Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397279.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.0, whole genome shotgun sequence
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: 2022356
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6073 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:4408 original size:7 final size:7
Alignment explanation
Indices: 4398--4736 Score: 130
Period size: 7 Copynumber: 50.3 Consensus size: 7
4388 CTAAACCCTA
4398 CCGAACC
1 CCGAACC
4405 CCGAACC
1 CCGAACC
4412 CCGAA-C
1 CCGAACC
4418 CCGAA-C
1 CCGAACC
4424 CCGAA-C
1 CCGAACC
*
4430 CGGAACC
1 CCGAACC
*
4437 CTGAACC
1 CCGAACC
*
4444 CTGAACC
1 CCGAACC
4451 CCGAACTC
1 CCGAAC-C
***
4459 TTAAACC
1 CCGAACC
**
4466 CTTAAACC
1 C-CGAACC
4474 CCAGAACC
1 CC-GAACC
* *
4482 CCAAAAC
1 CCGAACC
*
4489 CTGAGA-C
1 CCGA-ACC
4496 CCGAGA-C
1 CCGA-ACC
*
4503 CC-AAGC
1 CCGAACC
*
4509 CCGGACC
1 CCGAACC
4516 CCGAACC
1 CCGAACC
4523 CCGAACC
1 CCGAACC
4530 CCG-ACC
1 CCGAACC
*
4536 CCGCACC
1 CCGAACC
4543 CCG---C
1 CCGAACC
*
4547 CCGACCC
1 CCGAACC
4554 CCG-ACC
1 CCGAACC
*
4560 CCTCAACC
1 CC-GAACC
*
4568 CTGAACC
1 CCGAACC
*
4575 CTGAACC
1 CCGAACC
**
4582 CTTAA-C
1 CCGAACC
**
4588 CTTAACC
1 CCGAACC
*
4595 CGGAA-C
1 CCGAACC
4601 CCGAAACC
1 CCG-AACC
*
4609 CAGAACC
1 CCGAACC
4616 CCGAACC
1 CCGAACC
4623 CCGAACC
1 CCGAACC
4630 TCC--A-C
1 -CCGAACC
*
4635 CC-AAAC
1 CCGAACC
4641 CCGAACC
1 CCGAACC
*
4648 CCGACCC
1 CCGAACC
4655 CGCGAACC
1 C-CGAACC
*
4663 CGGAA-C
1 CCGAACC
4669 CCGAA-C
1 CCGAACC
* *
4675 CTGAAAC
1 CCGAACC
*
4682 CTGAACC
1 CCGAACC
* *
4689 CTGACCC
1 CCGAACC
4696 CCG-ACC
1 CCGAACC
4702 CCG-ACC
1 CCGAACC
*
4708 CCTAACC
1 CCGAACC
4715 CCTGAACC
1 CC-GAACC
4723 CCG-ACC
1 CCGAACC
4729 CC-AACC
1 CCGAACC
4735 CC
1 CC
4737 TAAACCCTAA
Statistics
Matches: 268, Mismatches: 39, Indels: 51
0.75 0.11 0.14
Matches are distributed among these distances:
4 6 0.02
5 3 0.01
6 74 0.28
7 146 0.54
8 39 0.15
ACGTcount: A:0.28, C:0.52, G:0.14, T:0.06
Consensus pattern (7 bp):
CCGAACC
Found at i:4695 original size:6 final size:7
Alignment explanation
Indices: 4559--4757 Score: 71
Period size: 7 Copynumber: 29.6 Consensus size: 7
4549 GACCCCCGAC
*
4559 CCCTCAA
1 CCCTGAA
4566 CCCTGAA
1 CCCTGAA
4573 CCCTGAA
1 CCCTGAA
*
4580 CCCTTAA
1 CCCTGAA
*
4587 -CCTTAA
1 CCCTGAA
*
4593 CCCGGAA
1 CCCTGAA
4600 CCC-GAAA
1 CCCTG-AA
*
4607 CCCAGAA
1 CCCTGAA
*
4614 CCCCGAA
1 CCCTGAA
*
4621 CCCCGAA
1 CCCTGAA
**
4628 -CCTCCA
1 CCCTGAA
*
4634 CCC-AAA
1 CCCTGAA
4640 CCC-GAA
1 CCCTGAA
* *
4646 CCCCGAC
1 CCCTGAA
*
4653 CCCGCGAA
1 CCC-TGAA
*
4661 CCCGGAA
1 CCCTGAA
4668 CCC-GAA
1 CCCTGAA
4674 -CCTGAA
1 CCCTGAA
*
4680 ACCTGAA
1 CCCTGAA
*
4687 CCCTGAC
1 CCCTGAA
*
4694 CCCCG-A
1 CCCTGAA
* *
4700 CCCCGAC
1 CCCTGAA
4707 CCCT-AA
1 CCCTGAA
4713 CCCCTGAA
1 -CCCTGAA
*
4721 CCCCG-A
1 CCCTGAA
*
4727 CCC-CAA
1 CCCTGAA
*
4733 CCCCTAAA
1 -CCCTGAA
*
4741 CCCTAAA
1 CCCTGAA
4748 CCCT-AA
1 CCCTGAA
4754 CCCT
1 CCCT
4758 AATAGAGTGC
Statistics
Matches: 154, Mismatches: 24, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
5 2 0.01
6 42 0.27
7 99 0.64
8 11 0.07
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (7 bp):
CCCTGAA
Found at i:4717 original size:27 final size:27
Alignment explanation
Indices: 4685--4750 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
4675 CTGAAACCTG
* *
4685 AACCCTGACCCCCGACCCCGACCCCTA
1 AACCCTGAACCCCGACCCCAACCCCTA
*
4712 ACCCCTGAACCCCGACCCCAACCCCTA
1 AACCCTGAACCCCGACCCCAACCCCTA
*
4739 AACCCTAAACCC
1 AACCCTGAACCC
4751 TAACCCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.58, G:0.08, T:0.08
Consensus pattern (27 bp):
AACCCTGAACCCCGACCCCAACCCCTA
Found at i:4737 original size:20 final size:21
Alignment explanation
Indices: 4699--4743 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
4689 CTGACCCCCG
*
4699 ACCCCGACCCCTAACCCCTGA
1 ACCCCGACCCCTAACCCCTAA
4720 ACCCCGACCCC-AACCCCTAA
1 ACCCCGACCCCTAACCCCTAA
4740 ACCC
1 ACCC
4744 TAAACCCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.27, C:0.60, G:0.07, T:0.07
Consensus pattern (21 bp):
ACCCCGACCCCTAACCCCTAA
Found at i:5545 original size:21 final size:21
Alignment explanation
Indices: 5502--5545 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5492 TTAAATATTT
* *
5502 TGTTGAAAATTTATTGATACA
1 TGTTGAAAATATATCGATACA
* *
5523 TGTTGATAATATATCGATGCA
1 TGTTGAAAATATATCGATACA
5544 TG
1 TG
5546 CAGTTCAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (21 bp):
TGTTGAAAATATATCGATACA
Found at i:8359 original size:31 final size:32
Alignment explanation
Indices: 8321--8383 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
8311 CCCAAGTATG
8321 TCTTTTCATCCTATTCCATCCACTC-AAATAA
1 TCTTTTCATCCTATTCCATCCACTCTAAATAA
8352 TCTTTTCATCCTATTCCATCCACTCTAAATAA
1 TCTTTTCATCCTATTCCATCCACTCTAAATAA
8384 ATAATCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.40
Consensus pattern (32 bp):
TCTTTTCATCCTATTCCATCCACTCTAAATAA
Found at i:17829 original size:21 final size:21
Alignment explanation
Indices: 17800--17852 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17790 TATCAAGACA
*
17800 TGACTACTTTGAAAGAAAGTAT
1 TGAC-ACTTTGAAAAAAAGTAT
*
17822 TGACACTTTTAAAAAAAGTAT
1 TGACACTTTGAAAAAAAGTAT
* *
17843 CGAGACTTTG
1 TGACACTTTG
17853 GTTGAAAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
TGACACTTTGAAAAAAAGTAT
Found at i:18966 original size:64 final size:64
Alignment explanation
Indices: 18794--18933 Score: 280
Period size: 64 Copynumber: 2.2 Consensus size: 64
18784 GACGTATTGA
18794 TGATTCCACATACTACATGAGTAAAGAACAAGCACATAATGTATGCTAAGTTACCATTGTGTGT
1 TGATTCCACATACTACATGAGTAAAGAACAAGCACATAATGTATGCTAAGTTACCATTGTGTGT
18858 TGATTCCACATACTACATGAGTAAAGAACAAGCACATAATGTATGCTAAGTTACCATTGTGTGT
1 TGATTCCACATACTACATGAGTAAAGAACAAGCACATAATGTATGCTAAGTTACCATTGTGTGT
18922 TGATTCCACATA
1 TGATTCCACATA
18934 TTATGTGAGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (64 bp):
TGATTCCACATACTACATGAGTAAAGAACAAGCACATAATGTATGCTAAGTTACCATTGTGTGT
Found at i:19163 original size:68 final size:68
Alignment explanation
Indices: 18940--19135 Score: 333
Period size: 68 Copynumber: 2.9 Consensus size: 68
18930 CATATTATGT
* *
18940 GAGATAAGAAGGAGCACATGATGTATGATATGTTGCAATTTATTTGATAATGACTTCACATACCA
1 GAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATTTATTTGATAATGACTTCACATACCA
19005 TAA
66 TAA
19008 GAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATTTATTTGATAATGACTTCACATACCA
1 GAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATTTATTTGATAATGACTTCACATACCA
19073 TAA
66 TAA
* * *
19076 GAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGTGATGATGA-TTC-CATA
1 GAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATTTATTTGATAATGACTTCACATA
19136 TGTTATATGA
Statistics
Matches: 123, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
66 4 0.03
67 3 0.02
68 116 0.94
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (68 bp):
GAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATTTATTTGATAATGACTTCACATACCA
TAA
Found at i:20940 original size:78 final size:79
Alignment explanation
Indices: 20767--20943 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 79
20757 TTTATTTCTT
* * * * * * *
20767 GAGATAATATCTAACTTGGATCAATTAAAATTTACTTATTGGTCATCTAAGTTATCTTTAAATAA
1 GAGATAATATTTAAATTTGACCAAGTAAAATTTACTTATTAGTCATCTAAGTTATCTTCAAATAA
*
20832 ATTAAGATAATTTA
66 ATAAAGATAATTTA
*
20846 GAGATAATATTTAAATTTGACCAAGTAAAATTTACTTATTAGTCATCTAATTTAT-TTCCAAA-A
1 GAGATAATATTTAAATTTGACCAAGTAAAATTTACTTATTAGTCATCTAAGTTATCTT-CAAATA
20909 AATAAAGATAATTTA
65 AATAAAGATAATTTA
20924 GAGATAA-ATTCTAAATTTGA
1 GAGATAATATT-TAAATTTGA
20944 TCATCCAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
77 3 0.03
78 33 0.38
79 51 0.59
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (79 bp):
GAGATAATATTTAAATTTGACCAAGTAAAATTTACTTATTAGTCATCTAAGTTATCTTCAAATAA
ATAAAGATAATTTA
Found at i:20997 original size:57 final size:56
Alignment explanation
Indices: 20888--20999 Score: 145
Period size: 57 Copynumber: 2.0 Consensus size: 56
20878 TACTTATTAG
* * *
20888 TCATCTAATTTATTTCCAAAAAATAAAGATAATTTAGAGATAAATTCTAAATTTGA
1 TCATCCAATTTATCTCCAAAAAATAAAGATAATTTAGAGATAAACTCTAAATTTGA
* * *
20944 TCATCCAATTTATCTCTAAATAAATTAAGATATTTTAGAGATAATACTC-AAATTTG
1 TCATCCAATTTATCTCCAAA-AAATAAAGATAATTTAGAGATAA-ACTCTAAATTTG
21000 TCCAATCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 17 0.35
57 28 0.58
58 3 0.06
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (56 bp):
TCATCCAATTTATCTCCAAAAAATAAAGATAATTTAGAGATAAACTCTAAATTTGA
Found at i:21204 original size:17 final size:17
Alignment explanation
Indices: 21182--21226 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
21172 ATGAACCACA
**
21182 GAGAAAGAAGGTCAAGG
1 GAGAAAGAAGAACAAGG
*
21199 GAGAAAGGAGAACAAGG
1 GAGAAAGAAGAACAAGG
21216 GAGAAAGAAGA
1 GAGAAAGAAGA
21227 TGATTTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.40, T:0.02
Consensus pattern (17 bp):
GAGAAAGAAGAACAAGG
Found at i:21307 original size:51 final size:51
Alignment explanation
Indices: 21217--21327 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
21207 AGAACAAGGG
*
21217 AGAAAGAAG-ATGATTTTGAAGAACCAAACCTCCAAAGTTCCACATATCCA
1 AGAAAGAAGAAAGATTTTGAAGAACCAAACCTCCAAAGTTCCACATATCCA
* * *
21267 AGAAAGAAGAAAGATTTTGAAG-ACCAAAGCCTTCACAGTTCCACATATCTA
1 AGAAAGAAGAAAGATTTTGAAGAACCAAA-CCTCCAAAGTTCCACATATCCA
*
21318 AGAAGGAAGA
1 AGAAAGAAGA
21328 TATAAAGACC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 15 0.28
51 39 0.72
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (51 bp):
AGAAAGAAGAAAGATTTTGAAGAACCAAACCTCCAAAGTTCCACATATCCA
Found at i:21499 original size:18 final size:18
Alignment explanation
Indices: 21476--21514 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21466 TATAAGACTC
*
21476 ATAAGAACCTTTAAGAAA
1 ATAAGAACCTTGAAGAAA
21494 ATAAGAACCTTGAAGAAA
1 ATAAGAACCTTGAAGAAA
21512 ATA
1 ATA
21515 TTCACTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (18 bp):
ATAAGAACCTTGAAGAAA
Found at i:21579 original size:38 final size:38
Alignment explanation
Indices: 21501--21693 Score: 146
Period size: 38 Copynumber: 5.1 Consensus size: 38
21491 AAAATAAGAA
* * *
21501 CCTTGAAGAAAATATTCACTCAAGATCAAGTCATATAC
1 CCTTGAAGAAAATATTCATTCAAGATCAAGTTATAAAC
* *
21539 CCTTGTAGAAAATATTCATTCAAGATCAAGTTGTAAAC
1 CCTTGAAGAAAATATTCATTCAAGATCAAGTTATAAAC
* * *
21577 CCTTGAAGCTGAGATCAAGTCA-T-AAGACTC-A--TA-AAAC
1 CCTTGAAG--AAAAT--ATTCATTCAAGA-TCAAGTTATAAAC
* * * * *
21614 GCTAGAAGAAAATATTCATTAAAGATCAAGTCATAGAC
1 CCTTGAAGAAAATATTCATTCAAGATCAAGTTATAAAC
* * * *
21652 CTTTGTAGAAAATATTCATTCAAGATCAAATTGTAAAC
1 CCTTGAAGAAAATATTCATTCAAGATCAAGTTATAAAC
21690 CCTT
1 CCTT
21694 AAAGCGAATT
Statistics
Matches: 117, Mismatches: 27, Indels: 22
0.70 0.16 0.13
Matches are distributed among these distances:
33 4 0.03
34 3 0.03
35 8 0.07
37 11 0.09
38 76 0.65
40 8 0.07
41 3 0.03
42 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (38 bp):
CCTTGAAGAAAATATTCATTCAAGATCAAGTTATAAAC
Found at i:21774 original size:70 final size:69
Alignment explanation
Indices: 21635--21822 Score: 204
Period size: 70 Copynumber: 2.7 Consensus size: 69
21625 ATATTCATTA
*
21635 AAGATCAAGTCATAGACCTTTGTAGAAA-ATATTCATTCAAGATCAAATTGTAAACCCTTAAAGC
1 AAGATCAAGTCATAGACCTTT-TA-AAACATATTCATTCAAGATCAAGTTGTAAACCCTTAAAGC
*
21699 GAATTC
64 AAATTC
* * * *
21705 AAGATCAAGTCATAGACCTTTTAAACACCTATTCATTCAAGATCAAGTTGTAGAA-TCTTGAAGT
1 AAGATCAAGTCATAGACCTTTTAAA-ACATATTCATTCAAGATCAAGTTGTA-AACCCTTAAAGC
21769 AAATTC
64 AAATTC
* * *
21775 AAGATCGAA-TCATAAGACC-CTTAAATACATATTCGTTCAAGATAAAGT
1 AAGATC-AAGTCAT-AGACCTTTTAAA-ACATATTCATTCAAGATCAAGT
21823 CATCATGACC
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
68 2 0.02
69 3 0.03
70 88 0.86
71 9 0.09
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (69 bp):
AAGATCAAGTCATAGACCTTTTAAAACATATTCATTCAAGATCAAGTTGTAAACCCTTAAAGCAA
ATTC
Found at i:45496 original size:23 final size:22
Alignment explanation
Indices: 45466--45535 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
45456 ACAAACATAA
45466 TTTTATTATAATTTAATAATAT
1 TTTTATTATAATTTAATAATAT
* ** *
45488 TTTGTATTAGAAGATAATTAA-ACC
1 TTT-TATTATAATTTAA-TAATA-T
*
45512 TTTTATTATAATTAAATAATAT
1 TTTTATTATAATTTAATAATAT
45534 TT
1 TT
45536 AATATTAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
22 8 0.23
23 21 0.60
24 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTATTATAATTTAATAATAT
Found at i:45672 original size:45 final size:45
Alignment explanation
Indices: 45576--45664 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
45566 AAATTTAAAT
* * *
45576 AATACTAAATAATATTCTTTATTACATTTATTGTATTCAAATAAC
1 AATATTAAATAATATTCTTTATAACATTTATTATATTCAAATAAC
*
45621 AATATTAAATAATATTCTTTATAATATTTATTATAGTT-AAATAA
1 AATATTAAATAATATTCTTTATAACATTTATTATA-TTCAAATAA
45665 TATTATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (45 bp):
AATATTAAATAATATTCTTTATAACATTTATTATATTCAAATAAC
Found at i:45694 original size:18 final size:19
Alignment explanation
Indices: 45641--45688 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
45631 AATATTCTTT
45641 ATAATATTTATTATAGTTAA
1 ATAATATTTATTATA-TTAA
45661 ATAATA-TTATTATATTAA
1 ATAATATTTATTATATTAA
45679 ATAATATTTA
1 ATAATATTTA
45689 AATATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATAATATTTATTATATTAA
Found at i:48466 original size:2 final size:2
Alignment explanation
Indices: 48459--48486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48449 CAAGTGTATT
48459 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
48487 CACATTATGA
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):
TA
Found at i:48647 original size:9 final size:10
Alignment explanation
Indices: 48624--48657 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
48614 TACTTGATGA
48624 AAAAATAATC
1 AAAAATAATC
48634 AAAAATAATC
1 AAAAATAATC
48644 AAAAATAATC
1 AAAAATAATC
48654 AAAA
1 AAAA
48658 GTTCTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATAATC
Found at i:55792 original size:19 final size:19
Alignment explanation
Indices: 55754--55792 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55744 TAACCATTAC
*
55754 AACTAAAAAGAAAAATAAA
1 AACTAAAAAGAAAAACAAA
55773 AACTAAGAAAG-AAAACAAA
1 AACTAA-AAAGAAAAACAAA
55792 A
1 A
55793 CAAATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (19 bp):
AACTAAAAAGAAAAACAAA
Found at i:66956 original size:2 final size:2
Alignment explanation
Indices: 66949--66981 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66939 TTTCAAATGA
66949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66982 AAGGTACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76911 original size:26 final size:26
Alignment explanation
Indices: 76854--76914 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
76844 GTAAATATGT
* *
76854 TTATATTTAAAGTATATATATATTAA
1 TTATATTTTAAGTATATATATAGTAA
**
76880 AAATATTTTAA-TATATATAATAGTAA
1 TTATATTTTAAGTATATAT-ATAGTAA
76906 TTATATTTT
1 TTATATTTT
76915 TTTATAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
TTATATTTTAAGTATATATATAGTAA
Found at i:77192 original size:21 final size:21
Alignment explanation
Indices: 77167--77206 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
77157 CACAAAATAG
*
77167 AAAGTAAATATATTTATATTA
1 AAAGTAAATATATATATATTA
**
77188 AAAGTGTATATATATATAT
1 AAAGTAAATATATATATAT
77207 AATAGGAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTA
Found at i:77676 original size:32 final size:32
Alignment explanation
Indices: 77640--77702 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
77630 AATTTTATGT
77640 AGTTCATCTTCTCTATTTATGTAAATTTATTA
1 AGTTCATCTTCTCTATTTATGTAAATTTATTA
* *
77672 AGTTCATTTTTTCTATTTATGTAAATTTATT
1 AGTTCATCTTCTCTATTTATGTAAATTTATT
77703 TCCCTTCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (32 bp):
AGTTCATCTTCTCTATTTATGTAAATTTATTA
Found at i:80045 original size:2 final size:2
Alignment explanation
Indices: 80038--80064 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80028 AGTATGTTCA
80038 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
80065 ATGCTGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:82513 original size:4 final size:4
Alignment explanation
Indices: 82504--82532 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
82494 TACAGCTGAC
82504 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
82533 AACAAGATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:88588 original size:12 final size:12
Alignment explanation
Indices: 88546--88588 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
88536 GCACAAGGTC
*
88546 TCTCTTTCTCTT
1 TCTCTCTCTCTT
* *
88558 TCTCTATCTCTG
1 TCTCTCTCTCTT
*
88570 TCGCTCTCTCTT
1 TCTCTCTCTCTT
88582 TCTCTCT
1 TCTCTCT
88589 TAGTCAAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.02, C:0.37, G:0.05, T:0.56
Consensus pattern (12 bp):
TCTCTCTCTCTT
Found at i:93511 original size:3 final size:3
Alignment explanation
Indices: 93503--93554 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
93493 GATAAAGGAC
93503 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
93551 ATA A
1 ATA A
93555 GAACCATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:104398 original size:12 final size:13
Alignment explanation
Indices: 104370--104411 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
104360 TTTGGGCTAC
104370 TAATTATAGAAAT
1 TAATTATAGAAAT
*
104383 TAATTA-AGATAT
1 TAATTATAGAAAT
*
104395 TAATAATTAGAAAT
1 TAATTA-TAGAAAT
104409 TAA
1 TAA
104412 AAGTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 6 0.25
14 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
TAATTATAGAAAT
Found at i:108848 original size:5 final size:5
Alignment explanation
Indices: 108838--108862 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
108828 TTAGCAGAAG
108838 AAGGA AAGGA AAGGA AAGGA AAGGA
1 AAGGA AAGGA AAGGA AAGGA AAGGA
108863 CATAGGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:122069 original size:103 final size:104
Alignment explanation
Indices: 121942--122147 Score: 360
Period size: 103 Copynumber: 2.0 Consensus size: 104
121932 TGTATAATCA
* *
121942 TTTTTAGCTAGAATTTGATGAATTTGAGTTGGGCTTTTGGTCTTTTTCTTTGAGATAATTCTTGG
1 TTTTTAGCTAGAATTTGATGAATTTGAGTTGGGCTTTTGGTCTCTTTCTTTAAGATAATTCTTGG
*
122007 GATTTGAATGTTGATGAGTTAAAGTTTCTTCCT-TTTTG
66 GATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTGTTTTG
* *
122045 TTTTTAGCTTGAATTTGATGAATTTGAGTTGGGCTTTTGGTCTCTTTCTTTAATATAATTCTTGG
1 TTTTTAGCTAGAATTTGATGAATTTGAGTTGGGCTTTTGGTCTCTTTCTTTAAGATAATTCTTGG
122110 GATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTGTTTT
66 GATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTGTTTT
122148 TAAGATTGAA
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 93 0.96
104 4 0.04
ACGTcount: A:0.20, C:0.08, G:0.21, T:0.50
Consensus pattern (104 bp):
TTTTTAGCTAGAATTTGATGAATTTGAGTTGGGCTTTTGGTCTCTTTCTTTAAGATAATTCTTGG
GATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTGTTTTG
Found at i:126186 original size:9 final size:9
Alignment explanation
Indices: 126172--126214 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
126162 CGGGTCATGC
126172 TTTTTGTTT
1 TTTTTGTTT
126181 TTTTTGTTTT
1 TTTTTG-TTT
*
126191 TGTTTTTTTT
1 T-TTTTGTTT
126201 GTTTTTGTTT
1 -TTTTTGTTT
126211 TTTT
1 TTTT
126215 GGTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 10 0.34
10 14 0.48
11 5 0.17
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:126192 original size:15 final size:15
Alignment explanation
Indices: 126172--126214 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
126162 CGGGTCATGC
126172 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
126187 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
126202 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
126215 GGTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTGTTTTTTTTG
Found at i:131795 original size:7 final size:7
Alignment explanation
Indices: 131783--131815 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
131773 AACACTCCTC
131783 TCCCCTT
1 TCCCCTT
131790 TCCCCTT
1 TCCCCTT
131797 TCCCCTT
1 TCCCCTT
131804 TCCCCTT
1 TCCCCTT
131811 TCCCC
1 TCCCC
131816 CTTAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (7 bp):
TCCCCTT
Found at i:156179 original size:29 final size:29
Alignment explanation
Indices: 156142--156227 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 29
156132 TGGTGGACTT
*
156142 GGTGGCTTGTAAGGGGTGTAGGAGTTGGC
1 GGTGCCTTGTAAGGGGTGTAGGAGTTGGC
* *
156171 GGTGCCTTGTAAGGAGGCGTAGGAGTTGGT
1 GGTGCCTTGTAAGG-GGTGTAGGAGTTGGC
156201 GGTGCCTTGTAAGGGGTGCT-GGAGTTG
1 GGTGCCTTGTAAGGGGTG-TAGGAGTTG
156228 TCGGAGGCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.45
30 28 0.55
ACGTcount: A:0.14, C:0.09, G:0.49, T:0.28
Consensus pattern (29 bp):
GGTGCCTTGTAAGGGGTGTAGGAGTTGGC
Found at i:156214 original size:59 final size:59
Alignment explanation
Indices: 156141--156288 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 59
156131 ATGGTGGACT
* *
156141 TGGTGGCTTGTAAGGGGTGTAGGAGTTGGCGGTGCCTT-GTAAGGAGGCGTAGGAGTTGG
1 TGGTGGCTTGTAAGGGGTGTAGGAGTTGGCGGAGCCTTGGT-AGGAGGCGCAGGAGTTGG
* * * * * *
156200 TGGTGCCTTGTAAGGGGTGCT-GGAGTTGTCGGAGGCTTGGTTGGAGGCGCCGGAGTTGT
1 TGGTGGCTTGTAAGGGGTG-TAGGAGTTGGCGGAGCCTTGGTAGGAGGCGCAGGAGTTGG
* *
156259 TGGTGGCTTGTATGGGGGTGAAGGAGTTGG
1 TGGTGGCTTGTA-AGGGGTGTAGGAGTTGG
156289 GGGTTTAATG
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 57 0.78
60 16 0.22
ACGTcount: A:0.13, C:0.09, G:0.49, T:0.28
Consensus pattern (59 bp):
TGGTGGCTTGTAAGGGGTGTAGGAGTTGGCGGAGCCTTGGTAGGAGGCGCAGGAGTTGG
Found at i:156285 original size:30 final size:29
Alignment explanation
Indices: 156140--156287 Score: 98
Period size: 30 Copynumber: 5.0 Consensus size: 29
156130 AATGGTGGAC
* *
156140 TTGGTGGCTTGTAAGGGGTGTAGGAGTTG
1 TTGGTGGCTTGTAGGGGGTGCAGGAGTTG
** * * * *
156169 GCGGTGCCTTGTAAGGAGGCGTAGGAGTTG
1 TTGGTGGCTTGT-AGGGGGTGCAGGAGTTG
* * * *
156199 GTGGTGCCTTGTAAGGGGTGCTGGAGTTG
1 TTGGTGGCTTGTAGGGGGTGCAGGAGTTG
* * * * * *
156228 TCGGAGGCTTGGTTGGAGGCGCCGGAGTTG
1 TTGGTGGCTT-GTAGGGGGTGCAGGAGTTG
*
156258 TTGGTGGCTTGTATGGGGGTGAAGGAGTTG
1 TTGGTGGCTTGTA-GGGGGTGCAGGAGTTG
156288 GGGGTTTAAT
Statistics
Matches: 88, Mismatches: 28, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
29 29 0.33
30 59 0.67
ACGTcount: A:0.13, C:0.09, G:0.49, T:0.29
Consensus pattern (29 bp):
TTGGTGGCTTGTAGGGGGTGCAGGAGTTG
Found at i:156322 original size:45 final size:48
Alignment explanation
Indices: 156271--156697 Score: 320
Period size: 44 Copynumber: 9.4 Consensus size: 48
156261 GTGGCTTGTA
* *
156271 TGGGGGTGAAGGAGTTGGGGGTTTA-ATGGGGAGCG-GGAGCCTTG-G
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
*
156316 TGGGGGTGCAGGAGTT-GGGGTTTATATGGGGAGAGTAGGAGCCTTGAC
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAG-AGGAGCCTTGAC
* * * *
156364 CGGGGGTGTAGGAGTTGGGGG-TTATACGGGG-GAGTAGGAGCCTCGAC
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAG-AGGAGCCTTGAC
* * *
156411 TGGGGTGTG--GGAGTT-GGGGTTT-TACGGGGAG-TAGGAGCCTCGAC
1 TGGGG-GTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
** * * *
156455 TGGGGGTGTGGGAGTT-GGGGTTTGTACGGGG-GAGTAGGAGCCTCGAC
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAG-AGGAGCCTTGAC
* * * *
156502 TGGGGTGTG--GGAGTTGGGGGTTTGTACGGGGAG-TAGGAGCCTCGAC
1 TGGGG-GTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
* * * *
156548 T-GGGGTG-TGGAGTT-GGGG-TTGTACGGGGAG-TAGGA-CCTTGAC
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
* * *
156590 T-GGGGTGCAGGACTT-GGGGTTTATATGGGGAG-TAGGAGCCTTGAC
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
* * *
156635 T-GGGGTG-AGGAGTT-GGGGTTTGTATGGAG-GATAGGAGCCTTGAC
1 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
* *
156679 T-GGGGTGCAGGACTTGGGG
1 TGGGGGTGAAGGAGTTGGGG
156698 CTGTGTACGG
Statistics
Matches: 339, Mismatches: 20, Indels: 45
0.84 0.05 0.11
Matches are distributed among these distances:
42 13 0.04
43 30 0.09
44 86 0.25
45 78 0.23
46 38 0.11
47 60 0.18
48 30 0.09
49 4 0.01
ACGTcount: A:0.15, C:0.10, G:0.51, T:0.24
Consensus pattern (48 bp):
TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGAGAGAGGAGCCTTGAC
Found at i:156428 original size:46 final size:46
Alignment explanation
Indices: 156273--156710 Score: 441
Period size: 46 Copynumber: 9.7 Consensus size: 46
156263 GGCTTGTATG
* ** ** * *
156273 GGGGTGAAGGAGTTGGGGGTT-TAATGGGGAGCGGGAGCCTTG-GT
1 GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
* * * * * *
156317 GGGGGTGCAGGAGTTGGGGTTTATATGGGGAGAGTAGGAGCCTTGACCG
1 -GGGGTGTAGGAGTTGGGGGTTGTACGGGG-GAGTAGGAGCCTCGA-CT
*
156366 GGGGTGTAGGAGTTGGGGGTTATACGGGGGAGTAGGAGCCTCGACT
1 GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
* *
156412 GGGGTGTGGGAGTT-GGGGTTTTAC-GGGGAGTAGGAGCCTCGACT
1 GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
* *
156456 GGGGGTGTGGGAGTTGGGGTTTGTACGGGGGAGTAGGAGCCTCGACT
1 -GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
*
156503 GGGGTGTGGGAGTTGGGGGTTTGTAC-GGGGAGTAGGAGCCTCGACT
1 GGGGTGTAGGAGTTGGGGG-TTGTACGGGGGAGTAGGAGCCTCGACT
*
156549 GGGGTGT-GGAGTT-GGGGTTGTAC-GGGGAGTAGGA-CCTTGACT
1 GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
* * * * * *
156591 GGGGTGCAGGACTTGGGGTTTATA-TGGGGAGTAGGAGCCTTGACT
1 GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
* * * *
156636 GGGGTG-AGGAGTTGGGGTTTGTATGGAGGA-TAGGAGCCTTGACT
1 GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
* * *
156680 GGGGTGCAGGACTTGGGGCTGTGTACGGGGG
1 GGGGTGTAGGAGTTGGGGGT-TGTACGGGGG
156711 TCTGGAGTTG
Statistics
Matches: 347, Mismatches: 31, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
42 13 0.04
43 22 0.06
44 77 0.22
45 77 0.22
46 80 0.23
47 52 0.15
48 26 0.07
ACGTcount: A:0.15, C:0.10, G:0.51, T:0.24
Consensus pattern (46 bp):
GGGGTGTAGGAGTTGGGGGTTGTACGGGGGAGTAGGAGCCTCGACT
Found at i:156452 original size:44 final size:45
Alignment explanation
Indices: 156318--156709 Score: 472
Period size: 44 Copynumber: 8.6 Consensus size: 45
156308 AGCCTTGGTG
* * * * *
156318 GGGGTGCAGGAGTTGGGGTTTATATGGGGAGAGTAGGAGCCTTGACCG
1 GGGGTGTAGGAGTTGGGGTTTGTA-CGGG-GAGTAGGAGCCTCGA-CT
* *
156366 GGGGTGTAGGAGTTGGGGGTTATACGGGGGAGTAGGAGCCTCGACT
1 GGGGTGTAGGAGTTGGGGTTTGTAC-GGGGAGTAGGAGCCTCGACT
*
156412 GGGGTGTGGGAGTTGGGGTTT-TACGGGGAGTAGGAGCCTCGACT
1 GGGGTGTAGGAGTTGGGGTTTGTACGGGGAGTAGGAGCCTCGACT
*
156456 GGGGGTGTGGGAGTTGGGGTTTGTACGGGGGAGTAGGAGCCTCGACT
1 -GGGGTGTAGGAGTTGGGGTTTGTAC-GGGGAGTAGGAGCCTCGACT
*
156503 GGGGTGTGGGAGTTGGGGGTTTGTACGGGGAGTAGGAGCCTCGACT
1 GGGGTGTAGGAGTT-GGGGTTTGTACGGGGAGTAGGAGCCTCGACT
*
156549 GGGGTGT-GGAGTTGGGG-TTGTACGGGGAGTAGGA-CCTTGACT
1 GGGGTGTAGGAGTTGGGGTTTGTACGGGGAGTAGGAGCCTCGACT
* * * * *
156591 GGGGTGCAGGACTTGGGGTTTATATGGGGAGTAGGAGCCTTGACT
1 GGGGTGTAGGAGTTGGGGTTTGTACGGGGAGTAGGAGCCTCGACT
* *
156636 GGGGTG-AGGAGTTGGGGTTTGTATGGAGGA-TAGGAGCCTTGACT
1 GGGGTGTAGGAGTTGGGGTTTGTACGG-GGAGTAGGAGCCTCGACT
* * *
156680 GGGGTGCAGGACTTGGGGCTGTGTACGGGG
1 GGGGTGTAGGAGTTGGGG-TTTGTACGGGG
156710 GTCTGGAGTT
Statistics
Matches: 316, Mismatches: 17, Indels: 25
0.88 0.05 0.07
Matches are distributed among these distances:
42 13 0.04
43 26 0.08
44 77 0.24
45 59 0.19
46 71 0.22
47 45 0.14
48 25 0.08
ACGTcount: A:0.15, C:0.10, G:0.50, T:0.24
Consensus pattern (45 bp):
GGGGTGTAGGAGTTGGGGTTTGTACGGGGAGTAGGAGCCTCGACT
Found at i:156483 original size:91 final size:91
Alignment explanation
Indices: 156326--156685 Score: 482
Period size: 91 Copynumber: 4.0 Consensus size: 91
156316 TGGGGGTGCA
* * * * *
156326 GGAGTTGGGGTTTATATGGGGAGAGTAGGAGCCTTGACCGGGGGTGTAGGAGTTGGGGGTTATAC
1 GGAGTTGGGGTTTATA-CGGG-GAGTAGGAGCCTCGA-CTGGGGTGTAGGAGTTGGGGTTTGTAC
156391 GGGGGAGTAGGAGCCTCGACTGGGGTGTG
63 GGGGGAGTAGGAGCCTCGACTGGGGTGTG
*
156420 GGAGTTGGGGTTT-TACGGGGAGTAGGAGCCTCGACTGGGGGTGTGGGAGTTGGGGTTTGTACGG
1 GGAGTTGGGGTTTATACGGGGAGTAGGAGCCTCGACT-GGGGTGTAGGAGTTGGGGTTTGTACGG
156484 GGGAGTAGGAGCCTCGACTGGGGTGTG
65 GGGAGTAGGAGCCTCGACTGGGGTGTG
*
156511 GGAGTTGGGGGTTTGTACGGGGAGTAGGAGCCTCGACTGGGGTGT-GGAGTTGGGG-TTGTAC-G
1 GGAGTT-GGGGTTTATACGGGGAGTAGGAGCCTCGACTGGGGTGTAGGAGTTGGGGTTTGTACGG
* **
156573 GGGAGTAGGA-CCTTGACTGGGGTGCA
65 GGGAGTAGGAGCCTCGACTGGGGTGTG
* * * * *
156599 GGACTTGGGGTTTATATGGGGAGTAGGAGCCTTGACTGGGGTG-AGGAGTTGGGGTTTGTATGGA
1 GGAGTTGGGGTTTATACGGGGAGTAGGAGCCTCGACTGGGGTGTAGGAGTTGGGGTTTGTACGGG
*
156663 GGA-TAGGAGCCTTGACTGGGGTG
66 GGAGTAGGAGCCTCGACTGGGGTG
156686 CAGGACTTGG
Statistics
Matches: 244, Mismatches: 15, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
87 44 0.18
88 28 0.11
89 29 0.12
90 7 0.03
91 81 0.33
92 17 0.07
93 25 0.10
94 13 0.05
ACGTcount: A:0.16, C:0.10, G:0.50, T:0.25
Consensus pattern (91 bp):
GGAGTTGGGGTTTATACGGGGAGTAGGAGCCTCGACTGGGGTGTAGGAGTTGGGGTTTGTACGGG
GGAGTAGGAGCCTCGACTGGGGTGTG
Found at i:161007 original size:2 final size:2
Alignment explanation
Indices: 161000--161026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
160990 ACATACAAAC
161000 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
161027 AGAGATGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:169271 original size:2 final size:2
Alignment explanation
Indices: 169264--169292 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
169254 ACTAAGCATA
169264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
169293 AACAACTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:203208 original size:27 final size:28
Alignment explanation
Indices: 203168--203221 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
203158 AACTATTAAA
*
203168 ATATATAT-ACAAAATTTTAAAAATTTC
1 ATATATATAAAAAAATTTTAAAAATTTC
*
203195 ATATGTATAAAAAAATTTTAAAAATTT
1 ATATATATAAAAAAATTTTAAAAATTT
203222 TGAAAGGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (28 bp):
ATATATATAAAAAAATTTTAAAAATTTC
Found at i:236469 original size:143 final size:143
Alignment explanation
Indices: 236211--236500 Score: 580
Period size: 143 Copynumber: 2.0 Consensus size: 143
236201 AAAAGCTCAA
236211 CATGTGGGCCACTTTTATATCAGCTACTTGCATTGGACAACACTGTCCAACTTTTTGTACAAGGA
1 CATGTGGGCCACTTTTATATCAGCTACTTGCATTGGACAACACTGTCCAACTTTTTGTACAAGGA
236276 GGGTCACATCTCACAACTAACACCAATTGAATACATCATGAAAAGAAATATATGTAATGTATATC
66 GGGTCACATCTCACAACTAACACCAATTGAATACATCATGAAAAGAAATATATGTAATGTATATC
236341 ATCACATAGTCAT
131 ATCACATAGTCAT
236354 CATGTGGGCCACTTTTATATCAGCTACTTGCATTGGACAACACTGTCCAACTTTTTGTACAAGGA
1 CATGTGGGCCACTTTTATATCAGCTACTTGCATTGGACAACACTGTCCAACTTTTTGTACAAGGA
236419 GGGTCACATCTCACAACTAACACCAATTGAATACATCATGAAAAGAAATATATGTAATGTATATC
66 GGGTCACATCTCACAACTAACACCAATTGAATACATCATGAAAAGAAATATATGTAATGTATATC
236484 ATCACATAGTCAT
131 ATCACATAGTCAT
236497 CATG
1 CATG
236501 GATGTAATAA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 147 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (143 bp):
CATGTGGGCCACTTTTATATCAGCTACTTGCATTGGACAACACTGTCCAACTTTTTGTACAAGGA
GGGTCACATCTCACAACTAACACCAATTGAATACATCATGAAAAGAAATATATGTAATGTATATC
ATCACATAGTCAT
Found at i:243878 original size:129 final size:129
Alignment explanation
Indices: 243644--243891 Score: 374
Period size: 129 Copynumber: 1.9 Consensus size: 129
243634 ATAACAACAA
* * *
243644 AGTTTTCATACTTTTCCAAACTGAACAGGAGAAAATGATAGCATCTCAAAAATGCAGAATTTTCT
1 AGTTTTCATACTTCTCCAAACTAAACAGGAGAAAATGATAGCATCTCAAAAATGCACAATTTTCT
* ** * *
243709 ATGACATGCAGTTTTGGAGCTTAAGAACATATTATTCTCAATCTTCCCAAATTCCATTTGCTAG
66 AGGACATGCAGTTTTGGAGCTTAAGAACATAAAATCCTCAATCTTCACAAATTCCATTTGCTAG
*
243773 AGTTTTCATACTTCTCCAAACTAAACTGGAGAAAAT-ATAAGCATCTCAAAAATGCACAATTTTC
1 AGTTTTCATACTTCTCCAAACTAAACAGGAGAAAATGAT-AGCATCTCAAAAATGCACAATTTTC
*
243837 TAGGACATGCAGTTTT-GATGCTTAAGTACATAAAATCCTCAATCTTCACAAATTC
65 TAGGACATGCAGTTTTGGA-GCTTAAGAACATAAAATCCTCAATCTTCACAAATTC
243892 TACAATTGCT
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
128 4 0.04
129 103 0.96
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (129 bp):
AGTTTTCATACTTCTCCAAACTAAACAGGAGAAAATGATAGCATCTCAAAAATGCACAATTTTCT
AGGACATGCAGTTTTGGAGCTTAAGAACATAAAATCCTCAATCTTCACAAATTCCATTTGCTAG
Found at i:284343 original size:2 final size:2
Alignment explanation
Indices: 284336--284376 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
284326 CCACCCACTA
284336 TC TC TC TC -C T- TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
284375 TC
1 TC
284377 AAACAGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:288705 original size:37 final size:35
Alignment explanation
Indices: 288635--288706 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
288625 TTGTCAGGTT
* * *
288635 CCAAGTTTAAAGACAACCTTGACTGATTCGATGGA
1 CCAAGTTCAAAGACAACCTTGACTAATTAGATGGA
*
288670 CCAAGTTCAAAGACAATATCTTGACTAATTAGATGGA
1 CCAAGTTCAAAGAC-A-ACCTTGACTAATTAGATGGA
288707 TTATTAGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 13 0.42
36 1 0.03
37 17 0.55
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (35 bp):
CCAAGTTCAAAGACAACCTTGACTAATTAGATGGA
Found at i:289215 original size:19 final size:20
Alignment explanation
Indices: 289170--289218 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
289160 TTAAAAATAT
* *
289170 AAATATTTAATTATATAATTG
1 AAATATTT-ATTATATAAGTC
*
289191 ATATATTTATTA-ATAAGTC
1 AAATATTTATTATATAAGTC
289210 AAATATTTA
1 AAATATTTA
289219 AGTGTAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 13 0.54
20 4 0.17
21 7 0.29
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AAATATTTATTATATAAGTC
Found at i:289621 original size:107 final size:108
Alignment explanation
Indices: 289429--289637 Score: 339
Period size: 107 Copynumber: 1.9 Consensus size: 108
289419 TTAAATGACT
* * *
289429 AAATATGTTGATCTAGTTACAACTTTCACAATTTACAAATACACATTCTTTTCAAATTATTCAAC
1 AAATATATTGATATAATTACAACTTTCACAATTTACAAATACACATTCTTTTCAAATTATTCAAC
* *
289494 TCTTACTCAATTTACTTTTTATTTAAATTTACTCAAATTAGAA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGAA
* * *
289537 AAATATATTGATATAATTACAATTTTCACAA-TTACTAATACACATTCTTTTGAAATTATTCAAC
1 AAATATATTGATATAATTACAACTTTCACAATTTACAAATACACATTCTTTTCAAATTATTCAAC
289601 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
289638 ATTTTTTATG
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 66 0.71
108 27 0.29
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.43
Consensus pattern (108 bp):
AAATATATTGATATAATTACAACTTTCACAATTTACAAATACACATTCTTTTCAAATTATTCAAC
TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGAA
Found at i:299355 original size:184 final size:185
Alignment explanation
Indices: 299046--299409 Score: 570
Period size: 184 Copynumber: 2.0 Consensus size: 185
299036 AATTAATTAT
* * * *
299046 ATTTAATATTTAATTAATTATAATGGTACTTGACACTTGTTGATGCAAGCAATTAAAAAAATTTT
1 ATTTAATATTTAATTAATTATAATGGCACTTAACACATATTGATGCAAGCAATTAAAAAAATTTT
* * * *
299111 TAAAATTTTGTCAACAGATAATAATTGTTAGAAACAGATAATTCGATTAACTTTGTTTGAAAGTA
66 AAAAATTTTGTCAACAGATAATAATTGTTAGAAACAAATAATTCGATTAAATTTGTTTGAAAATA
* * *
299176 ATTATATATATTGAAAAACCAATAGACATAATTGTTAGAAAC-AACAATGCCTAA
131 ATTATATATATTGAAAAACCAACAAACATAACTGTTAGAAACAAACAATGCCTAA
*
299230 ATTTAATATTTAATTAATTATAATGGCACTTAACACATATTGATGCAAGCAATTAAAATAATTTT
1 ATTTAATATTTAATTAATTATAATGGCACTTAACACATATTGATGCAAGCAATTAAAAAAATTTT
*
299295 AAAAATTTTGTCAACAGATAATAATTGTT-GCAAACAAATAGTTCGATTAAATTTGTTTGAAAAT
66 AAAAATTTTGTCAACAGATAATAATTGTTAG-AAACAAATAATTCGATTAAATTTGTTTGAAAAT
* *
299359 AATTATATCTATTGAAAAACCAACAAATATAACTGTTAGAAACAAACAATG
130 AATTATATATATTGAAAAACCAACAAACATAACTGTTAGAAACAAACAATG
299410 TATATCTGAA
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
183 1 0.01
184 155 0.95
185 7 0.04
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (185 bp):
ATTTAATATTTAATTAATTATAATGGCACTTAACACATATTGATGCAAGCAATTAAAAAAATTTT
AAAAATTTTGTCAACAGATAATAATTGTTAGAAACAAATAATTCGATTAAATTTGTTTGAAAATA
ATTATATATATTGAAAAACCAACAAACATAACTGTTAGAAACAAACAATGCCTAA
Found at i:300299 original size:34 final size:35
Alignment explanation
Indices: 300230--300303 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
300220 AAATTTAAAT
* * *
300230 TTAAATAATCAAAAATAAATTTCTCAAATATCAAC
1 TTAAATAATCAAAAATAAATTACTCAAACAACAAC
300265 TTAAATAA-CTAAAAATAAA-TACTCAAACAACAAC
1 TTAAATAATC-AAAAATAAATTACTCAAACAACAAC
300299 TTAAA
1 TTAAA
300304 CAACATTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (35 bp):
TTAAATAATCAAAAATAAATTACTCAAACAACAAC
Found at i:302882 original size:4 final size:4
Alignment explanation
Indices: 302873--302899 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
302863 GATTATTTGT
302873 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
302900 TATACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:309962 original size:19 final size:19
Alignment explanation
Indices: 309920--309963 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
309910 AATATAATTT
* * *
309920 ATATATTAATAATTAAATA
1 ATATATTAAAAAGTAAAAA
*
309939 TTATATTAAAAAGTAAAAA
1 ATATATTAAAAAGTAAAAA
309958 ATATAT
1 ATATAT
309964 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATATTAAAAAGTAAAAA
Found at i:310657 original size:21 final size:20
Alignment explanation
Indices: 310623--310661 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
310613 TAAAATACAT
*
310623 TTATATTTTTTTAATTATTA
1 TTATATTATTTTAATTATTA
310643 TTATAATTATTTTAATTAT
1 TTAT-ATTATTTTAATTAT
310662 GACAATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTTAATTATTA
Found at i:317752 original size:2 final size:2
Alignment explanation
Indices: 317745--317790 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
317735 TCTTTCAGAT
*
317745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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
317787 -A TA T
1 TA TA T
317791 TTGTTATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
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:337859 original size:3 final size:3
Alignment explanation
Indices: 337846--337889 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
337836 AGAAAGAGAT
*
337846 AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
337890 TTCTTAGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:340522 original size:2 final size:2
Alignment explanation
Indices: 340515--340556 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
340505 GTGTTCTTGC
*
340515 AT AT AT AT AT AT AT AT AT AT AT AT TT 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 AT AT AT AT
340557 GGGGAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:348959 original size:2 final size:2
Alignment explanation
Indices: 348954--348999 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
348944 TATACGTGTG
* *
348954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
348996 TA TA
1 TA TA
349000 CAAATCTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:360763 original size:5 final size:5
Alignment explanation
Indices: 360755--360779 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
360745 CATAACAGCT
360755 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
360780 ATTATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:360864 original size:17 final size:17
Alignment explanation
Indices: 360842--360875 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
360832 ATATAATATT
360842 TTAATTATTAATAATAA
1 TTAATTATTAATAATAA
*
360859 TTAATTATTAATTATAA
1 TTAATTATTAATAATAA
360876 AAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTATTAATAATAA
Found at i:360881 original size:17 final size:17
Alignment explanation
Indices: 360844--360899 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
360834 ATAATATTTT
* **
360844 AATTATTAATAATAATT
1 AATTATTAATTATAAAA
360861 AATTATTAATTATAAAA
1 AATTATTAATTATAAAA
360878 AATTATTTAATTTATAATAA
1 AATTA-TTAA-TTATAA-AA
360898 AA
1 AA
360900 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 19 0.58
18 4 0.12
19 6 0.18
20 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATTAATTATAAAA
Found at i:360881 original size:21 final size:22
Alignment explanation
Indices: 360842--360900 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
360832 ATATAATATT
360842 TTAATTATTAATAATAATTAATT-A
1 TTAATTA-TAA-AA-AATTAATTAA
*
360866 TTAATTATAAAAAATTATTTAA
1 TTAATTATAAAAAATTAATTAA
* *
360888 TTTATAATAAAAA
1 TTAATTATAAAAA
360901 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 14 0.45
23 3 0.10
24 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATTATAAAAAATTAATTAA
Found at i:360901 original size:21 final size:21
Alignment explanation
Indices: 360841--360901 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
360831 TATATAATAT
*
360841 TTTAA-TTATTAATAATAATTA
1 TTTAATTTA-TAATAAAAATTA
* * *
360862 ATT-ATTAATTATAAAAAATTA
1 TTTAATTTATAAT-AAAAATTA
360883 TTTAATTTATAATAAAAAT
1 TTTAATTTATAATAAAAAT
360902 ATAAAAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.13
21 19 0.63
22 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATTTATAATAAAAATTA
Found at i:360934 original size:29 final size:31
Alignment explanation
Indices: 360871--360933 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
360861 AATTATTAAT
* *
360871 TATAAAAAATT-ATTTAATTTATAATAAAAA
1 TATAAAAAATTAATTAAATATATAATAAAAA
360901 TATAAAAAATTAATTAAATATA-AATAAATAA
1 TATAAAAAATTAATTAAATATATAATAAA-AA
360932 TA
1 TA
360934 ATAATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TATAAAAAATTAATTAAATATATAATAAAAA
Found at i:367893 original size:3 final size:3
Alignment explanation
Indices: 367885--367916 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
367875 TGGGAACCAA
367885 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
367917 GATGCTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:370329 original size:202 final size:203
Alignment explanation
Indices: 369970--370369 Score: 495
Period size: 202 Copynumber: 2.0 Consensus size: 203
369960 TTTATCCATA
* *
369970 ATTATATATATGAAATTAATGATATAACTTATATTATAATGTTTTATATCAAAATTTGTATAAAT
1 ATTATATATATGAAATTAATGATATAAATTATATTATAATATTTTATATCAAAA-TTGTAT-AAT
* * * ** ** *
370035 AATAACTAATAATAAATAATATGTTACAACATCTAAAATGATAGTTAATAAACTTATTAAGTGTA
64 AATAACTAATAACAAACAATATGTTACAAAATCTAAAATGATAACTAATAAACTTACCAAGTGAA
* * *
370100 ATCATATAAATAAAGTTTATTATAAATTATAATAATACTTATGTATAAATTAAATATATATATCA
129 ATCATATAAATAAACTTTATCATAAATTATAATAATACTTAGGTATAAATTAAATATATATAT-A
370165 TATATTACTTT
193 TATATTACTTT
*
370176 ATTATATATAT-ACAATTAATGATATAAATTATATATTTAAATATTTTATATC-AAA-TGTAT-A
1 ATTATATATATGA-AATTAATGATATAAATTATAT-TAT-AATATTTTATATCAAAATTGTATAA
* * * * * *
370237 -AATAACTAATTACAAACAATATGTTATAAAATTTAAAATGATAACTAATAAAGTTACCCATTGA
63 TAATAACTAATAACAAACAATATGTTACAAAATCTAAAATGATAACTAATAAACTTACCAAGTGA
* * * *
370301 AATCATATAAATAAACTTTATCATAAATTATAGTAATGCTTCGGTATAAATTAAATATATGTATA
128 AATCATATAAATAAACTTTATCATAAATTATAATAATACTTAGGTATAAATTAAATATATATATA
370366 TATA
193 TATA
370370 ATATATTTAT
Statistics
Matches: 167, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
201 5 0.03
202 107 0.64
203 1 0.01
205 6 0.04
206 31 0.19
207 5 0.03
208 12 0.07
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (203 bp):
ATTATATATATGAAATTAATGATATAAATTATATTATAATATTTTATATCAAAATTGTATAATAA
TAACTAATAACAAACAATATGTTACAAAATCTAAAATGATAACTAATAAACTTACCAAGTGAAAT
CATATAAATAAACTTTATCATAAATTATAATAATACTTAGGTATAAATTAAATATATATATATAT
ATTACTTT
Found at i:373924 original size:12 final size:12
Alignment explanation
Indices: 373904--373938 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
373894 TTATGACATA
* *
373904 AATGGAACCTGT
1 AATGTAACCTAT
373916 AATGTAACCTAT
1 AATGTAACCTAT
373928 AATGTAACCTA
1 AATGTAACCTA
373939 AAAGCAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (12 bp):
AATGTAACCTAT
Found at i:379037 original size:27 final size:27
Alignment explanation
Indices: 378998--379050 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
378988 CACACTACAT
378998 AGTGTATCAGAAGTTGAAGCTAAGAAG
1 AGTGTATCAGAAGTTGAAGCTAAGAAG
* *
379025 AGTGTATCGGAAGTTGATGCTAAGAA
1 AGTGTATCAGAAGTTGAAGCTAAGAA
379051 AATGGCTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.30, T:0.25
Consensus pattern (27 bp):
AGTGTATCAGAAGTTGAAGCTAAGAAG
Found at i:383153 original size:25 final size:26
Alignment explanation
Indices: 383107--383189 Score: 78
Period size: 31 Copynumber: 2.9 Consensus size: 26
383097 TTAAAATAAA
383107 TTTATTTTTTCATTATAGTAAATTAAA-TT
1 TTTATTTTTT-ATT-T--TAAATTAAATTT
383136 TTTATTTTTTATTTTAAATTAAAATATTTT
1 TTTATTTTTTATTTTAAATT--AA-A-TTT
383166 TTTATATTTTTATTTTAAATTAAA
1 TTTAT-TTTTTATTTTAAATTAAA
383190 ATAAATTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
25 6 0.12
27 3 0.06
28 5 0.10
29 12 0.25
30 7 0.15
31 15 0.31
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTATTTTTTATTTTAAATTAAATTT
Found at i:383178 original size:31 final size:31
Alignment explanation
Indices: 383125--383202 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
383115 TTCATTATAG
*
383125 TAAATTAAATTTTTAT-TTTTTATTTTAAAT
1 TAAAATAAATTTTTATATTTTTATTTTAAAT
**
383155 TAAAATATTTTTTTATATTTTTATTTTAAAT
1 TAAAATAAATTTTTATATTTTTATTTTAAAT
383186 TAAAATAAATTTTTATA
1 TAAAATAAATTTTTATA
383203 ATTAATAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 13 0.31
31 29 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TAAAATAAATTTTTATATTTTTATTTTAAAT
Found at i:383280 original size:11 final size:11
Alignment explanation
Indices: 383250--383281 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
383240 TTATCATCTT
*
383250 ATATTTATATG
1 ATATTTATGTG
383261 ATATTTATGTG
1 ATATTTATGTG
383272 ATATTTATGT
1 ATATTTATGT
383282 AATTATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (11 bp):
ATATTTATGTG
Found at i:389734 original size:33 final size:30
Alignment explanation
Indices: 389643--389730 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
389633 CAAGAGCAAA
*
389643 AAGAAGATAAACGACAACACCATCATCAAG
1 AAGAAGATAAACAACAACACCATCATCAAG
**
389673 AAGAAGATAAACAACAACAGAATCATCAAG
1 AAGAAGATAAACAACAACACCATCATCAAG
* * *
389703 AAGAAGATAAAGAAGAACAACATCATCA
1 AAGAAGATAAACAACAACACCATCATCA
389731 TCAAAAGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.10
Consensus pattern (30 bp):
AAGAAGATAAACAACAACACCATCATCAAG
Found at i:389795 original size:45 final size:45
Alignment explanation
Indices: 389682--389800 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
389672 GAAGAAGATA
* * * *
389682 AACAACAACAGAATCATCAAGAAGAAGATAAAGAAGAACAACATC
1 AACAACAACAGAATCATCGAGAAGAAGAGAAACAACAACAACATC
* * * ** *
389727 ATCATCAAAAGCTTCA-AGAAGAAGAAGAGAAACAACAACAACATC
1 AACAACAACAGAATCATCG-AGAAGAAGAGAAACAACAACAACATC
*
389772 AAGAACAACAGAATCATCGAGAAGAAGAG
1 AACAACAACAGAATCATCGAGAAGAAGAG
389801 CAAGAGCAAC
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.57, C:0.18, G:0.16, T:0.09
Consensus pattern (45 bp):
AACAACAACAGAATCATCGAGAAGAAGAGAAACAACAACAACATC
Found at i:393518 original size:27 final size:27
Alignment explanation
Indices: 393488--393553 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 27
393478 AGAAAATTAT
* *
393488 ATTAAAAATGAAAATAAAATTTATAAG
1 ATTAAAAATAAAAATAAAATATATAAG
* * *
393515 ATTATAATAAAAAAAATAAAATATATGAT
1 ATTA-AA-AATAAAAATAAAATATATAAG
393544 ATTAAAAATA
1 ATTAAAAATA
393554 TATTTAAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 7 0.23
28 4 0.13
29 20 0.65
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (27 bp):
ATTAAAAATAAAAATAAAATATATAAG
Found at i:394556 original size:17 final size:17
Alignment explanation
Indices: 394534--394578 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
394524 CTTGATGTTG
394534 TAATGGTGGCTTAGTGC
1 TAATGGTGGCTTAGTGC
394551 TAATGGTGGCTTAGTGC
1 TAATGGTGGCTTAGTGC
394568 TAATGGTGGCT
1 TAATGGTGGCT
394579 CTTGTGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.36, T:0.36
Consensus pattern (17 bp):
TAATGGTGGCTTAGTGC
Found at i:409156 original size:117 final size:116
Alignment explanation
Indices: 408950--409171 Score: 347
Period size: 117 Copynumber: 1.9 Consensus size: 116
408940 TTTGGATAGT
** *
408950 ATAATTTCTCATGGAAGACTCTAGTAGTGTTTCCATAATAACGAAAATAAAGAGATCATTGTATA
1 ATAATTTCTCATGGAAGACTCTAGTAGTCCTTCCATAACAACGAAAATAAAGAGATCATTGTATA
*
409015 CATGAAGAAGAATTCGTAAAGCAAGCTTCTTCAAATAAAGAGGATAGTGAAA
66 CAAGAAGAAGAATTCGTAAAGCAAGCTTCTTC-AATAAAGAGGATAGTGAAA
* *
409067 ATAA-TTCTTCATGGAGGACTCTAGTAGTCCTTCCATAACAACGAAAATAAAGAGATCGTTGTAT
1 ATAATTTC-TCATGGAAGACTCTAGTAGTCCTTCCATAACAACGAAAATAAAGAGATCATTGTAT
* *
409131 ACAAGAAGTAGAATTCGTAAAGCAAGTTTCTTCAATAAAGA
65 ACAAGAAGAAGAATTCGTAAAGCAAGCTTCTTCAATAAAGA
409172 AGAGAGCGAA
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
116 11 0.11
117 85 0.89
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (116 bp):
ATAATTTCTCATGGAAGACTCTAGTAGTCCTTCCATAACAACGAAAATAAAGAGATCATTGTATA
CAAGAAGAAGAATTCGTAAAGCAAGCTTCTTCAATAAAGAGGATAGTGAAA
Found at i:409975 original size:12 final size:12
Alignment explanation
Indices: 409958--409982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
409948 CATGTCCTTG
409958 AAGAAAGAAATA
1 AAGAAAGAAATA
409970 AAGAAAGAAATA
1 AAGAAAGAAATA
409982 A
1 A
409983 TAATTACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAGAAAGAAATA
Found at i:420771 original size:30 final size:30
Alignment explanation
Indices: 420737--420798 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
420727 AATCGAGCTC
* *
420737 TTATATTTTTATTTTGATTAAAATAAACCT
1 TTATACTTTTATTTTGAATAAAATAAACCT
*
420767 TTATACTTTTATTTTGAATCAAATAAACCT
1 TTATACTTTTATTTTGAATAAAATAAACCT
420797 TT
1 TT
420799 GTAATTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (30 bp):
TTATACTTTTATTTTGAATAAAATAAACCT
Found at i:422749 original size:2 final size:2
Alignment explanation
Indices: 422738--422772 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
422728 TCCCTTTTGG
422738 AT AT AT -T 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 AT
422773 GTATGTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:439055 original size:107 final size:107
Alignment explanation
Indices: 438869--439083 Score: 405
Period size: 107 Copynumber: 2.0 Consensus size: 107
438859 TGGGAGAGGA
*
438869 ACAAGGACACCCTAGCTTTTCTTTGAAGTGCCCTAAATATGCTGTAAGGCAGATCTCTTTCCTTT
1 ACAAGGACACCCTAGCTTTTCTTTAAAGTGCCCTAAATATGCTGTAAGGCAGATCTCTTTCCTTT
438934 CCAAAGGTTTTCCAATGCAAGTGATCAAATAAATGATAAACT
66 CCAAAGGTTTTCCAATGCAAGTGATCAAATAAATGATAAACT
438976 ACAAGGACACCCTAGCTTTTCTTTAAAGTGCCCTAAATATGCTGTAAGGCAGATCTCTTTCCTTG
1 ACAAGGACACCCTAGCTTTTCTTTAAAGTGCCCTAAATATGCTGTAAGGCAGATCTCTTTCCTT-
439041 T-CAAAGGTTTTCCAATGCAAGTGATCAAATAAATGATAAACT
65 TCCAAAGGTTTTCCAATGCAAGTGATCAAATAAATGATAAACT
439083 A
1 A
439084 TAACCCAATT
Statistics
Matches: 106, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
107 105 0.99
108 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (107 bp):
ACAAGGACACCCTAGCTTTTCTTTAAAGTGCCCTAAATATGCTGTAAGGCAGATCTCTTTCCTTT
CCAAAGGTTTTCCAATGCAAGTGATCAAATAAATGATAAACT
Found at i:443746 original size:15 final size:15
Alignment explanation
Indices: 443722--443752 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
443712 AAATGCATCT
443722 TGATTATAATTATAA
1 TGATTATAATTATAA
*
443737 TGATTTTAATTATAA
1 TGATTATAATTATAA
443752 T
1 T
443753 ATATGACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
TGATTATAATTATAA
Found at i:443848 original size:18 final size:18
Alignment explanation
Indices: 443813--443869 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
443803 TCATATTTTA
*
443813 TATTAAAATTAAATATAAT
1 TATTAAAATT-TATATAAT
*
443832 TATTAAAATTTATATAAA
1 TATTAAAATTTATATAAT
* * *
443850 AATTTAAATTTAAATAAT
1 TATTAAAATTTATATAAT
443868 TA
1 TA
443870 GTAATAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAAAATTTATATAAT
Found at i:443909 original size:31 final size:31
Alignment explanation
Indices: 443871--443929 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
443861 AAATAATTAG
*
443871 TAATAATTA-ATTTAAATTTTTATATAAATTT
1 TAATAATTATATTT-AATTTTAATATAAATTT
443902 TAATAATTATATTTAATTTTAATATAAA
1 TAATAATTATATTTAATTTTAATATAAA
443930 ATATGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TAATAATTATATTTAATTTTAATATAAATTT
Found at i:451233 original size:90 final size:90
Alignment explanation
Indices: 451039--451242 Score: 279
Period size: 90 Copynumber: 2.3 Consensus size: 90
451029 AACTCGTATT
* * *
451039 CTCATAATAATTATATGAATTAATGTTTTAAATATATAATATATAAAATATTTTAAAATTTTTGA
1 CTCATAATAATGATATGAATTAATGTTTTAAATATATAATATATAAAATATTTAAAAAATTTTGA
451104 AAATTAAATATTTTCTTTATTTATG
66 AAATTAAATATTTTCTTTATTTATG
**
451129 CTCATAATGGTGATATGAATTAATGTTTTAAATATATAATATATAAAATATTTGGAAAAAAATTT
1 CTCATAATAATGATATGAATTAATGTTTTAAATATATAATATATAAAATATTT---AAAAAATTT
*
451194 T-AAAATTAAATA-TTT-TTTATTTATT
63 TGAAAATTAAATATTTTCTTTATTTATG
* * *
451219 TTCGTAATAATGATATAAATTAAT
1 CTCATAATAATGATATGAATTAAT
451243 ATTATTTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
90 78 0.78
91 3 0.03
92 11 0.11
93 8 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (90 bp):
CTCATAATAATGATATGAATTAATGTTTTAAATATATAATATATAAAATATTTAAAAAATTTTGA
AAATTAAATATTTTCTTTATTTATG
Found at i:464890 original size:5 final size:5
Alignment explanation
Indices: 464880--464908 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
464870 AAATATTATC
464880 AATCT AATCT AATCT AATCT AATCT AATC
1 AATCT AATCT AATCT AATCT AATCT AATC
464909 GGTATCATGT
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:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
AATCT
Found at i:466808 original size:27 final size:27
Alignment explanation
Indices: 466770--466823 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
466760 AGCCCTAAAA
466770 ATTCCATTACTTTCTGATCAAAATAAT
1 ATTCCATTACTTTCTGATCAAAATAAT
466797 ATTCCATTACTTTCTGATCAAAATAAT
1 ATTCCATTACTTTCTGATCAAAATAAT
466824 TTATCTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTCCATTACTTTCTGATCAAAATAAT
Found at i:470847 original size:18 final size:18
Alignment explanation
Indices: 470824--470860 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
470814 TAGATGATAT
470824 ATTATTTAAAAAAATTAA
1 ATTATTTAAAAAAATTAA
*
470842 ATTATTTAAATAAATTAA
1 ATTATTTAAAAAAATTAA
470860 A
1 A
470861 ATAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATTTAAAAAAATTAA
Found at i:470907 original size:21 final size:21
Alignment explanation
Indices: 470869--470910 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
470859 AAATAAATTT
470869 TTTATTATATTTAATTAAATA
1 TTTATTATATTTAATTAAATA
*
470890 TTTA-TATATTTATTTTAAATA
1 TTTATTATATTTA-ATTAAATA
470911 AATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATTATATTTAATTAAATA
Found at i:471669 original size:27 final size:28
Alignment explanation
Indices: 471631--471703 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
471621 TATATAAAAA
471631 ATTTAAATAAATTTT-TATTTTTATTCT
1 ATTTAAATAAATTTTATATTTTTATTCT
*
471658 ATTT-AATCAAATTATTATATTTTTATTTT
1 ATTTAAAT-AAATT-TTATATTTTTATTCT
471687 ATATTAAATAAATTTTA
1 AT-TTAAATAAATTTTA
471704 ATAACTAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 3 0.08
27 9 0.22
28 2 0.05
29 16 0.40
30 7 0.17
31 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTAAATAAATTTTATATTTTTATTCT
Found at i:475938 original size:19 final size:18
Alignment explanation
Indices: 475906--475952 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
475896 TGTGAAGACA
* * *
475906 TAATATTTTGAAAACTTT
1 TAATTTTTTAAAAAATTT
475924 TGAATTTTTTAAAAAATTT
1 T-AATTTTTTAAAAAATTT
475943 TAATTTTTTA
1 TAATTTTTTA
475953 TTATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TAATTTTTTAAAAAATTT
Found at i:476005 original size:31 final size:29
Alignment explanation
Indices: 475937--476006 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
475927 ATTTTTTAAA
* *
475937 AAATTTTA-ATTTTTTATTATATTTAATT
1 AAATTTTATATTTTTTATTAAATTAAATT
* *
475965 ACATTTTTATATTTTTATTTTAAATTAAATT
1 A-AATTTTATATTTTT-TATTAAATTAAATT
475996 AAATATTTATA
1 AAAT-TTTATA
476007 ATAATTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 6 0.18
30 8 0.24
31 18 0.55
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
AAATTTTATATTTTTTATTAAATTAAATT
Found at i:476583 original size:16 final size:16
Alignment explanation
Indices: 476562--476604 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
476552 CTCGACTAGT
*
476562 ATGTTTGGCATGGTTC
1 ATGTTTGGCACGGTTC
476578 ATGTTTGGCACGGTTC
1 ATGTTTGGCACGGTTC
476594 ATGTTTGGCAC
1 ATGTTTGGCAC
476605 TTGGCAGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.40
Consensus pattern (16 bp):
ATGTTTGGCACGGTTC
Found at i:487150 original size:12 final size:12
Alignment explanation
Indices: 487112--487157 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
487102 AATATTTTTT
487112 AATATAAAAATGC
1 AATATAAAAAT-C
487125 AA-ATAAAAA-C
1 AATATAAAAATC
487135 -ATATAAAAATC
1 AATATAAAAATC
487146 AATATGAAAAAT
1 AATAT-AAAAAT
487158 AAAATATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.03
10 8 0.28
11 1 0.03
12 11 0.38
13 8 0.28
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (12 bp):
AATATAAAAATC
Found at i:492564 original size:3 final size:3
Alignment explanation
Indices: 492515--492548 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
492505 GGTCGTCTTT
*
492515 GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
492549 GTCAGGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:503017 original size:2 final size:2
Alignment explanation
Indices: 503010--503040 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
503000 TAAATAGGGG
503010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
503041 CACATACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:503454 original size:7 final size:7
Alignment explanation
Indices: 503442--503481 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
503432 TCAGGTTACA
503442 CGTGAGT
1 CGTGAGT
503449 CGTGAGT
1 CGTGAGT
503456 CGTGAGT
1 CGTGAGT
*
503463 CGTGACT
1 CGTGAGT
*
503470 CGTGACT
1 CGTGAGT
503477 CGTGA
1 CGTGA
503482 AACTCATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.28
Consensus pattern (7 bp):
CGTGAGT
Found at i:507969 original size:59 final size:59
Alignment explanation
Indices: 507876--507989 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
507866 AACCAAAGAA
*
507876 CTAAATGTTCTTAATCTAATTGACTTAGAATTTATTGTCATCAACTCATCATACCCGAG
1 CTAAATGTTCTTAATCTAATTGACTTAGAATTTATTGCCATCAACTCATCATACCCGAG
* * *
507935 CTAAATGTTCTTAATCTAATTGAGTTGGATTTTATTGCCATCAACTCATCATACC
1 CTAAATGTTCTTAATCTAATTGACTTAGAATTTATTGCCATCAACTCATCATACC
507990 TAAGAGTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (59 bp):
CTAAATGTTCTTAATCTAATTGACTTAGAATTTATTGCCATCAACTCATCATACCCGAG
Found at i:513654 original size:2 final size:2
Alignment explanation
Indices: 513641--513679 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
513631 AAGCTGACAT
*
513641 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
513680 AGTTACCGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:514990 original size:16 final size:16
Alignment explanation
Indices: 514971--515020 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
514961 CTTTAAGTGC
514971 TTGATGCCTTCAATCT
1 TTGATGCCTTCAATCT
* * *
514987 TTGAT-AC-TCAGTCC
1 TTGATGCCTTCAATCT
*
515001 TTGATGCCTTCGATCT
1 TTGATGCCTTCAATCT
515017 TTGA
1 TTGA
515021 CACTCAATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 13 0.52
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (16 bp):
TTGATGCCTTCAATCT
Found at i:515006 original size:30 final size:30
Alignment explanation
Indices: 514970--515026 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
514960 GCTTTAAGTG
*
514970 CTTGATGCCTTCAATCTTTGATACTCAGTC
1 CTTGATGCCTTCAATCTTTGACACTCAGTC
*
515000 CTTGATGCCTTCGATCTTTGACACTCA
1 CTTGATGCCTTCAATCTTTGACACTCA
515027 ATTTTGCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (30 bp):
CTTGATGCCTTCAATCTTTGACACTCAGTC
Found at i:516369 original size:24 final size:24
Alignment explanation
Indices: 516333--516379 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
516323 AAGCTGCGAT
516333 GCCTGATCAGCTGAATTTTGGGAC
1 GCCTGATCAGCTGAATTTTGGGAC
* * *
516357 GCCTGCTCGGCTGATTTTTGGGA
1 GCCTGATCAGCTGAATTTTGGGA
516380 AGCTGATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (24 bp):
GCCTGATCAGCTGAATTTTGGGAC
Found at i:522959 original size:25 final size:25
Alignment explanation
Indices: 522881--522960 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
522871 ATAATTTTGT
*
522881 ATTGAGTAATAATTTTGAGCTAGTG
1 ATTGAGTAATAATTTTGAGCTATTG
* * *
522906 ATTGAGTTGAA-AAATATGA--TTTTG
1 ATTGAG-T-AATAATTTTGAGCTATTG
522930 TATTGAGTAATAATTTTGAGCTATTG
1 -ATTGAGTAATAATTTTGAGCTATTG
522956 ATTGA
1 ATTGA
522961 TTGAGTACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
23 2 0.05
24 10 0.24
25 17 0.40
26 11 0.26
27 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (25 bp):
ATTGAGTAATAATTTTGAGCTATTG
Found at i:528020 original size:18 final size:19
Alignment explanation
Indices: 527997--528033 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
527987 AAATAATAAA
527997 AAATT-ATTTAAAAATTTT
1 AAATTAATTTAAAAATTTT
*
528015 AAATTAATTTAAAACTTTT
1 AAATTAATTTAAAAATTTT
528034 TTAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTAATTTAAAAATTTT
Found at i:533180 original size:2 final size:2
Alignment explanation
Indices: 533173--533212 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
533163 TATTGAATAC
*
533173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
533213 GGTGGATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:544172 original size:116 final size:113
Alignment explanation
Indices: 543956--544173 Score: 301
Period size: 116 Copynumber: 1.9 Consensus size: 113
543946 CCAGGCTCCC
*
543956 ACAGCCCACGAGTCCCGATTCCCCCTGCGGCCCTGCTCGCACCCTCCGCTCCCAAGAGTCCTTTT
1 ACAGCCCACGAGTCCCGATTCCCCCTGCGGCCCTGCCCGCACCCTCCGCTCCCAAGAGTCCTTTT
* * * * *
544021 GGGTGATTCCCGATTCCCTCTGCGGCCCTGCCCCCCGTCTCACAGTTG
66 GGATGATTCCCGATTCCCCCCGCGACCCTCCCCCCCGTCTCACAGTTG
* * *
544069 ACAGTCCCACGAGTCCCGATTCCCCCTGCTGCCCTGCCCGCCCCCCTCCGACTCCCAGGAGTCCT
1 ACAG-CCCACGAGTCCCGATTCCCCCTGCGGCCCTGCCCG-CACCCTCCG-CTCCCAAGAGTCCT
* *
544134 TTTGGATGATTCCCGATTCCCCCCGCTACCCCCTCCCCCC
63 TTTGGATGATTCCCGATTCCCCCCGCGACCCTC-CCCCCC
544174 ACTCAAGTGT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
113 4 0.04
114 33 0.37
115 8 0.09
116 39 0.43
117 6 0.07
ACGTcount: A:0.11, C:0.49, G:0.19, T:0.21
Consensus pattern (113 bp):
ACAGCCCACGAGTCCCGATTCCCCCTGCGGCCCTGCCCGCACCCTCCGCTCCCAAGAGTCCTTTT
GGATGATTCCCGATTCCCCCCGCGACCCTCCCCCCCGTCTCACAGTTG
Found at i:545584 original size:20 final size:16
Alignment explanation
Indices: 545551--545600 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
545541 ACATTCACAC
*
545551 TTTTATTTTATTTTTGA
1 TTTTAATTTATTTTT-A
545568 TTTAATAATTATATTTTTA
1 TTT--TAATT-TATTTTTA
545587 TTTTAATTTATTTT
1 TTTTAATTTATTTT
545601 ATCTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
19 8 0.28
20 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTAATTTATTTTTA
Found at i:547254 original size:28 final size:28
Alignment explanation
Indices: 547223--547308 Score: 77
Period size: 33 Copynumber: 2.9 Consensus size: 28
547213 TAAAATATAT
547223 AATACAAA-AAATTATATTAAGAAATAAA
1 AATA-AAATAAATTATATTAAGAAATAAA
*
547251 AATAAAATATATAAGATTATAATAAGAAATAAA
1 AAT--AA-A-ATAA-ATTATATTAAGAAATAAA
* *
547284 AATAAAATATATGATATTAA-AAATA
1 AATAAAATAAATTATATTAAGAAATA
547309 TATTTAAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
27 5 0.10
28 11 0.23
29 4 0.08
30 3 0.06
31 3 0.06
32 2 0.04
33 20 0.42
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (28 bp):
AATAAAATAAATTATATTAAGAAATAAA
Found at i:547277 original size:33 final size:33
Alignment explanation
Indices: 547210--547295 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
547200 AAAAAAATTA
* * * *
547210 AAATAAAATATATAATACAAAAAATTATATTAAG
1 AAATAAAA-ATAAAATATATAAAATTATAATAAG
*
547244 AAATAAAAATAAAATATATAAGATTATAATAAG
1 AAATAAAAATAAAATATATAAAATTATAATAAG
547277 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
547296 GATATTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 39 0.83
34 8 0.17
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAG
Found at i:555101 original size:20 final size:19
Alignment explanation
Indices: 555087--555132 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
555077 ATTTATCATT
555087 TTTATTTTTCTTTTAATTG
1 TTTATTTTTCTTTTAATTG
* *
555106 TTTATTTTT-TTTAAATTT
1 TTTATTTTTCTTTTAATTG
555124 TATTATTTT
1 T-TTATTTT
555133 GTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTATTTTTCTTTTAATTG
Found at i:555698 original size:23 final size:23
Alignment explanation
Indices: 555672--555719 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
555662 AATAAAAAAT
*
555672 AAAAATAAAATAAAGTGAATGCA
1 AAAAATAAAAGAAAGTGAATGCA
**
555695 AAAAATGGAAGAAAGTGAATGCA
1 AAAAATAAAAGAAAGTGAATGCA
555718 AA
1 AA
555720 CCTCATGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAGAAAGTGAATGCA
Found at i:557308 original size:2 final size:2
Alignment explanation
Indices: 557301--557343 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
557291 TTGGTTTAAG
557301 AT AT AT AT 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 AT AT AT AT
557343 A
1 A
557344 ACATGGCGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:564002 original size:16 final size:16
Alignment explanation
Indices: 563983--564033 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
563973 CAATAATTAT
*
563983 AAAAGCAAATATAA-A
1 AAAAACAAATATAATA
563998 AAAAACAAA-ATAATA
1 AAAAACAAATATAATA
*
564013 ATAATATCAAATATAATA
1 A-AA-AACAAATATAATA
564031 AAA
1 AAA
564034 TTTAACATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.13
15 10 0.33
16 2 0.07
17 7 0.23
18 7 0.23
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAAACAAATATAATA
Found at i:574680 original size:90 final size:87
Alignment explanation
Indices: 574572--574743 Score: 220
Period size: 90 Copynumber: 1.9 Consensus size: 87
574562 GACTGGGTCT
* *
574572 CATGACTTAGAATAAAAGGAGAGCAACATCCAGCACATAAAAGAAAAAGAGGAGAGATTAGG-TT
1 CATGACTTAGAATAAAAGGAGAACAACATCCAGCACAGAAAAG--AAA-AGGAGAGATTAGGTTT
574636 AAATTAAGGCTTTCGTTTAAATTTTG
63 AAATTAAGGCTTTC-TTTAAATTTTG
* * *** * *
574662 CATGGCTTAGAATAAAAGGAGAATAGTGTTCAGCACAGAAAAGAAAAGGAGAGATTAGGTTTAAG
1 CATGACTTAGAATAAAAGGAGAACAACATCCAGCACAGAAAAGAAAAGGAGAGATTAGGTTTAAA
574727 TTAAGGCTTTCTTTAAA
66 TTAAGGCTTTCTTTAAA
574744 ATTATTACGA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
87 19 0.26
88 18 0.25
90 35 0.49
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (87 bp):
CATGACTTAGAATAAAAGGAGAACAACATCCAGCACAGAAAAGAAAAGGAGAGATTAGGTTTAAA
TTAAGGCTTTCTTTAAATTTTG
Found at i:574831 original size:2 final size:2
Alignment explanation
Indices: 574826--574860 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
574816 ATAAAGTATT
*
574826 AC AC AC AC AC AC AC AC AC AC AC AC AG AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
574861 GATATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.46, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:581817 original size:41 final size:40
Alignment explanation
Indices: 581754--581876 Score: 178
Period size: 41 Copynumber: 3.1 Consensus size: 40
581744 CTAAACATTA
581754 GGCTTACAAGTTGAAAGTCCCAAATACTAACTGTTAAGGT
1 GGCTTACAAGTTGAAAGTCCCAAATACTAACTGTTAAGGT
*
581794 GGCTCTACAAGTTGAAAGGCCCAAATACTAACTGTTAAGGT
1 GGCT-TACAAGTTGAAAGTCCCAAATACTAACTGTTAAGGT
** * *
581835 GGCTT-CTTGGT-AAAGTCCCAGATACTAACTGTTAAGGT
1 GGCTTACAAGTTGAAAGTCCCAAATACTAACTGTTAAGGT
581873 GGCT
1 GGCT
581877 CCTTGGTGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
38 29 0.38
39 3 0.04
40 5 0.07
41 39 0.51
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (40 bp):
GGCTTACAAGTTGAAAGTCCCAAATACTAACTGTTAAGGT
Found at i:581869 original size:38 final size:39
Alignment explanation
Indices: 581765--581885 Score: 163
Period size: 38 Copynumber: 3.1 Consensus size: 39
581755 GCTTACAAGT
** *
581765 TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTCTACAAGT
1 TGAAAGTCCCAAATACTAACTGTTAAGGTGGCT-T-CTTGG
*
581806 TGAAAGGCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
1 TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
* *
581845 T-AAAGTCCCAGATACTAACTGTTAAGGTGGCTCCTTGG
1 TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
581883 TGA
1 TGA
581886 TACATTGTAG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 35 0.49
39 4 0.06
40 1 0.01
41 32 0.44
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (39 bp):
TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
Found at i:585336 original size:4 final size:4
Alignment explanation
Indices: 585327--585357 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
585317 TGTCCCACGT
*
585327 TTTA TTTA TTTA TTTG TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
585358 TTGATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Done.