Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 22 of 135
Found at i:6087187 original size:23 final size:23
Alignment explanation
Indices: 6087110--6087175 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
6087100 GTCATGAGGC
*
6087110 AGAGGAAAAGTATGCCACAAGAT
1 AGAGGAAAAGTATGCCACAAGGT
*
6087133 AGAGGAAAAGCATGCCACAAGGT
1 AGAGGAAAAGTATGCCACAAGGT
6087156 AGAGGAAAAGTATGCCACAA
1 AGAGGAAAAGTATGCCACAA
6087176 TGGCAGATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.47, C:0.15, G:0.27, T:0.11
Consensus pattern (23 bp):
AGAGGAAAAGTATGCCACAAGGT
Found at i:6091946 original size:2 final size:2
Alignment explanation
Indices: 6091939--6091966 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6091929 TCACACCAGC
6091939 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
6091967 TCAATTTTGA
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:6098418 original size:18 final size:18
Alignment explanation
Indices: 6098390--6098424 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6098380 CAGTAGCAGG
6098390 AGAAGTGAAG-AAGAAAA
1 AGAAGTGAAGAAAGAAAA
6098407 AGAAGATGAAGAAAGAAA
1 AGAAG-TGAAGAAAGAAA
6098425 GGGAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (18 bp):
AGAAGTGAAGAAAGAAAA
Found at i:6110428 original size:14 final size:14
Alignment explanation
Indices: 6110409--6110436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6110399 AAAAGTAAAG
6110409 CGGAAGCGAGTGGC
1 CGGAAGCGAGTGGC
6110423 CGGAAGCGAGTGGC
1 CGGAAGCGAGTGGC
6110437 TGGATTGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.50, T:0.07
Consensus pattern (14 bp):
CGGAAGCGAGTGGC
Found at i:6111940 original size:3 final size:3
Alignment explanation
Indices: 6111932--6111971 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6111922 TCTTTTTTAT
6111932 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6111972 AACTATCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6117455 original size:24 final size:23
Alignment explanation
Indices: 6117427--6117471 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6117417 ATGTCACCAT
6117427 AATATCATTTATGCCACGTGTCAA
1 AATATCA-TTATGCCACGTGTCAA
* *
6117451 AATATTATTATGTCACGTGTC
1 AATATCATTATGCCACGTGTC
6117472 TCAAACTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (23 bp):
AATATCATTATGCCACGTGTCAA
Found at i:6122525 original size:70 final size:70
Alignment explanation
Indices: 6122409--6122548 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
6122399 TCTAATCTCG
6122409 ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
1 ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
6122474 TCATA
66 TCATA
* *
6122479 ATCAGAAATTTTATTTCCTGCAACTTGTGAGTTTTCTACCATTTTGCCCTTATTATGCATGTGCA
1 ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
6122544 TCATA
66 TCATA
6122549 CCCTATGTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (70 bp):
ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
TCATA
Found at i:6128046 original size:21 final size:22
Alignment explanation
Indices: 6128009--6128051 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
6127999 ACACAGTGAG
6128009 AAAACAATAAGAAAATAACAAC
1 AAAACAATAAGAAAATAACAAC
6128031 AAAACAATAA-AAAATAACAAC
1 AAAACAATAAGAAAATAACAAC
6128052 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.74, C:0.14, G:0.02, T:0.09
Consensus pattern (22 bp):
AAAACAATAAGAAAATAACAAC
Found at i:6128621 original size:15 final size:15
Alignment explanation
Indices: 6128596--6128629 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6128586 CACGAGAAAT
6128596 AAAATTACTTTACAAA
1 AAAATTACTTTA-AAA
6128612 AAAATT-CTTTAAAA
1 AAAATTACTTTAAAA
6128626 AAAA
1 AAAA
6128630 AAGGGGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 5 0.28
16 6 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTACTTTAAAA
Found at i:6128631 original size:16 final size:16
Alignment explanation
Indices: 6128596--6128630 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6128586 CACGAGAAAT
*
6128596 AAAATTACTTTACAAA
1 AAAATTACTTTAAAAA
6128612 AAAATT-CTTTAAAAA
1 AAAATTACTTTAAAAA
6128627 AAAA
1 AAAA
6128631 AGGGGAATCG
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:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACTTTAAAAA
Found at i:6133492 original size:25 final size:27
Alignment explanation
Indices: 6133438--6133489 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
6133428 TTTTTATTTT
*
6133438 TTTCAAACTCTTAAATATCGGATAGAA
1 TTTCAAACTCTTAAATATCGGAGAGAA
*
6133465 TTTCAAA-T-TTAAATAATCTGAGAGA
1 TTTCAAACTCTTAAAT-ATCGGAGAGA
6133490 TTTTTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 9 0.41
27 7 0.32
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (27 bp):
TTTCAAACTCTTAAATATCGGAGAGAA
Found at i:6134282 original size:15 final size:16
Alignment explanation
Indices: 6134262--6134295 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6134252 AATTTTTTAA
6134262 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
6134277 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
6134293 AAA
1 AAA
6134296 ATTAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:6136342 original size:25 final size:23
Alignment explanation
Indices: 6136300--6136347 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
6136290 TTTGAGTTAA
6136300 CAAAAATATTTTATATTTGATTTT
1 CAAAAATATTTTATATTT-ATTTT
6136324 CAAATAATATTTT-TCATTTATTTT
1 CAAA-AATATTTTAT-ATTTATTTT
6136348 ATTCGAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (23 bp):
CAAAAATATTTTATATTTATTTT
Found at i:6139459 original size:11 final size:11
Alignment explanation
Indices: 6139443--6139469 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6139433 CAGCTTAGCT
6139443 AAACATAAAGA
1 AAACATAAAGA
6139454 AAACATAAAGA
1 AAACATAAAGA
6139465 AAACA
1 AAACA
6139470 CTGGTATAAA
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:0.74, C:0.11, G:0.07, T:0.07
Consensus pattern (11 bp):
AAACATAAAGA
Found at i:6142787 original size:20 final size:19
Alignment explanation
Indices: 6142744--6142787 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
6142734 TGATCTTTTT
*
6142744 TTTTAATATTCAAAATATA
1 TTTTAATATTCAAAATAAA
* *
6142763 GTTTATATATTCAAATTAAA
1 TTTTA-ATATTCAAAATAAA
6142783 TTTTA
1 TTTTA
6142788 CAAATAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAATATTCAAAATAAA
Found at i:6144031 original size:30 final size:33
Alignment explanation
Indices: 6143970--6144043 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 33
6143960 CCTATTTACT
6143970 TAAAATAA-ATAATTTCAGTCAAAATAAAATTAAG
1 TAAAATAACA-AATTTCAGTCAAAATAAAATT-AG
6144004 -AAAATAACAAATTT-AGTC-AAA-AAAATTAG
1 TAAAATAACAAATTTCAGTCAAAATAAAATTAG
6144033 TAAAATAACAA
1 TAAAATAACAA
6144044 CTTTGAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
29 2 0.05
30 16 0.42
31 3 0.08
32 4 0.11
33 12 0.32
34 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAATAACAAATTTCAGTCAAAATAAAATTAG
Found at i:6144520 original size:11 final size:11
Alignment explanation
Indices: 6144504--6144529 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6144494 CACTTCACAA
6144504 AATTGCAATCT
1 AATTGCAATCT
6144515 AATTGCAATCT
1 AATTGCAATCT
6144526 AATT
1 AATT
6144530 ATACTTGCCA
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (11 bp):
AATTGCAATCT
Found at i:6145460 original size:42 final size:42
Alignment explanation
Indices: 6145378--6145465 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
6145368 ACTCATCAAC
*
6145378 AAACTAAACCCAAATATAATTTCATTATTCAAAAATACTCAT
1 AAACTAAACCCAAATATAATTTCATTATTCAAAAACACTCAT
* *
6145420 AAACTAAACTCAAATATAATTTTA-T-TTCTAAATAACACTCAT
1 AAACTAAACCCAAATATAATTTCATTATTC-AAA-AACACTCAT
6145462 AAAC
1 AAAC
6145466 AACTCTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 3 0.07
41 4 0.10
42 34 0.83
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (42 bp):
AAACTAAACCCAAATATAATTTCATTATTCAAAAACACTCAT
Found at i:6146026 original size:5 final size:5
Alignment explanation
Indices: 6146016--6146044 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6146006 GAACAAATAT
6146016 ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
6146045 AAATTCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:6155882 original size:30 final size:33
Alignment explanation
Indices: 6155821--6155894 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 33
6155811 ACTATTTACT
6155821 TAAAATAA-ATAATTTCAGTCAAAATAAAATTAAG
1 TAAAATAACA-AATTTCAGTCAAAATAAAATT-AG
6155855 -AAAATAACAAATTT-AGTC-AAA-AAAATTAG
1 TAAAATAACAAATTTCAGTCAAAATAAAATTAG
6155884 TAAAATAACAA
1 TAAAATAACAA
6155895 CTTTGAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
29 2 0.05
30 16 0.42
31 3 0.08
32 4 0.11
33 12 0.32
34 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAATAACAAATTTCAGTCAAAATAAAATTAG
Found at i:6159801 original size:6 final size:6
Alignment explanation
Indices: 6159792--6159821 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
6159782 ATAGTGATAG
6159792 ATATTT ATATTT ATATTT ATATTTT ATATT
1 ATATTT ATATTT ATATTT ATA-TTT ATATT
6159822 AAATCACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:6160009 original size:41 final size:39
Alignment explanation
Indices: 6159922--6160013 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 39
6159912 TTAAAAATAA
* * * *
6159922 TTTTTAATACAATAAAATATTTATTATATTTATTTGTAT
1 TTTTTAATATAATAAAACATTTATTATATATATTGGTAT
6159961 TTTTTAATATAATAAAACATTTATTATATATA-TGGTAGT
1 TTTTTAATATAATAAAACATTTATTATATATATTGGTA-T
6160000 GTTTGTTAATATAA
1 -TTT-TTAATATAA
6160014 ATATTTTGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 4 0.09
39 30 0.65
40 3 0.07
41 9 0.20
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (39 bp):
TTTTTAATATAATAAAACATTTATTATATATATTGGTAT
Found at i:6160096 original size:16 final size:15
Alignment explanation
Indices: 6160071--6160117 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
6160061 AAAGTATTAT
6160071 AACT-TTTTAAAAAA
1 AACTATTTTAAAAAA
*
6160085 AATTAGTTTTAAATAAA
1 AACTA-TTTTAAA-AAA
*
6160102 AACTAATTTAAAAAA
1 AACTATTTTAAAAAA
6160117 A
1 A
6160118 TTAAATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.11
15 4 0.15
16 13 0.48
17 7 0.26
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (15 bp):
AACTATTTTAAAAAA
Found at i:6163147 original size:52 final size:52
Alignment explanation
Indices: 6163090--6163194 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
6163080 CCCAATGCTG
*
6163090 AATTAACACATCTAATTGTAACCATAATCATAACTATGTTGTTGTTATTATT
1 AATTAACACATCTAATTGTAACCATAATCATAACTATGTTGTTATTATTATT
*
6163142 AATTAACACATCTAATTGTAACCATAATCATAGCTATGTTGTTATTATTATT
1 AATTAACACATCTAATTGTAACCATAATCATAACTATGTTGTTATTATTATT
6163194 A
1 A
6163195 CCTTGTGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (52 bp):
AATTAACACATCTAATTGTAACCATAATCATAACTATGTTGTTATTATTATT
Found at i:6170550 original size:90 final size:91
Alignment explanation
Indices: 6170396--6170574 Score: 306
Period size: 90 Copynumber: 2.0 Consensus size: 91
6170386 CACATCATCT
* *
6170396 ATGATCCAGTTCAATTAAAAAAAGATACATCATCTTTGATTTGAAAGTTTAGTCCAAATGTACAT
1 ATGATCCAGTCCAATTAAAAAAAGACACATCATCTTTGATTTGAAAGTTTAGTCCAAATGTACAT
*
6170461 ATGATGTAGAAAAAAAGATGATATAG
66 ATGATGTAGAAAAAAAAATGATATAG
* *
6170487 ATGATCCCGTCCAATT-AAAAAAGACACATCATCTTTGATTTGGAAGTTTAGTCCAAATGTACAT
1 ATGATCCAGTCCAATTAAAAAAAGACACATCATCTTTGATTTGAAAGTTTAGTCCAAATGTACAT
6170551 ATGATGTAGAAAAAAAAATGATAT
66 ATGATGTAGAAAAAAAAATGATAT
6170575 GTCCTCTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 69 0.83
91 14 0.17
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (91 bp):
ATGATCCAGTCCAATTAAAAAAAGACACATCATCTTTGATTTGAAAGTTTAGTCCAAATGTACAT
ATGATGTAGAAAAAAAAATGATATAG
Found at i:6170751 original size:27 final size:29
Alignment explanation
Indices: 6170693--6170758 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
6170683 TTTTCAACTA
*
6170693 TTTTATTTATCTTAAATAAGATTTTATAT
1 TTTTATTTATATTAAATAAGATTTTATAT
*
6170722 TTTTA-TTATATTAAATTA-ATTTTATAT
1 TTTTATTTATATTAAATAAGATTTTATAT
*
6170749 TTTAATTTAT
1 TTTTATTTAT
6170759 GAACTCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.39
28 15 0.45
29 5 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATTTATATTAAATAAGATTTTATAT
Found at i:6171904 original size:17 final size:18
Alignment explanation
Indices: 6171873--6171906 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6171863 AAACTACATT
6171873 TTTAAAAATAGATATATG
1 TTTAAAAATAGATATATG
6171891 TTTAAAAATA-ATATAT
1 TTTAAAAATAGATATAT
6171907 AATAAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTAAAAATAGATATATG
Found at i:6172094 original size:31 final size:29
Alignment explanation
Indices: 6172059--6172124 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
6172049 ATCCTAAAAT
*
6172059 TATACACGAA-TTATGATTTAATGTGTAATTG
1 TATACACGAACTT-TGATTT--TGTGCAATTG
* *
6172090 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACACGAACTTTGATTTTGTGCAATTG
6172119 TATACA
1 TATACA
6172125 TAAAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.45
31 15 0.48
32 2 0.06
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (29 bp):
TATACACGAACTTTGATTTTGTGCAATTG
Found at i:6172122 original size:29 final size:30
Alignment explanation
Indices: 6172058--6172125 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
6172048 AATCCTAAAA
* *
6172058 TTATACACGAATTATGATTTAATGTGTAATT
1 TTATACATGAATTATGATTT-ATGTGCAATT
*
6172089 GTATACATGAACTT-TGATTT-TGTGCAATT
1 TTATACATGAA-TTATGATTTATGTGCAATT
6172118 TTATACAT
1 TTATACAT
6172126 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 15 0.47
31 15 0.47
32 2 0.06
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (30 bp):
TTATACATGAATTATGATTTATGTGCAATT
Found at i:6174492 original size:26 final size:27
Alignment explanation
Indices: 6174444--6174495 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6174434 TTGAAGTAAT
*
6174444 TAAAAAACAATAGAAAGATTAAATTTG
1 TAAAAAAAAATAGAAAGATTAAATTTG
* *
6174471 TAAAAAAAAATATAATGA-TAAATTT
1 TAAAAAAAAATAGAAAGATTAAATTT
6174496 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (27 bp):
TAAAAAAAAATAGAAAGATTAAATTTG
Found at i:6175560 original size:105 final size:105
Alignment explanation
Indices: 6175378--6175587 Score: 359
Period size: 105 Copynumber: 2.0 Consensus size: 105
6175368 GATATAAAAA
* * *
6175378 ATATTAAAAGTAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACGTAAGGCTCCT
1 ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAAGCTCCT
* *
6175443 ATTAACTTCATTTTTTAGTTAAAAGTATGAA-ACGCTCTAT
66 ATTAAATTCATTTTTTAGTTAAAAATATGAACA-GCTCTAT
6175483 ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAAGCTCCT
1 ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAAGCTCCT
6175548 ATTAAATTCATTTTTTAGTTAAAAATATGAACAGCTCTAT
66 ATTAAATTCATTTTTTAGTTAAAAATATGAACAGCTCTAT
6175588 TTCCTTTTAA
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
105 98 0.99
106 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.38
Consensus pattern (105 bp):
ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAAGCTCCT
ATTAAATTCATTTTTTAGTTAAAAATATGAACAGCTCTAT
Found at i:6182232 original size:39 final size:39
Alignment explanation
Indices: 6182189--6182265 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
6182179 GTCAGTCAAC
* * *
6182189 AAAATGCGAAATTTA-CTAGAATGCTTAGTGGGATTGAAG
1 AAAATG-GAAAATTATCCAGAATGCTTAGTGGGACTGAAG
*
6182228 AAAATGGAAAATTATCCAGAATTCTTAGTGGGACTGAA
1 AAAATGGAAAATTATCCAGAATGCTTAGTGGGACTGAA
6182266 AGGATTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 7 0.21
39 26 0.79
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (39 bp):
AAAATGGAAAATTATCCAGAATGCTTAGTGGGACTGAAG
Found at i:6188746 original size:19 final size:17
Alignment explanation
Indices: 6188704--6188747 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 17
6188694 ATATTTATAA
6188704 ACTCTCCAAGTAATGGC
1 ACTCTCCAAGTAATGGC
6188721 A-TCTCCAAGTAATGGTAC
1 ACTCTCCAAGTAATGG--C
6188739 ACTCTCCAA
1 ACTCTCCAA
6188748 ACAACAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
18 2 0.08
19 7 0.29
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.25
Consensus pattern (17 bp):
ACTCTCCAAGTAATGGC
Found at i:6192108 original size:30 final size:31
Alignment explanation
Indices: 6192044--6192108 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
6192034 AAATAAAATT
* * *
6192044 TTTTGAATAGTTCAGTGATTTAAATGAAAAC
1 TTTTGAACAATTCAGTGATTAAAATGAAAAC
* *
6192075 TTTTGAACAATTCAGTGA-TAAAATTATAAC
1 TTTTGAACAATTCAGTGATTAAAATGAAAAC
6192105 TTTT
1 TTTT
6192109 TTAATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
TTTTGAACAATTCAGTGATTAAAATGAAAAC
Found at i:6193515 original size:19 final size:19
Alignment explanation
Indices: 6193482--6193565 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 19
6193472 TTTTTTCGAT
*
6193482 TTTTATAAAA-GTTACAAA
1 TTTTATAAAATTTTACAAA
6193500 TTTTATAAAATTTTAC-AA
1 TTTTATAAAATTTTACAAA
* * *
6193518 TCTTTTTAAATTTTTA-ATA
1 T-TTTATAAAATTTTACAAA
* *
6193537 TTTTCATTAAAATTTAATAAA
1 TTTT-A-TAAAATTTTACAAA
6193558 TTTTATAA
1 TTTTATAA
6193566 CTTTTATTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
18 16 0.31
19 21 0.40
20 9 0.17
21 6 0.12
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (19 bp):
TTTTATAAAATTTTACAAA
Found at i:6193570 original size:9 final size:9
Alignment explanation
Indices: 6193482--6193572 Score: 51
Period size: 9 Copynumber: 9.7 Consensus size: 9
6193472 TTTTTTCGAT
6193482 TTTTATAAA
1 TTTTATAAA
** *
6193491 AGTTACAAA
1 TTTTATAAA
6193500 TTTTATAAAA
1 TTTTAT-AAA
*
6193510 TTTTA-CAA
1 TTTTATAAA
*
6193518 TCTTTTTAAA
1 T-TTTATAAA
6193528 TTTT-TAATA
1 TTTTATAA-A
6193537 TTTTCATTAAAA
1 TTTT-A-T-AAA
*
6193549 TTTAATAAA
1 TTTTATAAA
*
6193558 TTTTATAAC
1 TTTTATAAA
6193567 TTTTAT
1 TTTTAT
6193573 TGATCTTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
8 6 0.10
9 36 0.58
10 12 0.19
11 1 0.02
12 5 0.08
13 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (9 bp):
TTTTATAAA
Found at i:6207682 original size:25 final size:25
Alignment explanation
Indices: 6207654--6207701 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
6207644 GGTGGCATTC
**
6207654 AATAGAGATTTCCTATTTAAGTAAT
1 AATAGAGAACTCCTATTTAAGTAAT
6207679 AATAGAGAACTCCTATTTAAGTA
1 AATAGAGAACTCCTATTTAAGTA
6207702 TTGTTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (25 bp):
AATAGAGAACTCCTATTTAAGTAAT
Found at i:6215264 original size:24 final size:24
Alignment explanation
Indices: 6215237--6215286 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
6215227 TCATACCATT
6215237 ATTTATTTTAAACACTGCACAGTC
1 ATTTATTTTAAACACTGCACAGTC
6215261 ATTTATTTTAAACACTGCACAGTC
1 ATTTATTTTAAACACTGCACAGTC
6215285 AT
1 AT
6215287 CTTAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (24 bp):
ATTTATTTTAAACACTGCACAGTC
Found at i:6215841 original size:15 final size:15
Alignment explanation
Indices: 6215821--6215853 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6215811 GGGTTTGGTC
6215821 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
*
6215836 TTGGTTCAATTGGGT
1 TTGGTTCAAATGGGT
6215851 TTG
1 TTG
6215854 AGCTTAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.33, T:0.45
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:6221778 original size:12 final size:13
Alignment explanation
Indices: 6221740--6221789 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
6221730 TAAAAATTCC
6221740 TAAATTAAAAT-AA
1 TAAA-TAAAATAAA
6221753 T-AATAATAAT-AA
1 TAAATAA-AATAAA
6221765 TAAAT-AAATAAA
1 TAAATAAAATAAA
6221777 TAAATAAAATAAA
1 TAAATAAAATAAA
6221790 AATATTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 16 0.48
13 11 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:6222900 original size:11 final size:11
Alignment explanation
Indices: 6222884--6222934 Score: 84
Period size: 11 Copynumber: 4.6 Consensus size: 11
6222874 GAACGATCAA
6222884 CGGTCAACGGT
1 CGGTCAACGGT
*
6222895 CGGTCAATGGT
1 CGGTCAACGGT
6222906 CGGTCAACGGT
1 CGGTCAACGGT
*
6222917 CGATCAACGGT
1 CGGTCAACGGT
6222928 CGGTCAA
1 CGGTCAA
6222935 TGGTTTGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (11 bp):
CGGTCAACGGT
Found at i:6222981 original size:15 final size:15
Alignment explanation
Indices: 6222961--6222994 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6222951 GGGTTTGGTG
6222961 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
*
6222976 TTGGTTCAATTGGGT
1 TTGGTTCAAATGGGT
6222991 TTGG
1 TTGG
6222995 GCTTAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:6235543 original size:19 final size:19
Alignment explanation
Indices: 6235519--6235562 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
6235509 GCAAACATTT
6235519 TTTAAATTAATAT-TTAAAA
1 TTTAAATTAAT-TCTTAAAA
*
6235538 TTTAAATTAATTCTTAAAT
1 TTTAAATTAATTCTTAAAA
6235557 TTTAAA
1 TTTAAA
6235563 ATATTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATTAATTCTTAAAA
Found at i:6237544 original size:18 final size:17
Alignment explanation
Indices: 6237523--6237579 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 17
6237513 AAATAATTTA
6237523 AAAATTATAAAAATATTC
1 AAAA-TATAAAAATATTC
*
6237541 AAAA-ATAAAAATAACTTTA
1 AAAATATAAAAAT-A--TTC
6237560 AAAATATAAAAA-ATTC
1 AAAATATAAAAATATTC
6237576 AAAA
1 AAAA
6237580 AAAAAGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 14 0.42
17 1 0.03
18 5 0.15
19 6 0.18
20 7 0.21
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAATATTC
Found at i:6237568 original size:36 final size:34
Alignment explanation
Indices: 6237513--6237584 Score: 110
Period size: 36 Copynumber: 2.1 Consensus size: 34
6237503 TAGCATCAAT
6237513 AAATAATTTAAAAATTATAAAAATATTCAAAAATAA
1 AAATAATTTAAAAATTATAAAAA-ATTCAAAAA-AA
6237549 AAATAACTTTAAAAA-TATAAAAAATTCAAAAAAA
1 AAATAA-TTTAAAAATTATAAAAAATTCAAAAAAA
6237583 AA
1 AA
6237585 GTACATGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 4 0.11
35 9 0.26
36 14 0.40
37 8 0.23
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.26
Consensus pattern (34 bp):
AAATAATTTAAAAATTATAAAAAATTCAAAAAAA
Found at i:6237580 original size:18 final size:18
Alignment explanation
Indices: 6237511--6237581 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
6237501 TGTAGCATCA
* * *
6237511 ATAAATAATTTAAAAATT
1 ATAAAAAATTCAAAAAAT
6237529 ATAAAAATATTC-AAAAAT
1 ATAAAAA-ATTCAAAAAAT
*
6237547 A-AAAATAACTT-TAAAAAT
1 ATAAAA-AA-TTCAAAAAAT
6237565 ATAAAAAATTCAAAAAA
1 ATAAAAAATTCAAAAAA
6237582 AAAGTACATG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 7 0.16
18 29 0.67
19 7 0.16
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAAATTCAAAAAAT
Found at i:6242333 original size:137 final size:137
Alignment explanation
Indices: 6242056--6242314 Score: 412
Period size: 137 Copynumber: 1.9 Consensus size: 137
6242046 ACATAGATAA
* * *
6242056 AATTAATATATGAATTTGAGTTATGCAAAATATTAATTGTATATATTTTACCTAATTTATTAATA
1 AATTAATATATGAATTTGAGTTATACAAAATACTAATTGTATATATTTTACCAAATTTATTAATA
6242121 TAAACATTATATTAATTAATTTCGGTCAAAATAAAAAAGACATGAAAATTAATATTCCTTTGTAA
66 TAAACATTATATTAATTAATTTCGGTCAAAATAAAAAAGACATGAAAATTAATATTCCTTTGTAA
6242186 AGAATAT
131 AGAATAT
*
6242193 AATTAATATATGAATTTTA-TTCATACAAAATACTAATTGTATATATTTTACCAAATTTATTAAT
1 AATTAATATATGAATTTGAGTT-ATACAAAATACTAATTGTATATATTTTACCAAATTTATTAAT
* * * * *
6242257 ATAAATAGTTATATTAATTACTTTTGGTCAAAATATAAAAGACATGATAATTAATATT
65 ATAAACA-TTATATTAATTAATTTCGGTCAAAATAAAAAAGACATGAAAATTAATATT
6242315 GTTTGAAATA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
136 2 0.02
137 63 0.57
138 46 0.41
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (137 bp):
AATTAATATATGAATTTGAGTTATACAAAATACTAATTGTATATATTTTACCAAATTTATTAATA
TAAACATTATATTAATTAATTTCGGTCAAAATAAAAAAGACATGAAAATTAATATTCCTTTGTAA
AGAATAT
Found at i:6242994 original size:17 final size:17
Alignment explanation
Indices: 6242972--6243061 Score: 117
Period size: 17 Copynumber: 5.3 Consensus size: 17
6242962 CCATTTTTAA
*
6242972 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
*
6242989 AAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTT
*
6243006 AAATTTAATTTAAGTTT
1 AAATTTATTTTAAGTTT
*
6243023 AAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTT
* * *
6243040 AAAATTATTCTAAATTT
1 AAATTTATTTTAAGTTT
6243057 AAATT
1 AAATT
6243062 GATAATATCC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 64 1.00
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:6243003 original size:11 final size:11
Alignment explanation
Indices: 6242987--6243040 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
6242977 TATTTTAAGG
6242987 TTAAATTTATT
1 TTAAATTTATT
*
6242998 TTAAATTTAAAT
1 TTAAATTT-ATT
*
6243010 TT-AATTTAAGT
1 TTAAATTT-ATT
6243021 TTAAATTTATT
1 TTAAATTTATT
6243032 TTAAATTTA
1 TTAAATTTA
6243041 AAATTATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 29 0.76
12 9 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:6244940 original size:30 final size:28
Alignment explanation
Indices: 6244904--6245220 Score: 210
Period size: 29 Copynumber: 10.8 Consensus size: 28
6244894 AGAAATCACG
6244904 TTTTGACCCTCAAACTATCCAAAAATTACA
1 TTTT-ACCCTCAAACT-TCCAAAAATTACA
6244934 TTTTGACCCT-AAACTTTTCCAAAAATTACA
1 TTTT-ACCCTCAAAC--TTCCAAAAATTACA
* * *
6244964 TTTTAGCCCTCAAACTTCTAAAAATCAAAA
1 TTTTA-CCCTCAAACTTCCAAAAAT-TACA
6244994 TTTTACCC-CTAAACTTTCCAAAAATTACA
1 TTTTACCCTC-AAAC-TTCCAAAAATTACA
* *
6245023 TTTCAACCCCCAAACTTTCCAAAAATTACA
1 TTT-TACCCTCAAAC-TTCCAAAAATTACA
* ** * *
6245053 TTTTGCCCTTGAACTTTCAAAAATCACA
1 TTTTACCCTCAAACTTCCAAAAATTACA
** * *
6245081 TTTTTACCCTCGTACTT-AAAAAATTCATA
1 -TTTTACCCTCAAACTTCCAAAAATT-ACA
* * * *
6245110 TTTTTGCCCCCGAACTTCTAAAAAATTACA
1 -TTTTACCCTCAAACTTC-CAAAAATTACA
* *
6245140 TTTTTACCC-CGGAACTTCCAAAAATCACCA
1 -TTTTACCCTC-AAACTTCCAAAAATTA-CA
* * *
6245170 TTTTACGCTCAAGCATCCAAAAATTACCA
1 TTTTACCCTCAAACTTCCAAAAATTA-CA
**
6245199 TTTTACCCTCAATTTTCCAAAA
1 TTTTACCCTCAAACTTCCAAAA
6245221 GTTCGACTTC
Statistics
Matches: 235, Mismatches: 36, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
28 19 0.08
29 109 0.46
30 93 0.40
31 14 0.06
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (28 bp):
TTTTACCCTCAAACTTCCAAAAATTACA
Found at i:6245020 original size:59 final size:58
Alignment explanation
Indices: 6244904--6245220 Score: 218
Period size: 59 Copynumber: 5.4 Consensus size: 58
6244894 AGAAATCACG
*
6244904 TTTTGACCCTCAAACTATCCAAAAATTACATTTTGA-CCCTAAACTTTTCCAAAAATTACA
1 TTTTAACCCTCAAACT-TCCAAAAATTACATTTT-ACCCCTAAAC-TTTCCAAAAATTACA
* * * *
6244964 TTTTAGCCCTCAAACTTCTAAAAATCAAAATTTTACCCCTAAACTTTCCAAAAATTACA
1 TTTTAACCCTCAAACTTCCAAAAAT-TACATTTTACCCCTAAACTTTCCAAAAATTACA
* * * * * *
6245023 TTTCAACCCCCAAACTTTCCAAAAATTACATTTTGCCCTTGAACTTT-CAAAAATCACA
1 TTTTAACCCTCAAAC-TTCCAAAAATTACATTTTACCCCTAAACTTTCCAAAAATTACA
* ** * * * ** *
6245081 TTTTTACCCTCGTACTT-AAAAAATTCATATTTTTGCCCCCGAAC-TTCTAAAAAATTACA
1 TTTTAACCCTCAAACTTCCAAAAATT-ACA-TTTTACCCCTAAACTTTC-CAAAAATTACA
* * * * * *
6245140 TTTTTACCC-CGGAACTTCCAAAAATCACCATTTTA-CGCTCAAGC-ATCCAAAAATTACCA
1 TTTTAACCCTC-AAACTTCCAAAAATTA-CATTTTACCCCT-AAACTTTCCAAAAATTA-CA
**
6245199 TTTT-ACCCTCAATTTTCCAAAA
1 TTTTAACCCTCAAACTTCCAAAA
6245221 GTTCGACTTC
Statistics
Matches: 204, Mismatches: 40, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
56 7 0.03
57 6 0.03
58 56 0.27
59 91 0.45
60 44 0.22
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (58 bp):
TTTTAACCCTCAAACTTCCAAAAATTACATTTTACCCCTAAACTTTCCAAAAATTACA
Found at i:6245047 original size:89 final size:89
Alignment explanation
Indices: 6244910--6245089 Score: 240
Period size: 89 Copynumber: 2.0 Consensus size: 89
6244900 CACGTTTTGA
** *
6244910 CCCTCAAACTATCCAAAAATTACATTTTGACCCTAAACTTTTCCAAAAATTACATTTTAGCCCTC
1 CCCTCAAACTATCCAAAAATTACATTTCAACCCCAAACTTTTCCAAAAATTACATTTT-GCCCTC
6244975 AAAC-TTCTAAAAATCAAAATTTTAC
65 AAACTTTC-AAAAATCAAAATTTTAC
* *
6245000 CCCT-AAACTTTCCAAAAATTACATTTCAACCCCCAAAC-TTTCCAAAAATTACATTTTGCCCTT
1 CCCTCAAACTATCCAAAAATTACATTTCAA-CCCCAAACTTTTCCAAAAATTACATTTTGCCCTC
* * *
6245063 GAACTTTCAAAAATCACATTTTTAC
65 AAACTTTCAAAAATCAAAATTTTAC
6245088 CC
1 CC
6245090 TCGTACTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
88 25 0.31
89 44 0.55
90 11 0.14
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (89 bp):
CCCTCAAACTATCCAAAAATTACATTTCAACCCCAAACTTTTCCAAAAATTACATTTTGCCCTCA
AACTTTCAAAAATCAAAATTTTAC
Found at i:6245217 original size:29 final size:28
Alignment explanation
Indices: 6244904--6245220 Score: 151
Period size: 30 Copynumber: 10.8 Consensus size: 28
6244894 AGAAATCACG
*
6244904 TTTTGACCCTCAAACTATCCAAAAATTACA
1 TTTT-ACCCTCAACCT-TCCAAAAATTACA
* *
6244934 TTTTGACCCTAAACTTTTCCAAAAATTACA
1 TTTT-ACCCTCAAC-CTTCCAAAAATTACA
* * * *
6244964 TTTTAGCCCTCAAACTTCTAAAAATCAAAA
1 TTTTA-CCCTCAACCTTCCAAAAAT-TACA
* *
6244994 TTTTACCCCTAAACTTTCCAAAAATTACA
1 TTTTA-CCCTCAACCTTCCAAAAATTACA
* * *
6245023 TTTCAACCCCCAAACTTTCCAAAAATTACA
1 TTT-TACCCTC-AACCTTCCAAAAATTACA
* * * *
6245053 TTTTGCCCTTGAA-CTTTCAAAAATCACA
1 TTTTACCC-TCAACCTTCCAAAAATTACA
* * *
6245081 TTTTTACCCTCGTA-CTT-AAAAAATTCATA
1 -TTTTACCCTC-AACCTTCCAAAAATT-ACA
* * *
6245110 TTTTTGCCCCCGAA-CTTCTAAAAAATTACA
1 -TTTTACCCTC-AACCTTC-CAAAAATTACA
*
6245140 TTTTTACCC-CGGAA-CTTCCAAAAATCACCA
1 -TTTTACCCTC--AACCTTCCAAAAATTA-CA
* * *
6245170 TTTTACGCTCAAGCATCCAAAAATTACCA
1 TTTTACCCTCAACCTTCCAAAAATTA-CA
**
6245199 TTTTACCCTCAATTTTCCAAAA
1 TTTTACCCTCAACCTTCCAAAA
6245221 GTTCGACTTC
Statistics
Matches: 226, Mismatches: 46, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
28 21 0.09
29 97 0.43
30 99 0.44
31 9 0.04
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (28 bp):
TTTTACCCTCAACCTTCCAAAAATTACA
Found at i:6257047 original size:78 final size:78
Alignment explanation
Indices: 6256929--6257863 Score: 903
Period size: 78 Copynumber: 12.0 Consensus size: 78
6256919 GGTAGATTAT
* * **
6256929 AGCCGTTCGATCTTTTACCCCGAGCATGGGGCAGATCATCACCAGCCAATCTCTTACCTTGAGCC
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
*
6256994 TGGGGTAGATTGC
66 TGGGGCAGATTGC
* * * *
6257007 AGCCATTCGCTCTCTTACCCCGAGCTTGGGGCAGATCATCACCAACCAATCTCTTACCTCGAG-C
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
* *
6257071 TCGAGGCAGATTAC
66 T-GGGGCAGATTGC
* * * * * * * * * *
6257085 AGCTGTTCGATCTCTTACCCCAAGCCTAGAGCAAATCATTACCAACTAATCTCTTACCCCGAGCT
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
*
6257150 TGGGGCAGATTAC
66 TGGGGCAGATTGC
** * * * *
6257163 AATCGTTTGATCTCTTTCCCCGAGCTTGGGGTAGATCATCACCAACCAATCTCTTACCCCGAG-C
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
* * *
6257227 TCGGGTCAGGTTGT
66 T-GGGGCAGATTGC
** * * * * *
6257241 AGTTGTTCGATCTCTTACCTCAAGCTTGGGGCAAATAATCACCAGCCAATCTCTTACCTCGAGCC
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
* *
6257306 TAGGGCAGATTGT
66 TGGGGCAGATTGC
* * * * *
6257319 AGTCGTTCGATCTCTTACCCCGAGCTTGGGGCAAAGCATCATCAGCCAATCTCTTACCCTGAGCC
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
** *
6257384 CAGGGCAGGTTGC
66 TGGGGCAGATTGC
* * * ** * * *
6257397 AGCTGTTCGATCTCTAACCCCAAGCTTAAGACAGATCATCACCAGCCAATCTCTTGCCCTGAG-C
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
*
6257461 TCGGGGCA-AGTTAC
66 T-GGGGCAGA-TTGC
** * * * * * *
6257475 AGTTGTTCGATCTCTTACCCCAAGCCTGGGACAGATCATCACTAGCCAATATCTTACCCCAAGCC
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
** **
6257540 T-GGATAGATTAT
66 TGGGGCAGATTGC
** * * * * *
6257552 AATCATTCGATCTCTTACCCCGAGCTTAGGACAGATCATCACCAACCAATCTCTTACCCTGAGCC
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
*
6257617 TTGGGCAGATTGC
66 TGGGGCAGATTGC
* * * * *
6257630 AACCATTCGATCTCTTACCTCGAGCTTGGGGCAGATCATCACCAGCTAATCTCTTACCCCGAGCT
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
*
6257695 TGAGGCAGATTGC
66 TGGGGCAGATTGC
* * * * * * ** *
6257708 AGTCATTCAATCTCTTACTCCGAGCTTGGGGCAAATCATCATCAGTTAATCTCTTACCCCGAGCT
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
6257773 TGGGGCAGATTGC
66 TGGGGCAGATTGC
* * * * *
6257786 AACCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATAATCATCAGCCAATCTC--ACCCCGATCA
1 AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
*
6257849 TGGGGCAGATGGC
66 TGGGGCAGATTGC
6257862 AG
1 AG
6257864 TCATTCGAAG
Statistics
Matches: 708, Mismatches: 140, Indels: 20
0.82 0.16 0.02
Matches are distributed among these distances:
76 21 0.03
77 65 0.09
78 617 0.87
79 5 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (78 bp):
AGCCGTTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCC
TGGGGCAGATTGC
Found at i:6257227 original size:39 final size:39
Alignment explanation
Indices: 6256938--6257858 Score: 403
Period size: 39 Copynumber: 23.7 Consensus size: 39
6256928 TAGCCGTTCG
* * **
6256938 ATCTTTTACCCCGAGCATGGGGCAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
** * * *
6256977 ATCTCTTACCTTGAGCCTGGGGTAGAT--TGCAGCCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAT-CA-CCATTCA
* **
6257016 CTCTCTTACCCCGAGCTTGGGGCAGATCATCACCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* * * * ** *
6257055 ATCTCTTACCTCGAGCTCGAGGCAGATTA-CAGCTGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCA-CCATTCA
* * * * * * *
6257094 ATCTCTTACCCCAAGCCTAGAGCAAATCATTACCA-ACTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTC-A
* * * **
6257133 ATCTCTTACCCCGAGCTTGGGGCAGATTA-CAATCGTTTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATC-ACCATTCA
* * **
6257172 ATCTCTTTCCCCGAGCTTGGGGTAGATCATCACCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* * * ** *** *
6257211 ATCTCTTACCCCGAGCTCGGGTCAGGTTGT-AGTTGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCA-CCATTCA
* * * * **
6257250 ATCTCTTACCTCAAGCTTGGGGCAAATAATCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* * * ** * * *
6257289 ATCTCTTACCTCGAGCCTAGGGCAGATTGT-AGTCGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCA-CCATTCA
* * * **
6257328 ATCTCTTACCCCGAGCTTGGGGCAAAGCATCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* *** * ** *
6257367 ATCTCTTACCCTGAGCCCAGGGCAGGT--TGCAGCTGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAT-CA-CCATTCA
* * ** * **
6257406 ATCTCTAACCCCAAGCTTAAGACAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* * * * *** *
6257445 ATCTCTTGCCCTGAGCTCGGGGCA-AGTTA-CAGTTGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-TCATCA-CCATTCA
* * * * **
6257484 ATCTCTTACCCCAAGCCTGGGACAGATCATCACTAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* * * ** * * * *
6257523 ATATCTTACCCCAAGCCT-GGATAGATTATAATCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* * **
6257561 ATCTCTTACCCCGAGCTTAGGACAGATCATCACCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* *
6257600 ATCTCTTACCCTGAGCCTT-GGGCAGAT--TGCAACCATTCG
1 ATCTCTTACCCCGAG-CTTGGGGCAGATCAT-C-ACCATTCA
* *
6257639 ATCTCTTACCTCGAGCTTGGGGCAGATCATCACCA-GCTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTC-A
* *
6257678 ATCTCTTACCCCGAGCTTGAGGCAGAT--TGCAGTCATTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAT-CA-CCATTCA
* * *
6257717 ATCTCTTACTCCGAGCTTGGGGCAAATCATCATCAGTT-A
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCA-TTCA
* *
6257756 ATCTCTTACCCCGAGCTTGGGGCAGAT--TGCAACCGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAT-C-ACCATTCA
* * **
6257795 ATCTCTTACCCCGAGCTTGGGGCAGATAATCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
* *
6257834 ATCTC--ACCCCGATCATGGGGCAGAT
1 ATCTCTTACCCCGAGCTTGGGGCAGAT
6257859 GGCAGTCATT
Statistics
Matches: 631, Mismatches: 210, Indels: 84
0.68 0.23 0.09
Matches are distributed among these distances:
37 23 0.04
38 49 0.08
39 533 0.84
40 21 0.03
41 5 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCATCACCATTCA
Found at i:6258298 original size:17 final size:17
Alignment explanation
Indices: 6258276--6258399 Score: 158
Period size: 17 Copynumber: 7.3 Consensus size: 17
6258266 ATTTTTTTAA
*
6258276 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
**
6258293 AAATTTATTTTAAAATT
1 AAATTTATTTTAAGTTT
6258310 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
* *
6258327 AAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTT
*
6258344 AAATTTAATTTAAGTTT
1 AAATTTATTTTAAGTTT
*
6258361 AAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTT
* * *
6258378 AAAATTATTCTAAATTT
1 AAATTTATTTTAAGTTT
6258395 AAATT
1 AAATT
6258400 GATAATGTCA
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 93 1.00
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:6258317 original size:34 final size:34
Alignment explanation
Indices: 6258276--6258399 Score: 185
Period size: 34 Copynumber: 3.6 Consensus size: 34
6258266 ATTTTTTTAA
* *
6258276 AAATTTATTTTAAGGTTAAATTTATTTTAAAATT
1 AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
*
6258310 AAATTTATTTTAAGTTTAAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
*
6258344 AAATTTAATTTAAGTTTAAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
* * *
6258378 AAAATTATTCTAAATTTAAATT
1 AAATTTATTTTAAGTTTAAATT
6258400 GATAATGTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 81 1.00
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (34 bp):
AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
Found at i:6258322 original size:11 final size:11
Alignment explanation
Indices: 6258291--6258378 Score: 63
Period size: 11 Copynumber: 7.8 Consensus size: 11
6258281 TATTTTAAGG
6258291 TTAAATTTATT
1 TTAAATTTATT
* *
6258302 TTAAAATTAAAT
1 TT-AAATTTATT
* *
6258314 TT-ATTTTAAGT
1 TTAAATTT-ATT
*
6258325 TTAAATTTGTT
1 TTAAATTTATT
*
6258336 TTAAATTTAAAT
1 TTAAATTT-ATT
*
6258348 TT-AATTTAAGT
1 TTAAATTT-ATT
6258359 TTAAATTTATT
1 TTAAATTTATT
6258370 TTAAATTTA
1 TTAAATTTA
6258379 AAATTATTCT
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
10 3 0.05
11 36 0.60
12 21 0.35
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:6258327 original size:6 final size:6
Alignment explanation
Indices: 6258291--6258399 Score: 79
Period size: 6 Copynumber: 19.2 Consensus size: 6
6258281 TATTTTAAGG
* * * * **
6258291 TTAAAT TT-ATT TTAAAA TTAAAT TT-ATT TTAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
6258336 TTAAAT TTAAAT TT-AAT TTAAGT TTAAAT TT-ATT TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
6258382 TT--AT TCTAAAT TTAAAT T
1 TTAAAT T-TAAAT TTAAAT T
6258400 GATAATGTCA
Statistics
Matches: 78, Mismatches: 17, Indels: 16
0.70 0.15 0.14
Matches are distributed among these distances:
4 2 0.03
5 21 0.27
6 52 0.67
7 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:6260257 original size:27 final size:29
Alignment explanation
Indices: 6260226--6260421 Score: 116
Period size: 30 Copynumber: 6.7 Consensus size: 29
6260216 CTGAATTATC
*
6260226 CAAAAATTACGTTTTGACCCT-AACTTTT
1 CAAAAATTACATTTTGACCCTAAACTTTT
*
6260254 -AAAAATTACATTTTGACCTTAAACTTTT
1 CAAAAATTACATTTTGACCCTAAACTTTT
* * * *
6260282 CCAAAAATTAAATTTTAGCCCCCAAAC-TTC
1 -CAAAAATTACATTTT-GACCCTAAACTTTT
* * *
6260312 CAAAAAACT-CATTTTTACCACCAAAC-TTT
1 C-AAAAATTACATTTTGACC-CTAAACTTTT
* * * **
6260341 CTAAAAATCACATTTTAACCACTGAACTTCC
1 C-AAAAATTACATTTTGACC-CTAAACTTTT
* * **
6260372 CAAAAATTACATTTTTACGCTCGTAC-TTT
1 CAAAAATTACATTTTGACCCT-AAACTTTT
*
6260401 CAAAAATTACATTTTTACCCT
1 CAAAAATTACATTTTGACCCT
6260422 CGTACTTCCA
Statistics
Matches: 132, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
27 18 0.14
28 9 0.07
29 43 0.33
30 53 0.40
31 9 0.07
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTGACCCTAAACTTTT
Found at i:6260347 original size:59 final size:61
Alignment explanation
Indices: 6260274--6260389 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 61
6260264 TTTTGACCTT
* * *
6260274 AAACTTTTCCAAAAATTAAATTTTAGCCCCCAAACTTCCAAAAAACT-CATTTTTACCACC
1 AAACTTTTCCAAAAATCAAATTTTAACCACCAAACTTCCAAAAAACTACATTTTTACCACC
* * ** * *
6260334 AAAC-TTTCTAAAAATCACATTTTAACCACTGAACTTCCCAAAAATTACATTTTTAC
1 AAACTTTTCCAAAAATCAAATTTTAACCACCAAACTTCCAAAAAACTACATTTTTAC
6260390 GCTCGTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
59 33 0.72
60 13 0.28
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.32
Consensus pattern (61 bp):
AAACTTTTCCAAAAATCAAATTTTAACCACCAAACTTCCAAAAAACTACATTTTTACCACC
Found at i:6260408 original size:29 final size:29
Alignment explanation
Indices: 6260343--6260473 Score: 122
Period size: 29 Copynumber: 4.4 Consensus size: 29
6260333 CAAACTTTCT
* * *
6260343 AAAAATCACATTTTAACCACT-GAACTTCCC
1 AAAAATTACATTTTTACC-CTCGTACTT-CC
* *
6260373 AAAAATTACATTTTTACGCTCGTACTTTC
1 AAAAATTACATTTTTACCCTCGTACTTCC
6260402 AAAAATTACATTTTTACCCTCGTACTTCC
1 AAAAATTACATTTTTACCCTCGTACTTCC
* * * * *
6260431 AAAAATCATATTTTTGCCCCCG-AGCATCC
1 AAAAATTACATTTTTACCCTCGTA-CTTCC
6260460 AAAAATTATCATTT
1 AAAAATTA-CATTT
6260474 CATCCTCAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.01
29 59 0.70
30 24 0.29
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTCGTACTTCC
Found at i:6260489 original size:29 final size:29
Alignment explanation
Indices: 6260457--6260552 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
6260447 CCCCCGAGCA
* * *
6260457 TCCAAAAATT-ATCATTTCATCCTCAATTT
1 TCCAAAAATTCAAC-TTTAATCCTAAATTT
*
6260486 TCCAAAAGTTCAACTTTAATCCTAAATTT
1 TCCAAAAATTCAACTTTAATCCTAAATTT
* * *
6260515 TTCAAAAATTTCAATTTTAACCCTAAATTCT
1 TCCAAAAA-TTCAACTTTAATCCTAAATT-T
*
6260546 TCGAAAA
1 TCCAAAA
6260553 TCACATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 28 0.52
30 20 0.37
31 6 0.11
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.39
Consensus pattern (29 bp):
TCCAAAAATTCAACTTTAATCCTAAATTT
Found at i:6260528 original size:30 final size:29
Alignment explanation
Indices: 6260459--6260553 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
6260449 CCCGAGCATC
* *
6260459 CAAAAATTATC-ATTTCATCCTCAA-TTTT
1 CAAAAATT-TCAATTTAATCCTAAATTTTT
* *
6260487 CCAAAAGTTCAACTTTAATCCTAAATTTTT
1 CAAAAATTTCAA-TTTAATCCTAAATTTTT
* *
6260517 CAAAAATTTCAATTTTAACCCTAAATTCTT
1 CAAAAATTTCAA-TTTAATCCTAAATTTTT
*
6260547 CGAAAAT
1 CAAAAAT
6260554 CACATTTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 10 0.19
30 35 0.65
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (29 bp):
CAAAAATTTCAATTTAATCCTAAATTTTT
Found at i:6260563 original size:30 final size:30
Alignment explanation
Indices: 6260500--6260563 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
6260490 AAAGTTCAAC
* * **
6260500 TTTAATCCTAAATTTTTCAAAAATTTCAAT
1 TTTAACCCTAAATTCTTCAAAAATCACAAT
* *
6260530 TTTAACCCTAAATTCTTCGAAAATCACATT
1 TTTAACCCTAAATTCTTCAAAAATCACAAT
6260560 TTTA
1 TTTA
6260564 TCTCGGACTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTAACCCTAAATTCTTCAAAAATCACAAT
Found at i:6265295 original size:20 final size:18
Alignment explanation
Indices: 6265267--6265353 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 18
6265257 CCATGTCAAC
*
6265267 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
6265287 AAATTATTTTTAAAATATA
1 AAATTA-TTTTAAAATATA
** *
6265306 AAATTATTAAAATTAATTTA
1 AAATTATTTTAA--AATATA
6265326 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
6265346 AAATTATT
1 AAATTATT
6265354 AAAATCATCA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
18 6 0.11
19 8 0.15
20 29 0.53
21 8 0.15
22 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:6265316 original size:28 final size:27
Alignment explanation
Indices: 6265276--6265329 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
6265266 CAAATAATTT
*
6265276 TAAAATTATTAAAATTATTTTTAAAATA
1 TAAAATTATTAAAATTA-ATTTAAAATA
6265304 TAAAATTATTAAAATTAATTTAAAAT
1 TAAAATTATTAAAATTAATTTAAAAT
6265330 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAAATTATTAAAATTAATTTAAAATA
Found at i:6265346 original size:40 final size:37
Alignment explanation
Indices: 6265271--6265358 Score: 142
Period size: 40 Copynumber: 2.3 Consensus size: 37
6265261 GTCAACAAAT
6265271 AATT-TTAAAATTATTAAAATTATTTTTAAAATATAA
1 AATTATTAAAATTATTAAAATTATTTTTAAAATATAA
6265307 AATTATTAAAATTAATTTAAAATTATTTTTTAAAATATAA
1 AATTATTAAAATT-A-TTAAAATTA-TTTTTAAAATATAA
6265347 AATTATTAAAAT
1 AATTATTAAAAT
6265359 CATCATCATC
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
36 4 0.08
37 8 0.17
38 1 0.02
39 9 0.19
40 26 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
AATTATTAAAATTATTAAAATTATTTTTAAAATATAA
Found at i:6271108 original size:21 final size:23
Alignment explanation
Indices: 6271070--6271111 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
6271060 CAGCAAATGA
6271070 TTTTAAAATTATTAAAATTATAT
1 TTTTAAAATTATTAAAATTATAT
6271093 TTTTAAAA-TA-TAAAATTAT
1 TTTTAAAATTATTAAAATTAT
6271112 GAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAAAATTATTAAAATTATAT
Found at i:6273606 original size:17 final size:19
Alignment explanation
Indices: 6273566--6273606 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
6273556 AATTCCAATG
6273566 CATTATTAAATTTATTATAA
1 CATT-TTAAATTTATTATAA
6273586 -ATTTTAAA-TTATTA-AA
1 CATTTTAAATTTATTATAA
6273602 CATTT
1 CATTT
6273607 AATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 10 0.50
18 5 0.25
19 3 0.15
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
CATTTTAAATTTATTATAA
Found at i:6273863 original size:5 final size:5
Alignment explanation
Indices: 6273853--6273878 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6273843 AAAATTATAC
6273853 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
6273879 TTATATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:6273913 original size:14 final size:15
Alignment explanation
Indices: 6273884--6273921 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6273874 AAATATTATA
*
6273884 TTAATAAAAATAAAT
1 TTAAGAAAAATAAAT
*
6273899 TTAAGAAAAATAATT
1 TTAAGAAAAATAAAT
6273914 TTAA-AAAA
1 TTAAGAAAA
6273922 CAAGAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
TTAAGAAAAATAAAT
Found at i:6274021 original size:16 final size:16
Alignment explanation
Indices: 6273994--6274032 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6273984 AATAAATTTT
*
6273994 TAATACAAATTTAGTAC
1 TAATA-AAATTTAATAC
*
6274011 TTATAAAATTTAATAC
1 TAATAAAATTTAATAC
6274027 TAATAA
1 TAATAA
6274033 TTTAACATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (16 bp):
TAATAAAATTTAATAC
Found at i:6274495 original size:42 final size:42
Alignment explanation
Indices: 6274436--6274520 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
6274426 ACCCAGACTG
*
6274436 TATAAATTTTGAGCCATCTGTTTGTTGAAACTTGGCCACGCC
1 TATAAATTTTGAGCCATCTGTTCGTTGAAACTTGGCCACGCC
6274478 TATAAATTTTGAGCCATCTGTTCGTTGAAACTTGGCCACGCC
1 TATAAATTTTGAGCCATCTGTTCGTTGAAACTTGGCCACGCC
6274520 T
1 T
6274521 TATCCACACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (42 bp):
TATAAATTTTGAGCCATCTGTTCGTTGAAACTTGGCCACGCC
Found at i:6278574 original size:24 final size:25
Alignment explanation
Indices: 6278538--6278584 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
6278528 TAAAAATCTT
6278538 TTTTAGAAATTAAAAT-ATTTAAAA
1 TTTTAGAAATTAAAATAATTTAAAA
** *
6278562 TTTTAGATTTTAAATTAATTTAA
1 TTTTAGAAATTAAAATAATTTAA
6278585 TTTTATTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTTAGAAATTAAAATAATTTAAAA
Found at i:6283697 original size:33 final size:33
Alignment explanation
Indices: 6283627--6283698 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
6283617 TGATTATTAG
* * *
6283627 ATACATCTACTCTAAGTACATTAATTAAACTAG
1 ATACATCTACTCTAAGTACATCAATTAAAATAA
* *
6283660 ATACATCTACTTTAA-TACATCCATTAAATATAA
1 ATACATCTACTCTAAGTACATCAATTAAA-ATAA
6283693 ATACAT
1 ATACAT
6283699 GCAAGTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (33 bp):
ATACATCTACTCTAAGTACATCAATTAAAATAA
Found at i:6298556 original size:17 final size:17
Alignment explanation
Indices: 6298531--6298566 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6298521 GGAAAAGGTG
*
6298531 GAGTACTTGTTCGTTGA
1 GAGTACTTGTTCGTAGA
*
6298548 GAGTTCTTGTTCGTAGA
1 GAGTACTTGTTCGTAGA
6298565 GA
1 GA
6298567 ACTCTTGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.31, T:0.39
Consensus pattern (17 bp):
GAGTACTTGTTCGTAGA
Found at i:6298572 original size:17 final size:17
Alignment explanation
Indices: 6298536--6298574 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6298526 AGGTGGAGTA
* **
6298536 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAACT
6298553 CTTGTTCGTAGAGAACT
1 CTTGTTCGTAGAGAACT
6298570 CTTGT
1 CTTGT
6298575 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (17 bp):
CTTGTTCGTAGAGAACT
Found at i:6299485 original size:22 final size:22
Alignment explanation
Indices: 6299458--6299505 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6299448 AAATAACATT
* *
6299458 AAAATAGTAAGAAAACAATAAG
1 AAAATAATAAGAAAACAACAAG
* *
6299480 AAAATAATGAGAAACCAACAAG
1 AAAATAATAAGAAAACAACAAG
6299502 AAAA
1 AAAA
6299506 CATCAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAATAATAAGAAAACAACAAG
Found at i:6302383 original size:6 final size:7
Alignment explanation
Indices: 6302366--6302395 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
6302356 ATCCATCCTT
6302366 TTTTTTA
1 TTTTTTA
6302373 TTTTTTA
1 TTTTTTA
6302380 TTTTTTA
1 TTTTTTA
6302387 -TTTTTA
1 TTTTTTA
6302393 TTT
1 TTT
6302396 AGCGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:6302385 original size:14 final size:13
Alignment explanation
Indices: 6302366--6302395 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
6302356 ATCCATCCTT
6302366 TTTTTTATTTTTTA
1 TTTTTTA-TTTTTA
6302380 TTTTTTATTTTTA
1 TTTTTTATTTTTA
6302393 TTT
1 TTT
6302396 AGCGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:6304547 original size:30 final size:30
Alignment explanation
Indices: 6304494--6304729 Score: 332
Period size: 30 Copynumber: 7.9 Consensus size: 30
6304484 GGATTTAGGG
* *
6304494 AAGTTTGGGGGT-AAAATGGTAATTTTTG-A
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAA
* * *
6304523 AAGTTTAGGGGGTCAAAATATAATTTTAGAA
1 AAGTTT-TGGGGTCAAAATGTAATTTTGGAA
**
6304554 AAGTTTTGGGGTCAAAATGTGGTTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * *
6304584 GAGTTTTGGGGTAAAAATGTAATTATGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
6304614 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
6304644 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
6304674 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
6304704 AAGTTTTGGGGTCTAAATATAATTTT
1 AAGTTTTGGGGTCAAAATGTAATTTT
6304730 TGAATAATTT
Statistics
Matches: 187, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
29 6 0.03
30 169 0.90
31 12 0.06
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:6305729 original size:3 final size:3
Alignment explanation
Indices: 6305718--6305763 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
6305708 CCTTTTTTTT
6305718 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6305764 ATTGATGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6306552 original size:6 final size:6
Alignment explanation
Indices: 6306543--6306642 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
6306533 TTTTTTTATG
* * ** * *
6306543 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
6306591 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
6306638 TTAAA
1 TTAAA
6306643 ATCAATTTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.05
5 7 0.09
6 54 0.72
7 4 0.05
8 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:6306589 original size:17 final size:16
Alignment explanation
Indices: 6306569--6306647 Score: 90
Period size: 17 Copynumber: 4.9 Consensus size: 16
6306559 AATTTTTATT
6306569 TAAATTTAAATTCAAA
1 TAAATTTAAATTCAAA
*
6306585 GTAAATTTAAA-T-AAT
1 -TAAATTTAAATTCAAA
*
6306600 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTCAAA
*
6306617 TAAATTTAAATTTAAA
1 TAAATTTAAATTCAAA
*
6306633 TAAATTTAAAATCAA
1 TAAATTTAAATTCAA
6306648 TTTAACTCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
14 10 0.19
15 2 0.04
16 20 0.37
17 22 0.41
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTCAAA
Found at i:6306603 original size:31 final size:32
Alignment explanation
Indices: 6306568--6306647 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
6306558 TAATTTTTAT
*
6306568 TTAAATTTAAATTCAAAGTAAATTTAAA-TAA
1 TTAAATTTAAATTCAAAATAAATTTAAATTAA
*
6306599 TTAAATTTAAATTTAAAATAAATTTAAATTTAA
1 TTAAATTTAAATTCAAAATAAATTTAAA-TTAA
* *
6306632 ATAAATTTAAAATCAA
1 TTAAATTTAAATTCAA
6306648 TTTAACTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAATTTAAATTCAAAATAAATTTAAATTAA
Found at i:6306659 original size:27 final size:27
Alignment explanation
Indices: 6306606--6306660 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
6306596 TAATTAAATT
*
6306606 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
* *
6306633 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
6306660 T
1 T
6306661 TAAACGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:6307115 original size:69 final size:68
Alignment explanation
Indices: 6306997--6307491 Score: 720
Period size: 68 Copynumber: 7.1 Consensus size: 68
6306987 GGAAATGATC
* *
6306997 TTGCTCTTATTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGAT
6307062 GACG
65 GACG
* * * *
6307066 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT
6307131 AGGAAACGATG
65 --G--AC---G
* * * *
6307142 TTACTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGAT
6307207 GACG
65 GACG
* *
6307211 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGGTG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
6307276 ACG
66 ACG
* * *
6307279 TCGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCTCTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
6307344 ACA
66 ACG
*
6307347 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
6307412 ACG
66 ACG
*
6307415 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGAT
*
6307480 AACG
65 GACG
6307484 TTGCTCTT
1 TTGCTCTT
6307492 GTTTGGTCTG
Statistics
Matches: 388, Mismatches: 28, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
68 195 0.50
69 128 0.33
71 1 0.00
72 2 0.01
73 2 0.01
74 1 0.00
76 58 0.15
77 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
ACG
Found at i:6307219 original size:145 final size:142
Alignment explanation
Indices: 6306956--6307491 Score: 734
Period size: 145 Copynumber: 3.8 Consensus size: 142
6306946 AAGATTTTGC
* * * * *
6306956 TATCCAACTTTACTTCAATTTCTAGAGGATAGGAAATGATCTTGCTCTTATTTCAATTTCAGAGA
1 TATCC-ACTCTACTTCAATTTCAAGAGGAT-GGAAACG-TGTTGCTCTTACTTCAATTTCAGAGA
*
6307021 TAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
63 TAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
* *
6307086 GAGATAAAGACTTGA
128 GAGATAAAGACGTGT
* * * *
6307101 TATCCAGTTTTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCTACTTCAATTTCAGAGA
1 TATCCA-CTCTACTTCAATTTCAAGAGGAT-GGAAACG-TGTTGCTCTTACTTCAATTTCAGAGA
* *
6307166 TGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
63 TAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
6307231 GAGATAAAGACGTGT
128 GAGATAAAGACGTGT
** *
6307246 TATCCACTCTACTTCAATTTCAAG-GG--GGTGAC--GTCGCTCTTACTTCAATTTCAGAGATAA
1 TATCCACTCTACTTCAATTTCAAGAGGATGGAAACGTGTTGCTCTTACTTCAATTTCAGAGATAA
* * *
6307306 AGACGTGTTATCC-TCTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAG
66 AGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAG
6307370 ATAAAGACGTGT
131 ATAAAGACGTGT
* *
6307382 TATCCACTCTACTTCAATTTCAAGGGGAT-G--AC--GTTGCTCTTACTTCAATTTCAGAGATGA
1 TATCCACTCTACTTCAATTTCAAGAGGATGGAAACGTGTTGCTCTTACTTCAATTTCAGAGATAA
*
6307442 AGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAACGTTGCTCTT
66 AGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTT
6307492 GTTTGGTCTG
Statistics
Matches: 356, Mismatches: 30, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
136 125 0.35
137 70 0.20
138 1 0.00
140 4 0.01
143 2 0.01
144 17 0.05
145 137 0.38
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (142 bp):
TATCCACTCTACTTCAATTTCAAGAGGATGGAAACGTGTTGCTCTTACTTCAATTTCAGAGATAA
AGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAG
ATAAAGACGTGT
Found at i:6319409 original size:29 final size:28
Alignment explanation
Indices: 6319369--6319626 Score: 87
Period size: 29 Copynumber: 8.8 Consensus size: 28
6319359 ATCGAGGTTA
* *
6319369 AAAATGGGATTTAGGGAAGTTTAGGGGT
1 AAAATGGAATTTAGGAAAGTTTAGGGGT
** *
6319397 AAAATGGTAATTTTTGAAAGTTTTGGGGT
1 AAAATGG-AATTTAGGAAAGTTTAGGGGT
** *
6319426 AAAATATAATTTTAGAAAAGTTTTA-GGGT
1 AAAATGGAA-TTTAGGAAAG-TTTAGGGGT
* * *
6319455 CAAAATGTG-GTTTTGGAAGAGTTT-CGGGT
1 -AAAATG-GAATTTAGGAA-AGTTTAGGGGT
* *
6319484 CAAAATGTAATTGT-GGAAAAGTTT-TGGGT
1 -AAAATGGAATT-TAGG-AAAGTTTAGGGGT
* * *
6319513 CAAAATGTAATTTTGGAAAAGTTTTAGGGTT
1 -AAAATGGAATTTAGG-AAAG-TTTAGGGGT
* * *
6319544 AAAATGTAATTTTGGAAAAGTTTTA-GGAT
1 AAAATGGAATTTAGG-AAAG-TTTAGGGGT
* * * *
6319573 CAAAATGTAATTTTGGAAAAGTTTTGAGGTT
1 -AAAATGGAATTTAGG-AAAGTTTAG-GGGT
* *
6319604 AAAATGTAATTTTAGAAAAGTTT
1 AAAATGGAA-TTTAGGAAAGTTT
6319627 TAAGGTTTAA
Statistics
Matches: 187, Mismatches: 26, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
28 10 0.05
29 90 0.48
30 77 0.41
31 10 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTAGGAAAGTTTAGGGGT
Found at i:6319412 original size:59 final size:59
Alignment explanation
Indices: 6319215--6319412 Score: 188
Period size: 59 Copynumber: 3.4 Consensus size: 59
6319205 TTGGGTTTTA
* *
6319215 AGGGGTAAAATGGTAATTTTT-GTGAAATCGGGGCTAAAAATGGAATTTA-GAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTAGGAAAGTTT
* * ** * * * * *
6319272 -GGGGAATAAAATGATAAATTTTGGCAAAAACAAGGTCAAAAATGAAATTTTGGAAAG-TT
1 AGGGG--TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTAGGAAAGTTT
* * * * * *
6319331 CGGAGGCAAAACGGTAAGTTTTGGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTT
1 AGG-GGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTAGGAAAGTTT
6319391 AGGGGTAAAATGGTAATTTTTG
1 AGGGGTAAAATGGTAATTTTTG
6319413 AAAGTTTTGG
Statistics
Matches: 106, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
56 4 0.04
58 14 0.13
59 75 0.71
60 11 0.10
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (59 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTAGGAAAGTTT
Found at i:6319478 original size:30 final size:30
Alignment explanation
Indices: 6319388--6319628 Score: 296
Period size: 30 Copynumber: 8.1 Consensus size: 30
6319378 TTTAGGGAAG
*
6319388 TTTAGGGGT-AAAATGGTAATTTTTG-AAAGT
1 TTTA-GGGTCAAAAT-GTAATTTTGGAAAAGT
* * *
6319418 TTTGGGGT-AAAATATAATTTTAGAAAAGT
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGT
** *
6319447 TTTAGGGTCAAAATGTGGTTTTGGAAGAG-
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGT
* *
6319476 TTTCGGGTCAAAATGTAATTGTGGAAAAGT
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGT
6319506 TTT-GGGTCAAAATGTAATTTTGGAAAAGT
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGT
*
6319535 TTTAGGGTTAAAATGTAATTTTGGAAAAGT
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGT
*
6319565 TTTAGGATCAAAATGTAATTTTGGAAAAGT
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGT
* *
6319595 TTT-GAGGTTAAAATGTAATTTTAGAAAAGT
1 TTTAG-GGTCAAAATGTAATTTTGGAAAAGT
6319625 TTTA
1 TTTA
6319629 AGGTTTAAAT
Statistics
Matches: 184, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
28 8 0.04
29 74 0.40
30 102 0.55
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
TTTAGGGTCAAAATGTAATTTTGGAAAAGT
Found at i:6319645 original size:60 final size:58
Alignment explanation
Indices: 6319397--6319628 Score: 304
Period size: 59 Copynumber: 3.9 Consensus size: 58
6319387 GTTTAGGGGT
* * *
6319397 AAAATGGTAATTTTTG-AAAGTTTTGGGGTAAAATATAATTTTAGAAAAGTTTTAGGGTC
1 AAAAT-GTAATTTTGGAAAAGTTTTGGGTTAAAATGTAATTTTAGAAAAGTTTTA-GGTC
** * * * * * *
6319456 AAAATGTGGTTTTGGAAGAGTTTCGGGTCAAAATGTAATTGTGGAAAAGTTTTGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGTTAAAATGTAATTTTAGAAAAGTTTTAGGTC
*
6319514 AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGATC
1 AAAATGTAATTTTGGAAAAGTTTT-GGGTTAAAATGTAATTTTAGAAAAGTTTTAGG-TC
6319574 AAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTAGAAAAGTTTTA
1 AAAATGTAATTTTGGAAAAGTTTTG-GGTTAAAATGTAATTTTAGAAAAGTTTTA
6319629 AGGTTTAAAT
Statistics
Matches: 150, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
58 31 0.21
59 65 0.43
60 54 0.36
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGTTAAAATGTAATTTTAGAAAAGTTTTAGGTC
Found at i:6320646 original size:3 final size:3
Alignment explanation
Indices: 6320635--6320671 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
6320625 TTTTTTTTAT
6320635 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6320672 ATTGATGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6321460 original size:6 final size:6
Alignment explanation
Indices: 6321451--6321550 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
6321441 TTTTTTTATG
* * ** * *
6321451 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
6321499 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
6321546 TTAAA
1 TTAAA
6321551 ATCAATTTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.05
5 7 0.09
6 54 0.72
7 4 0.05
8 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:6321497 original size:17 final size:16
Alignment explanation
Indices: 6321477--6321555 Score: 90
Period size: 17 Copynumber: 4.9 Consensus size: 16
6321467 AATTTTTATT
6321477 TAAATTTAAATTCAAA
1 TAAATTTAAATTCAAA
*
6321493 GTAAATTTAAA-T-AAT
1 -TAAATTTAAATTCAAA
*
6321508 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTCAAA
*
6321525 TAAATTTAAATTTAAA
1 TAAATTTAAATTCAAA
*
6321541 TAAATTTAAAATCAA
1 TAAATTTAAATTCAA
6321556 TTTAACTCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
14 10 0.19
15 2 0.04
16 20 0.37
17 22 0.41
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTCAAA
Found at i:6321511 original size:31 final size:32
Alignment explanation
Indices: 6321476--6321555 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
6321466 TAATTTTTAT
*
6321476 TTAAATTTAAATTCAAAGTAAATTTAAA-TAA
1 TTAAATTTAAATTCAAAATAAATTTAAATTAA
*
6321507 TTAAATTTAAATTTAAAATAAATTTAAATTTAA
1 TTAAATTTAAATTCAAAATAAATTTAAA-TTAA
* *
6321540 ATAAATTTAAAATCAA
1 TTAAATTTAAATTCAA
6321556 TTTAACTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAATTTAAATTCAAAATAAATTTAAATTAA
Found at i:6321567 original size:27 final size:27
Alignment explanation
Indices: 6321514--6321568 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
6321504 TAATTAAATT
*
6321514 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
* *
6321541 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
6321568 T
1 T
6321569 TAAACGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:6322272 original size:29 final size:29
Alignment explanation
Indices: 6322230--6322298 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
6322220 ATATATGAAC
6322230 TTTAATTTAATGTACAA-TGTAATACAT-AAAT
1 TTTAATTT--TGTACAATTGT-AT-CATGAAAT
*
6322261 TTTAATTTTGTAGAATTGTATCATGAAAT
1 TTTAATTTTGTACAATTGTATCATGAAAT
*
6322290 TTTTATTTT
1 TTTAATTTT
6322299 AGTTCAATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 20 0.59
30 3 0.09
31 8 0.24
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (29 bp):
TTTAATTTTGTACAATTGTATCATGAAAT
Found at i:6322472 original size:43 final size:42
Alignment explanation
Indices: 6322416--6322502 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 42
6322406 AATTTATTTT
* *
6322416 TATAAATATATATAATTGAATCAAAATAATAGTTTCTTATATA
1 TATAAATATATATAATTGAAGCAAAATAA-AGTTTCATATATA
* *
6322459 TATATATATATATAATTGAAGCAAAATAAAGTTTGATATATA
1 TATAAATATATATAATTGAAGCAAAATAAAGTTTCATATATA
6322501 TA
1 TA
6322503 ATTGCACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 13 0.32
43 27 0.68
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.40
Consensus pattern (42 bp):
TATAAATATATATAATTGAAGCAAAATAAAGTTTCATATATA
Found at i:6328718 original size:66 final size:66
Alignment explanation
Indices: 6328612--6328737 Score: 216
Period size: 66 Copynumber: 1.9 Consensus size: 66
6328602 TGAAAGTTAG
*
6328612 AACTTTGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
1 AACTTAGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
6328677 A
66 A
* * *
6328678 AACTTAGAAGAGTGCTTTAGGATTCATGGATGTAGTTTGACTAGGACCAAAACTGAATAA
1 AACTTAGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAA
6328738 TAGGATGTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (66 bp):
AACTTAGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
A
Found at i:6334518 original size:30 final size:30
Alignment explanation
Indices: 6334479--6334542 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
6334469 AAAAAATATG
*
6334479 AAAACTATTTATAAAAATTAAAAATTATAA
1 AAAAATATTTATAAAAATTAAAAATTATAA
* * * * *
6334509 AAAAATATTTGTAATATTTTAAAATTTTAA
1 AAAAATATTTATAAAAATTAAAAATTATAA
6334539 AAAA
1 AAAA
6334543 TTAATTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATATTTATAAAAATTAAAAATTATAA
Found at i:6336892 original size:19 final size:19
Alignment explanation
Indices: 6336851--6336899 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
6336841 TACTATTTCC
*
6336851 AAATACAAAAACATGTGAA
1 AAATACAAAAACAAGTGAA
*
6336870 AAATACAAAAAGAAGT-AA
1 AAATACAAAAACAAGTGAA
*
6336888 TAAATATAAAAA
1 -AAATACAAAAA
6336900 AGTTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.16
Consensus pattern (19 bp):
AAATACAAAAACAAGTGAA
Found at i:6338181 original size:21 final size:21
Alignment explanation
Indices: 6338156--6338206 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6338146 GAATTACGTA
* *
6338156 ATTTGGGTTTATAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
6338177 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
6338198 ATTTGGATT
1 ATTTGGATT
6338207 ATGCTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:6339953 original size:163 final size:164
Alignment explanation
Indices: 6339650--6339976 Score: 604
Period size: 164 Copynumber: 2.0 Consensus size: 164
6339640 ATCAAACGAA
*
6339650 AAGAGAAAGAAAAGGTTGTATGAAATTGTGATTTCACGTTATTCTTATTTTTTTATAAGAGAATG
1 AAGAGAAAGAAAAGATTGTATGAAATTGTGATTTCACGTTATTCTTATTTTTTTATAAGAGAATG
6339715 ACAAATCAGATTTTTTTCAGTATTTTTAATTAGATTTAATTATTTTAATGAGAAAAAACTAAAAA
66 ACAAATCAGATTTTTTTCAGTATTTTTAATTAGATTTAATTATTTTAATGAGAAAAAACTAAAAA
6339780 TCAGG-AAAAAAATTCAATTTGTCATTCATTTAT
131 TCAGGAAAAAAAATTCAATTTGTCATTCATTTAT
6339813 AAGAGAAAGAAAAGATTGTATGAAATTGTGATTTCACGTTATTCTTATTTTTTTATAAGAGAATG
1 AAGAGAAAGAAAAGATTGTATGAAATTGTGATTTCACGTTATTCTTATTTTTTTATAAGAGAATG
*
6339878 ACAAATCAGATTTTTTTTTAGTATTTTTAATTAGATTTAATTATTTTAATGAGAAAAAACTAAAA
66 ACAAATCAGA-TTTTTTTCAGTATTTTTAATTAGATTTAATTATTTTAATGAGAAAAAACTAAAA
*
6339943 ATCA-GAAAAAAAATTTAATTTGTCATTCATTTAT
130 ATCAGGAAAAAAAATTCAATTTGTCATTCATTTAT
6339977 TGAAAAGAGA
Statistics
Matches: 159, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
163 75 0.47
164 84 0.53
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (164 bp):
AAGAGAAAGAAAAGATTGTATGAAATTGTGATTTCACGTTATTCTTATTTTTTTATAAGAGAATG
ACAAATCAGATTTTTTTCAGTATTTTTAATTAGATTTAATTATTTTAATGAGAAAAAACTAAAAA
TCAGGAAAAAAAATTCAATTTGTCATTCATTTAT
Found at i:6341800 original size:2 final size:2
Alignment explanation
Indices: 6341793--6341826 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6341783 TTTATGGTAA
6341793 AT AT AT 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 AT AT AT
6341827 TTAATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6342702 original size:30 final size:30
Alignment explanation
Indices: 6342630--6342703 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
6342620 AAATTTTAAA
* *
6342630 TTAATAATGAT-AAATTTGTACTTTAACCT
1 TTAAAAATGATAAAATTTGTAATTTAACCT
**
6342659 TTCCAAATGATAAAATTT-TAATTTAATCCT
1 TTAAAAATGATAAAATTTGTAATTTAA-CCT
*
6342689 TTAAAAATTATAAAA
1 TTAAAAATGATAAAA
6342704 ATATAGACTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (30 bp):
TTAAAAATGATAAAATTTGTAATTTAACCT
Found at i:6346885 original size:14 final size:15
Alignment explanation
Indices: 6346857--6346885 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6346847 ATTGAAAAGC
6346857 AAAATATGAAAAGTT
1 AAAATATGAAAAGTT
6346872 AAAATA-GAAAAGTT
1 AAAATATGAAAAGTT
6346886 GACTGAACCT
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:0.00, G:0.14, T:0.24
Consensus pattern (15 bp):
AAAATATGAAAAGTT
Found at i:6354420 original size:5 final size:5
Alignment explanation
Indices: 6354410--6354435 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6354400 GAAAGTGGAG
6354410 GGAAA GGAAA GGAAA GGAAA GGAAA G
1 GGAAA GGAAA GGAAA GGAAA GGAAA G
6354436 AATCGGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:6355902 original size:30 final size:30
Alignment explanation
Indices: 6355866--6356302 Score: 371
Period size: 30 Copynumber: 14.8 Consensus size: 30
6355856 ATTACGGAGA
* *
6355866 CAAAATGTAATTTTGGAAAAATATAGGGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
* *
6355896 CAAAATGAAATTTTAGG-GAAGTTTAGGGGT
1 CAAAATGTAATTTT-GGAAAAGTTTAGGGGT
* * *
6355926 CAAAATGTAGTTCTGGAAAAGTTTAAGGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
* * * *
6355956 TAAAATGTGATTTTAGG-AAATTTTGGGGGT
1 CAAAATGTAATTTT-GGAAAAGTTTAGGGGT
* * *
6355986 CAAAATGTAATTTTTGAAAAATTTA-TGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
*
6356015 CAAAATGTAGTTTTGGAAAAGTTT-GAGGGT
1 CAAAATGTAATTTTGGAAAAGTTTAG-GGGT
* *
6356045 TAAAATGTGATTTTAGG-AAAGTTTAGGGGT
1 CAAAATGTAATTTT-GGAAAAGTTTAGGGGT
* * **
6356075 TAAAATGTGATTTTAGG--AAGTTTATGGTTT
1 CAAAATGTAATTTT-GGAAAAGTTTA-GGGGT
* *
6356105 CAAAATGTAATTTTGGAAATA-TTTAAGGTT
1 CAAAATGTAATTTTGGAAA-AGTTTAGGGGT
* *
6356135 TAAAATGTAATTTTAGG-AAAGTTTAAGGGT
1 CAAAATGTAATTTT-GGAAAAGTTTAGGGGT
* *
6356165 TAAAATGTAATTTTGGAATAGTTTA-GGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
* *
6356194 -TAAATGTAATTTTGGAAAAATTTAGGGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
* * *
6356223 TAAAATGTAA-TTTGG-GAAGTTT-GGAGT
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
* *
6356250 CAAAATGTAATTTTGGAAAAGTTTAGAGGA
1 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
** *
6356280 CAAAATACAATTTTGGAAGAGTT
1 CAAAATGTAATTTTGGAAAAGTT
6356303 CAAGGGCTTT
Statistics
Matches: 334, Mismatches: 53, Indels: 40
0.78 0.12 0.09
Matches are distributed among these distances:
27 13 0.04
28 31 0.09
29 58 0.17
30 217 0.65
31 14 0.04
32 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
CAAAATGTAATTTTGGAAAAGTTTAGGGGT
Found at i:6357249 original size:19 final size:18
Alignment explanation
Indices: 6357219--6357254 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
6357209 ATGACATTAA
6357219 TAATATTTTAAAATATAT
1 TAATATTTTAAAATATAT
6357237 TAATATATTTAAAATATA
1 TAATAT-TTTAAAATATA
6357255 AACAGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATTTTAAAATATAT
Found at i:6359759 original size:58 final size:58
Alignment explanation
Indices: 6359650--6359928 Score: 273
Period size: 58 Copynumber: 4.7 Consensus size: 58
6359640 AAATAGGGGC
* *
6359650 TAAAAATGGAACTTTGGAAAGTTCGAAGGGTAAAAATGGTAAATTTT-GGTAAAAACGAGGT
1 TAAAAAT-GAAATTTGGAAAGTTC-AGGGGT-AAAATGGT-AATTTTGGGTAAAAACGAGGT
* * *
6359711 TAAAAATGAAATTTGGAAGGTTCGGGGGTAAAATGGTAATTTTGGGTAAAATCGAGGT
1 TAAAAATGAAATTTGGAAAGTTCAGGGGTAAAATGGTAATTTTGGGTAAAAACGAGGT
* * *
6359769 T-AAAATGGAATTTAGGAAAGTTTAGGGGTAAAATGGTAATTTTTTGGTAAAATTA-G-GGT
1 TAAAAATGAAATTT-GGAAAGTTCAGGGGTAAAATGGTAA-TTTTGGGTAAAA--ACGAGGT
* * * * *
6359828 TAAAAATGGAATTTAGGAAAGTTTA--GGTAAAATGGTAATTTTGGGTGAAATCGGGGT
1 TAAAAATGAAATTT-GGAAAGTTCAGGGGTAAAATGGTAATTTTGGGTAAAAACGAGGT
* * **
6359885 TAAAAATGGAATTTTGGAAAGTTTAGGTATAAAATGGTAATTTT
1 TAAAAAT-GAAATTTGGAAAGTTCAGGGGTAAAATGGTAATTTT
6359929 TGAAAGTTTT
Statistics
Matches: 189, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
56 1 0.01
57 47 0.25
58 62 0.33
59 34 0.18
60 38 0.20
61 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (58 bp):
TAAAAATGAAATTTGGAAAGTTCAGGGGTAAAATGGTAATTTTGGGTAAAAACGAGGT
Found at i:6359879 original size:116 final size:116
Alignment explanation
Indices: 6359650--6359929 Score: 345
Period size: 117 Copynumber: 2.4 Consensus size: 116
6359640 AAATAGGGGC
* * *
6359650 TAAAAATGGAACTTTGGAAAGTTCGAAGGGTAAAAATGGTAA-ATTTTGGTAAAAACGAGGTTAA
1 TAAAAATGGAA-TTTGGAAAGTT-TAGGGGT-AAAATGGTAATTTTTTGGTAAAAACGAGGTTAA
* *
6359714 AAATGAAATTTGGAAGGTTCGGGGGTAAAATGGTAATTTTGGGTAAAATCGAGGT
63 AAATGAAATTTGGAAAGTTC-GAGGTAAAATGGTAATTTTGGGTAAAATCGAGGT
6359769 T-AAAATGGAATTTAGGAAAGTTTAGGGGTAAAATGGTAATTTTTTGGTAAAATTA-G-GGTTAA
1 TAAAAATGGAATTT-GGAAAGTTTAGGGGTAAAATGGTAATTTTTTGGTAAAA--ACGAGGTTAA
* * * *
6359831 AAATGGAATTTAGGAAAGTT-TAGGTAAAATGGTAATTTTGGGTGAAATCGGGGT
63 AAATGAAATTT-GGAAAGTTCGAGGTAAAATGGTAATTTTGGGTAAAATCGAGGT
**
6359885 TAAAAATGGAATTTTGGAAAGTTTAGGTATAAAATGGTAATTTTT
1 TAAAAATGGAA-TTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
6359930 GAAAGTTTTA
Statistics
Matches: 143, Mismatches: 11, Indels: 16
0.84 0.06 0.09
Matches are distributed among these distances:
116 41 0.29
117 72 0.50
118 28 0.20
119 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (116 bp):
TAAAAATGGAATTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTTGGTAAAAACGAGGTTAAAAA
TGAAATTTGGAAAGTTCGAGGTAAAATGGTAATTTTGGGTAAAATCGAGGT
Found at i:6359941 original size:30 final size:28
Alignment explanation
Indices: 6359765--6359937 Score: 108
Period size: 29 Copynumber: 6.0 Consensus size: 28
6359755 GGTAAAATCG
*
6359765 AGGT-TAAAATGGAATTTAGGAAAGTTT
1 AGGTATAAAATGGAATTTTGGAAAGTTT
** *
6359792 AGGGGTAAAATGGTAATTTTTTGGTAAA-ATT
1 AGGTATAAAATGG-AA--TTTTGG-AAAGTTT
*
6359823 AGGGT-TAAAAATGGAATTTAGGAAAGTTT
1 A-GGTAT-AAAATGGAATTTTGGAAAGTTT
**
6359852 AGG--TAAAATGGTAATTTTGGGTGAAA-TCG
1 AGGTATAAAATGG-AATTTT--G-GAAAGTTT
*
6359881 GGGT-TAAAAATGGAATTTTGGAAAGTTT
1 AGGTAT-AAAATGGAATTTTGGAAAGTTT
*
6359909 AGGTATAAAATGGTAATTTTTGAAAGTTT
1 AGGTATAAAATGG-AATTTTGGAAAGTTT
6359938 TAGGGTCAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 32
0.71 0.09 0.20
Matches are distributed among these distances:
26 7 0.06
27 13 0.11
28 25 0.22
29 29 0.25
30 11 0.10
31 18 0.16
32 12 0.10
ACGTcount: A:0.38, C:0.01, G:0.27, T:0.35
Consensus pattern (28 bp):
AGGTATAAAATGGAATTTTGGAAAGTTT
Found at i:6359949 original size:30 final size:29
Alignment explanation
Indices: 6359887--6359985 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
6359877 ATCGGGGTTA
* * *
6359887 AAAATGGAATTTTGGAAAG-TTTA-GGTAT
1 AAAATGTAATTTTTGAAAGTTTTAGGGT-C
6359915 AAAATGGTAATTTTTGAAAGTTTTAGGGTC
1 AAAAT-GTAATTTTTGAAAGTTTTAGGGTC
* * *
6359945 AAAATGTAGTTTTTTTAAA-TTTTGGGGTC
1 AAAATGTA-ATTTTTGAAAGTTTTAGGGTC
*
6359974 GAAATGTAATTT
1 AAAATGTAATTT
6359986 CTAGATAGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
28 8 0.14
29 31 0.53
30 17 0.29
31 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.41
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTTAGGGTC
Found at i:6361897 original size:6 final size:6
Alignment explanation
Indices: 6361886--6361936 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
6361876 TCATAATTTG
* *
6361886 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATAGTTGA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
6361935 AT
1 AT
6361937 AAATTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
8 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:6367451 original size:17 final size:18
Alignment explanation
Indices: 6367429--6367465 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
6367419 AGTAAACAAA
6367429 TTATTGAATTTT-TTAAT
1 TTATTGAATTTTATTAAT
*
6367446 TTATTGATTTTTATTAAT
1 TTATTGAATTTTATTAAT
6367464 TT
1 TT
6367466 TATTCATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTGAATTTTATTAAT
Found at i:6368318 original size:37 final size:37
Alignment explanation
Indices: 6368256--6368330 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
6368246 AGTTTGGCTC
*
6368256 AAATTTAATTTAAATAATAAAATATTTTAAA-ATTTT
1 AAATTTAATTTAAATAACAAAATATTTTAAATATTTT
* *
6368292 AAATTTAATTGTAAATTACAATATATTTTAAATATTTT
1 AAATTTAATT-TAAATAACAAAATATTTTAAATATTTT
6368330 A
1 A
6368331 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 10 0.29
37 18 0.53
38 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (37 bp):
AAATTTAATTTAAATAACAAAATATTTTAAATATTTT
Found at i:6368629 original size:17 final size:17
Alignment explanation
Indices: 6368607--6368656 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
6368597 TTTAATTTTT
6368607 ATATAAAAAATTAAAAA
1 ATATAAAAAATTAAAAA
* *
6368624 ATATAATACA-T-AAAA
1 ATATAAAAAATTAAAAA
6368639 ATATTAAAAATATTAAAA
1 ATA-TAAAAA-ATTAAAA
6368657 TAAGTGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 9 0.36
18 1 0.04
19 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
ATATAAAAAATTAAAAA
Found at i:6374546 original size:53 final size:53
Alignment explanation
Indices: 6374466--6374571 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
6374456 CTAGCCACTA
6374466 TGGGGGAGATTTTTAAGGGGGGTTAGAAGATGGAGGTTGAGGTGGATTGTATG
1 TGGGGGAGATTTTTAAGGGGGGTTAGAAGATGGAGGTTGAGGTGGATTGTATG
6374519 TGGGGGAGATTTTTAAGGGGGGTTAGAAGATGGAGGTTGAGGTGGATTGTATG
1 TGGGGGAGATTTTTAAGGGGGGTTAGAAGATGGAGGTTGAGGTGGATTGTATG
6374572 GGCTTACCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (53 bp):
TGGGGGAGATTTTTAAGGGGGGTTAGAAGATGGAGGTTGAGGTGGATTGTATG
Done.