATAATT-GACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCACCATCCC
*
40330447 TTTTCATTGTTGATGGTCGTCACC
65 TTTTCATTGTTAATGGTCGTCACC
* * * *
40330471 ATCCCTTTTCATAATTGACAGTCGAAGCTATCCCCTTTC-TTATTCGATAGTCA-AAGCTATCCC
1 ATCCCTTTTCATAATTGACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCA-CCATCCC
40330534 TTTTCATT
65 TTTTCATT
40330542 TGTTGATGAT
Statistics
Matches: 134, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
86 1 0.01
87 24 0.18
88 19 0.14
89 29 0.22
90 61 0.46
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (88 bp):
ATCCCTTTTCATAATTGACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCACCATCCCT
TTTCATTGTTAATGGTCGTCACC
Found at i:40330469 original size:29 final size:30
Alignment explanation
Indices: 40330292--40330483 Score: 147
Period size: 30 Copynumber: 6.4 Consensus size: 30
40330282 AATTGAAATT
** * *
40330292 ATCCCTTTTCATAGTTCGACAGTCG-AAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
* * * * * *
40330322 ATCCTTTTTCATAATTTGATAGTGGTCACT
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* ** *
40330352 ATCCCTTTTCATTGTTTAATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * *
40330382 ATCCCTTTTCATAATTGGATAGCCG-AAGCC
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
*
40330412 ATCCCTTTTCATAGTTCGATGGTCATCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* *
40330442 GTCCCTTTTCATTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
40330471 ATCCCTTTTCATA
1 ATCCCTTTTCATA
40330484 ATTGACAGTC
Statistics
Matches: 127, Mismatches: 32, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
29 24 0.19
30 101 0.80
31 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:40330503 original size:29 final size:30
Alignment explanation
Indices: 40330471--40330540 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
40330461 GGTCGTCACC
*
40330471 ATCCCTTTTCATAATT-GACAGTCGAAGCT
1 ATCCCTTTTCATAATTCGACAGTCAAAGCT
* * *
40330500 ATCCCCTTTC-TTATTCGATAGTCAAAGCT
1 ATCCCTTTTCATAATTCGACAGTCAAAGCT
40330529 ATCCCTTTTCAT
1 ATCCCTTTTCAT
40330541 TTGTTGATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.12
29 29 0.85
30 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAGTCAAAGCT
Found at i:40333628 original size:23 final size:23
Alignment explanation
Indices: 40333594--40333637 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
40333584 GTCAATTATT
40333594 ATTTTAATAATATTTTATTTAAA
1 ATTTTAATAATATTTTATTTAAA
40333617 ATTTT-ATGAATATTTTATTTA
1 ATTTTAAT-AATATTTTATTTA
40333638 TTTAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTTAATAATATTTTATTTAAA
Found at i:40341423 original size:16 final size:17
Alignment explanation
Indices: 40341402--40341434 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40341392 AAGTAGTTGA
40341402 TTGAAT-GATGTTTTGG
1 TTGAATCGATGTTTTGG
*
40341418 TTGAATCTATGTTTTGG
1 TTGAATCGATGTTTTGG
40341435 AGTACTCGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (17 bp):
TTGAATCGATGTTTTGG
Found at i:40344988 original size:42 final size:42
Alignment explanation
Indices: 40344929--40345010 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
40344919 CTACAAATTT
40344929 ATACCAAAGGCCTTAAAATTAGAGGAGGGCCGGTTACCTTTC
1 ATACCAAAGGCCTTAAAATTAGAGGAGGGCCGGTTACCTTTC
40344971 ATACCAAAGGCCTTAAAATTAGAGGAGGGCCGGTTACCTT
1 ATACCAAAGGCCTTAAAATTAGAGGAGGGCCGGTTACCTT
40345011 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (42 bp):
ATACCAAAGGCCTTAAAATTAGAGGAGGGCCGGTTACCTTTC
Found at i:40355038 original size:38 final size:38
Alignment explanation
Indices: 40354996--40355070 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
40354986 TAAACATTGA
*
40354996 ATATTACCTTTACTATTTTTAGAAAAAATCTTCATCTC
1 ATATTACCTTTACTATTTTTAGAAAAAATCCTCATCTC
40355034 ATATTACCTTTACTATTTTTAGAAAAAATCCTCATCT
1 ATATTACCTTTACTATTTTTAGAAAAAATCCTCATCT
40355071 TGAGAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.44
Consensus pattern (38 bp):
ATATTACCTTTACTATTTTTAGAAAAAATCCTCATCTC
Found at i:40355594 original size:23 final size:22
Alignment explanation
Indices: 40355551--40355594 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
40355541 AAATTATAAA
* *
40355551 ATATAAAAATATATATGTGTAC
1 ATATAAAAAAATATATATGTAC
40355573 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
40355595 TGTGAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:40356364 original size:21 final size:21
Alignment explanation
Indices: 40356327--40356381 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
40356317 AATCATATCT
40356327 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
40356346 TTTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
40356367 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
40356382 CCTTGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.31
21 22 0.69
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:40357196 original size:44 final size:45
Alignment explanation
Indices: 40357015--40357397 Score: 179
Period size: 44 Copynumber: 8.7 Consensus size: 45
40357005 GGATTATTGG
* * *
40357015 CTTCAATTTGCTCCACTACAACTTAGGGAGATAATATCT-GTAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * * * * * **
40357059 TTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGA-CTAGT-GG
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * ***
40357102 CTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCCGT
1 CTTCAATCTGC-TCCACTACTA-CTTAGGG-AGATAAGATCTAGTAAT
* *
40357147 CTTCAATTTGCTCCACTACTACTTACGGAGATAAGATCT-GTAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * * * * * *
40357191 TTTCAACCTACTCCACTGCTGCTTAGAGAGATAA-AGTCTA-CAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGA-TCTAGTAAT
* ** * * * **
40357235 CTTCAACCT-CTCCACTGTTGCTCAGGGAGATAAG-GCTAGT-GG
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * ***
40357277 CTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCCGT
1 CTTCAATCTGC-TCCACTACTA-CTTAGGG-AGATAAGATCTAGTAAT
* * *
40357322 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-CTAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * * *
40357366 -TTCAATCTACTCCACTGCTGCTCAGGGAGATA
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATA
40357398 GGATTCAAAA
Statistics
Matches: 252, Mismatches: 65, Indels: 45
0.70 0.18 0.12
Matches are distributed among these distances:
42 10 0.04
43 73 0.29
44 131 0.52
45 38 0.15
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
Found at i:40357259 original size:175 final size:175
Alignment explanation
Indices: 40357060--40357441 Score: 590
Period size: 175 Copynumber: 2.2 Consensus size: 175
40357050 ATCTGTAATT
40357060 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
* *
40357125 TTGGGAAGATAAGATTCGCCGTCTTCAATTTGCTCCACTACTACTTACGGAGATAAGATCTGTAA
66 TTGGGAAGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTACGGAGATAAGATCTCTAA
* *
40357190 TTTTCAACCTACTCCACTGCTGCTTAGAGAGATA-AAGTCTACAATC
131 -TTTCAACCTACTCCACTGCTGCTCAGAGAGATAGAAGTC-AAAATC
* *
40357236 TTCAACCT-CTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
* * *
40357300 TTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTCTAA
66 TTGGGAAGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTACGGAGATAAGATCTCTAA
* * * *
40357365 TTTCAATCTACTCCACTGCTGCTCAGGGAGATAGGATTCAAAATC
131 TTTCAACCTACTCCACTGCTGCTCAGAGAGATAGAAGTCAAAATC
*
40357410 TTCAACCTATTCCACTGCTGAC-CAGGGAGATA
1 TTCAACCTACTCCACTGCTG-CTCAGGGAGATA
40357442 GGATTCACAA
Statistics
Matches: 188, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
174 43 0.23
175 136 0.72
176 9 0.05
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (175 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
TTGGGAAGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTACGGAGATAAGATCTCTAA
TTTCAACCTACTCCACTGCTGCTCAGAGAGATAGAAGTCAAAATC
Found at i:40357428 original size:44 final size:44
Alignment explanation
Indices: 40357366--40357661 Score: 443
Period size: 44 Copynumber: 6.7 Consensus size: 44
40357356 GATCTCTAAT
* * *
40357366 TTCAATCTACTCCACTGCTG-CTCAGGGAGATAGGATTCAAAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
40357410 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * *
40357454 TTCAACCTATTCCACTGTTGACCTGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
40357498 TTCAACCTATTCCACTCCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* *
40357542 TTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
40357586 TTCAACCTATTCCACTGCTGACCAGAGAGATAGGATTCACAATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
40357630 TTCAACCTATTCCATTGCTGACCAGGAAGATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATA
40357662 AAGCTTTGTG
Statistics
Matches: 229, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
43 1 0.00
44 226 0.99
45 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:40358999 original size:21 final size:19
Alignment explanation
Indices: 40358975--40359018 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
40358965 GATTTTTTTC
*
40358975 TTTTTTGGTTTTTTGTGTGTT
1 TTTTTTGGGTTTTT-T-TGTT
40358996 TTTTTTGGGTTTTTTTGTT
1 TTTTTTGGGTTTTTTTGTT
40359015 TTTT
1 TTTT
40359019 GAATTGGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (19 bp):
TTTTTTGGGTTTTTTTGTT
Found at i:40364215 original size:23 final size:22
Alignment explanation
Indices: 40364175--40364217 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
40364165 AAAATATAAA
*
40364175 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
40364197 ATATAAGAAAAATATATATGT
1 ATATAA-AAAAATATATATGT
40364218 NATAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:40364658 original size:23 final size:22
Alignment explanation
Indices: 40364615--40364672 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40364605 AAAGGGTATC
* *
40364615 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40364636 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40364659 TGCATATCATATCT
1 TACAAATCATATCT
40364673 AATATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40377114 original size:28 final size:28
Alignment explanation
Indices: 40377082--40377137 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
40377072 ATTTTGAGTA
40377082 AGATTAAGATAAGGATGATAAATTTTAT
1 AGATTAAGATAAGGATGATAAATTTTAT
*
40377110 AGATTAAGATAATGATGATAAATTTTAT
1 AGATTAAGATAAGGATGATAAATTTTAT
40377138 TGTAGGACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (28 bp):
AGATTAAGATAAGGATGATAAATTTTAT
Found at i:40378920 original size:21 final size:21
Alignment explanation
Indices: 40378894--40378941 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 21
40378884 GATTGGGTCG
40378894 GGTAAGGGGTGTTACAATGTT
1 GGTAAGGGGTGTTACAATGTT
40378915 GGTAAGGGGTGTTACAATGTT
1 GGTAAGGGGTGTTACAATGTT
40378936 GTGTAA
1 G-GTAA
40378942 CAAGTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.38, T:0.33
Consensus pattern (21 bp):
GGTAAGGGGTGTTACAATGTT
Found at i:40391440 original size:82 final size:82
Alignment explanation
Indices: 40391303--40391519 Score: 425
Period size: 82 Copynumber: 2.6 Consensus size: 82
40391293 TGAGACTATT
*
40391303 ATTATATACATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATATCAATAAGTAAA
1 ATTATATAAATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATATCAATAAGTAAA
40391368 GACATGAAGATGTGTAC
66 GACATGAAGATGTGTAC
40391385 ATTATATAAATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATATCAATAAGTAAA
1 ATTATATAAATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATATCAATAAGTAAA
40391450 GACATGAAGATGTGTAC
66 GACATGAAGATGTGTAC
40391467 ATTATATAAATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATA
1 ATTATATAAATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATA
40391520 GCAAAAAGGA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 134 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (82 bp):
ATTATATAAATATTTAGAGTTAGAAGTATATAAAAATAGGTTTTAATAACATATCAATAAGTAAA
GACATGAAGATGTGTAC
Found at i:40393103 original size:132 final size:131
Alignment explanation
Indices: 40392954--40394007 Score: 1499
Period size: 132 Copynumber: 8.0 Consensus size: 131
40392944 TAACTTCAGG
* * *
40392954 GAGATA-AGATTAGTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
1 GAGATAGA-ATTACTGGCTTCAATGTACTCCACTGTAACAT-AGGGAGGTAAAATCTGCCATCTT
* * * * * * * *
40393018 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATTCTTCAATCTATTCCACTACTCCCC
64 CGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
40393083 AGA
129 AGA
*
40393086 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA-CATAGGGAGGTAAAATCTGCCATCTTC
*
40393151 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC-CAACC
65 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTC-CCC
40393215 AGA
129 AGA
* *
40393218 GAGATATAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA-CATAGGGAGGTAAAATCTGCCATCTTC
* * * *
40393283 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATCTATTCAACTGCTGCTCA
65 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
*
40393348 GG
130 GA
40393350 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCTT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAA-CATAGGGAGGTAAAATCTGCCATCTT
* * * * *
40393414 CGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCGATTCCACTGCTGCCC
64 CGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
*
40393479 AGG
129 AGA
* * *
40393482 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCATATT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAA-CATAGGGAGGTAAAATCTGCCATCTT
* * ** *
40393546 CGATCTACTCCACTACTACTTAGGGAGGCAAGATCTGCTATCTTCAATCTATTCCACTACTCCCC
64 CGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
*
40393611 AAA
129 AGA
*
40393614 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA-CATAGGGAGGTAAAATCTGCCATCTTC
*
40393679 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC-CAACC
65 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTC-CCC
40393743 AGA
129 AGA
*
40393746 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAC-ATAGGGAGGTAAAATCTGCCATCTTC
* * * * *
40393811 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATTTATTCAACTGCTGCTCA
65 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
*
40393876 GG
130 GA
*
40393878 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAA-CATAGGGAGGTAAAATCTGCCATCTT
* * * *
40393942 CGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCC
64 CGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
40394007 A
129 A
40394008 TCAATGTACT
Statistics
Matches: 837, Mismatches: 74, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
131 5 0.01
132 827 0.99
133 5 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (131 bp):
GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACATAGGGAGGTAAAATCTGCCATCTTCG
ATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCAG
A
Found at i:40393384 original size:264 final size:263
Alignment explanation
Indices: 40392954--40394206 Score: 1753
Period size: 264 Copynumber: 4.8 Consensus size: 263
40392944 TAACTTCAGG
* * *
40392954 GAGATAAGATTAGTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTC
1 GAGATAA-ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTC
* * * * * * *
40393019 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATTCTTCAATCTATTCCACTACTCCCCA
65 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
*
40393084 GAGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCT
130 GAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCT
* *
40393149 TCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAAC
195 TCGATATACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCCAAC
40393214 CAGA
260 CAGA
40393218 GAGATATAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTC
1 GAGATA-AATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTC
* * * * *
40393283 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATCTATTCAACTGCTGCTCA
65 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
*
40393348 GGGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATC
130 GAGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATC
* * ***
40393412 TTCGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCGATTCCACTGCTGC
194 TTCGATATACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCCAA
*
40393477 CCAGG
259 CCAGA
* * *
40393482 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCATATT
1 GAGA-TA-AATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
* ** *
40393546 CGATCTACTCCACTACTACTTAGGGAGGCAAGATCTGCTATCTTCAATCTATTCCACTACTCCCC
64 CGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
* *
40393611 AAAGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATC
129 AGAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATC
* *
40393676 TTCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
194 TTCGATATACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCCAA
40393741 CCAGA
259 CCAGA
* * *
40393746 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
1 GAGATA-AATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTC
* * * * * *
40393811 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATTTATTCAACTGCTGCTCA
65 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
* *
40393876 GGGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATC
130 GAGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATC
*
40393940 TTCGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTG----
194 TTCGATATACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCCAA
40394001 -C---
259 CCAGA
* * * * * *
40394002 ---------TGC--CCATCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCATATTCG
1 GAGATAAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCG
*
40394056 ATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC-CAACCA
66 ATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTC-CCCA
*
40394120 GAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA-CAATAGGGAGGTAAAATCCGCCATC
130 GAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATC-ATAGGGAGGTAAAATCTGCCATC
40394184 TTCGATATACTCCACTACTACTT
194 TTCGATATACTCCACTACTACTT
40394207 TGCCCAGGGA
Statistics
Matches: 888, Mismatches: 92, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
243 1 0.00
244 178 0.20
245 1 0.00
246 2 0.00
259 1 0.00
263 3 0.00
264 699 0.79
265 3 0.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (263 bp):
GAGATAAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCG
ATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCAG
AGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCTT
CGATATACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCCAACC
AGA
Found at i:40393681 original size:396 final size:393
Alignment explanation
Indices: 40392954--40394206 Score: 1825
Period size: 396 Copynumber: 3.2 Consensus size: 393
40392944 TAACTTCAGG
* *
40392954 GAGATA-AGATTAGTGGCTTCAATGTACTCCACTGTAAC-CTCAGGGAGGTAAAATCCGCCATCT
1 GAGATAGA-ATTACTGGCTTCAATGTACTCCACTGTAACAAT-AGGGAGGTAAAATCCGCCATCT
* * * * * * * * *
40393017 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATTCTTCAATCTATTCCACTACTCCC
64 TCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
* * *
40393082 CAGAG-AGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCA
129 CAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCA
*
40393146 TCTTCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC-
193 TCTTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCT
* *
40393210 CAACCAGAGAGATATAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTG
258 C-CCCA-AGAGATA-AATTA-TGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTG
* *
40393275 CCATCTTCGATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATCTATTCAACT
319 CCATCTTCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACT
** *
40393340 G-CTGCTCAGG
384 GCCAAC-CAGA
*
40393350 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATC-ATAGGGAGGTAAAATCTGCCATCT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAA-CAATAGGGAGGTAAAATCCGCCATCT
* * * *
40393413 TCGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCGATTCCACTGCTGCC
64 TCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
*
40393478 CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCAT
129 CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCAT
* * ** *
40393543 ATTCGATCTACTCCACTACTACTTAGGGAGGCAAGATCTGCTATCTTCAATCTATTCCACTACTC
194 CTTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTC
*
40393608 CCCAAAGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCC
259 CCC-AAGAGATA-AATTA-TGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCC
40393673 ATCTTCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC
321 ATCTTCGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC
40393738 CAACCAGA
386 CAACCAGA
40393746 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
* * * *
40393811 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATTTATTCAACTGCTGCTCA
66 GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCA
40393876 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
131 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
* * *
40393941 TCGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCC
196 TCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCC
* *
40394006 C------------A-----TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCATATT
261 CAAGAGATAAATTATGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTT
*
40394054 CGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
326 CGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
40394119 AGA
391 AGA
40394122 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
40394187 GATATACTCCACTACTACTT
66 GATATACTCCACTACTACTT
40394207 TGCCCAGGGA
Statistics
Matches: 792, Mismatches: 56, Indels: 38
0.89 0.06 0.04
Matches are distributed among these distances:
376 195 0.25
382 1 0.00
395 2 0.00
396 584 0.74
397 10 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (393 bp):
GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
GATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCA
GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
TCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCC
CAAGAGATAAATTATGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTT
CGATATACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
AGA
Found at i:40394095 original size:112 final size:112
Alignment explanation
Indices: 40393896--40394113 Score: 400
Period size: 112 Copynumber: 1.9 Consensus size: 112
40393886 ATTACTGGCT
*
40393896 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTAC
1 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
40393961 TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
66 TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
*
40394008 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCATATTCGATCTACTCCACTACTAC
1 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
* *
40394073 TTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC
66 TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGC
40394114 CAACCAGAGA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 102 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (112 bp):
TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
Found at i:40394197 original size:244 final size:244
Alignment explanation
Indices: 40393764--40394206 Score: 696
Period size: 244 Copynumber: 1.8 Consensus size: 244
40393754 ATTACTGGCT
* *
40393764 TCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTCGATATACTCCACTACTAC
1 TCAATGTACTCCACTGTAACAACAGGGAGGTAAAATCCGCCATATTCGATATACTCCACTACTAC
* * ** *
40393829 TTAGGGAGGTAAGATTTGAAATCTTCAATTTATTCAACTGCTGCTCAGGGAAGTAGAATTACTGG
66 TTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCAACTGCAACTCAGAGAAGTAGAATTACTGG
* *
40393894 CTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACT
131 CTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCCGCCATCTTCGATATACTCCACTACT
40393959 ACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
196 ACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
** *
40394008 TCAATGTACTCCACTGTAATC-ACAGGGAGGTAAAATTTGCCATATTCGATCTACTCCACTACTA
1 TCAATGTACTCCACTGTAA-CAACAGGGAGGTAAAATCCGCCATATTCGATATACTCCACTACTA
*
40394072 CTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAAC-CAGAG-AGATAGAATTAC
65 CTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCAACTG-CAACTCAGAGAAG-TAGAATTAC
*
40394135 TGGCTTCAATGTACTCCACTGTAA-CAATAGGGAGGTAAAATCCGCCATCTTCGATATACTCCAC
128 TGGCTTCAATGTACTCCACTGTAATC-ACAGGGAGGTAAAATCCGCCATCTTCGATATACTCCAC
40394199 TACTACTT
192 TACTACTT
40394207 TGCCCAGGGA
Statistics
Matches: 181, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
243 3 0.02
244 175 0.97
245 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (244 bp):
TCAATGTACTCCACTGTAACAACAGGGAGGTAAAATCCGCCATATTCGATATACTCCACTACTAC
TTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCAACTGCAACTCAGAGAAGTAGAATTACTGG
CTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCCGCCATCTTCGATATACTCCACTACT
ACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
Found at i:40395624 original size:8 final size:8
Alignment explanation
Indices: 40395613--40395662 Score: 54
Period size: 7 Copynumber: 6.6 Consensus size: 8
40395603 CCCTTTTTAC
40395613 TTTTTCAT
1 TTTTTCAT
40395621 TTTTTCA-
1 TTTTTCAT
40395628 TTTTTCA-
1 TTTTTCAT
40395635 -TTTTCAT
1 TTTTTCAT
*
40395642 TTTTTC-C
1 TTTTTCAT
40395649 TTTTTCAT
1 TTTTTCAT
40395657 ATTTTT
1 -TTTTT
40395663 TCGACTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
6 6 0.17
7 13 0.36
8 12 0.33
9 5 0.14
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:40395631 original size:15 final size:15
Alignment explanation
Indices: 40395613--40395662 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
40395603 CCCTTTTTAC
40395613 TTTTTCATTTTTTCA-
1 TTTTTCA-TTTTTCAT
40395628 TTTTTCA-TTTTCAT
1 TTTTTCATTTTTCAT
*
40395642 TTTTTCCTTTTTCAT
1 TTTTTCATTTTTCAT
40395657 ATTTTT
1 -TTTTT
40395663 TCGACTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
15 14 0.45
16 5 0.16
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCATTTTTCAT
Found at i:40395638 original size:21 final size:21
Alignment explanation
Indices: 40395614--40395656 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40395604 CCTTTTTACT
40395614 TTTTCATTTTTTCATTTTTCA
1 TTTTCATTTTTTCATTTTTCA
*
40395635 TTTTCATTTTTTCCTTTTTCA
1 TTTTCATTTTTTCATTTTTCA
40395656 T
1 T
40395657 ATTTTTTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCATTTTTTCATTTTTCA
Found at i:40396566 original size:13 final size:12
Alignment explanation
Indices: 40396518--40396566 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 12
40396508 CTCCTTTTTC
*
40396518 TTTTTTCTTTAT
1 TTTTTTTTTTAT
40396530 TTTTATTTTTTAT
1 TTTT-TTTTTTAT
40396543 TTTATTTTTTTAT
1 TTT-TTTTTTTAT
40396556 TTTTTTCTTTT
1 TTTTTT-TTTT
40396567 GACTTTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 7 0.21
13 25 0.76
14 1 0.03
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:40396566 original size:27 final size:27
Alignment explanation
Indices: 40396520--40396605 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
40396510 CCTTTTTCTT
40396520 TTTTCTTTATTTTTATT-TTTT-ATTTTA
1 TTTT-TTTATTTTT-TTCTTTTGATTTTA
*
40396547 TTTTTTTATTTTTTTCTTTTGACTTTGA
1 TTTTTTTATTTTTTTCTTTTGA-TTTTA
* *
40396575 TTTTTCT-TTTTCTTCTTTTGATTTTGA
1 TTTTTTTATTTTTTTCTTTTGATTTT-A
40396602 TTTT
1 TTTT
40396606 GATTTTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.04
26 16 0.31
27 23 0.45
28 10 0.20
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (27 bp):
TTTTTTTATTTTTTTCTTTTGATTTTA
Found at i:40396611 original size:27 final size:26
Alignment explanation
Indices: 40396549--40396614 Score: 96
Period size: 27 Copynumber: 2.5 Consensus size: 26
40396539 TTATTTTATT
40396549 TTTTTATTTTTTTCTTTTGACTTTGA
1 TTTTTATTTTTTTCTTTTGACTTTGA
* *
40396575 TTTTTCTTTTTCTTCTTTTGATTTTGA
1 TTTTTATTTTT-TTCTTTTGACTTTGA
*
40396602 TTTTGATTTTTTT
1 TTTTTATTTTTTT
40396615 GATTGAATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.09, C:0.08, G:0.08, T:0.76
Consensus pattern (26 bp):
TTTTTATTTTTTTCTTTTGACTTTGA
Found at i:40402624 original size:24 final size:24
Alignment explanation
Indices: 40402596--40402646 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
40402586 CCTAAAAAAA
*
40402596 TTTTAATTGTCCATAACCTCATTT
1 TTTTAATTGTCCATAACCCCATTT
*
40402620 TTTTAATTGTCTATAACCCCATTT
1 TTTTAATTGTCCATAACCCCATTT
40402644 TTT
1 TTT
40402647 CTCACAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTAATTGTCCATAACCCCATTT
Found at i:40403209 original size:14 final size:13
Alignment explanation
Indices: 40403192--40403251 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
40403182 TATTTAATTA
40403192 AATAAATATAATAT
1 AATAAATA-AATAT
*
40403206 AATAAAGTAAATCT
1 AATAAA-TAAATAT
40403220 AATAAAATAAATA-
1 AAT-AAATAAATAT
*
40403233 AGTAAATGAAATA-
1 AATAAAT-AAATAT
40403246 AATAAA
1 AATAAA
40403252 GAAACGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 4 0.10
13 12 0.31
14 18 0.46
15 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (13 bp):
AATAAATAAATAT
Found at i:40403216 original size:19 final size:18
Alignment explanation
Indices: 40403190--40403251 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
40403180 AATATTTAAT
*
40403190 TAAATAAATATAATATAA
1 TAAATAAATATAATAAAA
*
40403208 TAAAGTAAATCTAATAAAA
1 TAAA-TAAATATAATAAAA
* *
40403227 TAAATAAGTA-AATGAAA
1 TAAATAAATATAATAAAA
40403244 TAAATAAA
1 TAAATAAA
40403252 GAAACGAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 13 0.35
18 8 0.22
19 16 0.43
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (18 bp):
TAAATAAATATAATAAAA
Found at i:40403245 original size:22 final size:22
Alignment explanation
Indices: 40403190--40403251 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
40403180 AATATTTAAT
*
40403190 TAAATAAATATAATATAATAAAG
1 TAAATAAATAAAATA-AATAAAG
*
40403213 TAAATCTAATAAAATAAAT-AAG
1 TAAAT-AAATAAAATAAATAAAG
40403235 TAAATGAAAT-AAATAAA
1 TAAAT-AAATAAAATAAA
40403252 GAAACGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.21
22 11 0.32
23 8 0.24
24 8 0.24
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
TAAATAAATAAAATAAATAAAG
Found at i:40404039 original size:24 final size:26
Alignment explanation
Indices: 40403985--40404039 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
40403975 GTGTTTTGCA
40403985 ATTGAAATAGATTGATTTGATATATG
1 ATTGAAATAGATTGATTTGATATATG
*
40404011 A-TGAAAT-TATTGAATTT-ATAT-TG
1 ATTGAAATAGATTG-ATTTGATATATG
40404034 ATTGAA
1 ATTGAA
40404040 TTGAATTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.12
24 12 0.46
25 10 0.38
26 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (26 bp):
ATTGAAATAGATTGATTTGATATATG
Found at i:40404520 original size:21 final size:20
Alignment explanation
Indices: 40404472--40404520 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
40404462 GAAAAGCTAT
*
40404472 TTGAATAGAAAGTATGAGAT
1 TTGAATAGAAAGTATGAGAA
40404492 TTGAAATAGCAATAG-ATGAGAA
1 TTG-AATAG-AA-AGTATGAGAA
40404514 TTGAATA
1 TTGAATA
40404521 TGTTATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 9 0.36
22 11 0.44
23 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (20 bp):
TTGAATAGAAAGTATGAGAA
Found at i:40409278 original size:23 final size:24
Alignment explanation
Indices: 40409250--40409294 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40409240 AGAAAAGATC
40409250 TTTCTTTCCA-GTGTTTGTTCCCT
1 TTTCTTTCCAGGTGTTTGTTCCCT
* *
40409273 TTTCTTTGCAGGTTTTTGTTCC
1 TTTCTTTCCAGGTGTTTGTTCC
40409295 TTGATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.04, C:0.22, G:0.16, T:0.58
Consensus pattern (24 bp):
TTTCTTTCCAGGTGTTTGTTCCCT
Found at i:40418274 original size:378 final size:378
Alignment explanation
Indices: 40417579--40418339 Score: 1504
Period size: 378 Copynumber: 2.0 Consensus size: 378
40417569 CGATAGCAAC
40417579 AAAAACCAAGCCCTCGATAATATTAAGGTAACAAAATGTTAATGTCATCTATAATGCTTGGGAAA
1 AAAAACCAAGCCCTCGATAATATTAAGGTAACAAAATGTTAATGTCATCTATAATGCTTGGGAAA
40417644 TAGTTTCATTTATATTTACTTGATTAACTTGTGTTTTTTGTTTTTTGTAGGCGAGGTTTGCTTTA
66 TAGTTTCATTTATATTTACTTGATTAACTTGTGTTTTTTGTTTTTTGTAGGCGAGGTTTGCTTTA
40417709 GAGGTCTCGGATGCTTATGTAAAGAAGGCATTGGGAAAAAGATGGAGAGACAACAAAAGTACTTT
131 GAGGTCTCGGATGCTTATGTAAAGAAGGCATTGGGAAAAAGATGGAGAGACAACAAAAGTACTTT
*
40417774 GAAGAAAAATTATTATAAGACAAAAATAACCCTCGATGAGAAATTGCAAAATGTCCCGCCGGGTA
196 GAAGAAAAATTATTATAAGACAAAAACAACCCTCGATGAGAAATTGCAAAATGTCCCGCCGGGTA
40417839 TGTTGAGGTGCCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAATAAAGGCGAGGTATGACGT
261 TGTTGAGGTGCCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAATAAAGGCGAGGTATGACGT
40417904 ACTTCTAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACT
326 ACTTCTAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACT
40417957 AAAAACCAAGCCCTCGATAATATTAAGGTAACAAAATGTTAATGTCATCTATAATGCTTGGGAAA
1 AAAAACCAAGCCCTCGATAATATTAAGGTAACAAAATGTTAATGTCATCTATAATGCTTGGGAAA
40418022 TAGTTTCATTTATATTTACTTGATTAACTTGTGTTTTTTGTTTTTTGTAGGCGAGGTTTGCTTTA
66 TAGTTTCATTTATATTTACTTGATTAACTTGTGTTTTTTGTTTTTTGTAGGCGAGGTTTGCTTTA
40418087 GAGGTCTCGGATGCTTATGTAAAGAAGGCATTGGGAAAAAGATGGAGAGACAACAAAAGTACTTT
131 GAGGTCTCGGATGCTTATGTAAAGAAGGCATTGGGAAAAAGATGGAGAGACAACAAAAGTACTTT
*
40418152 GAAGAAAAATTATTATAAGACAAAAACAACCCTCGATGAGAAATTGCAAAATGTCCCGCTGGGTA
196 GAAGAAAAATTATTATAAGACAAAAACAACCCTCGATGAGAAATTGCAAAATGTCCCGCCGGGTA
40418217 TGTTGAGGTGCCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAATAAAGGCGAGGTATGACGT
261 TGTTGAGGTGCCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAATAAAGGCGAGGTATGACGT
40418282 ACTTCTAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACT
326 ACTTCTAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACT
40418335 AAAAA
1 AAAAA
40418340 ATTTCATAAC
Statistics
Matches: 381, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
378 381 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (378 bp):
AAAAACCAAGCCCTCGATAATATTAAGGTAACAAAATGTTAATGTCATCTATAATGCTTGGGAAA
TAGTTTCATTTATATTTACTTGATTAACTTGTGTTTTTTGTTTTTTGTAGGCGAGGTTTGCTTTA
GAGGTCTCGGATGCTTATGTAAAGAAGGCATTGGGAAAAAGATGGAGAGACAACAAAAGTACTTT
GAAGAAAAATTATTATAAGACAAAAACAACCCTCGATGAGAAATTGCAAAATGTCCCGCCGGGTA
TGTTGAGGTGCCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAATAAAGGCGAGGTATGACGT
ACTTCTAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACT
Found at i:40419108 original size:21 final size:20
Alignment explanation
Indices: 40419082--40419148 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
40419072 CGACAACTTA
40419082 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGC-GAAGCGAGGG
* *
40419103 AAGCAGCGGCTACAGCGAGGG
1 AAGCAGAGGCGA-AGCGAGGG
* * *
40419124 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGC-GAAGCGAGGG
40419145 AAGC
1 AAGC
40419149 GGAGCAGAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.31, C:0.19, G:0.46, T:0.03
Consensus pattern (20 bp):
AAGCAGAGGCGAAGCGAGGG
Found at i:40419149 original size:21 final size:21
Alignment explanation
Indices: 40419095--40419152 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
40419085 CAGAGGCGGA
* *
40419095 AGCGAGGGAAGCAGCGGCTAC
1 AGCGAGGGAAGCGGAGGCTAC
*
40419116 AGCGAGGGAAGCGGAGGCTGC
1 AGCGAGGGAAGCGGAGGCTAC
*
40419137 AGCGAGAGAAGCGGAG
1 AGCGAGGGAAGCGGAG
40419153 CAGAGCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.48, T:0.03
Consensus pattern (21 bp):
AGCGAGGGAAGCGGAGGCTAC
Found at i:40419388 original size:14 final size:14
Alignment explanation
Indices: 40419369--40419402 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
40419359 ATTGCTATTG
40419369 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
40419383 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
40419397 GTTGCT
1 GTTGCT
40419403 ACAGGAGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.56
Consensus pattern (14 bp):
GTTGCTTTTGAATT
Found at i:40419533 original size:43 final size:43
Alignment explanation
Indices: 40419467--40419556 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
40419457 GTTTTTGTAT
* * * *
40419467 AAAAGCGCCACTAAAGAATATGTTCTTTAGCGGCATTTGTAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAACGGCATTTATAAA
* *
40419510 AAAAACGCCGCTAAATAACATGTTCTTTAACGGCATTTATAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAACGGCATTTATAAA
40419553 AAAA
1 AAAA
40419557 CGCTGCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (43 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAACGGCATTTATAAA
Found at i:40420920 original size:19 final size:17
Alignment explanation
Indices: 40420865--40420920 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
40420855 AGAAGAACAA
40420865 GAAGA-AAGAAGAGAAAG
1 GAAGACAAG-AGAGAAAG
*
40420882 GAAGAGAAGAGAGAAA-
1 GAAGACAAGAGAGAAAG
*
40420898 GAAGCCAAGTAGAGAAAG
1 GAAGACAAG-AGAGAAAG
40420916 TGAAG
1 -GAAG
40420921 GAGTAAGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 7 0.21
17 19 0.58
18 3 0.09
19 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.36, T:0.04
Consensus pattern (17 bp):
GAAGACAAGAGAGAAAG
Found at i:40424855 original size:30 final size:30
Alignment explanation
Indices: 40424821--40424882 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
40424811 ACTTATTTTA
40424821 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
40424851 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
40424881 TT
1 TT
40424883 CCTTATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:40425000 original size:18 final size:18
Alignment explanation
Indices: 40424965--40425004 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
40424955 GAAATATTTA
*
40424965 TTTTGATGTTTTTAATAT
1 TTTTGATGTTTATAATAT
40424983 TTTTGATGTATTATATATAT
1 TTTTGATGT-TTATA-ATAT
40425003 TT
1 TT
40425005 AAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTGATGTTTATAATAT
Found at i:40427973 original size:133 final size:132
Alignment explanation
Indices: 40427733--40427974 Score: 319
Period size: 133 Copynumber: 1.8 Consensus size: 132
40427723 GATGCTAAAT
**
40427733 AAAAGGTAACAATATCGTATCGATACTTGATAAAACTTTGAAATTCAAAATGCCAATTTTGTATC
1 AAAAGGTAACAATATCGTATCGATACTTGATAAAACTTTGAAAAACAAAATGCCAATTTTGTATC
* * * *
40427798 GATACCGAAAAAGGTATCGATAAAAGTGTACCACTATTGATACTTGAAAAAAATTATCGATACCA
66 AATACCAAAAAAGGTATCAATAAAAGTGTA-CACTATCGATACTTGAAAAAAATTATCGATACCA
40427863 AGC
130 AGC
* * *
40427866 AAAAGGTATCGATATCGTATCGATACTTGATAAATATTTTGAAAAACAAAATGCC-ATTTTCG-A
1 AAAAGGTAACAATATCGTATCGATACTTGATAAA-ACTTTGAAAAACAAAATGCCAATTTT-GTA
* *
40427929 TCAATACTAAAAAAGGTATCAATAAAATTGTGA-ATCTATCGATACT
64 TCAATACCAAAAAAGGTATCAATAAAAGTGT-ACA-CTATCGATACT
40427975 CAACTAAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
132 1 0.01
133 74 0.79
134 19 0.20
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (132 bp):
AAAAGGTAACAATATCGTATCGATACTTGATAAAACTTTGAAAAACAAAATGCCAATTTTGTATC
AATACCAAAAAAGGTATCAATAAAAGTGTACACTATCGATACTTGAAAAAAATTATCGATACCAA
GC
Found at i:40428012 original size:133 final size:132
Alignment explanation
Indices: 40427744--40428012 Score: 296
Period size: 133 Copynumber: 2.0 Consensus size: 132
40427734 AAAGGTAACA
** * *
40427744 ATATCGTATCGATACTTGATAAAACTTTGAAATTCAAAATGCCAATTTTGTATCGATACCGAAAA
1 ATATCGTATCGATACTTGATAAAACTTTGAAAAACAAAATGCCAATTTTGTATCAATACCAAAAA
* * * *
40427809 AGGTATCGATAAAAGTGTACCACTATTGATACTTGAAAAAAATTATCGATACCAAGCAAAAGGTA
66 AGGTATCAATAAAAGTGTA-CACTATCGATACTTCAAAAAAATTATCGATACCAAGCAAAAAGTA
*
40427874 TCG
130 CCG
* *
40427877 ATATCGTATCGATACTTGATAAATATTTTGAAAAACAAAATGCC-ATTTTCG-ATCAATACTAAA
1 ATATCGTATCGATACTTGATAAA-ACTTTGAAAAACAAAATGCCAATTTT-GTATCAATACCAAA
* * * **
40427940 AAAGGTATCAATAAAATTGTGA-ATCTATCGATAC-TCAACTAAATTTATCGATA-CTTGACAAA
64 AAAGGTATCAATAAAAGTGT-ACA-CTATCGATACTTCAA-AAAAATTATCGATACCAAG-CAAA
40428002 AAGTACCG
125 AAGTACCG
40428010 ATA
1 ATA
40428013 CCAAATCAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
132 6 0.05
133 89 0.78
134 19 0.17
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (132 bp):
ATATCGTATCGATACTTGATAAAACTTTGAAAAACAAAATGCCAATTTTGTATCAATACCAAAAA
AGGTATCAATAAAAGTGTACACTATCGATACTTCAAAAAAATTATCGATACCAAGCAAAAAGTAC
CG
Found at i:40432289 original size:53 final size:53
Alignment explanation
Indices: 40432218--40432323 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
40432208 GATAAGTATT
* *
40432218 ATATTAATTTAATATTAAATTGATTAAGTTTAATTATAGTTGAACTCTCTAAA
1 ATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAA
40432271 ATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAA
1 ATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAA
40432324 CTCCCCCTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (53 bp):
ATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAA
Found at i:40439848 original size:7 final size:7
Alignment explanation
Indices: 40439825--40439877 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
40439815 ATAATATATT
40439825 TAAATTA
1 TAAATTA
*
40439832 TTAA-TA
1 TAAATTA
40439838 TAAATTA
1 TAAATTA
40439845 TAAATTA
1 TAAATTA
40439852 TAAATTA
1 TAAATTA
40439859 TAAACTTA
1 TAAA-TTA
40439867 TTAAAATTA
1 -T-AAATTA
40439876 TA
1 TA
40439878 TTAATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.12
7 24 0.60
8 4 0.10
9 4 0.10
10 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (7 bp):
TAAATTA
Found at i:40447303 original size:28 final size:29
Alignment explanation
Indices: 40447236--40447301 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
40447226 TTTGGAACAA
*
40447236 GACTAAAATTGACTAATTTGAAAAGTATAAT
1 GACTAAAATTGACTAAATT--AAAGTATAAT
*
40447267 -ATTAAAATTGACTAAATTAAAGTATAAT
1 GACTAAAATTGACTAAATTAAAGTATAAT
40447295 GACTAAA
1 GACTAAA
40447302 TTCACAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 10 0.32
29 5 0.16
30 16 0.52
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.32
Consensus pattern (29 bp):
GACTAAAATTGACTAAATTAAAGTATAAT
Found at i:40453959 original size:19 final size:19
Alignment explanation
Indices: 40453914--40453959 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
40453904 CCATAGTCGT
* *
40453914 TTTTTAAAAATAAACTAAG
1 TTTTTAAAAATAAACAAAA
*
40453933 TCTTTTAAAGATAAACAAAA
1 T-TTTTAAAAATAAACAAAA
40453953 TTTTTAA
1 TTTTTAA
40453960 TTTGACTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (19 bp):
TTTTTAAAAATAAACAAAA
Found at i:40458563 original size:31 final size:31
Alignment explanation
Indices: 40458528--40458608 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
40458518 TGACGTTTTC
40458528 ATCTTGTTTCAACATCTTCCCAATCTATTGA
1 ATCTTGTTTCAACATCTTCCCAATCTATTGA
* *
40458559 ATCTTGCTTCAACATCTTCCTAATCTATTGA
1 ATCTTGTTTCAACATCTTCCCAATCTATTGA
40458590 ATCTTGTTTCAACATCTTC
1 ATCTTGTTTCAACATCTTC
40458609 TAAATATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.25, C:0.26, G:0.06, T:0.43
Consensus pattern (31 bp):
ATCTTGTTTCAACATCTTCCCAATCTATTGA
Found at i:40461736 original size:21 final size:20
Alignment explanation
Indices: 40461711--40461749 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40461701 TACTTTTAAA
40461711 TATCAATCAACATTCTAAATT
1 TATCAATCAACA-TCTAAATT
* *
40461732 TATCATTTAACATCTAAA
1 TATCAATCAACATCTAAA
40461750 ACCACAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (20 bp):
TATCAATCAACATCTAAATT
Found at i:40466096 original size:15 final size:17
Alignment explanation
Indices: 40466065--40466096 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
40466055 TTCTAATACG
40466065 TTAAACTTTACTTATGA
1 TTAAACTTTACTTATGA
40466082 TTAAA-TTTA-TTATGA
1 TTAAACTTTACTTATGA
40466097 AAAAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAAACTTTACTTATGA
Found at i:40466441 original size:30 final size:31
Alignment explanation
Indices: 40466407--40466469 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
40466397 TACAGTTAAA
*
40466407 TTATCACTTT-GATACATGTACTTT-ATTTTG
1 TTATCACTTTGGACAC-TGTACTTTCATTTTG
* *
40466437 TTATCAGTTTGGCCACTGTACTTTCATTTTG
1 TTATCACTTTGGACACTGTACTTTCATTTTG
40466468 TT
1 TT
40466470 TGGAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (31 bp):
TTATCACTTTGGACACTGTACTTTCATTTTG
Found at i:40467915 original size:27 final size:27
Alignment explanation
Indices: 40467877--40467932 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
40467867 TTAGACTTAA
* * *
40467877 TTAAAAATTAAGGTGAATATTAC-TTT
1 TTAAAAAATAAGGTCAATACTACATTT
40467903 TTAAAAGAATAAGGTCAATACTACATTT
1 TTAAAA-AATAAGGTCAATACTACATTT
40467931 TT
1 TT
40467933 TATTTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (27 bp):
TTAAAAAATAAGGTCAATACTACATTT
Found at i:40470092 original size:45 final size:44
Alignment explanation
Indices: 40470028--40470116 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 44
40470018 TTGTTTGATT
* *
40470028 TCCTGCTGATAGCCATTCTCTTTTGGGATTGCAAATAAGAGTTG
1 TCCTGCTGATAGCCATTCTCATCTGGGATTGCAAATAAGAGTTG
40470072 NTCCTGCTGATAGCCATTCTCATCTGGGATTGCAAATAAGAGTTG
1 -TCCTGCTGATAGCCATTCTCATCTGGGATTGCAAATAAGAGTTG
40470117 AGAGGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (44 bp):
TCCTGCTGATAGCCATTCTCATCTGGGATTGCAAATAAGAGTTG
Found at i:40471083 original size:20 final size:21
Alignment explanation
Indices: 40471051--40471106 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
40471041 TATATATGAA
* * *
40471051 AATTTGGAATTTTTTATAAAT
1 AATTTGTATTTTTTTAAAAAT
*
40471072 ATTTTG-ATTTTTTTAAAAAT
1 AATTTGTATTTTTTTAAAAAT
40471092 AATTTGTATTTTTTT
1 AATTTGTATTTTTTT
40471107 TGTTGAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
AATTTGTATTTTTTTAAAAAT
Found at i:40471314 original size:61 final size:61
Alignment explanation
Indices: 40471153--40471348 Score: 225
Period size: 61 Copynumber: 3.2 Consensus size: 61
40471143 TTTATATAAC
* * *
40471153 ATTTGGTACCTAAACTTGACACTTTTTTTCCTAATTTGGTACCTAAACTCTTTTTT-GGCCCA
1 ATTTGGTACCTGAACTTGACA-TTTTTTTCCTAATTTGATACCTAAACT-TTTTTTAGGCTCA
* * *
40471215 ATCTGTGTTACCTGAACTTTACACTTTTTT-CTAATTTGATACCTAAACTTTTTTTAGGCTCA
1 AT-T-TGGTACCTGAACTTGACATTTTTTTCCTAATTTGATACCTAAACTTTTTTTAGGCTCA
* * * * ** *
40471277 ATTTGGTACTTGAACTTGGCATTTTTTTCCTAATTTGACACATATCCTTTTTTTAGGTTCA
1 ATTTGGTACCTGAACTTGACATTTTTTTCCTAATTTGATACCTAAACTTTTTTTAGGCTCA
40471338 ATTTGGTACCT
1 ATTTGGTACCT
40471349 AAATTTATTA
Statistics
Matches: 113, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
60 20 0.18
61 44 0.39
62 27 0.24
63 7 0.06
64 15 0.13
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.46
Consensus pattern (61 bp):
ATTTGGTACCTGAACTTGACATTTTTTTCCTAATTTGATACCTAAACTTTTTTTAGGCTCA
Found at i:40471587 original size:22 final size:22
Alignment explanation
Indices: 40471545--40471587 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40471535 AAATAATATT
*
40471545 TTAATTAATAACTAAATTAATA
1 TTAATTAATAACTAAAGTAATA
40471567 TTAATTAA-AACTAAAAGTAAT
1 TTAATTAATAACT-AAAGTAAT
40471588 TGAACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAATTAATAACTAAAGTAATA
Found at i:40471835 original size:92 final size:90
Alignment explanation
Indices: 40471738--40471921 Score: 228
Period size: 92 Copynumber: 2.0 Consensus size: 90
40471728 AGAAAAAAGA
** *
40471738 TTAGGTACCAAATTAGGAAAAAGAGTCGTGTTCAGG-TACCAAATTGGACCCCTAAAAAT-TTTA
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTT-AGGATACCAAATTGGA--CCAAAAAATATTTA
40471801 AGTACCAAATTAAGAAAAAAATGTCAAGT
63 AGTACC-AATTAAGAAAAAAATGTCAAGT
* * *
40471830 TTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTGGATACCAAATTGGACCAAAAAATAGTTTAGG
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTAGGATACCAAATTGGACCAAAAAATA-TTTAAG
* **
40471895 TACCAATTAGGAAAAAGTTGTCAAGT
65 TACCAATTAAGAAAAAAATGTCAAGT
40471921 T
1 T
40471922 CAAGTATCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
90 8 0.10
91 22 0.28
92 50 0.62
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTAGGATACCAAATTGGACCAAAAAATATTTAAGT
ACCAATTAAGAAAAAAATGTCAAGT
Found at i:40471857 original size:31 final size:31
Alignment explanation
Indices: 40471797--40471921 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
40471787 CCCTAAAAAT
* * *
40471797 TTTAAGTACCAAATTAAGAAAAAAATGTCAAG
1 TTTAGGTACCAAATT-AGGAAAAAGTGTCAAG
40471829 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
1 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
**
40471860 TTT-GGATACCAAATT-GGACCAAAA-AAT--AG
1 TTTAGG-TACCAAATTAGGA--AAAAGTGTCAAG
40471889 TTTAGGTACC-AATTAGGAAAAAGTTGTCAAG
1 TTTAGGTACCAAATTAGGAAAAAG-TGTCAAG
40471920 TT
1 TT
40471922 CAAGTATCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
27 4 0.05
28 4 0.05
29 13 0.17
30 7 0.09
31 31 0.40
32 18 0.23
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.27
Consensus pattern (31 bp):
TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
Found at i:40477706 original size:52 final size:52
Alignment explanation
Indices: 40477633--40477735 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
40477623 AATTTATACA
40477633 TTTTTGAGATCGGTGCGTTGTATTCTAGCTAGCCCGTACCTCAATTTCTGAG
1 TTTTTGAGATCGGTGCGTTGTATTCTAGCTAGCCCGTACCTCAATTTCTGAG
* *
40477685 TTTTTGAGATCGTTGCTTTGTATTCTAGCTAGCCCGTACCTCAATTTCTGA
1 TTTTTGAGATCGGTGCGTTGTATTCTAGCTAGCCCGTACCTCAATTTCTGA
40477736 AAATTTTGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (52 bp):
TTTTTGAGATCGGTGCGTTGTATTCTAGCTAGCCCGTACCTCAATTTCTGAG
Found at i:40478533 original size:23 final size:23
Alignment explanation
Indices: 40478484--40478537 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40478474 CAGCTTGTAT
* * * *
40478484 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTCTCAACTCAACA
*
40478507 GAGCTTACCGTCTCAACTCAATA
1 GAGCTTACCGTCTCAACTCAACA
40478530 GAGCTTAC
1 GAGCTTAC
40478538 TATTTATCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (23 bp):
GAGCTTACCGTCTCAACTCAACA
Found at i:40478708 original size:191 final size:191
Alignment explanation
Indices: 40478384--40478764 Score: 699
Period size: 191 Copynumber: 2.0 Consensus size: 191
40478374 ATACTGAGCT
*
40478384 CGTTTGAACTTTAGAAAATCGTCGGATACGAGTGACTTGTCACTAGGGTTACCGTTTGGTCGAGC
1 CGTTTGAACTTTAAAAAATCGTCGGATACGAGTGACTTGTCACTAGGGTTACCGTTTGGTCGAGC
* *
40478449 TCCTGCATTTGTTGTAGACTCACCACAGCTTGTATGAGCTTACCGTTTCAGCTCTACGGAGCTTA
66 TCCTGCATTTGTTGCAGACTCACCACAACTTGTATGAGCTTACCGTTTCAGCTCTACGGAGCTTA
40478514 CCGTCTCAACTCAATAGAGCTTACTATTTATCAGCTCGGAATGAGCTTACCGATCATGGCC
131 CCGTCTCAACTCAATAGAGCTTACTATTTATCAGCTCGGAATGAGCTTACCGATCATGGCC
40478575 CGTTTGAACTTTAAAAAATCGTCGGATACGAGTGACTTGTCACTAGGGTTACCGTTTGGTCGAGC
1 CGTTTGAACTTTAAAAAATCGTCGGATACGAGTGACTTGTCACTAGGGTTACCGTTTGGTCGAGC
* *
40478640 TCCTGGATTTGTTGCGGACTCACCACAACTTGTATGAGCTTACCGTTTCAGCTCTACGGAGCTTA
66 TCCTGCATTTGTTGCAGACTCACCACAACTTGTATGAGCTTACCGTTTCAGCTCTACGGAGCTTA
* *
40478705 CCGTCTCAGCTCAATAGAGCTTACTGTTTATCAGCTCGGAATGAGCTTACCGATCATGGC
131 CCGTCTCAACTCAATAGAGCTTACTATTTATCAGCTCGGAATGAGCTTACCGATCATGGC
40478765 TCGAAAGAGC
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
191 183 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (191 bp):
CGTTTGAACTTTAAAAAATCGTCGGATACGAGTGACTTGTCACTAGGGTTACCGTTTGGTCGAGC
TCCTGCATTTGTTGCAGACTCACCACAACTTGTATGAGCTTACCGTTTCAGCTCTACGGAGCTTA
CCGTCTCAACTCAATAGAGCTTACTATTTATCAGCTCGGAATGAGCTTACCGATCATGGCC
Found at i:40478724 original size:23 final size:23
Alignment explanation
Indices: 40478675--40478728 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
40478665 CAACTTGTAT
* * *
40478675 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTCTCAGCTCAACA
*
40478698 GAGCTTACCGTCTCAGCTCAATA
1 GAGCTTACCGTCTCAGCTCAACA
40478721 GAGCTTAC
1 GAGCTTAC
40478729 TGTTTATCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (23 bp):
GAGCTTACCGTCTCAGCTCAACA
Found at i:40493561 original size:36 final size:36
Alignment explanation
Indices: 40493519--40493604 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
40493509 AGCTAATTAT
*
40493519 CTAACAGACAAATTGAAAATAATTAAAC-AGCACCAG
1 CTAACAG-CAAATTGAAAATAATTAAACAAACACCAG
* * * *
40493555 CTAACAGCTAATTGATAATGATTAAACAAACACTAG
1 CTAACAGCAAATTGAAAATAATTAAACAAACACCAG
*
40493591 CTAACAGCTAATTG
1 CTAACAGCAAATTG
40493605 GCATACCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 17 0.39
36 27 0.61
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (36 bp):
CTAACAGCAAATTGAAAATAATTAAACAAACACCAG
Found at i:40497277 original size:18 final size:18
Alignment explanation
Indices: 40497254--40497291 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40497244 TTAGGATTTT
*
40497254 TTTTTGTCTCAAAAGTGC
1 TTTTTGTCCCAAAAGTGC
*
40497272 TTTTTGTCCCAAATGTGC
1 TTTTTGTCCCAAAAGTGC
40497290 TT
1 TT
40497292 CTTATAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (18 bp):
TTTTTGTCCCAAAAGTGC
Found at i:40500156 original size:31 final size:31
Alignment explanation
Indices: 40500108--40500187 Score: 119
Period size: 31 Copynumber: 2.5 Consensus size: 31
40500098 AAAAATTTAG
40500108 CTTTTAAGGATCC-AAAATTTATTTTA-CCAA
1 CTTTTAAGGA-CCTAAAATTTATTTTATCCAA
40500138 CTTTTAAAGGACCTAAAATTTATTTTATCCAA
1 CTTTT-AAGGACCTAAAATTTATTTTATCCAA
40500170 CTTTTAAGGAACCTAAAA
1 CTTTTAAGG-ACCTAAAA
40500188 CCCTATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 7 0.15
31 22 0.48
32 17 0.37
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (31 bp):
CTTTTAAGGACCTAAAATTTATTTTATCCAA
Found at i:40501109 original size:9 final size:9
Alignment explanation
Indices: 40500997--40501111 Score: 54
Period size: 9 Copynumber: 12.0 Consensus size: 9
40500987 AAAAATCCAA
40500997 AAAAATA-T
1 AAAAATATT
40501005 AAAAACTATTTT
1 AAAAA-TA--TT
*
40501017 AAAAAAATT
1 AAAAATATT
40501026 AAAAATCATT
1 AAAAAT-ATT
**
40501036 AAAATTATAAA
1 AAAA--ATATT
40501047 AAAAATATT
1 AAAAATATT
* *
40501056 AAACTATTTTT
1 AAA--AATATT
40501067 AAAAA-ATTT
1 AAAAATA-TT
**
40501076 AAAACCATT
1 AAAAATATT
* *
40501085 AAAATTATA
1 AAAAATATT
40501094 AAAAATATT
1 AAAAATATT
40501103 AAAAATATT
1 AAAAATATT
40501112 TTTTAATATA
Statistics
Matches: 80, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
8 5 0.06
9 46 0.57
10 8 0.10
11 13 0.16
12 8 0.10
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATATT
Found at i:40501115 original size:49 final size:49
Alignment explanation
Indices: 40500995--40501128 Score: 166
Period size: 49 Copynumber: 2.7 Consensus size: 49
40500985 TAAAAAATCC
* * *
40500995 AAAAAAATA-TAAAAACTATTTTAAAAAAATTAAAAATCATTAAAATTAT
1 AAAAAAATATTAAAAA-TATTTTTAAAAAATTTAAAACCATTAAAATTAT
*
40501044 AAAAAAAATATT-AAACTATTTTTAAAAAATTTAAAACCATTAAAATTAT
1 -AAAAAAATATTAAAAATATTTTTAAAAAATTTAAAACCATTAAAATTAT
* *
40501093 -AAAAAATATTAAAAATATTTTTTAATATATTTAAAA
1 AAAAAAATATTAAAAATA-TTTTTAAAAAATTTAAAA
40501129 TTTTAAAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
47 10 0.14
48 5 0.07
49 46 0.62
50 12 0.16
51 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (49 bp):
AAAAAAATATTAAAAATATTTTTAAAAAATTTAAAACCATTAAAATTAT
Found at i:40512016 original size:23 final size:22
Alignment explanation
Indices: 40511988--40512034 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
40511978 AAGCCACCCC
* * *
40511988 TTTTATTTTATTTCTTTATTATT
1 TTTTATATAATTTATTT-TTATT
40512011 TTTTATATAATTTATTTTTATT
1 TTTTATATAATTTATTTTTATT
40512033 TT
1 TT
40512035 ACTAGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATATAATTTATTTTTATT
Found at i:40512225 original size:27 final size:26
Alignment explanation
Indices: 40512191--40512257 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
40512181 TTTTTTTCGA
* *
40512191 TTTATTTTTTATTTT-TATTTATTTATC
1 TTTATTTTTTATTTTGT-TTTAGTT-GC
* *
40512218 TTTCTTTTTAATTTTGTTTTAGTTGC
1 TTTATTTTTTATTTTGTTTTAGTTGC
40512244 TTTATTTTTTATTT
1 TTTATTTTTTATTT
40512258 ATTTTCTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 13 0.39
27 19 0.58
28 1 0.03
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTATTTTTTATTTTGTTTTAGTTGC
Found at i:40513262 original size:15 final size:16
Alignment explanation
Indices: 40513233--40513266 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40513223 CTTATTGTAA
*
40513233 AAAAAAAGAGCAAAAG
1 AAAAAAAGAGAAAAAG
40513249 AAAAAAAGA-AAAAAG
1 AAAAAAAGAGAAAAAG
40513264 AAA
1 AAA
40513267 TCGAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:40518334 original size:38 final size:38
Alignment explanation
Indices: 40518279--40518390 Score: 215
Period size: 38 Copynumber: 2.9 Consensus size: 38
40518269 ACTCAGATAT
40518279 AGTCATATTCCCCTATTTGAGTTCTAAAAATTCTTTAC
1 AGTCATATTCCCCTATTTGAGTTCTAAAAATTCTTTAC
*
40518317 AGTCATATTCCCTTATTTGAGTTCTAAAAATTCTTTAC
1 AGTCATATTCCCCTATTTGAGTTCTAAAAATTCTTTAC
40518355 AGTCATATTCCCCTATTTGAGTTCTAAAAATTCTTT
1 AGTCATATTCCCCTATTTGAGTTCTAAAAATTCTTT
40518391 CTTTTTCTGA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.44
Consensus pattern (38 bp):
AGTCATATTCCCCTATTTGAGTTCTAAAAATTCTTTAC
Found at i:40521486 original size:24 final size:24
Alignment explanation
Indices: 40521458--40521506 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40521448 CATTTTCTAC
40521458 CATAAATTTCAAAATTTTACCATA
1 CATAAATTTCAAAATTTTACCATA
40521482 CATAAATTTCAAAATTTTACCATA
1 CATAAATTTCAAAATTTTACCATA
40521506 C
1 C
40521507 TCATCCATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (24 bp):
CATAAATTTCAAAATTTTACCATA
Found at i:40526234 original size:17 final size:16
Alignment explanation
Indices: 40526179--40526235 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
40526169 TCGTAATTAT
40526179 GTTA-TTTAGAATTTGA
1 GTTATTTTA-AATTTGA
* *
40526195 ATTATTTTAAATTTAA
1 GTTATTTTAAATTTGA
**
40526211 GAGATTTCTAAATTTGA
1 GTTATTT-TAAATTTGA
40526228 GTTATTTT
1 GTTATTTT
40526236 CGTTTAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (16 bp):
GTTATTTTAAATTTGA
Found at i:40528273 original size:18 final size:19
Alignment explanation
Indices: 40528247--40528286 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
40528237 CCCGAAGGTG
*
40528247 AAAATGTGA-AGTTGGTTA
1 AAAAGGTGATAGTTGGTTA
*
40528265 AAAAGGTGATGGTTGGTTA
1 AAAAGGTGATAGTTGGTTA
40528284 AAA
1 AAA
40528287 GGATACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (19 bp):
AAAAGGTGATAGTTGGTTA
Found at i:40529681 original size:49 final size:43
Alignment explanation
Indices: 40529574--40529774 Score: 154
Period size: 43 Copynumber: 4.5 Consensus size: 43
40529564 TGTTTCTAAA
*
40529574 ATGACCTTTAGCGGCGCTTTTACCACAAACGCCGTTAAAGACC
1 ATGACCTTTAGCGGCGCTTATACCACAAACGCCGTTAAAGACC
* *
40529617 ATGACTTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGGTAAAGACC
1 ATGACCTTTAGCGGCGCTTATACCACAAACGCCG-T-----TAAAGACC
* * * * *
40529666 ATGACCTTTAGCGGCGCATT-T-CTAAAAAACACCGCTAAAGGCC
1 ATGACCTTTAGCGGCGC-TTATAC-CACAAACGCCGTTAAAGACC
* * * * * * *
40529709 ACGATCTTTAGCGACGCTTATCCCAAAAACGCCATTAAAAACC
1 ATGACCTTTAGCGGCGCTTATACCACAAACGCCGTTAAAGACC
* * *
40529752 ACGACCTTTAGCGACCCTTATAC
1 ATGACCTTTAGCGGCGCTTATAC
40529775 GCCACAATAA
Statistics
Matches: 127, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
42 2 0.02
43 87 0.69
44 2 0.02
48 1 0.01
49 33 0.26
50 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGCTTATACCACAAACGCCGTTAAAGACC
Found at i:40529731 original size:92 final size:91
Alignment explanation
Indices: 40529574--40529741 Score: 223
Period size: 92 Copynumber: 1.8 Consensus size: 91
40529564 TGTTTCTAAA
* * * * *
40529574 ATGACCTTTAGCGGCGCTTTTACCACAAACGCCGTTAAAGACCATGACTTTTAGCGGCGCTTATC
1 ATGACCTTTAGCGGCGCTTTTA-CAAAAACACCGCTAAAGACCACGACTTTTAGCGACGCTTATC
*
40529639 CCACAAACGCCGCTAAAGGTAAAGACC
65 CCAAAAACGCCGCTAAAGGTAAAGACC
*
40529666 ATGACCTTTAGCGGCGCATTTCTA-AAAAACACCGCTAAAGGCCACGA-TCTTTAGCGACGCTTA
1 ATGACCTTTAGCGGCGC-TTT-TACAAAAACACCGCTAAAGACCACGACT-TTTAGCGACGCTTA
40529729 TCCCAAAAACGCC
63 TCCCAAAAACGCC
40529742 ATTAAAAACC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
91 1 0.02
92 60 0.91
93 3 0.05
94 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (91 bp):
ATGACCTTTAGCGGCGCTTTTACAAAAACACCGCTAAAGACCACGACTTTTAGCGACGCTTATCC
CAAAAACGCCGCTAAAGGTAAAGACC
Found at i:40534434 original size:23 final size:23
Alignment explanation
Indices: 40534390--40534435 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40534380 AATGTTCGTA
* *
40534390 TTTTTTATTAATTTTTTATTTTG
1 TTTTTTATAAATTATTTATTTTG
40534413 TTTTTTATAAATTGATTT-TTTTG
1 TTTTTTATAAATT-ATTTATTTTG
40534436 CGGCGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (23 bp):
TTTTTTATAAATTATTTATTTTG
Found at i:40535125 original size:7 final size:7
Alignment explanation
Indices: 40535115--40535139 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40535105 ACTAACTCTT
40535115 AACCCCA
1 AACCCCA
40535122 AACCCCA
1 AACCCCA
40535129 AACCCCA
1 AACCCCA
40535136 AACC
1 AACC
40535140 ACTAACCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:40535219 original size:82 final size:82
Alignment explanation
Indices: 40535130--40535291 Score: 254
Period size: 82 Copynumber: 2.0 Consensus size: 82
40535120 CAAACCCCAA
* *
40535130 ACCCCAAA-CCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
1 ACCCCAAATCC-CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
40535194 ATCATAAACCCTAACCCG
65 ATCATAAACCCTAACCCG
* * *
40535212 ACCCCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACATTAATTAATCTAAA
1 ACCCCAAATCCCTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
*
40535277 TCCTAAACCCTAACC
66 TCATAAACCCTAACC
40535292 TAACACTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
82 71 0.97
83 2 0.03
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (82 bp):
ACCCCAAATCCCTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
TCATAAACCCTAACCCG
Found at i:40535314 original size:82 final size:82
Alignment explanation
Indices: 40535133--40535316 Score: 228
Period size: 82 Copynumber: 2.2 Consensus size: 82
40535123 ACCCCAAACC
* *
40535133 CCAAACCACT-AACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATC
1 CCAAATCACTAAACC-CTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATC
* *
40535197 ATAAACCCTAACCCGACC
65 ATAAACCCTAACCCAACA
* * * * * *
40535215 CCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACATTAATTAATCTAAATCC
1 CCAAATCACTAAACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATCA
*
40535280 TAAACCCTAACCTAACA
66 TAAACCCTAACCCAACA
*
40535297 CTAAATCTAC-AAACCCTAAA
1 CCAAATC-ACTAAACCCTAAA
40535317 TCCCTACCTC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
82 82 0.95
83 4 0.05
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.26
Consensus pattern (82 bp):
CCAAATCACTAAACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATCA
TAAACCCTAACCCAACA
Found at i:40535395 original size:14 final size:15
Alignment explanation
Indices: 40535378--40535409 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
40535368 CTTAAATCAG
40535378 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
40535392 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
40535407 AAT
1 AAT
40535410 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:40535825 original size:41 final size:41
Alignment explanation
Indices: 40535765--40536093 Score: 430
Period size: 41 Copynumber: 8.2 Consensus size: 41
40535755 AATGTTCAAT
40535765 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40535806 TAGAGATCTAAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * * *
40535847 TAAAGATCTAAGCATTAGCGGCGCTTTTTTAAAAATGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40535888 TAAAGATCTGAGTATTAGCGGCGCTTTCTCAAAAATGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
40535929 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40535970 TAAAGATCTGAGCATTAGCGGCACTTTTTTC-AAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGC-TTTCTCAAAAACGCCGC
*
40536011 T--A-A----AG-A-TAGCGGCGCTTT-TTAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40536042 TAAAGATCTGAGCATTAGCGGCACTTTTTTTC-AAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGC--TTTCTCAAAAACGCCGC
40536084 TAAAGATCTG
1 TAAAGATCTG
40536094 TAAGGTACAA
Statistics
Matches: 256, Mismatches: 18, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
30 1 0.00
31 14 0.05
32 8 0.03
33 2 0.01
34 3 0.01
38 3 0.01
39 2 0.01
40 8 0.03
41 186 0.73
42 28 0.11
43 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
Found at i:40536036 original size:31 final size:32
Alignment explanation
Indices: 40535985--40536048 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
40535975 ATCTGAGCAT
*
40535985 TAGCGGCACTTTTTTCAAAACGCCGCTAAAGA
1 TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
*
40536017 TAGCGGCGC-TTTTTAAAAACGCCGCTAAAGA
1 TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
40536048 T
1 T
40536049 CTGAGCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (32 bp):
TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
Found at i:40536062 original size:72 final size:74
Alignment explanation
Indices: 40535944--40536090 Score: 271
Period size: 72 Copynumber: 2.0 Consensus size: 74
40535934 ATCTGAGCAT
40535944 TAGCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCAC-TTTTTTCAAAACGC
1 TAGCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTTCAAAACGC
40536008 CGCTAAAGA
66 CGCTAAAGA
*
40536017 TAGCGGCGCTTT-TTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTTCAAAACGC
1 TAGCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTTCAAAACGC
40536081 CGCTAAAGA
66 CGCTAAAGA
40536090 T
1 T
40536091 CTGTAAGGTA
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 36 0.50
73 36 0.50
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (74 bp):
TAGCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTTCAAAACGC
CGCTAAAGA
Found at i:40536176 original size:40 final size:40
Alignment explanation
Indices: 40536126--40536261 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
40536116 GGGCTTAGAC
*
40536126 TTTTT-GCGGCGTTTTTCTAAAAAACGCCGCTAATGCT-AA
1 TTTTTAGCGGCGTTTTTCT-AAAAACGCCGCTAATGCTCGA
* * * *
40536165 TTTTTAGCGGCGCTTTCCTAGAAACGCTGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCTAAAAACGCCGCTAATGCTCGA
* * * *
40536205 TCTTTAGCGGCGTTTTACGT-AAAGCGCCACTAATGCTCGA
1 TTTTTAGCGGCGTTTTTC-TAAAAACGCCGCTAATGCTCGA
*
40536245 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
40536262 TGTCCAAACG
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 21 0.27
40 57 0.72
41 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCTAAAAACGCCGCTAATGCTCGA
Found at i:40538943 original size:44 final size:43
Alignment explanation
Indices: 40538850--40539184 Score: 203
Period size: 44 Copynumber: 7.7 Consensus size: 43
40538840 GATGCGATCT
* * * *
40538850 GCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCC
1 GCTCCACTACAACTTCAGGGAGATAAGAT-TATTACTTCAATCC
* * *
40538894 GCTCCACTACAGCCTT-AGGGAGATATGATTATTGACTTCAATCT
1 GCTCCACTACA-ACTTCAGGGAGATAAGATTATT-ACTTCAATCC
* * * *
40538938 GCTCCACTGCAACTTCAGGGAGATAAGATT-TGCTTCTTCGATCT
1 GCTCCACTACAACTTCAGGGAGATAAGATTAT--TACTTCAATCC
* *** * * *
40538982 GCCCCACTGTGACTTCAGGGGGATAAGATGTATTTAC-TCAGTCT
1 GCTCCACTACAACTTCAGGGAGATAAGAT-TA-TTACTTCAATCC
* * * ** * ** *
40539026 GCTCCACTGCAACCTCAGGGAAATAAGA-CCTGA-GGCGATCC
1 GCTCCACTACAACTTCAGGGAGATAAGATTATTACTTCAATCC
* * * * * *
40539067 ACTCTACTGCAACTTCAGAGAGATAAGATCGATTACTTTAATCC
1 GCTCCACTACAACTTCAGGGAGATAAGAT-TATTACTTCAATCC
* * *
40539111 GCTCCACTACAACCTCAGGGAGATAGGATTATTGACTTCAATCT
1 GCTCCACTACAACTTCAGGGAGATAAGATTATT-ACTTCAATCC
* * *
40539155 ACTCCACTGCAACCTCAGGGAGATAAGATT
1 GCTCCACTACAACTTCAGGGAGATAAGATT
40539185 TGCTTCTTCC
Statistics
Matches: 222, Mismatches: 56, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
41 28 0.13
43 13 0.06
44 173 0.78
45 7 0.03
47 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
GCTCCACTACAACTTCAGGGAGATAAGATTATTACTTCAATCC
Found at i:40539118 original size:129 final size:129
Alignment explanation
Indices: 40538943--40539182 Score: 295
Period size: 129 Copynumber: 1.9 Consensus size: 129
40538933 AATCTGCTCC
* * * * * *** * *
40538943 ACTGCAACTTCAGGGAGATAAGATTTGCTTCTTCGATCTGCCCCACTGTGACTTCAGGGGGATAA
1 ACTGCAACTTCAGAGAGATAAGATTCGATTCTTCAATCCGCCCCACTACAACCTCAGGGAGATAA
* * *
40539008 GATGTATTTAC-TCAGTCTGCTCCACTGCAACCTCAGGGAAATAAGACCTGAGGCGATCCACTCT
66 GAT-TATTGACTTCAATCTACTCCACTGCAACCTCAGGGAAATAAGACCTGAGGCGATCCACTCT
* *
40539072 ACTGCAACTTCAGAGAGATAAGA-TCGATTACTTTAATCCGCTCCACTACAACCTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTCGATT-CTTCAATCCGCCCCACTACAACCTCAGGGAGATA
* *
40539136 GGATTATTGACTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGA
65 AGATTATTGACTTCAATCTACTCCACTGCAACCTCAGGGAAATAAGA
40539183 TTTGCTTCTT
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
128 10 0.11
129 82 0.89
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (129 bp):
ACTGCAACTTCAGAGAGATAAGATTCGATTCTTCAATCCGCCCCACTACAACCTCAGGGAGATAA
GATTATTGACTTCAATCTACTCCACTGCAACCTCAGGGAAATAAGACCTGAGGCGATCCACTCT
Found at i:40539495 original size:87 final size:87
Alignment explanation
Indices: 40539347--40539760 Score: 567
Period size: 87 Copynumber: 4.7 Consensus size: 87
40539337 GCAATCGAGG
** * *
40539347 GGAGGCAAGGCTTTGTTTTTTATCTGTTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTT
* *
40539412 AACCAGCTCCATTGAAACCGAT
66 AACCAGCTCCACTGCAACCGAT
*
40539434 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGACAAGATCTGCTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTT
* * *
40539499 AACCCGCTCTACTGGAACCGAT
66 AACCAGCTCCACTGCAACCGAT
* * * * *
40539521 GGAGGCAAGGCTTTGTTTTTGATCTGCTCCACTGTCAATGTAGGAATGCAAGATCTGCTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTT
40539586 AACCAGCTCCACTGCAACCGAT
66 AACCAGCTCCACTGCAACCGAT
* * ** *
40539608 GGAGGCAAGGCTTTGTTTTCAATCTGCTTCGTTGTCAATGCAAAAAGGCAAGATCTGCTATCTTC
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTT
* * *
40539673 AACCTGCTCCACTGCAACCAAG
66 AACCAGCTCCACTGCAACCGAT
* * * *
40539695 GGAGGCAAGGCTTTGTTTCTTCGATCTGCTTCGTTGTCAATACAAGAAGGCAAGATCTACTATCT
1 GGAGGCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCT
40539760 T
64 T
40539761 CACTGATCTG
Statistics
Matches: 290, Mismatches: 35, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
87 245 0.84
88 2 0.01
89 43 0.15
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (87 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTT
AACCAGCTCCACTGCAACCGAT
Found at i:40539761 original size:45 final size:45
Alignment explanation
Indices: 40539625--40539762 Score: 111
Period size: 45 Copynumber: 3.1 Consensus size: 45
40539615 AGGCTTTGTT
* * *
40539625 TTCAATCTGCTTCGTTGTCAATGCAAAAAGGCAAGATCTGCTATC
1 TTCAATCTGCTTCGTTGTCAATACAAGAAGGCAAGATCTACTATC
* * ** * * * ** *
40539670 TTCAACCTGCTCCACTG-CAA-CCAAGGGAGGCAAG-GCTTTGTTTC
1 TTCAATCTGCTTCGTTGTCAATACAA-GAAGGCAAGATC-TACTATC
*
40539714 TTCGATCTGCTTCGTTGTCAATACAAGAAGGCAAGATCTACTATC
1 TTCAATCTGCTTCGTTGTCAATACAAGAAGGCAAGATCTACTATC
40539759 TTCA
1 TTCA
40539763 CTGATCTGTT
Statistics
Matches: 65, Mismatches: 23, Indels: 10
0.66 0.23 0.10
Matches are distributed among these distances:
43 4 0.06
44 26 0.40
45 31 0.48
46 4 0.06
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
TTCAATCTGCTTCGTTGTCAATACAAGAAGGCAAGATCTACTATC
Found at i:40541957 original size:17 final size:18
Alignment explanation
Indices: 40541919--40541958 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
40541909 TCATCTAGGT
40541919 TTTTCTCTTTTTCGTTC-
1 TTTTCTCTTTTTCGTTCA
* *
40541936 TTTTTTCTTTTTCTTTCA
1 TTTTCTCTTTTTCGTTCA
40541954 TTTTC
1 TTTTC
40541959 ATTTTGACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTCTCTTTTTCGTTCA
Done.