Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 17 of 211
Found at i:5410482 original size:17 final size:17
Alignment explanation
Indices: 5410460--5410492 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5410450 ACAGAGAAGG
*
5410460 AAAGAAGGAAAGAAAAA
1 AAAGAAAGAAAGAAAAA
5410477 AAAGAAAGAAAGAAAA
1 AAAGAAAGAAAGAAAA
5410493 GGGAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAAA
Found at i:5412004 original size:45 final size:45
Alignment explanation
Indices: 5411935--5412032 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
5411925 GCCGACTACT
* * * *
5411935 GTTACTGTTACTGATTCGATACTTTGTGTGTCGAATATTGTTACC
1 GTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTATTACC
* *
5411980 GTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATACTATTACT
1 GTTACTGTTACAGATTCGA-CACTTTGTGTGTCGAATACTATTACC
5412025 GTTACTGT
1 GTTACTGT
5412033 CACTGTTACC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.44
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTATTACC
Found at i:5417312 original size:23 final size:23
Alignment explanation
Indices: 5417279--5417322 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5417269 TGTGAGGTCC
*
5417279 GTAATATCCCGAAAATTACTATT
1 GTAATACCCCGAAAATTACTATT
5417302 GTAATACCCCGAAAATTACTA
1 GTAATACCCCGAAAATTACTA
5417323 CAGTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTATT
Found at i:5417328 original size:23 final size:23
Alignment explanation
Indices: 5417279--5417328 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5417269 TGTGAGGTCC
* **
5417279 GTAATATCCCGAAAATTACTATT
1 GTAATACCCCGAAAATTACTACA
5417302 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACTACA
5417325 GTAA
1 GTAA
5417329 GAAAGTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTACA
Found at i:5427548 original size:25 final size:24
Alignment explanation
Indices: 5427503--5427552 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
5427493 AAAATTTAAG
***
5427503 TATTTTTTATTTTATTCTATTTTT
1 TATTTTTTATTTTAAAATATTTTT
5427527 TATTTTTTATTTTTAAAATATTTTT
1 TATTTTTTA-TTTTAAAATATTTTT
5427552 T
1 T
5427553 GAAATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (24 bp):
TATTTTTTATTTTAAAATATTTTT
Found at i:5434375 original size:45 final size:45
Alignment explanation
Indices: 5434324--5434413 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
5434314 CAAAGACTTA
* *
5434324 ATCACATAAGGAGTTTCTAACATTTTTCACAAAGTAGATGAGGTT
1 ATCACATAAAGAGTTTCTAACATTTTTCACAAAGCAGATGAGGTT
5434369 ATCACATAAAGAGTTTCTAACATTTTTCACAAAGCAGATGAGGTT
1 ATCACATAAAGAGTTTCTAACATTTTTCACAAAGCAGATGAGGTT
5434414 TTCTCCATCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (45 bp):
ATCACATAAAGAGTTTCTAACATTTTTCACAAAGCAGATGAGGTT
Found at i:5438434 original size:67 final size:66
Alignment explanation
Indices: 5438325--5438458 Score: 223
Period size: 67 Copynumber: 2.0 Consensus size: 66
5438315 TTTCCATTTT
5438325 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTGC
1 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTGC
5438390 A
66 A
* * **
5438391 AGAGAGCACACTCCCGTGAACTTCATTCCTTACAGTGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCA-TCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
5438456 CA
65 CA
5438458 A
1 A
5438459 CGACAATTAC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 23 0.37
67 40 0.63
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (66 bp):
AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTGC
A
Found at i:5438616 original size:57 final size:57
Alignment explanation
Indices: 5438523--5438636 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
5438513 ACCTTAATTC
* *
5438523 AGATTACCCGTCCAGGCTAAATCCATTTTCCACATATTCTTCAAGAA-GGCTATATCA
1 AGATCACCCGTCCAAGCTAAATCCATTTTCCACATATTCTTC-AGAAGGGCTATATCA
* * *
5438580 AGATCACCCGTCCAAGCTAGAT-CTTTTTCACACATATTCTTCGGAAGGGCTATATCA
1 AGATCACCCGTCCAAGCTAAATCCATTTTC-CACATATTCTTCAGAAGGGCTATATCA
5438637 GGATAGGATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
56 9 0.18
57 41 0.82
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (57 bp):
AGATCACCCGTCCAAGCTAAATCCATTTTCCACATATTCTTCAGAAGGGCTATATCA
Found at i:5439389 original size:2 final size:2
Alignment explanation
Indices: 5439382--5439411 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5439372 TTGAATATTC
5439382 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
5439412 TCTCCTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5441668 original size:14 final size:13
Alignment explanation
Indices: 5441624--5441689 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 13
5441614 TTTGAAGTTT
5441624 AAATT-AAATATTA
1 AAATTAAAAT-TTA
5441637 AAATTAATAAATTT-
1 AAATT-A-AAATTTA
*
5441651 AAATTCAGAATTTA
1 AAATT-AAAATTTA
5441665 AAATTAAAATATTA
1 AAATTAAAAT-TTA
5441679 AAATTAAAATT
1 AAATTAAAATT
5441690 GTTTTATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 15 0.33
14 24 0.53
15 2 0.04
16 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
AAATTAAAATTTA
Found at i:5441687 original size:6 final size:6
Alignment explanation
Indices: 5441624--5441689 Score: 51
Period size: 6 Copynumber: 9.8 Consensus size: 6
5441614 TTTGAAGTTT
* *
5441624 AAATTA AATATTA AAATTAA TAAATTT AAATTCA GAATTTA AAATTAA
1 AAATTA AA-ATTA AAATT-A -AAATTA AAATT-A -AAATTA AAATT-A
5441672 AATATTA AAATTA AAATT
1 AA-ATTA AAATTA AAATT
5441690 GTTTTATGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
6 23 0.47
7 14 0.29
8 12 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (6 bp):
AAATTA
Found at i:5454765 original size:54 final size:54
Alignment explanation
Indices: 5454678--5454785 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
5454668 CATGCAAAAG
* * * * *
5454678 ATGTAATCAAACAATATTAAATTTAAGACATTAAAGCTCGAGTTTAACTAGAAA
1 ATGTAATCAAACAAAATTAAATGTAAGAAATTAAAACTCGAGCTTAACTAGAAA
* *
5454732 ATGTAATCAAGCAAAATTAAATGTAAGAAATTAAAACTCGAGCTTAACTTGAAA
1 ATGTAATCAAACAAAATTAAATGTAAGAAATTAAAACTCGAGCTTAACTAGAAA
5454786 GAAAATTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (54 bp):
ATGTAATCAAACAAAATTAAATGTAAGAAATTAAAACTCGAGCTTAACTAGAAA
Found at i:5455765 original size:31 final size:31
Alignment explanation
Indices: 5455713--5455785 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
5455703 CCCAAAGAGA
* *
5455713 TTAAGTACCAACTTAATAAAAAGTATAAAGT
1 TTAAGTACCAAATTAAGAAAAAGTATAAAGT
* * *
5455744 TTAAGTACCAAATTAGGAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAAGAAAAAGTATAAAGT
**
5455775 TTGGGTACCAA
1 TTAAGTACCAA
5455786 TTTGAACCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (31 bp):
TTAAGTACCAAATTAAGAAAAAGTATAAAGT
Found at i:5457921 original size:49 final size:46
Alignment explanation
Indices: 5457858--5457963 Score: 140
Period size: 49 Copynumber: 2.2 Consensus size: 46
5457848 TCTGAATAAG
*
5457858 AAAAGGCAAAACTACATCGTTTTGATAAACATTTACATTTTCTGAAGTT
1 AAAAGGCAAAACTACATCGTTTTGATAAACATTTAC-TTGTC--AAGTT
* * *
5457907 AAAAGGTAAAACTACGTCGTTTTGATAAATATTTACTTGTCAAGTT
1 AAAAGGCAAAACTACATCGTTTTGATAAACATTTACTTGTCAAGTT
*
5457953 AAAAGACAAAA
1 AAAAGGCAAAA
5457964 TCATTATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
46 14 0.27
48 4 0.08
49 33 0.65
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (46 bp):
AAAAGGCAAAACTACATCGTTTTGATAAACATTTACTTGTCAAGTT
Found at i:5461748 original size:23 final size:22
Alignment explanation
Indices: 5461721--5461776 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5461711 TGTTATTAAA
5461721 TTTTAATAAAATA-TTTAGTATAT
1 TTTTAATAAAATATTTTA-TAT-T
*
5461744 TTTTAAT-TAATATTTTATATT
1 TTTTAATAAAATATTTTATATT
5461765 TTTTAAATAAAA
1 TTTT-AATAAAA
5461777 ATAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 5 0.18
22 10 0.36
23 13 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAATAAAATATTTTATATT
Found at i:5461755 original size:22 final size:21
Alignment explanation
Indices: 5461721--5461776 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
5461711 TGTTATTAAA
5461721 TTTTAATAAAATATTTAGTATAT
1 TTTTAATAAAATATTT--TATAT
*
5461744 TTTTAAT-TAATATTTTATATT
1 TTTTAATAAAATATTTTATA-T
5461765 TTTTAAATAAAA
1 TTTT-AATAAAA
5461777 ATAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 10 0.36
23 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTAATAAAATATTTTATAT
Found at i:5465309 original size:18 final size:18
Alignment explanation
Indices: 5465286--5465321 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5465276 TTCTTTTTTT
5465286 CTTTTCTATTTTTATGAA
1 CTTTTCTATTTTTATGAA
*
5465304 CTTTTCTATTTTTTTGAA
1 CTTTTCTATTTTTATGAA
5465322 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (18 bp):
CTTTTCTATTTTTATGAA
Found at i:5474505 original size:3 final size:3
Alignment explanation
Indices: 5474497--5474528 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5474487 AATAAATAGG
*
5474497 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5474529 GGACTAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5474514 original size:15 final size:16
Alignment explanation
Indices: 5474491--5474525 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5474481 AATATAAATA
5474491 AATAGGTAATAATAAT
1 AATAGGTAATAATAAT
5474507 AATA-GTAATAATAAT
1 AATAGGTAATAATAAT
5474522 AATA
1 AATA
5474526 ATAGGACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (16 bp):
AATAGGTAATAATAAT
Found at i:5475675 original size:16 final size:17
Alignment explanation
Indices: 5475643--5475682 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5475633 CTTGCTGTAA
5475643 TGGGC-TTGTTTGGATT
1 TGGGCTTTGTTTGGATT
*
5475659 TGGGCTTTGTTT-TATT
1 TGGGCTTTGTTTGGATT
5475675 TGGG-TTTG
1 TGGGCTTTG
5475683 GCATTTGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 12 0.55
17 6 0.27
ACGTcount: A:0.05, C:0.05, G:0.35, T:0.55
Consensus pattern (17 bp):
TGGGCTTTGTTTGGATT
Found at i:5477491 original size:18 final size:18
Alignment explanation
Indices: 5477441--5477491 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5477431 TAAATATTTC
* *
5477441 TAAAAA-AATATTTTACA
1 TAAAAATAAAATTTTAAA
5477458 TAAAAATTAAAA-TTTAAA
1 TAAAAA-TAAAATTTTAAA
5477476 TAAAAATAAAATTTTA
1 TAAAAATAAAATTTTA
5477492 TTCAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 11 0.38
18 15 0.52
19 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATAAAATTTTAAA
Found at i:5481078 original size:21 final size:23
Alignment explanation
Indices: 5481033--5481079 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
5481023 GCCATGCCAG
*
5481033 TTTTTAATAGTAAAATGGATGAAT
1 TTTTTAATAG-AAAATGGATCAAT
5481057 TTTTTAATA-AAAAT-GATCAAT
1 TTTTTAATAGAAAATGGATCAAT
5481078 TT
1 TT
5481080 GCTCTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
24 9 0.41
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (23 bp):
TTTTTAATAGAAAATGGATCAAT
Found at i:5482955 original size:23 final size:23
Alignment explanation
Indices: 5482907--5482960 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
5482897 TTATCCTAGA
* *
5482907 TTATTATATTGTTTCAATATTGT
1 TTATTATATAGTTTCAATATTAT
*
5482930 TTATTATATAAGTTTTAA-ATTAT
1 TTATTATAT-AGTTTCAATATTAT
5482953 TTA-TATAT
1 TTATTATAT
5482961 TCATATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 16 0.59
24 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (23 bp):
TTATTATATAGTTTCAATATTAT
Found at i:5489467 original size:14 final size:14
Alignment explanation
Indices: 5489448--5489487 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5489438 ACTTGAACCT
*
5489448 TAAATTTTAGACTC
1 TAAATTTTAAACTC
5489462 TAAATTTTAAACTC
1 TAAATTTTAAACTC
*
5489476 TAAATCTTAAAC
1 TAAATTTTAAAC
5489488 CTTGGACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (14 bp):
TAAATTTTAAACTC
Found at i:5493572 original size:13 final size:12
Alignment explanation
Indices: 5493552--5493577 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5493542 CCCCAAGTTC
5493552 TTAAAAAAAATT
1 TTAAAAAAAATT
5493564 TTAAAAAAAATT
1 TTAAAAAAAATT
5493576 TT
1 TT
5493578 GATTTTCTAC
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:5504224 original size:9 final size:9
Alignment explanation
Indices: 5504203--5504241 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
5504193 GTTAGTTTTG
5504203 AAAATTACAA
1 AAAATTAC-A
5504213 AAAATTACA
1 AAAATTACA
*
5504222 AAAATTATA
1 AAAATTACA
5504231 AAAATTA-A
1 AAAATTACA
5504239 AAA
1 AAA
5504242 GCTAAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 4 0.14
9 16 0.57
10 8 0.29
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAATTACA
Found at i:5504347 original size:13 final size:14
Alignment explanation
Indices: 5504325--5504353 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5504315 GTTTATAAGT
5504325 TTTTTCTTTCAGTA
1 TTTTTCTTTCAGTA
5504339 TTTTT-TTTCAGTA
1 TTTTTCTTTCAGTA
5504352 TT
1 TT
5504354 AATACTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (14 bp):
TTTTTCTTTCAGTA
Found at i:5509655 original size:9 final size:9
Alignment explanation
Indices: 5509633--5510027 Score: 426
Period size: 9 Copynumber: 44.3 Consensus size: 9
5509623 TATAAGCTTG
5509633 CATAACTTA
1 CATAACTTA
*
5509642 CATAAATTA
1 CATAACTTA
*
5509651 AATAACTTA
1 CATAACTTA
5509660 CATAACTTA
1 CATAACTTA
5509669 CATAACTTA
1 CATAACTTA
*
5509678 CATAAATTA
1 CATAACTTA
*
5509687 AATAACTTA
1 CATAACTTA
*
5509696 CACAACTTA
1 CATAACTTA
*
5509705 CATTA--TA
1 CATAACTTA
*
5509712 CACAACTTA
1 CATAACTTA
5509721 CAT-ACATTA
1 CATAAC-TTA
*
5509730 AATAACTTA
1 CATAACTTA
5509739 CATAACTTA
1 CATAACTTA
*
5509748 CATAAATTA
1 CATAACTTA
*
5509757 CATAAATTA
1 CATAACTTA
*
5509766 AATAACTTA
1 CATAACTTA
5509775 CATAACTTA
1 CATAACTTA
*
5509784 CATAAATTA
1 CATAACTTA
*
5509793 CATAAATTA
1 CATAACTTA
*
5509802 CATAAATTA
1 CATAACTTA
5509811 -ATAAACTTA
1 CAT-AACTTA
5509820 CATAACTTA
1 CATAACTTA
*
5509829 CATAAATTA
1 CATAACTTA
*
5509838 AATAACTTA
1 CATAACTTA
5509847 CATAACTTA
1 CATAACTTA
*
5509856 CATAAATTA
1 CATAACTTA
* *
5509865 TATAAATTA
1 CATAACTTA
* *
5509874 AAAAACTTA
1 CATAACTTA
5509883 CATAACTTA
1 CATAACTTA
*
5509892 CATAAATTA
1 CATAACTTA
5509901 -ATAAACTTA
1 CAT-AACTTA
5509910 CATAACTTA
1 CATAACTTA
5509919 CATAACTTA
1 CATAACTTA
* *
5509928 GATTA--TA
1 CATAACTTA
*
5509935 CACAACTTA
1 CATAACTTA
*
5509944 CATAAATTA
1 CATAACTTA
*
5509953 AATAACTTA
1 CATAACTTA
*
5509962 CATAGCTTA
1 CATAACTTA
5509971 CATAACTTA
1 CATAACTTA
* *
5509980 TATAGCTTA
1 CATAACTTA
5509989 CATAACTTA
1 CATAACTTA
*
5509998 CATAAATTA
1 CATAACTTA
*
5510007 AATAACTTA
1 CATAACTTA
5510016 CATAACTTA
1 CATAACTTA
5510025 CAT
1 CAT
5510028 TATACACGCT
Statistics
Matches: 321, Mismatches: 55, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
7 9 0.03
8 6 0.02
9 300 0.93
10 6 0.02
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:5510237 original size:21 final size:21
Alignment explanation
Indices: 5510211--5510282 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
5510201 CTATAACTTA
*
5510211 AAGCAGAGG-TGGCAGCGAGGG
1 AAGCAGAGGCT-GCAGCGAGAG
5510232 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
5510253 AAGCAAAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
5510274 AAGCAGAGG
1 AAGCAGAGG
5510283 TTCAAAAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 46 0.98
22 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:5510716 original size:40 final size:40
Alignment explanation
Indices: 5510657--5510748 Score: 148
Period size: 40 Copynumber: 2.2 Consensus size: 40
5510647 AAAATTAGTG
5510657 GCGTTTTTCGTTAAGCGCCGCTAAAGAACATGATCTTTAGCC
1 GCGTTTTT--TTAAGCGCCGCTAAAGAACATGATCTTTAGCC
* *
5510699 GTGTTTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCG
1 GCGTTTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCC
5510739 GCGTTTTTTT
1 GCGTTTTTTT
5510749 TAAAAGCGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 40 0.85
42 7 0.15
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
GCGTTTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCC
Found at i:5511307 original size:34 final size:34
Alignment explanation
Indices: 5511264--5511329 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
5511254 AATAAAATAT
*
5511264 TTTTCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
5511297 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
5511330 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:5517969 original size:26 final size:26
Alignment explanation
Indices: 5517940--5517991 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5517930 AATAAAAGAG
5517940 TTCAATATCTTGAGTCTATTGACAAT
1 TTCAATATCTTGAGTCTATTGACAAT
5517966 TTCAATATCTTGAGTCTATTGACAAT
1 TTCAATATCTTGAGTCTATTGACAAT
5517992 AGGGTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (26 bp):
TTCAATATCTTGAGTCTATTGACAAT
Found at i:5518062 original size:36 final size:36
Alignment explanation
Indices: 5518015--5518086 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5518005 GTCCTTTCAA
5518015 AATGATGCTGATGTAATGTCTTAAATCAAGGATATG
1 AATGATGCTGATGTAATGTCTTAAATCAAGGATATG
5518051 AATGATGCTGATGTAATGTCTTAAATCAAGGATATG
1 AATGATGCTGATGTAATGTCTTAAATCAAGGATATG
5518087 GAATCTTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.33
Consensus pattern (36 bp):
AATGATGCTGATGTAATGTCTTAAATCAAGGATATG
Found at i:5518225 original size:51 final size:51
Alignment explanation
Indices: 5518165--5518270 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
5518155 ATGGTATTGA
5518165 TTGTGGTTTAAGGTCTACTTAGAAAAGACACATGTATAGTATGTAATTCGC
1 TTGTGGTTTAAGGTCTACTTAGAAAAGACACATGTATAGTATGTAATTCGC
* * *
5518216 TTGTGGTTTAAGGTTTACTTAGAAAAGACATATGTATAGTATGTAGTTCGC
1 TTGTGGTTTAAGGTCTACTTAGAAAAGACACATGTATAGTATGTAATTCGC
5518267 TTGT
1 TTGT
5518271 TACGAACACG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (51 bp):
TTGTGGTTTAAGGTCTACTTAGAAAAGACACATGTATAGTATGTAATTCGC
Found at i:5518532 original size:22 final size:19
Alignment explanation
Indices: 5518484--5518526 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5518474 AATTAAATTG
5518484 ATTTATT-TAAATTTTTAA
1 ATTTATTATAAATTTTTAA
5518502 ATTTATTATAAATTATTT-A
1 ATTTATTATAAATT-TTTAA
5518521 ATTTAT
1 ATTTAT
5518527 CATTATTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 13 0.57
20 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTATTATAAATTTTTAA
Found at i:5532096 original size:220 final size:220
Alignment explanation
Indices: 5531714--5532156 Score: 832
Period size: 220 Copynumber: 2.0 Consensus size: 220
5531704 AGGAGTAGGA
* *
5531714 AACTTTGTCAGAAGAGGCCACGACGGGTTCGTCACTAGCTCCAACCCCACAAGCGCCACCGGTGT
1 AACTTTGTCAGAAGAGGCCACGACGAGTTCGTCACTAGCTCCAACCCCACAAGCGCCACCGATGT
*
5531779 TTGCATTAAATCCCAATCAGTTCACTCCATATATTCCTGTTCATTTCATTAACCTCATGTTTTAT
66 TTGCATTAAATCCCAATCAGTTCACTCCATATATTCATGTTCATTTCATTAACCTCATGTTTTAT
*
5531844 TCACAAGCACCGCATTATGCACCACCGTAGCACCCTGTATCTACACTCCCGCAGGTACATATTTT
131 TCACAAGCACCGCATTATGCACCACCGTAGCACCCTGTATCTACACTCCCACAGGTACATATTTT
5531909 GGGGCACCTCCGTCCCCAACATATT
196 GGGGCACCTCCGTCCCCAACATATT
*
5531934 AACTTTGTCAGAAGAGGCCACGACGAGTTCGTCACTAGCTCCAACCCCACAAGCGCCACTGATGT
1 AACTTTGTCAGAAGAGGCCACGACGAGTTCGTCACTAGCTCCAACCCCACAAGCGCCACCGATGT
*
5531999 TTGCATTAAATCCCAATCAGTTCACTCCTTATATTCATGTTCATTTCATTAACCTCATGTTTTAT
66 TTGCATTAAATCCCAATCAGTTCACTCCATATATTCATGTTCATTTCATTAACCTCATGTTTTAT
5532064 TCACAAGCACCGCATTATGCACCACCGTAGCACCCTGTATCTACACTCCCACAGGTACATATTTT
131 TCACAAGCACCGCATTATGCACCACCGTAGCACCCTGTATCTACACTCCCACAGGTACATATTTT
5532129 GGGGCACCTCCGTCCCCAACATATT
196 GGGGCACCTCCGTCCCCAACATATT
5532154 AAC
1 AAC
5532157 CTCGATACTG
Statistics
Matches: 217, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 217 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.28
Consensus pattern (220 bp):
AACTTTGTCAGAAGAGGCCACGACGAGTTCGTCACTAGCTCCAACCCCACAAGCGCCACCGATGT
TTGCATTAAATCCCAATCAGTTCACTCCATATATTCATGTTCATTTCATTAACCTCATGTTTTAT
TCACAAGCACCGCATTATGCACCACCGTAGCACCCTGTATCTACACTCCCACAGGTACATATTTT
GGGGCACCTCCGTCCCCAACATATT
Found at i:5548672 original size:21 final size:21
Alignment explanation
Indices: 5548646--5548686 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5548636 ATCTGCTCAA
* *
5548646 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5548667 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5548687 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5553144 original size:19 final size:19
Alignment explanation
Indices: 5553120--5553157 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5553110 AATAAAAATA
*
5553120 TATTTT-TAATAATATAATT
1 TATTTTGTAA-AAAATAATT
5553139 TATTTTGTAAAAAATAATT
1 TATTTTGTAAAAAATAATT
5553158 GTTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTTTGTAAAAAATAATT
Found at i:5559629 original size:17 final size:18
Alignment explanation
Indices: 5559609--5559642 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5559599 CGAAAATGGT
5559609 ATAAAA-TTAAAAAAAAC
1 ATAAAAGTTAAAAAAAAC
5559626 ATAAAAGTTAAAAAAAA
1 ATAAAAGTTAAAAAAAA
5559643 AAGCTGGGGA
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:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
ATAAAAGTTAAAAAAAAC
Found at i:5559745 original size:13 final size:13
Alignment explanation
Indices: 5559727--5559795 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 13
5559717 CCATTCGGCT
5559727 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
5559740 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
*
5559753 GAAAAGGAAAAGAGAA
1 G--AAGGAGAAGA-AA
*
5559769 GAAAGGA-AAG-GA
1 G-AAGGAGAAGAAA
5559781 -AAGGAGAAGAAA
1 GAAGGAGAAGAAA
5559793 GAA
1 GAA
5559796 AAAGAAAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 5 0.11
11 3 0.06
12 2 0.04
13 16 0.34
14 3 0.06
15 15 0.32
16 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAAGGAGAAGAAA
Found at i:5559777 original size:5 final size:5
Alignment explanation
Indices: 5559749--5559815 Score: 57
Period size: 5 Copynumber: 13.4 Consensus size: 5
5559739 AGAAGGAGAA
* * * *
5559749 GAAAG AAAAG GAAAA GAGAA- GAAAG GAAAG GAAAG GAGAA- GAAAG AAAAA
1 GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG
*
5559799 GAAAG AAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GA
5559816 GAAGAGGGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
4 4 0.08
5 41 0.84
6 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:5559783 original size:30 final size:29
Alignment explanation
Indices: 5559728--5559813 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
5559718 CATTCGGCTG
*
5559728 AAGGAGAAGAAAG-AAGGAGAA-GAAAGAA
1 AAGGAAAAGAAAGAAAGGA-AAGGAAAGAA
*
5559756 AAGGAAAAGAGAAGAAAGGAAAGGAAAGGAG
1 AAGGAAAAGA-AAGAAAGGAAAGGAAA-GAA
* *
5559787 AA-GAAAGAAAAAGAAAGAAAAGGAAAG
1 AAGGAAA-AGAAAGAAAGGAAAGGAAAG
5559814 GAGAAGAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
28 9 0.18
29 6 0.12
30 28 0.57
31 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (29 bp):
AAGGAAAAGAAAGAAAGGAAAGGAAAGAA
Found at i:5559803 original size:20 final size:20
Alignment explanation
Indices: 5559732--5559803 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
5559722 CGGCTGAAGG
5559732 AGAAGAAAG-AAGGAGAAGAA
1 AGAA-AAAGAAAGGAGAAGAA
* *
5559752 AGAAAAGGAAAAGAGAAGAA
1 AGAAAAAGAAAGGAGAAGAA
* *
5559772 AGGAAAGGAAAGGAGAAGAA
1 AGAAAAAGAAAGGAGAAGAA
5559792 AGAAAAAGAAAG
1 AGAAAAAGAAAG
5559804 AAAAGGAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAAAAAGAAAGGAGAAGAA
Found at i:5559820 original size:20 final size:20
Alignment explanation
Indices: 5559741--5559803 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
5559731 GAGAAGAAAG
5559741 AAGGAGAAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAGGA
* *
5559761 AAAGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGA
*
5559781 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAGAAAGAAAAGGA
5559801 AAG
1 AAG
5559804 AAAAGGAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGAAAAGGA
Found at i:5560382 original size:130 final size:131
Alignment explanation
Indices: 5560227--5560494 Score: 457
Period size: 130 Copynumber: 2.1 Consensus size: 131
5560217 AAAAAACACT
5560227 CTAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAAT
1 CTAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAAT
* *
5560292 ATATTTTTTGAAAGTAATAAAA-TCCGAAAAAAATACAAACAAATGGCCGGAATAAGAGTTTTTT
66 ATATTTTTTGAAAGTAATAAAATTCCGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTT
5560356 A
131 A
* *
5560357 CTAAATTAATACATTTCAAGCATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAAT
1 CTAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAAT
* * * *
5560422 ATATTTTTTGAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
66 ATATTTTTTGAAAGTAATAAAATTCCGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTT
5560487 A
131 A
5560488 CTAAATT
1 CTAAATT
5560495 TATTTAAAGA
Statistics
Matches: 129, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
130 85 0.66
131 44 0.34
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (131 bp):
CTAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAAT
ATATTTTTTGAAAGTAATAAAATTCCGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTT
A
Found at i:5560539 original size:153 final size:154
Alignment explanation
Indices: 5560358--5561109 Score: 1119
Period size: 153 Copynumber: 4.9 Consensus size: 154
5560348 AGTTTTTTAC
*
5560358 TAAATTAATACATTTCAAGCATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
*
5560423 TA-TTTT-TTGAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
66 TATTTTTATTGAAAGTAATAAAATTCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
*
5560486 TACTAAATTTATTTAAAGAACACAG
131 TA-TAAATTTATTTAAAAAACACAG
*
5560511 TAAATTAATACATTTCAAACCTAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
*
5560576 TATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTT
66 TATTTTTATTGAAAGTAATAAAATTC-GGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTT
*
5560641 TT-T-AATTTATTTTAAAAAATACAG
130 TTATAAATTTA-TTTAAAAAACACAG
* * * *
5560665 TAAATTAATACATTTTAAACATAACGTACTAAAATAATGTAAAATAATAAAAAATGAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
* *
5560730 TATTTTTATTGAAAGTAATAAAATTTGGAAAAAAATACGAACAAATGGCCGAAATAAGGG-TTTT
66 TATTTTTATTGAAAGTAATAAAATTCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
*
5560794 T-T-AATTTATTTAAAAAACACAA
131 TATAAATTTATTTAAAAAACACAG
* **
5560816 TAAATTAATACATTTCAAACATAATGTACTAAAATGATGTAAAATAATAAAATATAAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
*
5560881 TATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTT
66 TATTTTTATTGAAAGTAATAAAATTCGG-AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTT
* *
5560946 TTAAAAATTTATTTAAAAAACACAC
130 TTATAAATTTATTTAAAAAACACAG
* * *
5560971 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATTAGAAAATTA-GAAAATAGT
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TACGAAAATAAT
* * * * * *
5561035 ATA-TTTT-TTAAAAGTAATAAAATTCAGAAAAAAAATACGAATAAATGGTCAAAATAAGGGTTT
65 ATATTTTTATTGAAAGTAATAAAATTC-GGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTT
5561098 TTTACTAAATTT
129 TTTA-TAAATTT
5561110 GTTTTGAAGT
Statistics
Matches: 549, Mismatches: 39, Indels: 21
0.90 0.06 0.03
Matches are distributed among these distances:
151 99 0.18
152 42 0.08
153 159 0.29
154 113 0.21
155 96 0.17
156 40 0.07
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (154 bp):
TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
TATTTTTATTGAAAGTAATAAAATTCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
TATAAATTTATTTAAAAAACACAG
Found at i:5560726 original size:16 final size:18
Alignment explanation
Indices: 5560694--5560729 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
5560684 CATAACGTAC
5560694 TAAAATAATGTAAAATAA
1 TAAAATAATGTAAAATAA
5560712 TAAAA-AATG-AAAATAA
1 TAAAATAATGTAAAATAA
5560728 TA
1 TA
5560730 TATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAAATAATGTAAAATAA
Found at i:5560916 original size:305 final size:302
Alignment explanation
Indices: 5560356--5561101 Score: 1129
Period size: 305 Copynumber: 2.4 Consensus size: 302
5560346 AGAGTTTTTT
* * *
5560356 ACTAAATTAATACATTTCAAGCATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAAATGAAAATAA
* * *
5560421 TATATTTTTTGAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
66 TATATTTTTTGAAAGTAATAAAATTAGGAAAAAAATACGAACAAATGGCCGAAATAAGGG-TTTT
* * *
5560486 TACTAAATTTATTTAAAGAACACAGTAAATTAATACATTTCAAACCTAATGTACTAAAATAATGT
130 T--T-AATTTATTTAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATAATGT
* *
5560551 AAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACG
192 AAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACG
*
5560616 AACAAAGGGCCGAAATAAGAGTTTTTTT-AATTTATTTTAAAAAATAC
257 AACAAAGGGCCGAAATAAG-GTTTTTTTAAATTTA-TTTAAAAAACAC
* * *
5560663 AGTAAATTAATACATTTTAAACATAACGTACTAAAATAATGTAAAATAATAAAAAATGAAAATAA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAAATGAAAATAA
*
5560728 TATATTTTTATTGAAAGTAATAAAATTTGGAAAAAAATACGAACAAATGGCCGAAATAAGGGTTT
66 TATA-TTTT-TTGAAAGTAATAAAATTAGGAAAAAAATACGAACAAATGGCCGAAATAAGGGTTT
*
5560793 TTTAATTTATTTAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATGATGTAA
129 TTTAATTTATTTAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
5560858 AATAATAAAATATAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAA
194 AATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAA
5560923 CAAAGGGCCGAAATAAGGTTTTTTTAAAAATTTATTTAAAAAACAC
259 CAAAGGGCCGAAATAAGGTTTTTTT--AAATTTATTTAAAAAACAC
*
5560969 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT--TAGAAAATTAGAAAAT
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA-AAAAAT-GAAAAT
* * * * * *
5561032 AGTATATTTTTTAAAAGTAATAAAATTCAGAAAAAAAATACGAATAAATGGTCAAAATAAGGGTT
64 AATATATTTTTTGAAAGTAATAAAATT-AGGAAAAAAATACGAACAAATGGCCGAAATAAGGGTT
5561097 TTTTA
128 TTTTA
5561102 CTAAATTTGT
Statistics
Matches: 403, Mismatches: 28, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
304 26 0.06
305 183 0.45
306 67 0.17
307 69 0.17
308 9 0.02
309 49 0.12
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (302 bp):
ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAAATGAAAATAA
TATATTTTTTGAAAGTAATAAAATTAGGAAAAAAATACGAACAAATGGCCGAAATAAGGGTTTTT
TAATTTATTTAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
TAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAACA
AAGGGCCGAAATAAGGTTTTTTTAAATTTATTTAAAAAACAC
Found at i:5561247 original size:41 final size:40
Alignment explanation
Indices: 5561149--5561247 Score: 96
Period size: 42 Copynumber: 2.4 Consensus size: 40
5561139 TAATATAAAA
* *
5561149 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTT
1 ACTAACAATAATACTAACTAAAACAATAATTAGGGTTTTT
* *
5561189 ACTAATC-CTAATAACTAACCATAATAACAAT-ATTA-GTTTTTT
1 ACTAA-CAATAAT-ACTAA-C-TAA-AACAATAATTAGGGTTTTT
5561231 ACTAACAATAATACTAA
1 ACTAACAATAATACTAA
5561248 GTAACGATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
40 8 0.17
41 12 0.25
42 16 0.33
43 7 0.15
44 5 0.10
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.34
Consensus pattern (40 bp):
ACTAACAATAATACTAACTAAAACAATAATTAGGGTTTTT
Found at i:5561498 original size:21 final size:20
Alignment explanation
Indices: 5561457--5561504 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
5561447 TTCTTCTCTT
5561457 TCTTTCTCCTTTCTCTATTC
1 TCTTTCTCCTTTCTCTATTC
* *
5561477 TCTTTCTCTCTTTTTCTTTTC
1 TCTTTCTC-CTTTCTCTATTC
*
5561498 TTTTTCT
1 TCTTTCT
5561505 GGCACCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTCTCCTTTCTCTATTC
Found at i:5561533 original size:15 final size:15
Alignment explanation
Indices: 5561513--5561548 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5561503 CTGGCACCAC
5561513 CTTCTTTTTCTTCTT
1 CTTCTTTTTCTTCTT
*
5561528 CTTCTTTTTCTTTTT
1 CTTCTTTTTCTTCTT
5561543 CTTCTT
1 CTTCTT
5561549 CAACTGGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
CTTCTTTTTCTTCTT
Found at i:5562135 original size:16 final size:16
Alignment explanation
Indices: 5562114--5562146 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5562104 TTCACATTGC
5562114 AAACG-AAAGTGATAGG
1 AAACGAAAAGTGA-AGG
5562130 AAACGAAAAGTGAAGG
1 AAACGAAAAGTGAAGG
5562146 A
1 A
5562147 GAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.55, C:0.06, G:0.30, T:0.09
Consensus pattern (16 bp):
AAACGAAAAGTGAAGG
Found at i:5563837 original size:16 final size:16
Alignment explanation
Indices: 5563816--5563887 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
5563806 TTTTGTATTA
5563816 TTTTAATATTAAATAT
1 TTTTAATATTAAATAT
* *
5563832 TTTTAAAATTAAATAA
1 TTTTAATATTAAATAT
* *
5563848 CTTTAATA-TAATTTAT
1 TTTTAATATTAA-ATAT
*
5563864 TTTAAATTAGTTAAATAT
1 TTTTAA-TA-TTAAATAT
5563882 TTTTAA
1 TTTTAA
5563888 AAATATTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
15 3 0.07
16 26 0.62
17 2 0.05
18 8 0.19
19 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
TTTTAATATTAAATAT
Found at i:5570670 original size:45 final size:46
Alignment explanation
Indices: 5570621--5570731 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 46
5570611 TGCCATAGTG
*
5570621 TCTTTCAATTATGGTCTTACTTAATT-ATGTCATGATGTCAAAGCA
1 TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
* * * * * *
5570666 TCTTTCAACTATGGTCGTA-TTTATTCTTGTTATGGTGTCATAGCA
1 TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
*
5570711 TCTTTCAGCTATGGTCTTACT
1 TCTTTCAACTATGGTCTTACT
5570732 CATTTTAGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
44 5 0.09
45 49 0.89
46 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (46 bp):
TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
Found at i:5572121 original size:13 final size:13
Alignment explanation
Indices: 5572098--5572151 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
5572088 TTTAAACCAA
*
5572098 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
5572111 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
5572124 ACTTTTTACATAGC
1 ACTTTTCA-AAAGC
5572138 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
5572151 A
1 A
5572152 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:5572138 original size:27 final size:26
Alignment explanation
Indices: 5572098--5572151 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
5572088 TTTAAACCAA
5572098 ACTTTTTAAAAGCACTTCTCAAAAGC
1 ACTTTTTAAAAGCACTTCTCAAAAGC
* *
5572124 ACTTTTTACATAGCACTTTTCAAAAGC
1 ACTTTTTA-AAAGCACTTCTCAAAAGC
5572151 A
1 A
5572152 TTGCCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (26 bp):
ACTTTTTAAAAGCACTTCTCAAAAGC
Found at i:5574154 original size:17 final size:17
Alignment explanation
Indices: 5574113--5574157 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5574103 CGAAACCCCA
5574113 AGAGAAAATGAAAAATG
1 AGAGAAAATGAAAAATG
* *
5574130 AAAAAAAAT-AATAAATG
1 AGAGAAAATGAA-AAATG
5574147 AGAGAAAATGA
1 AGAGAAAATGA
5574158 TGTGAGAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (17 bp):
AGAGAAAATGAAAAATG
Found at i:5575627 original size:29 final size:30
Alignment explanation
Indices: 5575567--5575628 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
5575557 ACGTACACAT
* *
5575567 TTGTACCAAAATCAAAGTTTATGTTTATAA
1 TTGTACCAAAATCAAAGTTAATGTTCATAA
5575597 TTGTA-CAAAATCAAAGTTAATGTATCA-AA
1 TTGTACCAAAATCAAAGTTAATGT-TCATAA
5575626 TTG
1 TTG
5575629 CACATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (30 bp):
TTGTACCAAAATCAAAGTTAATGTTCATAA
Found at i:5586166 original size:12 final size:12
Alignment explanation
Indices: 5586124--5586164 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5586114 TAATTCCCAC
*
5586124 TAATAATAATAA
1 TAATAATAATAT
*
5586136 TAATAATATTAT
1 TAATAATAATAT
*
5586148 TAATACTAATAT
1 TAATAATAATAT
5586160 TAATA
1 TAATA
5586165 CTTACCTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:5587349 original size:21 final size:21
Alignment explanation
Indices: 5587325--5587367 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5587315 AATAATAGCT
5587325 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
5587346 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
5587367 A
1 A
5587368 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:5587518 original size:35 final size:35
Alignment explanation
Indices: 5587464--5587531 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
5587454 TATTTAATAA
* *
5587464 TATAATATCATTATAATTTAATTATCATAAATTCG
1 TATAATATAATTATAATTTAAATATCATAAATTCG
*
5587499 TATAATATAAATTAT-ATTTAAATATCATTAATT
1 TATAATAT-AATTATAATTTAAATATCATAAATT
5587532 ATATAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (35 bp):
TATAATATAATTATAATTTAAATATCATAAATTCG
Found at i:5588146 original size:14 final size:14
Alignment explanation
Indices: 5588127--5588153 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5588117 TTTCTTCATC
5588127 AGAATTATAAGTTG
1 AGAATTATAAGTTG
5588141 AGAATTATAAGTT
1 AGAATTATAAGTT
5588154 ATTTATTTTG
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:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (14 bp):
AGAATTATAAGTTG
Found at i:5593277 original size:11 final size:11
Alignment explanation
Indices: 5593263--5593289 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5593253 AAAAAGGACA
5593263 AAAAAAAAAAG
1 AAAAAAAAAAG
5593274 AAAAAAAAAAG
1 AAAAAAAAAAG
5593285 AAAAA
1 AAAAA
5593290 GAAACCAACC
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5593288 original size:17 final size:16
Alignment explanation
Indices: 5593262--5593293 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5593252 GAAAAAGGAC
5593262 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAA
5593278 AAAAAAGAAAAAGAAA
1 AAAAAA-AAAAAGAAA
5593294 CCAACCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAA
Found at i:5599744 original size:46 final size:46
Alignment explanation
Indices: 5599677--5599765 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
5599667 ATCCTCTTTA
5599677 AGGGAGTTGTGAAGATCAATGGTCGAGATATAAGGTCATAGGTAAG
1 AGGGAGTTGTGAAGATCAATGGTCGAGATATAAGGTCATAGGTAAG
5599723 AGGGAGTTGTGAAGATCAATGGTCGAGATATAAGGTCATAGGT
1 AGGGAGTTGTGAAGATCAATGGTCGAGATATAAGGTCATAGGT
5599766 CATTAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.07, G:0.35, T:0.25
Consensus pattern (46 bp):
AGGGAGTTGTGAAGATCAATGGTCGAGATATAAGGTCATAGGTAAG
Found at i:5603764 original size:109 final size:105
Alignment explanation
Indices: 5603626--5603958 Score: 454
Period size: 109 Copynumber: 3.1 Consensus size: 105
5603616 AGAATAGGAG
* *
5603626 AAAAAGTAAAAAAAAAAATTTAGTGGTGGCCTGCCAATGGCCTGCATCACCTTTTTTGTAGGAAT
1 AAAAAGT--AAAAAAAAATTTTGTGGTGGCCTGCCAATGGCCTGCACCACCTTTTTTGT-GGAAT
5603691 TTTTTTTACTTTTTTCGTGTCAAAAGAAAGTATCAGTATACGA
63 TTTTTTTACTTTTTTCGTGTCAAAAGAAAGTATCAGTATACGA
5603734 AAAAAGTTAAAAAAAAATTTTTGGTGGTGGCCTGCCAATGG-CTGACACCACCTTTTTTGTGGGA
1 AAAAAG-TAAAAAAAAA-TTTT-GTGGTGGCCTGCCAATGGCCTG-CACCACCTTTTTTGT-GGA
* * *
5603798 ATTTTTTTTTTACATTTTTCGTGTCAAAAGAAGGTATTAGTATACGA
61 A--TTTTTTTTACTTTTTTCGTGTCAAAAGAAAGTATCAGTATACGA
* *
5603845 AAAAAGTAAAAAAAGAATTTTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGGATTTT
1 AAAAAGTAAAAAAA-AATTTTGTGGTGGCCTGCCAATGGCCTGCACCACCTTTTTTGTGGAATTT
* * * *
5603910 TTTTTACTTTTTTAGTATCAATAGCAAGTATCAGTATAC-A
65 TTTTTACTTTTTTCGTGTCAAAAGAAAGTATCAGTATACGA
5603950 AAAAAGTAA
1 AAAAAGTAA
5603959 TTTTTTTTTG
Statistics
Matches: 202, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
105 10 0.05
106 35 0.17
107 9 0.04
108 15 0.07
109 70 0.35
110 14 0.07
111 49 0.24
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (105 bp):
AAAAAGTAAAAAAAAATTTTGTGGTGGCCTGCCAATGGCCTGCACCACCTTTTTTGTGGAATTTT
TTTTACTTTTTTCGTGTCAAAAGAAAGTATCAGTATACGA
Found at i:5616677 original size:1 final size:1
Alignment explanation
Indices: 5616671--5616699 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
5616661 TCATAGATAC
5616671 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5616700 CAAGAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5623545 original size:16 final size:16
Alignment explanation
Indices: 5623524--5623591 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
5623514 TTTGGTTCGC
5623524 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
5623540 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
5623556 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
5623572 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
5623588 TGTA
1 TGTA
5623592 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5623844 original size:16 final size:16
Alignment explanation
Indices: 5623807--5623848 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5623797 TTAATCATAT
*
5623807 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5623823 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5623838 TTAAAATATAT
1 TTAAAATATAT
5623849 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5623855 original size:14 final size:15
Alignment explanation
Indices: 5623816--5623857 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5623806 TTTAAACATA
*
5623816 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5623831 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5623845 A-TATAATTTAATA
1 ATTATAATTAAATA
5623858 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5624052 original size:26 final size:28
Alignment explanation
Indices: 5624023--5624083 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
5624013 CATGAATTTG
*
5624023 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
5624049 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
5624077 TAAAATT
1 TATAATT
5624084 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:5628009 original size:18 final size:20
Alignment explanation
Indices: 5627973--5628009 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5627963 AAAAATCATA
*
5627973 AAAATATTTAAAATTTTAAC
1 AAAATATTTAAAATGTTAAC
5627993 AAAAT-TTTAAAA-GTTAA
1 AAAATATTTAAAATGTTAA
5628010 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAATATTTAAAATGTTAAC
Found at i:5644472 original size:2 final size:2
Alignment explanation
Indices: 5644465--5644497 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5644455 ATACTGAAGA
5644465 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5644498 TGTATATGCA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5648610 original size:15 final size:15
Alignment explanation
Indices: 5648576--5648604 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5648566 TATGACTAAT
5648576 AATTGAATTTAACTA
1 AATTGAATTTAACTA
5648591 AATTG-ATTTAACTA
1 AATTGAATTTAACTA
5648605 CTATTGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
AATTGAATTTAACTA
Found at i:5649779 original size:6 final size:6
Alignment explanation
Indices: 5649770--5649872 Score: 161
Period size: 6 Copynumber: 16.8 Consensus size: 6
5649760 AGTACAAATT
* * *
5649770 ATATAC ATATAG ACATAC ATACATAT ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC AT--ATAC ATATAC ATATAC ATATAC ATATAC
5649820 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
5649868 ATATA
1 ATATA
5649873 GGCCTTATCA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
6 84 0.94
8 5 0.06
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:5649785 original size:8 final size:8
Alignment explanation
Indices: 5649769--5649860 Score: 58
Period size: 8 Copynumber: 11.5 Consensus size: 8
5649759 AAGTACAAAT
5649769 TATATACA
1 TATATACA
*
5649777 TATAGACA
1 TATATACA
*
5649785 TACATACA
1 TATATACA
*
5649793 TATATATA
1 TATATACA
*
5649801 CATATACA
1 TATATACA
* *
5649809 TATACATA
1 TATATACA
* *
5649817 TACATATA
1 TATATACA
*
5649825 CATATACA
1 TATATACA
* *
5649833 TATACATA
1 TATATACA
* *
5649841 TACATATA
1 TATATACA
*
5649849 CATATACA
1 TATATACA
5649857 TATA
1 TATA
5649861 CATATACATA
Statistics
Matches: 60, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
8 60 1.00
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (8 bp):
TATATACA
Found at i:5655121 original size:16 final size:18
Alignment explanation
Indices: 5655100--5655132 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5655090 TTACCTACAA
5655100 AATTTTA-AT-AGATTTG
1 AATTTTAGATAAGATTTG
5655116 AATTTTAGATAAGATTT
1 AATTTTAGATAAGATTT
5655133 TTATAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (18 bp):
AATTTTAGATAAGATTTG
Found at i:5661132 original size:19 final size:21
Alignment explanation
Indices: 5661051--5661126 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
5661041 ATTTTCGAGG
5661051 ATATACAATCTTAGATAT-A-
1 ATATACAATCTTAGATATGAT
*
5661070 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
5661091 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
5661112 ATATACAATCTTAGA
1 ATATACAATCTTAGA
5661127 AGATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 17 0.32
20 1 0.02
21 35 0.66
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:5668688 original size:18 final size:19
Alignment explanation
Indices: 5668662--5668705 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
5668652 ATCCCAGCCC
*
5668662 ATATTAAATATATA-TAAT
1 ATATAAAATATATATTAAT
5668680 ATATAAAATATATATTTAAT
1 ATATAAAATATATA-TTAAT
5668700 ATATAA
1 ATATAA
5668706 TTCTGGTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
20 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAAATATATATTAAT
Found at i:5669790 original size:15 final size:15
Alignment explanation
Indices: 5669770--5669799 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5669760 AACATCTGTA
5669770 CATTATTTCACATAT
1 CATTATTTCACATAT
5669785 CATTATTTCACATAT
1 CATTATTTCACATAT
5669800 TTCTCTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTATTTCACATAT
Found at i:5670048 original size:76 final size:76
Alignment explanation
Indices: 5669922--5670070 Score: 271
Period size: 76 Copynumber: 2.0 Consensus size: 76
5669912 TTTATCACAT
* *
5669922 ATTACTTAATAAATACAGTCAATTTATTATCTATTATATTTAATCATTATCAAGCCTTATTCCTC
1 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCCTC
5669987 ACTTATTCTTC
66 ACTTATTCTTC
*
5669998 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
1 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCCTC
5670063 ACTTATTC
66 ACTTATTC
5670071 AACATATAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.46
Consensus pattern (76 bp):
ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCCTC
ACTTATTCTTC
Found at i:5670107 original size:18 final size:18
Alignment explanation
Indices: 5670086--5670134 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5670076 ATAAATTTGT
5670086 AATTAAATATCATATTAA-
1 AATTAAAT-TCATATTAAC
* *
5670104 AATTATATTCATTTTAAC
1 AATTAAATTCATATTAAC
*
5670122 AATTAACTTCATA
1 AATTAAATTCATA
5670135 ATCAAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAATTCATATTAAC
Found at i:5672066 original size:15 final size:15
Alignment explanation
Indices: 5672046--5672077 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5672036 TCTATTTTAA
*
5672046 TAATATTAGGATAAT
1 TAATATTAAGATAAT
5672061 TAATATTAAGATAAT
1 TAATATTAAGATAAT
5672076 TA
1 TA
5672078 TTAAGGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (15 bp):
TAATATTAAGATAAT
Found at i:5680650 original size:15 final size:15
Alignment explanation
Indices: 5680632--5680660 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5680622 TATATATTTA
5680632 TAAATTAAAATATAC
1 TAAATTAAAATATAC
5680647 TAAATTAAAATATA
1 TAAATTAAAATATA
5680661 AAAAACAAAT
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:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATTAAAATATAC
Found at i:5681354 original size:29 final size:30
Alignment explanation
Indices: 5681316--5681377 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
5681306 GCAACTATAA
* *
5681316 TTTTGAGTTAATTGATATGA-TTTATAATT
1 TTTTAAGTTAATTGATATAATTTTATAATT
* **
5681345 TTTTAAGTTATTTTTTATAATTTTATAATT
1 TTTTAAGTTAATTGATATAATTTTATAATT
5681375 TTT
1 TTT
5681378 ATTTTTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTTAAGTTAATTGATATAATTTTATAATT
Found at i:5681361 original size:22 final size:23
Alignment explanation
Indices: 5681336--5681396 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
5681326 ATTGATATGA
5681336 TTTATAATTTTTTAAGTTAT-TT
1 TTTATAATTTTTTAAGTTATATT
* * *
5681358 TTTATAATTTTATAATTTTTATT
1 TTTATAATTTTTTAAGTTATATT
5681381 TTTATATATTTTTTAA
1 TTTATA-ATTTTTTAA
5681397 ATACTATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 17 0.52
23 8 0.24
24 8 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATAATTTTTTAAGTTATATT
Found at i:5681394 original size:17 final size:18
Alignment explanation
Indices: 5681353--5681395 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5681343 TTTTTTAAGT
5681353 TATTTTTTATAATTTTATA
1 TATTTTTTAT-ATTTTATA
5681372 -A-TTTTTAT-TTTTATA
1 TATTTTTTATATTTTATA
5681387 TATTTTTTA
1 TATTTTTTA
5681396 AATACTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.32
16 1 0.05
17 13 0.59
18 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTTATATTTTATA
Found at i:5691074 original size:89 final size:89
Alignment explanation
Indices: 5691022--5691517 Score: 714
Period size: 89 Copynumber: 5.6 Consensus size: 89
5691012 TAGGACATGC
* * * * * *
5691022 TATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCT-ATTTTTTTCGATCTACTCCACC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTCGATCTGCTTCGCC
* *
5691086 ACCAGTATGGGGAGACAAGATCTG
66 ACCAGTATGGGAAGGCAAGATCTG
* * * * *
5691110 TTTCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTC-TTCGATTTGCGTCGCC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTCGATCTGCTTCGCC
*
5691174 ACCAGTATGGGAAGGCAAGATCTAT
66 ACCAGTATGGGAAGGCAAGATCT-G
* *
5691199 TATCTTTGATCTACTTCACGCCGGTACATAAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTCGATCTGCTTCGCC
5691263 ACCAGTATGGGAAGGCAAGATCTAG
66 ACCAGTATGGGAAGGCAAGATCT-G
*
5691288 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTCGATCTGCTTCGCC
5691352 ACCAGTATGGGAAGGCAAGATCTGG
66 ACCAGTATGGGAAGGCAAGATCT-G
* *
5691377 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GATATGCTTCGCC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTCGATCTGCTTCGCC
5691441 ACCAGTATGGGAAGGCAAGATCTGG
66 ACCAGTATGGGAAGGCAAGATCT-G
* * *
5691466 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAATATCTTCTTTTCTTT
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTCTTT
5691518 TCAGCCTGCT
Statistics
Matches: 376, Mismatches: 28, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
88 71 0.19
89 296 0.79
90 9 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (89 bp):
TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTCGATCTGCTTCGCC
ACCAGTATGGGAAGGCAAGATCTG
Found at i:5691077 original size:44 final size:43
Alignment explanation
Indices: 5691024--5691507 Score: 329
Period size: 45 Copynumber: 10.9 Consensus size: 43
5691014 GGACATGCTA
*
5691024 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATT
* * * *** * *
5691067 TTTTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT
1 TCTTT-GATCTACTTCA-CGCCAGTACATGAAGACAAGATCTATT
* *
5691112 TCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATT
* * * * * * *** *
5691156 TCTTCGATTTGCGTCGCCACCAGTATGGGAAGGCAAGATCTATT
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTATT
* * *
5691200 ATCTTTGATCTACTTCACGCCGGTACATAAAGACAAGATCTGCTT
1 -TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATT
* * * *** * *
5691245 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTA
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTA-TT
* *
5691290 TCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATT
* * * *** * * *
5691334 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTA
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCT-ATT
* *
5691379 TCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATT
* * * * *** * * *
5691423 TCTTTGATATGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTA
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCT-ATT
* *
5691468 TCTCTGATCTACTTCACGCCAGTACATGAAGACAATATCT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
5691508 TCTTTTCTTT
Statistics
Matches: 325, Mismatches: 105, Indels: 21
0.72 0.23 0.05
Matches are distributed among these distances:
43 22 0.07
44 150 0.46
45 153 0.47
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATT
Found at i:5691179 original size:133 final size:131
Alignment explanation
Indices: 5691042--5691484 Score: 379
Period size: 133 Copynumber: 3.3 Consensus size: 131
5691032 CTACTTCACG
* * * *
5691042 CCAGTACATGAAGATAAGATCTATTTTTTTCGATCTACTCCACCACCAGTATGGGGAGACAAGAT
1 CCAGTACATGAAGACAAGATCTATTTCTTT-GATCTACTTCACCACCAGTATGGGAAGACAAGAT
* * *
5691107 CTGTTTCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTCTTCGATTTGCGTCG
65 CTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TTTCTTCGATATGCTTCG
5691172 CCA
129 CCA
*** * * * ****
5691175 CCAGTATGGGAAGGCAAGATCTATTATCTTTGATCTACTTCA-CGCCGGTACATAAAGACAAGAT
1 CCAGTACATGAAGACAAGATCTATT-TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGAT
* * * *** * * * *
5691239 CTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATC-TCTGATCTACT
65 CTG-TTTCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCT-GTTTCTTC-GATATGCT
* *
5691303 TC-ACG
126 TCGCCA
* * * *
5691308 CCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGAT
1 CCAGTACATGAAGACAAGATCT-ATTTCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGAT
* * *
5691373 CTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATATGCTTC
65 CT-GTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TTTCTTCGATATGCTTC
5691438 GCCA
128 GCCA
*** * * * *
5691442 CCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCAC
1 CCAGTACATGAAGACAAGATCT-ATTTCTTTGATCTACTTCAC
5691485 GCCAGTACAT
Statistics
Matches: 233, Mismatches: 66, Indels: 21
0.73 0.21 0.07
Matches are distributed among these distances:
132 19 0.08
133 111 0.48
134 101 0.43
135 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (131 bp):
CCAGTACATGAAGACAAGATCTATTTCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATC
TGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTCTTCGATATGCTTCGCC
A
Found at i:5691464 original size:45 final size:44
Alignment explanation
Indices: 5690941--5691491 Score: 324
Period size: 44 Copynumber: 12.4 Consensus size: 44
5690931 GTTTTCCTCA
* * * * *
5690941 ATCTACTTCGCCACCAGTATGGGAAGATAAAATCTG-TATATTCG
1 ATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * * * * *
5690985 ATCCACTTCGCTACC-GATATAGAAAGATAGGA-CATGCTATCTTTG
1 ATCTACTTC-CCACCAG-TATGGGAAGACAAGATC-TGCTTTCTTTG
* * *** * * *
5691030 ATCTACTTCACGCCAGTACATGAAGATAAGATCT-ATTTTTTTCG
1 ATCTACTTCCCACCAGTATGGGAAGACAAGATCTGCTTTCTTT-G
* *
5691074 ATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TTTCTTTG
1 ATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * *** * *
5691118 ATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTCTTCG
1 ATCTACTTCCCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * * *
5691162 ATTTGCGTCGCCACCAGTATGGGAAGGCAAGATCT-ATTATCTTTG
1 ATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGCTT-TCTTTG
* * * ****
5691207 ATCTACTTCACGCCGGTACATAAAGACAAGATCTGCTTTCTTTG
1 ATCTACTTCCCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * *
5691251 ATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAG-TATCTCTG
1 ATCTACTTC-CCACCAGTATGGGAAGACAAGATCT-GCTTTCTTTG
* * ***
5691296 ATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTG
1 ATCTACTTCCCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * * *
5691340 ATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTG
1 ATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * ***
5691385 ATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTG
1 ATCTACTTCCCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * * * *
5691429 ATATGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTG
1 ATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
* *
5691474 ATCTACTTCACGCCAGTA
1 ATCTACTTCCCACCAGTA
5691492 CATGAAGACA
Statistics
Matches: 374, Mismatches: 116, Indels: 34
0.71 0.22 0.06
Matches are distributed among these distances:
43 27 0.07
44 177 0.47
45 169 0.45
46 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTACTTCCCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
Found at i:5692827 original size:8 final size:7
Alignment explanation
Indices: 5692783--5692824 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
5692773 TTAGCCTCTC
5692783 CATTTTT
1 CATTTTT
5692790 -ACTTTTT
1 CA-TTTTT
5692797 CATTTTT
1 CATTTTT
5692804 CA-TTTT
1 CATTTTT
5692810 CATCTTTT
1 CAT-TTTT
5692818 CATTTTT
1 CATTTTT
5692825 TCACATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:5693717 original size:22 final size:22
Alignment explanation
Indices: 5693689--5693733 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5693679 AGTTTGGCAG
5693689 AAAAATCCAAAAGAATGAAAGA
1 AAAAATCCAAAAGAATGAAAGA
**
5693711 AAAAATCGTAAAGAATGAAAGA
1 AAAAATCCAAAAGAATGAAAGA
5693733 A
1 A
5693734 CATTTGCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.07, G:0.16, T:0.11
Consensus pattern (22 bp):
AAAAATCCAAAAGAATGAAAGA
Found at i:5696768 original size:101 final size:102
Alignment explanation
Indices: 5696590--5696795 Score: 387
Period size: 101 Copynumber: 2.0 Consensus size: 102
5696580 TCAATGAATG
5696590 CGAAGAGAAATCATGTTTTTTTAAAAAAACTTTTGATTTTCGACAAGAAGACAAAACATAACCAA
1 CGAAGAGAAATCATGTTTTTTTAAAAAAACTTTTG--TTTCGACAAGAAGACAAAACATAACCAA
5696655 TTCATGGCTCGACTCTCTAAAATTTCCCAGTGGAGTCGC
64 TTCATGGCTCGACTCTCTAAAATTTCCCAGTGGAGTCGC
5696694 CGAAGAGAAATCATGTTTTTTTAAAAAAACTTTTG-TTCGACAAGAAGACAAAACATAACCAATT
1 CGAAGAGAAATCATGTTTTTTTAAAAAAACTTTTGTTTCGACAAGAAGACAAAACATAACCAATT
5696758 CATGGCTCGACTCTCTAAAATTTCCCAGTGGAGTCGC
66 CATGGCTCGACTCTCTAAAATTTCCCAGTGGAGTCGC
5696795 C
1 C
5696796 AAGCTGTTGA
Statistics
Matches: 102, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
101 67 0.66
104 35 0.34
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (102 bp):
CGAAGAGAAATCATGTTTTTTTAAAAAAACTTTTGTTTCGACAAGAAGACAAAACATAACCAATT
CATGGCTCGACTCTCTAAAATTTCCCAGTGGAGTCGC
Found at i:5699393 original size:17 final size:17
Alignment explanation
Indices: 5699371--5699434 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
5699361 AATCTTAGAG
5699371 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
5699388 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
5699407 TTCTAATTGTATATAGC
1 TTCTAATTGTATACAGC
*
5699424 TTTTAATTGTA
1 TTCTAATTGTA
5699435 GCCCTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 4 0.11
19 11 0.30
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:5699410 original size:36 final size:36
Alignment explanation
Indices: 5699363--5699433 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
5699353 GATTATGTAA
5699363 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
5699399 TCTTAGAGTTCTAATTGTATATAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
5699434 AGCCCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:5699412 original size:19 final size:19
Alignment explanation
Indices: 5699362--5699418 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
5699352 TGATTATGTA
5699362 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
5699381 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
5699398 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
5699417 AT
1 AT
5699419 ATAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:5704296 original size:17 final size:17
Alignment explanation
Indices: 5704274--5704318 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5704264 AATCTTAGAG
5704274 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
5704291 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAAC
*
5704308 TTTTAATTGTA
1 TTCTAATTGTA
5704319 GCCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:5707376 original size:14 final size:15
Alignment explanation
Indices: 5707352--5707390 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5707342 TTTTGAAAGC
5707352 TAAAGTTAAAAATA-T
1 TAAA-TTAAAAATACT
*
5707367 TATATTAAAAATACT
1 TAAATTAAAAATACT
5707382 TAAATTAAA
1 TAAATTAAA
5707391 TTATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (15 bp):
TAAATTAAAAATACT
Found at i:5718605 original size:29 final size:30
Alignment explanation
Indices: 5718546--5718615 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
5718536 GCTAGTAGTT
* *
5718546 TATAAAATTTGAATCAAATTAAAATATCATA
1 TATAAAA-TTGAATAAAATCAAAATATCATA
*
5718577 TATAAAATTGTATAAAATCAAAAT-TCATA
1 TATAAAATTGAATAAAATCAAAATATCATA
*
5718606 TATAACATTG
1 TATAAAATTG
5718616 CATATTAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 14 0.40
30 14 0.40
31 7 0.20
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (30 bp):
TATAAAATTGAATAAAATCAAAATATCATA
Found at i:5718631 original size:31 final size:28
Alignment explanation
Indices: 5718546--5718635 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 28
5718536 GCTAGTAGTT
* *
5718546 TATAAAATTTGAATCAAATTAAAATATCATA
1 TATAAAA-TTGTAT-AAAATAAAAT-TCATA
5718577 TATAAAATTGTATAAAATCAAAATTCATA
1 TATAAAATTGTATAAAAT-AAAATTCATA
* *
5718606 TATAACATTGCATATTAAACTAAAATTCAT
1 TATAAAATTG--TA-TAAAATAAAATTCAT
5718636 GTGTAGTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 18 0.35
30 10 0.20
31 18 0.35
32 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (28 bp):
TATAAAATTGTATAAAATAAAATTCATA
Found at i:5730526 original size:12 final size:13
Alignment explanation
Indices: 5730503--5730535 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5730493 ACAAATACAA
5730503 AATTATATTAATT
1 AATTATATTAATT
5730516 AATTA-ATTAATT
1 AATTATATTAATT
5730528 -ATTATATT
1 AATTATATT
5730536 TTATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 10 0.53
13 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATTATATTAATT
Found at i:5731244 original size:31 final size:29
Alignment explanation
Indices: 5731177--5731234 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
5731167 AAAATTTTAC
*
5731177 GTATAAAATTACATAAAATCAAAATTCCT
1 GTATAAAATTACATAAAACCAAAATTCCT
*
5731206 GTTTAAAATTACATATTAAACCAAAATTC
1 GTATAAAATTACATA--AAACCAAAATTC
5731235 ATTGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
31 11 0.44
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (29 bp):
GTATAAAATTACATAAAACCAAAATTCCT
Found at i:5733422 original size:21 final size:22
Alignment explanation
Indices: 5733379--5733431 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
5733369 TATTTTGATT
**
5733379 TTTTTAAAAAATTTTAACTATAA
1 TTTTTAAAAAA-TTTAAAAATAA
5733402 TTTTTAAAAAA-TTAAAAATAA
1 TTTTTAAAAAATTTAAAAATAA
*
5733423 -TCTTAAAAA
1 TTTTTAAAAA
5733432 TAAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 8 0.30
23 11 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTTAAAAAATTTAAAAATAA
Found at i:5733826 original size:8 final size:8
Alignment explanation
Indices: 5733813--5733841 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5733803 TCAATAAATA
5733813 AAATTATT
1 AAATTATT
5733821 AAATTATT
1 AAATTATT
5733829 AAA-TATT
1 AAATTATT
5733836 AAATTA
1 AAATTA
5733842 AAATAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:5740991 original size:50 final size:50
Alignment explanation
Indices: 5740900--5740998 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
5740890 GCATTATTCT
* * * * * *
5740900 AATCAATGTCAAATAGAAGGAGAGAAGTTCTATATGGATTCTACTTGTAC
1 AATCAATATCAAATAAAAGAAGAGAAGTTATATACGAATTCTACTTGTAC
*
5740950 AATCAATATCAAATAAAAGAAGAGTAGTTATATACGAATTCTACTTGTA
1 AATCAATATCAAATAAAAGAAGAGAAGTTATATACGAATTCTACTTGTA
5740999 TTTTATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (50 bp):
AATCAATATCAAATAAAAGAAGAGAAGTTATATACGAATTCTACTTGTAC
Found at i:5743383 original size:3 final size:3
Alignment explanation
Indices: 5743377--5743411 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5743367 GCTGGGGTTG
* *
5743377 TCT TCT TCT TCT TCT TCT CCT TCT CCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5743412 CTCAGACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:5755610 original size:14 final size:15
Alignment explanation
Indices: 5755588--5755616 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5755578 GTGTGTATTA
5755588 GAAAGAAAAAAAAAG
1 GAAAGAAAAAAAAAG
5755603 GAAA-AAAAAAAAAG
1 GAAAGAAAAAAAAAG
5755617 AGAGAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAAAAAG
Found at i:5764284 original size:53 final size:52
Alignment explanation
Indices: 5764132--5764330 Score: 185
Period size: 53 Copynumber: 3.9 Consensus size: 52
5764122 TCACATATCA
* * *
5764132 CACACCGAAGCCATAGCCTAGCTATGGTCTTACAC-G--G-A-A-ATCACATAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATATCAC--AT
* * * * * * * * *
5764180 CACACTGATGTCATATCCCAGATATGATCTGACACGGAAATCACATATCACAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACAG-AAGCACATATCACAT
5764233 CACACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATAGTCACAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATA-TCACAT
* * *
5764286 CACACCGATGCCATAGCCTAGCTATGGTCTTATGCGGAAGCACAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAGCACAT
5764331 GATAATCACA
Statistics
Matches: 122, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
48 27 0.22
49 1 0.01
52 8 0.07
53 80 0.66
54 1 0.01
55 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (52 bp):
CACACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATATCACAT
Found at i:5767525 original size:14 final size:14
Alignment explanation
Indices: 5767499--5767527 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5767489 TGGTTAATGA
5767499 GTATATATATTTTT
1 GTATATATATTTTT
5767513 GTATA-ATATTTTT
1 GTATATATATTTTT
5767526 GT
1 GT
5767528 TTTAAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (14 bp):
GTATATATATTTTT
Found at i:5769234 original size:21 final size:21
Alignment explanation
Indices: 5769180--5769236 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
5769170 TAGCTCTCAC
5769180 GAGCTTCTGTTTAACTTATAT
1 GAGCTTCTGTTTAACTTATAT
* ** * *
5769201 GAGTTTCCATTTAACTTTTTT
1 GAGCTTCTGTTTAACTTATAT
5769222 GAGCTTCTGTTTAAC
1 GAGCTTCTGTTTAAC
5769237 CCTTATGGGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (21 bp):
GAGCTTCTGTTTAACTTATAT
Found at i:5769304 original size:21 final size:21
Alignment explanation
Indices: 5769224--5769318 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
5769214 ACTTTTTTGA
*
5769224 GCTTCTGTTTAACCCTTATGG
1 GCTTCTGTTCAACCCTTATGG
* ** * *
5769245 GTTTCCATTCAACTCTTATGA
1 GCTTCTGTTCAACCCTTATGG
*
5769266 GCTTCCGTTCAACCCTTATGG
1 GCTTCTGTTCAACCCTTATGG
* * * * *
5769287 GTTTCTGTTTAGCTCTTATGT
1 GCTTCTGTTCAACCCTTATGG
5769308 GCTTCTGTTCA
1 GCTTCTGTTCA
5769319 GCCTTCAGGC
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (21 bp):
GCTTCTGTTCAACCCTTATGG
Found at i:5769318 original size:42 final size:42
Alignment explanation
Indices: 5769180--5769318 Score: 145
Period size: 42 Copynumber: 3.3 Consensus size: 42
5769170 TAGCTCTCAC
* * * * * *
5769180 GAGCTTCTGTTTAA-CTTATATGAGTTTCCATTTAACTTTTTT
1 GAGCTTCTGTTCAACCCT-TATGGGTTTCCATTCAACTCTTAT
*
5769222 GAGCTTCTGTTTAACCCTTATGGGTTTCCATTCAACTCTTAT
1 GAGCTTCTGTTCAACCCTTATGGGTTTCCATTCAACTCTTAT
* ** * *
5769264 GAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCTCTTAT
1 GAGCTTCTGTTCAACCCTTATGGGTTTCCATTCAACTCTTAT
*
5769306 GTGCTTCTGTTCA
1 GAGCTTCTGTTCA
5769319 GCCTTCAGGC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 81 0.98
43 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (42 bp):
GAGCTTCTGTTCAACCCTTATGGGTTTCCATTCAACTCTTAT
Found at i:5769578 original size:19 final size:18
Alignment explanation
Indices: 5769545--5769580 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5769535 ATTTATGTTT
5769545 AACTTATTAAACTTACTA
1 AACTTATTAAACTTACTA
*
5769563 AACTTCATTAAGCTTACT
1 AACTT-ATTAAACTTACT
5769581 TGTGTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (18 bp):
AACTTATTAAACTTACTA
Found at i:5773037 original size:50 final size:50
Alignment explanation
Indices: 5772975--5773076 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
5772965 TAGCAGAGAA
5772975 GACTACTCGGTTGAAGCACTATCCTAGACGAATCAAAAAGGTACAATTTT
1 GACTACTCGGTTGAAGCACTATCCTAGACGAATCAAAAAGGTACAATTTT
*
5773025 GACTACTTGGTTGAAGCACTATCCTAGACGAATCAAAAAGGTACAATTTT
1 GACTACTCGGTTGAAGCACTATCCTAGACGAATCAAAAAGGTACAATTTT
5773075 GA
1 GA
5773077 TTAAGTATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (50 bp):
GACTACTCGGTTGAAGCACTATCCTAGACGAATCAAAAAGGTACAATTTT
Found at i:5782156 original size:2 final size:2
Alignment explanation
Indices: 5782144--5782187 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5782134 ACCAAAATTT
5782144 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5782185 TA T
1 TA T
5782188 TCATGTCGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5782643 original size:88 final size:86
Alignment explanation
Indices: 5782484--5782725 Score: 245
Period size: 88 Copynumber: 2.7 Consensus size: 86
5782474 CTTAACAGTG
* *
5782484 TAAAAAG-CCCTCAAAGTTTTTCAAGAAAAGCAATTAAGCCCCTGTTTTATTTTTTGCACTCAAT
1 TAAAAAGACCCTCAAA-TTTTTTAAAAAAAGCAATTAAGCCCC---TTT-TTTTTTGCACTCAAT
* * *
5782548 TGCGTACTTAAACTTTCAAAATGTAT
61 TGCGTACTTAAACTGTCAAAATATAC
* *
5782574 TAAAAAGACCTTCAAATTTTTTAAAAAAAAAGCAATTAAGCCCCTTTTTTTTTGCACTCAATTGG
1 TAAAAAGACCCTCAAATTTTTT--AAAAAAAGCAATTAAGCCCCTTTTTTTTTGCACTCAATTGC
*
5782639 GTACTTGAACTGTCAAAATATAC
64 GTACTTAAACTGTCAAAATATAC
* * *** *
5782662 CAAAAA-AGCCGTCAAATTTTTTTTTAAAAGCAATTAAGCCCCTACTTTTTTTTTACACTCAATT
1 TAAAAAGA-CCCTCAAATTTTTTAAAAAAAGCAATTAAG-CCC--CTTTTTTTTTGCACTCAATT
5782726 TCCAAAATGC
Statistics
Matches: 131, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
86 13 0.10
87 4 0.03
88 54 0.41
89 22 0.17
90 12 0.09
91 7 0.05
92 19 0.15
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (86 bp):
TAAAAAGACCCTCAAATTTTTTAAAAAAAGCAATTAAGCCCCTTTTTTTTTGCACTCAATTGCGT
ACTTAAACTGTCAAAATATAC
Found at i:5782921 original size:26 final size:27
Alignment explanation
Indices: 5782877--5782931 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
5782867 AATTAAAGTT
*
5782877 ATAAAAATTATTAA-ATTTTAATAAAA
1 ATAAAAAATATTAATATTTTAATAAAA
* * *
5782903 ATAAAAAATATTTATTTTTTATTAAAA
1 ATAAAAAATATTAATATTTTAATAAAA
5782930 AT
1 AT
5782932 TAGAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATAAAAAATATTAATATTTTAATAAAA
Found at i:5782940 original size:11 final size:11
Alignment explanation
Indices: 5782926--5782960 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
5782916 ATTTTTTATT
*
5782926 AAAAATTA-GA
1 AAAAATTATAA
5782936 AAAAATTATAA
1 AAAAATTATAA
5782947 AAAAATTATAA
1 AAAAATTATAA
5782958 AAA
1 AAA
5782961 TCATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:5782947 original size:19 final size:19
Alignment explanation
Indices: 5782925--5783007 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
5782915 TATTTTTTAT
*
5782925 TAAAAATTAGAAAAAATTA
1 TAAAAATTATAAAAAATTA
*
5782944 TAAAAAAATTAT-AAAAATCA
1 T--AAAAATTATAAAAAATTA
*
5782964 TAAAATATTATAAAATA-TA
1 TAAAA-ATTATAAAAAATTA
*
5782983 TATAAATATATAAAAAATTA
1 TAAAAAT-TATAAAAAATTA
5783003 TAAAA
1 TAAAA
5783008 TTTTATAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
18 6 0.12
19 19 0.37
20 18 0.35
21 8 0.16
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (19 bp):
TAAAAATTATAAAAAATTA
Done.