Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 48 of 208
Found at i:13303919 original size:69 final size:69
Alignment explanation
Indices: 13303795--13303925 Score: 181
Period size: 69 Copynumber: 1.9 Consensus size: 69
13303785 AGAGGTTTAG
* * *
13303795 GGTGTAAGACTACAGTTTGGCTATGGAAACCAATAGAGTCCGCCGAGACAATAAACATGAGAATT
1 GGTGTAAGACTACAGCTCGGCTATGGAAACCAATAGAGTCCGCCAAGACAATAAACATGAGAATT
13303860 ATGA
66 ATGA
* * * * * *
13303864 GGTGTAAGACTATAGCTCGGCTATGGCAACCAATGGAGTCTGCCAATACATTAAACATGAGA
1 GGTGTAAGACTACAGCTCGGCTATGGAAACCAATAGAGTCCGCCAAGACAATAAACATGAGA
13303926 CCTGATGGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (69 bp):
GGTGTAAGACTACAGCTCGGCTATGGAAACCAATAGAGTCCGCCAAGACAATAAACATGAGAATT
ATGA
Found at i:13306355 original size:25 final size:26
Alignment explanation
Indices: 13306299--13306357 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
13306289 ATTTTACCAA
*
13306299 TGGTAAAA-TGTCAAAATGTTATTAG
1 TGGTAAAATTATCAAAATGTTATTAG
*
13306324 -GGATAAAATTATCAAAATTTTATT-G
1 TGG-TAAAATTATCAAAATGTTATTAG
13306349 TGGTAAAAT
1 TGGTAAAAT
13306358 AGGGATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 2 0.07
25 12 0.41
26 15 0.52
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.37
Consensus pattern (26 bp):
TGGTAAAATTATCAAAATGTTATTAG
Found at i:13308295 original size:11 final size:11
Alignment explanation
Indices: 13308279--13308305 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13308269 TATTTTTTAA
13308279 TTTTAAAATAC
1 TTTTAAAATAC
13308290 TTTTAAAATAC
1 TTTTAAAATAC
13308301 TTTTA
1 TTTTA
13308306 TTAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:13308378 original size:30 final size:31
Alignment explanation
Indices: 13308344--13308413 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
13308334 AATACTTCTT
13308344 TAATTTTTTAATTTTAAAAT-ATTTTTAAAA
1 TAATTTTTTAATTTTAAAATAATTTTTAAAA
***
13308374 TAATTTTTTAATTTTATTTTAATTTTTAAAA
1 TAATTTTTTAATTTTAAAATAATTTTTAAAA
*
13308405 TAAATTTTT
1 TAATTTTTT
13308414 GGTATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TAATTTTTTAATTTTAAAATAATTTTTAAAA
Found at i:13308557 original size:5 final size:5
Alignment explanation
Indices: 13308547--13308576 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13308537 TTTTTTTCTG
*
13308547 GGCCC GGCCC GACCC GGCCC GGCCC GGCCC
1 GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC
13308577 ATGAGCACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.60, G:0.37, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:13310343 original size:21 final size:22
Alignment explanation
Indices: 13310310--13310350 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13310300 AGAATTAACA
**
13310310 GTTCATCTGTAACG-ACTAGTG
1 GTTCATCCATAACGTACTAGTG
13310331 GTTCATCCATAACGTACTAG
1 GTTCATCCATAACGTACTAG
13310351 CAGCTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (22 bp):
GTTCATCCATAACGTACTAGTG
Found at i:13310535 original size:106 final size:108
Alignment explanation
Indices: 13310308--13310556 Score: 331
Period size: 106 Copynumber: 2.3 Consensus size: 108
13310298 GAAGAATTAA
* * *
13310308 CAGTTCATCTGTAACGACTAGTGGTTCATCCATAACGTACTAGCAGCTTGTCTGCAAACTTCTTT
1 CAGTTCATCTGCAACGACTAATGGTTTATCCATAACGTACTAGCAGCTTGTCTGCAAA--TC-TT
* * *
13310373 TTTTATCTAAAAATTTTGGTGGTTCATCCATAATTTTTATTACTGG
63 TTTTATCTAAAAATTCTAGTGGTTCATCCACAATTTTTATTACTGG
* * * *
13310419 CAGTTCATCTGCAACGACTAATGGTTTATCCATAACGTATTGGCAGCTTGTTTGTAAA-C-TTTT
1 CAGTTCATCTGCAACGACTAATGGTTTATCCATAACGTACTAGCAGCTTGTCTGCAAATCTTTTT
* *
13310482 TATTTGAAAATTCTAGTGGTTCATCCACAATTTTTATTACTGG
66 TATCTAAAAATTCTAGTGGTTCATCCACAATTTTTATTACTGG
**
13310525 CAGTTCATCTGCAATTACTAATGGTTTATCCA
1 CAGTTCATCTGCAACGACTAATGGTTTATCCA
13310557 CAACACAGTG
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
106 72 0.58
108 1 0.01
111 51 0.41
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (108 bp):
CAGTTCATCTGCAACGACTAATGGTTTATCCATAACGTACTAGCAGCTTGTCTGCAAATCTTTTT
TATCTAAAAATTCTAGTGGTTCATCCACAATTTTTATTACTGG
Found at i:13314463 original size:16 final size:15
Alignment explanation
Indices: 13314438--13314467 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13314428 GTTTATTTGT
13314438 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
13314453 AAAAAAGAAAAAAAA
1 AAAAAA-AAAAAAAA
13314468 AGGGCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:13314463 original size:17 final size:16
Alignment explanation
Indices: 13314438--13314469 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
13314428 GTTTATTTGT
13314438 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
13314454 AAAAAGAAAAAAAAAG
1 AAAAA-AAAAAAAAAG
13314470 GGCAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:13317320 original size:13 final size:14
Alignment explanation
Indices: 13317299--13317335 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
13317289 TCCAAGTGAG
13317299 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
13317313 AT-AAATAACTAAA
1 ATAAAATAATTAAA
13317326 ATAAAATAAT
1 ATAAAATAAT
13317336 AAATCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:13328881 original size:42 final size:43
Alignment explanation
Indices: 13328834--13328917 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
13328824 TTTTTATAAT
* *
13328834 AAACGCCGCTATAGACCATGGTCTTTCGCGGC-CTTACCCAAC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGACGCTTACCCAAC
*
13328876 AAACGCCGCTATAGGCCATGGTCTTTAGCGACGCTTACCCAA
1 AAACGCCGCTATAGACCATGGTCTTTAGCGACGCTTACCCAA
13328918 TAAATGCTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 29 0.76
43 9 0.24
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGGTCTTTAGCGACGCTTACCCAAC
Found at i:13329343 original size:21 final size:21
Alignment explanation
Indices: 13329317--13329370 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
13329307 AGCTGTTCTG
13329317 CTTCCCTCGCTGCAACCTCTA
1 CTTCCCTCGCTGCAACCTCTA
* * *
13329338 CTTCCCTCGCTGCAGCCTTTG
1 CTTCCCTCGCTGCAACCTCTA
*
13329359 CTTCTCTCGCTG
1 CTTCCCTCGCTG
13329371 TCGCATCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.07, C:0.44, G:0.15, T:0.33
Consensus pattern (21 bp):
CTTCCCTCGCTGCAACCTCTA
Found at i:13329443 original size:21 final size:21
Alignment explanation
Indices: 13329419--13329458 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13329409 TTTCGTTGAA
*
13329419 CCTCAGCTTCTCTCGCTGCTG
1 CCTCAGCTTCTCTCACTGCTG
*
13329440 CCTCTGCTTCTCTCACTGC
1 CCTCAGCTTCTCTCACTGC
13329459 CGCATCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.45, G:0.15, T:0.35
Consensus pattern (21 bp):
CCTCAGCTTCTCTCACTGCTG
Found at i:13329463 original size:87 final size:87
Alignment explanation
Indices: 13329330--13329535 Score: 256
Period size: 87 Copynumber: 2.4 Consensus size: 87
13329320 CCCTCGCTGC
* * * * *
13329330 AACCTCTA-CTTCCCTCGCTGCAGCCTTTGCTTCTCTCGCTGTCGCATCTGCTTTAAGATGCT-G
1 AACCTC-AGCTTCTCTCGCTGCTGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGATG-TAG
13329393 CTGGAGTTCTTCA-TACTTTCGTTG
64 CTGGAGTTCTTCATTACTTT-GTTG
* *
13329417 AACCTCAGCTTCTCTCGCTGCTGCCTCTGCTTCTCTCACTGCCGCATCTGTTTTAAGTTGTAGCT
1 AACCTCAGCTTCTCTCGCTGCTGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGATGTAGCT
* *
13329482 GGAGTTCTTCATTTCTTTTTTG
66 GGAGTTCTTCATTACTTTGTTG
* * *
13329504 AACCTCAGCTTCTCTCGATGTTGCCTCCGCTT
1 AACCTCAGCTTCTCTCGCTGCTGCCTCTGCTT
13329536 TAAGTTGTGT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
86 2 0.02
87 97 0.93
88 5 0.05
ACGTcount: A:0.12, C:0.31, G:0.17, T:0.39
Consensus pattern (87 bp):
AACCTCAGCTTCTCTCGCTGCTGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGATGTAGCT
GGAGTTCTTCATTACTTTGTTG
Found at i:13329466 original size:21 final size:21
Alignment explanation
Indices: 13329424--13329466 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13329414 TTGAACCTCA
* * *
13329424 GCTTCTCTCGCTGCTGCCTCT
1 GCTTCTCTCACTGCCGCATCT
13329445 GCTTCTCTCACTGCCGCATCT
1 GCTTCTCTCACTGCCGCATCT
13329466 G
1 G
13329467 TTTTAAGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.42, G:0.19, T:0.35
Consensus pattern (21 bp):
GCTTCTCTCACTGCCGCATCT
Found at i:13331656 original size:15 final size:15
Alignment explanation
Indices: 13331628--13331663 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13331618 TTAATAAAAG
*
13331628 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
13331642 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
13331657 GAAAACA
1 GAAAACA
13331664 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:13334863 original size:73 final size:73
Alignment explanation
Indices: 13334630--13334878 Score: 408
Period size: 74 Copynumber: 3.4 Consensus size: 73
13334620 ATAACTATCA
13334630 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCGTTTT
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTAT-AAAAACGAAGTCGTTTT
*
13334695 GGTTAAAAT
65 GGTTAAACT
*
13334704 TTTGTGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATACAAAACGAAGTCGTTTT
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATA-AAAACGAAGTCGTTTT
13334769 GGTTAAACT
65 GGTTAAACT
* *
13334778 TTTGCGGCGTTTTTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCCTTTTG
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
13334843 GTTAAACT
66 GTTAAACT
* * * *
13334851 TTTGTGGCGTTTTTACAATAAACGCCGC
1 TTTGCGGCGTTTGTACCAGAAACGCCGC
13334879 AAATTCGTGC
Statistics
Matches: 166, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
73 50 0.30
74 116 0.70
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (73 bp):
TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
GTTAAACT
Found at i:13336051 original size:41 final size:41
Alignment explanation
Indices: 13335959--13336052 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
13335949 GCTAGCTACA
*
13335959 AAACGCCGCTAATGCTCCGGTCTTCAGCGGCGTTTTATAAT
1 AAACGCCGCTAATGCTCCGGTCTTCAGCGGCGTTTTATAAG
* * * * *
13336000 ATATGCCGCTAATGCTGCGGTTTTTAGCGGCGCTTTT-TAAG
1 AAACGCCGCTAATGCTCCGGTCTTCAGCGGCG-TTTTATAAG
*
13336041 AAACGTCGCTAA
1 AAACGCCGCTAA
13336053 AGACCTAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCCGGTCTTCAGCGGCGTTTTATAAG
Found at i:13336068 original size:41 final size:41
Alignment explanation
Indices: 13336023--13336216 Score: 234
Period size: 41 Copynumber: 4.7 Consensus size: 41
13336013 GCTGCGGTTT
* * *
13336023 TTAGCGGCGCTTTTTAAGAAACGTCGCTAAAGACC-TAAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGT-AGCA
13336064 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
*
13336105 TTAGCGGCGCGTTGTAAAAAACGCCGCTAAAGACC-TGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGT-AGCA
* * * *
13336146 TTAGCGGCGCATAT-TAGAAAACGCTGCGAAAGACCGTAGCA
1 TTAGCGGCGC-TTTGTAAAAAACGCCGCTAAAGACCGTAGCA
* *
13336187 TTAGCGGCGATTATGT-AAAAGCGCCGCTAA
1 TTAGCGGCGCTT-TGTAAAAAACGCCGCTAA
13336217 GGGCCCCAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
40 2 0.02
41 126 0.95
42 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
Found at i:13338735 original size:35 final size:35
Alignment explanation
Indices: 13338657--13338745 Score: 96
Period size: 35 Copynumber: 2.5 Consensus size: 35
13338647 GAACTTTCAA
13338657 TTTTAAAAATTA-T-TTTTTTTCAAAATATAATTAT
1 TTTTAAAAATTATTATTTTTTTC-AAATATAATTAT
*
13338691 TTTTAAAAAATTATTATTTTGTTTC-AATTTAATT-T
1 TTTT-AAAAATTATTATTTT-TTTCAAATATAATTAT
*
13338726 CTTTTAAAAAGTATTATTTT
1 -TTTTAAAAATTATTATTTT
13338746 AAGAAAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
34 4 0.08
35 23 0.48
36 13 0.27
37 4 0.08
38 4 0.08
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (35 bp):
TTTTAAAAATTATTATTTTTTTCAAATATAATTAT
Found at i:13339599 original size:31 final size:29
Alignment explanation
Indices: 13339539--13339604 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
13339529 AAGTTGTGGA
* *
13339539 TTTAGTCATTATACTTTGATTTGATTAAT
1 TTTAGTCATTATACTTTGAATTGAGTAAT
*
13339568 TTTAGTCATTATACTTTTTGAATTGGGTAAT
1 TTTAGTCATTATAC--TTTGAATTGAGTAAT
13339599 TTTAGT
1 TTTAGT
13339605 TTTTGTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 14 0.44
31 18 0.56
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.55
Consensus pattern (29 bp):
TTTAGTCATTATACTTTGAATTGAGTAAT
Found at i:13341831 original size:6 final size:6
Alignment explanation
Indices: 13341820--13341847 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13341810 AAAATTAATT
13341820 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
13341848 GCTACAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:13348536 original size:34 final size:34
Alignment explanation
Indices: 13348425--13348536 Score: 147
Period size: 34 Copynumber: 3.3 Consensus size: 34
13348415 TTAATACTCA
13348425 ATAAGCATGACTT-TTGCTACCGTATTGATATGTT
1 ATAAGCATG-CTTATTGCTACCGTATTGATATGTT
* * * *
13348459 ATAAGCAT-ATCTACTGCTACCGTATTGATCTATT
1 ATAAGCATGCT-TATTGCTACCGTATTGATATGTT
*
13348493 ATAAGCATGCTTATTGCTACTGTATTGATATGTT
1 ATAAGCATGCTTATTGCTACCGTATTGATATGTT
13348527 ATAAGCATGC
1 ATAAGCATGC
13348537 CATATTGCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
32 1 0.02
33 1 0.02
34 63 0.95
35 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (34 bp):
ATAAGCATGCTTATTGCTACCGTATTGATATGTT
Found at i:13348661 original size:45 final size:45
Alignment explanation
Indices: 13348611--13348715 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 45
13348601 TGTTTACATC
* * *
13348611 GATTAGTGGTTTATCCACAA-CATATTAGCATCTTTTATCTGTATT
1 GATTAGTGGTTTATCCA-AACCATATTAGCAACTTTTATCTGCACT
* *
13348656 GATTAGTAGTTTATCCAAACCGTATTAGCAACTTTTATCTGCACT
1 GATTAGTGGTTTATCCAAACCATATTAGCAACTTTTATCTGCACT
*
13348701 GATTACTGGTTTATC
1 GATTAGTGGTTTATC
13348716 ACTACACCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 2 0.04
45 50 0.96
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (45 bp):
GATTAGTGGTTTATCCAAACCATATTAGCAACTTTTATCTGCACT
Found at i:13348750 original size:12 final size:12
Alignment explanation
Indices: 13348733--13348758 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13348723 CAAAACAGGC
13348733 TTTTAGCGGCGT
1 TTTTAGCGGCGT
13348745 TTTTAGCGGCGT
1 TTTTAGCGGCGT
13348757 TT
1 TT
13348759 GGATAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:13348975 original size:41 final size:41
Alignment explanation
Indices: 13348917--13349047 Score: 217
Period size: 41 Copynumber: 3.2 Consensus size: 41
13348907 TGAGCTTTCG
13348917 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
13348958 GGGCTTTAGCGGTGTTTTTGAGATAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
13348999 GGGCTTTAGCGGCGTTTTTTAGAAAACGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
13349040 GGGATTTA
1 GGGCTTTA
13349048 AAATAATTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.30
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:13349380 original size:21 final size:20
Alignment explanation
Indices: 13349356--13349397 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 20
13349346 ATGTGTTAAG
13349356 GGTTTATGGTTTTAGGGTTTA
1 GGTTTATGG-TTTAGGGTTTA
13349377 GGTTTATGGTTTAGGGTTTA
1 GGTTTATGGTTTAGGGTTTA
13349397 G
1 G
13349398 ATTAACTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (20 bp):
GGTTTATGGTTTAGGGTTTA
Found at i:13349394 original size:14 final size:14
Alignment explanation
Indices: 13349326--13349397 Score: 67
Period size: 15 Copynumber: 5.1 Consensus size: 14
13349316 TTAAAGGTTG
*
13349326 GGGTTTAAGGTTTA
1 GGGTTTATGGTTTA
*
13349340 GAGG-TTATGTGTTAA
1 G-GGTTTATG-GTTTA
13349355 GGGTTTATGGTTTTA
1 GGGTTTATGG-TTTA
13349370 GGGTTTA-GGTTTA
1 GGGTTTATGGTTTA
* *
13349383 TGGTTTAGGGTTTA
1 GGGTTTATGGTTTA
13349397 G
1 G
13349398 ATTAACTAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
13 10 0.21
14 16 0.33
15 22 0.46
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (14 bp):
GGGTTTATGGTTTA
Found at i:13349397 original size:7 final size:7
Alignment explanation
Indices: 13349326--13349397 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
13349316 TTAAAGGTTG
13349326 GGGTTTA
1 GGGTTTA
*
13349333 AGGTTTA
1 GGGTTTA
13349340 GAGG-TTA
1 G-GGTTTA
* *
13349347 TGTGTTAA
1 -GGGTTTA
13349355 GGGTTTA
1 GGGTTTA
*
13349362 TGGTTTTA
1 -GGGTTTA
13349370 GGGTTTA
1 GGGTTTA
13349377 -GGTTTA
1 GGGTTTA
*
13349383 TGGTTTA
1 GGGTTTA
13349390 GGGTTTA
1 GGGTTTA
13349397 G
1 G
13349398 ATTAACTAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
6 6 0.12
7 34 0.67
8 11 0.22
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:13349601 original size:14 final size:15
Alignment explanation
Indices: 13349572--13349609 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
13349562 AATAATTATA
13349572 TATGGATTTAGAGAT
1 TATGGATTTAGAGAT
*
13349587 TATGGA-TTAGGGAT
1 TATGGATTTAGAGAT
13349601 TATGG-TTTA
1 TATGGATTTA
13349610 AGGGTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGAGAT
Found at i:13349630 original size:21 final size:21
Alignment explanation
Indices: 13349596--13349674 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
13349586 TTATGGATTA
*
13349596 GGGA-TTATGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
13349616 GGGATTTAAGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
* * *
13349637 AGGAGTTAGAGG-TTAAGAGTT
1 GGGATTTA-AGGTTTAAGGGTT
*
13349658 AGGGATTTCAGGGTTTA
1 -GGGATTT-AAGGTTTA
13349675 GGATTTAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.09
21 29 0.62
22 10 0.21
23 4 0.09
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.35
Consensus pattern (21 bp):
GGGATTTAAGGTTTAAGGGTT
Found at i:13355921 original size:43 final size:43
Alignment explanation
Indices: 13355830--13356849 Score: 496
Period size: 43 Copynumber: 23.2 Consensus size: 43
13355820 TGTTTTTAGT
* * * * **
13355830 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
13355872 GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
**
13355915 AACGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
13355958 GGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * *
13356001 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * *
13356044 GGCGTTTGT-GCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCTTTTGTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGG------TCT-T-G-AGC---TATAGC
* *** * *
13356098 GGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCCCAATCTCTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* *** * ** *
13356141 GGCGTTTATTTCTAAAAACGCCG-TAAAAGTTTGTGGCGTTGA-AAACAGC
1 GGCGTTT-GTGGGAAAAGCGCCGCT-AAAG---GT--C-TTGAGCTATAGC
* * * ** * * * *** * *
13356190 GGCACTTTTTGCG----GCGCTTTCAAAAACGCCGCAAATACTTTTAGC
1 GGC-GTTTGTGGGAAAAGCGC-CGC-TAAAGGTC-TTGA-GC-TATAGC
*
13356235 GGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * *
13356278 GGCTTTTGTGGGAAAAGCGCTGCTAAAGGCCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* ** *
13356321 GGCGTTTGTGGGAAAAGCGCCACTAAAGACCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * *** *
13356364 GGCGTTTGT-GCAAAAGCGCTGCTAAAGGTCCCAATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * * *
13356406 GGCGTTTGT-GGAACATGCGCCGCTGAAGGTCCTGATCTATGGC
1 GGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTCTTGAGCTATAGC
* *
13356449 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-CGAATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG-AGCTATAGC
* *** * * * * *
13356492 GGCGTTTATTTCTAAAAACGCCAC-AAAAGT-TTGCGGCGTTGAAAACAGC
1 GGCGTTT-GTGGGAAAAGCGCCGCTAAAGGTCTTG-AGC--T----ATAGC
* * * ** * *** * *
13356541 GGCACTTTTTGCG----GCG-CTTTAAAAAATGTCGCAAATACTTTTAGC
1 GGC-GTTTGTGGGAAAAGCGCCGCT---AAAGGTC-TTGA-GC-TATAGC
* *
13356586 AGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * *
13356629 GGCTTTTGTGGGAAAAGCGCCGCTAAAGGCCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * *
13356672 GGCGTTTGTGGGAAAAGCGCCACTAAAGGCCTTGATCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * *** *
13356715 GACGTTTGT-GCAAAAGCGCCGCTAAAGGTCCCAATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * * * *
13356757 GGCGTTTG-AGGAACAGGCACCGCTAAAGATCCTGATCTATAGC
1 GGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * * *
13356800 GGCATTTGTGGGAAAAGCACCGTTAAAGGTCATGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
13356843 GACGTTT
1 GGCGTTT
13356850 ATTTCTAAAA
Statistics
Matches: 749, Mismatches: 169, Indels: 119
0.72 0.16 0.11
Matches are distributed among these distances:
42 120 0.16
43 463 0.62
44 48 0.06
45 19 0.03
46 12 0.02
47 6 0.01
48 13 0.02
49 27 0.04
50 9 0.01
51 1 0.00
54 13 0.02
55 18 0.02
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
Found at i:13356123 original size:55 final size:54
Alignment explanation
Indices: 13356040--13356143 Score: 172
Period size: 55 Copynumber: 1.9 Consensus size: 54
13356030 CCTTGATCTA
*
13356040 TAGCGGCGTTTGTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCTTTTG
1 TAGCGGCGTTTCTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCTTTTG
* *
13356094 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCCCAATCTCTAGCGGC
1 TAGCGGCGTTTCT-GCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGC
13356144 GTTTATTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 12 0.26
55 34 0.74
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (54 bp):
TAGCGGCGTTTCTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCTTTTG
Found at i:13356594 original size:351 final size:351
Alignment explanation
Indices: 13355868--13356873 Score: 1451
Period size: 351 Copynumber: 2.8 Consensus size: 351
13355858 GTTTGTTCTA
* * ** *
13355868 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGAGCTATAGCAACGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCTTTTGTGGGAAAAGC
* * * * * *
13355933 GCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTAT
66 GCCGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGCCTTGATCTAT
* ** *
13355998 AGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGG-CCTTGATCTATAGCGGCGTTTGTGCAA-AAGC
131 AGCGGCGTTTGT-GCAAAAGCGCCGCTAAAGGTCC-CAATCTATAGCGGCGTTTGTGGAACAAGC
* * *
13356061 GCCGCTAAAGGTCCCAATCTATAGCGGCTTTTGTAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAG
194 GCCGCTAAAGGT-CC--T-GAT-----C-TATG--GCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
* * * *
13356126 GTCCCAATCTCTAGCGGCGTTTATTTCTAAAAACGCCGTAAAAGTTTGTGGCGTTGAAAACAGCG
247 GTCCGAATCTATAGCGGCGTTTATTTCTAAAAACGCCGCAAAAGTTTGCGGCGTTGAAAACAGCG
*
13356191 GCACTTTTTGCGGCGCTTTCAAAAACGCCGCAAATACTTT
312 GCACTTTTTGCGGCGCTTTAAAAAACGCCGCAAATACTTT
13356231 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCTTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCTTTTGTGGGAAAAGC
* *
13356296 GCTGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGACCTTGATCTAT
66 GCCGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGCCTTGATCTAT
* *
13356361 AGCGGCGTTTGTGCAAAAGCGCTGCTAAAGGTCCCAATCTATAGCGGCGTTTGTGGAACATGCGC
131 AGCGGCGTTTGTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCGTTTGTGGAACAAGCGC
*
13356426 CGCTGAAGGTCCTGATCTATGGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCGAATCTATAG
196 CGCTAAAGGTCCTGATCTATGGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCGAATCTATAG
*
13356491 CGGCGTTTATTTCTAAAAACGCCACAAAAGTTTGCGGCGTTGAAAACAGCGGCACTTTTTGCGGC
261 CGGCGTTTATTTCTAAAAACGCCGCAAAAGTTTGCGGCGTTGAAAACAGCGGCACTTTTTGCGGC
* *
13356556 GCTTTAAAAAATGTCGCAAATACTTT
326 GCTTTAAAAAACGCCGCAAATACTTT
*
13356582 TAGCAGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCTTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCTTTTGTGGGAAAAGC
13356647 GCCGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGCCTTGATCTAT
66 GCCGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGCCTTGATCTAT
* * * * *
13356712 AGTGACGTTTGTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCGTTTGAGGAACAGGCAC
131 AGCGGCGTTTGTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCGTTTGTGGAACAAGCGC
* * * * * *
13356777 CGCTAAAGATCCTGATCTATAGCGGCATTTGTGGGAAAAGCACCGTTAAAGGTCATG-ATCTATA
196 CGCTAAAGGTCCTGATCTATGGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-CGAATCTATA
* *
13356841 GCGACGTTTATTTCTAAAAATGCCGCAAAAGTT
260 GCGGCGTTTATTTCTAAAAACGCCGCAAAAGTT
13356874 GAAAATAGCG
Statistics
Matches: 590, Mismatches: 50, Indels: 18
0.90 0.08 0.03
Matches are distributed among these distances:
351 397 0.67
352 1 0.00
353 3 0.01
354 1 0.00
359 2 0.00
360 1 0.00
362 40 0.07
363 145 0.25
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (351 bp):
TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCTTTTGTGGGAAAAGC
GCCGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGCCTTGATCTAT
AGCGGCGTTTGTGCAAAAGCGCCGCTAAAGGTCCCAATCTATAGCGGCGTTTGTGGAACAAGCGC
CGCTAAAGGTCCTGATCTATGGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCGAATCTATAG
CGGCGTTTATTTCTAAAAACGCCGCAAAAGTTTGCGGCGTTGAAAACAGCGGCACTTTTTGCGGC
GCTTTAAAAAACGCCGCAAATACTTT
Found at i:13361347 original size:18 final size:18
Alignment explanation
Indices: 13361324--13361360 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13361314 GTATATGCAA
*
13361324 AACACTCGATACATATAC
1 AACACTCAATACATATAC
13361342 AACACTCAATACATATAC
1 AACACTCAATACATATAC
13361360 A
1 A
13361361 TATATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.27, G:0.03, T:0.22
Consensus pattern (18 bp):
AACACTCAATACATATAC
Found at i:13393823 original size:8 final size:8
Alignment explanation
Indices: 13393805--13393847 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
13393795 ATGAGATGCT
13393805 ATGGACTAA
1 ATGG-CTAA
13393814 ATGGCTAA
1 ATGGCTAA
13393822 ATGGCTAA
1 ATGGCTAA
13393830 ATGGCTAA
1 ATGGCTAA
13393838 ATGGACTAA
1 ATGG-CTAA
13393847 A
1 A
13393848 ATAAACCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.73
9 9 0.27
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (8 bp):
ATGGCTAA
Found at i:13393831 original size:16 final size:17
Alignment explanation
Indices: 13393805--13393847 Score: 79
Period size: 16 Copynumber: 2.6 Consensus size: 17
13393795 ATGAGATGCT
13393805 ATGGACTAAATGGCTAA
1 ATGGACTAAATGGCTAA
13393822 ATGG-CTAAATGGCTAA
1 ATGGACTAAATGGCTAA
13393838 ATGGACTAAA
1 ATGGACTAAA
13393848 ATAAACCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (17 bp):
ATGGACTAAATGGCTAA
Found at i:13400625 original size:26 final size:26
Alignment explanation
Indices: 13400589--13400638 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
13400579 CTGATCAAAA
13400589 AGGGGTTGCTAAGTGCGGATTCCCTT
1 AGGGGTTGCTAAGTGCGGATTCCCTT
*
13400615 AGGGGTTGCTAAGTGCTGATTCCC
1 AGGGGTTGCTAAGTGCGGATTCCC
13400639 CGAATTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCGGATTCCCTT
Found at i:13400658 original size:67 final size:68
Alignment explanation
Indices: 13400548--13400679 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 68
13400538 ATTGAATGTA
*
13400548 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGG-GGTTGCTAAGTGCGGATTCC
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGTGGTTGCGAAGTGCGGATTCC
13400612 CTT
66 CTT
* * * * *
13400615 AGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTC-TAAAGGTGGTTGCGAAGTGCTGATTC
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGA-TCAAAAAGGTGGTTGCGAAGTGCGGATTC
13400679 C
65 C
13400680 ATCGTATCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 37 0.65
68 20 0.35
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (68 bp):
AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGTGGTTGCGAAGTGCGGATTCC
CTT
Found at i:13400665 original size:42 final size:43
Alignment explanation
Indices: 13400618--13400768 Score: 139
Period size: 42 Copynumber: 3.6 Consensus size: 43
13400608 TTCCCTTAGG
* *
13400618 GGTTGCTAAGTGCTGATTCC-CCGAATTATTGATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTATAAAGGT
* * * * *
13400660 GGTTGCGAAGTGCTGATTCCATCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTAT-AAAGGT
* * * * * *
13400703 GGTTGCTATGTGTTGATTCC-CCGTATCACTGAATAT-AAGTT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTATAAAGGT
*
13400744 GGTTGCTATGTGCTGATTCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
13400769 GTAATGGTTA
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 3 0.03
41 19 0.22
42 33 0.38
43 28 0.32
44 5 0.06
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTATAAAGGT
Found at i:13406590 original size:19 final size:20
Alignment explanation
Indices: 13406542--13406590 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
13406532 ATCTCTAATC
13406542 CTTATTCTCTCAAACTTATCA
1 CTTATTCTCTCAAACTTAT-A
*
13406563 CTT-TTCTCTCAAATTTAT-
1 CTTATTCTCTCAAACTTATA
13406581 CTTATTCTCT
1 CTTATTCTCT
13406591 TACACTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 6 0.23
20 14 0.54
21 3 0.12
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (20 bp):
CTTATTCTCTCAAACTTATA
Found at i:13408270 original size:42 final size:42
Alignment explanation
Indices: 13408191--13408418 Score: 167
Period size: 42 Copynumber: 5.4 Consensus size: 42
13408181 TTTAGTCGAC
* * * * * *
13408191 GATGCACTTATGTGCCAGTGTATTTTCTTTGGTTCATCTGAT
1 GATGCACTTACGTGCCAGTATATTTGCTTCGGCTCATCCGAT
* *
13408233 GATGCACTTACGTGCCAGTATATTTGCTTCGGCTCATCCAAA
1 GATGCACTTACGTGCCAGTATATTTGCTTCGGCTCATCCGAT
* * * * * * *
13408275 GATGCATTTACATGTCATTATATTTGCTTCAGTTCATTCGAT
1 GATGCACTTACGTGCCAGTATATTTGCTTCGGCTCATCCGAT
* * * * *
13408317 GATGCACCTTATGTGCCATTATAATTGCTTTGGC-C-TGCCAAT
1 GATGCA-CTTACGTGCCAGTATATTTGCTTCGGCTCAT-CCGAT
* *
13408359 AATGCAC-TACGTGTGCCAGTATATTTCCTTCGGC-CTATCCGAT
1 GATGCACTTAC--GTGCCAGTATATTTGCTTCGGCTC-ATCCGAT
* *
13408402 GATGCACTAAGGTGCCA
1 GATGCACTTACGTGCCA
13408419 AATTGATATG
Statistics
Matches: 142, Mismatches: 37, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 107 0.75
43 29 0.20
44 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (42 bp):
GATGCACTTACGTGCCAGTATATTTGCTTCGGCTCATCCGAT
Found at i:13409920 original size:21 final size:20
Alignment explanation
Indices: 13409883--13409930 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
13409873 AAAATTTATT
13409883 AAAAATTAAAAAGATTACAA
1 AAAAATTAAAAAGATTACAA
* * *
13409903 AAAATATTTAAAATATTATAA
1 AAAA-ATTAAAAAGATTACAA
13409924 AAAAATT
1 AAAAATT
13409931 CAAAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATTAAAAAGATTACAA
Found at i:13415795 original size:44 final size:44
Alignment explanation
Indices: 13415718--13415824 Score: 171
Period size: 44 Copynumber: 2.4 Consensus size: 44
13415708 ACATCACTTG
*
13415718 TCACCTGTTACTGATCAGATAAGTGTACATAAAGCTACCACCTA
1 TCACTTGTTACTGATCAGATAAGTGTACATAAAGCTACCACCTA
* *
13415762 TCACTTGTCACTGATCAGATAAGTGTAGC-TAAAGCTACCACTTA
1 TCACTTGTTACTGATCAGATAAGTGTA-CATAAAGCTACCACCTA
13415806 TCACTTGTTACTGATCAGA
1 TCACTTGTTACTGATCAGA
13415825 AGTACTCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
44 57 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (44 bp):
TCACTTGTTACTGATCAGATAAGTGTACATAAAGCTACCACCTA
Found at i:13419049 original size:24 final size:27
Alignment explanation
Indices: 13419008--13419056 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
13418998 ATACTAGGTT
13419008 TTTTCTCCTAGTTAAACTCT-ATTATC
1 TTTTCTCCTAGTTAAACTCTGATTATC
*
13419034 TTTTC-CC-AGTTGAACTCTGATTA
1 TTTTCTCCTAGTTAAACTCTGATTA
13419057 ATGTAGGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTCTCCTAGTTAAACTCTGATTATC
Found at i:13423520 original size:92 final size:91
Alignment explanation
Indices: 13423363--13423550 Score: 243
Period size: 92 Copynumber: 2.1 Consensus size: 91
13423353 GACAGTGTGT
* ** * * *
13423363 TGGGCCGTGTGCTCGGCCACGTGAGATATACGGGCGTATGAGCCACACAGTCTAGTTGAGGTAGG
1 TGGGCCGTATGCTCAACCACGTGAGACACACAGGCGTATGAGCCACACAGTCTAGTTGAGGTAGG
* * *
13423428 GTATGTGGGCCATACATTTTTGCCTGG
66 G-ATGTGGGCCACACATTTTGGCCTAG
* * *
13423455 TGGGCCGTATGCTCAACCATGTGAGACACACAGGCGTGTGAGCCACACGGTCTAGTT-ATGGTAG
1 TGGGCCGTATGCTCAACCACGTGAGACACACAGGCGTATGAGCCACACAGTCTAGTTGA-GGTAG
13423519 GGATGTGGGCCACACATTTTGGCCTAG
65 GGATGTGGGCCACACATTTTGGCCTAG
13423546 TGGGC
1 TGGGC
13423551 TGTGTGGGTC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
91 28 0.34
92 55 0.66
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.24
Consensus pattern (91 bp):
TGGGCCGTATGCTCAACCACGTGAGACACACAGGCGTATGAGCCACACAGTCTAGTTGAGGTAGG
GATGTGGGCCACACATTTTGGCCTAG
Found at i:13430212 original size:25 final size:24
Alignment explanation
Indices: 13430170--13430218 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
13430160 GTCATTAGGG
*
13430170 TTACCGATTCCAGCTCGTATGAGC
1 TTACCGATACCAGCTCGTATGAGC
13430194 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATAC-CAGCTCGTATGAGC
13430219 ATACATGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (24 bp):
TTACCGATACCAGCTCGTATGAGC
Found at i:13434350 original size:17 final size:20
Alignment explanation
Indices: 13434305--13434350 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 20
13434295 TTATGAAGAA
13434305 TTAATTATAAATATAATAGTT
1 TTAA-TATAAATATAATAGTT
*
13434326 TTATTATAAA-ATAA-A-TT
1 TTAATATAAATATAATAGTT
13434343 TTAATATA
1 TTAATATA
13434351 GAAAAGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
19 4 0.17
20 6 0.26
21 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAATATAAATATAATAGTT
Found at i:13438381 original size:18 final size:17
Alignment explanation
Indices: 13438327--13438394 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 17
13438317 ATAATTATTT
13438327 TAAATTATAT-TTTATAG
1 TAAATTATATATTT-TAG
*
13438344 TATTATATATTATGATTTTAG
1 TA-AAT-TA-TAT-ATTTTAG
*
13438365 TAAATTCATATATTTTAT
1 TAAATT-ATATATTTTAG
13438383 TAAATTATATAT
1 TAAATTATATAT
13438395 AATTTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.19
18 14 0.33
19 6 0.14
20 6 0.14
21 5 0.12
22 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TAAATTATATATTTTAG
Found at i:13438401 original size:19 final size:18
Alignment explanation
Indices: 13438358--13438394 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13438348 ATATATTATG
*
13438358 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATTCATAT
13438376 ATTTTATTAAATT-ATAT
1 ATTTTATTAAATTCATAT
13438393 AT
1 AT
13438395 AATTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTATTAAATTCATAT
Found at i:13438567 original size:44 final size:45
Alignment explanation
Indices: 13438512--13438608 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 45
13438502 CTATTACACA
* * *
13438512 TCTATTCCATTCAACCAAACACAAGAATACC-ATTATGCCTCTAT
1 TCTATTACATTCAACCAAACAAAAGAATACCTATTACGCCTCTAT
*
13438556 TCTATTACATTCAACCAAACAAAAGATTACCTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACAAAAGAATACCTATTACGCCTCTAT
*
13438601 TCCATTAC
1 TCTATTAC
13438609 GCATCTATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 28 0.60
45 19 0.40
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (45 bp):
TCTATTACATTCAACCAAACAAAAGAATACCTATTACGCCTCTAT
Found at i:13438609 original size:16 final size:16
Alignment explanation
Indices: 13438588--13438640 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
13438578 AAGATTACCT
13438588 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
13438604 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
13438620 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
13438636 ATTAC
1 ATTAC
13438641 AGCCAACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:13441196 original size:18 final size:18
Alignment explanation
Indices: 13441173--13441235 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
13441163 TTATATATAA
13441173 TTTTATGTAATTTAAATT
1 TTTTATGTAATTTAAATT
**
13441191 TTTTATGTTTTTCTAAATT
1 TTTTATGTAATT-TAAATT
*
13441210 TTTT-TATATATTTAATTATT
1 TTTTATGTA-ATTTAA--ATT
13441230 TTTTAT
1 TTTTAT
13441236 ATATCTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 15 0.43
19 12 0.34
20 7 0.20
21 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATGTAATTTAAATT
Found at i:13442523 original size:16 final size:16
Alignment explanation
Indices: 13442498--13442540 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
13442488 ATAATTTACC
* * *
13442498 TTAATTATTTTTATTT
1 TTAATAATTTTAAATT
13442514 TTAATAATTTTAAATT
1 TTAATAATTTTAAATT
13442530 TTAATTAATTT
1 TTAA-TAATTT
13442541 ATGGATGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATAATTTTAAATT
Found at i:13442894 original size:31 final size:32
Alignment explanation
Indices: 13442859--13442918 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
13442849 AAAATTTCTA
* * *
13442859 TATTATATAAATATATAATAT-AATATGCAAT
1 TATTATATAAAAACATAAAATAAATATGCAAT
13442890 TATTATATAAAAACATAAAATAAATATGC
1 TATTATATAAAAACATAAAATAAATATGC
13442919 GTACATTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (32 bp):
TATTATATAAAAACATAAAATAAATATGCAAT
Found at i:13444241 original size:18 final size:17
Alignment explanation
Indices: 13444196--13444243 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
13444186 GAAAAGGCAC
*
13444196 GAAAAAGAAGAAAGAAG
1 GAAAAAGAAAAAAGAAG
**
13444213 GAAAATTAAAACAAGAAG
1 GAAAAAGAAAA-AAGAAG
13444231 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
13444244 AAACAGACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (17 bp):
GAAAAAGAAAAAAGAAG
Found at i:13447722 original size:40 final size:40
Alignment explanation
Indices: 13447666--13447818 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
13447656 ATTATATACT
* * *
13447666 GAAATGTATGCACTTTCGATCCATACATACTGAATCTACT
1 GAAATGTATGCACTTTCGAGCCATACCTACTGAATCTACC
* *
13447706 GAAATGTATGCGCTTTCGAGCTATACCTACTGAATCTACC
1 GAAATGTATGCACTTTCGAGCCATACCTACTGAATCTACC
* *
13447746 GAAATGTATGCTCTTTCGAGCCATACCTATTGAATCTACC
1 GAAATGTATGCACTTTCGAGCCATACCTACTGAATCTACC
* * *
13447786 AAAAAGCATGCACTTTCGAGCCATACCTACTGA
1 GAAATGTATGCACTTTCGAGCCATACCTACTGA
13447819 TTATATTGAA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (40 bp):
GAAATGTATGCACTTTCGAGCCATACCTACTGAATCTACC
Found at i:13447830 original size:80 final size:80
Alignment explanation
Indices: 13447659--13447830 Score: 218
Period size: 80 Copynumber: 2.1 Consensus size: 80
13447649 ATGTTGTATT
* ** * * *
13447659 ATATACTGAAATGTATGCACTTTCGATCCATACATACTGAATCTACTGAAATGTATGCGCTTTCG
1 ATATACTGAAATGTATGCACTTTCGAGCCATACATACTGAATCTACCAAAAAGCATGCACTTTCG
*
13447724 AGCTATACCTACTGA
66 AGCCATACCTACTGA
* * * * *
13447739 ATCTACCGAAATGTATGCTCTTTCGAGCCATACCTATTGAATCTACCAAAAAGCATGCACTTTCG
1 ATATACTGAAATGTATGCACTTTCGAGCCATACATACTGAATCTACCAAAAAGCATGCACTTTCG
13447804 AGCCATACCTACTGA
66 AGCCATACCTACTGA
* *
13447819 TTATATTGAAAT
1 ATATACTGAAAT
13447831 ATTGTACAGA
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (80 bp):
ATATACTGAAATGTATGCACTTTCGAGCCATACATACTGAATCTACCAAAAAGCATGCACTTTCG
AGCCATACCTACTGA
Found at i:13457731 original size:15 final size:16
Alignment explanation
Indices: 13457706--13457740 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
13457696 AACAAATAAA
*
13457706 AAAAATCAAAAATTTT
1 AAAAATCAAAAATATT
13457722 AAAAAT-AAAAATATT
1 AAAAATCAAAAATATT
13457737 AAAA
1 AAAA
13457741 GGAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATCAAAAATATT
Found at i:13458337 original size:21 final size:22
Alignment explanation
Indices: 13458295--13458350 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 22
13458285 TATTAATTTT
* *
13458295 TATTTTT-TAAACTTTATTTAA
1 TATTTTTATAAATTTTATATAA
13458316 TATTTTTATAAATTTTA-ATAA
1 TATTTTTATAAATTTTATATAA
* *
13458337 T-GTTTTACAAATTT
1 TATTTTTATAAATTT
13458351 ACAAATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 8 0.27
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTTTTATAAATTTTATATAA
Found at i:13461108 original size:2 final size:2
Alignment explanation
Indices: 13461101--13461125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13461091 AGTCATATTC
13461101 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13461126 AAGCATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13465666 original size:12 final size:12
Alignment explanation
Indices: 13465640--13465678 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
13465630 TTTGTGTTTG
13465640 TATATATATTAAT
1 TATATATA-TAAT
13465653 TATATATATAAT
1 TATATATATAAT
* *
13465665 TATAAATTTAAT
1 TATATATATAAT
13465677 TA
1 TA
13465679 CTTTTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATATAAT
Found at i:13471929 original size:25 final size:25
Alignment explanation
Indices: 13471882--13471941 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 25
13471872 CTAGGCACCC
13471882 ATTTTATTATTCATATAATATAACAAT
1 ATTTTATTATT-ATATAATATAA-AAT
13471909 ATTTTATTATT-TATACA-ATAAAAT
1 ATTTTATTATTATATA-ATATAAAAT
13471933 ATGTTTATT
1 AT-TTTATT
13471942 GGTGACTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.16
25 14 0.45
26 1 0.03
27 11 0.35
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTTATTATTATATAATATAAAAT
Found at i:13488999 original size:14 final size:14
Alignment explanation
Indices: 13488980--13489006 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13488970 ACGTGTTCTG
13488980 TTTGTTTTTAATTA
1 TTTGTTTTTAATTA
13488994 TTTGTTTTTAATT
1 TTTGTTTTTAATT
13489007 TTTAAATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTGTTTTTAATTA
Found at i:13489170 original size:27 final size:28
Alignment explanation
Indices: 13489122--13489188 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
13489112 TTTTTTACAA
* * *
13489122 ATATTAAATTATTTATATAATTTTATTAT
1 ATATTATATT-TTTATAAAATTGTATTAT
*
13489151 ATATTATATTTTT-TAAAATTGTATTTT
1 ATATTATATTTTTATAAAATTGTATTAT
*
13489178 CTATTAT-TTTT
1 ATATTATATTTT
13489189 AATGTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.12
27 17 0.52
28 3 0.09
29 9 0.27
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
ATATTATATTTTTATAAAATTGTATTAT
Found at i:13490866 original size:17 final size:19
Alignment explanation
Indices: 13490846--13490886 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
13490836 ATAACTTTAA
*
13490846 AAAATATA-TAATA-CATC
1 AAAATATACTAAAATCATC
13490863 AAAA-ATACTAAAATCATC
1 AAAATATACTAAAATCATC
13490881 AAAATA
1 AAAATA
13490887 AATATTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 8 0.40
19 1 0.05
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATACTAAAATCATC
Found at i:13490868 original size:18 final size:18
Alignment explanation
Indices: 13490845--13490884 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13490835 TATAACTTTA
*
13490845 AAAAATA-TATAATACATC
1 AAAAATACTAAAAT-CATC
13490863 AAAAATACTAAAATCATC
1 AAAAATACTAAAATCATC
13490881 AAAA
1 AAAA
13490885 TAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATACTAAAATCATC
Found at i:13493370 original size:19 final size:19
Alignment explanation
Indices: 13493346--13493465 Score: 150
Period size: 19 Copynumber: 6.0 Consensus size: 19
13493336 AATCTTCAAG
13493346 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13493365 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
13493384 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
*
13493405 GATATGCAATCTTGGATAT
1 GATATGCAATCTTAGATAT
13493424 GATATGCAATCTTGGAAGATAT
1 GATATGCAATCTT---AGATAT
* *
13493446 GATTTTGTAATCTTAGATAT
1 GA-TATGCAATCTTAGATAT
13493466 TTAATTTGTA
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
19 51 0.56
20 6 0.07
21 18 0.20
22 7 0.08
23 9 0.10
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:13493392 original size:40 final size:38
Alignment explanation
Indices: 13493346--13493465 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 38
13493336 AATCTTCAAG
13493346 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
* *
13493384 GATATATGCAATCTTGGATATGATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCTTAGATAT
* *
13493424 GATATGCAATCTTGGAAGATATGATTTTGTAATCTTAGATAT
1 GATATGCAATCTT---AGATATGA-TATGCAATCTTAGATAT
13493466 TTAATTTGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
38 13 0.19
40 36 0.51
41 7 0.10
42 14 0.20
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:13496104 original size:88 final size:88
Alignment explanation
Indices: 13495450--13496077 Score: 932
Period size: 88 Copynumber: 7.1 Consensus size: 88
13495440 AAGATAACGA
* * * * * * * *
13495450 ATCTTGTCTTCATGCACCGACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTGGGTTATA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
* * *
13495515 GCGGAGCAGGTTAAAAATAGCAG
66 GTGGAGCAGGTTGAAGATAGCAG
* * * *
13495538 ATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCAAAGATACCAGTCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
*
13495603 GTGGAGCAGGTTGAAGATAGTAG
66 GTGGAGCAGGTTGAAGATAGCAG
* * *
13495626 ATCTTGCCTTCCTGTACCGACAGCGAAACAGATCGAAGATACCAGCCTTACCTCCCTGGGTCGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
* * *
13495691 GTGGATCAGGTTGAAAATAACAG
66 GTGGAGCAGGTTGAAGATAGCAG
* *
13495714 ATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCGGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
13495779 GTGGAGCAGGTTGAAGATAGCAG
66 GTGGAGCAGGTTGAAGATAGCAG
* * *
13495802 ATCTTGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
13495867 GTGGAGCAGGTTGAAGATAGCAG
66 GTGGAGCAGGTTGAAGATAGCAG
** * * *
13495890 ATCTTGCCTTCCTGTACCGACAATGAAGCAGATCAAAGATACCAGCATTGCCTCCCTGGGTCGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
13495955 GTGGAGCAGGTTGAAGATAGCAG
66 GTGGAGCAGGTTGAAGATAGCAG
** *
13495978 ATCTTGCCTTCCTGTTTCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
13496043 GTGGAGCAGGTTGAAGATAGCAG
66 GTGGAGCAGGTTGAAGATAGCAG
*
13496066 ATCTTGTCTTCC
1 ATCTTGCCTTCC
13496078 CATACTGGTG
Statistics
Matches: 487, Mismatches: 53, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 487 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (88 bp):
ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
GTGGAGCAGGTTGAAGATAGCAG
Found at i:13496119 original size:45 final size:45
Alignment explanation
Indices: 13496055--13496235 Score: 183
Period size: 42 Copynumber: 4.1 Consensus size: 45
13496045 GGAGCAGGTT
*
13496055 GAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * **
13496100 GAAGAAAGTAGATCTTGTCTT--CAT-GTATTGGCGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* *** ** *
13496142 GAAGAAAGCATATCTTGTCTTCATGTA-TCGGT-ATGAAATAGATC
1 GAAGAAAGCAGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATC
* **
13496186 AAAGGTAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
13496231 GAAGA
1 GAAGA
13496236 TACAAGTCTT
Statistics
Matches: 104, Mismatches: 26, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
42 34 0.33
43 3 0.03
44 34 0.33
45 33 0.32
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (45 bp):
GAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
Found at i:13496237 original size:264 final size:262
Alignment explanation
Indices: 13495450--13496168 Score: 704
Period size: 264 Copynumber: 2.7 Consensus size: 262
13495440 AAGATAACGA
* * * * * * * * *
13495450 ATCTTGTCTTCATGCACCGACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTGGGTTATA
1 ATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
* * * * * *
13495515 GCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCAAAGATAC
66 GTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCC-GCATCAACAGCGAAGCAGATCGAAGAAAC
* * * * * * * * * *
13495580 CAGTCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGTAGATCTTGCCTTCCTGTACCG
130 CAGCCTTGCCTCCATGGATTG-AGCGAAGCAGATCGAAGAAAGCAGATCTTGCCTTCATGTACCG
** * * * ** * * * * * *
13495645 ACAGCGAAACAGATCGAAGATACCAGCCTTACCTCCCTGGGTCGTAGTGGATCAGGTTGAAAATA
194 ACAATGAAACAGATCAAAGATACCAGCATTGCCTCCCTGACTCGTAGCGAAGCAGATCGAAGATA
*
13495710 ACAG
259 GCAG
*
13495714 ATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCGGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
*
13495779 GTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGATAC
66 GTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCC-GCATCAACAGCGAAGCAGATCGAAGAAAC
* * * * * * * *
13495844 CAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCG
130 CAGCCTTGCCTCCATGGATTG-AGCGAAGCAGATCGAAGAAAGCAGATCTTGCCTTCATGTACCG
* ** * * * *
13495909 ACAATGAAGCAGATCAAAGATACCAGCATTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATA
194 ACAATGAAACAGATCAAAGATACCAGCATTGCCTCCCTGACTCGTAGCGAAGCAGATCGAAGATA
13495974 GCAG
259 GCAG
**
13495978 ATCTTGCCTTCCTGTTTCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
* **** *
13496043 GTGGAGCAGGTTGAAGATAGCAGATCTTGTCTTCC-CATACTGGTGGCGAAGTAGATCGAAGAAA
66 GTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCGCAT-C-AACAGCGAAGCAGATCGAAGAAA
** * * * * * * *
13496107 GTAGATCTTGTCTTCATGTATTG-GCGAAGTAGATCGAAGAAAGCATATCTTGTCTTCATGTA
129 CCAG-CCTTGCCTCCATGGATTGAGCGAAGCAGATCGAAGAAAGCAGATCTTGCCTTCATGTA
13496169 TCGGTATGAA
Statistics
Matches: 399, Mismatches: 53, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
262 3 0.01
263 31 0.08
264 353 0.88
265 12 0.03
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (262 bp):
ATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTA
GTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCGCATCAACAGCGAAGCAGATCGAAGAAACC
AGCCTTGCCTCCATGGATTGAGCGAAGCAGATCGAAGAAAGCAGATCTTGCCTTCATGTACCGAC
AATGAAACAGATCAAAGATACCAGCATTGCCTCCCTGACTCGTAGCGAAGCAGATCGAAGATAGC
AG
Found at i:13496604 original size:19 final size:19
Alignment explanation
Indices: 13496580--13496673 Score: 143
Period size: 19 Copynumber: 4.8 Consensus size: 19
13496570 AATCTTCAAG
13496580 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13496599 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
13496618 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
* *
13496639 GATATGCAATATTGGATAT
1 GATATGCAATCTTAGATAT
13496658 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
13496674 AGATATGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 51 0.74
21 18 0.26
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:13496626 original size:40 final size:38
Alignment explanation
Indices: 13496580--13496680 Score: 143
Period size: 40 Copynumber: 2.7 Consensus size: 38
13496570 AATCTTCAAG
*
13496580 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATATTAGATAT
* *
13496618 GATATATGCAATCTTGGATATGATATGCAATATTGGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATATTAGATAT
13496658 GATATGCAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
13496681 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
36 6 0.11
37 1 0.02
38 15 0.26
40 35 0.61
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATATTAGATAT
Found at i:13498910 original size:18 final size:17
Alignment explanation
Indices: 13498887--13498939 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 17
13498877 TAATATCATC
13498887 AATATATAAAAAATATA
1 AATATATAAAAAATATA
*
13498904 TAATATAGTAAAAAATGTA
1 -AATATA-TAAAAAATATA
13498923 AATATCATAATAAAATA
1 AATAT-ATAA-AAAATA
13498940 AAGATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (17 bp):
AATATATAAAAAATATA
Found at i:13510344 original size:5 final size:6
Alignment explanation
Indices: 13510330--13510399 Score: 50
Period size: 6 Copynumber: 10.5 Consensus size: 6
13510320 GAAGTCTAAG
*
13510330 AAAATA AAAATAA AACAACTA AAAACA AAAATA AAAATTTTAA AAAATA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAA---T-A AAAATA
* *
13510379 AAAATA AAACTA AAAAGA AAA
1 AAAATA AAAATA AAAATA AAA
13510400 GAAATAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
6 34 0.65
7 6 0.12
8 5 0.10
9 2 0.04
10 5 0.10
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:13512076 original size:20 final size:20
Alignment explanation
Indices: 13512051--13512092 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13512041 TAATAAAAAC
13512051 AAAAAATAATAAA-AATAATT
1 AAAAAA-AATAAATAATAATT
*
13512071 AAAAAACATAAATAATAATT
1 AAAAAAAATAAATAATAATT
13512091 AA
1 AA
13512093 TAATTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAAAATAAATAATAATT
Found at i:13512094 original size:27 final size:27
Alignment explanation
Indices: 13512045--13512099 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
13512035 TAATAGTAAT
13512045 AAAAACAAAAAATAATAAAAATAATTA
1 AAAAACAAAAAATAATAAAAATAATTA
* *
13512072 AAAAAC-ATAAATAATAATTAATAATTA
1 AAAAACAAAAAATAATAA-AAATAATTA
13512099 A
1 A
13512100 TGAAATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAAACAAAAAATAATAAAAATAATTA
Found at i:13530103 original size:184 final size:184
Alignment explanation
Indices: 13529789--13530163 Score: 678
Period size: 184 Copynumber: 2.0 Consensus size: 184
13529779 GGTCATTCGT
13529789 CTTTGTGATGAATGACTTTATTACTATTTGATATCAATTGATTTTTAATTAAGGAAGATGTAATG
1 CTTT-TGATGAATGACTTTATTACTATTTGATATCAATTGATTTTTAATTAAGGAAGATGTAATG
* *
13529854 GTTACCATGAGATAAAATATGACCATGTTGGGAGAATGGATGTATCCCAAATAGATTAAAGATAT
65 GTTACAATGAGATAAAATATGACCATGTAGGGAGAATGGATGTATCCCAAATAGATTAAAGATAT
* *
13529919 CCTATGAGGGTAACACACTTATGATAAGGTCATTGGATGAACACTTATCGAGTAA
130 CCTATGAGGGTAACACACATATGATAAGGTCATTGGATGAACACTGATCGAGTAA
13529974 CTTTTGATGAATGACTTTATTACTATTTGATATCAATTGATTTTTAATTAAGGAAGATGTAATGG
1 CTTTTGATGAATGACTTTATTACTATTTGATATCAATTGATTTTTAATTAAGGAAGATGTAATGG
* * *
13530039 TTACAATGGGATAAAATATGACCATGTAGGGAGAGTGGATGTATCTCAAATAGATTAAAGATATC
66 TTACAATGAGATAAAATATGACCATGTAGGGAGAATGGATGTATCCCAAATAGATTAAAGATATC
13530104 CTATGAGGGTAACACACATATGATAAGGTCATTGGATGAACACTGATCGAGTAA
131 CTATGAGGGTAACACACATATGATAAGGTCATTGGATGAACACTGATCGAGTAA
13530158 CTTTTG
1 CTTTTG
13530164 TAATGGTATG
Statistics
Matches: 183, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
184 179 0.98
185 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (184 bp):
CTTTTGATGAATGACTTTATTACTATTTGATATCAATTGATTTTTAATTAAGGAAGATGTAATGG
TTACAATGAGATAAAATATGACCATGTAGGGAGAATGGATGTATCCCAAATAGATTAAAGATATC
CTATGAGGGTAACACACATATGATAAGGTCATTGGATGAACACTGATCGAGTAA
Found at i:13530646 original size:16 final size:17
Alignment explanation
Indices: 13530614--13530648 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13530604 TAGAATTGGG
*
13530614 TTGAAAAAATTATTTAA
1 TTGAAAAAATTAATTAA
13530631 TTGAAAAAA-TAATTAA
1 TTGAAAAAATTAATTAA
13530647 TT
1 TT
13530649 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
TTGAAAAAATTAATTAA
Found at i:13533548 original size:17 final size:17
Alignment explanation
Indices: 13533526--13533561 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
13533516 CTTCTATAGT
13533526 ATGTAGCATCATTCACA
1 ATGTAGCATCATTCACA
13533543 ATGTAGCATCATTCACA
1 ATGTAGCATCATTCACA
13533560 AT
1 AT
13533562 AGTGGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (17 bp):
ATGTAGCATCATTCACA
Found at i:13536451 original size:20 final size:20
Alignment explanation
Indices: 13536426--13536471 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
13536416 AGATGAGCTA
** *
13536426 TTTCTTAAATTGTCTTGTTC
1 TTTCTTAAATAATCTTCTTC
*
13536446 TTTCTTGAATAATCTTCTTC
1 TTTCTTAAATAATCTTCTTC
13536466 TTTCTT
1 TTTCTT
13536472 TGAACAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTCTTAAATAATCTTCTTC
Found at i:13540278 original size:19 final size:20
Alignment explanation
Indices: 13540244--13540281 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13540234 TTATTCCAAG
*
13540244 GAATTGTCTTAGAAAATGAT
1 GAATTGTCTAAGAAAATGAT
13540264 GAATTGT-TAAGAAAATGA
1 GAATTGTCTAAGAAAATGA
13540282 GCTTGGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (20 bp):
GAATTGTCTAAGAAAATGAT
Found at i:13548532 original size:14 final size:15
Alignment explanation
Indices: 13548506--13548534 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13548496 TGTTATAGAA
13548506 TAAATAGACAAAGAG
1 TAAATAGACAAAGAG
13548521 TAAATA-ACAAAGAG
1 TAAATAGACAAAGAG
13548535 AATGGGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (15 bp):
TAAATAGACAAAGAG
Found at i:13549877 original size:22 final size:22
Alignment explanation
Indices: 13549851--13549893 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
13549841 GCCCGGCCCG
13549851 TTTTTAATTAAAATTAAAATTTT
1 TTTTTAA-TAAAATTAAAATTTT
13549874 TTTTTAATAAAATTAAAATT
1 TTTTTAATAAAATTAAAATT
13549894 AATTGTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAATTTT
Found at i:13549906 original size:22 final size:22
Alignment explanation
Indices: 13549854--13549910 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
13549844 CGGCCCGTTT
** *
13549854 TTAATTAAAATTAAAATTTTTTT
1 TTAA-TAAAATTAAAATTAATTG
13549877 TTAATAAAATTAAAATTAATTG
1 TTAATAAAATTAAAATTAATTG
*
13549899 TTAGTAAAATTA
1 TTAATAAAATTA
13549911 TCAAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTAATAAAATTAAAATTAATTG
Found at i:13550016 original size:9 final size:9
Alignment explanation
Indices: 13549983--13550010 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13549973 TTTATCAAAT
13549983 TATTAATTG
1 TATTAATTG
13549992 TATTAATTG
1 TATTAATTG
13550001 TATTAATTG
1 TATTAATTG
13550010 T
1 T
13550011 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:13550020 original size:68 final size:68
Alignment explanation
Indices: 13549899--13550108 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
13549889 AAATTAATTG
*
13549899 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
13549962 TGA
66 TGA
13549965 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
13550030 TGA
66 TGA
*
13550033 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
13550098 TGA
66 TGA
13550101 TTAGTAAA
1 TTAGTAAA
13550109 ACAAACTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:13550063 original size:9 final size:9
Alignment explanation
Indices: 13550051--13550078 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13550041 TTTATCAAAT
13550051 TATTAATTG
1 TATTAATTG
13550060 TATTAATTG
1 TATTAATTG
13550069 TATTAATTG
1 TATTAATTG
13550078 T
1 T
13550079 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:13550228 original size:23 final size:24
Alignment explanation
Indices: 13550181--13550226 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
13550171 AAATAAACTT
13550181 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
13550205 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
13550227 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:13551939 original size:2 final size:2
Alignment explanation
Indices: 13551932--13551959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13551922 TGTGAATTAC
13551932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13551960 GATGGCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13566945 original size:28 final size:27
Alignment explanation
Indices: 13566887--13566941 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13566877 TCGATTCCCA
13566887 CATAGATTTTTTAGTACTATGTTAGTT
1 CATAGATTTTTTAGTACTATGTTAGTT
13566914 CATAGATTTTTTAGTACTATGTTAGTT
1 CATAGATTTTTTAGTACTATGTTAGTT
13566941 C
1 C
13566942 CATAACACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (27 bp):
CATAGATTTTTTAGTACTATGTTAGTT
Found at i:13571588 original size:27 final size:27
Alignment explanation
Indices: 13571558--13571613 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
13571548 CATTTAATGA
13571558 TGATTAGTGGACATGATATTTGGATGG
1 TGATTAGTGGACATGATATTTGGATGG
13571585 TGATTAGTGGACATGATATTTGGATGG
1 TGATTAGTGGACATGATATTTGGATGG
13571612 TG
1 TG
13571614 CATGTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.04, G:0.34, T:0.38
Consensus pattern (27 bp):
TGATTAGTGGACATGATATTTGGATGG
Found at i:13581518 original size:38 final size:38
Alignment explanation
Indices: 13581471--13581575 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 38
13581461 ACAAGGTTGT
* * *
13581471 ATCTTGTTATATTACTCGAGAATCTGCAACT-AGACTAG
1 ATCTCGTTATATTACCCGAGAATCTACAA-TAAGACTAG
*
13581509 ATCTCGTTATATTACCCGAGAATCTACAATAAGGCTAG
1 ATCTCGTTATATTACCCGAGAATCTACAATAAGACTAG
* * *
13581547 ATCTCGTTATATTACACAAGACTCTACAA
1 ATCTCGTTATATTACCCGAGAATCTACAA
13581576 CAAATGCTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 1 0.02
38 58 0.98
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (38 bp):
ATCTCGTTATATTACCCGAGAATCTACAATAAGACTAG
Found at i:13583223 original size:45 final size:45
Alignment explanation
Indices: 13583156--13583414 Score: 374
Period size: 45 Copynumber: 5.8 Consensus size: 45
13583146 GTCTGATTCA
* * * *
13583156 TGATTCCATAGCGTCCTTCAGCTATGGTCTTACTCGTTAGAATCG
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCG
* *
13583201 TGATGCCATGACGTCTTTCAGCTATGGTCTTACTCATTAAAATCG
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCG
* **
13583246 TGATGTCATAACGTCTTTCAAATATGGTCTTACTCGTTAAAATCG
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCG
* * *
13583291 TGATGACATAACGTCTTTCAGTTGTGGTCTTACTCGTTAAAATCG
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCG
* * *
13583336 TGATGCCATAACATCTTTCAGCTATGGTCTTACTCTTTAAAATTG
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCG
*
13583381 TGATGCCATAACGTCTGTCAGCTATGGTCTTACT
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACT
13583415 TGCTATGGTC
Statistics
Matches: 191, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 191 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCG
Found at i:13583354 original size:135 final size:138
Alignment explanation
Indices: 13583153--13583517 Score: 421
Period size: 135 Copynumber: 2.6 Consensus size: 138
13583143 TTCGTCTGAT
** * * * * *
13583153 TCATGATTCCATAGCGTCCTTCAGCTATGGTCTTACTCGTTAGAATCGTGATGCCATGACGTCTT
1 TCATGATGACATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCGTGATGCCATAACATCTT
* *
13583218 TCAGCTATGGTCTTACTCATTAAAATCGTGATGTCATAACGTCTTTCA-A-A-TATGGTCTTACT
66 TCAGCTATGGTCTTACTCATTAAAATCGTGATGCCATAACGTCTGTCACATACTATGGTCTTACT
13583280 CGTTAAAA
131 CGTTAAAA
* * *
13583288 TCGTGATGACATAACGTCTTTCAGTTGTGGTCTTACTCGTTAAAATCGTGATGCCATAACATCTT
1 TCATGATGACATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCGTGATGCCATAACATCTT
* *
13583353 TCAGCTATGGTCTTACTCTTTAAAATTGTGATGCCATAACGTCTGTCAGCTATGGTCTTACTTGC
66 TCAGCTATGGTCTTACTCATTAAAATCGTGATGCCATAACGTCTGTCA-C-A------TA----C
13583418 TATGGTCTTACTCGTTAAAA
119 TATGGTCTTACTCGTTAAAA
* * * * *
13583438 TCATGATGCCATAACCTCTTTCAGCTATGGTCTTACTAGTTAAAATCATGATGCCATAACATTTT
1 TCATGATGACATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCGTGATGCCATAACATCTT
*
13583503 TTAGCTATGGTCTTA
66 TCAGCTATGGTCTTA
13583518 TTCAGTTCTG
Statistics
Matches: 192, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
135 99 0.52
138 1 0.01
145 1 0.01
150 91 0.47
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (138 bp):
TCATGATGACATAACGTCTTTCAGCTATGGTCTTACTCGTTAAAATCGTGATGCCATAACATCTT
TCAGCTATGGTCTTACTCATTAAAATCGTGATGCCATAACGTCTGTCACATACTATGGTCTTACT
CGTTAAAA
Found at i:13583421 original size:15 final size:15
Alignment explanation
Indices: 13583401--13583429 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13583391 ACGTCTGTCA
13583401 GCTATGGTCTTACTT
1 GCTATGGTCTTACTT
13583416 GCTATGGTCTTACT
1 GCTATGGTCTTACT
13583430 CGTTAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (15 bp):
GCTATGGTCTTACTT
Found at i:13583429 original size:60 final size:60
Alignment explanation
Indices: 13583356--13583474 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
13583346 ACATCTTTCA
* ** *
13583356 GCTATGGTCTTACTCTTTAAAATTGTGATGCCATAACGTCTGTCAGCTATGGTCTTACTT
1 GCTATGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTGTCAGCTATGGTCTTACTT
*
13583416 GCTATGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTTTCAGCTATGGTCTTACT
1 GCTATGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTGTCAGCTATGGTCTTACT
13583475 AGTTAAAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.39
Consensus pattern (60 bp):
GCTATGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTGTCAGCTATGGTCTTACTT
Found at i:13583446 original size:105 final size:105
Alignment explanation
Indices: 13583315--13583517 Score: 316
Period size: 105 Copynumber: 1.9 Consensus size: 105
13583305 CTTTCAGTTG
* ** *
13583315 TGGTCTTACTCGTTAAAATCGTGATGCCATAACATCTTTCAGCTATGGTCTTACTCTTTAAAATT
1 TGGTCTTACTCGTTAAAATCATGATGCCATAACATCTTTCAGCTATGGTCTTACTAGTTAAAATC
* *
13583380 GTGATGCCATAACGTCTGTCAGCTATGGTCTTACTTGCTA
66 ATGATGCCATAACATCTGTCAGCTATGGTCTTACTTGCTA
*
13583420 TGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTTTCAGCTATGGTCTTACTAGTTAAAATC
1 TGGTCTTACTCGTTAAAATCATGATGCCATAACATCTTTCAGCTATGGTCTTACTAGTTAAAATC
* * *
13583485 ATGATGCCATAACATTTTTTAGCTATGGTCTTA
66 ATGATGCCATAACATCTGTCAGCTATGGTCTTA
13583518 TTCAGTTCTG
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (105 bp):
TGGTCTTACTCGTTAAAATCATGATGCCATAACATCTTTCAGCTATGGTCTTACTAGTTAAAATC
ATGATGCCATAACATCTGTCAGCTATGGTCTTACTTGCTA
Found at i:13583480 original size:45 final size:45
Alignment explanation
Indices: 13583416--13583517 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
13583406 GGTCTTACTT
* *
13583416 GCTATGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTTTCA
1 GCTATGGTCTTACTAGTTAAAATCATGATGCCATAACATCTTTCA
* *
13583461 GCTATGGTCTTACTAGTTAAAATCATGATGCCATAACATTTTTTA
1 GCTATGGTCTTACTAGTTAAAATCATGATGCCATAACATCTTTCA
13583506 GCTATGGTCTTA
1 GCTATGGTCTTA
13583518 TTCAGTTCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (45 bp):
GCTATGGTCTTACTAGTTAAAATCATGATGCCATAACATCTTTCA
Found at i:13583556 original size:150 final size:150
Alignment explanation
Indices: 13583268--13583562 Score: 376
Period size: 150 Copynumber: 2.0 Consensus size: 150
13583258 GTCTTTCAAA
* * * * *
13583268 TATGGTCTTACTCGTTAAAATCGTGATGACATAACGTCTTTCAGTTGTGGTCTTACTCGTTAAAA
1 TATGGTCTTACTCGTTAAAATCATGATGACATAACCTCTTTCAGCTATGGTCTTACTAGTTAAAA
* * * * * *
13583333 TCGTGATGCCATAACATCTTTCAGCTATGGTCTTACTCTTTAAAATTGTGATGCCATAACGTCTG
66 TCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCGTTAAAAGTATAATGCCACAACGTCTG
*
13583398 TCAGCTATGGTCTTACTTGC
131 TCAACTATGGTCTTACTTGC
*
13583418 TATGGTCTTACTCGTTAAAATCATGATGCCATAACCTCTTTCAGCTATGGTCTTACTAGTTAAAA
1 TATGGTCTTACTCGTTAAAATCATGATGACATAACCTCTTTCAGCTATGGTCTTACTAGTTAAAA
* * * *** **
13583483 TCATGATGCCATAACATTTTTTAGCTATGGTCTTATTCAGTT-CTGGTATAATGCCACAGTGTCT
66 TCATGATGCCATAACATCTTTCAGCTATGGTCTTACTC-GTTAAAAGTATAATGCCACAACGTCT
*
13583547 TTCAACTATGGTCTTA
130 GTCAACTATGGTCTTA
13583563 TTTTTTTCTT
Statistics
Matches: 122, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
150 120 0.98
151 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (150 bp):
TATGGTCTTACTCGTTAAAATCATGATGACATAACCTCTTTCAGCTATGGTCTTACTAGTTAAAA
TCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCGTTAAAAGTATAATGCCACAACGTCTG
TCAACTATGGTCTTACTTGC
Found at i:13584165 original size:17 final size:17
Alignment explanation
Indices: 13584143--13584179 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
13584133 TCAAGTCCTT
13584143 ACATTTTTA-TCACTTTA
1 ACATTTTTAGTC-CTTTA
13584160 ACA-TTTTAGTCCTTTA
1 ACATTTTTAGTCCTTTA
13584176 ACAT
1 ACAT
13584180 AAAATTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.49
Consensus pattern (17 bp):
ACATTTTTAGTCCTTTA
Found at i:13585203 original size:14 final size:15
Alignment explanation
Indices: 13585184--13585221 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
13585174 ACTAACTTTT
13585184 AATTCAATAATT-AA
1 AATTCAATAATTCAA
13585198 AATTC-ATCAATTCAA
1 AATTCAAT-AATTCAA
13585213 AATTCAATA
1 AATTCAATA
13585222 TAAAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.10
14 9 0.43
15 8 0.38
16 2 0.10
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:13586821 original size:54 final size:54
Alignment explanation
Indices: 13586747--13586945 Score: 181
Period size: 54 Copynumber: 3.7 Consensus size: 54
13586737 AAAATGACCA
* * *
13586747 AAATACCCTCAAAGGATAAAATGACTGAAATACCCCTAAAGGGTAAAATGATTG
1 AAATACCCCCGAAGGATAAAATAACTGAAATACCCCTAAAGGGTAAAATGATTG
* * * * * *
13586801 AAATACCCCCGAAGGGTAAAATGA-TAGAAATACCCTCGAAA-AGT-AAATAATCG
1 AAATACCCCCGAAGGATAAAATAACT-GAAATACCC-CTAAAGGGTAAAATGATTG
* * * *
13586854 AAATACCCCCGGAGGATAAAATAATTGAAATACCCCCAAAGGGTAAAATGACTG
1 AAATACCCCCGAAGGATAAAATAACTGAAATACCCCTAAAGGGTAAAATGATTG
* * * **
13586908 AAATA-CGCCTATAGGGTAAAATAACTGTTATACCCCTA
1 AAATACCCCCGA-AGGATAAAATAACTGAAATACCCCTA
13586946 GGAGATGAAA
Statistics
Matches: 116, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
52 4 0.03
53 43 0.37
54 65 0.56
55 4 0.03
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.20
Consensus pattern (54 bp):
AAATACCCCCGAAGGATAAAATAACTGAAATACCCCTAAAGGGTAAAATGATTG
Found at i:13586884 original size:53 final size:54
Alignment explanation
Indices: 13586747--13586902 Score: 172
Period size: 53 Copynumber: 2.9 Consensus size: 54
13586737 AAAATGACCA
* * * * * * *
13586747 AAATACCCTCAAAGGATAAAATGACTGAAATACCCCTAAAGGGTAAAATGATTG
1 AAATACCCCCGAAGGATAAAATGATTGAAATACCCCGAAAGAGTAAAATAATCG
* *
13586801 AAATACCCCCGAAGGGTAAAATGATAGAAATACCCTCGAAA-AGT-AAATAATCG
1 AAATACCCCCGAAGGATAAAATGATTGAAATACCC-CGAAAGAGTAAAATAATCG
* * * *
13586854 AAATACCCCCGGAGGATAAAATAATTGAAATACCCCCAAAGGGTAAAAT
1 AAATACCCCCGAAGGATAAAATGATTGAAATACCCCGAAAGAGTAAAAT
13586903 GACTGAAATA
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
52 4 0.05
53 40 0.48
54 36 0.43
55 4 0.05
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.18
Consensus pattern (54 bp):
AAATACCCCCGAAGGATAAAATGATTGAAATACCCCGAAAGAGTAAAATAATCG
Found at i:13586934 original size:27 final size:27
Alignment explanation
Indices: 13586747--13586943 Score: 159
Period size: 27 Copynumber: 7.3 Consensus size: 27
13586737 AAAATGACCA
* * *
13586747 AAATACCCTCAAAGGATAAAATGACTG
1 AAATACCCCCAAAGGGTAAAATAACTG
* * *
13586774 AAATACCCCTAAAGGGTAAAATGATTG
1 AAATACCCCCAAAGGGTAAAATAACTG
* *
13586801 AAATACCCCCGAAGGGTAAAATGA-TAG
1 AAATACCCCCAAAGGGTAAAATAACT-G
* *
13586828 AAATACCCTCGAAA-AGT-AAATAA-TCG
1 AAATACCC-CCAAAGGGTAAAATAACT-G
** * *
13586854 AAATACCCCCGGAGGATAAAATAATTG
1 AAATACCCCCAAAGGGTAAAATAACTG
*
13586881 AAATACCCCCAAAGGGTAAAATGACTG
1 AAATACCCCCAAAGGGTAAAATAACTG
* * *
13586908 AAATACGCCTATAGGGTAAAATAACTG
1 AAATACCCCCAAAGGGTAAAATAACTG
**
13586935 TTATACCCC
1 AAATACCCC
13586944 TAGGAGATGA
Statistics
Matches: 137, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
25 2 0.01
26 17 0.12
27 114 0.83
28 4 0.03
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATACCCCCAAAGGGTAAAATAACTG
Found at i:13600511 original size:1 final size:1
Alignment explanation
Indices: 13600507--13600536 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
13600497 ACGTTTTTCC
13600507 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13600537 GCGCTTTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13603492 original size:40 final size:41
Alignment explanation
Indices: 13603431--13603512 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 41
13603421 ACCGTCAAAG
*
13603431 ACAGAATTTTTTTTTTCTTACCTAATTGTATGGTCCCATCC
1 ACAGAATTTTTTTTTTCTTACCGAATTGTATGGTCCCATCC
*
13603472 ACAGAA-TTTTTTTTTCTTACCGAATTGTATGGTCTCATCC
1 ACAGAATTTTTTTTTTCTTACCGAATTGTATGGTCCCATCC
13603512 A
1 A
13603513 TGGAATGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 33 0.85
41 6 0.15
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (41 bp):
ACAGAATTTTTTTTTTCTTACCGAATTGTATGGTCCCATCC
Found at i:13603808 original size:20 final size:20
Alignment explanation
Indices: 13603783--13603823 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
13603773 AGGAAAACAT
13603783 ATATTAA-AATAAAAATAAAA
1 ATATTAATAA-AAAAATAAAA
*
13603803 ATATTAATAAAAAACTAAAA
1 ATATTAATAAAAAAATAAAA
13603823 A
1 A
13603824 AATCATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
ATATTAATAAAAAAATAAAA
Found at i:13604159 original size:21 final size:20
Alignment explanation
Indices: 13604131--13604170 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
13604121 TTGTTATCTT
13604131 AAATTTAA-ACTAAATAATAA
1 AAATTTAAGA-TAAATAATAA
13604151 AAATGTTAAGATAAATAATA
1 AAAT-TTAAGATAAATAATA
13604171 TATTTTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 13 0.72
22 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (20 bp):
AAATTTAAGATAAATAATAA
Found at i:13604747 original size:18 final size:18
Alignment explanation
Indices: 13604710--13604744 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13604700 TAATTAATAA
*
13604710 CTTATATTTTTATGATTT
1 CTTATATTTTTATAATTT
13604728 CTTAT-TTTTTATAATTT
1 CTTATATTTTTATAATTT
13604745 TCTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTATATTTTTATAATTT
Found at i:13605136 original size:10 final size:11
Alignment explanation
Indices: 13605110--13605135 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13605100 ATTTATATAA
13605110 AAAAATATTTT
1 AAAAATATTTT
13605121 AAAAATATTTT
1 AAAAATATTTT
13605132 AAAA
1 AAAA
13605136 TTAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:13605598 original size:19 final size:20
Alignment explanation
Indices: 13605561--13605597 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
13605551 TTATAGTATT
*
13605561 TATATATTTTTAAAATTTTC
1 TATATATTTCTAAAATTTTC
13605581 TATA-ATTTCT-AAATTTT
1 TATATATTTCTAAAATTTT
13605598 TATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATATTTCTAAAATTTTC
Found at i:13606056 original size:34 final size:34
Alignment explanation
Indices: 13606016--13606140 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 34
13606006 AATAAATCAA
* *
13606016 GGTTTAGAGTTTTTTTAAAAATTAATTAAATTTG
1 GGTTTAGAGTTTTTTAAAAAATTAATTAAATTAG
* ** * *
13606050 GTTTTAG-GGGTTTTAAATAAATAAATTAAATTGG
1 GGTTTAGAGTTTTTTAAA-AAATTAATTAAATTAG
13606084 GGTTTAGAG-TTTTTAAGAAAATTAATTAAATTAG
1 GGTTTAGAGTTTTTTAA-AAAATTAATTAAATTAG
*
13606118 GGTTTAG-TTTTTTTAAAATAATT
1 GGTTTAGAGTTTTTTAAAA-AATT
13606141 TTGTGTTTAG
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
33 9 0.12
34 64 0.85
35 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (34 bp):
GGTTTAGAGTTTTTTAAAAAATTAATTAAATTAG
Found at i:13606573 original size:251 final size:251
Alignment explanation
Indices: 13606227--13606748 Score: 744
Period size: 251 Copynumber: 2.1 Consensus size: 251
13606217 TTTTGTATTT
* *
13606227 TTTTCCTACAGTAGTTTCAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAA
1 TTTT-CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAA
* * * * *
13606292 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC-TCTTT
65 ACACTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTTC-TT
* * * *
13606356 TTCTATAGTAGTTCTTAAAAAAATAATTTTGA-GAAGACGGTTCTGAAAAAATAGTGTCAAAAAC
129 TTCTACAGTAGTTCCTAAAAAAAAAATTTT-ACGAAGACAGTTCTGAAAAAATAGTGTCAAAAAC
* * * * *
13606420 GCTTCAAGCAAGATGCATTTTCAGCAAAATTATTGAAAAAAGCTCCCACGTGGACGCTCA
193 GCTTCAAGCAAGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACGTGGACACT-A
* * *
13606480 TTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAA-ATAGTGTCAAAAA
1 TTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAAA
* *
13606544 TACTTCAAGCAGGATGCACTATTAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTTCTTTT
66 CACTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTTCTTTT
*
13606609 CTACAGTAGTTCCTAAAAAAAAAATTTTACGAAGACAGTTCTGAAAAAATAGTGTCAAAAATGCT
131 CTACAGTAGTTCCTAAAAAAAAAATTTTACGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCT
* * * * *
13606674 TCATGCAGGATGCACTATCAACAAAATTACTGAAAAAAGCTTCCACGTTGACACTT
196 TCAAGCAAGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACGTGGACACTA
13606730 TTTTCTACAGTAGTTCCTG
1 TTTTCTACAGTAGTTCCTG
13606749 CTTGGCCTTA
Statistics
Matches: 239, Mismatches: 28, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
250 19 0.08
251 171 0.72
252 45 0.19
253 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (251 bp):
TTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAAA
CACTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTTCTTTT
CTACAGTAGTTCCTAAAAAAAAAATTTTACGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCT
TCAAGCAAGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACGTGGACACTA
Found at i:13606575 original size:125 final size:126
Alignment explanation
Indices: 13606226--13606748 Score: 721
Period size: 126 Copynumber: 4.2 Consensus size: 126
13606216 ATTTTGTATT
* * * *
13606226 TTTTTCCTACAGTAGTTTCAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAA
1 TTTTT-CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAA
* * *
13606291 AACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
65 AACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTC
* * *
13606353 TTTTTCTATAGTAGTTCTTAAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * *
13606418 ACGCTTCAAGCAAGATGCATTTTCAGCAAAATTATTGAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTC
* * *
13606479 ATTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTG-AAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
** * *
13606543 ATACTTCAAGCAGGATGCACTATTAGCAAAATTACTGAAAAAAGCTCCCACATGGACACT-
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTC
* * *
13606603 TCTTTTCTACAGTAGTTCCTAAAAAAAAAATTTT-ACGAAGACAGTTCTGAAAAAATAGTGTCAA
1 T-TTTTCTACAGTAGTTCCTGAAAAAATAATTTTGA-GAAGACGGTTCTGAAAAAATAGTGTCAA
* * * * *
13606667 AAATGCTTCATGCAGGATGCACTATCAACAAAATTACTGAAAAAAGCTTCCACGTTGACACT-
64 AAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTC
13606729 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
13606749 CTTGGCCTTA
Statistics
Matches: 354, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.00
125 125 0.35
126 223 0.63
127 5 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTC
Found at i:13609101 original size:13 final size:13
Alignment explanation
Indices: 13609083--13609117 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
13609073 AGTTCTTTAT
13609083 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
13609096 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
13609109 TGCTTTTGA
1 TGCTTTTGA
13609118 AGAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.43
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:13611252 original size:72 final size:72
Alignment explanation
Indices: 13611133--13611303 Score: 249
Period size: 72 Copynumber: 2.4 Consensus size: 72
13611123 AAAATAATAT
** * *
13611133 ATAAACAACTATTGATAAAACTA-ATTTAGTATAAATAAGTAGAACATAAATTCAATATCCAAAG
1 ATAAACAACTATTGATAAAACTAGATTTAACATAAATAAATAGAACATAAATTCAATATCCAAAA
13611197 ACCAAAC
66 ACCAAAC
* *
13611204 ATAAGCAACTATTAATAAAACTAGA-TTACACATAAATAAATAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTTA-ACATAAATAAATAGAACATAAATTCAATATCCAAA
13611268 AACCAAAC
65 AACCAAAC
*
13611276 ATAAATAACTATTGATAAAACTAG-TTTA
1 ATAAACAACTATTGATAAAACTAGATTTA
13611304 GCATTGTTGT
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
71 24 0.27
72 64 0.73
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTTAACATAAATAAATAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:13611749 original size:18 final size:18
Alignment explanation
Indices: 13611728--13611793 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
13611718 CCCATCAATT
13611728 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
13611746 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
13611764 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
13611782 TGAACATCATTT
1 TGAACATCATTT
13611794 CTTATATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:13616515 original size:2 final size:2
Alignment explanation
Indices: 13616508--13616540 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13616498 TGGTATAAAA
13616508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13616541 AAATATTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.